Contents. Inhoudsopgave 5

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Contents 1

Faculty of Sciences Description Organisation of the faculty Objectives of the Faculty Board of the faculty Student Council Office of the faculty Departments Educational Organisation Board of Education Education and External Affairs Office Programmes Educational Committee Examination Board Research organisation Research groups Research Schools

13 13 13 13 13 14 14 14 15 15 16 16 18 18 19 19 20

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Education Exact Sciences Academic calendar Master coordinators Monitoring students' progress Educational rules Admission requirements for the Master Enrolment procedures VU - UvA Enrolment procedure courses Interim examinations and practical work Master Thesis Final Exams Degree ceremonies Attendance certificate Right of appeal Education and Examination Rules Rules and Regulations of the Examination Board Educational quality control Educational Committees Assessment of education Students' associations AIK MENS STORM VCSVU Studying abroad Orientation on the Labour Market Stichting Bèta Bedrijvencontactdag Amsterdam Professional Associatons Belgisch/Nederlandse Vereniging voor Kunstmatige Intelligentie (BNVKI)

23 23 23 23 24 24 24 24 24 26 26 26 27 27 28 28 28 28 29 29 29 29 29 29 30 30 30 31 31

1.1 1.2 1.2.1 1.2.2 1.2.3 1.2.4 1.2.5 1.3 1.3.1 1.3.2 1.3.3 1.3.4 1.3.5 1.4 1.4.1 1.4.2

2.1 2.2 2.3 2.4 2.4.1 2.4.2 2.4.3 2.4.4 2.4.5 2.4.6 2.4.7 2.4.8 2.4.9 2.4.10 2.4.11 2.5 2.5.1 2.5.2 2.6 2.6.1 2.6.2 2.6.3 2.6.4 2.7 2.8 2.8.1 2.9 2.9.1

Inhoudsopgave

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2.9.2 2.9.3 2.9.4 2.9.5 2.9.6 2.9.7 2.9.8 2.9.9 2.9.10

Centrum voor Wiskunde en Informatica (CWI) Koninklijke Nederlandse Chemie Vereninging (KNCV) Koninklijk Wiskundig Genootschap Nederlands Genootschap voor Informatica (NGI) Nederlandse Natuurkundige Vereniging (NNV) Nederlandse Astronomenclub (NAC) Netwerk voor Informaticae Mathematicae en Fysicae (NIMF) Thomas Stieltjes Instituut for Mathematics Vereniging voor Statistiek en Operations Research (VVS)

31 31 31 31 31 31 32 32 32

3

Study Facilities Opening hours Education Office Books and Tutorials Library Announcement and Information Facilities Educational rooms Computer facilities Digital learning environment Printing and copy facilities Safety and Environment Opening hours of the buildings Students' ID Card Disabled Bicycle parking racks / bicycle repair shop

33 33 33 33 34 34 34 34 35 35 35 35 36 36

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Master Artificial Intelligence The domain of the Master Objectives Final attainment level Requirements for the Master Master programmes Intelligent Internet Applications Programme First year Second year Recommended optional courses Cognitive Science Programme Programme for students having a Bachelor in AI Programme for students having a Bachelor in Psychology Organisation Dynamics and Self Organisation Programme Programme for students having a Bachelor in AI Programme for students having a Bachelor in Biology or Medical Biology Knowledge Management and Knowledge Technology Programme First year Second year Recommended optional courses

37 37 38 38 38 39 39 39 40 40 40 40 40 41 42 42 42 43 44 45 45 45 46 46

3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 3.9 3.10 3.11 3.12 3.13

4.1 4.2 4.3 4.4 4.5 4.6 4.6.1 4.6.2 4.6.3 4.6.4 4.7 4.7.1 4.7.2 4.7.3 4.8 4.8.1 4.8.2 4.8.3 4.9 4.9.1 4.9.2 4.9.3 4.9.4

4.10 4.10.1 4.10.2 4.10.3 4.10.4 4.11 4.11.1 4.11.2 4.11.3 4.11.4 4.12 4.12.1 4.13 4.13.1 4.14 4.14.1 4.15 4.15.1 4.16 4.16.1 4.16.2

Technical Artificial Intelligence Programme First year Second year Recommend optional courses Interdisciplinary Applications AI and Law Programme for students having a Bachelor in AI Programme for students having a Bachelor in Law AI and Linguistics AI and Communication Programma Society oriented variant Programma Final-projects and Training on the job Programme Elective courses outside the department Programme Educational possibilities after the Master Programme Training as a researcher

46 46 47 47 47 47 48 48 49 49 50 51 51 51 52 52 53 53 53 53 53

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Master Bioinformatics The domain of the Master Objectives Final attainment level Requirements for the Master Master programme Programme Compulsory courses Optional courses Traineeships Educational possibilities after the Master Programme Professional associations

55 55 56 56 57 57 58 58 58 59 59 59 60

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Master Business Mathematics and Informatics Objectives Final attainment level Requirements for the Master Part-time studying The Variants of the Master Society oriented variant Programme Compulsory courses Optional courses Mathematics Optional coursus BMI Research variant Programme

61 61 61 61 61 62 62 62 62 63 63 63 63

5.1 5.2 5.3 5.4 5.5 5.6 5.6.1 5.6.2 5.6.3 5.7 5.7.1 5.8

6.1 6.2 6.3 6.4 6.5 6.6 6.6.1 6.6.2 6.6.3 6.6.4 6.7 6.7.1

Inhoudsopgave

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6.7.2 6.7.3 6.7.4 6.8 6.8.1 6.9 6.9.1 6.9.2 6.10 6.10.1 6.10.2 6.10.3 6.10.4 6.10.5 6.11 6.11.1 6.12 6.12.1

Compulsory courses Optional courses Mathematics Optional courses BMI Communication variant Programme The Dual Master's Programme Programme Optional courses Mathematics Educational possibilities after the master Programme Training as a researcher in BMI Training as a researcher in Mathematics Training as a researcher in Computer Science Training as a researcher in Artificial Intelligence Optional courses Programme External master project Programme

63 64 64 64 64 65 65 65 66 66 66 66 66 67 67 67 67 67

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Master Computer Science The domain of the Master Objectives Final attainment level Requirements for the Master Master programmes Internet and Web Technology Programme First year Second year Parallel Computing and Visualisation Programme First year Second year Software Engineering Programme First year Second year Multimedia Programme First year Second year Formal Methods en Software Verification Programme First year Second year Technical Artificial Intelligence Programme First year Second year Information and Communication Technology

69 69 69 69 70 70 71 71 71 72 72 72 72 73 73 73 73 74 74 74 74 75 75 75 75 76 76 76 77 77 77

7.1 7.2 7.3 7.4 7.5 7.6 7.6.1 7.6.2 7.6.3 7.7 7.7.1 7.7.2 7.7.3 7.8 7.8.1 7.8.2 7.8.3 7.9 7.9.1 7.9.2 7.9.3 7.10 7.10.1 7.10.2 7.10.3 7.11 7.11.1 7.11.2 7.11.3 7.12

7.12.1 7.12.2 7.12.3 7.13 7.13.1 7.14 7.14.1 7.15 7.15.1 7.16 7.16.1 7.17 7.17.1

Programme of this Society oriented variant First year Second year Society oriented variant Programma Communication variant Programma Master projects and Training on the job Programme Educational possibilities after the Master, training as a researcher Programme Graduate schools Introduction

77 78 78 79 79 79 79 80 80 81 81 81 81

8

Master Information Sciences Business Information Science The domain of the Master Objectives Final attainment level Requirements for the Master Master Programme Multimedia & Culture The domain of the Master Objectives Final attainment level Requirements for the Master Master Programme

83 83 83 83 83 84 86 86 86 87 87 88 89

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Master Medical Natural Sciences Objectives Final attainment level Requirements for the Master Structure of the training Part-time studying Dual training Master Programmes Physics of Life Department of Physics and Medical Technology (Vumc) Bioinformatics / Genomics Integrative Bioinformatics Institute VU (FEW, FALW, Vumc) Biomolecular Complexity MSc Biomolecular complexity (MSc BMC) Molecular Medicine Department of Pharmacochemistry Current research themes Society oriented variant Programma Communication / Education variant Differentiatie C/E variant

8.1 8.1.1 8.1.2 8.1.3 8.1.4 8.1.5 8.2 8.2.1 8.2.2 8.2.3 8.2.4 8.2.5

9.1 9.2 9.3 9.4 9.5 9.6 9.7 9.8 9.8.1 9.9 9.9.1 9.10 9.10.1 9.11 9.11.1 9.11.2 9.12 9.12.1 9.13 9.13.1

Inhoudsopgave

91 91 91 92 92 93 93 93 94 94 96 96 99 99 104 104 105 107 107 107 108

9

9.13.2 9.13.3 9.14 9.14.1 9.14.2 9.14.3 9.14.4 9.14.5

Communicatie variant Educatie variant Minors Physiology at the Institute for Cardiovascular Research VU, Laboratorium voor Fysiologie, Vumc Stagemogelijkheden Laboratorium voor FysiologieThema 1: Verbetering van hartfunctie bij hartfalen Thema 2: Verbetering van vaatfunctie bij metabole ziekten Molecular Cell Biology at the Department of Molecular Cell Biology, Vumc Stageopdrachten Dietetiek

10

108 109 109 109 109 110 110 111

Master Pharmaceutical Sciences 10.1 Objectives 10.2 Final attainment level 10.3 Requirements for the Master 10.4 Structure of the training 10.5 Part-time studying 10.6 Dual training 10.7 Research tracks 10.7.1 Drug Design & Synthesis 10.7.2 Drug Discovery & Target Finding 10.7.3 Computational Medicinal Chemistry & Toxicology 10.7.4 Drug Disposition & Safety Assessment 10.7.5 Biomolecular & Drug Analysis 10.8 Programme Pharmaceutical Sciences 10.8.1 Master's programme 10.8.2 Compulsory courses 10.8.3 Basic courses 10.8.4 Advanced courses 10.8.5 Optional courses (Major/Minor) 10.9 Society oriented variant 10.9.1 Programma 10.10 Communication / Education variant 10.10.1 Differentiatie C/E variant 10.10.2 Communicatie variant 10.10.3 Educatie variant 10.11 Overige vakken

113 113 113 114 114 115 115 115 116 116 117 117 118 118 118 118 118 118 119 119 119 120 120 120 121 121

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Exam parts

Inhoudsopgave

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Exact Sciences

1

1.1

Faculty of Sciences Description The Faculty of Sciences is divided into five departments, each containing a number of sections. The courses at the faculty are taught by lecturers from each of these five departments. Only organisational and policy-related matters are dealt with at faculty level. The five departments within the Faculty of Sciences are: • Computer Science • Physics and Astronomy • Chemistry and Pharmaceutical Sciences • Mathematics • History, Philosophy and Social Aspects of Science Tuition is also provided for target groups outside of the Faculty, in particular to students of Econometrics and Arts subjects. Scientific research is sometimes conducted in a multidisciplinary context with researchers from other faculties at the VU or from other institutes.

1.2

Organisation of the faculty

1.2.1

Objectives of the Faculty The Faculty of Sciences aims to provide tuition and to conduct research in the sciences, more specifically the subjects Computer Science, Physics and Astronomy, Chemistry and Pharmaceutical Sciences, Mathematics and the connected multidisciplinary fields.

1.2.2

Board of the faculty The Faculty Board consists of three professors from the departments of Computer Science, Physics and Astronomy, Chemistry and Pharmaceutical Sciences and Mathematics, one of whom is the dean. The Board is supplemented by the Operational Director, a member of the support staff and a student from one of the faculty’s programmes, all acting in an advisory role. The powers and duties of the Faculty Board include: • organising and co-ordinating teaching and scientific research; where teaching is concerned. This task is largely delegated to the Board of Education; • drawing up the Education and Examination Regulations for each educational programme offered by the Faculty and evaluating these regulations on a regular basis; • supervising the implementation of the Education and Examination Regulations and the research programmes. For these purposes, the Board can issue directives to the departments; • appointing the Board of Education; • setting up the Examination Board and appointing its members; • appointing the members of the Programme Committees; • drawing up the procedural regulations for the teaching programme; • determining the Faculty’s annual research programme and policy plan.

Faculty of Sciences

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The members of the Faculty Board are: prof. dr. W. Hogervorst (Physics and Astronomy Department), dean prof. dr. E.J. Baerends (Chemistry and Pharmaceutical Sciences Department) prof. dr. J. van Mill (Mathematics Department) drs. D. Schinkelshoek (Operational Director), advisor R.F. Schmidt (support staff), advisor N. Zonneveld (student), advisor 1.2.3

Student Council Student participation in the board of the Faculty takes place via the Faculty Student Council. The Faculty Student Council meets with the Faculty Staff Council (which represents all faculty personnel) in a Joint Faculty Meeting to determine their position on the following issues: • approval of the Education and Examination Regulations of the various programmes; • issuing advice on the departments’ professor and lecturer plans; • issuing budgetary advice; • amendments to the faculty regulations. The members of the Faculty Student Council are: Guus Harms (Physics) Kirsten Valkenburg (Mathematics) Sebastiaan Janssens (Physics/Mathematics) Paulien Out (Business Mathematics and Informatics) Cynthia Maan (Physics) Anette Houweling (Medical Natural Sciences) Manon van Tunen (Medical Natural Sciences) General e-mail address: [email protected]

1.2.4

Office of the faculty The Faculty Office is part of the Faculty Service Centre. The Faculty Service Centre also includes the Precision Mechanics and Glass Instrumentation Group, the Electronics Group and the Computer Support Group (IT Group). The Faculty Office includes: the Faculty Secretariat, the Personnel and Organisation Department, the Accounts Department, the Health Safety and Environment Department and the Education and External Affairs Office. The head of the Faculty Office is the Operational Director, D. Schinkelshoek. Postal address: Vrije Universiteit Faculty of Sciences De Boelelaan 1081-1083 1081 HV Amsterdam Phone: +31 (0) 20 44 47500 fax (020) 44 47509

1.2.5

14

Departments A department is defined as an organisation of people working together in a particular subject area. Each department consists of a head of department, academic staff, support staff and students who contribute to the department’s teaching and/or research Exact Sciences

programme. The department also undertakes activities in the field of public relations, the organisation of public lectures and the like. Each department is run by a department head, who is one of the department’s professors, appointed by the Faculty Board for a term of three years. The responsibilities of the department head include: • the teaching carried out within the department; this task is largely delegated to the department’s management team; • the Education and Examination Regulations for the teaching programmes within the department; • the research carried out within the department; • the department’s professor and lecturer plan. The department heads are: Computer Science: prof. dr. A.E. Eiben Physics and Astronomy: prof. dr. P.J.G. Mulders Chemistry and Pharmaceutical Sciences: prof. dr. H. Irth Mathematics: prof. dr. A.W. van der Vaart History, Philosophy and Social Aspects of Science: prof. dr. F.H. van Lunteren

1.3

Educational Organisation The responsibility for organising the Faculty of Sciences’ teaching programmes is in the hands of the Faculty Board. However, the actual implementation of this task has been delegated to the Board of Education.

1.3.1

Board of Education The Faculty’s Board of Education is charged with organising and co-ordinating the teaching within the departments, as well as the teaching intended for other programmes at the university. The Board of Education, after consulting the departments, puts forward a proposal for the allocation of teaching staff to the various educational units. It also carries out evaluations to ensure that the quality of the teaching is maintained. The Board also prepares inspections and advises on the recruitment of teaching staff. A member of the Board of Education takes part in the appraisals of teaching staff and acts as an informant in the evaluation of professors. The Board of Education consists of four members of academic staff, each of whom are selected from one of the four departments Computer Science, Physics and Astronomy, Chemistry and Pharmaceutical Sciences, and Mathematics. The Faculty Board appoints one of the members of the Board of Education to the position of head (or Educational Director) for a period of three years. The members of the Board of Education are: prof. dr.W.H. Mager (Chemistry, Pharmaceutical Sciences and Medical Natural Sciences), chairperson dr. J.P. Dekker (Physics and Astronomy) dr. F. van Schagen ( Mathematics and Business Mathematics & Informatics) dr. J.M. van Wouwe (Computer Science, Artificial Intelligence and Information Sciences) vacancy (student), advisor dr M. Witte (Head of the Education and External Affairs Office), advisor Faculty of Sciences

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1.3.2

Education and External Affairs Office The Education and External Affairs Office takes care of the student administration and the planning and organization of lectures and examinations. In addition the Office also provides policy support to the administrative bodies and the Educational Director. It also takes care of public relations for the Faculty and provides information to potential students. The members of the Education and External Affairs Office are: dr. M. Witte (head), Room S3.56, Phone: +31 (0) 20 44 47730 Education Office, Room S3.11: C.M.L. Berkeveld (Medical Natural Sciences), Phone: +31 (0) 20 44 47657 A.J. Bikker-Burggraaf (assistant education co-ordinator), Phone: +31 (0) 20 44 47486 N. Brouwenstijn (Chemistry and Pharmaceutical Sciences), Phone: +31 (0) 20 44 47663 E.H. Pauw (Mathematics and Computer Science Bachelor’s), Phone: +31 (0) 20 44 47655 P. Rinsma (Physics and Astronomy), Phone: +31 (0) 20 44 47664 J. van Schie (education office co-ordinator), Phone: +31 (0) 20 44 47662 M. Sotiriou (desk), Phone: +31 (0) 20 44 47660 J.J.W. Trimbach (Mathematics and Computer Science Master’s), Phone: +31 (0) 20 44 47661 PR and Information: B. Blasweiler, Room P3.22, Phone: +31 (0) 20 44 47517 C.M.A. Fruitier, Room P3.54, Phone: +31 (0) 20 44 47507 M.J. Veenkamp, Room P3.62, Phone: + 31 (0) 20 44 47732 M.A.H. Vermond, Room P3.22, Phone: +31 (0) 20 44 47651 International Relations: J. Furman, Room P3.62, Phone: +31 (0) 20 44 47499

1.3.3

Programmes The new University programme structure features three-year courses which lead to a Bachelor’s degree and which are open to students with an appropriate pre-university background. Following this, there are programmes of one or two years leading to a Master’s degree. The table below contains an overview of all the programmes within the Faculty of Sciences. Master programmes

Name Artificial Intelligence: Intelligent Internet Applications Knowledge Management and Technology Self Organising Systems Interdisciplinary Applications Cognitive Science AI and Communication Bioinformatics Biomolecular Sciences**

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Exact Sciences

Programme Full time

Full time Full time

Business Mathematics and Informatics Chemistry: Analytical Sciences* Laser Sciences / Molecular Photoscience* Biochemistry Molecular Design, Synthesis and Catalysis* Computational and Theoretical Sciences* Chemistry and Education Chemistry and Communication Chemistry and Business Computer Science: Internet en Web-technology Parallel Computing and Visualisation Software Engineering Multimedia Formal Methods and Software Verification Technical Artificial Intelligence Information- and Communication Technology Computer Science and Communication Information Science: Business Informatics Multimedia and Culture Mathematics*: Fundamental Mathematics Application Oriented Mathematics Mathematics with Life Sciences Mathematics and Communication Mathematics and Education Medical Natural Sciences: Physics of Life Molecular Medicine Bioinformatics/Genomics Bio Complex Systems MNS and Communication MNS and Management Parallel and Distributed Computer Systems *** Pharmaceutical Sciences / Pharmacochemistry: Drug Discovery & Target Finding Drug Disposition & Safety Assessment Drug Design & Synthesis Computational Medicinal Chemistry & Toxicology Biomolecular & Drug Analysis Pharmacochemistry and Communication Pharmacochemistry and Business Physics: Biophysics and Physics of Complex Systems Computational Physics Laser Sciences / Molecular Photoscience* Condensed Matter Science* Particle and Astroparticle Physics* Theoretical Physics* Physics and Business Physics and Communication Physics and Education Stochastics and Financial Mathematics*

Full time Part time Dual Full time

Full time

Full time Full time Part time

Full time

Full time Full time

Full time

Full time

* Together with the Universiteit van Amsterdam.

Faculty of Sciences

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** Together with the Faculteit der Aard- en Levenswetenschappen. *** See for further information of this master http://www.cs.vu.nl/masters/compsys/ 1.3.4

Educational Committee Each programme has a programme committee. The programme committee advises the head of department and the board of the Faculty of Sciences on matters relating to education. The programme committee also carries out class evaluations and, every year, it also advises on the Education and Examination Regulations. Three members of the programme committee are drawn from the academic staff. The remaining three are students. The director of education and the programme advisor are consultant members.

1.3.5

Examination Board The Faculty Board sets up the Examination Board, made up of members of the academic staff responsible for the education in these programmes. For each programme or group of programmes is a sub-committee in the examination board. The Board draws up rules with regard to proper examination procedure and also administers the examinations. It allocates examiners and can give them guidelines on evaluating the examinations. The Board also draws up the Rules and Guidelines for Examinations and Interim Examinations. Membership of the Examination Board is not open to students. http://www.few.vu.nl/onderwijs/reglementen-en.html Examination Board (executive management): prof. dr. D. Lenstra, chairperson prof. dr. M. van Veldhuizen, secretary Sub-committees Physics and Astronomy: prof. dr. D. Lenstra, chairperson dr. J.P. Dekker, secretary dr. W.A. Sterrenburg Chemistry and Pharmaceutical Sciences: prof. dr. H.A. Raué, chairperson prof. dr. K. Lammertsma, secretary dr. H. Lingeman prof. dr. R. Leurs, advisor prof. dr. S. Stolte, advisor Mathematics and Computer Science: prof. dr. F.M.T. Brazier, chairperson prof. dr. M. van Veldhuizen, secretary prof. dr. A.C.M. Ran dr. ir. T. Koetsier dr. C.M. Jonker Medical Sciences: dr. H. Lingeman, chairperson dr. J.P. Dekker, secretary prof. dr. A.C.M. Ran

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Exact Sciences

1.4

Research organisation Research takes place within the various departments of the Faculty. In the interests of promoting multidisciplinary research, the Faculty Board can set up research institutes. The Faculty’s Laser Centre is such a research institute.

1.4.1

Research groups A department’s research activities take place in research groups. These groups participate in a number of research schools and research institutes. The Department of Physics and Astronomy contains the following research groups: • Subatomic Physics and Nuclear Physics Measurement Methods head: prof. dr. ing. J.F.J. van den Brand Secretarial support: Ms P.H. Koning, Room T2.24, Phone: +31 (0) 20 44 47459 • Theoretical Physics head: prof. dr. F. MacKintosh Secretarial support: Ms P.H. Koning, Room T2.24, Phone: +31 (0) 20 44 47459 • Solid State Physics head: prof. dr. R.P. Griessen Secretarial support: Ms P.H. Koning, Room T2.24, Phone: +31 (0) 20 44 47459 • Biophysics head: prof. dr. R. van Grondelle Secretarial support: Ms Y.M. de Bruin, Room T2.04, Phone: +31 (0) 20 44 47890 • Physics of Complex Systems head: prof. dr. C.F. Schmidt Secretarial support Physics of Complex Systems: Ms G.J. Rijnsburger, Room U0.21, Phone: +31 (0) 20 44 47891 • Physics Practicals and Didactics head: dr.P.J. Blankert secretarial support: Ms Y.M. de Bruin, Room T2.04, Phone: +31 (0) 20 44 47890 • Atomic Physics and Laser Physics head: prof. dr. W.M.G. Ubachs secretarial support: Ms Y.M. de Bruin, Room T2.04, Phone: +31 (0) 20 44 47890 • Physics Computer Science head: prof. dr. ir. H.E. Bal secretarial support: Ms P.H. Koning, Room T2.24, Phone: +31 (0) 20 44 47459 The Department of Chemistry and Pharmaceutical Sciences contains the following research groups: • Analytical Chemistry and Applied Spectroscopy head: prof. dr. C. Gooijer secretarial support: Ms G.M. Cassée, Room M3.28, Phone: +31 (0) 20 44 47544 • Biochemistry and Molecular Biology head: prof. dr. S.M. van der Vies secretarial support: Ms N. Ramdjan, Room KB2.46, Phone: +31 (0) 20 44 47555 • Organic and Anorganic Chemistry head: prof. dr. K. Lammertsma secretarial support: Ms J.M. Sisto-Rijken, Room N3.38, Phone: +31 (0) 20 44 47480 • Medicinal Chemistry head: prof. dr. R. Leurs secretarial support: Ms L. de Wit, Room P2.46, Phone: +31 (0) 20 44 47600 Faculty of Sciences

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• Molecular Toxicology head: prof. dr. N.P.E. Vermeulen secretarial support: Ms L. de Wit, Room P2.46, Phone: +31 (0) 20 44 47600 • Physical Chemistry head: prof. dr. S. Stolte secretarial support: Ms T.M. de Jonge, Room O1.31, Phone: +31 (0) 20 44 47644 • Theoretical Chemistry head: prof. dr. E.J. Baerends secretarial support: Ms P. van Berkum, Room R1.54, Phone: +31 (0) 20 44 47519

The Department of Mathematics contains the following research groups: • Geometry head: prof. dr. J. van Mill secretarial support: Ms M.W.S. Titawano, Room S3.38, Phone: +31 (0) 20 44 47700 • Analysis head: prof. dr. J. Hulshof secretarial support: Ms M.W.S. Titawano, Room S3.38, Phone: +31 (0) 20 44 47700 • Stochastics head: prof. dr. R.W.J. Meester secretarial support: Ms M.W.S. Titawano, Room S3.38, Phone: +31 (0) 20 44 47700 The Department of Computer Science contains the following research groups: • Information Management and Software Engineering head: prof. dr. J.C. van Vliet secretarial support: Ms E. Lammers, Room T3.06c, Phone: +31 (0) 20 44 47718 • Computer Systems head: prof. dr. A.S. Tanenbaum secretarial support: Ms I. Thomson, Room S3.54, Phone: +31 (0) 20 44 47483 • Artificial Intelligence head: prof. dr. J. Treur secretarial support: Ms I. Thomson, Room S3.54, Phone: +31 (0) 20 44 47483 • Theoretical Computer Science head: prof. dr. A.E. Eiben secretarial support: Ms E. Lammers, Room T3.06c, Phone: +31 (0) 20 44 47718 • Business Informatics head: prof. dr. J.M. Akkermans secretarial support: Ms E. Lammers, Room T3.06c, Phone: +31 (0) 20 44 47718 • Bioinformatics head: prof. dr. J. Heringa secretarial support: Ms I. Thomson, Room S3.54, Phone: +31 (0) 20 44 47483 1.4.2

Research Schools A research school is a cooperative venture between institutes in a certain field of research. Its aim is to organise a high-quality four-year educational program for its Ph.D. students and to facilitate and stimulate co-operation and communication between its members and stakeholders, including leading (industrial) companies in the field. A research school can be approved as such by the Royal Netherlands Academy of Arts and Sciences. The Department of Physics and Astronomy participates in five research schools:

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Exact Sciences

SAF (Subatomic Physics) NOVA (Netherlands Research School for Astronomy) • Biocentrum Amsterdam (Biophysics) • COM-OP (Condensed Matter and Optical Physics) (biophysics, solid state physics, atomic physics, theoretical physics) The Physics and Astronomy Department is the leading party in COM-OP, Prof. D. Lenstra is director, Dr D.G. de Groot is executive manager and Ms P. de Koning is management assistant/secretary. • FANTOM (Fundamental and Applied Nuclear and Atomic Physics) (nuclear physics measurement methods). The Department of Physics and Astronomy is affiliated with the Netherlands Research School of Theoretical Physics (LOTN). The department also participates in the COMPAS research institute (Condensed Matter, Physics and Atomic Spectroscopy) (Director: Prof. D. Lenstra) and is an indirect partner in NIKHEF, the Netherlands’ national institute for subatomic physics. •

•

The Department of Chemistry and Pharmaceutical Sciences participates in the following research schools, recognized by the Royal Netherlands Academy of Arts and Sciences: • Biocentrum Amsterdam • Leiden/Amsterdam Centre for Drug Research • Holland Research School for Molecular Chemistry The Department of Mathematics participates in the Thomas Stieltjes Institute for Mathematics together with the mathematics departments of the University of Amsterdam, Delft University of Technology, Eindhoven University of Technology, University of Leiden and Erasmus University, Rotterdam. The Stieltjes Institute works together with the Centre for Mathematics and Computer Science. From their third year, students can take what are known as the ‘Stieltjes classes’. These are detailed in the information guide published by the Stieltjes Institute and (subject to approval) can count towards a Master's degree or the educational requirements set for trainee research assistants (AIOs). A reference copy of the Stieltjes Institute information guide is available at the Education Office. General information on the Stieltjes Institute can be found at: http://www.math.leidenuniv.nl/~stieltjes. The Departments of Computer Science and Artificial Intelligence are associated with the following research schools: • SIKS (Dutch Research School for Information and Knowledge Systems) • IPA (Institute for Programming Research and Algorithmics) • OZL (Dutch Research School in Logic) • ASCI (Advanced Simulation and Computing)

Faculty of Sciences

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Exact Sciences

2

2.1

Education Exact Sciences Academic calendar The academic year is divided into six teaching periods of eight, eight, four, eight, eight and four weeks respectively. The final week of each period is reserved to tests. Two weeks are devoted to re-sits. One is after the second period and the other is at the end of the summer holiday. Period 1 2 3 4 5 6

Dates Mon 06/09/04 to Fr 29/10/04 Mon 01/11/04 to Fr 07/01/05 Mon 10/01/05 to Fr 04/02/05 Mon 07/02/05 to Fr 01/04/05 Mon 04/04/05 to Fr 03/06/05 Mon 06/06/05 to Fr 01/07/05

Week numbers 37 to 44 45 to 1 2 to 5 6 to 13 14 to 22 23 to 26

There are no classes on the following days: December Mon 27 till January Fri 7 March Fri 25: Good Friday March Mon 28: Easter Monday May Thurs 5: Ascension Day May Fri 6: Mandatory day off May Mon 16: White Monday Also look on the website: http://www.few.vu.nl/onderwijs/roosters/periode04-05.html The study advisor and the section educational coordinator can assist you in drawing up your study programme.

2.2

Master coordinators For each of the master's programmes there are Master programme coordinators to consult when you want to put together your master study programme. This is also the individual with whom you agree matters relating to your masters thesis (when should you start, who will supervise you? etc). Thus, any questions that you have concerning the programme aspects of the master's course can be put to this person. The master coordinators are named in the educational chapters of each study.

2.3

Monitoring students' progress A programme consists of examination components, which are also referred to as 'subjects'. Each examination component carries a number of ECTS credits. The exact number of credits for each component is given in the Education and Examination Rules (OER). The Master's programmes are each worth 120 creditpoints, exept the Master Information Sciences and the Master Medical Natural Sciences these are each worth 60 creditpoints. Twice a year, each student receives a computer printout giving full details of their course results up to that time. At least twice a year, in order to Education Exact Sciences

23

monitor students' progress, the Education Office produces a cohort-based summary of all interim examination results for each programme. These summaries are analysed by the programme coordinator who is most closely involved. This can result in action focused either on individual students (if they are achieving poor results), or on a programme committee or a Director of Education (if the problems in question are of a collective nature).

2.4

Educational rules The rules on which these regulations were originally based, can be found in the Faculty's web page: http://www.few.vu.nl/onderwijs/reglementen-en.html

2.4.1

Admission requirements for the Master The admission requirements for the Master are described in the specific parts per study in this guide. Students who want to follow a master programme at the VU should contact the Master coordinator.

2.4.2

Enrolment procedures VU - UvA Because several master's programmes are offered in cooperation with the Universiteit van Amsterdam VU-students who follow classes at the UvA have to enrol as a 'bijvak' student at the UvA. For the academic year 2004-2005 VU-students have to follow this procedure: • The student has to register at the UvA as a 'bijvak' student. At the moment this has to be done again each year. • The VU master's programme coordinator will arrange a 'bijvak student' registration form, to be send to the students study address. The student must send in or hand over to the Central Registration Office of the UvA the following documents: • the registration form for 'bijvak' student. Address: Studentencentrum, Vendelstraat 2, 1012 XX Amsterdam, phone: +31 (0 ) 20 525 4889.

2.4.3

Enrolment procedure courses For all the courses and examinations registration is compulsory. Generally this is done via the ‘TISVU’ procedure. Sometimes the student has to contact the lecturer directly. Registration of courses At the latest three weeks prior to the starting date of the course the starting via http://tisvu.vu.nl/HTM/TISVULogin.htm

2.4.4

24

Interim examinations and practical work Registering for interim examinations Candidates for each written interim examination must register via TISVU (interim examination information system) no later than 8 days prior to the interim examination in question. TISVU manuals are available from the Education Office. In the case of oral interim examinations, individual arrangements can be made with the lecturer in question. With regard to practicals, candidates must either register using TISVU, via the Blackboard page of the lecturer in question, or at the Education Office.

Exact Sciences

Cancellation of interim examination or practical Those who are unable to attend an interim examination for which they have already registered must deregister via TISVU no later than 8 days prior to the examination in question. Publication of results of interim examinations Results will be published as soon as possible, but no later than twenty working days after completion of the written interim examination. They will be posted on the notice boards opposite the Education Office desk in the S3 corridor. In the case of oral interim examinations, candidates are immediately informed of the results via an interim examination form that they are required to bring to the interim examination in question. The lecturer records the grade on the form, which is then signed or initialled. The results of practicals will be made known within twenty-two working days after the completion of these components. They will either be posted on the notice boards opposite the Education Office desk in the S3 corridor or they will be handed out personally to each individual student, in the form of an official document. All examination components receive a grade that is either a whole number or an extension of .5. Grades of 5.0 or less correspond to fail, while grades of 6.0 and above mean a pass. Markers are not allowed to give final grades of between 5.0 and 6.0. If a student sits the interim examination for a given component more than once, then the highest mark counts. Right to inspection For at least thirty days after publication of the results of a written interim examination, students can request an opportunity to inspect their assessed work. Upon request, they will also be provided with a copy of the work in question. Students may inspect their work either at the Education Office desk or at the office of the lecturer in question. Registration of course results All course results are processed by the Education Office and stored in a student administration system. Students can inspect the recorded results for themselves, via TISVU. Exemptions Students who have previously successfully completed a comparable course component at another institute of higher education can ask the examination board to grant them an exemption from the relevant interim examination or practical. This request should be accompanied by information concerning the institute involved, the date of the course component examination in question and the name of the lecturer concerned. Students should also indicate the study load of the relevant course component (in terms of credits). In addition, detailed information must be supplied concerning the content of the course component in question. The student is notified in writing concerning the exemptions granted by the examination board. A copy of this document is also sent to the Education Office. The validity of course results Successfully completed examinations of the Master remain valid for four years. In cases where the period that has elapsed since a student successfully completed the

Education Exact Sciences

25

interim examination in a given component exceeds the stipulated term, the examination board may decide that the individual in question must sit an additional or replacement interim examination in that component before being permitted to sit the relevant examination. 2.4.5

Master Thesis Depending on the selected profile, students must complete a research project of 36 credits (M and C/E profile) or 60 credits (O profile). The mandatory elements of a research project are the literature survey, designing and performing research and presenting both verbal and written reports on the project. Approximately six months prior to the start of the research project, the subject of the project, its duration and the period in which it will take place must be agreed with the master programme coordinator. The chapter about the Master contains a description of possible research topics in each of the various specialisation's (main subjects). Literature Thesis Students can prepare a literature thesis (‘scriptie’) on a single topic, one that is not directly related to their specialisation of 12 credits. Approximately three months before students plan to start work on the literature thesis, the subject of the thesis, the duration of the work and the period in which it will take place must be agreed with the relevant programme coordinator.

2.4.6

Final Exams Students should register for examinations using an application form, which must be requested at the Education Office at least two weeks before the meeting of the examination board. The following documents should be submitted when requesting the form: 1. the university registration card; 2. an examination board approval of the examination programme / selected subjects. Students are urgently reminded that, at the time of the application, they must already have met all of the requirements for sitting the examination. This means that the Education Office must have been informed of the results of all examination components. For details of the dates of examination board meetings and of the degree ceremony, see the table Degree ceremonies 2004/2005. The master's or doctoral examination ceremony will be arranged by each subexamination committee separately (Physics and Astronomy, Chemistry and Pharmaceutical Sciences, Mathematics and Computers Science, and Medical Natural Sciences).

2.4.7

26

Degree ceremonies Last examination request 8th September 2004

Date of Examination 22th September 2004

6th October 2004

20th October 2004

3rd November 2004

17th November 2004

Exact Sciences

Degree Ceremony 12th October 2004 13th October 2004 14th October 2004 14th December 2004 15th December 2004 16th December 2004 14th December 2004 15th December 2004

(1) (2) (3) (1) (2) (3) (1) (2)

1st December 2004

15th December 2004

12th January 2005

26th January 2005

2nd February 2005

23th February 2005

2nd March 2005

16th March 2005

6th April 2005

20th April 2005

4th May 2005

18th May 2005

8th June 2005

22th June 2005

8th June 2005 *

31th August 2005

16th December 2004 15th February 2005 16th February 2005 17th February 2005 15th February 2005 16th February 2005 17th February 2005 19th April 2005 20th April 2005 21th April 2005 19th April 2005 20th April 2005 21th April 2005 14th June 2005 15th June 2005 16th June 2005 14th June 2005 15th June 2005 16th June 2005 23th August 2005 24th August 2005 25th August 2005 13th September 2005 14th September 2005 15th September 2005

(3) (1) (2) (3) (1) (2) (3) (1) (2) (3) (1) (2) (3) (1) (2) (3) (1) (2) (3) (1) (2) (3) (1) (2) (3)

(1) doctoral- and master examination ceremony Physics and Astronomy (2) doctoral- and master examination ceremony Mathematics and Computers Science (3) doctoral- and master examination Chemistry and Pharmaceutical Sciences *) Note: This date is out of the ordinary. Students who want to sit for the examination of August have to hand in their application form at the Educational Office not later than June 8. This is possible even if grades for some subjects miss because of re-sits in August or completion of the master thesis. Arrangements should be made with the Educational Office as to when the last results should be handed in. You should therefore keep an eye on the 'News' and on the notice boards near the Education Office. 2.4.8

Attendance certificate Those who terminate their studies without successfully completing the final examinations can obtain an attendance certificate from the examination board, provided that they have successfully completed at least two course components. The attendance certificate lists those examination components that have been successfully completed.

2.4.9

Right of appeal Students who wish to object to a mark that they have been awarded should first approach the relevant lecturer. If this fails to produce a satisfactory solution, the student in question should then approach the chairperson of the examination board.


27

Examination Appeals Board For complaints about the decisions of the examination board students might contact the Examination Appeals Board. An appeal can be lodged with this body by students who object to the results of interim or final examinations, to the evaluation of study assignments and theses, or to the way in which they have been treated. For details see the VU Student Statute (general section of the study guide), which contains a description of the procedure involved and the grounds for appeal. Appeals must be lodged within thirty days of the decision in question. Further information on this topic can be obtained from the Student General Counselling Service. The Student General Counselling Service can be reached via the general Student Services Desk in the central hall of the main building, De Boelelaan 1105, room 0A11, which is open on weekdays from 10 a.m. to 5 p.m. It is also possible to make an appointment with the Student General Counselling Service by calling +31-(0)204445020. 2.4.10

Education and Examination Rules There are Education and Examination Rules (OER) for every programme that is offered by the faculty. In addition to specifying the purpose of the Master, the OER also contains information on the rules and guidelines concerning teaching arrangements for the Master's, examinations and interim examinations, obtaining exemptions, requisite educational background, progress in the course of studies, study advice etc. For further details, see the Education and Examination Rules http://www.few.vu.nl/onderwijs/reglementen-en.html Since it is a legal document, it is written in Dutch.

2.4.11

Rules and Regulations of the Examination Board The examination board of the Faculty of Sciences, which draws up rules to ensure that the interim examinations proceed correctly, is appointed by the faculty board (see chapter 2). It also conducts the final examinations. The board appoints examiners and can provide them with guidelines on the evaluation of the interim examinations. It also sets out further Rules and Guidelines for interim and final examinations. For further details, see the examination board's Rules and Regulations for Examination http://www.few.vu.nl/onderwijs/reglementen-nl.html Since it is a legal document, it is written in Dutch.

2.5 2.5.1

Educational quality control Educational Committees The educational committee advises the director of education, the head of the department and the board of the Faculty of Sciences on matters relating to education, including class evaluations. Every year, it also advises on the Education and Examination Rules. Academic staff makes up half of the membership of the programme committee, the other half are students. The director of education and the study advisor are consultant members. The Chairpersons of the Educational Committees are: Artificial Intelligence: dr. C.M. Jonker Business Mathematics and Informatics: prof. dr. A.C.M. Ran Chemistry: dr. M.W.G. de Bolster

28

Exact Sciences

Computer science: dr. R.C. de Vrijer Financial Mathematics and Stochastics: prof. dr. M. van Veldhuizen Information Science: dr. J. Gordijn Mathematics: prof. dr. M. van Veldhuizen Medical Natural Sciences: dr. G.J.L. Wuite Pharmaceutical Sciences: dr. M.W.G. de Bolster Physics and Astronomy: prof. dr. R.P. Griessen 2.5.2

2.6

Assessment of education The faculty is constantly endeavouring to improve the quality of its programmes. As part of this effort, students are asked to express their views on this matter by filling in questionnaires or being interviewed. The results of these surveys are discussed with the lecturers and during meetings of the programme committees. A summary of the assessment procedure is available for inspection, at the Education Office.

Students' associations

2.6.1

AIK AIK is the student association for all students in Physics and Astronomy at the Faculty of Sciences. Address: Students' associations Aik, room SK.12, phone: +31 (0) 20 44 47989, email: [email protected], website: http://www.nat.vu.nl/~aik/

2.6.2

MENS MENS is the student association for all students in Medical Natural Sciences at the Faculty of Sciences. Address: room TK.18, phone: +31 (0) 20 44 47613, e-mail: [email protected], website: http://www.few.vu.nl/mens

2.6.3

STORM STORM (STudent Organisation for Mathematicians) is a student association for all students in the Mathematics and Computer Science departments of the Faculty of Sciences. STORM has two rooms, one is used for socialising and the other is for board meetings. These are in S0.10 and T0.28 on the ground floor, phone: +31 (0) 20 44 47666, e-mail: [email protected], website: http:// www.cs.vu.nl/storm

2.6.4

VCSVU The VCSVU is a flourishing association with approximately 160 members who are students at the Department of Chemistry and Pharmaceutical Sciences. The VCSVU is also responsible for putting together a periodical called Papieren Binding. Address VCSVU: room M1.54 and room N1.57, phone: +31 (0) 20 44 47510, e-mail [email protected], website: http://www.vcsvu. Educational trips for Chemistry and Pharmaceutical Sciences students The association Stichting Studiereizen Chemiestudenten, SSC was set up to deal with the financial risks and the know-how associated with organizing an educational trips abroad. In principle, every student is given the opportunity to take part in an educational trip in the course of his or her studies. For further information see: http://www.chem.vu.nl/studiereis


29

2.7

Studying abroad There are plenty of good reasons for completing part of your studies in a foreign country. These include cultural interest, personal development, widening the course of study, moving on to the second phase of the programme, and adding lustre to your curriculum vitae. The Faculty of Sciences offers you various opportunities to complete part of your studies abroad. For instance, there are cooperation agreements with partner institutions within the framework of the Erasmus/Socrates programme. The advantages of studying at a partner institution are that you are not required to pay extra tuition fees, arranging for your stay is a fairly simple matter, and you can usually obtain a grant. When studying abroad, you can either attend lectures or complete a final project (or a combination of these activities). In some instances, after first consulting the parties in question, you can make use of the contracts that other faculties have signed with partner institutions. There is also the opportunity of studying in the United States, within the framework of the International Student Exchange Program (ISEP). You pay the usual tuition fees to the VU, plus € 3,000 for one semester's study in the US. This is inclusive of meals and accommodation. You also pay $ 300 in registration costs. If you wish to complete part of your final project at a foreign institution with which neither the VU nor the Faculty of Sciences has signed an agreement, then you may be eligible for a 'free movers' grant. Grants are awarded on a competitive basis. In all cases, it is essential that you start making preparations at least six months prior to departure. In order to ensure that your credits will be recognized, it is important that you maintain your registration as a student of the VU throughout your period of study abroad. Further details about studying abroad can be found at: www.vu.nl -> studenten -> internationaal. One particularly useful site is: www.nuffic.nl. Alternatively, you can make an appointment with the International representative of the Faculty of Sciences, Jasperina Furman. E-mail: [email protected].

2.8 2.8.1

Orientation on the Labour Market Stichting Bèta Bedrijvencontactdag Amsterdam Each year, the Stichting Bèta Bedrijvencontactdag Amsterdam (Foundation for the Company Recruitment of Exact Science Students in Amsterdam) or SBBA organises a company recruitment day for exact science students studying at the Vrije Universiteit (VU) and the University of Amsterdam (UvA). The annual company recruitment day takes place on the first Thursday in April, and is held alternately in the buildings of the VU and those of the UvA. The company recruitment day is primarily aimed at senior students and PhD students. In March, these students each receive an invitation and a copy of the programme, which contains a registration form. The recruitment day includes an Info Market, where companies present themselves. There are also a number of lecture series, in which individual companies have the

30

Exact Sciences

opportunity to inform the public about the employment opportunities that they can offer exact science students. Students can request a personal interview with a given company by completing and submitting the curriculum vitae (CV) that is enclosed with the registration form. Students whose CVs are of interest to the companies concerned are invited to the interview days, which take place some time after the recruitment days, usually in May. The SBBA is made up of students of the VU and the UvA. Further details concerning the SBBA or the company recruitment day can be obtained from the Foundation's website: www.sbba.nl.

2.9

Professional Associatons

2.9.1

Belgisch/Nederlandse Vereniging voor Kunstmatige Intelligentie (BNVKI) The BNVKI is the professional association for everyone in Belgium and the Netherlands involved with Artificial Intelligence, both from academia and industry. The association organising the yearly Belgisch Nederlandse AI Congres (BNAIC), and publishes 6 times per year a newsletter. The BNVKI has reduced membership fees for students. For more information: http://www.cs.unimaas.nl/~bnvki

2.9.2

Centrum voor Wiskunde en Informatica (CWI) The CWI is a research institute for mathematics and computer science, located in Amsterdam. The CWI has the largest library on these subjects in the Netherlands. Frequently there are lectures and colloquia at the CWI. More information is available on the website http://www.cwi.nl

2.9.3

Koninklijke Nederlandse Chemie Vereninging (KNCV) The Royal Netherlands Chemical Society KNCV, is the professional organization for chemists and chemical engineers in The Netherlands. For more information see the website: http://www.kncv.nl

2.9.4

Koninklijk Wiskundig Genootschap The Dutch Mathematical Society is called “Koninklijk Wiskundig Genootschap”. Members receive the “Nieuw Archief voor Wiskunde”. For more information see the website http://www.wiskgenoot.nl

2.9.5

Nederlands Genootschap voor Informatica (NGI) The NGI is the Dutch Society for Computer Science.Information about the Ngi and its activities can be found on the website http://www.ngi.nl

2.9.6

Nederlandse Natuurkundige Vereniging (NNV) In the NNV a large number of graduated Dutch physicists are united. Students can become a member at a reduced rate, so they will be informed of everything that is going on in the field of physics. Address: Prins Mauritslaan 29-39, Postbus 302, 1170 AH Badhoevedorp, phone: +31 (0) 20 658 0228

2.9.7

Nederlandse Astronomenclub (NAC) The Dutch Astronomers Club aims to promote the study of astronomy in the Netherlands. Of this club almost all astronomers are a member. Students of


31

astronomy and/or physics can become a memeber as soon as the have completed two course years. Secretary: dr. S.J. Hogeveen, e-mail: s.j. [email protected] 2.9.8

Netwerk voor Informaticae Mathematicae en Fysicae (NIMF) NIMF is the Dutch network of women working in the areas of mathematics, physics, astronomy, computer science and other related beta-subjects. For information consult the website http://www.science.uva.nl/misc/nimf/ or write to Stichting NIMF, Da Costalaan 23, 2281 SB Rijswijk

2.9.9

Thomas Stieltjes Instituut for Mathematics Thomas Stieltjes Institute for Mathematics is a research institue for mathematics, in which participate both uniersities in Amsterdam, the universities in Delft, Eindhoven, Leiden and Rotterdam. The Institute cooperates with the Centre for Mathematics and Computer Science (CWI) in Amsterdam and the European Institute for Studies of Randomness (EURANDOM) in Eindhoven. For more information see the website http://www.stieltjes.org

2.9.10

32

Vereniging voor Statistiek en Operations Research (VVS) The VVS is the Dutch society for Statistics and Operations Research. Members receive Statistica Neerlandica (four times per year), Kwantitatieve Methoden (three times per year) and Stator (four times per year). More information can be found on the website of the VVS: http://www.vvs-or.nl

Exact Sciences

3

3.1

Study Facilities Opening hours Education Office During opening hours, you can ask your questions about grades, exams and classes to the staff of the Education Office desk, in room S3.11. The desk is open from 10.30 to 13.30 each day. Outside opening hours, the Education Office can be reached via phone: +31 (0) 20 44 47660 or e-mail: [email protected]

3.2

Books and Tutorials Textbooks, syllabi, lecture notes, etc can be obtained from the VU bookshop in the main building. Wherever possible, student associations will collectively purchase the textbooks for the courses. These will then be sold at reduced prices at the start of the relevant course of lectures. Textbooks can usually be borrowed from the library also.

3.3

Library The science and mathematics library contains sub-collections for Computer Science, Physics and Astronomy, Chemistry, Mathematics, History, Philosophy and Social Aspects of Science, Earth Sciences and Biology, as well as an Environmental Sciences collection. The collection of books and journals can be searched using the online public catalogue (OPC). Using this system, you can search by author(s), title, key word, or systematic code (Library of Congress Classification and National Library of Medicine Classification, Mathematics Subject Classification, Chemical Signatures). Articles in journals can be traced using electronic bibliographies (CD-ROMs and Internet). The ACM Guide to Computing Literature (volumes from 1980), MathSciNet (from 1940), PubMed (from 1952), Web of Science (from 1945 ) and Chemical Abstracts (12th & 13th Collective index as well as the volumes for 19972002) are available via the campus network (Internet). Most of the collections can be explored freely, without requiring the mediation of library staff. A large number of journals is available online and in full text form. Students must show their student chip card if they wish to take library materials out on loan. Journals are not available for loan. However, the library does have its own photocopying facilities. The library holds at least one copy of any book that is recommended or mandatory reading for given interim examinations. The UBVU (Library of the Vrije Universiteit) website provides detailed information about lending facilities, photocopying facilities, library regulations, other libraries at the VU, reading rooms and catalogues. Subject librarian/computerized literature survey: Mr M.G. Gerzon, room P6.20, phone: +31 (0) 20 44 45238 Ms A.A. de Maesschalck, room P6.20, phone: +31 (0) 20 44 45238 The science and mathematics library is located on the sixth floor of the Mathematics and Sciences building (W & N building). It can be reached via the entrance at 1083 De Boelelaan (P wing). Opening times: Monday to Friday from 9 a.m. to 5 p.m. The reading rooms are open from Monday to Friday, from 9 a.m. to 5.45 p.m. Desk telephone number: +31 (0) 20 44 45230, Library website: http://www.ubvu.vu.nl .

Study Facilities

33

3.4

Announcement and Information Facilities • • • •

•

3.5

Information about lectures and examination timetables can be found at the Educational Office or at the site www.few.vu.nl/onderwijs/index-en.html Information about courses on Blackboard website http://bb.vu.nl or on the of the course. Information on study results and registration for courses and examinations can be found on TISVU: tisvu.vu.nl. Announcements regarding changes in lecture or interim examination timetables, the results of interim examinations, notices concerning practicals, etc are posted on Internet, in the vufew.announce newsgroup, on www.few.vu.nl/onderwijs/index-en.html and on the notice-boards opposite the Education Office desk in the S3 corridor. Copies of lecture and interim examination timetables can also be obtained from the Education Office.

Educational rooms Lectures and tutorials are held in the bètagebouw (Science building). If they have not been reserved the R2 lecture rooms can be used as reading rooms. There are also special study areas in the science and mathematics library. Special lecture rooms on the first floor of the U and T wings have been equipped for laboratory experiments.

3.6

Computer facilities Students can use the computer systems provided, which run either Windows or Unix, to carry out tasks associated with their course of study. Rooms equipped with these computer systems are located in building sections P4, P3, S3, S1 and N1. The computer classrooms are available to students of the faculty from Monday to Friday from 8.30 a.m. to 10.30 p.m. At given times, the classrooms can be reserved for courses or for specific groups of users. Notices containing details of these times are affixed to the classroom door. At the start of the course, each first-year student is assigned an e-mail address and a log-in account. This account is not activated until the user has signed a declaration that he will observe the rules governing the use of the account. These rules are roughly as follows: the account is made available for the purposes of study, commercial activities are not permitted, copyright rules must be observed, normal codes of conduct apply. Those needing assistance with computer problems should contact the helpdesk, which is in room S4.09a of the Mathematics and Sciences building (W & N building). Physics students have a separate status, since they use laptops. They have log-in and printing facilities in the physics practical classrooms and in U0.30.

3.7

Digital learning environment Classes make use of the Blackboard digital learning environment, which can be accessed via Internet (http://bb.vu.nl). Blackboard contains general information about every course, including details of the timetable, the lecturers and the class' objectives. Blackboard also contains information related to the lectures or practicals, such as assignments, visualisation, sheets and web links. Students can place completed assignments (including group assignments) on Blackboard, and inspect one another's results. They can also use Blackboard to find out if there have been any last-minute changes to the lecture timetable.

34

Exact Sciences

3.8

Printing and copy facilities Photocopy machines are located at various points throughout the building. These are fitted with photocopy charge card readers. Photocopy charge cards can be purchased at the W & N Service Point, De Boelelaan 1085a, room M0.18, phone: +31 (0) 20 44 45888. Students are entitled to make use of certain printing facilities. These will vary, depending on the student's programme. Details of these arrangements can be obtained from the helpdesk, which is in room S4.09a of the Mathematics and Sciences building (W & N building).

3.9

Safety and Environment The Faculty of Sciences' Safety and Environmental Officer is: K. Maurer, room P3.12, phone: +31 (0) 20 44 47501 or tracer *97271, e-mail [email protected] Students can discuss any safety and environmental issues with this official. The official presents several information meetings on the subjects of safety, environment and working with computer monitors. At the first meeting, each student is issued with a copy of the safety regulations. Further information, and the rules on which these regulations were originally based, can be found in the: • Working Conditions Act; • Faculty of Science information booklet; • Faculty's web page.

3.10

Opening hours of the buildings There is free access to the Mathematics and Sciences building (W & N building) from Monday to Friday from 7.00 a.m. to 7.00 p.m. In addition, the building is accessible via the entrance at De Boelelaan 1085 from Monday to Friday from 7 p.m. to 10.30 p.m. At all other times, anyone present in the building must be in possession of a security pass. Security passes can be obtained from the W & N Service Point, De Boelelaan 1085a, room M0.18, phone: +31 (0) 20 44 45888. Both the W & N building and the faculty will be closed from Saturday 25-12-2004 to Saturday 01-012005.

3.11

Students' ID Card Each registered student is issued with a student chip card. Students are notified when their chip cards are ready for collection. Chip cards can be collected from the Student Services Desk in the central hall of the main building of the VU, room 0A-11. The Student Services Desk is open on weekdays from 10 a.m. to 5 p.m. The card acts as a pass for the university library. The chip card can also be used as a security pass for the Mathematics and Sciences building (W & N building), outside normal opening hours. Such use must be authorized by the head of the faculty. Finally, students with a physical disability can use the card as a parking permit. This is subject to a number of conditions. Details can be obtained from the W & N Service Point, De Boelelaan 1085a, room M0.18, phone: +31 (0) 20 44 45888, or from other VU service points.

Study Facilities

35

3.12

Disabled Access to the W & N building for the disabled is via the ramp at the 1083a entrance. There are toilets for the disabled in N0.54, M1.66 and S3.70.

3.13

Bicycle parking racks / bicycle repair shop The cellar of the W & N building contains both open and closed-off areas of bicycle parking racks. Access to the closed-off area of bicycle parking racks is by means of a special pass, which can be obtained from the W & N Service Point, De Boelelaan 1085a, room M0.18, phone: +31 (0) 20 44 45888. The 'Klavertje Vier' bicycle repair shop is located in the cellar of the main building of the Vrije Universiteit at De Boelelaan 1081, phone +31 (0) 20 44 49425.

36

Exact Sciences

4

4.1

Master Artificial Intelligence The domain of the Master Research in Artificial Intelligence concerns the analysis and modelling of tasks that are commonly assumed to require human intelligence, as well as the design of systems that can perform or support such tasks. Such research requires a wide varience of activities, from observing and interviewing human expert to designing and implementing computer programs, and creating mathematical models. Artificial Intelligence integrates computer science with (cognitive) psychology. Other ingredients are biology, linguistics, philosophy and logic, all used to understand and describe the underlying principles of human cognitive processes, including reasoning and natural language understanding. For these reasons Artificial Intelligence is a broad and multi-disciplinary research area. It is possible to study Artificial Intelligence at the Vrije Universiteit since 1991. The programme consists of a Bachelors study (taking 3 years) and a Master study (taking 2 years). The Bachelors study is dedicated to providing the student with a broad and thorough basis in Artificial Intelligence, whereas the Masters provides the student with an opportunity to specialise in an area and further deepen his knowledge of AI in general. Both Bachelors and Masters studies are organised by the Faculty of Sciences in close cooperation with the Faculty of Psychology and Pedagogy, and the Faculties of Linguistics and Law. Furthermore, the students can follow courses at the Universiteit van Amsterdam. Information about the Bachelor programme can be found in a separate study guide. The Vrije Universiteit offers a big variety of Master programmes in Artificial Intelligence. Currently, the following programmes are available: • Intelligent Internet Applications (Research Programme) • Cognitive Science (Research Programme) • Organisation Dynamics and Self Organisation (Research Programme) • Knowledge Management and Knowledge Technology (Societal Programme) • Technical Artificial Intelligence (Research Programme) • Interdisciplinary Applications (Societal Programme) • AI and Communication (Societal Programme) • "Maatschappelijke Variant" (Societal Programme) The latest information can always be found at: http://www.cs.vu.nl/ai/masters/. Depending on the chosen Master programme the student attends lectures in other faculties, for example Psychology, Linguistics, Economy, Law, Social Sciences, and Biology. Graduation projects vary from practical to rather fundamental, depending on the preferences and capacities of the students. Students can go to companies, research institutes or universities either in The Netherlands or abroad. Examples of projects and locations, and more information on what such a project entails, can be found at: http://www.cs.vu.nl/ai > Term Projects. Masters in Artificial Intelligence are employed by companies that develop AI-systems either for their own company (for example banks, insurance companies) or in commission for other companies (software companies). Masters in AI are also Master Artificial Intelligence

37

employed as consultants, for example for the management of knowledge within organisations. Research and education is another area where masters in AI build a future for themselves, for example at universities or research institutes doing research in Artificial Intelligence. Study advice is open to all. You can contact advisors Vera Stebletsova, email [email protected], and Martijn Schut (international students), email [email protected]. Furthermore, the website http:www.cs.vu.nl/ai/ contains information on study advice regarding Artificial Intelligence.

4.2

Objectives The Master programmes in Artificial Intelligence aim to provide the student with the knowledge, experience, and insights in Artificial Intelligence needed to carry out his/her professional duties autonomously, as well as to prepare the student for further education for the profession of teacher, or scientific researcher.

4.3

Final attainment level After graduation the student in Artificial Intelligence (AI) is expected to be critical in a scientific manner, to be aware of the social aspects of the creation of intelligent systems to support humans in their duties, and to possess knowledge, experience, and insights regarding: • knowledge acquisition and knowledge modelling; • methods for the design of AI-systems, such as knowledge-based systems, multiagent systems; • techniques for search and optimalisation, such as genetic algorithms and neural networks; • the architecture and operation of AI-systems; • the important programming paradigms for AI; • the determination of requirements that an AI-system has to meet; • the theoretical foundations of Artificial Intelligence; • subjects from philosophy, computer science, logic, psychology, language understanding and mathematics relevant for AI; • specialistic subjects in one or more of the research areas of AI. The graduate is capable of: practical application of the learned both alone as well as in a team; • clear oral and written presentation of the results of his/her work; • making good use of the literature on AI. •

4.4

Requirements for the Master For the Master programmes in Artificial Intelligence, students may enrol who have a Bachelor or Drs diploma in Artificial Intelligence obtained at a Dutch university (Utrecht, Nijmegen, Amsterdam (VU, UvA), Groningen, Maastricht). Some of the programmes are open to students who have a Bachelor, Drs or Master diploma in Computer Science, Psychology, Biology, or Law obtained at a Dutch institute or university of quality recognised by the Vrije Universiteit.

38

Exact Sciences

Some of the programmes are also open to people with other diplomas, University or HBO, who are kindly invited to contact us if interested in following a Master programme at our Department.

4.5

Master programmes For the Master in Artificial Intelligence, a number of different programmes are offered from which the student can choose. Below we briefly give the content of each programme. You can find more information http://www.cs.vu.nl/ai/masters. AI programmes: • Intelligent Internet Applications (Research Programme) • Cognitive Science (Research Programme) • Organisation Dynamics and Self Organisation (Research Programme) • Knowledge Management and Knowledge Technology (Societal Programme) • Technical Artificial Intelligence (Research Programme) • Interdisciplinary Applications (Societal Programme) • AI and Communication (Societal Programme) • "Maatschappelijke Variant" (Societal Programme) For psychology courses, please note that registration through the TISVU system is only possible for courses that count as first or second year Bachelor courses Psychology. All other courses require the student to register personally at the "Faculteit der Psychologie en Pedagogiek". The regulation regarding tentaminations can be found in the study guide of that Faculty through http://www.psy.vu.nl.

4.6 4.6.1

Intelligent Internet Applications Programme Future perspective: This Master programme contains elements so that the graduate student has a good overview of the contemporary literature regarding applications of intelligent websites and intelligent agents on the Internet. Furthermore, the student learns techniques and methods from Artificial Intelligence that are used in Internet applications. The master graduate student is a capable designer of intelligent web-sites, and applications based on intelligent agents. The student ensures that his/her designs respect the needs of the company for which the design is meant. Graduate students can work for any company interested in bringing intelligent applications to the Internet. Audience: The programme aims at students with aptitude for science, and having an interest for the application of artificial intelligence on modern communication technologies such as the Internet. Objectives and final attainment level: The objective of the programme is to endow the student with the developments on the area of artificial intelligence and modern communication technology, and to prepare for a profession as researcher or expert in a company. The curriculum must give a good preparation on PhD research. It is expected from the graduate to be critical in a scientific manner, to be aware of societal aspects of information technology and of the creation of intelligent systems and to possess knowledge, capabilities and insights related to: • knowledge acquisition and knowledge modelling Master Artificial Intelligence

39

methods of designing AI systems, specifically on internet applications based on intelligent agents • techniques for search and optimalization • architectures of AI systems • the design of intelligent websites • the contemporary literature on intelligent internet applications, including websites and internet agents and the graduate is expected to be capable of • working individually as well as in teams • reporting verbally and written professionally on his/her work • consulting specialist literature.

•

4.6.2

First year Also 27 cp optional courses. Course code 400111 400110 400081 400153 400152

4.6.3

150005 400016 400052

4.7.1

40

Course name

Behaviour Dynamics Master Project Artificial Intelligence

Stp.

Period

6 7 4 8 8

1 1 and 2 1 and 2 1 and 2 2 and 3

Stp.

Period

6 30

1 and 2 4, 5 en 6

Recommended optional courses Course code 400010

4.7

Evolutionary Computing E-Business Innovation User Interface Design Intelligent Web Applications I Intelligent Interactive Distributed Systems

Second year Also 24 cp optional courses. Course code 400113 400285

4.6.4

Course name

Course name Bedrijfsmodellering en requirements engineering Inleiding wijsgerige antropologie Computernetwerken Network Programming

Stp.

Period

7

1 en 2

6 5 9

28.03.2005 - 27.05.2005 4 en 5 5 and 6

Cognitive Science Programme Future perspective: A training in Cognitive Science prepares students well for many of the careers of the future, not only to become a researcher in this field, but also including humancomputer interaction, human factors design, medical analysis, information technology, data retrieval, and education.

Exact Sciences

Audience: The programme aims at AI students as well as Psychology students with an interest for a multi-disciplinary scientific training. Remarks: "Neural Models of Cognitive Processes" is called "Neural Networks" at the Faculty of Psychology. • "Onderzoeksmethoden Dataverzamelingstechnieken voor AI " is worth 6 ects, being half of the course "Onderzoeksmethoden I : dataverzamelingstechnieken" (12 ects) at the Faculty of Psychology. • "Opzetten van Onderzoek" will be given in an number of different variant, check for the latest information http://www.cs.vu.nl/ai/education-en.html. • Courses not taught in 03/04: "Perception", and "Knowledge Representation". • Courses not taught in 04/05: "Neural Models of Cognitive Processes". • For students of previous years: "Cognitive Neuroscience" is now called "hersenen en gedrag" at the Faculty of Psychology, teacher: Stims.

•

Specifics: This programme is organised in close cooperation with the Faculty of Psychology and can be entered by AI students and Psychology students. 4.7.2

Programme for students having a Bachelor in AI First year Also 12 cp optional courses. Course code 812025 815047 815048 813023 815050 813001 812001 813010

Course name

Onderzoeksmethoden I voor AI: Dataverzamelingstechnieken Perceptie Informatieverwerking Opzetten van Onderzoek Kennisrepresentatie Toegepaste Cognitieve Psychologie Thema: Aandacht in het brein Hersenen en Gedrag

Second year Also 6 cp optional courses. Course code 400111 400113 815051 815049 400285

Course name

Evolutionary Computing Behaviour Dynamics Neural models of cognitive processes Denken en beslissen Master Project Artificial Intelligence

Recommended optional courses Course code 400154 812005 800159

Course name

Machine Learning Onderzoeksmethoden II-A: Dataanalysetechnieken Geheugen

Master Artificial Intelligence

Stp.

Period

6 6 6 6 6 6 6 6

1 2 en 4 3 4 en 5 5 5 en 6

Stp.

Period

6 6 6 6 30

1 1 and 2 1 en 2 1 en 2 4, 5 en 6

Stp.

Period

6 12

1 and 2 5 en 6

4

41

4.7.3

Programme for students having a Bachelor in Psychology First year Also 6 cp optional courses. Course code 815051 400043 815049 400054 400312 815048 400126 400270 400132 400293

Course name

Neural models of cognitive processes Logische taal en redeneermethoden Denken en beslissen Design of Multi-Agent Systems Human-Computer Interaction Informatieverwerking Kennissystemen Programmeren in Prolog Neural Networks Project AI

Second year Also 6 cp optional courses. Course code 815047 400111 400113 815050 400285

Course name

Perceptie Evolutionary Computing Behaviour Dynamics Kennisrepresentatie Master Project Artificial Intelligence

Recommended optional courses Course code 400154 800159

4.8 4.8.1

Course name

Machine Learning Geheugen

Stp.

Period

6 5 6 6 5 6 4 4 6 6

1 en 2 1 en 2 1 en 2 2 2 and 3 2 en 4 4 5 5 6

Stp.

Period

6 6 6 6 30

1 1 1 and 2 4 en 5 4, 5 en 6

Stp.

Period

6 4

1 and 2

Organisation Dynamics and Self Organisation Programme Future perspective: After completion of this Master programme, the student • has an overview of the literature an practice in the area of organisation dynamics and self organisation • has mastered methods and techniques for modeling various types of organisations and their dynamics • is capable of constructing models of dynamic organisations with which can be simulated and experimented • is capable of conducting application-directed AI research in combination with other fields of research. Students of this programme can function in industry through a variety of different often management-related professions, within a diversity of institutions and companies, for example, in strategic management and organisation advising. Audience: Students with an interest in analysing, modeling, simulating and experimenting with dynamics properties.

42

Exact Sciences

Objectives and final attainment level: In this multi-disciplinary programme, elements from biology, social sciences, economics and computer science are integrated. By continuously generating new and diverse variants, organisms of increasingly large complexity are realised during biological evolution. Methods have been developed in AI (evolutionary methods, genetic algorithms), with which these evolution processes can be simulated. In nature, evolution leads to organisms that have such adapted to their environments that they can survive; in AI, evolution leads to acceptable solutions for problems. These methods turn out to be well applicable for the discovery of structure in large quantities of data (datamining). In biological populations, the interaction between organisms can also be further analysed, determining largely how successfully an organism can function; this is the subject of ecology and population dynamics. Concerning social sciences, models have been developed with which dynamic organisations can be described and simulated. Such methods are used in organisation theory to analyse large organisation and analyse and support processes of change within such organisations. In economics, simulation models are being developed in the area of market mechanisms, in which the behaviour of individuals leads to patterns in the economics as a whole. The student graduated in this Programme: has a good overview of the contemporary literature and practice in the area of self organising systems • has mastered methods and techniques for the modeling of dynamic organisation forms • is capable of, in cooperation with people from related scientific disciplines, modeling, simulating, and experimenting with dynamic organisation forms • is capable of doing applied AI research in cooperation with other scientific disciplines.

•

4.8.2

Programme for students having a Bachelor in AI First year Also 30 cp optional courses Course code 60422070 400111 470063 400188 703000

Course name

Advanced Methods for Applied Economic Research Evolutionary Computing Evolutiebiologie Organisational Dynamics Organisatietheorie (bacheloropleiding)

Second year Also 16 cp optional courses. Course code 400125 400113 400285

Course name

Knowledge Management and Modeling Behaviour Dynamics Master Project Artificial Intelligence


Stp.

Period

6

1

6 6 6 6

1 14.03.2005 - 08.04.2005 3 5e en 6e: dinsdagmorgen en donderdagmiddag

Stp. 6 6 30

Period 1 and 2 1 and 2 4, 5 en 6

43

Recommended optional courses

4.8.3

Course code 470503

Course name

Dynamic Energy Budgets

6

150005 470053

Inleiding wijsgerige antropologie Evolutionaire genetica

6 6

Period Study year 2004-2005, details will follow 28.03.2005 - 27.05.2005 29.11.2004 - 24.12.2004

Programme for students having a Bachelor in Biology or Medical Biology First year Also 1 cp optional courses. Course code 400125 400090 400150 400054 400188 400085 400126 400151 400270 400132 400201 703000

Course name

Knowledge Management and Modeling Zelforganiserende systemen Inleiding programmeren I Design of Multi-Agent Systems Organisational Dynamics Inleiding programmeren II practicum Kennissystemen Inleiding programmeren II Programmeren in Prolog Neural Networks Project Kennissystemen Organisatietheorie (bacheloropleiding)

Second year Also 4 cptional courses. Course code 400111 400154 400113 400108 400285

Course name

Evolutionary Computing Machine Learning Behaviour Dynamics Data Mining Techniques Master Project Artificial Intelligence

Recommended optionl courses

44

Stp.

Stp. 6 5 4 6 6 2 4 3 4 6 7 6

Stp. 6 6 6 6 30

Course code 470503

Course name

Dynamic Energy Budgets

6

150005 470053

Inleiding wijsgerige antropologie Evolutionaire genetica

6 6

Exact Sciences

Stp.

Period

1 and 2 1 en 2 1 en 2 2 3 4 4 4 5 5 5 en 6 5e en 6e: dinsdagmorgen en donderdagmiddag

Period 1 1 and 2 1 and 2 1 and 2 4, 5 en 6

Period Study year 2004-2005, details will follow 28.03.2005 - 27.05.2005 29.11.2004 - 24.12.2004

4.9 4.9.1

Knowledge Management and Knowledge Technology Programme Future perspective: An increasingly number of companies starts to document knowledge in the company with the use of knowledge acquisition and knowledge modeling techniques from AI. By doing this, the conduct of business is being simplified. Also with change processes in companies, automated knowledge intensive methods can be used, together with elements from economics and organisation psyhology. For graduates, these is a multi-disciplinary field of labour. Via company internships and company funded research projects there is good contact with industry. Audience: This programme aims at students with an aptitude for science, with an interest for the application of artificial intelligence on company management. Objectives and final attainment level: The programme has as objective to endow the student with developments in the areas of artficial intelligence and the modern conduct of company and to prepare for a profession as information analyst or knowledge managers in a company. A training in the company organisation is supposed to be part of the education. It is expected from the graduant to be critical in a scientific manner, is aware of societal aspects of information technology and of the creation of intelligent systems and posesses knowledge, capabilities and insights related to: • the workings of computer systems, including information systems and knowledge-based systems • knowledge acquisition and knowledge modelling • architecture of AI systems • techniques for search and optimalization • company organisation • technological, economic and social aspects of information in companies • methods and techniques in the area of knowledge management and capable to • work individually as well as in teams • clearly report verbally and written on his/her work • consult specialist literature.

4.9.2

First year Also 25 cp optional courses. Course code 400111 400125 400153 400010 400067

Course name

Evolutionary Computing Knowledge Management and Modeling Intelligent Web Applications I Bedrijfsmodellering en requirements engineering Project Software Engineering


Stp.

Period

6 6 8 7

1 1 and 2 1 and 2 1 en 2

8

5 en 6

45

4.9.3

Second year Also 18 cp optional courses. Course code 400113 400195 400285

4.9.4

Behaviour Dynamics Kwaliteitszorg van de informatievoorziening Master Project Artificial Intelligence

Recommended optional courses Course code 60111030 400137 400115 400108 400029 150006 400117 400164 400292

4.10

Course name

Course name

Management en organisatie 1.1 Object-Oriented Software Development Logical Verification: Applied Logic Data Mining Techniques Inleiding besliskunde Inleiding wetenschapsfilosofie Protocol Validation Object-Oriented Software Development Practical Ontology Engineering

Stp.

Period

6 5

1 and 2 1 en 2

30

4, 5 en 6

Stp.

Period

3 4 6 6 6 6 6 9

1 1 and 2 1 and 2 1 and 2 1 en 2 30.08.2004 - 22.10.2004 5 and 6 5 and 6

3

6

Technical Artificial Intelligence Programme for students having a Bachlor in Computer Science

4.10.1

Programme Future perspective: The graduate student of this Master programme is capable of applying techniques from Computer Science to problems of an Artificial Intelligence nature, e.g., designing knowledge-based systems or multi-agent systems. This technically adapt graduate, furthermore, has learned proven AI techniques in the areas of machine learning, neural networks, knowledge representation, and evolutionary computing. Graduate students are well equiped for work in companies that create intelligent applications. Audience: The programme aims at students with a Bachelor in Computer Science, having an interest in Artificial Intelligence. Objectives and final attainment level: The objective of the programme is to endow the student with the developments on the area of artificial intelligence and computer science, and to prepare for a profession as researcher or expert in a company. The curriculum must give a good preparation on PhD research. It is expected from the graduate to be critical in a scientific manner, to be aware of societal aspects of information technology and of the creation of intelligent systems and to possess knowledge, capabilities and insights related to: • knowledge acquisition and knowledge modelling • methods of designing AI systems, specifically based on intelligent agents • techniques for search and optimalization • adaptive applications

46

Exact Sciences

• the contemporary literature on adaptive applications and agent-based systems and the graduate is expected to be capable of • working individually as well as in teams • reporting verbally and written professionally on his/her work • consulting specialist literature.

4.10.2

First year Also 5 cp optional courses. Course code 400111 400154 400054 400059 400083 400132 400201 400123 811012

4.10.3

400285

Period

6 6 6 7

1 1 and 2 2 4

6 6 7 8 4

4 en 5 5 5 en 6 5 en 6

Course name

Stp.

Period

8 8

1 and 2 2 and 3

30

4, 5 en 6

Intelligent Web Applications I Intelligent Interactive Distributed Systems Master Project Artificial Intelligence

Recommend optional courses The course Dutch for foreigners is also an option. Course code 400125 400108 811003 400188

4.11

Stp.

Evolutionary Computing Machine Learning Design of Multi-Agent Systems Practicum Ontwerp van multi-agent systemen Web-gebaseerde kennisrepresentatie Neural Networks Project Kennissystemen Facetten van de AI Inleiding in de Psychologie voor AI

Second year Also 14 cp optional courses. Course code 400153 400152

4.10.4

Course name

Course name

Knowledge Management and Modeling Data Mining Techniques Functieleer Organisational Dynamics

Stp.

Period

6 6 6 6

1 and 2 1 and 2 2 en 3 3

Interdisciplinary Applications Occupational perspective: This variant allows students to integrate Artificial Intelligence intensively with another discipline, like Psychology (see the special variant Cognitive Science), Law, or Linguistics. Graduates will work in a company, for a research institute, or a governmental institute in close cooperation with others of the chosen discipline. Target population: This variant is intended for those students that like to specialise in one of the mentioned disciplines.


47

Objectives and final attainment level: These will be discussed seperately for AI and Law and for AI and Linguistics. 4.11.1

AI and Law In the research area AI & Law two main streams can be recognised. The first is practical or applied AI & Law, aiming to develop proper legal applications. Examples are legal databases, automated role management and legal advisory systems. The second is theoretical AI & Law or computational theory of law. This second stream is interested in foundations of and insights into Law and legal reasoning, as well as in testing AI-techniques within the legal domain. Recent research themes are validation of legal knowledge-based systems, dialogue models of legal reasoning, distributed applications. In legal practice gradually more computer applications are being realised. The judiciary and police automate their administration. Lawyer's offices develop knowhow-systems to manage the available knowledge and improve their market position. The government develops systems to aid civil servants in the drafting of legislation and the execution. These systems vary from administrative systems and databases to knowledge-based systems. Even for lawyers law is not always easy to comprehend. The development of legal knowledge-based systems, therefore, requires not only knowledge of AI, but also knowledge of Law. The Master variant, therefore, comprises an introduction to Law and, amongst others, courses in Civil law, Constitutional Law, Criminal Law, and Governmental Law. For more information, please contact one of the study advisors of AI (Martijn Schut ([email protected]) and Vera Stebletsova ([email protected])) or Arno Lodder ([email protected]) from the department of Law. A graduate of the Master variant AI & Law: • Has a good overview of the current literature and practice in the area of AI & Law. • In cooperation with jurists, is capable of starting and carrying out projects in AI and Law.

4.11.2

Programme for students having a Bachelor in AI Compulsory courses Also 36 cp elective courses. Students must also follow the course IT analyse Jurisprudentie Internetrecht. Course code 200201

200105 201542 400111 400113 200108

48

Course name

Stp.

Period

Rechtzoeken (B2/BN2)

2.9

Beginselen privaatrecht II (B1) Verdieping Informatietechnologie voor juristen (M) Evolutionary Computing Behaviour Dynamics Beginselen bestuursrecht (B1)

5.7 9

Rechtzoeken wordt doorgaans tweemaal per jaar gegeven: direct na de zomervakantie en direct na de kerstvakantie. Let goed op de collegeroosters voor de precieze datum. 02 / 13 06 / 15

6 6 5.7

1 1 and 2 14 / 26

Exact Sciences

200367 200101 400285 200104 200102 200103

IT en recht (B3/M) Inleiding (B1) Master Project Artificial Intelligence Beginselen staatsrecht (B1) Beginselen strafrecht (B1) Beginselen privaatrecht I (B1)


60111030 400110 400115 150007 200206 400117

4.11.3

Course name

Encyclopedie der rechtswetenschap I (B1) Management en organisatie 1.1 E-Business Innovation Logical Verification: Applied Logic Inleiding wijsgerige ethiek Encyclopedie der rechtswetenschap II (B2/BN2) Protocol Validation

16 / 26 36 / 40 4, 5 en 6 41 / 05 41 / 52 41 / 52

Stp.

Period

8.6

06 / 22

3 7 6 6 8.6

1 1 and 2 1 and 2 25.10.2004 - 17.12.2004 38 / 52

6

5 and 6

Programme for students having a Bachelor in Law Compulsory courses Also 17 cp elective courses. Students must also follow the course IT analyse Jurisprudentie Internetrecht. Course code 201542 400111 400110 400113 400043 200367 400054 400312 400126 815050

Course name

Verdieping Informatietechnologie voor juristen (M) Evolutionary Computing E-Business Innovation Behaviour Dynamics Logische taal en redeneermethoden IT en recht (B3/M) Design of Multi-Agent Systems Human-Computer Interaction Kennissystemen Kennisrepresentatie


60111030 400115 150007 200206 400117

4.11.4

6 5.8 30 5.7 5.7 5.7

Course name

Encyclopedie der rechtswetenschap I (B1) Management en organisatie 1.1 Logical Verification: Applied Logic Inleiding wijsgerige ethiek Encyclopedie der rechtswetenschap II (B2/BN2) Protocol Validation

Stp.

Period

9

06 / 15

6 7 6 5 6 6 5 4 6

1 1 and 2 1 and 2 1 en 2 16 / 26 2 2 and 3 4 4 en 5

Stp.

Period

8.6

06 / 22

3 6 6 8.6

1 1 and 2 25.10.2004 - 17.12.2004 38 / 52

6

5 and 6

AI and Linguistics An important aspect of intelligent behaviour is the ability to use language to communicate. Natural languages are highly symbolic, tightly structured communication systems. Linguistic research focuses on the methods and techniques Master Artificial Intelligence

49

needed to analyse the structure of natural languages and to use natural language in computer systems. Such linguistic knowledge can be applied to the creation of user interfaces to knowledge-based systems, automated support in the writing of technical manuals, and automated information retrieval from huge text sources. There is a growing demand for supporting linguistic technology in the development of intelligent spelling checkers, thesauri, and knowledge representation of terms and concepts in domains of application. Artificial Intelligence techniques are, in turn, put to good use in linguistics, for example in the development of an extended electronic corpus of spoken and written Dutch, or is the maintenance of a knowledge-base of Dutch and Belgian governmental terminology. Retrieving information from such large databases requires a good conceptual model, and a suitable format for the lexicon. The variant AI and Linguistics incorporates courses in Linguistics that focus on the following three aspects: corpuslinguistics, lexicology, and terminology. The graduate of this variant: • Has a good overview of the current literature and practice in the area of AI & Linguistics. • Is capable, in cooperation with linguists, of initiating and executing projects involving AI and Linguistics. Programme for students having a Bachelor in AI Teaching of courses in the Faculty of Arts cannot be guaranteed to be in English. Compulsory courses Also 41 cp optional courses. Course code 540117 513702 400111 400113 540118 539155 540150 400285 540114 539151

Course name

Lex: Lexicale semantiek 1 ACW: Theorie van woord en beeldrelaties 1: Inleiding semiotiek Evolutionary Computing Behaviour Dynamics Lex: Lexicale semantiek 2 Atw: Corpustaalkunde Lex: Het relationele lexicon Master Project Artificial Intelligence Lex: Terminologie, inleiding Atw: Inleiding syntaxis

Recommended optional courses Course code 539152 539163 500013 539170 539602 539162

4.12

Course name

Atw: Psycholinguïstiek Atw: Inleiding morfologie Let alg: Taalgebruikstheorie Morphology Topics in Anthroplogical Linguistics Atw: Fonologie

Stp.

Period

5 5

1 1

6 6 5 5 5 30 5 5

1 1 and 2 2 2 4 4, 5 en 6 5 5

Stp.

Period

5 5 5 10 5 5

1 2 4 4 and 5 5 5

AI and Communication As for all study programmes offered at the Faculty of Sciences a Communication variant is offered. This programme is open for any student having a Bachelor.

50

Exact Sciences

Teaching in these variant is mainly in Dutch. Therefore we also give the requirements in Dutch. 4.12.1

Programma Het programma omvat een reeks cursussen, waarvan de eerste twee verplicht zijn. Op twee momenten kan er een keuze gemaakt worden tussen alternatieven ('Communicatie en Educatie via Internet' of 'Wetenschap Technologie & Samenlevingsstudies' en 'Informatie Representatie en Multimedia' of Gezondheidscommunicatie). Het jaar wordt afgesloten met een verplichte scriptie van 9 studiepunten en een korte stage van 18 studiepunten. De Communicatie variant wordt georganiseerd door de afdeling Wetenschapscommunicatie van de Faculteit Aard- en Levenswetenschappen. Contactpersoon voor de Communicatie variant is drs. I. van Veen, tel. (020) 44 47214, e-mail: [email protected]. Programmacoördinator is dr. J. Willems, e-mail: [email protected]. Communicatie variant

Tevens scriptie van 9 sp en stage van 18 sp Vakcode 471007 471014 471006 471025 470087 471015 470553 471027 471026

4.13

Vaknaam Interpersoonlijke communicatie Wetenschapsjournalistiek Communicatiewetenschappen Popular Science Writing Gezondheidscommunicatie Information Representation/ Multimedia 1 Wetenschap, technologie en samenleving studies Communicatie en educatie via internet Museologie en buitenschoolse educatie

Stp. 3 6 6 3 6 6

Periode 01.11.2004 - 12.11.2004 04.10.2004 - 29.10.2004 06.09.2004 - 01.10.2004 07.02.2005 - 8.02.2005 10.01.2005 - 04.02.2005 10.01.2005 - 04.02.2005

3

15.11.2004 - 26.11.2004

3 6

15.11.2004 - 26.11.2004 29.11.2004 - 24.12.2004

Society oriented variant As for all study programmes offered at the Faculty of Sciences a Society variant is offered. This programme is open for any student having a Bachelor. Teaching in these variant is mainly in Dutch. Therefore we also give the requirements in Dutch.

4.13.1

Programma De Maatschappij variant speelt in op de toenemende behoefte die universiteiten, het bedrijfsleven, de overheid en andere maatschappelijke instellingen hebben aan academische professionals die in staat zijn om complexe vraagstukken te analyseren en maatschappelijke systemen te beïnvloeden. Hierbij kun je denken aan acceptatieen milieuproblemen rond de introductie van genetisch gemodificeerd voedsel, ethische dilemma's rond de toepassing van voorspellende geneeskunde (diagnostiek), toenemende vraagsturing in wetenschappelijk onderzoek en de implementatie van maatschappelijk verantwoord ondernemen. Tijdens de opleiding leer je kennis van verschillende wetenschappelijke disciplines samen met kennis uit de maatschappij te integreren. De opleiding is zowel theoretisch als praktisch georiënteerd met concrete cursussen over beleid, management en ondernemerschap op het gebied van onder andere gezondheid en milieu. Je kunt ook deelnemen aan het masterprogramma Master Artificial Intelligence

51

Beleid Management en Ondernemerschap welke wordt verzorgd door de afdeling Biologie en Samenleving van de faculteit der Aard en levenswetenschappen (FALW; prof. dr. J. Bunders, kamer A0.68, telefoon: (020) 44 47030). Je kunt rechtstreeks in deze masteropleiding instromen met een universitaire bachelor in de bèta wetenschappen. De meest recente informatie vind je op onze website: www.falw.vu.nl/masters. M-variant

Tevens scriptie van 9 sp en stage van 18 sp. Vakcode 470556 470557 470553

Vaknaam Inleiding Beleidswetenschappen Inleiding Organisatie en Management Wetenschap, technologie en samenleving studies

Stp. 7 5 3

Periode 06.09.2004 - 08.10.2004 11.10.2004 - 29.10.2004 15.11.2004 - 26.11.2004

Stp. 3 9

Periode 01.11.2004 - 12.11.2004 10.01.2005 - 18.02.2005

M-variant keuzevakken

Mogelijke vakken. Vakcode 470558 470559

4.14 4.14.1

Vaknaam Ondernemerschap I Ondernemerschap II

Final-projects and Training on the job Programme Each Master programme is finished with a graduation project or internship. This can be an individual project as well as a group project. Information about graduation projects and internships can be found on the Internet pages of the AI divisions and on http://www.cs.vu.nl/ai/msc-projects/index-en.html. Internships proposed by the student him/herself need approval in advance from a member of staff, who will also be involved with supervising the project. Concerning graduation projects, the following rules are important: • The size of the graduation projects is as such that with adequate foreknowledge and complete study, the project can be finished within 6 months. • Students can in principle only start their graduation project if they have completed all other exam parts. In case one part must still be completed, approval of the project leader is required to start the project. In case more than one part must be completed, explicit approval of the board of exam is required. • The student participates in the KIM (Kunstmatige Intelligentie Meeting). In some cases, the amount of participation may be determined by the lecturer. More information can be found on http://www.cs.vu.nl/ai/kim-en.html. • Upon project completion, a meeting will be held with all involved in the project, in which a short evaluation will be made and a judgement will be made under responsibility of the lecturer. When the final judgement is that the student work is not sufficient, a supplement will be required from the student. The rules for graduation internships are similar to those for graduation projects. For details, please contact the study advisor.

52

Exact Sciences

4.15 4.15.1

4.16 4.16.1

Optional courses outside the department Programme The student is advised to also consider following courses at other universities to get a programme that best fits his/her interests. Specific topics offered at other universities are, for example, image processing, cryptography, sensor informatics, data & knowledge modelling, computer graphics, embedded systems, robotics. Before entering a course, the student needs to register at that university for the study that offers that course. The student needs his/her VU-collegekaart for that registration. Example universities that offer interesting courses for an AI-student are the University of Amsterdam (UvA), Utrecht University, University of Nijmegen, Leiden University, University of Groningen, University of Maastricht. The student is advised to consult the study guides and web pages of these universities to get a better insight in the kind of courses offered.

Educational possibilities after the Master Programme The AI Master programmes provide an excellent basis for a Ph. D. study in Artificial Intelligence or other research areas, such as Computer Science, and Cognitive Science. Each year the faculty offers a number of Ph. D. student positions. Graduate students with execellent grades are invited to apply for one of these positions. A Ph.D. student position is normally awarded for 4 years, during which time the Ph.D. student is expected to finish his Ph.D. thesis. Ph. D. Students are supervised by a full professor, whereas daily supervision is sometimes performed by another member of the scientific staff. Aside from his/her research task (which includes following specialised courses and seminars), the Ph. D. student is also expected to contribute to the education of others. All Ph. D. Students are registered with SIKS, i.e., the Dutch research school for Information and Knowledge Systems, http://www.siks.nl. SIKS guarantees an excellent training programme for the Ph. D. student and a high level of research attainment with respect to the accepted Ph. D. theses. The Department of Artificial Intelligence of the Faculty of Sciences offers Ph.D. student positions in one of the following areas: • Knowledge technology and knowledge representation; (prof. dr. F. van Harmelen, [email protected]). • Agent systems and their dynamics, also offering interesting cooperation opportunities on cognitive science, biology and organisation theory; (prof. dr. J. Treur, [email protected], dr. C.M. Jonker, [email protected]). • Computational intelligence; (prof. dr. G. Eiben, [email protected]). Students interested in a Ph.D. student position can contact either the persons mentioned or one of the study advisors M.C. Schut ([email protected]) or V. Stebletsova ([email protected]).

4.16.2

Training as a researcher All training as a researcher at the Department of Artificial Intelligence is carried out under the auspices of SIKS, the Dutch research school for Information and Knowledge Systems, http://www.siks.nl. Master Artificial Intelligence

53

54

Exact Sciences

5

5.1

Master Bioinformatics The domain of the Master Research in Bioinformatics in its broadest definition concerns the analysis of informational processes within living systems with the help of computers. To do this succesfully, Bioinformatics actively uses and integrates contributions from areas such as Mathematics, Computer Science, Chemistry, Medicine and Biology. Bioinformatics has recently become one of the keywords in the life sciences as well as in Biotechnological and Pharmaceutical industries. Although in essence the field is quite old and bioinformatics techniques developed over the years have come of age, the field has gained major prominence relatively recently, owing mostly to the worldwide human genome projects and subsequent structural and functional genomics initiatives. While the complete human genome sequence has been obtained at relatively little cost of around two billion Euros, the current investments in for example proteomics industries amount to orders of magnitude more. Also other genomic technologies, aimed at gaining insight in human physiological functioning such as microarray (gene chip) technology, have attracted multi-billion Euro investments both in industry and academia. Currently, many new small/medium enterprises (SMEs) and large international biotechnological and pharmaceutical companies are actively recruiting bioinformaticians, but experience hardship in doing so due to the lack of individuals with proper training. Similar problems are encountered at national academic centres in The Netherlands, particularly in microarray centres. As the interpretation of the data coming from all the above largescale projects is crucially depending on the application and creation of new bioinformatics techniques, it is clear that a broad based and integrative master's curriculum in bioinformatics at the Vrije Universiteit is timely. It is possible to study for a Master's degree at the Vrije Universiteit as of September 2003. The international Bioinformatics Master study takes 2 years and is organised by the Integrative Bioinformatics Institute VU (IBIVU), a multidisciplinary centre within the Vrije Universiteit in which three faculties (Faculty of Sciences; Faculty of Earth and Life Sciences; and the Faculty of Psychology) and the VU Medical Centre take part. To prepare for the Bioinformatics master course, various Bachelor programmes at the Vrije Universiteit offer integral courses in Bioinformatics, such as Medical and Natural Sciences and Biomolecular Sciences. These Bachelor programmes (taking 3 years) are dedicated to providing the student with a broad and thorough basis in each of their areas of study, which is indispensable for starting the Bioinformatics Master programme. The Bioinformatics Master's provides the student with an opportunity to deepen his/her knowledge of the various aspects of Bioinformatics, while the student has ample possibility to specialise in one or a few areas of choice. It is expected that the breadth and flexibility of the masters programme resulting from the multidisciplinary setup of the Integrative Bioinformatics Institute as well as the emphasis on creating bioinformatics tools from the strong embedding in the Informatics department (e.g. AI, Computer Systems) will be attractive for students. The Bioinformatics Master studies are currently organised by the Faculty of Sciences and the Faculty of Earth and Life Sciences. The latest information can always be found at: http://www.cs.vu.nl/~ibivu/teaching/. Master Bioinformatics

55

Depending on the individual furnishing of his/her Master programme, the student can attend lectures in other faculties and centres, for example Biology or the Centre for Neurogenomics and Cognitive Research (CNCR). Graduation projects can vary from practical to rather fundamental, depending on the preferences and capacities of the students. Students can also go to companies, research institutes or universities either in The Netherlands or abroad. Study advice is open to all. Advisor Prof.dr. Jaap Heringa can be contacted at all times. Furthermore, the website http://www.cs.vu.nl/~ibivu/teaching/ contains information regarding the international Bioinformatics Master programme.

5.2

Objectives Bioinformatics can be viewed as an extensive and challenging research discipline, which requires bioinformatics practitioners to have a well-developed concept of the art of doing science, a high ability for (mathematical) abstraction, a broadly developed knowledge, an ability to quickly absorb and integrate novel concepts, strong problem-solving skills, and well-developed practical proficiencies in the area of computer science. The 2-year bioinformatics master's programme at the VU should aim to deliver students with the world view, knowledge and practical ability to conduct sound bioinformatics research in a wide range of application areas and different environments. The programme should therefore offer core techniques and formalisms to every student, while allowing sufficient differentiation and choice in research projects and practical applications. It is hoped that the programme will draw students to continue studying bioinformatics at the VU towards a PhD.

5.3

Final attainment level After graduation the master in Bioinformatics is expected to be critical in a scientific manner, to be aware of the societal aspects of bioinformatics research, and to possess knowledge, experience, and insights regarding the following: As mentioned in the introduction, Bioinformatics research is now firmly positioned in the scientific limelight, and is generating substantial -and sometimes unrealisticexpectation. Students should be able to recognise good and bad research. Bioinformatics research is often used early on in cost intensive bio-medical development cycles (e.g. to define leads in drug discovery): errors can be costly. Bioinformatics research interfaces many other scientific disciplines. Students should have knowledge concerning all neighbouring disciplines, and also have an ability to deal with incomplete knowledge and mental pictures, while still being able to ask appropriate research questions. Paraphrasing the classical statement of the eminent geneticist Theodosious Dobzhansky: ""Nothing in Biology makes sense except in the light of evolution"" would give for bioinformatics research: ""Nothing in bioinformatics makes sense except in the light of Biology"". Biology is the science area of complexity and inconsistency, where mathematical and physical concepts seem to derail frequently. Students should be trained to deal with these complexities. Bioinformatics methods often have to be devised with an ill-defined standard of truth (e.g. multiple alignment, sequence database searching). Many mathematical concepts and novel computational techniques are being implemented in bioinformatics techniques at a rapid pace. To be able to place these

56

Exact Sciences

innovations, students should have a sound knowledge of statistics, modelling techniques and formalisms, and multivariate statistics. Examples of new concepts are novel machine learning techniques (e.g. recent implementations of Support Vector Machines in bioinformatics methods), parallel and distributed (Grid) computing, etc. Bioinformatics research requires skills to use and understand many different computational methods. Bioinformatics research often involves development of novel methods and/or databases. Students should be confident in programming using different computer languages. Bioinformatics techniques and databases are mostly available via the Internet. Students need web-related computational skills. Quoting another eminent molecular biologist Sydney Brenner ""Bioinformatics research ranges from book-keeping to real art"". Students need to develop the skills and mentality to allow this full range of activities. The graduate is expected to be capable of: practical application of the learned both alone as well as in a team; clear oral and written presentation of the results of his/her work; making good use of the literature and other knowledge sources relating to Bioinformatics.

5.4

Requirements for the Master Since bioinformatics is an inherently multi-disciplinary field, prospective students can be expected from many walks of life, although particular interest in the Bioinformatics masters is expected from bachelors (or equivalent) in Computer Science, Mathematics, Physics, Chemistry, Biology, Medical Natural Sciences, Pharmaceutical Sciences and Medicine. The programme is open to students who have a Bachelor, Drs or Master diploma obtained at a Dutch institute or foreign university of quality recognised by the Vrije Universiteit. The prospective student should have a thorough interest and experience in biomolecular and computational sciences. Some experience in programming is required. The programme is also open to students with other diplomas from universities or other research/teaching institutions they deem equivalent. These are kindly invited to contact us if interested in following the international Master programme in Bioinformatics at the Integrative Bioinformatics Institute VU.

5.5

Master programme Future perspective: Employment prospects are excellent and appear relatively independent from economic conditions. Arguably, there is currently no other field in the Life Sciences with such positive job opportunities. Programme: The full Master"s programme in Bioinformatics takes two years and is worth 120 credits (within the European Community Course Credit Transfer System). As a rule, the student will take approximately nine months of courses (45 credits) and complete

Master Bioinformatics

57

fifteen months of practical training (75 credits). It is also possible to take individual sections of the programme, leading to degree component certificates at Master's level. Unless otherwise stated, the tuition is in English. The classes consist of: Compulsory courses Optional courses First traineeship (Major) Second traineeship (Minor) Optional third traineeship

30 credits 15-18 credits 30-60 credits 15-30 credits 15-30 credits

Every student is allocated a mentor to help put together the Master's programme that suits him or her best, using a flexible approach and in full consultation. You also have the option to choose courses at other departments, in consultation with your mentor.

5.6 5.6.1

Programme Compulsory courses Course code 430047 430045 430046 430049 430048

5.6.2

Course name Genome Analysis: Structural and Functional Genomics Sequence Analysis DNA Protein Structure-Function Analysis and Prediction Integrative Bioinformatics and Genomics Bioinformatic Data Analysis and Tools

Stp.

Period

6

1

6 6

2 3

6 6

5 5 and 6

Optional courses Optional courses are provided by the IBIVU, and the Biology, Mathematics and Computer Science Departments at the VU. Course code 400303 400111 400114 400161 400108 400154 400171 400132 400296

Course name

Introduction to Bioinformatics Evolutionary Computing Scientific Visualisation Parallel programming Data Mining Techniques Machine Learning Statistical Models Neural Networks Statistical Genetics

Stp.

Period

6 6 4 6 6 6 4 6 6

1 1 and 2 1 and 2 1 and 2 1 and 2 1 and 2 5 Spring

Specific optional courses in Bioinformatics

The two courses will be provided upon demand and sufficient interest. Vakcode 400303 400296

Vaknaam Introduction to Bioinformatics Statistical Genetics

Further courses in Computer Science

58

Exact Sciences

Stp. 6 6

Periode

Spring

Vakcode 400304 400114 400115 400154 400132

Vaknaam Parallel Computing Scientific Visualisation Logical Verification: Applied Logic Machine Learning Neural Networks

Stp. 6 4 6 6 6

Periode 1 and 2 1 and 2 1 and 2 5

Stp. 4 4

Periode 1 and 2 not fixed

Further courses in Mathematics Vakcode 400171 400135

5.6.3

Vaknaam Statistical Models Statistic and Probability Seminar

Traineeships Your traineeships will account for 75 of your credits. You will complete two or three traineeships, one of which will be more extensive than the others (minimum of 30 credits). The IBIVU's broad, multidisciplinary structure allows you to work on a wide variety of subjects at the VU. External traineeships are also possible. Your third traineeship can also take the form of a literature survey. Projects can be chosen in fundamental bioinformatics research or more applied in the following associated areas: • Structural/functional genomics • Proteomics • Pharmaco-genomics • Biophysics • Genetical epidemiology Possible themes for student projects in data mining include: Gene expression • Genome mapping • Protein folding • Neuronal networks • Macromolecular crowding • Ion channel kinetics • Integrative cell modelling • Positron emission tomography (PET) imaging • Linking gene expression to Comparative Genomic Hybridization (CGH) data

•

5.7 5.7.1

Educational possibilities after the Master Programme Each year the Integrative Bioinformatics Institute VU or its member faculties offer a number of Ph.D. student positions. Graduate students with excellent grades are invited to apply for one of these positions. A Ph.D. student position is normally awarded for 4 years, during which time the Ph.D. student is expected to finish his Ph.D. thesis. Ph.D. Students are supervised by a full professor, whereas daily supervision is sometimes performed by another member of the scientific staff. Aside

Master Bioinformatics

59

from his/her research task (which includes following specialised courses and seminars), the Ph.D. student is also expected to contribute to the education of others. Students interested in a Ph.D. student position can contact Prof.dr. Jaap Heringa ([email protected]).

5.8

Professional associations Netherlands BioInformatics Centre (NBIC), BIOinformatics Application Services Provider (BIOASP), Dutch Bioinformatics Training Association (BioTrain).

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Exact Sciences

6

6.1

Master Business Mathematics and Informatics Objectives The Master's programme in Business Mathematics and Informatics (BMI) is a multidisciplinary programme, geared to improving business processes by applying a combination of methods based on mathematics, computer science and business management. The Master's programme BMI will deepen your knowledge of these methods and give you the opportunity to specialize in areas like business process optimization, computational intelligence and financial risk management. Much more so than in the Bachelor's programme, business problems will be the center of attention and the motivation for the methods to be learned from the three subdiscplines. The Master's programme is concluded by an external master project of half a year.

6.2

Final attainment level At the end of his/her studies the master BMI has: knowledge of advanced methods from mathematics and computer science that are applicable to business and industrial processes; • expertise in analysing, modeling and solving organisational, management- and decision problems in a practical context; • knowledge of and expertise with a broad selection of software packages that are in use in business and industry; • the capacity to work in an interdisciplinary team, in particular: sufficient knowledge of theory and practice in the area of business economy, organisation and administration to communicate and collaborate with experts in these areas; • presentation and communication skills on a level befitting the master.

•

6.3

Requirements for the Master One gains direct entry to the Master's programme in BMI if one has a Bachelor's degree in the subject. Permission is granted to start the Master's programme if at most 18 cp of the Bachelor's programme still have to be done. Those who have a Bachelor's degree in Business Mathematics from an institute of higher education, or a Bachelor's degree in Mathematics or Econometrics from a university, will be admitted to the Master's programme with some additional requirements. Those additional requirements depend on the precise nature of the Bachelor's programme. If one has a Bachelor's degree in a related subject from a university or institute of higher education in the Netherlands or abroad, the Examination Board may set additional requirements. One is advised to contact the student advisor.

6.4

Part-time studying The part time programme is ment for those who have another occupation besides the study. The programme is based on the assumption that the student has at least 20 hours each week available for study, and has the possibility to follow courses during at least 2 days per week. The programme is the same as the programme for full time Master Business Mathematics and Informatics

61

students. There are no separate classes for part time students, neither are there separate exams for those students.

6.5

The Variants of the Master There are four variants: a society oriented variant, research variant, a dual variant and a communication oriented variant. In contrast to many other master's programmes, the standard programme is the society oriented variant. The programmes are shortly described below.

6.6 6.6.1

Society oriented variant Programme This is the standard master's programme. The goal of the programme is to prepare students for a career in business, industry, or within governmental or research facilities, with (possibly only initially) a major quantitative aspect. The emphasis will be on a broad and multidisciplinary education, preparing the student for a role as an academically trained quantitative professional in a multidisciplinary organisation. Even so, the possibility to continue after the Master in a PhD programme exists also for this variant. There are at present three specializations possible: Business Process Optimization This subject underscores the multidisciplinary nature of BMI: you will tackle quantitative business problems with the aid of mathematical algorithms which are then implemented in decision-support systems. All aspects of this subject are addressed from the perspective of interrelationships. Computational Intelligence Computational Intelligence (CI) is a collective name for various fields of application and problem-solving techniques. Typical CI applications are optimization and data mining. CI offers a succesful pragmatic approach to actual problems. Financial Risk Management This specialization prepares you for a quantitative position in the financial world. The subjects covered include the pricing of derivatives, such as share options, and risk management. You will deal with both practical and theoretical aspects of the discipline.

6.6.2

Compulsory courses Course code 400157 400108 400107 400010 400213 400286

62

Course name

Modeling of Business Processes Data Mining Techniques ICT in a social context Bedrijfsmodellering en requirements engineering Project Optimalisation of Business Processes Master Project Business Mathematics and Informatics

Exact Sciences

Stp.

Period

6 6 4 7

1 and 2 1 and 2 1 and 2 1 en 2

6

3

37

4, 5 en 6

400352 400206

6.6.3

6 6

5 variabel

Stp.

Period

6 4 6 6 5 6

1 and 2 1 and 2 4 and 5 4 en 5 4 en 5 5

Optional courses Mathematics

BMI optional courses Mathematics

2 out of 6 Course code 400336 400171 400180 400076 400019 400260

6.6.4

Stochastic Processes for Finance BWI werkstuk

Course name Caput Stochastic Optimization Statistical Models Mathematical System Theory Toegepaste analyse: financiele wiskunde Discrete wiskunde Optimization of Business Processes

Optional coursus BMI

BMI optional courses BMI

At least 6 cp has to be chosen out of this list or the list of optional courses Mathematics. Course code 61311020 400111 400214 400165 61331060 61321010 400132

6.7

Course name

Business Intelligence Evolutionary Computing Simulation Performance Analysis of Communication Networks Logistics Financial Risk Management Neural Networks

Stp.

Period

6 6 5 6

1 1 1 and 2 1 and 2

6 6 6

4 4 5

Research variant

6.7.1

Programme This variant is for students aiming at continuing after the Masters degree for a PhD degree. The emphasis will be less on a broad education and more on specialization, compared with the society oriented variant. The external master's project which concludes the master's programme may, in special cases, be replaced by an internal research project in this variant. There is a possibility of applying for a pre-aio scholarship for those students who will continue as an aio (PhD student). More information can be obtained from the student advisor. For a description of possible specializations see above under the Society oriented variant.

6.7.2

Compulsory courses Course code 400157 400108 400107 400213

Course name

Modeling of Business Processes Data Mining Techniques ICT in a social context Project Optimalisation of Business Processes

Master Business Mathematics and Informatics

Stp.

Period

6 6 4 6

1 and 2 1 and 2 1 and 2 3

63

400352

6.7.3

6

5



2 out of 6 Course code 400336 400171 400180 400076 400019 400260

6.7.4

Stochastic Processes for Finance

Course name Caput Stochastic Optimization Statistical Models Mathematical System Theory Toegepaste analyse: financiele wiskunde Discrete wiskunde Optimization of Business Processes

Stp.

Period

6 4 6 6 5 6

1 and 2 1 and 2 4 and 5 4 en 5 4 en 5 5

Optional courses BMI

BMI optional courses BMI

At least 6 cp has to be chosen out of this list or the list of optional courses Mathematics. Course code 61311020 400111 400214 400165 61331060 61321010 400132

6.8

Course name

Business Intelligence Evolutionary Computing Simulation Performance Analysis of Communication Networks Logistics Financial Risk Management Neural Networks

Stp.

Period

6 6 5 6

1 1 1 and 2 1 and 2

6 6 6

4 4 5

Communication variant If the non-compulsory part of the program is filled in the following way, then one can study in the communication variant. The scriptie replaces the BWI-werkstuk.

6.8.1

Programme This variant is intended for students with an interest in the communication on science towards the public (e.g. through science journalism or science museums). In this variant the study points that are in other variants intended for a specialization are now used to follow two courses: 'Wetenschapsjournalistiek' (6 cp) and 'Communicatiewetenschap' (6 cp), do a 'scriptie' (9 cp) and a short 'stage' (18 cp). The 'scriptie' replaces the 'BWI werkstuk'. It should be stressed that this short 'stage' can in no way be done as (part of) the requirement to do a final term project. Course code 471014 471006 471027

64

Course name

Wetenschapsjournalistiek Communicatiewetenschappen Communicatie en educatie via internet

Exact Sciences

Stp. 6 6 3

Period

04.10.2004 - 29.10.2004 06.09.2004 - 01.10.2004 15.11.2004 - 26.11.2004

6.9 6.9.1

The Dual Master's Programme Programme The dual master's programme combines work and study. During this programme the student is employed part time, and studies part time. The work has to be relevant for the study. The external master's project is incorporated in the work, although supervision of the external master's project has to involve at least one university staffmember. In addition the student gets some credit points for the work time. Moreover, it is possible to do the BMI paper (6 cp) on a case-study that is work related, provided the case-study is combined with a sound theoretical basis. This makes the total of work related credit points, including the external master's project, 60, being the equivalent of one year of study. Typically, a student participating in the dual master's programme should expect to obtain the Master's diplom after two and a half year. Admission to the dual master's programme is granted to those who have a BMI Bachelor's degree. For those with another univerisity Bachelor's degree, such as Mathematics, Econometrics, Computer Science, or a Bachelor's degree from an institute of higher education, admission may be granted on an individual basis. Those seeking admission to the dual master's programme should realise that admission also depends on obtaining suitable employment. The VU has contacts with a number of companies that are interested in participating in this programme. For more information concerning the dual master's programme, contact the coordinator for the external master's project, or the student advisor, dr. R.F. Swarttouw (e-mail: [email protected], tel. (020) 44 47787). The total of non-work related credit points should be at least 60. Master's programme (Dual variant) work related: 17 cp, possibly 6 cp for the 'BWI werkstuk' and 37 for the external master project. The 'BWI werkstuk' can be a case study taken from the work environment, provided there is enough theoretical foundation added. Course code 400157 400108 400107 400010 400352 400206

6.9.2

Course name Modeling of Business Processes Data Mining Techniques ICT in a social context Bedrijfsmodellering en requirements engineering Stochastic Processes for Finance BWI werkstuk

Stp.

Period

6 6 4 7

1 and 2 1 and 2 1 and 2 1 en 2

6 6

5 variabel

Stp.

Period

6 4

1 and 2 1 and 2



2 out of 6 Course code 400336 400171

Course name Caput Stochastic Optimization Statistical Models


65

400180 400076 400019 400260

6.10

Mathematical System Theory Toegepaste analyse: financiele wiskunde Discrete wiskunde Optimization of Business Processes

6 6 5 6

4 and 5 4 en 5 4 en 5 5

Educational possibilities after the master

6.10.1

Programme Each year the faculty offers a number of Ph.D. student positions. Graduate students with excellent grades are invited to apply for one of these positions. A Ph.D. student position is normally awarded for 4 years, during which time the Ph.D. student is expected to finish his Ph.D. thesis. Ph.D. Students are supervised by a full professor, whereas daily supervision is sometimes performed by another member of the scientific staff. Aside from his/her research task (which includes following specialised courses and seminars), the Ph.D. student is also expected to contribute to the education of others.

6.10.2

Training as a researcher in BMI Within the research groups in Mathematics, Computer Science and Artificial Intelligence there are several possibilities to do a Ph.D. project on BMI related topics. We mention here in particular optimization, queuing theory, statistics, systems and control theory, computational intelligence and topics from business informatics. Any BMI masters student interested in pursuing a Ph.D. degree is requested to contact the student advisor, dr. R.F. Swarttouw ([email protected]).

6.10.3

Training as a researcher in Mathematics The department of Mathematics of the Faculty of Sciences offers Ph.D. student positions in one of the following areas: • Statistics • Probability Theory • Operations Research • Partial Differential Equations • Operator Theory • Mathematical Systems Theory • Geometry • Topology Students interested in a Ph.D. student position can contact the student advisor dr. F. van Schagen ([email protected]). All training as a researcher at the Department of Mathematics is carried out under the auspices of the Thomas Stieltjes Institute for Mathematics http://www.math.leidenduniv.nl/~stieltjes

6.10.4

66

Training as a researcher in Computer Science The department of Computer Science of the Faculty of Sciences offers Ph.D. student positions in one of the following areas: • Information Systems • Computer Systems • Software Engineering • Theoretical Computer Science Exact Sciences

•

Bioinformatics

Students interested in a Ph.D. student position can contact the student advisor. 6.10.5

Training as a researcher in Artificial Intelligence The Department of Artificial Intelligence of the Faculty of Sciences offers Ph.D. student positions in one of the following areas: • Knowledge technology and knowledge representation; (prof. dr. F. van Harmelen, [email protected]). • Agent systems and their dynamics, also offering interesting cooperation opportunities on cognitive science, biology and organisation theory; (prof. dr. J. Treur, [email protected], dr. C.M. Jonker, [email protected]). • Computational intelligence; (prof. dr. G. Eiben, [email protected]). Students interested in a Ph.D. student position can contact either the persons mentioned or one of the study advisors. All training as a researcher at the Department of Artificial Intelligence is carried out under the auspices of SIKS, the Dutch research school for Information and Knowledge Systems, http://www.siks.nl.

6.11 6.11.1

Optional courses Programme Although the master's programmes consist partly of compulsary courses, there is still a lot of freedom to design a programme according to the students interest. This freedom can be used to pursue a specialization, of which three have already been described shortly, but it can also be used to widen the horizon a bit. Apart from this there is a national master's programme in Mathematics. Some of the courses offered there are suitable for BMI students. In additon the 'Landelijk Netwerk Mathematische Besliskunde' offers master-level courses in operations research. See htttp://www.math.leidenuniv.nl/~lnmb. The choice of courses needs the approval of the Examination Board. One is advised to consult with the student advisor first.

6.12 6.12.1

External master project Programme Each Master's programme is concluded by an external master project. This is in principle a project to be carried out within a business, industry or research facility other than the departments of Mathematics and Computer Science. Only in special cases can this be replaced by an internal research project. Although the master's project will mostly be an individual project, group projects are possible. Internships proposed by the student him/herself need approval in advance from a member of the staff who will also be involved in the supervision of the project. More information can be obtained from the webpage of the 'stagebureau' http://www.few.vu.nl/onderwijs/stage/index-nl.html


67

Concerning masters projects the following rules are important: The size of the project is such that with adequate foreknowledge and no other work to do in parallel, the project can be concluded in half a year. • Students can in principle only start their external masters project if they have completed all other courses. In case one course is still to be completed approval of the project leader is required to start the project. In case more than one course is still to be completed, explicit approval of the examination board is required. • Before starting the project it has to be approved by the BMI stage committee. In order to get this approval a short description (1 or 2 pages) should be handed in at the 'stagebureau'. this description should consist of the following items: - name of the company and the department - name of the supervisor(s) within the company - name of the student - starting date and length of the project - short problem formulation - clear formulation of the role the student has to play in the project and what his/her contribution shoul be - indication of the goals of the project and what the deliverables are (e.g., a mathematical model, a set of programs, a comparitive investigation, experimental data etc.) • Upon completion of the project, a meeting will be held with all involved in the project, in which a short evaluation will be made and a final judgement will be given under responsibility of the first advisor from within the staff of FEW. When the final judgement is that the work is unsatisfactory, a supplement will be required from the student(s).

•

68

Exact Sciences

7

7.1

Master Computer Science The domain of the Master The field of Computer Science is concerned with obtaining knowledge about notions, methods and skills connected with the operation and applications of computers. The technical side of Computer Science includes such subjects as programming, operating systems, computer networks, data structures, the theoretical foundations of computer science and the use of mathematics and logic. In the heart of Computer Science we find methodological disciplines like software engineering, conceptual modelling and specification methods. Furthermore there is a rich assortment of applications, like parallel computing, visualisation, security, databases, internet and web, electronic commerce, artificial intelligence, multimedia, protocol validation and managerial aspects. Students who want to follow the Master Program in Computer Science are supposed to possess already a solid basis in this field at the Bachelor level, especially in computer architecture, computer networks, software engineering and the theoretical foundations of computer science. In the Master Programme in Computer Science there are several specializations, which we list here: • Parallel Computing an Visualisation • Internet and Web Technology • Software Engineering • Formal Methods and Software Verification • Technical Artificial Intelligence • Multimedia • Information and Communication Technology

7.2

Objectives The Master Programme in Computer Science aims to provide the student with the knowledge, experience and insights needed to autonomously carry out his/her professional duties as a computer scientist. The Master Programme is designed to offer a solid basis for a career in business as well as to prepare the student for further education as scientific researcher or teacher.

7.3

Final attainment level After graduation, the student in Computer Science is expected to have developed a critical, scientific attitude, to be aware of the societal aspects of information technology and to possess knowledge, experience, and insights regarding: • the operation of computer systems, including operating systems, computer networks, information systems and knowledge systems; • the most important programming paradigms; • determining software requirements; • software design methods; • the theoretical foundation of Computer Science; • subjects from mathematics, statistics and logic relevant for Computer Science; • specialist subjects in one or more of the research areas of Computer Science. The graduate is capable of: Master Computer Science

69

• • •

7.4

practical application of the learned both alone as well as in a team; clear oral and written presentation of the results of his/her work; making good use of the literature on Computer Science.

Requirements for the Master For the Master programmes in Computer Science, students may enrol who have a Bachelor's degree in Computer Science obtained at a Dutch university, including the technical universities of Delft, Eindhoven and Twente. Admission of students with other diplomas always needs the approval of the Examination Board. If there are gaps in the student"s knowledge that might hinder the successful completion of a Master in Computer Science, the requirement can be made that some extra courses are followed, by way of a pre-master education of at most 60 cp. If the gap is too big for that, the student will first have to do a Bachelor exam in Computer Science. Depending on the level of his or her previous education the student may then be exempted from a, possibly considerable, part of the Bachelor programme. We now mention some specific situations. A Bachelor diploma in Computer Science of a foreign university of quality is likely to qualify, such at the discretion of the Examination Board. Also students with another Bachelor diploma obtained at a Dutch or foreign university can apply for admission to the Master Programme in Computer Science. In each individual case it will be judged whether the student's Bachelor fits the chosen specialization of the Master Programme and whether and to what extent a pre-master track is required. With some Bachelor diplomas, such as Artificial Intelligence, Information Science, Mathematics, etcetera, a smooth transfer is especially likely (although this may still depend on the chosen specialization of the Master in Computer Science). Only with some Bachelor diplomas from Dutch HBO-institutions is it likely that a pre-master track of 60 cp will suffice for admittance to the Master Programme in Computer Science. The best fit is to be expected with the HIO (Hogere Informatica) specialization. Other specializations, such as HAEO Business Informatics, do not match as good; enrolment for a Master"s in Information Science might be a better choice. For students with an HBO-Bachelor degree the Free University requires an additional assessment test; further details can be found at the VU-website: http://www.vu.nl/aankomende_studenten/index.cfm

7.5

Master programmes The Master Programme in Computer Science offers eight different specializations, from which the student can choose. • •

70

Parallel Computing and Visualisation Internet and Web Technology

Exact Sciences

• • • • • •

Software Engineering Multimedia Formal Methods and Software Verification Technical Artificial Intelligence Information and Communication Technology Communication and Education

Below we give concise descriptions, which are meant to give an impression of the character of the specializations. Each specialization has a web page and for each specialization there is a contact person. Consulting the web pages and speaking with one or more of the contact persons may be helpful in making a good choice. Once a specialization is chosen, the student, should make a study plan, specifying the courses that will be followed in the Master Programme. The total amount of cp that is required for obtaining a Master's degree is 120. Fixed elements of the Master Programme are a master project of 37 cp and a literature study of 6 cp. Mostly the literature study will also involve participation in a seminar. As to the remaining 77 cp, the curriculum of each specialization consists of a fixed part, a compulsary part and a variable part, where choice is possible. In the tables given below the fixed part is specified and some suggestions are given for the choices that have to be made. The study plan should be approved by the Examination Board. It can be changed, but then the approval of the Examination Board has to be renewed.

7.6

Internet and Web Technology

7.6.1

Programme It needs no saying that Internet and World Wide Web play an ever more central role in out society. This specialization is concerned large-scale computer systems, especially computer networks and the Internet. Important topics are: Internet and Web protocols, distributed systems, network security, development tools for network applications, peer-to-peer technology, etc.

7.6.2

First year Compulsory courses, 6 cp Theoretical Computer Science, 4 cp Mathematics and 6 cp other optional courses Compulsory courses Course code 400162 400161 400130 400127 400196 400052

Course name

Parallel Programming Practical Parallel programming Distributed Systems Network Security Bedrijfssystemen practicum Network Programming

Master Computer Science

Stp. 6 6 6 6 9 9

Period

1 and 2 1 and 2 1 and 2 4 and 5 4, 5 en 6 5 and 6

71

Optional choices 1 out of 2 Course code 400137 400170

Course name

Object-Oriented Software Development Software Architecture

Optional choice Theoretical Computer Science at least 6 cp Course code 400117

Course name

Protocol Validation

Optional choice Mathematics at least 4 cp Course code 400178

7.6.3

4 6

1 and 2 2 and 3

Stp.

Period

6

5 and 6

Stp.

Period

4

5

Course name

ICT in a social context

Stp.

Period

4

1 and 2

Parallel Computing and Visualisation

7.7.1

Programme The parallel computing approach to difficult and complex computations is to use a (large) number of computers instead of one, and let these computers work simultaneously. The technical focus is on the construction of efficient and correct software that can be executed in parallel. A central application is the use of advanced graphical techniques to optimally display large quantities of data. Other important applications can be found for example in the field of bio-informatics. Parallel computing and visualisation are at the cutting edge of what computers can do.

7.7.2

First year Compulsory courses, 6 cp Theoretical Computer Science, 4 cp Mathematics and 9 cp other optional courses Compulsory courses Course code 400162 400114 400161 400130 400106 400196

72

Kansrekening en Statistiek

Period

Second year Compulsory courses, 11 cp elective courses, 6 cp Literature study and 37 cp Master Project Course code 400107

7.7

Course name

Stp.

Course name

Parallel Programming Practical Scientific Visualisation Parallel programming Distributed Systems Computer Graphics Bedrijfssystemen practicum

Exact Sciences

Stp. 6 4 6 6 6 9

Period

1 and 2 1 and 2 1 and 2 1 and 2 1 and 2 4, 5 en 6

Optional courses 1 out of 2 Course code 400137 400170

Course name Object-Oriented Software Development Software Architecture

Optional choice Theoretical Computer Science at least 6 cp Course code 400211 400117

Course name

Distributed Algorithms Protocol Validation


7.7.3


Period

4 6

1 and 2 2 and 3

Stp.

Period

6 6

4 and 5 5 and 6

Stp.

Period

4

5


7.8

Course name

Stp.

Course name


Stp.

Period

4

1 and 2

Software Engineering

7.8.1

Programme Some people define software engineering as: 'the application of a systematic, quantifiable approach to the development, execution and maintenance of software. It is a broad and comprehensive field, in which engineering plays an important part, next to psychological and managerial aspects. Keywords are evolution and complexity.

7.8.2

First year Compulsory courses, 6 cp Theoretical Computer Science, 4 cp Mathematics and 9 cp other optional courses Compulsory courses Course code 400137 400130 400144 400100 400170

Course name

Object-Oriented Software Development Distributed Systems Databases II Caput Software Asset Management Software Architecture


Stp.

Period

4 6 6 7 6

1 and 2 1 and 2 1 and 2 1 en 2 2 and 3

73


Course name

Project ISO Object-Oriented Software Development Practical


Course name

Protocol Validation


7.8.3

4, 5 en 6 5 and 6

Stp.

Period

6

5 and 6

Stp.

Period

4

5

Course name


Stp.

Period

4

1 and 2

Multimedia

7.9.1

Programme Multimedia is a rapidly developing application- and research area. Because of the arrival of broadband Internet we speak of digital convergence, the combination of formerly disjoint media, as in interactive television. Connected with the efficient use of multimedia is the rich palette of research questions in the field of authoring, information retrieval, human computer interaction, software architecture and 3Dgraphics. In the specialization Multimedia there is special attention for the use of 3D virtual environments for the disclosure of multimedia information. Depending on interest and expertise, authoring and design problems can have the focus, or more technical aspects in the field of software architecture communication and 3D graphics.

7.9.2

First year Compulsory courses, 4 cp Mathematics and 20 cp other optional courses Compulsory courses Course code 400050 400137 400130 400106

74


9 9

Period


7.9

Course name

Stp.

Course name

Multimedia Authoring I -Web3D/VRML Object-Oriented Software Development Distributed Systems Computer Graphics

Exact Sciences

Stp.

Period

6

1

4 6 6

1 and 2 1 and 2 1 and 2

400170 400164

7.9.3

Software Architecture Object-Oriented Software Development Practical

Course name

Logical Verification: Applied Logic ICT in a social context Multimedia Authoring II -- Virtual Environments


Course name

Logical Verification: Applied Logic


7.10.1

2 and 3 5 and 6

Second year Compulsory courses, 6 cp Literature study and 37 cp Master Project Compulsory courses Course code 400115 400107 400051

7.10

6 9

Course name


Stp.

Period

6 4 6

1 and 2 1 and 2 2

Stp.

Period

6

1 and 2

Stp.

Period

4

5

Formal Methods en Software Verification Programme Because of the increasing complexity of software, the automatic verification of specifications becomes ever more important. Since the number of states of a system easily reaches astronomical proportions, complete testing is impossible and partial testing often insufficient. This is especially important for safety-critical or even lifecritical systems. This specialization is concerned with formal methods for the specification and verification of software systems. Three theoretical disciplines play a central role: term rewriting, process algebra and co-induction. Tools developed from process algebra are used in protocol validation. Term rewriting is used in the execution of equational specifications and lies at the basis of functional programming and proof checking. Co-induction is the prime method for analyzing infinitary processes. Furthermore, there are several verification methods originating from logic, like model checking, in which temporal logic is used, and type theory. Typical courses: Logical Verification, Protocol Validation, Term Rewriting Systems.

7.10.2

First year Compulsory courses, 8 cp elective courses, 4 cp Mathematics and 9 cp Practical work Computer Science Compulsory courses Course code 400115

Course name

Logical Verification: Applied Logic


Stp.

Period

6

1 and 2

75

400130 400107 400121

Distributed Systems ICT in a social context Term Rewriting Systems

Optional courses 1 1 out of 2 Course code 400137 400170

Course name

Course name

Course name

Period

4 6

1 and 2 2 and 3

Stp.

Period

6 6

4 and 5 5 and 6

Stp.

Period

6 6

4 and 5 5

Stp.

Period

Network Security Neural Networks


Stp.

Distributed Algorithms Protocol Validation


1 and 2 1 and 2 4 and 5

Object-Oriented Software Development Software Architecture


6 4 6

Course name


4

Optional choice Practical work Computer Science at least 9 cp Course code 400164

7.10.3

7.11.1

76

Object-Oriented Software Development Practical

Stp.

Period

9

5 and 6

Second year 6 cp Theoretical Computer Science, 10 cp optional courses, 6 cp Seminar and 37 cp Master Project optional choice Theoretical Computer Science Course code 400122

7.11

Course name

5

Course name

Advanced Logic

Stp.

Period

6

1 and 2

Technical Artificial Intelligence Programme In this specialization the realisation of intelligent computer programs is the central subject. Artificial intelligence uses a great number of techniques from computer

Exact Sciences

science and also plays a part in the development of these techniques, often inspired by human cognition. In this programme the student can choose between the existing techniques. Analysing, modelling and implementing of human knowledge, leading to a computer program that can reason with symbolic representations of this knowledge is the subject of Knowledge Technology. In Knowledge Discovery and Data Mining the computer is used for recognition of structures in raw data, from which conclusions can be drawn. 7.11.2

First year Compulsory courses, 4 cp elective courses and 4 cp Mathematics Compulsory courses Course code 400111 400122 400130 400054 400121 400270 400132 400201

Course name

Evolutionary Computing Advanced Logic Distributed Systems Design of Multi-Agent Systems Term Rewriting Systems Programmeren in Prolog Neural Networks Project Kennissystemen


Course name Object-Oriented Software Development Software Architecture


7.11.3

7.12.1


Period

6 6 6 6 6 4 6 7

1 1 and 2 1 and 2 2 4 and 5 5 5 5 en 6

Stp.

Period

4 6

1 and 2 2 and 3

Stp.

Period

4

5

Second year compulsory courses, 7 cp optional courses, 6 cp Literature Study and 37 cp Master Project compulsory courses Course code 400154 400107

7.12

Course name

Stp.

Course name

Machine Learning ICT in a social context

Stp.

Period

6 4

1 and 2 1 and 2

Information and Communication Technology Programme of this Society oriented variant This specialization is aimed at the education of computer scientists considering a career with companies or administrative institutions. It is taught partly in Dutch. The master project of 37 cp has the form of an internship at a company or institution outside the Department of Computer Science. A minor of at least 26 cp is Master Computer Science

77

compulsary, broadening the view with courses from, e.g., the economical sciences. Moreover the courses with a more applied character dominate in the curriculum. For the minor the following 3 options have been pre-defined, but also other combinations are possible. (The options given here are in Dutch.) 1. Bedrijfskunde / Economie: Management en Organisatie Management of Information Systems Management Accounting 2. Computerrecht: Inleiding Recht Bachelorvak rechten Informatica en Recht 3. Multimedia: Multimedia Authoring I ACW: Geschiedenis Woord- en Beeldrelaties 3 Multimedia Authoring II 7.12.2

First year Compulsory courses, 6 cp Theoretical Computer Science, 4 cp Mathematics and 29 cp optional courses for both years including a Minor of 26 cp Compulsory courses Course code 400125 400130 400100 400170 400058

Course name

Knowledge Management and Modeling Distributed Systems Caput Software Asset Management Software Architecture Project ISO

Optional choice Theoretical Computer Science Course code 400122

Course name

Advanced Logic


7.12.3


6 6 7 6 9

Period

1 and 2 1 and 2 1 en 2 2 and 3 4, 5 en 6

Stp.

Period

6

1 and 2

Stp.

Period

4

5

Second year compulsory courses, 6 cp Literature Study and 37 cp Master Project compulsory courses Course code 400107

78

Course name

Stp.

Course name


Exact Sciences

Stp.

Period

4

1 and 2

7.13


7.13.1

Programma De Maatschappij variant speelt in op de toenemende behoefte die universiteiten, het bedrijfsleven, de overheid en andere maatschappelijke instellingen hebben aan academische professionals die in staat zijn om complexe vraagstukken te analyseren en maatschappelijke systemen te beïnvloeden. Hierbij kun je denken aan acceptatieen milieuproblemen rond de introductie van genetisch gemodificeerd voedsel, ethische dilemma's rond de toepassing van voorspellende geneeskunde (diagnostiek), toenemende vraagsturing in wetenschappelijk onderzoek en de implementatie van maatschappelijk verantwoord ondernemen. Tijdens de opleiding leer je kennis van verschillende wetenschappelijke disciplines samen met kennis uit de maatschappij te integreren. De opleiding is zowel theoretisch als praktisch georiënteerd met concrete cursussen over beleid, management en ondernemerschap op het gebied van onder andere gezondheid en milieu. Je kunt ook deelnemen aan het masterprogramma Beleid Management en Ondernemerschap welke wordt verzorgd door de afdeling Biologie en Samenleving van de faculteit der Aard en levenswetenschappen (FALW; prof. dr. J. Bunders, kamer A0.68, telefoon: (020) 44 47030). Je kunt rechtstreeks in deze masteropleiding instromen met een universitaire bachelor in de bèta wetenschappen. De meest recente informatie vind je op onze website: www.falw.vu.nl/masters. M-variant



Stp. 7 5 3

Periode 06.09.2004 - 08.10.2004 11.10.2004 - 29.10.2004 15.11.2004 - 26.11.2004

Stp. 3 9

Periode 01.11.2004 - 12.11.2004 10.01.2005 - 18.02.2005



7.14


Communication variant As for all study programmes offered at the Faculty of Sciences a Communication variant is offered. This programme is open for any student having a Bachelor. Teaching in these variant is mainly in Dutch. Therefore we also give the requirements in Dutch.

7.14.1

Programma Het programma omvat een reeks cursussen, waarvan de eerste twee verplicht zijn. Op twee momenten kan er een keuze gemaakt worden tussen alternatieven ('Communicatie en Educatie via Internet' of 'Wetenschap Technologie & Master Computer Science

79

Samenlevingsstudies' en 'Informatie Representatie en Multimedia' of Gezondheidscommunicatie). Het jaar wordt afgesloten met een verplichte scriptie van 9 studiepunten en een korte stage van 18 studiepunten. De Communicatie variant wordt georganiseerd door de afdeling Wetenschapscommunicatie van de Faculteit Aard- en Levenswetenschappen. Contactpersoon voor het C-profiel is drs. I. van Veen, tel. (020) 44 47214, e-mail: [email protected]. Programmacoördinator is dr. J. Willems, e-mail: [email protected]. Communicatie variant


7.15 7.15.1


Stp. 3 6 6 3 6 6

Periode 01.11.2004 - 12.11.2004 04.10.2004 - 29.10.2004 06.09.2004 - 01.10.2004 07.02.2005 - 8.02.2005 10.01.2005 - 04.02.2005 10.01.2005 - 04.02.2005

3

15.11.2004 - 26.11.2004

3 6

15.11.2004 - 26.11.2004 29.11.2004 - 24.12.2004

Master projects and Training on the job Programme The Master programme is concluded with a Master project or internship. This can be an individual project as well as a group project. Information about graduation projects and internships can be found on the Internet pages of the research groups of the Department of Computer Science. A graduation project has to be supervised by a staff member. Internships proposed by the student him/herself need approval in advance from a member of staff, who will cooperate with supervising the project. Concerning graduation projects, the following rules are important: • The size of the Master projects is such that a project can be finished within 6 months of full-time occupation. • Students can in principle only start their graduation project if they have completed all other exam parts. In case one part must still be completed, approval of the project leader is required to start the project. In case more than one part must be completed, explicit approval of the Examination Board is required. • Upon project completion, a meeting will be held with all involved in the project, in which the student's work will be assessed and a judgement will be made under responsibility of the supervising member of staff. When the final judgement is that the student work is not sufficient, a supplement will be required from the student. The rules for graduation internships are similar to those for graduation projects.

80

Exact Sciences

7.16 7.16.1

Educational possibilities after the Master, training as a researcher Programme Each year the faculty offers a number of Ph.D. student positions; sometimes extra positions are available that are financed by NWO via specialised research projects. Graduate students with excellent grades are invited to apply for one of these positions. A Ph.D. student position is normally awarded for 4 years, during which time the Ph.D. student is expected to finish a doctoral thesis. A Ph.D. student obtains a full professor as supervisor, whereas the daily supervision will sometimes be performed by another member of the scientific staff. Aside from his/her research task (which includes following specialised courses and seminars), the Ph. D. student is also expected to contribute to regular teaching tasks. All Ph.D. students are registered with one of the research schools in which the Department of Computer Science participates: IPA, SIKS or OZSL. Training as a researcher is possible in one of the following disciplines: Information Systems; • Computer Systems; • Artificial Intelligence; • Software Engineering; • Theoretical Computer Science; • Bio-informatics. Students interested in a Ph.D. student position can contact one of the study advisors or a professor or staff member under whose supervision they would like to conduct their research.

•

7.17 7.17.1

Graduate schools Introduction The main task of a Ph.D. student is to do research, leading to a dissertation. Since everything has to be learned, the Ph.D. student is supposed to get training in doing research, and also to get additional education in his/her research area. The graduate education preparing for a Ph.D. is provided by the Dutch research schools. These research schools are institutions in which several universities participate. Their aim is to coordinate research activities in a specific area and to organize training programmes for Ph.D. students in that area. The Department of Computer Science of the Vrije Universiteit participates in three research schools: IPA It is the principal goal of the Institute for Programming research and Algorithmics (IPA) to educate researchers in the field of programming research and algorithmics; this research area comprises: • the study and development of formalisms, methods and techniques to design, analyze, and construct software systems and components Website: http://www.win.tue.nl/ipa


81

SIKS The scientific mission of the Dutch Research School for Information and Knowledge systems (SIKS) is to perform high-level fundamental and applied research in the field of information and knowledge systems, from the perspectives of the following scientific areas: • database systems • information systems • knowledge engineering • software engineering • theoretical computer science and applied logic Website: http://www.cs.uu.nl/siks OZSL The aim of the Dutch Graduate School in Logic (OZSL, for Onderzoeksschool Logika) is to guide the development of logic research, as a core part of an emerging new science of information processing. More in particular, the school is active in the research areas of: • logic in computer science • logic and artificial intelligence • logic, philosophy and linguistics The OZSL also encourages the development of new areas where logic, viewed as the science of the formal aspects of information processing, could play an important role. Website: http://www.ozsl.uva.nl ASCI The research in the Advanced School for Computing and Imaging (ASCI) focuses on two main themes: • Computer Systems: methods and techniques for the design and implementation of advanced computer systems, especially parallel, distributed, embedded and realtime systems. • Imaging Systems: methods and techniques for the analysis and synthesis of images. These two areas frequently overlap, creating areas of fruitful research. For example, advanced imaging systems often need massive parallel computing systems due to the amount of data to be processed. Similarly, when imaging, distributedsystems and real-time systems are combined, we get multimedia, another increasingly important area. Website: http://www.asci.tudelft.nl

82

Exact Sciences

8

8.1 8.1.1

Master Information Sciences Business Information Science The domain of the Master Research in Business Information Science is aimed at theory development, effective structuring, processing, and communication of information, using ICT. In the field of Business Information Science information processes of individuals and organisations are studied, not only from a technological perspective but also from the cognitive, social and organizational perspectives. Business Information Science at the Vrije Universiteit strikes a healthy balance by combining technology and information with people, culture and organisation, while the approach is defined by multidisciplinary and multicultural cooperation. Business Information Science at the Vrije Universiteit builds on a solid computer science foundation. For these reasons Business Information Science at the VU makes for a broad and multidisciplinary research area where the confrontation between the exact and social sciences is continuously challenged. The aim of Business Information Science is to develop people capable of solving complex problems in teams and concerned with the availability, application and use of complex information systems. The school seeks to train masters in Business Information Science equipped with the knowledge and skill that allow for broad employability, based on strong research driven technological innovation and with a clear orientation toward applicability in society. Both the Bachelors and Masters studies are organised by the Faculty of Sciences. Information about the Bachelor programme can be found in a separate study guide. The latest information on the masters in Business Information Science can always be found at http://www.cs.vu.nl/bi/masters/ Study advice is open to all. Advisor prof.dr. J.F. Schreinemakers (masters) can be contacted via secretary Elly Lammers ([email protected]).

8.1.2

Objectives The Master programmes in Information Sciences/Business Information Science aim to provide students with knowledge, experience and insights in Information Science and its supporting disciplines to carry out professional duties autonomously and at academic levels as well as to prepare the student for further education for the professions of teacher, scientific researcher or designer. Furthermore, the Master programme seeks to promote insight in the coherence of the sciences and to develop a sense of social responsibility.

8.1.3

Final attainment level After graduation the student in Information Sciences/Business Information Science (IS/BI) is expected to be critical in a scientific manner, to be aware of the multidisciplinary aspects of information systems, and to possess knowledge, experience, and insights regarding:

Master Information Sciences

83

• • •

8.1.4

novel developments and issues in IS/BI and possess knowledge of research relevant for contemporary problem solving concerning such issues; independent problem definition and goal setting of a research project; independent execution of advanced projects and the subsequent reporting both verbally and in writing.

Requirements for the Master For the Master programmes in Information Sciences/Business Information Science, students may enrol who have a Bachelor or Drs diploma in Information Sciences/Business Information Science from the VU. The following students may conditionally enrol in the Master programme IS/BI : Academic bachelor in Computer Science, Business Mathematics and Informatics under the condition of at minimum a pass for the following components: a. Information Sciences/Business Information Science courses: • Business Modelling & Requirements Engineering • Information System Development project • Quality of Information management b. Management courses • Marketing • Enterprise systems and E-Business • Accounting c. Computer Science courses: Programming I and II • Software Engineering (lectures) • Databases I • Suggested: Computer Networks •

d. Social science oriented courses In case of deficiencies of afore mentioned requirements [a-d], admission will only take place after successful participation (at minimum a pass) in the homologation package as determined by the study coach under requirements [a-d] mentioned above and while the total of the deficiencies does not exceed 30 ECTS. Students meeting these requirements can start with the master programme whenever the sum of required ECTS is 30 or less. In special cases the exam committee has the authority to deviate from these rules to accommodate. In case the student already has a HBO bachelor degree of one of the following programmes • HEAO-BI • Informatiekunde • Informatica (HIO) • HTS-Technische Computerkunde, then the student may enrol in an one-year pre-master programme in Business Information Science (total 60 ECTS). The pre-master programme allows form enrolment in the master programme in Business Information Science. The detailed

84

Exact Sciences

composition of the pre-master programme depends on the courses taken and successfully passed at the HBO and is determined on an individual basis. In any case and in addition to the requirements for the mentioned bachelor diploma's, the following courses are required to be successfully passed at the required academic level: Business Information Science courses: Business Modelling & Requirements Engineering • Information System Development lab • Quality of Information management •

Managerial courses: Enterprise Resource Planning • E-Business • Accounting • Marketing

•

Computer Science courses: Programming I en II • Software Engineering (lectures) • Databases I • Suggested: Computer Networks •

Social science oriented courses In the majority of the cases HBO-"instromers" will be required to follow a substantial number of the above courses at the VU, and will in general conform to one year of academic studies. At the end of this year successful students enrol in the one-year Master of Science programme. In practice, these regulations mean that students with the aforementioned HBO bachelor may be expected to obtain a master degree in Information Science from VU over a two year period. The HBO pre-master programme consists of subparts from Information Science, Computer Science and Management Science. In any case the programme will be composed in such a way that all courses mentioned are mastered at the required academic levels. The detailed composition of the programme will take place in consultation between the student and the director of master studies in information science. The latter will propose the specific programme design for approval to the exam committee. In case that the exam committee determines that certain courses have already been passed and at sufficient academic levels an exemption may be granted by the committee for the corresponding VU exams. Contact persons: Prof.dr. J.M. Akkermans (tel 020-4447718, [email protected]) dr. J. Gordijn (020-4447769, [email protected]) Ir. M.P.H. Huntjes (tel 020-4447747, [email protected])


85

8.1.5

Master Programme The master year is divided into two parts. During the first part in fall (time period 1, 2, and 3) students will take a number of courses based on recent research in Business Information Science. The emphasis will be on our own departmental research at the Free University. The second part of the Master year is focused on the final traineeship and the writing of a master thesis. It is strongly preferred to carry out the final traineeship at an external organisation. The final traineeship results in a written master thesis. Please note that: Students are required to select from { Knowledge management and modelling, Ontology Engineering en Software Architecture} at least two courses. • HBO-students following the two year master-track, enrolled in the study period 2003-2004 are not obliged to select "Design of experiments and analysis of variance". • Students entering the Master after graduating from the Information Science/Business Information Science Bachelor may already have taken compulsory courses of the Master IS/BI. These students will be required to take elective courses with a minimum of one (1) point from Computer Science and a minimum of one (1) point from Management Science; • Students enrolling from a Academic Bachelor comparable to the IS/BI Bachelor are required to compensate deficiencies with Free University bachelor courses and electives up to a maximum of 30 credit points. In addition, these students are assumed not to have taken one or more master courses. In this case all compulsory master courses will need to be taken, as well as the compulsory electives in Computer Science and in Management Science. •

Table: the master year schematically Compulsory courses Course code 400110 400310 400290 400284

Course name

E-Business Innovation Design of Experiments and Analysis of Variance Qualitative Research Methods for the Information Sciences Master Project Information Sciences

Stp.

Period

7 2

1 and 2 2

3

3

30

4, 5 en 6

Optional courses Students can also follow electives computer science and/or management science Course code 400125 400170 400292

8.2 8.2.1

86

Course name

Knowledge Management and Modeling Software Architecture Ontology Engineering

Stp.

Period

6 6 3

1 and 2 2 and 3 6

Multimedia & Culture The domain of the Master Research in Multimedia & Culture is aimed at theory development, development of design methods and techniques, assessment of multimedia products and productions, Exact Sciences

and design of modern interactive systems for cultural applications and for multicultural audiences. In the field of Multimedia & Culture modern technology design and use by individuals and organisations are studied, not only from a technological perspective but also from the cognitive, artistic/creative, social and organizational perspectives. Multimedia & Culture, as a specialisation in Information Sciences at the Vrije Universiteit strikes a healthy balance by combining technology and information design with people, arts and crafts, culture and organisation. The approach is defined by multidisciplinary and multicultural cooperation. The application domain should be considered interactive systems and multimedia products and productions in cultural domains in the broad sense, ranging from education, publishing and library applications, cultural history, broadcasting, arts, to games and amusement industry. Multimedia & Culture at the Vrije Universiteit builds on a solid computer science foundation. For these reasons Multimedia & Culture at the VU defines for a broad and multidisciplinary research area where the confrontation between the exact sciences, arts and design sciences, and social sciences is continuously challenged. The aim of Multimedia & Culture is to develop people capable to solve complex problems in teams and concerned with design, availability, application and use of complex multimedia and information systems. The school seeks to train masters in Multimedia & Culture equipped with the knowledge and skill that allow for broad employability, based on strong research driven technological innovation with a clear orientation toward applicability in society. Both the Bachelors and Masters studies Multimedia & Culture are organised by the Faculty of Sciences. Information about the Bachelor programme can be found in a separate study guide. The latest information on the bachelors and masters in Multimedia & Culture can always be found at http://www.cs.vu.nl/~mmc. Study advice is open to all. Study coordinator Dr. Gerrit C. van der Veer can be contacted via secretary Elly Lammers ([email protected]). 8.2.2

Objectives The Master programme in Information Sciences - Multimedia & Culture aims to provide the students with the knowledge, experience and insights in this specific domain of Information Sciences and its supporting disciplines to carry out his/her professional duties autonomously and at academic levels as well as to prepare the student for further education for the profession of teacher, scientific researcher or designer. Furthermore, the Master programme seeks to promote insight in the coherence of the sciences and to develop a sense of social responsibility.

8.2.3

Final attainment level After graduation the student in Information Sciences - Multimedia & Culture is expected to be critical in a scientific manner, to be aware of the multidisciplinary aspects of multimedia and information systems and its applications in cultural domains and in different cultures, and to possess knowledge, experience, and insights regarding: • novel developments and issues in Multimedia & Culture and state of the art knowledge of research relevant for contemporary problem solving concerning such issues;


87

• •

8.2.4

independent problem definition and goal setting of a research project; independent execution of advanced projects and the subsequent reporting both verbally and in writing.

Requirements for the Master For the Master programmes in Information Sciences - Multimedia & Culture students may enrol unconditionally, who have a Bachelor certificate Information Sciences Multimedia & Culture from the VU. The following students may conditionally enrol in the Master programme Information Sciences - Multimedia & Culture : • Academic bachelor in Computer Science, Information Sciences, Literature & Arts (Word and Image, Communication Sciences), or Industrial Design; • Higher Vocational Education (HBO) Bachelors in Computer Science or Interaction Design; under the condition of at minimum a pass for the following components: • Multimedia technology courses equivalent to 12 ECTS at academic level; • History of Western Culture classes equivalent to 6 ECTS at academic level; • Artistic design classes equivalent to 6 ECTS at academic level; • Humanities, User centred design / Cognitive Ergonomics courses equivalent to 12 ECTS at academic level; • Computer Science classes equivalent to 24 ECTS at academic level. In case of deficiencies of afore mentioned requirements [a-e], admission will only take place after successful participation (at minimum a pass) in the homologation package as determined by the study coordinator under requirements [a-e] mentioned above and while the total of the deficiencies does not exceed 60 ECTS. Students with deficiencies of a maximum of 60 ECTS have to enrol in the pre-master programme. In special cases the exam committee has the authority to deviate from these rules to accommodate. The bachelor of science diploma Multimedia & Culture allows subsequent enrolment in the master programme in Multimedia & culture without further conditions. The detailed composition of the bachelor of science programme depends on the courses taken and successfully passed during prior education and is determined on an individual basis. The detailed composition of the programme will take place in consultation between the student and the study coordinator. The latter will propose the specific programme design for approval to the examination committee. The Masters Multimedia & Culture is in principle a full time day curriculum. Even though there is no formal part time variant, it is in fact possible to take each year only part of the classes or fullfill other requirements like the traineeship, and to combine the study with a (part time) job. In this case carefullplanning and agreement of the study coordinator is mandatory. Contact persons: Dr. G.C. van der Veer (tel 020-4447718, [email protected])

88

Exact Sciences

8.2.5

Master Programme The master year is structured into two parts. In the first part (see the table below) students will take a number of courses. These classes regard 3 groups: design (text design, multimedia design case), computer science applications (software architecture, and e-business innovation), and domain specific methodology. Apart from this the student has to choose either a qualitative research methodology class, or a class on ontology engineering. This part will take a total of 30 ECTS. The second part of the Masters is focused on the final traineeship and the writing of a master thesis. For those who intend to enter a career in industry or cultural institutes, it is strongly preferred to carry out the final traineeship at an external organisation. For students who envision a continuation of their education, i.e., a PhD study, a research internship at the university is suggested where the student participates in a research project of the Vrije Universiteit. The final traineeship results in a written master thesis. This part will take the equivalent of a half year of student time. The project can be done individually or in a small group, the thesis will normally be written individually. Each thesis will be presented and discussed in a public session. Remarks: Please note that students enrolling from a Bachelor comparable to the VU Bachelor Multimedia & Culture are required to compensate deficiencies with Free University bachelor courses and electives up to a maximum of 60 credit points (see 1.2.5.). On the other hand, these students may have taken courses that are considered equivalent to one or more of the compulsory or listed master courses. In this case the student can apply for exemption from those master courses with the study coordinator. Remarks: MMC students should choose between Ontology Engineering and Qualitative research methods in the information sciences Course code 400287 400110 400310 400311 400170 400158 400290 400284 400292

Course name

Text Interface Design E-Business Innovation Design of Experiments and Analysis of Variance Applied Multivariate Analysis Software Architecture Multimedia Design Casus Qualitative Research Methods for the Information Sciences Master Project Information Sciences Ontology Engineering


Stp.

Period

3 7 2

1 1 and 2 2

4 6 6 3

2 2 and 3 2 and 3 3

30 3

4, 5 en 6 6

89

90

Exact Sciences

9

9.1

Master Medical Natural Sciences Objectives The Master course in Medical Natural Sciences aims • to educate students towards independent academic professionals. The corresponding skills encompass the ability to perform fundamental medicalnatural scientific research as well as to apply existing medical-natural scientific knowledge in new medical or clinical settings; • to stimulate interdisciplinary collaboration in the development of science from a medical-natural scientific background; • to teach students skills, knowledge and insight into a specialist area of the medical-natural science field, with a focus on insight into, and approaches towards, medical-natural scientific questions; • to offer education that is competence- and student-based, and meets high international standards; • to train students to acquire know-how in an international context; • to offer an inspiring academic study environment and doable study tracks to a demanding and heterogeneous student population. • to teach students how to develop the ability to transfer acquired knowledge to others.

9.2

Final attainment level The graduated Medical Natural scientist • is able to survey - and make good use of - scientific literature in the relevant subareas of medical natural sciences; • is able to survey the interdisciplinary character of medical natural sciences and to make good use of these interdisciplinary features; • is able to break in a sub-area of medical natural sciences within a reasonable amount of time; is able to formulate a research work plan, on the basis of a global presentation of questions from the field of medical natural sciences; • is able to tackle - apart from the main subject of study - an academic question in a second sub-area of medical natural sciences; • is able to analyse and interpret results of scientific research, and to draw conclusions upon them; • is versatile in many tasks in which knowledge and research skills in the field of medical natural sciences are required; • has sufficient knowledge of - and insight into - the role in society of medical natural sciences, in order to arrive at a responsible choice of profession; • has insight into the role of medical natural sciences in a durable society; • is able to collaborate with others, to transfer knowledge, to give an oral presentation (in English), to compose a written report (in English) or an internationally accessible scientific publication, and to take active part in a scientific discussion; • is able to set up scientific experiments including the corresponding controls, in a manner that meets proper quality standards, and to evaluate these; • is able to put results obtained and conclusions drawn into the context of data obtained by others;

Master Medical Natural Sciences

91

• •

is able to evaluate one's own functioning, both by self-reflection and in discussion with others; is acquainted with the ethical aspects related to the field of medical natural sciences.

Additional attainment level per variant: O-variant: the graduated Master of Science in Medical Natural Sciences has a broad experience with acquiring chemical knowledge and has some experience with performing chemical research in an independent manner. M-variant: the graduated Master of Science in Medical Natural Sciences has the ability to perform projects in society with applications of chemical know-how and methods, both as an individual as in a team. C/E-variant: the graduated Master of Science in Medical Natural Sciences is able to work in education or science communication. If the graduate has finished the education for teacher, he/she is qualified for the function of teacher in Dutch vwoeducation.

9.3

Requirements for the Master Direct admission to the Master's programme in Medical Natural Sciences is possible with a Bachelor's degree in Medical Natural Sciences. If you have a Bachelor's degree in a related subject, you will have to satisfy certain entry requirements depending on the track you have in mind. Candidates with a Bachelor's degree from an institute of higher vocational education require a declaration of equivalence from the Examination Board. The progamme provides limited opportunities to fill specific gaps in your knowledge or technical skills.

9.4

Structure of the training The Master's programme of Medical Natural Sciences offers three different profiles for graduation: • Research profile (O - variant) • Management/Business-oriented profile (M - variant) • Communication-education profile (C / E - variant) Schematic overview of the Master course Medical Natural sciences (in cp):

92

Exact Sciences

Profile Compulsory courses (Major) Research project (Major) (including report) Literature thesis and colloquium Minor programme (obligatory in O-variant) Internship (e.g. at a company) M or C projects High school teacher education Ethics Optional program O-variant For example Deficiency courses Extension research project Clinical internship Industrial internship Training abroad Apha or Gamma courses

O 24 42

M 18 33

C 18 33

E 18 33

12

6

6

6

21-27

-

-

-

-

18

18

-

-

42 -

42 -

60

3 12-18

3

3

3

120

120

120

max.12 18 18 18

Total (cp)

120

NB 1. With respect to the composition of the optional programme (O-variant), additional requirements may apply, depending on the chosen master specialisation (track). NB 2. Extension of the Major-research project should preferably be external (other university, company, abroad). Students should arrange the composition of their Master's programme in consult with the Master's coordinator. The exam committee formally has to approve the composition and extent of the Master's programme.

9.5

Part-time studying In principle this Master's programme is full-time.

9.6

Dual training Under specific conditions, a tailored Master's programme can be composed, in which in-service training is included.

9.7

Master Programmes Students who have chosen to follow the research-oriented variant (O-profile) first have to choose a specialist track. A choice can be made from the programmes in • Physics of Life • Bioinformatics / Genomics Master Medical Natural Sciences

93

• • • •

Biomolecular complexity Molecular Medicine Medical Natural Sciences and Business (M-variant) Medical Natural Sciences and Communication / Education (C/E variant)

Each track encompasses at least compulsory (theoretical) courses, a research project including Master thesis (Major), literature thesis and colloquium, and optional courses or training (see scheme). Generally spoken these students may aim at continuing their study with PhD education, in order to obtain an executive job as researcher, group leader etcetera at university, research institution, government or (industrial) company.

9.8 9.8.1

Physics of Life Department of Physics and Medical Technology (Vumc) The department of Physics and Medical Technology (PMT) is a professional organisation for physics and medical technology in education, research and support of patient care in the VU medical center. The department covers and supports a wide range of medical care and employs about 30 physicists/engineers and 50 technicians. Research is often carried out in multidisciplinary teams and related to research projects of the department PMT of to one of the other 45 departments in the Vumc. The research is devoted to: clarifying the physical principles which are the basis of human functioning from the cellular level to the level of the intact human being. • the development of new techniques and methods to assess function parameters in man in normal and pathological situations.

•

The main research projects of the department are related to: • cardio-, circulatory and pulmonary physics • neuro-physics • skeletal physics • ophthalmo-physics Important techniques that are being developed are: • MRI tagging techniques (MRI) • Image analysis • Functional magnetic resonance • Magneto-encephalography (MEG) • Electrical-impedance tomography (EIT) • Corneatopography In the department there are frequently practicals and research projects for students. Contactpersons: General: prof.dr. R.M. Heethaar, head of the department ([email protected]) dr.ir. B.J. ten Voorde, staffcoordinator ([email protected]) Cardio-, circulatory and pulmonary physics: 94

Exact Sciences

MRI: dr. M.B.M. Hofman ([email protected]), dr. J.T. Marcus ([email protected]) EIT: dr.ir. H. van Genderingen ([email protected]) Neurophysics: dr. J.C. de Munck ([email protected]) Skeletal physics: dr.ir. Th. Smit ([email protected]) Ohthalmophysics: dr. G.L. van der Heijde ([email protected]) Radiotherapy: dr. J. Cuijpers ([email protected]) The schedule below indicates the courses that are given in this specialization. For more information contact the co-ordinators.


95

Onderwe rp Optica / golven

Titel Onderwerp

Toepassing Elektriciteit, magnetisme, elektrodynamica, elektronica

Signaalverwerking

Titel Onderwerp Toepassing


Atoom-, kern fysica; structuur der materie

Titel Onderwerp

Kwantumfysica / kwantum mechanica

Toepassing Titel Onderwerp Toepassing

Stromingsleer / transport verschijnselen


9.9 9.9.1

96

Invulling Optica en geluidsgolven Functioneren van gezichts- en gehoor zintuig, perceptie eigenschappen van het oog, afbeelding met ultra geluid Echografie, microscoop Echografie, microscoop Bio electrodynamica Vergelijking van Lorentz-Maxwell, electro fysiologie EEG, ECG, hersenen, spieren, pacemakers, MEG, voorwaartse en inverse problemen, elektrische veiligheid Kwantitatieve analyse Digitale signaal analyse, medische statistiek (toetsingstheorema, experiment design), model vorming, numerieke analyse Beeld reconstructie Wordt open gelaten. Onderzocht moet worden wat reeds in de bachelor gegeven is. Toegepaste kwantum fysica Laser fysica, fluorescentie Pulsoxymetrie, fluorescentie technieken in de kliniek, lasertechnieken in de kliniek Fysica van circulatie en ventilatie Stromingsvergelijking (NavierStokes, elasticiteitstheorema), fysische mechanisme van hart en long Moderne cardiovasculaire en ventilatoire apparatuur, thermodilutie

Bioinformatics / Genomics Integrative Bioinformatics Institute VU (FEW, FALW, Vumc) Bioinformatics research is concerned with the information processes in living systems and with designing and applying methods to analyse and integrate biological (genomic) data. It therefore has a central position among research fields like pharmaceutics, biotechnology, gene technology, anthropology, agriculture, forensic science and chemistry, as well as clinical research and industrial applications.

Exact Sciences

Bioinformatics is a multidisciplinary field encompassing disciplines such as computer science, statistics, medicine, genomics, molecular biology, cell physiology, etc. The Integrative Bioinformatics Institute In addition to a growing Bioinformatics Department, the VU recently founded a broad-based bioinformatics institute, the Integrative Bioinformatics Institute VU (IBIVU). This is a multidisciplinary institute which brings together three faculties (Sciences, Earth and Life Sciences, Psychology and Education) and the VU University Medical Center with the joint aim of expanding the knowledge of genetic and cellular processes which play a key role in areas such as multifactorial diseases (e.g. cancer), soil ecology (ecogenomics), neurobiology and biocomplexity. The IBIVU combines, in addition to core bioinformatics, expertise from areas including: mathematics (biostatistics, stochastics), artificial intelligence, high-performance computing, scientific visualization, molecular cell physiology, genetic psychology and genomics. An overview of bioinformatics master courses open to MNW students Sequence Analysis Course/workshop studying theory and using techniques of sequence database searching, pairwise and multiple alignment, profile searching, and phylogeny (6 credits). DNA/Protein Structure-Function Analysis and Prediction Course/workshop studying theory of DNA/protein sequence- structure-function relationships and providing hands-on experience of associated methods (6 credits). Genome Analysis: Structural and Functional Genomics Course studying theory and methods of genome mining, gene and gene function prediction, gene clustering, and genomic networks (6 credits). Bioinformatic Data Analysis and Tools Course offering theory and methods in applied multivariate statistics, MCMC, data mining, and bioinformatics methods development (6 credits). Integrative Bioinformatics and Genomics Theory and practice of integrative approaches and databases within bioinformatics, including E-cell modelling, AI (agent systems), metabolic pathways (metabolome), and integrative data mining of genome, proteome, metabolome, and physiome data (6 credits). MNW-Bioinformatics Research project (major) including master thesis Your traineeships will account for 42 of your credits. The IBIVU's broad, multidisciplinary structure allows you to work on a wide variety of subjects at the VU. Current research themes in tools development within the Bioinformatics Section (FEW) that can be joined: • Genomic repeats detection: at least 50% of genomic sequences (including human) contain sequence repeats, which are implicated in cellular functioning and disease. Finding repeats is a difficult problem as they can have diverged beyond recognition through evolutionary time. Available methods to delineate repeats are not sensitive enough, such that improvements must be made. A project is ongoing to design new repeats detection methods and to make some of our in-house methods genome-ready by speed optimisation and implementation on high-


97

•

•

•

throughput (cluster) computers. The ultimate aim is to mine every available nucleotide and protein sequence to delineate 'all' internal sequence repeats, and to develop a repeats database. Multiple sequence alignment (MSA): The most important technique in molecular biology for gaining understanding about a given protein family is constructing a multiple alignment of a set of sequences. The MSA technique is also indispensable in comparative genomics research. We are currently developing the T-COFFEE and PRALINE methods, and work on designing new strategies to improve MSA. These strategies include novel ways to include evolutionary information and the integration of other bioinformatics prediction techniques (e.g. protein secondary structure prediction, residue accessible surface prediction) to better match the sequences. In addition to better methods we also work on new quality control and visualisation schemes. Homology searching: By far the most important current technique to get clues about the function of a given query sequence, for which no knowledge (annotation) is available, is by comparing that sequence with annotated sequences residing in sequence databases. The most widely used bioinformatics method worldwide at present is the method BLAST that incorporates a search strategy that leaves room for improvement. We are designing new and improved techniques to recognise homologous sequences for a given query sequence. The research includes the integration of predicted protein structural information, new filtering rules, and novel techniques from computer science (e.g. suffix trees). Gene finding: only a fraction of the genes in most genomes are currently known. For understanding cellular functioning and treating diseases it is important to develop better gene prediction techniques. We recently started a project to enhance gene prediction by combining available methods and applying new machine learning techniques.

Contact person: Prof. dr. Jaap Heringa Head, Bioinformatics Section / Room R-441 Sci. Dir., Integrative Bioinformatics Institute VU (IBIVU) Tel. +31 20 4447649 Fax. +31 20 4447653 Email: [email protected] Internet: ibivu.cs.vu.nl Mail address: Bioinformatics Section, FEW/Inf, Vrije Universiteit, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands Course code 430047 430045 470707 430046 430049 430048

98

Course name Genome Analysis: Structural and Functional Genomics Sequence Analysis Ethics DNA Protein Structure-Function Analysis and Prediction Integrative Bioinformatics and Genomics Bioinformatic Data Analysis and Tools

Exact Sciences

Stp.

Period

6

1

6 3 6

2 24.01.2005 - 04.02.2005 3

6 6

5 5 and 6

9.10 9.10.1

Biomolecular Complexity MSc Biomolecular complexity (MSc BMC) Participating sections • Biochemistry and Molecular Biology (FEW/BMB) Co-ordinator: Prof. dr. S.M. van der Vies, KB258 tel. (44) 47548, [email protected] Physics of Complex Systems (FEW/FCS) Co-ordinator: Dr. ir. G.J.L. Wuite, T061, tel.(44) 47987, [email protected] •

• Biophysics (FEW/BF) Co-ordinator: Prof.dr. R. Van Grondelle, S162, tel. (44) 47930, [email protected]

Introduction The research projects that are offered in the MSc Biomolecular Complexity are multi disciplinary and may take place either in one or in both the sections FCS - BMB or in teh section BF (see below). The interdisciplinary character of this MSc programme means that students will gain biochemical as well as biophysical experience. The first year of the program will be spend primarily on course work while the second part will be focused on the actual research. The research consists of a major period of 9 months and a minor period of 3 months. The latter part may be done outside the participating sections. The MSC-BMC is organised by de sections Biochemistry and Molecular Biology and Physics of Complex Systems List of current available research projects Mechanisms of Motor Proteins • Dynamics of DNA Enzymes • Cytoskeleton / Semi-flexible Polymers • Viral structural biology • Protein networks and Signal transduction • Protein misfolding and Parkinson's disease • Biology of Molecular Chaperone Complexes • Ribosome assembly

•

For more information read the individual descriptions of the projects below. Research subjects often changes in the sections, so for more information on the current projects contact the co-ordinators. Background The research programme of the Section of Physics of Complex Systems focuses on experimental studies of biological and biologically inspired systems. Until quite recently, these processes could only be investigated on a bulk level, which meant handling large numbers of molecules simultaneously resulting in the detection of averaged behaviour of these molecules. The stresses and forces that molecules exert on each other in the course of reactions were not directly measurable. This situation has changed rapidly thanks to the development of methods for manipulating single molecules. Methods such as optical tweezers and scanning force microscopy (SFM) make it possible to follow the movements, forces and strains that develop during the Master Medical Natural Sciences

99

course of a reaction in real-time and at a single molecule level. The area of research includes biochemical processes as diverse as protein folding, DNA elasticity, proteininduced bending of DNA, the stress-induced catalysis of enzymes, and the behaviour of molecular motors such as kinesin, myosin, and RNA polymerase. The general theme relating the projects is the study of dynamic physical properties of complex biological macromolecules, using a combination of microscopes and single molecule manipulation techniques, combined with physical modelling. The research programme of the Section of Biochemistry and Molecular Biology focuses on experimental studies of large protein-containing complex systems, such as molecular chaperone machines, ribosomes and protein networks for signalling. These complex systems have in common that they are composed of large numbers of proteins and/or RNA which have to interact with each other in a unique way and unique sequence, so that protein folding, ribosome assembly and signal transduction occur properly inside a living cell. Correct folding of a newly synthesised amino acid chain is required to obtain an active three-dimensional protein structure. For reason that are unclear proteins sometimes don't fold correctly and end up as aggregates which are found in certain cells of people with Parkinson, Alzheimer and Type II diabetes. Protein networks regulate signal transduction which plays an important role during cell proliferation (cancer), in the immune response (infection) and during adaptation to changes in osmolarity (kidneys), while ribosome assembly has been linked to protein networks that regulate cellular metabolism, the cell cycle and stress adaptation. The complex systems are studied both inside the living cell (in vivo) using two model organisms: Escherichia coli (bacterium) and Saccharomyces cerevisiae (baker's yeast) as well as in well-defined in vitro set-ups with purified components. The total research programme makes use of an elaborate number of genetics, molecular biological, biochemical and biophysical techniques such as: DNA isolation, modification en transformation, PCR, DNA hybridisation, genetic screen technology, gene deletion and/or mutation, Tandem Affinity Purification (TAP) of protein complexes (proteomics), protein chromatography, electrophoresis, immunedetection, fluorescence microscopy and a variety of spectroscopic methods among which Förster Resonance Energy Transfer (FRET) fluorescence. Depending on the project a different selection of these techniques is used. Description of current projects 1) Mechanisms of Motor Proteins Lecturers: Prof. Dr. C.F. Schmidt, Dr. ir. E.J. Peterman, U022, tel. (44)47576, [email protected] Biological motor proteins are studied in single-molecule experiments with the goal of understanding the physical principles of biological force generation in a multitude of active transport processes. Motor proteins are the ubiquitous nanometer scale mechanical engines at the basis of many crucial processes of life. Examples are intracellular transport processes, cell division, cell locomotion, and in complex large scale assemblies also macroscopic motion, such as muscle contraction, or flagella motion. The non-equilibrium dynamics of these specialised enzymes, usually embedded in a complex regulatory and functional environment, are the essence of their function.

100

Exact Sciences

2) Dynamics of DNA Enzymes Lecturers: Dr. ir. G.J.L. Wuite, T061, tel.(44) 47987, [email protected], Dr. ir. E.J. Peterman The research in this project focuses on experimentally exploring the dynamic function of DNA enzymes. For example, many DNA enzymes perform highly complex mechanical tasks in replication, transcription, or packing of DNA, of which the detailed dynamics are not yet understood. Single molecule experiments using optical tweezers technology and scanning force microscopy will be used for the exploration of the highly complex mechanical tasks of these enzymes. Knowing the dynamic physical processes of the interaction of these bio-molecules is a very important part of the understanding of this machinery. The increasingly microscopic and quantitative analysis, possible with single molecule methods, will push the limits towards progressively more exact and physical/mathematical understanding of molecular functions. This goal is spanning boundaries between biology, biochemistry, physics, and mathematics. 3) Cytoskeleton / Semiflexible Polymers Lecturer: Prof. dr. C.F. Schmidt, T013, tel. 44 47972, [email protected] The mechanical frame work or cytoskeleton of eukaryotic cells consists of a complex assembly of filamentous proteins, interacting with a multitude of accessory proteins, effecting for example cross-linking, length control, bundling, polymerisation control. This composite polymer structure governs the internal organisation of most plant and animal cells, serves as a transport network for active intracellular transport, and drives cellular motility, for example in cell division, cell growth or cell locomotion. It is also responsible for the mechanical rigidity of cells and the response of cells to external mechanical stresses. The network of actin network is a highly dynamic structure, being locally assembled and disassembled, which plays a crucial role in cellular response to stresses. This project focuses on the investigation of these networks of semi-flexible protein, in vitro and also in living cells, with the goal of understanding the functional principles of the cytoskeleton. Semi-flexible polymers are a so far not well-understood new class of polymers also with potential use as technical materials. 4) Viral structural biology Lecturers: Dr. ir. G.J.L. Wuite, T061, phone: (44) 47987, [email protected], Prof. dr. C.F. Schmidt • Many complex biological structures and materials, for example bones, spider silk or snail shells, have extraordinary physical properties far superior in certain aspects to man made materials. Understanding the construction principles of these materials is a challenge to physics, and holds the promise of delivering a future generation of bio-mimicking technical materials. Viruses are the simplest, smallest and often most rugged forms of life. Nature had to solve some extraordinary design challenges to construct these nanometer-sized machines. In this project we focus on the investigation of the micro-mechanical properties of viral shells using Scanning Force Microscopy (SFM). The experiments will be performed in collaboration with theoretical modelling as well as finite element numerical modelling.


101

5) Protein networks and Signal transduction Lecturers: Dr. M. Siderius, KA273, phone (44) 47569, [email protected], Prof. dr. S.M. van der Vies. Protein networks such as signal transduction pathways ensure that internal and external stimuli are translated into the proper cellular responses. The major components of the signal transduction pathways are proteins (often kinases) that are found either in an active or a non-active conformation. Some of the "signalling" proteins function in several different signal transduction pathways (hence the term "protein networks"). In this project the regulation of signalling will be studied with a focus on the MAPK (Mitogen Activated Protein Kinase) pathways and the role molecular chaperones play in the organisation of the signalling particles. The external stimulus that will be used is increased osmolarity and the organism for this study is yeast. Different techniques such as genetic screen technology, gene deletion and/or mutation, Tandem Affinity Purification (TAP) of protein complexes (proteomics) and fluorescence microscopy will be utilised. 6) Protein misfolding and Parkinson's disease Lecturers: Dr. H. van Heerikhuizen, KA263A, tel. (44) 47573, [email protected], Dr. C.J. Vos. Parkinson's disease (PD) is one of the most common forms of neurological disorders in humans. Characteristic of PD is the presence of intracytoplasmic protein aggregates (Lewis bodies) in certain parts of the brain. These Lewis bodies are composed of fibril-like aggregates of the presynaptic protein a-synucleine, which for unknown reasons is not folded correctly. In this project the yeast cell will be used to produce human a-synucleine. The folding of a-synucleine and the involvement of molecular chaperones in this process will be analysed In addition the folding behaviour of single a-synucleine point mutants, which have been identified in certain families that have a rare familial, autosomale dominant form of PD, will be examined. Different techniques such as DNA isolation, modification en transformation, PCR, DNA hybridisation, genetic screen technology, gene deletion and/or mutations and immunodetection will be utilised. 7) Biology of Molecular Chaperones Complexes Lecturers: Prof. Dr. S.M. van der Vies, KB 258 phone (44) 47548, [email protected], Dr. H. van Heerikhuizen Molecular chaperones are complex biological systems that are usually composed of several different types of protein. These large protein complexes facilitate protein folding, transport of polypeptides across membranes, activation of signalling molecules and protein degradation and are thus very important in all organisms. This project focuses on the GroEL.gp31 chaperone complex that facilitates the folding of a viral capsid protein. We aim to understand the way by which the polypeptide chain is folded inside the chaperone complex and what the physical interactions. Folding of the viral capsid protein will be studied inside the host cell (Escherichia coli) as well as in vitro. Different techniques like DNA isolation, modification en transformation, PCR, protein chromatography, electrophoresis, immune-detection, refolding assays, fluorescence spectroscopy will be used.

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Exact Sciences

8) Ribosome assembly Lecturers: Dr. J.C. Vos, G277a, phone (44) 47558, [email protected], Prof. dr. H.A. Raué Ribosomes are large RNA/protein complexes that produce amino acid chains of various lengths. A ribosome is composed of 78 different ribosomal proteins and 4 different ribosomal RNAs. In addition about 100 trans-acting factors and several snoRNP complexes are involved in the assembly and the processing of the precursor ribosomal RNA. The aim of this project is to identify and characterise proteins that are needed for the processing of the ribosomal RNA at site A2 in Saccharomyces cerevisiae. In addition, the recently identified trans-acting protein Rio2p kinase, which is required for the processing to the 18S ribosomal RNA, will be characterised. Techniques such as genetic screens, gene deletion and/or mutation, antibiotics sensitivity assays and Tandem Affinity Purification (TAP) of protein complexes (proteomics) will be used. Department of Biophysics The research group investigates molecular processes and structures in living matter. The research is mainly aimed at the primary processes of photosynthesis; the conversion of light energy into a durable form, for instance by plants. To be more specific, the research is aimed at: The absorption of light by chlorophyll-containing proteins and ultrafast transfer of excitation energy. It is very important to determine how the chlorophyll molecules are organized and how the very efficient transfer of excitation energy occurs. Charge separation in the photosynthetic reaction centre. The reaction centre is a chlorophyll-containing protein that is capable, after excitation with light, of storing the captured energyin the form of a separated pair of charges. In this process several intermediate components are involved, in which the first step lasts less than a picosecond. Later steps are slower and the energy transfer is completed after about a microsecond. The efficiency of the total process is very high. Nonlinear optical phenomena in biological/photosynthetic systems. Because photosynthetic systems contain many coupled pigments, the optical properties of this material are strongly nonlinear when excited with high-intensity light. The study of these properties tells us much about all kinds of dynamic processes. In addition, dynamics and structures of DNA-protein complexes are studied with spectroscopic techniques. The research group has many spectroscopic setups. The ultrafast phenomena from about 100 femtoseconds to 1 nanosecond are studied with two advanced laser systems that can produce these kind of short light pulses. The research group also has a number of versatile experimental setups that are used to study steady-state, polarized absorption and fluorescence spectroscopy with high resolution and, if necessary, at very low temperatures. There is also equipment available to study phenomena on a time scale slower than a nanosecond.


103

Contact persons: Prof dr R. van Grondelle, S162, tel 44 47930, [email protected] Dr J.P. Dekker, S130, tel. 44 47931, [email protected] Course code 430052 430051 430050 420084 430054 470707 430055 430057 430056

9.11 9.11.1

Course name

Stp.

Principles of Molecular Biochemistry Principles of Biophysics Introduction to Bio-Complexity Advanced Biophysics Advanced Structural Biology Ethics Techniques in Molecular Biophysics Biological Networks and Signal Transduction Molecular Biology

Period

6 6 6 6 6 3 6 6

1 1 1 2 2 24.01.2005 - 04.02.2005 3 4

6

4

Molecular Medicine Department of Pharmacochemistry General introduction During the Master's of Molecular Medicine students can specialise themselves by doing a Major in one of the following disciplins: • • •

Drug Discovery & Target Finding (Molecular Pharmacology) Drug Disposition & Safety (Molecular Toxicology) Biomolecular & Drug Analysis

The research training in the three specialisations takes place in the following sections: Section Medicinal Chemistry (prof.dr. Leurs) • Drug Discovery & Target Finding (Molecular Pharmacology) Section Molecular Toxicology (prof. Vermeulen): • Drug Disposition and Safety (Molecular Toxicology) Section Analytical Chemistry and Applied Spectroscopy (prof. H. Irth): • Biomolecular & Drug Analysis Students are urged to contact the mastercoordinator of Molecular Medicine as soon as possible with their choice of research group. Research training (Major) will be wound up with a Master thesis and an oral presentation. Research training (Minor) ends with a written report. Master programme Molecular Medicine An overview of the available courses is given below. Compulsory courses Principles of Pharmaceutical Sciences / Pharmacochemistry Molecular pharmacology and toxicology of drugs 104

Exact Sciences

Bioanalytical Aspects of drug discovery I Introductory course specialisation Pharmacodynamics of drug action Drug toxicity: concepts and experimental approaches Advanced courses specialisation Receptor structure and function Drug Disposition and Safety Assessment Bio-Analytical Aspects of Drug Discovery II Optional courses Drug Registration and Safety Assessment In vitro Pharmacology / Toxicology and High-Throughput Screening (Pharmaco / Toxico) Genomics and -proteomics Courses LACDR Courses MNW Courses Chemistry 9.11.2

Current research themes Drug Discovery & Target Finding (Dr. M.J. Smit, O-226, tel. (020) 44 475 79 / Dr. R.A. Bakker, Prof. Dr. Leurs) To gain experience in formulating a scientific question, setting up and carrying out molecular pharmacological experiments, to answer that question, interpreting data obtained, designing further experiments and reporting both orally and in writing. The student will participate in one of the research projects within the research programme "Structure-function relationships of biological active compounds: G protein coupled receptors and their ligands". The membrane-bound G protein coupled receptors play a key role in cellular (patho) physiology and are currently one of the most favored drug targets. Research focuses on the histaminergic receptors, with emphasise on the recently cloned H3 (multiple isoforms) and H4 (new potential target inflammation) receptors and recently initiated new line on human and viralencoded chemokine receptors. Interest is directed at the ligand-receptor interaction and signaling pathways activated by these receptors. Research topics comprise intriguing pharmacological concepts such as constitutive activity and dimerization of receptors and their role in the process of drug discovery. Besides classical pharmacological, molecular biological approaches, cell culture techniques and modern techniques (reportergene, fluorescent techniques) are applied to obtain more insight in the receptors. Research is performed in close collaboration with the synthetical and computational groups in order to ensure a multidisciplinary approach. Drug Disposition & Safety Assessment (Dr. J.N.M. Commandeur, room P-256, tel. (020) 44 47595 ; Prof. Dr. N.P.E. Vermeulen,) Training in and gaining experience in defining a scientific research question, designing and carrying out molecular toxicological experiments to answer that


105

question, validating and interpreting of the experimental data, evaluating and discussing the results and the perspectives, and reporting both orally and in writing. The research performed in the division of Molecular Toxicology, is focussed on the role of biotransformation enzymes in the bioactivation and detoxification of xenobiotics, and the characterisation of the structure and properties of the metabolites formed. In the research training, students can participate in one of the research projects carried out at this division. Subjects of the research projects include: expression of wild-type and mutant cytochrome P450s (P450s) and characterisation of their structural and catalytic properties; investigation of dynamics of P450s using various (laser)spectroscopical methods (RAMAN, FRET, NMR); development and use of wild-type and mutant P450s as bioreactors to produce bioactive compounds; development of automated high-resolution bioaffinity screening and detection systems using cytochrome P450s and estrogen receptors as detector proteins; development and evalution of selenium-containing compounds as chemoprotective compounds; development of biomonitoring methods for oxidative stress; role of biotransformation in estrogenic properties of xenobiotica. Research is performede in close cooperation with the computational group. Biomolecular & Drug Analysis (Prof. Dr. H. Irth, Dr. H. Lingeman, room M-330, tel. (020) 44 47539) To obtain knowledge and experience in the field of biomolecular and drug analysis, getting acquainted with various analytical approaches to study protein-ligand interactions, drug-matrix interactions, development of quantitative bio-analytical and pharmaceutical methods and reporting both orally and in writing. The main goals is to improve the selectivity and sensitivity / analyte detectability of total analytical systems. With large series of samples such as frequently encountered in real-life screening (e.g. biological samples) or monitoring studies, speed of analysis is another aspect of current interest. The emphasis, therefore, is on the development of on-line and, preferably, fully automated systems. This implies that much attention is devoted to the design and optimization of multidimensional methods. In this context important developments are in coupled-column systems, in combination with on-line bio-specific reaction and mass-spectrometric detection. The emphasis will be on systems that can be used for drug-protein interactions, determination of metabolic products, enzymes, proteins, nucleotides, receptors, etc. Course code 430063 435674 470707 435597 435686 435682 435598 435681 435680

106

Course name Principles of Molecular Medicine Molecular Pharmacology and Toxicology of Drugs Ethics Bio-Analytical Aspects of Drug Discovery I Pharmacodynamics of Drug Action Drug Toxicity: Basic Concepts and Experimental Approaches Bio-Analytical Aspects of Drug Discovery II Advanced Course on Drug Disposition & Safety Assessment (Molecular Toxicology) Receptor Structure and Function

Exact Sciences

Stp.

Period

6 6

1 2

3 6

24.01.2005 - 04.02.2005 3

3 3

4 4

6

4, 5 and 6

6

4, 5 and 6

6

4, 5 and 6

9.12


9.12.1

Programma De Maatschappij variant speelt in op de toenemende behoefte die universiteiten, het bedrijfsleven, de overheid en andere maatschappelijke instellingen hebben aan academische professionals die in staat zijn om complexe vraagstukken te analyseren en maatschappelijke systemen te beïnvloeden. Hierbij kun je denken aan acceptatieen milieuproblemen rond de introductie van genetisch gemodificeerd voedsel, ethische dilemma's rond de toepassing van voorspellende geneeskunde (diagnostiek), toenemende vraagsturing in wetenschappelijk onderzoek en de implementatie van maatschappelijk verantwoord ondernemen. Tijdens de opleiding leer je kennis van verschillende wetenschappelijke disciplines samen met kennis uit de maatschappij te integreren. De opleiding is zowel theoretisch als praktisch georiënteerd met concrete cursussen over beleid, management en ondernemerschap op het gebied van onder andere gezondheid en milieu. Je kunt ook deelnemen aan het masterprogramma Beleid Management en Ondernemerschap welke wordt verzorgd door de afdeling Biologie en Samenleving van de faculteit der Aard en levenswetenschappen (FALW; prof. dr. J. Bunders, kamer A0.68, telefoon: (020) 44 47030). Je kunt rechtstreeks in deze masteropleiding instromen met een universitaire bachelor in de bèta wetenschappen. De meest recente informatie vind je op onze website: www.falw.vu.nl/masters. Course code 470707

Course name Ethics

Stp.

Period

3

24.01.2005 - 04.02.2005

Stp. 7 5 3

Periode 06.09.2004 - 08.10.2004 11.10.2004 - 29.10.2004 15.11.2004 - 26.11.2004

Stp. 3 9

Periode 01.11.2004 - 12.11.2004 10.01.2005 - 18.02.2005

M-variant





9.13


Communication / Education variant The teaching in these variant is mainly in Dutch. Therefore we also give the requirements in Dutch.


107

9.13.1

Differentiatie C/E variant Binnen het C/E profiel is specialiseren mogelijk in de richting van communicatie (C) of educatie (E). Beide hebben een omvang van 60 studiepunten. Binnen de richting Educatie kan de lerarenopleiding gedaan worden die leidt tot de bevoegdheid om les te geven in de bovenbouw van het voortgezet onderwijs en het hoger beroepsonderwijs. De bekwaamheidseisen die leiden tot die eerstegraads bevoegdheid zijn landelijk vastgelegd door het samenwerkingsorgaan beroepskwaliteit leraren (SBL). Om het E-profiel te kunnen volgen moeten de cursussen Oriëntatie op Communicatie en Educatie deel 1 en deel 2 van ieder 6 studiepunten (vakcodes 990005 en 990007) met succes zijn afgerond. Het volgen van deze cursussen is niet vereist voor het C-profiel. Vanaf 2004 zal de oriëntatie voor het Communicatie-profiel beperkt worden tot de cursus Oriëntatie op Communicatie en Educatie deel 1 (vakcode 990005).

9.13.2

Communicatie variant Het programma omvat een reeks cursussen, waarvan de eerste twee verplicht zijn. Op twee momenten kan er een keuze gemaakt worden tussen alternatieven ('Communicatie en Educatie via Internet' of 'Wetenschap Technologie & Samenlevingsstudies' en 'Informatie Representatie en Multimedia' of Gezondheidscommunicatie). Het jaar wordt afgesloten met een verplichte scriptie van 9 studiepunten en een korte stage van 18 studiepunten. De Communicatie variant wordt georganiseerd door de afdeling Wetenschapscommunicatie van de Faculteit Aard- en Levenswetenschappen. Contactpersoon voor het C-profiel is drs. I. van Veen, tel. (020) 44 47214, e-mail: [email protected]. Programmacoördinator is dr. J. Willems, e-mail: [email protected]. Course code 470707

Course name Ethics

Stp.

Period

3

24.01.2005 - 04.02.2005

Stp. 3 6 6 3 6 6

Periode 01.11.2004 - 12.11.2004 04.10.2004 - 29.10.2004 06.09.2004 - 01.10.2004 07.02.2005 - 8.02.2005 10.01.2005 - 04.02.2005 10.01.2005 - 04.02.2005

3

15.11.2004 - 26.11.2004

3 6

15.11.2004 - 26.11.2004 29.11.2004 - 24.12.2004

Communicatie variant


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Exact Sciences

9.13.3

Educatie variant Voor het behalen van de eerstegraadsbevoegdheid kan in januari of in september gestart worden. De lerarenopleiding bestaat uit een aantal onderdelen die parallel aan elkaar en aan een stage op een school voor voortgezet onderwijs gegeven worden.. Studenten die in het C deel de cursus interpersoonlijke communicatie en de cursus museologie en buitenschoolse educatie volgen krijgen in de lerarenopleiding een vrijstelling voor de keuzemodulen, een deel van het praktijkonderzoek en een deel van algemene didactiek De lerarenopleiding wordt verzorgd door het Onderwijscentrum VU. Hier kan ook meer informatie omtrent de invulling van de lerarenopleiding worden verkregen. Secretariaat Onderwijs, tel. (020) 44 49222, e-mail: [email protected]. Course code 470707

Course name Ethics

Stp. 3

Period 24.01.2005 - 04.02.2005

Educatie variant Vakcode 990003 990002 990001 990000 990004

9.14

Vaknaam Praktijkonderzoek Praktijk 1 en 2 Algemene didactiek / pedagogiek 1 en 2 Vakdidactiek 1 en 2 Keuzemodulen

Stp. 8 30 9 30 4

Periode 30-08-2004 / 31-08-2005 30-08-2004 / 31-08-2005 30-08-2004 / 31-08-2005

Minors

9.14.1

Physiology at the Institute for Cardiovascular Research VU, Laboratorium voor Fysiologie, Vumc Het Laboratorium voor Fysiologie is een onderdeel van het Instituut voor Cardiovasculair Onderzoek (ICaR-VU) van het VU Medisch Centrum. Binnen onze afdeling maar ook in de andere afdelingen van het ICaR-VU zijn een aantal stagemogelijkheden. Een volledig en actueel onverzicht van de onderzoekprojecten binnen het ICaR-VU is te vinden op http://www.icar.med.vu.nl onder "Research". Hieronder volgt een kort overzicht van de stagemogelijkheden binnen het Laboratorium voor Fysiologie. De coordinatie van stages wordt verzorgd door Dr W.J. van der Laarse (tel. 48110/48115).

9.14.2

Stagemogelijkheden Laboratorium voor FysiologieThema 1: Verbetering van hartfunctie bij hartfalen Hierbij wordt de functie onderzocht van gezond en ziek hartspierweefsel om te komen tot een beter begrip van de ziekteprocessen en uiteindelijk tot een verbetering van de hartfunctie bij patiënten met hartfalen. Reperfusie schade en ischemische preconditionering. Dit betreft onderzoek naar contractiele eigenschappen, energiemetabolisme en calciumhomeostasis tijdens acuut zuurstoftekort en de daarop volgende reoxygenatie van het hartspierweefsel. Speciale aandacht wordt gegeven aan de effecten van anaesthetica en de


109

signaaltransductieprocessen die leiden tot preconditionering (bescherming tegen zuurstoftekort). Hypertrofie en hartfalen. Het doel van dit onderzoek is om te bepalen in welke mate cellulaire veranderingen verantwoordelijk zijn voor cardiale dysfunctie. Hierbij wordt aandacht besteed aan acute problemen (ischemie; atriaal fibrilleren; spiervermoeidheid) en chronische problemen (compensatoire hypertrofie na volumeen drukoverbelasting tgv hartkleplekkage of -vernauwing; eindstadium hartfalen). Dit onderzoek wordt uitgevoerd aan biopten van hartpatiënten, dunne stripjes hartspierweefsel en geïsoleerde hartspiercellen. Speciale aandacht wordt gegeven aan functionele parameters zoals krachtontwikkeling, zuurstof en ATP gebruik, calcium gevoeligheid, veranderingen in eiwitsamenstelling en fosforylering. Projectleiders: Dr C. Boer, Dr J. van der Velden, Dr W.J. van der Laarse, Dr A. Muller, Dr R. Musters, Dr W.S. Simonides, Dr G.J.M. Stienen. 9.14.3

Thema 2: Verbetering van vaatfunctie bij metabole ziekten Vaatfunctie omvat onder andere de regulatie van de weefselperfusie door veranderingen in vaatdiameter, microvasculaire permeabiliteit en interacties tussen bloedcellen en de vaatwand.Onderzoek wordt verricht naar de lange termijn veranderingen (jaren) bij diabetes en hypertensie en de korte termijn effecten (uren, dagen) bij bijv. hemodialyse en shock. Een nieuw onderzoeksveld richt zich op angiogenese, de aanmaak en uitgroei van nieuwe bloedvaten. Speciale aandacht wordt gegeven aan de relatie tussen mediators van de vaattonus (bijv. angiotensine) en hypertensie, veranderingen in vaatdiameter en vaatpermeabiliteit en intravitaal microscopie voor de bestudering van het rollen van leukocyten over de vaatwand. Moleculair biologische studies richten zich op de veranderingen in endotheelfunctie bij diabetes, activatie van cellen in de vaatwand door o.m. cytokines. Projectleiders: Prof. Dr V. van Hinsbergh, Dr A.A. van Lambalgen, Dr G. van Nieuw Amerongen, Dr P. Sipkema, Prof. Dr G.J. Tangelder.

9.14.4

Molecular Cell Biology at the Department of Molecular Cell Biology, Vumc Het onderzoek van de afdeling Moleculaire Celbiologie (ontstaan uit een fusie van Medische chemie / Celbiologie en Immunologie) concentreert zich rond immunologische thema's. In het bijzonder wordt aandacht besteed aan de verschillende aspecten van 'ontsteking'. Het onderzoek is ondergebracht binnen 7 onderzoekthema's die veelal in nauwe samenwerking met klinische afdelingen worden bestudeerd. Dat zijn: • Modulatie van ontstekingsprocessen • Ontsteking in de buikholte en tumorimmunologie (met twee fundamentele onderzoekslijnen gerelateerd aan buikvliesontsteking en dikke darm kanker) • Mucosale immuniteit (o.a. aanleg en organisatie van lymfoïde organen) • Ontsteking in het centraal zenuwstelsel (met name multiple sclerose) • Genomics van chronische ontsteking, met name reuma • Dendritische celadhesie (afweer tegen tumoren en virussen) • Glyco-immunologie (eiwit-suiker intereacties bij cellulaire communicatie, infectie en ontsteking) Afdelingshoofd is mw. Prof dr C.D. Dijkstra. Stage-coördinator is dr R.H.J. Beelen. Spreekuur: elke dinsdag 13.00 - 13.30 u in kamer J-288 (faculteit Geneeskunde). Tel. 020 44 48055 of 48080; email: [email protected]

110

Exact Sciences

9.14.5

Stageopdrachten Dietetiek Onderzoek naar de relatie(s) tussen radiotherapie, kwaliteit van leven en gewichtsverloop Globale achtergrond opdracht Bij de afdeling radiotherapie is een databestand van ongeveer 1000 KNO patiënten beschikbaar met de volgende gegevens: • Diagnose/tumorstadium • Bestralingsvelden, bestralingsintensiteit • Kwaliteit van leven • Gewichtsverloop Doel van de opdracht: In kaart brengen relaties tussen radiotherapie - kwaliteit van leven - gewichtsverloop bij specifieke tumorsoorten en -stadia Aard van de werkzaamheden 2 mnd. inlezen/ meedraaien in praktisch werk en literatuur onderzoek 2 mnd complementeren databestand 2 mnd data analyse, beschrijven resultaten, aanzet artikel Gewenst eindproduct Artikel Duur en periode van de opdracht 6 maanden Begeleider / contactpersoon opdracht • Caroline Panis, diëtist, Dr. P. Doornaert, radiotherapeut, Ir. Hinke Kruizenga, onderzoeker en diëtist • VU medisch centrum • Dienst Diëtetiek en Voedingswetenschappen • 0B 120 • Telefoon nr: 020-444 3221 • [email protected] Voedingstoestand en radiotherapie Globale achtergrond opdracht Van 2000 tot 2003 is door de afdeling Diëtetiek en Voedingswetenschappen een prospectief, beschrijvend onderzoek uitgevoerd naar het verloop van de voedingstoestand, lichaamsamenstelling, energieverbruik en kwaliteit van leven bij 100 patiënten die gedurende 6-7 weken radiotherapie ondergaan in het hoofdhalsgebied. Gedurende dit onderzoek zijn veel gegevens verzameld die aan de hand van diverse vraagstellingen verder uitgewerkt moeten worden. Aard van de werkzaamheden 1 mnd. literatuur onderzoek 1 tot 2 mnd data-analyse 2 tot 3 mnd beschrijven resultaten/ aanzet artikel Gewenst eindproduct Aanzet tot een wetenschappelijk artikel of een onderzoeksverslag Duur en periode van de opdracht 4 tot 6 maanden Begeleider / contactpersoon opdracht • Ir. Hinke Kruizenga (diëtist-onderzoeker) en dr. Marian van Bokhorst (diëtistonderzoeker)


111

• • • • •

VU medisch centrum Dienst Diëtetiek en Voedingswetenschappen 0B 120 Telefoon nr: 020-444 1407 Emailadres: [email protected]

De gevolgen van ondervoeding door ziekte op de lichaamsamenstelling Globale achtergrond opdracht Ondervoeding bij ziekte is een groot probleem in de klinische en poliklinische praktijk. Gewichtsverlies bij ziekte resulteert niet alleen in afname van vetmassa maar vooral in afname van spiermassa. Dit kan grote gevolgen hebben voor het herstel van een patiënt. Korte opdracht omschrijving Door middel van data analyse en literatuurstudie antwoord geven op de onderzoeksvragen: 1 Waaruit bestaat gewichtsverlies bij ziekte: vetmassa of vetvrije massa? 2 Is dit te verklaren? 3 Is dit afwijkend van de literatuur? 4 Welke methoden zijn het meest geschikt om gewichtsverlies te analyseren? 5 Is gewichtsverlies (vetmassa of vetvrije massa) bij ziekte een onafhankelijke voorspellende parameter voor beloop? Aard van de werkzaamheden 1 maand literatuurstudie 1 - 2 maanden data-analyse 2 - 3 maanden verslag/ aanzet artikel Gewenst eindproduct Dataset, verslag en / of (aanzet tot) artikel Duur en periode van de opdracht 4 tot 6 maanden Begeleider / contactpersoon opdracht • Ir. Hinke Kruizenga (diëtist-onderzoeker) en dr. Marian van Bokhorst (diëtistonderzoeker)) • VU medisch centrum • Dienst Diëtetiek en Voedingswetenschappen • 0B 120 • Telefoon nr: 020-444 1407 Emailadres: [email protected]

112

Exact Sciences

10

10.1

Master Pharmaceutical Sciences Objectives The objective of the Master's in Pharmaceutical Sciences is to provide students with such knowledge, abilities and insight in general pharmacochemistry and pharmacochemistry specializations, that they are able to work as a chemical professional (including the profession as teacher), or are qualified for a training to scientific researcher or designer. The education also aims at enlarging the insight in science as a whole and in its role in society.

10.2

Final attainment level The graduated Master of Science in Pharmaceutical Sciences is expected to have sufficient insight in pharmacochemistry and related fields (chemistry, physics, mathematics, biology and informatics) in order to be able to perform pharmacochemical research; • to have sufficient basal know-how of, and insight in pharmacochemistry in order to be able to get acquainted with a sub-area of pharmacochemistry at a specialist level within a short time; • to have sufficient expert knowledge of, and insight in at least one sub-area of pharmacochemistry in order to be able to perform scientific research in an independent way; • to be able to acquire (literature) information necessary to perform chemical research, to set up and perform a research project, and to report on it, both written and orally; • to master subject-specific methods and techniques in order to perform pharmacochemical research; • to be aware of the role of pharmacochemistry, and his/her role as a pharmacochemist, in society, and to be aware of the international character of science; • to be familiar with the professional possibilities in the labor market after graduation.

•

Additional attainment level per variant: O-variant: the graduated Master of Science in Pharmaceutical Sciences has a broad experience with acquiring chemical knowledge and has some experience with performing chemical research in an independent manner. M-variant: the graduated Master of Science in Pharmaceutical Sciences has the ability to perform projects in society with applications of chemical know-how and methods, both as an individual as in a team. E/C-variant: the graduated Master of Science in Pharmaceutical Sciences is able to work in education or science communication. If the graduate has finished the education for teacher, he/she is qualified for the function of teacher in Dutch vwoeducation.

Master Pharmaceutical Sciences

113

10.3

Requirements for the Master The Master is open to students • with a bachelor's degree in Pharmaceutical Sciences • with a bachelor's degree in Chemistry • who have followed a similar programme at another (foreign) University • with a bachelor's degree in a relevant Dutch hbo-education • with sufficient knowledge of the English language (level of Dutch vwoexamination) Students who want to specialize in the Education-variant must have succesfully completed the third year bachelor orientation course on education (12 cp).

10.4

Structure of the training The Master programme Pharmaceutical Sciences offers three different variants for graduation: • Research variant (O-variant) • Management/Business-oriented variant (M-variant) • Communication-Education variant (C/E-variant) The global composition of each variant is indicated below: Variant Compulsory courses Compulsory courses specialization Research project (Major) (including report) Colloquium and Thesis Practical training (company training) M or C projects Educational training Optional programme Ethics and portfolio academic skills Total cp

O 24 6-9

M 12 6-9

C 12 6-9

E 12 6-9

42

33-36

33-36

33-36

12 -

6 18

6 18

6 -

27-30 6

30 12 -

30 12 -

60 -

120

120

120

120

During the Master's in Pharmaceutical Sciences students can specialize themselves by doing a Major in one of the following disciplines: • Drug Discovery & Target Finding (Molecular Pharmacology) • Drug Disposition & Safety (Molecular Toxicology) • Drug Design & Synthesis • Computational Medicinal Chemistry & Toxicology • Biomolecular & Drug Analysis Each of these specializations consists of compulsory introductory and advanced courses, a research training, and colloquium/literature thesis.

114

Exact Sciences

The optional programme of the O-variant can consist of: Extension of the Major-research project *) Minor research project Theoretical courses (Minor) α- or γ-oriented courses Practical training (company training) Specialistic courses (Major)

6 – 18 18 – 24 6 – 12 6 – 18 18 6 – 18

*) The extension of the Major research project should be external (other university, company, abroad). • •

10.5

The optional programme of the M- and C-variants should consist of courses related to business (M-variant) or communication (C-variant). Students should arrange the composition of their master's programme in consult with the mastercoordinator. The composition and extent of the master's programme should be formally approved by the examination board.

Part-time studying In principle this master's programme is full-time.

10.6

Dual training Under specific conditions, a tailored master's programme can be composed, in which in-service training is included.

10.7

Research tracks Research training: minimum 42 cp Master coordinator dr. J.N.M. Commandeur, room P2.56, tel. (020) 4447595 Students graduating with the O-variant often continue as PhD-student in order to obtain positions such as scientific researcher, group leader etc. at universities, research institutes, government and industry. In the Master in Pharmaceutical Sciences students can specialize in one out of five disciplines: Section Medicinal Chemistry (prof.dr. Leurs) • Drug Design and Synthesis • Drug Discovery & Target Finding (Molecular Pharmacology) Section Molecular Toxicology (prof. Vermeulen) • Computational Medicinal Chemistry & Toxicology • Drug Disposition and Safety (Molecular Toxicology) Section Analytical Chemistry and Applied Spectroscopy (prof. H. Irth) • Biomolecular & Drug Analysis Students are urged to contact the master coordinator of Pharmaceutical Sciences as soon as possible with their choice of research group. Research training (Major) will Master Pharmaceutical Sciences

115

be wound up with a Master thesis and an oral presentation. Research training (Minor) ends with a written report. 10.7.1

Drug Design & Synthesis Contact: Dr. I. De Esch, room G-343a, tel. (020) 44 47602, Prof. Dr. R. Leurs To gain experience in formulating a scientific question in the field of Drug Synthesis, setting up and carrying out experiments to answer that question, interpreting data obtained, designing further experiments and reporting both orally and in writing. The student will participate in one of the research projects within the Departmental research programme "Structure-function relationships of biological active compounds: G-protein coupled receptors and their ligands". The membrane-bound G-protein coupled receptors play a key role in cellular (patho)physiology and are currently one of the most favoured drug targets. Research focuses on the histaminergic receptors, with emphasis on the recently cloned H3 (multiple isoforms) and H4 (new potential target inflammation) receptors and recently initiated new line on human and viral-encoded chemokine receptors. Interest is directed at the ligandreceptor interaction and signalling pathways activated by these receptors. Research topics involve the design and synthesis of ligands which interact with these G-protein coupled receptors. The study of structure-activity relationships within a series of these ligands is an important next step. The results will be used to design new structures. Techniques used are those common in modern drug synthesis. Intermediates and endproducts have to be characterized by analytical tools (chromatography, NMR, MS, etc.). Research is performed in close collaboration with the molecular pharmacology and computational groups in order to ensure a multidisciplinary approach.

10.7.2

Drug Discovery & Target Finding Contact: Dr. M.J. Smit, O-226, tel. (020) 44 475 79 / Dr. R.A. Bakker, Prof. Dr. Leurs To gain experience in formulating a scientific question, setting up and carrying out molecular pharmacological experiments, to answer that question, interpreting data obtained, designing further experiments and reporting both orally and in writing. The student will participate in one of the research projects within the research programme "Structure-function relationships of biological active compounds: G protein coupled receptors and their ligands". The membrane-bound G protein coupled receptors play a key role in cellular (patho) physiology and are currently one of the most favoured drug targets. Research focuses on the histaminergic receptors, with emphasise on the recently cloned H3 (multiple isoforms) and H4 (new potential target inflammation) receptors and recently initiated new line on human and viralencoded chemokine receptors. Interest is directed at the ligand-receptor interaction and signaling pathways activated by these receptors. Research topics comprise intriguing pharmacological concepts such as constitutive activity and dimerization of receptors and their role in the process of drug discovery. Besides classical pharmacological, molecular biological approaches, cell culture techniques and modern techniques (reportergene, fluorescent techniques) are applied to obtain more insight in the receptors. Research is performed in close collaboration with the synthetical and computational groups in order to ensure a multidisciplinary approach.

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10.7.3

Computational Medicinal Chemistry & Toxicology Contact: Prof.dr. N.P.E. Vermeulen (room P.222; tel. 47590, dr. B.C. Oostenbrink, dr. A. Feenstra To obtain knowledge and experience in the field of computational medicinal chemistry and bioinformatics, getting acquainted with various computational approaches to study protein-ligand interactions, and reporting both orally and in writing. The student will participate in one of the research projects within the group of Computational Medicinal Chemistry and Toxicology (CMCT). In this group various aspects of the specific binding of small molecules to biomacromolecules, such as the binding of agonists and antagonists to receptors and substrates and inhibitors to enzymes, are studied by computational techniques. The aim of these studies is to predict and/or rationalize the affinity and biological activity of chemicals on the basis of their chemical and physical properties. Some of the techniques that are utilized are conformational analysis, high quality ab initio calculations, generation of 'pharmacophore' models by comparing geometries, binding energy, charge distributions etc. of ligands and substrates. Furthermore, protein models are developed by homology modeling. Proteins which are studied include biotransformation enzymes (cytochrome P450s, beta-lyases), and receptors (histamine receptors, chemokine receptors and estrogen receptors). Ligands will be docked in these models with molecular dynamics simulations. The results of these projects will be used to rationalize experimental binding and activity data and to suggest specific amino acid mutations for experimental validation of the computational models. The latter is done in close cooperation with the experimental groups.

10.7.4

Drug Disposition & Safety Assessment Contact: Dr. J.N.M. Commandeur, room P-256, tel. (020) 44 47595; Prof. Dr. N.P.E. Vermeulen Training in and gaining experience in defining a scientific research question, designing and carrying out molecular toxicological experiments to answer that question, validating and interpreting of the experimental data, evaluating and discussing the results and the perspectives, and reporting both orally and in writing. The research performed in the division of Molecular Toxicology, is focused on the role of biotransformation enzymes in the bioactivation and detoxification of xenobiotics, and the characterization of the structure and properties of the metabolites formed. In the research training, students can participate in one of the research projects carried out at this division. Subjects of the research projects include: expression of wild-type and mutant cytochrome P450s (P450s) and characterization of their structural and catalytic properties; investigation of dynamics of P450s using various (laser)spectroscopical methods (RAMAN, FRET, NMR); development and use of wild-type and mutant P450s as bioreactors to produce bioactive compounds; development of automated high-resolution bioaffinity screening and detection systems using cytochrome P450s and estrogen receptors as detector proteins; development and evaluation of selenium-containing compounds as chemoprotective compounds; development of biomonitoring methods for oxidative stress; role of biotransformation in estrogenic properties of xenobiotica. Research is performed in close cooperation with the computational group.


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10.7.5

10.8

Biomolecular & Drug Analysis Contact: Prof. Dr. H. Irth, Dr. H. Lingeman, room M-330, tel. (020) 44 47539 To obtain knowledge and experience in the field of biomolecular and drug analysis, getting acquainted with various analytical approaches to study protein-ligand interactions, drug-matrix interactions, development of quantitative bio-analytical and pharmaceutical methods and reporting both orally and in writing. The main goal is to improve the selectivity and sensitivity / analytical detectability of total analytical systems. With large series of samples such as frequently encountered in real-life screening (e.g. biological samples) or monitoring studies, speed of analysis is another aspect of current interest. The emphasis, therefore, is on the development of on-line and, preferably, fully automated systems. This implies that much attention is devoted to the design and optimization of multidimensional methods. In this context important developments are in coupled-column systems, in combination with on-line bio-specific reaction and mass-spectrometric detection. The emphasis will be on systems that can be used for drug-protein interactions, determination of metabolic products, enzymes, proteins, nucleotides, receptors, etc.

Programme Pharmaceutical Sciences

10.8.1

Master's programme An overview of the available courses is given below. A description of the various courses can be found in the chapter Course Descriptions.

10.8.2

Compulsory courses Course code 435675 435674 435673 435597

10.8.3

Course code 435689

435671

Course name

Synthetic Approaches in Medicinal Chemistry I Pharmacodynamics of Drug Action Drug Toxicity: Basic Concepts and Experimental Approaches Computational Medicinal Chemistry and Toxicology I

Advanced courses Course code 435685 435672

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Principles of Pharmaceutical Scienses / Pharmacochemistry Molecular Pharmacology and Toxicology of Drugs Computational Design and Synthesis of Drugs Bio-Analytical Aspects of Drug Discovery I

Basic courses

435686 435682

10.8.4

Course name

Course name

Synthetic Approaches in Medicinal Chemistry II Computational Medicinal Chemistry and

Exact Sciences

Stp.

Period

6

1

6

2

6

2

6

3

Stp.

Period

3

4

3 3

4 4

3

4

Stp.

Period

6

4, 5 and 6

6

4, 5 and 6

435680 435598 435681

10.8.5

10.9

Toxicology II Receptor Structure and Function Bio-Analytical Aspects of Drug Discovery II Advanced Course on Drug Disposition & Safety Assessment (Molecular Toxicology)

6 6

4, 5 and 6 4, 5 and 6

6

4, 5 and 6

Optional courses (Major/Minor) Optional courses (Major / Minor) • Biochemical mechanisms of toxicology • Capita Pharmacochemistry • Drug Registration and Safety Assessment • In vitro Pharmacology and High-Throughput Screening • In vitro Toxicology and High-Throughput Screening • (Pharmaco / Toxico) Genomics and -proteomics • Combinatorial Chemistry • Protein Modeling & Bioinformatics • Courses LACDR (Leiden - Amstersdam Centre of Drug Research) • Courses MNW • Courses Chemistry


10.9.1

Programma De Maatschappij variant speelt in op de toenemende behoefte die universiteiten, het bedrijfsleven, de overheid en andere maatschappelijke instellingen hebben aan academische professionals die in staat zijn om complexe vraagstukken te analyseren en maatschappelijke systemen te beïnvloeden. Hierbij kun je denken aan acceptatieen milieuproblemen rond de introductie van genetisch gemodificeerd voedsel, ethische dilemma's rond de toepassing van voorspellende geneeskunde (diagnostiek), toenemende vraagsturing in wetenschappelijk onderzoek en de implementatie van maatschappelijk verantwoord ondernemen. Tijdens de opleiding leer je kennis van verschillende wetenschappelijke disciplines samen met kennis uit de maatschappij te integreren. De opleiding is zowel theoretisch als praktisch georiënteerd met concrete cursussen over beleid, management en ondernemerschap op het gebied van onder andere gezondheid en milieu. Je kunt ook deelnemen aan het masterprogramma Beleid Management en Ondernemerschap welke wordt verzorgd door de afdeling Biologie en Samenleving van de faculteit der Aard en levenswetenschappen (FALW; prof. dr. J. Bunders, kamer A0.68, telefoon: (020) 44 47030). Je kunt rechtstreeks in deze masteropleiding instromen met een universitaire bachelor in de bèta wetenschappen. De meest recente informatie vind je op onze website: www.falw.vu.nl/masters.


119

M-variant



Stp. 7 5 3

Periode 06.09.2004 - 08.10.2004 11.10.2004 - 29.10.2004 15.11.2004 - 26.11.2004

Stp. 3 9

Periode 01.11.2004 - 12.11.2004 10.01.2005 - 18.02.2005



10.10


Communication / Education variant The teaching in these variant is mainly in Dutch. Therefore we also give the requirements in Dutch.

10.10.1

Differentiatie C/E variant Binnen het C/E profiel is specialiseren mogelijk in de richting van communicatie (C) of educatie (E). Beide hebben een omvang van 60 studiepunten. Binnen de richting Educatie kan de lerarenopleiding gedaan worden die leidt tot de bevoegdheid om les te geven in de bovenbouw van het voortgezet onderwijs en het hoger beroepsonderwijs. De bekwaamheidseisen die leiden tot die eerstegraads bevoegdheid zijn landelijk vastgelegd door het samenwerkingsorgaan beroepskwaliteit leraren (SBL). Om het E-profiel te kunnen volgen moeten de cursussen Oriëntatie op Communicatie en Educatie deel 1 en deel 2 van ieder 6 studiepunten (vakcodes 990005 en 990007) met succes zijn afgerond. Het volgen van deze cursussen is niet vereist voor het C-profiel. Vanaf 2004 zal de oriëntatie voor het Communicatie-profiel beperkt worden tot de cursus Oriëntatie op Communicatie en Educatie deel 1 (vakcode 990005).

10.10.2

Communicatie variant Het programma omvat een reeks cursussen, waarvan de eerste twee verplicht zijn. Op twee momenten kan er een keuze gemaakt worden tussen alternatieven ('Communicatie en Educatie via Internet' of 'Wetenschap Technologie & Samenlevingsstudies' en 'Informatie Representatie en Multimedia' of Gezondheidscommunicatie). Het jaar wordt afgesloten met een verplichte scriptie van 9 studiepunten en een korte stage van 18 studiepunten. De Communicatie variant wordt georganiseerd door de afdeling Wetenschapscommunicatie van de Faculteit Aard- en Levenswetenschappen. Contactpersoon voor het C-profiel is drs. I. van Veen, tel. (020) 44 47214, e-mail: [email protected]. Programmacoördinator is dr. J. Willems, e-mail: [email protected].

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Communicatie variant


10.10.3


Stp. 3 6 6 3 6 6

Periode 01.11.2004 - 12.11.2004 04.10.2004 - 29.10.2004 06.09.2004 - 01.10.2004 07.02.2005 - 8.02.2005 10.01.2005 - 04.02.2005 10.01.2005 - 04.02.2005

3

15.11.2004 - 26.11.2004

3 6

15.11.2004 - 26.11.2004 29.11.2004 - 24.12.2004

Educatie variant Voor het behalen van de eerstegraadsbevoegdheid kan in januari of in september gestart worden. De lerarenopleiding bestaat uit een aantal onderdelen die parallel aan elkaar en aan een stage op een school voor voortgezet onderwijs gegeven worden.. Studenten die in het C deel de cursus interpersoonlijke communicatie en de cursus museologie en buitenschoolse educatie volgen krijgen in de lerarenopleiding een vrijstelling voor de keuzemodulen, een deel van het praktijkonderzoek en een deel van algemene didactiek De lerarenopleiding wordt verzorgd door het Onderwijscentrum VU. Hier kan ook meer informatie omtrent de invulling van de lerarenopleiding worden verkregen. Secretariaat Onderwijs, tel. (020) 44 49222, e-mail: [email protected]. Educatie variant Vakcode 990003 990002 990001 990000 990004

10.11

Vaknaam Praktijkonderzoek Praktijk 1 en 2 Algemene didactiek / pedagogiek 1 en 2 Vakdidactiek 1 en 2 Keuzemodulen

Stp. 8 30 9 30 4

Periode

Stp.

Period

30-08-2004 / 31-08-2005 30-08-2004 / 31-08-2005 30-08-2004 / 31-08-2005

Overige vakken Course code 435684 435670

Course name Capita Pharmacochemistry Biochemical Mechanisms of Toxicology


6 6

Throughout the year. Throughout the year.

121

122

Exact Sciences

11 naam code docent studiepunten contacturen periode doel

inhoud

werkwijze literatuur toetsing doelgroep opmerkingen onderwijs

Exam parts ACW: Theorie van woord en beeldrelaties 1: Inleiding semiotiek 513702 prof.dr. L.H. Hoek 5 28 (28 college) 1 Eerste kennismaking met de elementaire begrippen van de semiotiek; inleiding in de semiotische methodologie en semiotische analyse van de interactie tussen de mens en zijn omgeving aan het eind van de twintigste eeuw De volgende onderwerpen komen aan de orde: wat is semiotiek, tekenstructuur, tekens en betekenis, constructie van de werkelijkheid, codes en codificatie, semiosis, mythologie en ideologie, semiotiek van de massamedia Combinatie van hoor- en werkcollege; presentatie en discussie van onderwerpen aan de hand van een handboek K.L. Kim, Caged in Our Own Signs: A Book About Semiotics, 1996, Norwood (N), Ablex Publishing Corporation Schriftelijk tentamen 1e jaars studenten ACW Inschrijven verplicht via TISVU college

subject Advanced Biophysics code 420084 co-ordinators dr.ir. G.J.L. Wuite (tel 020-4447987, [email protected]); dr. J.P. Dekker (tel. 020-4447931, [email protected]) lecturers dr. J.P. Dekker; prof.dr. R. van Grondelle; prof.dr. K.J. Hellingwerf; dr.ir. G.J.L. Wuite; dr.ir. E.J.G. Peterman credits 6 period 2 aim To obtain knowledge about the current techniques and uses of biophysics for the understanding of biological systems. content Part one will highlight the basic reactions that play a role in photobiology, with respect to: (i) the underlying photochemistry, (ii) the structure and dynamics of the components that catalyse these processes and (iii) their biological function. With a focus on the kinetics of complex chemical reactions, molecular reaction dynamics, femtochemistry, reaction mechanisms of biological enzymes, electron and proton transport, energy transfer, exciton interactions, functioning of photoactive proteins, Part two will focus on current topics in the field of single molecule biophysics. Topic such as the movement of organisms (chemotaxis and Brownian motion), protein folding and self-assembly will be discussed. In addition, single molecule experiments will be considered using recent papers. form of tuition • Tutorials/discussions of book material, papers and lecture notes. • Self-study. literature Various review papers combined into a syllabus.

Exam parts

123

mode of assessment Oral presentation based on a research paper covering one the topics. entry requirements Msc students with Bachelor Physics, Chemistry or Medical Natural Sciences. Msc student with Bachelor in Biology, which have followed the course Principles of Biophysics. target audience Msc students with Bachelor Physics, Chemistry or Medical Natural Sciences. Msc student with Bachelor in Biology, which have followed the course Principles of Biophysics. remarks Registration for this course via https://tisvu.vu.nl/HTM/TISVULogin.htm, one week prior to the start. For the course schedules please refer to http://www.few.vu.nl/onderwijs/roosters. subject Advanced Course on Drug Disposition & Safety Assessment (Molecular Toxicology) code 435681 lecturer prof.dr. N.P.E. Vermeulen (tel. 4447590; [email protected]) credits 6 period 4, 5 and 6 aim Obtaining an in-depth overview and knowledge of drug disposition and safety assessment, with emphasis on molecular and biochemical mechanisms. content After a general introduction in toxicology, drug absorption, drug distribution, drug elimination, drug metabolism and toxic kinetics will be treated. More general mechanisms of toxicity, such as e.g. mutagenesis, carcinogenesis, developmental toxicity and idiosyncratic drug reactions, will then be treated. Subsequently, organ-selective toxicities of drugs and other chemicals will be treated, with special emphasis on molecular and biochemical mechanism and structure dependencies. Methods to test toxicities as well as the evaluation of toxicities in terms of safety- and health risks will also be treated. Special attention will be given to biotransformation enzymes and their role in drug toxication and detoxication and to the most recent developments in molecular toxicology. form of tuition Lectures, tutorials and self-study. literature Casarett and Doull's Toxicology, The Basic Science of Poisons, 6th edition, Pergamon Press, New York, and selected research papers mode of assessment Written examination. entry requirements Course "Biotransformation and Bio-activation of Drugs" or equivalent courses. target audience mPhar remarks Please contact the secretary four weeks prior to the start of the course (email: [email protected]). subject code credits period lecturer content

124

Advanced Logic 400122 6 1 and 2 dr. R.C. de Vrijer Being a continuation of the first year course 'Inleiding Logica' (Introduction to Logic), this course is about advanced systems of logic with applications in the field of Computer Science and Artificial Intelligence. In particular, several forms of modal logic (e.g. temporal logic, epistemic logic,

Exact Sciences

form of tuition mode of assessment entry requirements target audience subject code credits contact period lecturers content

literature examination format class

dynamic logic and non-monotonic logic will be treated). Lectures and practice sessions. Written exam. Inleiding Logica (400119). mAI, mCS (also suitable as an optional course for Mathematics) Advanced Methods for Applied Economic Research 60422070 6 36 hours (36 lecture) 1 prof.dr. M. Lindeboom; prof.dr. G.J. van den Berg (and other close colleagues) Knowledge of when and how to apply appropriate statistical research methods in practical situations is a must for every economist working in a professional environment. This holds for the analyst at a research department of a (governmental) organisation who needs to apply these methods in practice, as well as for the policy maker who needs to interpret (technical) research reports. This courses serves these professionals and is a perfect complement to the course 'Micro Economics for Policy'. The focus is on research methods used in micro economic policy analyses. We discuss methods for the analyses of cross-sectional and panel data and illustrate regression techniques and techniques for the analyses of qualitative data (the decision of mode of transportation, the decision whether or not to invest, the decision of whether or not to work etc). The methods are demonstrated by applications in labour economics, public economics, transport economics and health care analyses. This course also deals with the evaluation of programmes or interventions by large bodies like governments, hospitals or firm. The government, for instance, spends a substantive amount of money on a number of social programs targeted at bringing the unemployed back to work. Evaluation of the effectiveness of these programs is essential, yet not trivial because of selective application, self- selection by the unemployed and heterogeneous responses. We discuss the relevant methods and illustrate these with practical examples of recently implemented governmental programmes. To be announced written examination lecture

Advanced Structural Biology 430054 prof.dr. S.M. van der Vies prof.dr. S.M. van der Vies; dr. H. van Heerikhuizen 6 2 To acquire knowledge the molecular principles and mechanisms of protein structure, folding and dynamics. content The molecular properties of the structural elements of DNA, lipds and proteins and the organisation into higher order structures such as heleices, strands, barrels etc. will be discussed as well as the different forces and

subject code co-ordinator lecturers credits period aim

Exam parts

125

form of tuition literature

mode of assessment entry requirements target audience remarks

interactions that are responsible for the structure, function and flexibility of proteins. The molecular basis of protein folding both in vitro as well as inside the living cell and the role of folding factors such as molecular chaperones and folding enzymes will be discussed. Folding in different cellular compartments and the consequences of mis folding, aggregation and stress will be considered. In addition, the realtion between protein misfolding and neuro degenerating diseases such as Alzheimer and Parkinson¿s will be discussed. Attention shall also be given to the different techniques that can be utilised to study protein structure, folding and dynamics. • Lectures • Tutorials/discussions of book material and scientific papers • Self-study Book `Introduction to protein structure" by Carl Branden & John Tooze, ISBN0-8153-2305-0 and recent scientific publications among which `Molecular Chaperones in the cytosol: from nascent chain to folded protein¿. Science 295, 1852-1858 (2002) by F.-U. Hartl & M. Hayer-Hartl and `Protein folding and its link to human disease¿ Biochem. Soc. Symp. 68, 126 by C. Dobson. Written exam or review paper Bachelor in Medical Natural Sciences, Chemistry, Pharmaceutical Sciences or (Medical Biology). Bachelor in Physics plus content of the course Principles of Molecular Biochemistry Msc students with Bachelor in Medical Natural Sciences. Chemistry, Physics, Pharmaceutical Sciences or (Medical) Biology. Application for this course should reach Prof. Van der Vies (tel. 47548, Email: [email protected]) at least 2 weeks before the starting date of the course.

blackboard onderwijs

Algemene didactiek / pedagogiek 1 en 2 990001 9 Diverse Docenten 30.08.2004 - 31.08.2005 Bij algemene didactiek / pedagogiek spelen de leservaringen op school een belangrijke rol. Daarmee in samenhang komen bij de colleges algemene onderwijskundige en pedagogische inzichten onder andere via literatuurstudie aan de orde en wordt geoefend met en gereflecteerd op het begeleiden van leerprocessen. Het gaat daarbij om onderwerpen als orde, verschillen tussen leerlingen en leerstijlen. Reflectie op het eigen leerproces en dat van mede dio's via besprekingen van leerervaringen en het maken van een persoonlijk ontwikkelingsplan nemen een belangrijke plaats in. Het onderwijs wordt voor een belangrijk deel verzorgd door docenten van het cluster (alfa, bèta, gamma). Er wordt gestreefd naar een samenhang tussen vakdidactische en algemeen didactische / pedagogische aspecten in het onderwijsaanbod. Reader kan bij aanvang van de cursus aangeschaft worden. opdracht opdrachten worden opgenomen in het portfolio Ja werkcollege (30.08.2004 - 31.08.2005)

126

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naam code studiepunten docent periode inhoud

literatuur toetsing

subject code credits period lecturers aim content

form of tuition literature mode of assessment entry requirements target audience remarks naam code docent studiepunten contacturen periode doel inhoud

werkwijze literatuur toetsing entreevoorwaarden doelgroep opmerkingen onderwijs

Applied Multivariate Analysis 400311 4 2 dr.ir. G. Jongbloed; dr. G.C. van der Veer; dr. J.F. Hoorn Conceptual understanding, practical analysis and visualisation of multivariate data. We first introduce matrix representation and visualization techniques of multivariate data. Then multivariate methods such as regression analysis, principal component analysis, multidimensional scaling and factor analysis are considered. Also the more advanced Structural Equation Models (SEM) will be considered. Classes Applied multivariate data analysis, B.S. Everitt and G. Dunn, Exercises Descriptive statistics (comparable with the course "toegepaste statistiek" in the third year) mIS, mCS Homework consists of exercises to be completed using the statistical package R. Classes are in English. Atw: Corpustaalkunde 539155 prof.dr. P.T. van Reenen 5 28 (28 college) 2 Het ontwikkelen van inzicht in taalvariatieverschijnselen op basis van grote taalbestanden. Onderwerpen die binnen dit college vallen zijn bijvoorbeeld: Etymologisch onderzoek nieuwe stijl; het vervaardigen van dialectkaarten op computer; taalverandering. Centraal in alle benaderingen is het gebruik van grote taalkundige databestanden op computer. Ze betreffen moderne Nederlandse dialecten (in samenwerking met het Meertens Instituut), Middelnederlands, ook Middelnederduits, Oudfrans. Hoor/werkcollege plus practicum In overleg met de docent Werkstuk: opdracht aan de hand van eigen onderzoek Beginnerscursus UNIX (te volgen in periode 1; contactpersoon Erik Akkerman) 3e jaars studenten Taalwetenschap • Het college heeft plaats op het Meertens Instituut • Inschrijven verplicht via TISVU college

naam Atw: Fonologie code 539162 docent dr. C.M. Struijke

Exam parts

127

studiepunten contacturen periode doel

inhoud werkwijze literatuur toetsing doelgroep opmerkingen onderwijs voorkennisvak naam code docent studiepunten contacturen periode doel

inhoud werkwijze literatuur toetsing doelgroep opmerkingen onderwijs

5 28 (28 werkcollege) 5 Het ontwikkelen van inzicht in de fonologische systematiek van taal, van het vermogen om een wetenschappelijke publicatie hierover uit de (inter)nationale vakliteratuur zelfstandig te kunnen bestuderen en evalueren, en van het vermogen om zelfstandig een analyse te maken van fonologische verschijnselen. Bestudering van een tekstboek Fonologie Werkcolleges (thuis voorbereiden met behulp van opdrachten/vragen) C. Gussenhoven & H. Jacobs, Understanding Phonology, London: Arnold 1998 Schriftelijk tentamen aan het einde van periode 5 2e jaars studenten Taalwetenschap (ATW, Lexicologie, TTW), CIW, de talen Inschrijven verplicht via TISVU werkcollege 500011: Let alg: Algemene taalwetenschap, inleiding Atw: Inleiding morfologie 539163 drs. C. Blom 5 28 (28 werkcollege) 2 Het ontwikkelen van inzicht in de morfologische systematiek van taal, van het vermogen om een wetenschappelijke publicatie hierover uit de (inter)nationale vakliteratuur zelfstandig te kunnen bestuderen en evalueren en van het vermogen om zelfstandig een analyse te maken van morfologische verschijnselen. Bestudering van een tekstboek Morfologie Werkcolleges (thuis voorbereiden met behulp van opdrachten/vragen) G.E. Booij & A. van Santen. Morfologie. De woordstructuur van het Nederlands. Amsterdam: Amsterdam University Press, 1998 (2e druk) Schriftelijk tentamen aan het einde van periode 2 2e jaars studenten Taalwetenschap-ATW, 3e jaars studenten Taalwetenschap-Lexicologie en CIW, en de talen Inschrijven verplicht via TISVU werkcollege

Atw: Inleiding syntaxis 539151 dr. B.L.J. Los 5 28 (28 werkcollege) 5 Het verwerven van vaardigheden om met behulp van een theoretisch model inzicht te verkrijgen in de syntactische structuur van een taal. inhoud Inleiding in de generatieve syntaxis: de bouw van woordgroepen, lexicale en functionele projecties, de verplaatsing van constituenten werkwijze 2 x 2 uur werkcollege

naam code docent studiepunten contacturen periode doel

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literatuur Van Gelderen, E. (2002) An introduction to the grammar of English. Amsterdam/Philadelphia: John Benjamins toetsing Schriftelijk tentamen doelgroep Verplicht voor 1e jaars studenten Taalwetenschap: ATW, TTW en Lexicologie opmerkingen Inschrijven verplicht via TISVU onderwijs werkcollege naam code docent studiepunten contacturen periode doel inhoud

literatuur toetsing doelgroep opmerkingen onderwijs voorkennisvak

Atw: Psycholinguïstiek 539152 dr. C.M. Struijke 5 28 (28 werkcollege) 1 Het verwerven van inzicht in taalproductie en taalperceptie, en in psycholinguïstische vraagstellingen en inzichten. Bij het luisteren naar taal en het spreken ervan spelen allerlei processen een rol. Het doel van deze cursus is deze processen te identificeren en bestuderen. Wij kijken daarvoor naar de belangrijkste studies binnen het vakgebied aan de hand van het tekstboek en een enkel wetenschappelijk artikel. Deze studies toetsen voornamelijk theorieën aan de hand van gegevens die verzameld zijn door observatie en experimentatie. Door het bestuderen van dit onderzoek zullen we dus ook inzicht krijgen in experimentele methodologie binnen het vakgebied. De resultaten van het te bestuderen onderzoek kunnen leiden tot verificatie, falsificatie of aanpassing van taalgebruikersmodellen die uitgebreid besproken zullen worden. • Carroll, David W. 1999, Psychology of Language, 4th Edition, Pacific Grove, CA: Brooks/Cole • Uit te reiken artikel en hand-outs Opdrachten en tentamen 2e jaars studenten Taalwetenschap en minorstudenten (m.n. studenten talen, studenten Psychologie of Artificiële Intelligentie) Inschrijven verplicht via TISVU werkcollege 500011: Let alg: Algemene taalwetenschap, inleiding (of 1e jaar Taalwetenschap)

BWI werkstuk 400206 6 variabel de student beschrijft voor een deskundige manager (de manager bezit algemene deskundigheid) op een heldere wijze (beknopt en zakelijk) een probleem. inhoud naar aanleiding van een probleemstelling voert de student zelfstandig een (literatuur)onderzoek uit. De student legt de resultaten schriftelijk vast en geeft een mondelinge presentatie. De nadruk wordt gelegd op het bedrijfsgerichte aspect van de studie, naast wiskunde en informatica aspecten. toetsing werkstuk en voordracht.

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doelgroep mBMI. opmerkingen Meer informatie: www.cs.vu.nl/stagebureau docenten het werkstuk wordt begeleid door een docent, deskundig op het gebied van het door de student gekozen onderwerp contact drs. Miriam Maëla ([email protected]) naam code studiepunten periode docent doel

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Bedrijfsmodellering en requirements engineering 400010 7 1 en 2 dr. A.T. Schreiber Na dit vak is de student in staat: - een probleem- en veranderingsanalyse uit te voeren met betrekking tot een IT vraagstuk in een bedrijfsmatige context; op modelmatige wijze in kaart te brengen hoe een informatiesysteem als oplossing past in bedrijfsstrategie en bedrijfsproces; - verschillende methodieken toe te passen voor het eliciteren van door de organisatie te stellen eisen aan een te ontwikkelen informatiesysteem. Het vak BedrijfsModellering en Requirements Engineering (BMRE)behandelt de analyse van bedrijfsvraagstukken, waarbij introductie of uitbreiding van een informatiesysteem een van de mogelijke oplossingen is. Dit omvat de activiteiten en methodieken die nodig zijn om (1) een probleemanalyse uit te voeren met betrekking tot IT vraagstukken in een bedrijfsmatige context; (2) te modelleren hoe een gewenst informatiesysteem past in het bedrijfsproces en aan te geven welke eventuele veranderingen daarbij wenselijk zijn; (3) het ontwikkelen en toetsen van het te stellen pakket van eisen aan een te bouwen informatiesysteem. Het vak bestaat uit een college met een tentamen (4 sp) en een practicum (3 sp). Beide moeten voldoende zijn. Syllabus Tentamen plus practicumverslag. 2BI, 2MMC, 3I, 3BWI, mBMI

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Bedrijfssystemen practicum 400196 9 4, 5 en 6 ir. M.P.H. Huntjens Practisch ervaring op doen met de stof van het vak Bedrijfssystemen Drie opgaven over drie onderwerpen uit Bedrijfssystemen practicum zie Bedrijfssystemen Via practicumopgaven 3I Bedrijfssystemen

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Beginselen bestuursrecht (B1) 200108 5.7 prof.mr. J. Struiksma (kamer 6A-23 tel. (020) 44 46267) week 14 - 26

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doel Met het vak Beginselen bestuursrecht wordt beoogd de student inzicht te geven in de basisbegrippen en hoofdlijnen van het bestuursrecht. De bedoeling is de student een kern aan kennis en inzicht mee te geven waarop later in de bachelorfase zal moeten worden teruggegrepen. Daarnaast wordt van de student verwacht dat deze in staat zal zijn de te verwerven kennis toe te passen op een casus. inhoud Na een algemene kennismaking met het huidige bestuursrecht, zullen worden besproken de organisatie van het openbaar bestuur, de toedeling van de bevoegdheden aan bestuursorganen en de verschillende wijzen waarop het bestuur in het dagelijks leven kan ingrijpen. Voorts wordt ingegaan op de bestuursrechtelijke normen die door het bestuur bij de uitoefening van zijn bevoegdheden in acht genomen moeten worden. Daarnaast zal enige aandacht worden besteed aan de handhaving van bestuursrechtelijke regels. Tot slot zullen de beginselen van het systeem van rechtsbescherming tegen de overheid aan de orde worden gesteld. werkwijze Het vak is opgenomen in blackboard. Daar is uitgebreide informatie opgenomen over het collegeschema, literatuur, opdrachten en tentamen. literatuur • F.C.M.A. Michiels, Hoofdzaken van het bestuursrecht, Kluwer, laatste druk. • syllabus Beginselen bestuursrecht. (De syllabus is verkrijgbaar in de VU-boekhandel.) toetsing Het tentamen zal schriftelijk worden afgenomen. blackboard Bij deze cursus wordt blackboard gebruikt. Zodra de blackboardcursus toegankelijk is, is deze te bereiken voor studenten van de VU. onderwijs algemeen (week 14 - 26) naam code studiepunten coördinator periode doel

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Beginselen privaatrecht I (B1) 200103 5.7 mr. J.L. Smeehuijzen (kamer 6A-34, tel. (020) 4 446287) week 41 - 52 Het verwerven van inzicht in de verhouding van het privaatrecht tot andere rechtsgebieden en in de opbouw van de boeken 3, 5 en 6 BW. Het verwerven van kennis van de basisbegrippen van het vermogensrecht in de boeken 3, 5, 6 en 7 BW. Het verwerven van kennis van de belangrijkste regels op het gebied van het goederenrecht. Het verwerven van vaardigheid in het oplossen van casus en het daarbij kunnen toepassen van bovengenoemde kennis. Op de hoorcolleges behandelen de docenten de hoofdlijnen van de stof en belichten zij moeilijke onderdelen. Op de werkcolleges staat het oefenen met de stof centraal aan de hand van casus. Derhalve wordt van de student een actieve voorbereiding en deelname verwacht. • C.C. van Dam en A.J. Verheij (red.), Privaatrecht als opdracht, Ars Aequi Libri, Nijmegen, 6e druk 2001; • Syllabus Beginselen Privaatrecht I (verkrijgbaar in de VU-boekhandel). Het tentamen is schriftelijk en bestaat uit enkele casus. De arrestenbundels mogen niet worden meegenomen. Bij deze cursus wordt blackboard gebruikt. Zodra de blackboardcursus

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Beginselen privaatrecht II (B1) 200105 5.7 mr. J.M. Verhagen (kamer 6A-38, tel. (020) 44 46293) prof.mr. A.J. Akkermans; mr. J.M. Verhagen; prof.mr. C.E.C. Jansen (e.a.) week 2 - 13 Het leerdoel van het vak Beginselen privaatrecht II is dat de student de belangrijkste regels op het gebied van het verbintenissenrecht, waaronder het algemene overeenkomstenrecht en het onrechtmatige daadsrecht alsmede de wetsartikelen uit de Boeken 3, 6 en 7 van het Burgerlijk Wetboek waarin deze regels zijn vervat, efficiënt en doeltreffend kan toepassen op eenvoudige feitelijke situaties (casus). Op de hoorcolleges behandelen de docenten de hoofdlijnen van de stof en belichten zij moeilijke onderdelen. Op de werkcolleges staat het oefenen met de stof centraal aan de hand van casus. Derhalve wordt van de studenten een actieve voorbereiding en deelname verwacht. • C.C. van Dam en A.J. Verheij (red.), Privaatrecht als opdracht, Nijmegen: Ars Aequi Libri 2001, zesde druk; • A.V.T. de Bie en J. de Jong van Lier, Zeug geel 113, Deventer: W.E.J. Tjeenk Willink 2004, vierde druk; • Syllabus Beginselen Privaatrecht II (verkrijgbaar in de VU boekhandel). Het tentamen is schriftelijk en bestaat uit enkele casus. Bij deze cursus wordt blackboard gebruikt. Zodra de blackboardcursus toegankelijk is, is deze te bereiken voor studenten van de VU. algemeen (week 2 - 13)

Beginselen staatsrecht (B1) 200104 5.7 prof.mr.drs. B.P. Vermeulen (kamer 6A-19, tel. (020) 44 46264) week 41 - 5 Het kennen van de elementaire begrippen van het nationale en het internationale publiekrecht, het kunnen toepassen van deze begrippen op eenvoudige casus en het inzicht hebben in het functioneren van een democratische rechtsstaat, mede binnen de internationale rechtsruimte. inhoud Aan de orde komen onderwerpen als de betekenis van constitutie, grondwet en internationale verdragen, de inrichting en de werking van de staatkundige samenleving, grondrechten, begrippen als rechtsstaat en democratie alsmede verschillende soorten regelgeving. Bovendien worden de ontwikkeling van de bevoegdheden van de Nederlandse overheid in het licht van het internationale en Europese recht alsmede de rechtsbescherming tegen de overheid binnen het geheel van de Nederlandse staatsinrichting behandeld. werkwijze Het hoorcollege heeft het karakter van een algemene inleiding. Daarnaast worden werkcolleges verzorgd, waarin dieper op de verschillende onderdelen van de stof wordt ingegaan. Op de werkcolleges wordt een actieve deelname verwacht in die zin, dat men de bijbehorende vragen en opdrachten uit het Werkboek heeft voorbereid. Zowel op de hoor- als op de werkcolleges dient

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men een wetgevingsbundel paraat te hebben. Bij deze cursus wordt blackboard gebruikt. literatuur • Hoor- en werkcollegestof; • M.C. Burkens, H.R.B.M. Kummeling, B.P. Vermeulen, R.J.G.M. Widdershoven, Beginselen van de democratische rechtsstaat, Deventer (meest recente druk); • M.L.W.M. Viering e.a., Staatsrecht. Jurisprudentie 1849-1999, Ars Aequi, Nijmegen 2003. • Syllabus Beginselen staatsrecht (verkrijgbaar in de VU-boekhandel). toetsing Schriftelijk tentamen. Bij het tentamen mag gebruik worden gemaakt van een niet-geannoteerde wetgevingseditie. opmerkingen Spreekuur: volgens afspraak. blackboard Bij deze cursus wordt Blackboard gebruikt. Zodra de Blackboardcursus toegankelijk is, is deze te bereiken voor studenten van de VU. onderwijs algemeen (week 41 - 5) Beginselen strafrecht (B1) 200102 5.7 mr. B. de Wilde (kamer 5A-32, tel. (020) 44 46233) mr. C.J. Petiet; mr. B. de Wilde; mr. M.J. Kronenberg; mr. E. Pans week 41 - 52 Het aanleren van elementair inzicht in het geldende strafrecht, waarbij de systematiek van het materiële en het formele strafrecht centraal staan. De student moet tijdens het tentamen in staat zijn casus op het gebied van materieel en formeel strafrecht op te lossen. inhoud Het vak beoogt elementair inzicht te verschaffen in het strafrechtelijke systeem, waarbij materieel en formeel strafrecht zoveel mogelijk met elkaar in verband worden gebracht. De belangrijkste materieelrechtelijke leerstukken 'zoals opzet en culpa, strafuitsluitingsgronden en poging' en de hoofdlijnen van het strafproces, inclusief mensenrechten, komen aan de orde. werkwijze • Hoorcolleges. Tijdens de hoorcolleges wordt het onderwerp van de desbetreffende week ingeleid. Het onderwerp wordt in grote lijnen uiteengezet en wordt geïllustreerd aan de hand van voorbeelden. Het eerste hoorcollege is een inleiding tot rechtsbronnen die voor de bestudering van het strafrecht van belang zijn. • Werkcolleges. Tijdens de werkcolleges wordt dieper op de stof ingegaan. De opdrachten voor de desbetreffende week besproken in hoorcollegevorm. Voor deze colleges wordt voorbereiding niet geëist, maar wel ten zeerste aanbevolen. Iedere week maken casusvragen deel uit van de werkgroepopdrachten. In de laatste week wordt een recent tentamen besproken aan de hand van de modelantwoorden en modelnormering. Op deze manier worden studenten vertrouwd gemaakt met het beantwoorden van casusvragen aan de hand van de wet, het EVRM en de jurisprudentie. • Werkgroepen. Studenten die actiever en dieper op de stof willen ingaan kunnen deelnemen aan de intensieve werkgroepen. Voor deze werkgroepen is voorbereiding verplicht. Tijdens de werkgroepen komt dezelfde stof aan de orde als tijdens de werkcolleges.

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Blackboard. Bij dit vak wordt gebruik gemaakt van Blackboard. Hierop worden onder andere mededelingen gedaan en collegedictaten en andere documenten gepubliceerd. • M.J. Kronenberg & B. de Wilde, Grondtrekken van het Nederlandse strafrecht, Deventer: Kluwer 2003, ISBN 9013004776, prijs ¿ 31,00 • Syllabus Werkboek Beginselen strafrecht • Syllabus Jurisprudentie Beginselen strafrecht • Het boek en de syllabi zijn verkrijgbaar in de VU Boekhandel. Schriftelijk tentamen met open vragen, waarbij de nadruk ligt op casusoplossen. Bij deze cursus wordt Blackboard gebruikt. Zodra de Blackboardcursus toegankelijk is, is deze te bereiken voor studenten van de VU. algemeen (week 41 - 52) •

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Behaviour Dynamics 400113 6 1 and 2 dr. C.M. Jonker; prof.dr. J. Treur This course teaches analysis and modelling of the dynamics of behaviour in Artificial, Biological, Cognitive and Social systems. Behavioural dynamics occurs in different forms, contexts and complexity. During the course examples of such behaviour are studied coming from software systems (e.g., knowledge- and agent-based systems), biology (e.g., functioning of the blood circulatory system, bacteries), cognition (e.g., the dynamics of beliefs, desires and intentions, emotions and feelings, complex reasoning tasks). The dynamics of behaviour of such systems is analysed (including verification and validation), modelled, and simulated in this course using dedicated techniques and tools. form of tuition Combination of lectures and practical assignments. literature Online reader mode of assessment Examination and practical assignments. Both grades should be at least 5.5 to pass the course. subject code credits period lecturers content

Bio-Analytical Aspects of Drug Discovery I 435597 dr. H. Lingeman 6 3 Introduction to the bio-analytical aspects related to drug discovery focusing on proteomics, genomics and metabolomics, as well as the techniques used for screening and monitoring procedures. content An overview of the drug development process will be given dealing with preclinical and clinical development. Followed by the specific roles for bioanalysis in drug development. Aspects like lead optimization, screening for pharmacokinetic properties, absorption, metabolic stability screening, toxicity screening, ADME studies, metabolite identification and characterization. Most of these aspects will be illustrated with clinical or pharmacokinetic applications and therapeutic drug monitoring and the focus will be on the separation / detection systems used for these applications.

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In the second part the fundamental strategies for bio-analytical sample preparation and analysis will be discussed. Techniques like protein precipitation, liquid-liquid extraction, solid-phase extraction, restrictedaccess media, molecularly-imprinted polymers and immuno-affinity extraction will be introduced. With respect to the separation / detection the basics and potential of liquid chromatography / mass spectrometry combinations will be dealt with. Lectures and tutorials. High Throughput Bioanalytical Sample Preparation: Methods and Automation Strategies, D.A. Wells, Elsevier 2003. Written examination. Basic knowledge of analytical chemistry, pharmacology and toxicology. mPhar Bio-Analytical Aspects of Drug Discovery II 435598 dr. H. Lingeman; prof.dr. H. Irth 6 4, 5 and 6 In depth study on the bio-analytical aspects related to target- and lead discovery of drugs focusing on proteomics, genomics, metabolomics, highthroughput / high-resolution screening and monitoring of biological effects by using bio-markers. During this course the potential of modern analytical and imuunological techniques (e.g., sample preparation, separation, detection, identification) used in target- and lead-discovery will be discussed. The emphasis will be on the treatment of advanced sample preparation techniques (i.e. automation, high-throughput / combinatorial chemistry, miniaturization), advanced separation modes (i.e. chromatography, electrophoresis) and bio-specific (i.e. enzymatic, immunological) assays and mass-spectrometric methods. The techniques will be discussed in relation with pharmacokinetic studies - the applicability of the various techniques with within the different stages of ADME will be discussed. Structure-activity relationships dealing with the relation between technology and structure will be highlighted. Finally, biological-effect monitoring, for proteomics and genomics, exposure monitoring, pharmacokinetics and plasma / serum analyses will be dealt with. Lectures and tutorials. Hand-outs and monograph(s) indicated by the lecturer. Written examination. Basic knowledge of analytical chemistry, pharmacology and toxicology. mPhar Please contact the mastercoordinator four weeks prior to the start of the course (e-mail: [email protected]). Biochemical Mechanisms of Toxicology 435670 dr. J.N.M. Commandeur (tel. 4447595, [email protected]) 6

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period Throughout the year. aim To get acquainted with cellular mechanisms underlying the toxicity and carcinogenicity of drugs and other chemicals. content Cellular transport and selective accumulation of poptentially toxic drugs; xenobiotic-induced oxidative stress, cell injury, signalling and gene regulation, disruption of calcium homeostasis; mechanisms of necrotic and apoptotic cell death; impairment of cell proliferation and tissue repair, immune mechanisms; cytokine-mediated toxicity, nuclear-receptor-mediated toxicity; disruption of cellular energy production by xenobiotics, interaction of xenobiotics with ion transporters, specific inactivation of enzymes and other proteins. form of tuition Self study. literature "Mechanistic Toxicology" by UA Boelsterly, (Taylor&Francis, 2003, ISBN 0-415-28459-7). mode of assessment Written examination. entry requirements Knowledge of basic principles of drug action and biochemistry. target audience mPhar remarks Please contact the mastercoordinator four weeks prior to the start of the course (e-mail: [email protected]). subject code credits period lecturers aim

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Bioinformatic Data Analysis and Tools 430048 6 5 and 6 dr. J. Kleinjung; prof.dr. J. Heringa A theoretical and practical bioinformatics course on the fundamentals of bioinformatics tools and tool creation for biological data mining. Goals: • At the end of the course, students will be aware of the issues, methodology and available bioinformatics tools for • At the end of the course, students will have hands-on experience in molecular modeling and studying structure-function relationships. Theory: • Inverse protein folding, introduction to statistical thermodynamics of soft and biological matter (5 lectures), genetic algorithm, repeat recognition tools and concepts (e.g. transitivity), molecular mechanics simulations, (hidden) Markov models, pattern recognition, machine learning techniques Practical: Assignment Statistical Thermodynamics, Assignment hidden Markov modelling 13 Lectures (2 two-hour lectures per week) Assignment introductions, Computer practicals, Hands-on support E-course material (slides, assignment material, papers): http://ibivu.cs.vu.nl Books: Biological Physics. Energy, Information, Life. Philip Nelson. 600 pages , W H Freeman & Co., (July 2003), ISBN: 0716743728 Assignment results and oral or written exam (depending on number of course students) A completed course Sequence Analysis and DNA/Protein Structure-Function Analysis and Prediction is a strong advantage. Some experience in

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programming is required. target audience Students with Bachelor degree in Physics, Chemistry, Mathematics, Computer Science, Biology, Medical Natural Sciences or Medicine, with a strong interest and some basic knowledge in Bioinformatics remarks The course is taught in English. subject code co-ordinator lecturers credits period aim

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Biological Networks and Signal Transduction 430057 dr. M.H. Siderius dr. M.H. Siderius; guests 6 4 • To obtain knowledge and insight into the different ways cells co-ordinate and organise signal transduction pathways • To learn to understand cellular signalling networks from reading and discussing scientific literature Signal transduction pathways control many of the essential features of cells, ranging from metabolism. Cell cycle progression, differentiation and response to the environment to, for example, induced cell death. In order to ensure the proper responses to a certain stimulus, co-ordination of the different signalling events in the cell in crucial. The structure and function of the different components of cellular signalling and the way in which integration of the signal is achieved will be discussed. General mechanisms of the organisation of signal transduction biomolecules (proteins), subcellular localisation, protein-protein interactions, scaffolding and portein maturation will all be considered. Furthermore, a range of technologies that can be utilised to study signalling networks will be addressed. • Lectures • Discussion of scientific papers and book reviews • Student presentation • Problem solving • Lecture notes • Collected scientific papers Written exam or review paper Bachelor courses Molecular Cell Biology I and II (MNS Bachelor programme) or Biochemistry and Molecular Signalling course (Chemistry and Pharmaceutial Sciences Bachelor programme). Bsc in Medical Natural Sciences, Chemistry, Pharmaceutical Sciences or (Medical Biology). Bachelor in Physics plus content of the course Principles of Molecular Biochemistry and Advanced Structural Biology. Msc students with Bachelo in Medical Natural Sciences. Chemistry, Pharmaceutical Sciences or (Medical) Biology. Application for this course should reach Prof. Van der Vies (tel. 47564, Email: [email protected] at least 2 weeks before the starting date of the course. Business Intelligence 61311020 6 28 (8 practicum, 20 hoorcollege)

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1 drs. J.F.M. Feldberg drs. J.F.M. Feldberg; prof.dr. A.E. Eiben Het doel van dit vak is zowel het creëren van een elementair business intelligence referentiekader als het leren werken met en toepassen van een 'state-of-the-art' business intelligence oplossing. Studenten die dit vak gevolgd hebben moeten in staat zijn om in een organisatorische context actief mee te denken en te beslissen over het nut, de toepassing, de ontwikkeling en de consequenties van de toepassing van business intelligence systemen. Dit referentiekader moet tevens voldoende aanknopingspunten bieden om zelfstandig de aangereikte kennis en kunde te verdiepen en te verbreden. Het vak wordt primair vanuit een managementperspectief gegeven waarbij de techniek een ondersteunende rol vervult. Over het algemeen geldt dat organisaties geen gebrek aan gegevens hebben. Mede door het gebruik van ERP-systemen (enterprise resource planning), CRM-systemen (customer relationship management) en de groei van toepassingen op het gebied van Internet en e-commerce, beschikken organisaties over grote hoeveelheden verschillende soorten gegevens (markt, product, personeel, logistiek, financieel, etc.). Effectief en efficiënt gebruik van deze gegevens kan bijdragen aan de realisatie van houdbaar concurrentievoordeel. Echter, het ontwikkelen van de vaardigheden en systemen die noodzakelijk zijn om gegevens om te zetten in actiegerichte kennis en resultaten is voor veel organisaties een probleem. Door softwareleveranciers worden hulpmiddelen en systemen aangeboden (onder de noemer: business intelligence (BI) oplossingen) die kunnen worden ingezet ter ondersteuning van besluitvormingsprocessen. Om deze BI producten met succes te kunnen gebruiken is kennis van deze producten en hun toepassingsmogelijkheden nodig, alsmede vaardigheden om de juiste basisgegevens te verzamelen, te analyseren en te verdichten. In het college wordt het begrip Business Intelligence breed opgevat. Hoewel de kern van het vak zich richt op 'fact based decision making', data warehousing, online analytical processing (OLAP), data mining en (e)business intelligence systems, komen ook verwante beslissingsondersteunende systemen aan de orde, zoals: Decision Support Systems (DSS), Group DSS Executive Information Systems en Expert Systems. Middels een practicum wordt ook ruim aandacht besteed aan de toepassing van BI oplossingen. Het vak wordt gegeven in de vorm van hoorcolleges. Parallel aan de hoorcolleges wordt een practicum georganiseerd waarin studenten zelfstandig leren werken met een business intelligence oplossing die door veel organisaties wordt gebruikt. Binnen deze oplossing worden gegevens gebruikt die afkomstig zijn van verschillende ondernemingen. De practica zijn interactief van opzet en worden mede ondersteund door een digitale toetsomgeving. De studenten krijgen online opdrachten dan wel opgaven, waarvan de resultaten tijdens de collegecyclus digitaal zullen worden getoetst en beoordeeld (real time!). Literatuur wordt nog nader bekend gemaakt. Aanvullend studiemateriaal wordt via de digitale leeromgeving elektronisch dan wel d.m.v. een reader ter beschikking gesteld. schriftelijk tentamen

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65% van het eindcijfer. De toetsen bij het practicum tellen voor 35% mee voor het eindcijfer. Er wordt intensief gebruik gemaakt van een digitale toetsomgeving, alle toetsen en het tentamen worden digitaal afgenomen. onderwijs hoorcollege practicum subject code co-ordinator lecturers credits period aim

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Capita Pharmacochemistry 435684 dr. J.N.M. Commandeur (tel. 4447595; [email protected]) prof.dr. N.P.E. Vermeulen; prof.dr. R. Leurs; prof.dr. H. Irth; dr. H. van der Goot; dr. J.H.N. Meerman; dr. J.N.M. Commandeur; dr. M.J. Smit; dr. H. Lingeman 6 Throughout the year. Deepening of knowledge of specific aspects of pharmaceutical sciences/pharmacochemistry (e.g. related to the major/minor) or broadening of knowledge of fields related to pharmaceutical sciences/pharmacochemistry. Subjects of this course/caput are optional and may vary, depending on the rest of the programme and/or on the interests of the MSc-student. The following subjects can be selected: • Drug registration and safety assessment • In vitro pharmacology and toxicology and high-throughput screening • Pharmaco-/toxicogenomics and -proteomics • Protein modeling and bioinformatics • Combinatorial chemistry • Pharmacological basis of drug action Self-study. Depending on the course/caput. Oral or written examination Basic principles of pharmacochemistry. mPhar Please contact the mastercoordinator four weeks prior to the start of the course (e-mail: [email protected]).

Caput Financial Stochastics 400220 7 prof.dr. A.W. van der Vaart This course is not given in this form in 2004/05. A course with a similar contents is given by Andreas Kyprianou at the University of Utrecht within the joint master program Stochastics and Financial Mathematics of VU/UVA/UU. See http://www.math.vu.nl/sto/onderwijs/sfm content This course is concerned with "financial engineering", the theory of the pricing of financial derivatives, such as options. Mathematical speaking a financial derivative is a measurable function of the sample paths of a given collection of stochastic processes, called asset processes. The (economic) theory of no-arbitrage pricing as developed by Black, Scholes and Merton, shows

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that the "correct" price of such a derivative is equal to the cost of starting a so-called replicating portfolio. It turns out that this price can also be written as an expectation of the discounted derivative under a certain probability measure that makes the (discounted) asset processes martingales. This leads to the basic pricing formula, which can next be specialized to many different derivative and many models for the asset price processes. Of special interest and complexity are models for interest rates. A basic set of interest rate products are bonds, which are papers that give a fixed payment of one unit after a fixed time interval., called a term. The price of a bond with a given term, which is tradable during its term, is called a discount rate. A model for the collection of all discount rates is called a term structure. Given such a term structure it is possible to price derivatives on the interest rates. Asset processes can be modelled as diffusion processes (solutions of stochastic differential equations), or more generally as semimartingales. Economic notions such as completeness of a market, or the nonexistence of arbitrage, can then be described through mathematical notions such as existence or uniqueness of a martingale measure. This course starts with a brief review of semimartingales and stochastic calculus, where it is assumed that the students already have some experience with Ito stochastic integrals. Next we discuss martingale respresentation theorems, which are results saying that every martingale relative to a filtration generated by a given martingale (e.g. Brownian motion) can be expressed as a stochastic integral relative to this martingale. The remainder of the course is concerned with financial calculus, including derivative pricing, (Black-Scholes and exotic products, American style options, Asian options), and interest rate models (Heath-Jarrow-Morton, short rate). • Ioannis Karatzas &Steve Shreve, Methods of Mathematical Finance • P.J. Hunt & J.E. Kennedy, Financial Derivatives in Theory and Practice • lecture notes. Oral or written exam, or paper. required knowledge: Measure theoretic probability, stochastic integration mMath, mBMI, mSFM website: http://www.cs.vu.nl/sto/onderwijs/fw/

Caput Software Asset Management 400100 7 1 en 2 prof.dr. C. Verhoef; prof.dr. H.M.P. Kersten; prof.dr. J.C. van Vliet; dr.ing. J. Gordijn; dr. S. Brinkkemper aim Gain insight in IT costs, benefits, risks, and returns on information technology. content In this class we treat several techniques to aid in software cost estimation. We discuss how IT migrates from cost issue to strategic asset, and how to

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come to grips with this important production factor. We provide insight in how to support decision making on IT investment issues. Examples from the Financial and Insurance industry, and independent software vendors are discussed. With IT benchmarks we obtain insight in the risks of IT developmtn and the operational costs of IT. We introduce the notion of an IT portfolio, and how to perform quantitative analyses with it, to aid in justifying IT investments. Seminar with presentations of staff and students. Articles and chapters from books. Essay on selected topics from articles. You can do this individually or in a group of 3 persons max. Software Engineering (400071), a little statistical background is helpful. mCS, mIS, mBMI, mAI Caput Stochastic Optimization 400336 6 1 and 2 prof.dr. G.M. Koole Theory and algorithms for stochastic optimization are treated and applied to controlled queueing systems. We will discuss aspects of semi-Markov decision theory and their applications in certain queueing systems. In a programming assignment the students implement optimization algorithms and experiment with them. Experience with the more theoretical subjects is obtained through homework. Lecture notes (will be handed out during lectures). Programming and written exercises. Stochastische Methoden (400074) and a programming language. mBMI, mMath, mSFM and exchange students. • This course is given in English • Registration for this course via https://tisvu.vu.nl/HTM/TISVULogin.htm, one week prior to the start. For the course schedules please refer to http://www.few.vu.nl/onderwijs/roosters.

Communicatie en educatie via internet 471027 drs I. van Veen; J. Bruin 3 15.11.2004 - 26.11.2004 Na afloop van de module hebben de studenten: • inzicht in de theorie en praktijk van wetenschapscommunicatie via internet; • inzicht in het planmatig inzetten van tekst, beelden, multimedia en infographics; • ervaring met het produceren en bewerken van tekst, beelden, multimedia en infographics. inhoud • Doelgroepgerichte wetenschapscommunicatie via internet; • Content management (voor statische en dynamische websites); • Theorie en vraagstukken rond website usability;

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Content productie (tekst, beeld, multimedia, fotografie en infographics). Zelfstudie; • Interactieve responsie- en werkcolleges; • Trainingssessies; • Hoorcolleges. Boek in combinatie met artikelen. Wordt voor aanvang van de cursus nader bekend gemaakt. Beoordeling aan de hand van individuele producten en het functioneren tijdens de practica en werkcolleges. Masterstudenten van de faculteiten Aard- en Levenswetenschappen en Exacte Wetenschappen. De cursus Wetenschapsjournalistiek dient met succes te zijn afgerond •

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Communicatiewetenschappen 471006 dr. C.M. Koolstra 6 06.09.2004 - 01.10.2004 • Kennismaken met basisbegrippen van de communicatiewetenschap; • Kennismaken met communicatieprocessen vanuit een interpersoonlijk, organisatorisch en maatschappelijk perspectief; • Kennismaken met onderzoeksmethoden die vaak in de communicatiewetenschap worden gebruikt (survey, inhoudsanalyse, en experiment) • Leren communicatieprocessen in wetenschappelijke termen te beschrijven met het doel theorieën toe te passen en elementaire voorspellingen te doen; We leven in een communicatiemaatschappij. Volgens EU-schattingen houdt meer dan de helft van de beroepsbevolking zich bezig met een of andere vorm van communicatie. Men noemt hen ook wel communicatiewerkers. Om zinvol te kunnen functioneren in een communicatiemaatschappij heb je niet alleen communicatie-vaardigheden nodig (zoals schrijven, spreken en illustreren), maar moet je ook inzicht hebben in de wetmatigheden, ideeën en vooronderstellingen die daaraan ten grondslag liggen. Wat is communicatie? Welke media zijn belangrijk? Wat is een doelgroep? Wat is interactieve communicatie? Hoe effectief zijn publiekscampagnes? Een inleiding in de communicatiewetenschap leidt je uiteraard niet op tot communicatiewetenschapper; daarvoor heb je een aantal jaren studie nodig. Maar basale kennis van en inzicht in de communicatie-wetenschap is noodzakelijk om op een adequaat niveau met communicatiewetenschappers te communiceren, bijvoorbeeld bij het opzetten van een campagne of het evalueren daarvan. Een combinatie van hoorcolleges, werkgroepbijeenkomsten en zelfstudie. Boek: Severin, W. J. & Tankard, J. W. (2001). Communication theories: Origins, methods, and uses in the mass media. New York: Longman. [5th edition]. Een aantal wetenschappelijke artikelen (via Blackboard). • Participatie in de werkgroepen. • Een groepswerkopdracht. • Een schriftelijk tentamen, welke voor een deel uit meerkeuze vragen zal

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Computational Design and Synthesis of Drugs 435673 dr. I. de Esch (tel. 4447841, G343a, [email protected]) dr. I. de Esch; dr. A. Feenstra; dr. B.C. Oostenbrink 6 2 To gain insight and experience in the molecular modeling tools that enable (rational) drug design and planning a route to synthesize the ligand. In the post-genome era, an overwhelming amount of data describing the molecular characteristics of the targets is becoming available. For example, the structure of many proteins is being determined using Xray analysis and NMR techniques. Furthermore, high-throughput screening results in massive amounts of data that reveal the molecular properties of the ligands that are able to have interaction with the drug targets. In this course, several techniques that can help to translate this data into novel ligands will be discussed and demonstrated. Specific topics include crystal structure analysis, the building of homology models, docking of ligands, calculating binding free energy and affinity of ligands for the protein, de novo structure generation, and pharmacophore modelling. These techniques generate ideas for novel compounds. Because a design that cannot be synthesized is by definition a useless design, the synthetic feasibility is a key and integral part of the design process. Therefore, it is important to be able to define a synthetic pathway for the preparation of the designs. In this course, this aspect will be covered by a case study. For a specific design, a versatile and robust synthesis route has to be defined. A thorough literature search, in combination with detailed study of the reactions involved will result in a report that describes the suggested chemistry in detail. Lectures, tutorials and self study. F.A. Carey and R.J. Sundberg, Advanced Organic Chemistry, Parts B. Written examination, preparation of a report. Knowledge of basic organic chemistry. mPhar Please contact the coordinator four weeks prior to the start of the course (email: [email protected]).

Computational Medicinal Chemistry and Toxicology I 435671 dr. J.N.M. Commandeur (room P.256, tel. 4447595) ir. K.A. Feenstra; dr. B.C. Oostenbrink 3 4 To get acquainted with the principles and applications of modern molecular modeling and computer assisted drug design in medicinal chemistry. content Introduction to the basics of computational medicinal chemistry. The theory and methods of modeling of ligands will be discussed. An introduction to the modeling of proteins will be given. Methods for the automatic retrieval of pharmacophore keys and other relevant features from chemical databases are


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evaluated. The use of such data, combined with methods for calculating receptor affinity, for structure-based drug design is another topic. Lectures, tutorials and self-study. H.-D. Höltje and G. Folkers, Molecular Modeling, Basic Principles and Applications, and several recent review articles. Written examination. Courses "Biologische activiteit en chemische structuur" and "Computational Chemistry". mPhar Please contact the mastercoordinator four weeks prior to the start of the course (e-mail: [email protected]). Computational Medicinal Chemistry and Toxicology II 435672 dr. J.N.M. Commandeur (room P.256, tel. 4447595) dr. B.C. Oostenbrink; ir. K.A. Feenstra; prof.dr. N.P.E. Vermeulen 6 4, 5 and 6 Providing theoretical background on molecular modeling and computer assisted drug design, and an overview of recent developments, applications and trends. Methods and techniques of molecular modeling, quantum and molecular mechanics, advanced ab initio methods, energy minimization, conformational analysis, molecular interactions, molecular dynamics simulations, free energy calculations. Protein structure prediction, sequence analysis and protein folding. Chemoinformatics: chemical databases and database searching. The use of molecular modeling and chemoinformatics for de novo drug design: molecular docking procedures and scoring functions, molecular similarity searching; structure-based de novo design, genetic algorithms; QSAR, multiple linear regression, discriminant analysis, neural networks, partial least-squares methods and molecular field analysis. Lectures, tutorials and self-study. A. R. Leach, Molecular Modelling: principles and applications (ISBN 0-58238210-6) , and several recent review articles. Written or oral examination. Basic knowledge of computational chemistry and drug design as provided in the course "Computational Medicinal Chemistry and Toxicology". mPhar Please contact the mastercoordinator four weeks prior to the start of the course (e-mail: [email protected]). Computer Graphics 400106 6 1 and 2 dr. T. Kielmann The goal of the course is twofold: • The students shall get theoretical insights and practical knowledge that allows them to implement graphics applications. • The students shall get basic knowledge about the implementation

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techniques for computer graphics and their implications on graphics hardware. The course has a top-down structure, starting with the applications. In parallel with the lectures, programming assignments need to be worked on. These assignments use OpenGL and the C programming language. Topics of the lecture are: • Graphics programming with OpenGL • Color, input, interaction • Transformations (translation, rotation, scaling, shear) • 3-dimensional viewing (projections, perspective) • Light and shading • Implementation of a renderer (clipping, anti-aliasing) • Modeling (object hierarchies, scene graphs) • Advanced topics (texture mapping, curves and surfaces) Lectures (in English) and programming assignments. Edward Angel, Interactive Computer Graphics, 3rd edition, Addison Wesley. Written exam and programming assignments. The assignments contribute 2/3 to the final grade. The exam contributes 1/3. Both parts need to be graded sufficient in order to get the credit points. Introduction to programming. mCS, fourth year (and higher) students of FEW (and other faculties). This course is given in English. Computernetwerken 400016 5 4 en 5 prof.dr.ir. M.R. van Steen Het inzichtelijk maken van de architectuur van computernetwerken. De nadruk ligt op het behandelen van de architectuur van communicatieprotocollen, zowel voor hoog- als laagniveau-communicatie. Onderwerpen die aan de orde komen zijn: de fysieke laag, de datalinklaag, de netwerklaag, de transportlaag en de applicatielaag. Voorbeelden die aan de orde komen zijn onder meer het Internet, Internet via de kabel, Bluetooth, en draadloze netwerken. Veel aandacht wordt ook besteed aan beveiligen van netwerken. Hoorcollege A.S. Tanenbaum, Computer Networks, 4th edition, Prentice-Hall, 1996. Schriftelijk. 2I, 2BI, 2MMC, 3BI Er zal de mogelijkheid worden geboden om halverwege de collegereeks een toets te doen. Het daarvoor behaalde cijfer kan worden meegenomen in het bepalen van het eindcijfer. Nadere gegevens zullen bij aanvang van het college worden bekendgemaakt. - Veronderstelde voorkennis voor het college: Datastructuren (400145) en Computerorganisatie (400017) - Vereist voor deelname aan het tentamen: Inleiding Computersystemen (400033).

subject DNA Protein Structure-Function Analysis and Prediction code 430046

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6 3 prof.dr. J. Heringa; dr. J. Kleinjung A theoretical and practical bioinformatics course on the analysis and prediction of structure-function relationships of DNA and protein molecules. The course provides an introduction to the molecular principles of structure and function, available bioinformatics analysis and prediction techniques, and biological databases. Goals: • At the end of the course, students will be aware of the major issues, methodology and . • At the end of the course, the student will have hands-on experience in molecular modeling and studying structure-function relationships. Theory: • Protein folding and energetics, experimental structure determination, protein fold families, protein structure databases, protein secondary structure prediction, fold prediction, molecular modeling, protein-protein interactions, DNA/RNA structure/function, DNA/RNA structure prediction Practical: Assignment homology modelling, Assignment immunocomplex modelling 13 Lectures (2 two-hour lectures per week) Assignment introductions, Computer practicals, Hands-on support E-course material: http://ibivu.cs.vu.nl Books: Carl Branden & John Tooze (1998). Introduction to Protein Structure. 2nd Edition or higher. Garland Science, 410 pp., ISBN 0815323050. Assignment results and oral or written exam (depending on number of course students) Bachelor Physics, Chemistry, Mathematics, Computer Science, Biology, Medical Natural Sciences. A completed course Sequence Analysis is a strong advantage. Students with Bachelor Physics, Chemistry, Mathematics, Computer Science, Biology, Medical Natural Sciences or Medicine, with a strong interest and some basic knowledge in Bioinformatics The course is taught in English. Data Mining Techniques 400108 6 1 and 2 dr. W.J. Kowalczyk The course will provide a survey of basic data mining techniques and their applications for solving real life problems. After a general introduction to Data Mining we will discuss some "classical" algorithms like Naive Bayes, Decision Trees, Association Rules, etc., and some recently discovered methods like boosting, Support Vector Machines, co-learning. In the second part of the course a number of most successful applications of data mining will be discussed: marketing, fraud detection, text and Web mining, bioinformatics. In addition to lectures there will be an extensive practical part, where students will experiment with various data mining algorithms and

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data sets. The grade for the course will be based on these practical assignments (i.e., there will be no final examination). Lectures and compulsory practical work. Ian H. Witten, Eibe Frank, Data Mining: Practical Machine Learning Tools and Techniques with Java Implementations, Morgan Kaufman, 2000. Additionally, a collection of articles in electronic form. Computerpracticum. Vereist voor deelname aan het tentamen: Kansrekening en Statistiek of Algemene Statistiek. Aanbevolen: Machine Learning. mBMI, mCS, mAI Databases II 400144 6 1 and 2 dr. W. de Jonge Some of the topics that will be treated are: disk storage, record and file organizations, index structures, query processing and optimization, transaction processing, concurrency control, recovery, object identifiers, keys, surrogates, static classes, dynamic classes, role classes. The course will consist of lectures and homework. Details about the homework will be given in the first lecture. - Elmasri & Navathe, Fundamentals of Database Systems, (fourth edition), Addison-Wesley, 2003. - Various material to be announced or made available via the Web. (See, in due time, the info made accessible via URL: www.cs.vu.nl/~wiebren) To be determined. Prerequisite knowledge: Databases I mCS This course is not necessarily given each year. (E.g. only if there are enough participants.) Denken en beslissen 815049 6 160 (3 tentamen, 20 hoorcollege, 137 zelfstudie) 1 en 2 dr. E.A. Das-Smaal Kennis opdoen over theorieën, onderzoeksmethoden en praktijk m.b.t. het menselijk oordeel, rationeel denken, dilemma´s, keuze en planning. Wat is `rationeel' denken? Wat weerhoudt ons daar zoal van? Hoe kunnen we onze denken beslisprocessen verbeteren? Hoe redeneren en kiezen we in onzekere (risico) situaties? Wat is daarbij de invloed van (morele) opvattingen en emoties? Hoorcollege. Baron, J. (2000) Thinking and Deciding (3rd ed.). New York: Cambridge University Press. tentamen Schriftelijk tentamen, open eind vragen. Het vak wordt in 2004/2005 niet gegeven, maar in 2005/2006 wel

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Design of Experiments and Analysis of Variance 400310 2 2 dr.ir. G. Jongbloed; dr. G.C. van der Veer; dr. J.F. Hoorn Learn how to design experiments and analyse the results of these by ANOVA. Not only in theory, also in practice using a statistical package. In order to be able to draw conclusions from experiments or surveys, it is necessary that the design of the study is well chosen. In this course some well known designs (completely randomized, randomized block etc.) and the associated analyses of variance are discussed. Classes The definitive choice of a text book can in due time be found on math.vu.nl/~geurt Exercises Descriptive statistics (comparable to third year course "toegepaste statistiek") mIS, mCS Homework consists of computer exercises, to be handled using the statistical package R (http://www.r-project.org/). Classes are in English. Design of Multi-Agent Systems 400054 6 2 dr. C.M. Jonker; dr. V.N. Stebletsova This course discusses the design techniques of knowledge-based systems that consist of various intelligent agents and centers around the notion of compositional architecture. The design method used is DESIRE. A number of examples of agent models and generic task models are treated. In the associated practical work in spring, hands on experience is gained in the design of compositional multi-agent and knowledge systems using DESIRE tools. Combination of lectures and practical assignments. Syllabus On the basis of both the homework assingments and a written exam. Knowledge of Kennissytemen (400126) and Logische Taal en Redeneermethoden (400043). 3AI, 3I, mCS More information can be found on: http://www.cs.vu.nl/~ovm Discrete wiskunde 400019 5 4 en 5 dr. M.L.J. van de Vel Teltheorie met genererende functies en inclusie/exclusie. Grafentheorie (Euler- en Hamiltongrafen, bomen). Stromen in netwerken met algoritmen,

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toepassingen in scheduling, grafentheorie, enzovoort. Een eerste inleiding in de coderingstheorie. Hoorcollege met practicum. Dictaat "Combinatoriek, grafentheorie en getaltheorie" (open universiteit). Nota's "coderingstheorie" worden beschikbaar gesteld. Schriftelijk. 2W, mBMI, 3Ect dr. M.L.J. van de Vel Veronderstelde voorkennis: Calculus (400013), Lineaire Algebra (400042). Distributed Algorithms 400211 6 4 and 5 prof.dr. W.J. Fokkink To obtain a good understanding of a large range of distributed algorithms, with an emphasis on algorithms that are of importance for the course Distributed Systems. Transition systems, routing algorithms, wave and traversal algorithms, election protocols, termination detection, anonymous networks, synchronous networks, fault tolerance, failure detection. Lectures and exercise classes. Gerard Tel, Introduction to Distributed Algorithms, Cambridge University Press, 2000 (2nd edition). Written examen. Data Structures (400145) and Computer Networks (400016) 3I, 3BI, 3AI, mCS Distributed Systems 400130 6 1 and 2 prof.dr.ir. M.R. van Steen Provide insight into the design and implementation of modern distributed systems. We discuss the issues concerning the development of middleware systems for largescale computer networks. Principles that are discussed include communication, processes, naming, consistency and replication, fault tolerance, and security. These principles are further explained by means of different paradigms applied to distributed systems: object-based systems (CORBA), distributed file systems (NFS), document-based systems (the Web), and coordination-based systems (publish/subscribe systems and Jini). Explicit attention is paid to the practical feasibility and scalability of various solutions. For this reason, experimental (research) systems as well as commercially available systems are discussed. Lectures A.S. Tanenbaum, M. van Steen, Distributed Systems,Principles and Paradigms, Prentice-Hall (2002) Written exam. - Computer networks (400016). - Introduction to Computer Systems

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(400033). target audience mCS remarks • More information, slides and relevant literature, can be found on http://www.cs.vu.nl/~steen/ds/ • As a pre-announcement, note that there will be no lectures in 2005/2006! Details can be found on the Web site. subject code lecturer credits period aim content

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Drug Toxicity: Basic Concepts and Experimental Approaches 435682 dr. J.N.M. Commandeur (tel. 4447595, [email protected]) 3 4 To get acquainted with basic concepts and experimental approaches in molecular toxicological research. Enzymology of biotransformation enzymes; experimental approaches to identify (iso)enzymes involved in drug metabolism, enzyme kinetics, assessment of the formation of reactive intermediates and reactions with biological macromolecules, in vitro approaches to assess toxicity and genotoxicity of drugs, biochemical mechanisms leading to cell death, introduction to toxicogenomics and proteomics factors determining organselectivity of toxicants, genetic toxicology and chemical carcinogenesis. Lectures and case-studies. Casarett & Doull's Essentials of Toxicology (ISBN 0-07-138914-8) and supplemental materials. Written examination. Course Molecular Pharmacology and Toxicology of Drugs. mPhar Please contact the mastercoordinator four weeks prior to the start of the course (e-mail: [email protected]). Dynamic Energy Budgets 470503 prof.dr. S.A.L.M. Kooijman 6 Study year 2004-2005, details will follow

content A quantitative theory for processes of energy uptake and use by organisms is discussed. The focus is on relationship between different levels of biological organization (cells, organisms, populations), the role of modelling and statistics in practical biological research and the need of a mechanistic underpinning form of tuition Tele-course with weekly meetings of reporters literature S.A.L.M.Kooijman, Dynamic Energy and Mass Budgets in Biological Systems, 2000 Cambridge University Press, Great Britain ISBN 0-52178608-8. Costs about 40 euro (paperback) mode of assessment Software package DEB tool will be used to exercise the practical application of the DEB theory entry requirements BSc Biology

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E-Business Innovation 400110 7 drs. ing. J. Gordijn 1 and 2 dr.ing. J. Gordijn; drs. E. Schulten; prof.dr. J.M. Akkermans To understand and systematically analyze the multi-disciplinary aspects (strategy, business processes, technology issues, implementation) involved in innovations with information and communication technologies (ICT) in networked businesses. We will discuss theories and practical experiences, from different disciplines and industry sectors, covering some important recent topics in electronic business: formulation of strategy ; design and evaluation of e-business models; Web-languages such as XML and their use in standardization of products (music, information); content management; organizational readiness and technology/ systems requirements; future and perspectives of electronic business; Key topics will be exercised by small classroom workshops as part of an ebusiness strategy and implementation project to be carried out by the students. Combination of lectures, topical workshops and project. Reader with recent articles and lecture materials. On the basis of e-business project and workshops to be carried out during the course. Recommended is advance knowledge equivalent to : Bedrijfsmodellering , Software Engineering. 3BI, mIS, mCS, mBMI

Encyclopedie der rechtswetenschap I (B1) 200107 8.6 mr. J. Zwart (kamer 7A-37, tel. (020) 44 46326) prof.mr. A. Soeteman; drs. A.J. Wolthuis; mr. J. Zwart week 6 - 22 Het vak Encyclopedie der rechtswetenschap I bestaat uit twee onderdelen: Geschiedenis van de rechtsfilosofie (de omvangrijkste component) en Argumentatieleer. Bij Geschiedenis van de rechtsfilosofie gaat het om kennis van een aantal belangrijke stromingen in het westerse denken over recht en staat. Bij Argumentatieleer gaat het om kennis van de verschillende wijzen van argumentatie, die bij het juridische redeneren relevant zijn, en het kunnen toepassen daarvan op eenvoudige juridische teksten. inhoud In het onderdeel Geschiedenis worden een aantal teksten van belangrijke (rechts)filosofen vanaf Plato behandeld. In die teksten komen centrale vraagstukken rond recht, staat en macht, rond waarden als vrijheid en gelijkheid, betreffende de verhouding tussen recht en moraal en dergelijke aan de orde.

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In het kader van argumentatieleer komen de volgende onderwerpen aan de orde: (juridisch) redeneren, logica en recht, tekstanalyse, analyse van (juridische) argumentatie, drogredenen. Het onderwijs in beide onderdelen van Encyclopedie I wordt verzorgd in de vorm van hoorcolleges en werkcolleges. Bij de werkcolleges, waarin intensief de voorgeschreven stof wordt behandeld, wordt een actieve voorbereiding en deelname van de student verwacht in die zin, dat hij de in de literatuur geformuleerde vragen en opdrachten vooraf schriftelijk moet beantwoorden, respectievelijk uitvoeren. Bij deze cursus wordt blackboard gebruikt. • Reader Geschiedenis van de rechtsfilosofie 2005;' • Syllabus Juridische argumentatie 2005; • Collegestof. Het tentamen Encyclopedie I wordt schriftelijk afgenomen. Bij deze cursus wordt Blackboard gebruikt. Zodra de Blackboardcursus toegankelijk is, is deze te bereiken voor studenten van de VU. algemeen (week 6 - 22) Encyclopedie der rechtswetenschap II (B2/BN2) 200206 8.6 mr.drs. W.J. Veraart (kamer 7A-35, tel. (020) 444 6325 ) prof.mr. A. Soeteman; prof.dr. C.C.J.H. Bijleveld; mr.drs. W.J. Veraart week 38 - 52 De bedoeling van het vak Encyclopedie II is handvatten aan te reiken, die de studenten helpen (beter) te gaan nadenken over een aantal fundamentele vragen met betrekking tot het recht, inzicht te krijgen in sociaalmaatschappelijke aspecten van het recht en (beter) inzicht te krijgen in normatief-ethische aspecten van het recht. De volgende thema's komen onder andere aan de orde: • De verhouding tussen recht en moraal. • De grondslagen van de democratische rechtsstaat. • De grenzen van wetgeving. • Rechtsvinding. • Sociaal-wetenschappelijke bestudering van het recht. Het onderwijs zal in de vorm van twee uur hoorcolleges per week gedurende het eerste trimester worden verzorgd. De hoorcolleges dragen een ondersteunend karakter en dienen om de stof waar nodig uit te leggen, aan te vullen en te illustreren. Tevens worden tweemaal twee uur per week werkcolleges verzorgd waarin artikelen, arresten en stellingen nader worden uitgediept. Tijdens die werkcolleges is er ruimte voor debat. • G.J. Wiarda, Drie typen van rechtsvinding, Deventer, Tjeenk Willink, 1999 (vierde druk); • A. Soeteman, De droom van recht, Utrecht, Lemme 2000/2002; • Reader Encyclopedie II 2004-2005 (verkrijbaar in de VU-boekhandel); • Syllabus Encyclopedie II 2004-2005 (verkrijgbaar in de VU-boekhandel); • Collegestof. Schriftelijk tentamen met open vragen. Zie ook de informatie bij het vak "Rechtzoeken".

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blackboard Bij deze cursus wordt Blackboard gebruikt. Zodra de Blackboardcursus toegankelijk is, is deze te bereiken voor studenten van de VU. onderwijs algemeen (week 38 - 52) voorkennisvak 200107: Encyclopedie der rechtswetenschap I (B1) naam code docenten studiepunten periode doel

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Ethics 470707 prof.dr. J.T. de Cock Buning (coördinator); drs. H.J. Bout; Gastdocenten 3 24.01.2005 - 04.02.2005 Inzicht krijgen in de ethische aspecten van biologisch onderzoek en je eigen positie hierin als professioneel bioloog/biomedicus. Het verwerven van inzicht, kennis en vaardigheden m.b.t.: • analyseren van een ethisch probleem (reflectief evenwicht) • toepassen van de ethische toolbox op je eigen onderzoeksveld • het kunnen voeren van een scherpe maar constructieve discussie over de ethische uitgangspunten en consequenties van wetenschappelijk onderzoek. Deze cursus volgt op "Geschiedenis van de wetenschap" en bouwt voort op de waarneming dat de huidige manier van wetenschapbeoefening niet van zelfsprekend is. In deze cursus staat de wetenschapper van morgen centraal (jij dus) en hoe die, behalve kundig zou kunnen werken, ook op een professionele manier verantwoordelijkheid kan nemen. Met persoonlijke opinies kom je in ethische discussies niet ver. Pas wanneer we ethische kritiek of ethische besluiten rationeel kunnen koppelen aan breed gedragen ethische beginselen (bijvoorbeeld het gelijkheidsbeginsel of het recht op privacy) hebben we een punt. Als academicus weet je meer dan anderen. Hoe ga je met deze verantwoordelijkheid om? Heeft je toekomstige werkveld (onderzoek, onderwijs, beleid, communicatie) speciale ethische hot-spots en bestaan daar misschien speciale beroepscodes voor? De antwoorden op deze vragen zullen behandeld worden aan de hand van praktijkvoorbeelden, eigen ervaring en onderzoekopdrachten. Ca. de helft van de tijd zal besteed worden aan werkcolleges (inclusief gastcolleges). De andere helft van de tijd is bedoeld om in kleine werkgroepen verdiepingsopdrachten uit te voeren. Aanwezigheid is verplicht voor alle onderdelen. Ten slotte zal je de opdracht krijgen om de integriteitsaspecten van een onderzoeksgroep aan de VU in kaart te brengen. De cursus wordt afgesloten met presentaties en een forumdiscussie met hoogleraren van de VU. reader Een korte begrippen toets wordt halverwege de cursus afgenomen. Dit cijfer wordt gemiddeld met het groepscijfer voor de projectopdracht (inhoud en presentatie). Master biologie, biomedisch, BMO, Neuroscience, Molecular Science Verplichte cursus voor alle masters in the life sciences. Inlichtingen en aanmelden via [email protected]. Geen speciale

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Evolutiebiologie 470063 prof.dr. N.M. van Straalen (cursusleider); dr. J.H.C. Cornelissen 6 14.03.2005 - 08.04.2005 Kennismaking met de principes van de evolutieleer, verwerven van inzicht in de mechanismen van soortvorming, de diversiteit en onderlinge samenhang van bouwplannen van planten en dieren. Eindtermen De student is in staat: • de belangrijkste bewijzen voor evolutie te omschrijven; • de hoofdtijdperken in de evolutionaire geschiedenis aan te geven; • de mechanismen van soortvorming te omschrijven; • zelf een fylogenetische reconstructie te kunnen maken; • de hoofdgroepen van het planten- en dierenrijk te benoemen; • de bouwplannen van algen, mossen, varens en zaadplanten te beschrijven; • de bouwplannen van de hoofdgroepen van het dierenrijk te beschrijven; • de evolutionaire lijnen binnen de gewervelde dieren aan te geven; • de evolutie van de primaten en de mens te omschrijven; • met behulp van microscoop en eenvoudig snijmateriaal de externe morfologie van planten te achterhalen; • met behulp van microscoop en snijmateriaal de bouwplannen van de hoofdgroepen van het dierenrijk te achterhalen. In de cursus worden de principes van de evolutieleer geïllustreerd, met name de organische aspecten (ontstaan van bouwplannen, onderlinge samenhang en diversiteit binnen het plantenrijk en het dierenrijk). De stof omvat de volgende onderwerpen: • Evidentie voor evolutie; • Mechanismen van soortvorming; • Invloed van geologische gebeurtenissen op evolutie; • Classificatie en systematiek; • Fylogenie; • Diversiteit van algen, mossen, varens en zaadplanten; • Diversiteit van ongewervelde dieren; • Bouwplannen van gewervelde dieren, incl. primaten; • Evolutie van de mens; Hoorcolleges (38 uur); computerpractica (8 uur, aanwezigheid verplicht); voorcolleges (8 uur, aanwezigheid verplicht); snijpractica (32 uur, aanwezigheid verplicht); computer-ondersteund leren (20 uur); excursies (12 uur, verplichte deelname); tentamen (2 uur); onbegeleide zelfstudie (40 uur). M.W. Strickberger, Evolution, 3rd Ed., 2000. ISBN 0-7637-1066-0, prijs ongeveer 45 euro en een syllabus, prijs ongeveer 10 euro. Schriftelijk tentamen en verslag over de plantkunde-, dierkunde- en computerpractica en de excursies. Verplicht voor eerstejaars bachelorstudenten Biologie. Een laboratoriumjas tijdens de snijpractica is verplicht. Snijmaterialen kunnen aangeschaft worden bij het eerste practicum (ongeveer 25 euro).

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Evolutionaire genetica 470053 dr. J.M. Kooter (contactdocent); dr. H. Schat; dr. D. Roelofs 6 29.11.2004 - 24.12.2004 Verwerven van inzicht in: • dynamische karakter van genetisch materiaal • oorzaken van genetische variatie • evolutie van genomen bij pro- en eukaryoten • vergelijkende genomics • onstaan van nieuwe eigenschappen • soortvorming • gebruik van genomische databanken • modellen van de moleculaire oorsprong van leven • reconstructie van fylogenetische bomen met behulp van het computerprogramma PAUP • manieren waarbij genetische variatie wordt gebruikt om oorzaken van stochastische en deterministische processen af te leiden • toepassing van wiskundige regels die bestaan voor het gedrag van allelen van één of twee loci in ideale populaties, en voor genen met een kwantitatief effect • verschillende vormen van selectie en theoretische onderbouwing Theorie: • Populatiegenetica • Kwantitatieve genetica • Moleculaire evolutie van genomen • Ontstaan van species • Relatie Evolutie < > Ontwikkeling (evo-devo) • Moleculaire fylogenie • Analyse van genoomsequenties en genetische variatie bij de mens • "Origin of life" en RNA wereld Practicum: • Fylogenetische reconstructies met behulp van cladistisch computerprogramma • Lab practicum: verzamelen DNA datasets Literatuur studie • Hoorcolleges (40 uur) • Werkcolleges (verplicht, 10 uur) • Literatuurbespreking (verplicht, 9 uur) • Computer Prakticum (verplicht, 9 uur) • Lab. Practicum (verplicht, 8 uur) • Videopresentaties • Zelfstudie • Ondersteuning via Blackboard (Powerpoint presentaties) • Boek: 'Evolutionary Analysis', Scott Freeman and Jon C. Herron, Prentic Hall, Derde Editie, 2004. • Syllabus met studiemateriaal uit recente literatuur en samenvattingen Schriftelijk tentamen (0.8) en een literatuurbespreking (0.2). Beide moeten voldoende zijn. Studenten Biologie en Bio-medische Wetenschappen.

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opmerkingen De cursus wordt gegeven door de afdelingen Ontwikkelingsgenetica, Ecologie en Fysiologie van planten en Dierecologie. voorkennis Alle vakken uit het eerste jaar en Moleculaire Ontwikkelingsbiologie (470038). subject code credits period lecturer aim

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Evolutionary Computing 400111 6 1 prof.dr. A.E. Eiben To learn about computational methods based on Darwinian principles of evolution. To illustrate the usage of such methods as problem solvers and as simulation, respectively modelling tools.To gain hands-on experience in performing experiments. The course is treating various algorithms based on the Darwinian evolution theory. Driven by natural selection (survival of the fittest), an evolution process is being emulated and solutions for a given problem are being "bred". During this course all "dialects" within evolutionary computing are treated (genetic algorithms, evolutiestrategieën, evolutionary programming, genetic programming, and classifier systems). Applications in optimisation, constraint handling and machine learning are discussed. Specific subjects handled include: various genetic structures (representations), selection techniques, sexual and asexual genetic operators, (self-)adaptivity. If time permits, subjects in Artificial Life and Artificial Societies, and Evolutionary Art will be handled. Hands-on-experience is gained by a compulsory pogramming assignment. Oral lectures and compulsory pogramming assignment. The official course book is A.E. Eiben and J.E. Smith, Introduction to Evolutionary Computing, Springer, 2003 (ISBN 3-540-40184-9). Slides available from http://www.cs.vu.nl/~gusz/ecbook/ecbook.html Written exam and pogramming assignment (weighted average). mBMI, 3AI, mAI, mCS

Facetten van de AI 400123 8 5 en 6 dr. V.N. Stebletsova (coördinator, e-mail: [email protected]) De doelstelling van het college is tweeledig: (1) Kennisvermeerdering. De student doet uitvoerige kennis op over de zelfgepresenteerde onderwerpen. (2) Aanleren van vaardigheden. De student vergroot zijn/haar vaardigheden op de volgende gebieden: • hoe materiaal gezocht kan worden uit (bibliotheek en WWW); • schrijven van een overzichtsartikel; • presenteren; • verwerken van evaluaties. inhoud In dit werkcollege wordt aan de hand van artikelen een overzicht gegeven van een aantal belangrijke onderzoeksthema's binnen het vakgebied Kunstmatige Intelligentie. Enkele thema's die aan bod komen zijn:

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kennisrepresentatie (-talen, -systemen, -logische beschrijvingen, enzovoorts) • redeneertypen (redeneren met onzekerheid, metaredeneren, enzovoorts) • expliciet representeren van strategische kennis • kennisverwerving Studenten leren een literatuuronderzoek uit te voeren en daar zowel schriftelijk als mondeling verslag van te doen. De docenten leveren ondersteunend materiaal voor het aanleren van deze vaardigheden. Dit vak is vooral voor diegenen die in de AI willen afstuderen: AI-studenten en Informaticastudenten met specialisatie AI. Werkgroep. Gedurende het college voert elke student twee projecten uit onder begeleiding van een docent. Elk project bestaat uit het schrijven van een eigen artikel met bijbehorende presentatie. Het uitgevoerde project wordt tijdens speciale nabesprekingsbijeenkomsten besproken en geevalueerd door een docent. H.A.J.M. Lamers, "Hoe schrijf ik een wetenschappelijke tekst?", Coutinho, Bussum 1993. Dit vak wordt beoordeeld op basis van teksten, de presentaties en participatie m.b.t. discussie en beoordeling van mede-studenten. 3AI, mCS Informatie is te vinden op http://www.cs.vu.nl/¿faai/ Veronderstelde voorkennis: Kennissystemen(400126) of Ontwerp van Multi-agentsystemen (400054). •

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Financial Risk Management 61321010 6 28 (16 hoorcollege, 12 activerende werkvormen) 4 ir. F.W. van den Berg Het vak Financial Risk Management bouwt voort op de stof van Financial Management van het eerste en tweede jaar. Waarbij in Financial Management de optiek is vanuit het financiële beheer van een niet-financiële onderneming, ligt in dit vak het accent op de beheersing van financiële risico's, de werking van financiële markten en de rol die banken en financiële instellingen daarbij vervullen. De bedoeling is studenten additionele financiële ondergrond te geven voor het goed functioneren in een (junior) management functie in de FBI sector: Finance, Banking and Insurance (banken, verzekerings-maatschappijen, investeringsbedrijven, effecteninstellingen, beurs gerelateerde instellingen (AFM, Euronext, optiehandel), pensioenfondsen en beleggingsmaatschappijen). Het vak vormt een onderdeel van het specialisatie-traject in Finance. inhoud De volgende thema's komen aan de orde: • Bepaling en beheersing van de verschillende (financiële) risico's, zoals Liquidity risk, Sovereign risk, Insolvency risk, Interest Rate risk, Foreign Exchange risk etc. inclusief behandeling van concepten als Value-at-Risk, Stress Test, Immunization, Duration, Disintermediation, Securitization. • Assset Liability management (op inleidend niveau) en (International) Financial Risk management (incl. de toepassing van derivaten zoals swaps, opties, futures en forwards) om de gevolgen van schommelingen

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in renteniveaus en valutakoersen te beperken. Bancaire kredietverlening: kredietanalyse, risico-beoordeling, besluitvorming, kredietrisicomodel, procedures, zekerheden, covenants (leningsvoorwaarden), contractuele vastlegging. • Financiële producten: overzicht van de verschillende financieringsproducten variërend van bankleningen, hypothecaire leningen, revolving credits tot medium-term notes, project-financiering, (achtergestelde) schuldbewijzen, (converteerbare) obligaties, (preferente) aandelen en overig risicodragend kapitaal; hierbij wordt tevens aandacht gegeven aan de betreffende markten, de regelgeving en de eisen aan geldnemers en geldgevers. • Verschillende 'financiële schandalen', die het gevolg zijn van onvoldoende controle: zoals Barings -- Nick Leeson; junk bonds -Michael Milken; Savings & Loans banks in USA; Wall Street crash '29 '33; Oct. 1987 crash; LTCM - Long Term Capital Mgt.; problemen bij Continental Illinois Bank, Penn Square Bank, Bankers Trust Co., BCCI, Herstatt Bank, Credit Lyonais / Slavenburg Bank; insider trading -- Ivan Boesky; derivaten problemen bij Orange County / Procter & Gamble. Het vak wordt gegeven in de vorm van hoorcolleges. Parallel aan de hoorcolleges wordt een actieve werkvorm georganiseerd waarin studenten een Case bestuderen en deze groepsgewijs schriftelijk indienen. Studenten zullen ook groepsgewijs een presentatie maken over één van bovengenoemde 'financiële schandalen'. Al het materiaal incl. het tentamen is in het Engels. De colleges worden in het Engels gegeven, indien exchange studenten aanwezig zijn, anders in het Nederlands. De bedoeling is het vak vooral te benaderen vanuit de optiek van de geldgever (kapitaal-verstrekker), waarbij het accent ligt op het verlenen van financiering aan ondernemingen, en op het management van financiële ondernemingen (met name banken). Voor de te behandelen thema's zal het volgende boek worden gebruikt: Financial Institutions Management: A Risk Management Approach, Anthony Saunders en Marcia Millon Cornett, 2nd edition, McGraw-Hill, 2003 schriftelijk tentamen 50% van het eindcijfer. presentatie "financieel schandaal" (30%) paper 20% van het eindcijfer. Dit vak is een discipllinevak voor studenten BWS. Studenten economie kunnen het vak als keuzevak opnemen mits er voldoende plaats is. hoorcollege activerende werkvormen •

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Functieleer 811003 6 168 (15 paper, 3 tentamen, 15 practicum, 24 hoorcollege, 109 zelfstudie, 2 ondersteunend college) periode 2 en 3 docenten prof.dr. J.L. Theeuwes; dr. C.N.L. Olivers

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doel Kennismaking met de psychologische functieleer: de studie van algemene menselijke gedragsfuncties, zoals waarnemen, leren, geheugen, taal, beslissen, probleem-oplossen, aandacht en motoriek. inhoud In de cursus worden o.a. de biologische basis van gedrag, perceptie, aandacht, reactieprocessen en signaaldetectie besproken. Ook komen het geheugen, taal, beslissen en probleemoplossen aan de orde. werkwijze Hoorcolleges, Blackboardpractica via de computer, schrijven van een paper over de resultaten van een zelfgedaan experiment, responsiecollege. Hoorcolleges: Er zijn in totaal 12 hoorcolleges waarin de stof op hoofdlijnen wordt doorgenomen. Blackboardpractica via de computer: Naast de colleges zijn er 10 practica. Bij elk practicum worden via de computer een aantal vragen over de behandelde stof gesteld en doet de student zelf mee aan een aantal experimenten of demonstraties die representatief zijn voor bepaalde soorten onderzoek (b.v. op het gebied van signaaldetectie, visuele waarneming, taal, geheugen en neurale netwerken). De practica zullen worden gegeven in de computerruimte van FPP. Elke student zal een eigen computer tot zijn/haar beschikking hebben en via een unieke inlognaam inloggen. De student krijgt voor elk behaald practicum een punt. Het totaal aantal punten voor de practica bepaalt 10% van het eindcijfer. Paper: Tegen het eind van de cursus maakt elke student individueel een kort, paper over een zelfstandig uitgevoerd experiment. Het paper bevat de volgende onderdelen: titel, samenvatting, inleiding, methode, resultaten, discussie en referenties. Het paper wordt zowel op inhoud als op vorm beoordeeld. Het cijfer telt eveneens voor 10% mee bij de bepaling van het eindcijfer. Het paper wordt electronisch ingeleverd via Blackboard. Responsiecollege: De collegereeks eindigt met een responsiecollege, waarin studenten vragen over de stof aandragen ter voorbereiding van het tentamen. literatuur • Ashcraft, M.H. (2002). Cognition. Upper Saddle River, NY: Prentice Hall. • Syllabus Inleiding Functieleer 2003/2004 toetsing tentamen paper Multiple choice tentamen. Het tentamen telt voor 80% mee bij de bepaling van het eindcijfer, 10% wordt bepaald door de punten voor de practica en 10% door het cijfer voor het paper. Het eindcijfer wordt afgerond op gehele getallen. opmerkingen Alle studenten volgen in principe alle onderdelen van de cursus (dit geldt ook voor AI studenten). Deelname aan de practica en het paper is verplicht. Dit betekent dat minstens één practicum voldoende gemaakt, en een paper ingeleverd moet zijn, wil het tentamencijfer (vermenigvuldigd met bijbehorend gewicht) toegekend worden. Deelresultaten blijven in principe één jaar geldig. Aan practicum en paper moet tijdens de cursus voldaan worden en kunnen niet worden ingehaald of overgedaan. Eventuele vrijstellingen kunnen schriftelijk aangevraagd worden bij de Examencommissie van de Faculteit Psychologie en Pedagogiek. Verdere details staan in de syllabus. onderwijs hoorcollege practicum zelfstudie ondersteunend college

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Geheugen 800159 4 120 (3 tentamen, 18 hoorcollege, 99 zelfstudie) prof.dr. J.G.W. Raaijmakers Student vertrouwd maken met theorieën en onderzoekmethoden op het terrein van de geheugenpsychologie. Overzicht van de verschillende benaderingen en de theoretische achtergronden binnen de geheugenpsychologie. Aan de orde komt onder andere interferentie en vergeten; aandacht en geheugen; semantisch en episodisch geheugen; impliciete en expliciete geheugentaken; herkenning en herinnering; amnesie; associatieve netwerkmodellen. Hoorcolleges. Haberlandt, K. (1999) Human memory: Exploration and application. London: Allyn & Bacon. ISBN 020518992x. N.B. Boek minstens zes weken van te voren bestellen. tentamen Schriftelijk tentamen, open vragen. U kunt zich inschrijven voor de cursus door zich als bijvakstudent bij de UvA in te schrijven. (Tel. 020-5258080 bereikbaar ma t/m vr van 9-17 uur) U krijgt dan een inschrijfnummer. Houd er rekening mee dat dit een aantal weken in beslag neemt. Met dat inschrijfnummer kunt u zich, liefst uiterlijk twee weken voor aanvang, voor de cursus inschrijven bij het Onderwijsinstituut van Psychologie. (De balie is dagelijks geopend van 1014 uur.) hoorcollege zelfstudie

Genome Analysis: Structural and Functional Genomics 430047 6 1 dr. H. de Wit dr. D. Bald; dr R. Govers; dr A.S. Groffen; prof.dr. J. Heringa A 1-month intensive course for introduction to genomics and bioinformatics techniques used to analyse and integrate genomics data sets. content Static genome analyses: DNA, RNA and protein primary, secondary, tertiary en quaternary structures; genome sequencing, methods and annotation; genome projects (bacteria, yeast, plant, animal, human), bioinformatics and databases; COG, EST, SNP, motifs Dynamic genome analyses: transcriptome (arrays en clustering, QPCR, SAGE); proteomics (mass spectrometry, arrays, 2D gel electrophoresis, homology modeling); metabolomics (methods, interpretation, databases) Functional genetics: knock-out, reporter genes, expression vectors, promoter-probe studies; reverse genetics, RNAi, transgenese Integrative genome analyses: network modelling, Metabolic Control Analysis, biochemical databases; physiomics Application areas: medical genomics; ecogenomics; sociogenomics; pharmacogenomics; biotechnological genomics; ethical aspects

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form of tuition 15 short modules, each including a lecture, (computer) practical and self study Tutorials/discussions of book material, lecture notes Computer practicals Lab demonstrations: Students follow and assist an experienced postdoc/Ph D student performing a key experiment. Data evaluation and interpretation on site. literature Powerpoint presentations via Blackboard Book: A primer of genome science. Gibson G and Muse, SV, Sinauer Associates Inc Publishers, 2002, ISBN 0-87893-234-8 (pbk). E-course material: http://ibivu.cs.vu.nl mode of assessment Exam (50%), assignments (25%) and computer analyses (25%) entry requirements Bachelor Physics, Chemistry, Mathematics, Computer Science, Biology, Medical Natural Sciences. target audience Students with Bachelor Physics, Chemistry, Mathematics, Computer Science, Biology, or Medical Natural Sciences, with a strong interest in Bioinformatics remarks The course will be taught in Dutch; provisions can be made for English speakers. Gezondheidscommunicatie 470087 drs. A.M.C. Plass; dr M. Adriaanse; drs. J. Veldhuis 6 10.01.2005 - 04.02.2005 De cursus is bedoeld voor studenten met belangstelling voor communicatieprocessen bij gezondheidsbevordering en ziekte preventie. Het doel van de cursus is om inzicht te krijgen in 1) het bevorderen van de gezondheid van de hele samenleving of specifieke groepen, 2) de interactie tussen gedrag en omgeving en 3) het ontwikkelen van gezondheidsbevorderende interventies. Na deze cursus is de student in staat: - de volgende begrippen te onderscheiden/definiëren: communicatie/voorlichting, voorzieningen en regelgeving, gezondheidsvoorlichting en gezondheidsbevordering; de verschillende niveaus van omgeving: individueel, groep, organisatie, lokaal en samenleving. - een planningsmodel toe te passen op een concreet voorbeeld en de valkuilen te onderkennen in de planning van gezondheidscommunicatie. - het belang van de analyse van gezondheidsproblemen voor de planning van gezondheidscommunicatie te onderkennen, op te kunnen stellen en de uitkomsten te interpreteren. - de gereedschappen van de voorlichter en de daarbij passende literatuur te beschrijven en toe te passen op een concreet voorbeeld. - de uitkomsten van een analyse van gedrags- en omgevingsfactoren als mogelijke oorzaak van een gezondheidsprobleem te interpreteren inhoud In deze cursus worden de definities, concepten en theorieën rondom gezondheidscommunicatie/ -bevordering uiteengezet, alsook een aantal specifieke vormen van gezondheidscommunicatie: persuasief, informatief en educatief. Naast het bieden van een theoretisch kader is deze cursus tevens


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gericht op de praktische toepasbaarheid; o.m. analyse van een specifiek gezondheidsprobleem in combinatie met het definiëren van de doelgroep en het bedenken van een strategie om deze groep voor dit gezondheidsprobleem te bereiken. • Colleges • Werkcolleges • Gastcolleges • Opdrachten • Bezoek aan gezondheidsinstellingen • Zelfstudie Syllabus en aanvullende literatuur bij de colleges Beoordeling van opdrachten plus eindpresentatie Schriftelijk tentamen: multiple choice en open vragen Cursus Communicatiewetenschappen. Derdejaars studenten Gezondheidswetenschappen Vierdejaars bètastudenten met een specialisatie Hersenen en Gedrag 813010 dr. J.F. Stins 6 168 (3 tentamen, 20 hoorcollege, 145 zelfstudie) Overzicht van de recente theorieen over de biologische basis van cognitie en emoties en van de experimentele technieken die in de cognitieve neurowetenschappen worden gebruikt. De cursus begint met een korte opfrissing van de werking van het zenuwstelsel en een introductie van de belangrijkste meettechnieken op het terrein van hersenen en gedrag. Vervolgens worden de belangrijkste bevindingen en hun verbindende theorie behandeld op het terrein van de waarneming, de motoriek, aandacht, het geheugen, spraak, bewustzijn en emotie. Hoorcollege Gazzaniga M.S., Ivry, R.B., Mangun, R.B. (2002) Cognitive neuroscience, the biology of the mind, (2e druk), W.W. Norton and Company: New York and London, plus artikelen (wordt later bekend gemaakt). tentamen Schriftelijk tentamen; open eind vragen. hoorcollege zelfstudie

Human-Computer Interaction 400312 5 2 and 3 dr. G.C. van der Veer; dr. M. van Welie Explaining the User-Centered Design process and providing understanding of the interaction between people and information systems. The main goal is to teach students how to design and evaluate interactive systems that are easy to use and able to support people and organizations using them. content The usability aspects (cognitive ergonomic aspects) of human-computer

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interaction are related to both software engineering and to human aspects. This course introduces recent theories, approaches, and sources of HumanComputer Interaction to analyze and design Complex Interactive Systems. Several relevant schools are indicated, theories and techniques are discussed, and tools and applications are illustrated. The course also introduces some relevant basic notions about psychological aspects of computer use, aspects of organisational aspects of the introduction and application of information technology, and the theoretical basis for GTA (Groupware Task Analysis) and DUTCH (Design for Users and Tasks, from Concepts to Handles). Lectures A. Dix, J. Finlay, G. Abowd, R. Beale: Human-Computer Interaction, (3rd edition), Prentice Hall, London, 2004, ISBN 0-130-461091; Lecture notes and study guide on the website www.cs.vu.nl/~mmc/mci. Written essay and an examination 2BI, 2MMC, 3AI, 3I, mCS, mIS, the examination (including an accepted essay) needs to be passed to be able to participate in the course of User-Interface Design. See on the website www.cs.vu.nl/~mmc/mci. ICT in a social context 400107 4 1 and 2 drs. W. Rekers The class consists of three parts. - Part one, taught by Jan Willem van Doorn (Director Management Development CMG), deals with commercial, social and moral aspects of the application of ICT in society. - Part two deals with ICT and the law. It is taught by staff from the Institute for Information Technology and Law,Vrije Universiteit. - Part three concerns ethics and professional codes. Lectures (in Dutch) Lecture notes (in Dutch). Written exam (in Dutch). Organisation: Teun Koetsier. None. mCS, mBMI, 3AI, mAI, mIS This class is taught in Dutch. Foreign students preferably should not include this class in their programme.

naam IT en recht (B3/M) code 200367 IT en recht is een verplicht voorsorteervak voor de afstudeerrichting IT en recht. coördinator mr. K.J. Koelman (kamer 5A-31, tel. (020) 44 46217) docenten prof.mr. H.W.K. Kaspersen; mr. A.R. Lodder; mr. K.J. Koelman; prof.mr. A. Oskamp studiepunten 6 periode week 16 - 26 doel Verkenning van rechtsvragen die aan het gebruik van IT zijn verbonden en

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verkenning van mogelijkheden om IT te zetten ten behoeve van de rechtspraktijk. In het keuzevak IT & recht wordt een overzicht gegeven van de verschillende onderwerpen die tot het vakgebied behoren en van de (rechts)vragen die op deze gebieden actueel zijn. IT & Recht gaat in brede zin over de wisselwerking tussen informatietechnologie (IT) en het recht. Deze wisselwerking werkt twee kanten op. Aan de ene kant brengt het gebruik van informatietechnologie in het maatschappelijk verkeer problemen mee waarvoor het recht een oplossing dient te vinden. Deze rechtsvragen en de antwoorden daarop behoren tot het domein van het IT-recht. Aan de andere kant kan het gebruik van informatietechnologie juridisch werk ondersteunen. De vraag op welke wijze IT kan of dient te worden ingezet ten behoeve van de rechtspraktijk of de wetenschap is onderwerp van IT voor juristen. Bij het IT recht ligt de nadruk op het recht, bij de IT voor juristen ligt de nadruk op de toepassing van informatietechnologie voor en door juristen en onder welke juridische voorwaarden IT kan worden ingezet. Een aantal onderwerpen die aan de orde komen zijn: privacy en IT-systemen, bescherming van informatie op internet door het auteursrecht, domeinnamen en de juridische bescherming tegen misbruik daarvan, het recht rond de elektronische handel, strafrechtelijke handhaving op het internet, overzicht van internet als rechtsbron en de inzet van zogeheten `intelligent agents' (slimme, zelfdenkende IT) in de rechtspraktijk. Hoorcollege. syllabus IT & recht, verkrijgbaar in de VU-boekhandel. Schriftelijk tentamen met open vragen. Om deel te mogen nemen aan IT en recht moet men het hele eerste bachelorjaar hebben afgerond of een propedeuse recht gehaald hebben. algemeen (week 16 - 26) Informatieverwerking 815048 6 178 (3 tentamen, 18 hoorcollege, 157 zelfstudie) 2 en 4 dr. S.A. Los Kennismaking met de structuur en dynamiek van informatieverwerkingsprocessen. Structurele aspecten worden toegelicht aan de hand van discussies over informatieverwerkingsstadia en evidentie voor een centrale bottleneck. Dynamische aspecten worden toegelicht aan de hand van discussies over inhibitoire controle. Hoorcollege Reader met artikelen tentamen Tentamen met open vragen. hoorcollege zelfstudie

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Information Representation/ Multimedia 1 471015 dr. G.C. van der Veer; dr. J.F. Hoorn; J. Smit 6 10.01.2005 - 04.02.2005 In deze cursus wordt het begrip representatie systematisch behandeld, zowel vanuit de Psychologische kant van menselijke waarneming en informatieverwerking, als vanuit de kant van het ontwerpen van representaties met behulp van verschillende technieken. De cursus bevat theorie betreffende deze onderdelen met opgaven per onderdeel alsmede een ontwerpproject dat in groepen van ca. 3 personen zal worden uitgevoerd. Aanwezigheid is verplicht, en de cursus zal ca. 40 uur werk per week vereisen. literatuur Zie http://www.cs.vu.nl/~gerrit/Communicatie-Afbeeldingen toetsing De toetsing bestaat uit een combinatie van beoordelingen van: • huiswerkopgaven • presentatie eindproject • documentatie eindproject

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Inleiding (B1) 200101 5.8 mr. J. Zwart (kamer 7A-37, tel. (020) 444 6326) week 36 - 40 De student maakt kennis met alle onderdelen van het recht waar hij of zij in het eerste jaar mee geconfronteerd wordt. Centraal in het vak Inleiding staat het juridisch proces. Mede aan de hand van een aantal concrete gevallen, die in werkgroepen besproken zullen worden, wordt geïllustreerd hoe in strafrecht, in burgerlijk recht, in bestuursrecht en in Europees recht de procesgang is. Duidelijk zal ook worden dat in het proces bepaald wordt wat recht is. Maar daarvóór moet er altijd ook al recht zijn. Aandacht wordt daarom ook geschonken aan een eerste benadering van wat recht is en hoe recht tot stand gekomen is. Ook een aantal rechtshistorische aspecten van het proces wordt behandeld. Iedere week wordt zes uur hoorcollege en vijf uur werkcollege gegeven. Daarnaast is ruimte gereserveerd voor begeleiding door het mentoraat en excursies. Bij de cursus wordt blackboard gebruikt. Het te bestuderen materiaal is samengebundeld in een syllabus Inleiding, te verkrijgen bij de VU boekhandel. De collegestof is eveneens verplicht. Schriftelijk tentamen. De eerste vier weken van de studie wordt een allereerste oriëntatie in het recht gegeven. Het vak wordt onder verantwoordelijkheid van de sectie Encyclopedie gegeven door alle afdelingen en secties die eerste jaars onderwijs verzorgen. Ook worden onderdelen verzorgd door het mentoraat. Bij deze cursus wordt blackboard gebruikt. Zodra de blackboardcursus toegankelijk is, is deze te bereiken voor studenten van de VU. algemeen (week 36 - 40)

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Inleiding Beleidswetenschappen 470556 prof.dr. J.T. de Cock Buning 7 06.09.2004 - 08.10.2004 • Inzicht verwerven in beleidsprocessen; • Trainen in projectmatig werken in een praktijksituatie; • Trainen in interviewtechnieken en andere communicatieve vaardigheden; • Opdoen van ervaring met het schrijven van een beleidsadviesrapport. In deze cursus verdiep je je in de verschillende theoretische concepten rondom beleidswetenschappen, zowel op overheidsniveau als op instellingsniveau. dit deel van de cursus duurt een week en wordt afgesloten met een tentamen. Middels een projectopdracht leer je daarna deze concepten toe te passen op een praktijksituatie. Een groep van ongeveer 10 deelnemers wordt geconfronteerd met een actueel beleidsprobleem van een externe opdrachtgever van bijvoorbeeld het ministerie LNV of van de Nederlandse Patienten/Consumenten Federatie. Gevraagd wordt als een adviesteam te gaan functioneren en geheel zelfstandig in vier weken een beleidsadviesrapport voor te bereiden en te presenteren aan de externe opdrachtgever. Zelfstudie; werkcolleges; projectopdracht. Prof.dr. A. Hoogerwerf en prof.dr. M. Herweijer, Overheidsbeleid: Een inleiding in de beleidswetenschap, ISBN: 90-422-0157-6, prijs ongeveer 50 euro. Syllabus moet aangeschaft worden, kosten ongeveer 5 euro. Individuele toetsing door middel van een tentamen, individuele beoordeling aan de hand van individuele producten en het functioneren in de onderwijsgroep en een afgeleide van de beoordeling van groepsproducten. Onderdeel van de M-variant van de algemene Masters Biologie, Biomedische wetenschappen en van de Bèta brede Masters. Verplichte cursus in de Master Beleid, management en ondernemerschap voor natuur en levenswetenschappers. Inlichtingen en aanmelden via [email protected]. Bachelor vakken: 'Biologie, beleid & (kennis-)management' of 'Biomedisch beleid en (kennis-) management' of 'Beheer en beleid in de gezondheidswetenschappen'. Andere studierichtingen in overleg. Inleiding Organisatie en Management 470557 drs. M.B.M. Zweekhorst 5 11.10.2004 - 29.10.2004 • Inzicht verwerven in organisatiestructuren en managementprocessen; • Inzicht en praktijkervaring in projectleiderschap van een projectteam; • Trainen in communicatieve vaardigheden; • Kunnen reflecteren op de eigen stijl van leidinggeven; • Opstarten en begeleiden van een beleidsproject; • Teamrollen bij projectmanagement; • Omgaan met conflicten.

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inhoud In deze cursus verdiep je je gedurende de eerste week in de verschillende theoretische concepten rondom managementstudies en organisatiekunde, zowel op overheids- als op instellingsniveau. Daarna zal je twee weken als projectleider fungeren van één van de projectteams behorende bij de tweedejaarscursus Biomedisch/Biologie Beleid en (Kennis)management, Beheer en beleid in de gezondheidswetenschappen of de derdejaarscursus Duurzaamheid waarvoor een beleidsadviesrapport geschreven moet worden rondom een maatschappelijk biomedisch/biologisch probleem. Iedere dag zullen de projectleiders onder leiding van een docent reflecteren op het functioneren van het projectteam alsmede op hun eigen functioneren (ook in relatie tot persoonlijke leerdoelen). Vragen en problemen zullen eveneens aan de orde komen. werkwijze Zelfstudie; responsie- en werkcolleges; projectopdracht. literatuur Henry Mintzberg, Organisatiestructuren, ISBN: 90-5261-050-9, prijs: 32 euro. T. Gevers en T. Zijlstra, Praktisch Projectmanagement: handleiding bij het voorbereiden, realiseren en beheersen van projecten, 1995. Uitgever: Academic Service, Eindhoven, prijs: 17,50 euro. toetsing Individuele toetsing door middel van tentamen en aan de hand van functionering als projectleider. doelgroep Onderdeel van de M-variant van de algemene Masters Biologie, Biomedische wetenschappen en van de Bèta brede Masters. Verplichte cursus in de Master Beleid, management en ondernemerschap voor natuur en levenswetenschappers. opmerkingen Inlichtingen en aanmelden via [email protected] voorkennis Cursus Inleiding Beleidswetenschappen. naam code studiepunten periode docent doel inhoud


Inleiding besliskunde 400029 6 1 en 2 prof.dr. H.C. Tijms Kennis en inzicht hebben in het opstellen van OR-modellen en hun oplossingsmethoden. In deze inleiding zal het accent liggen op het opstellen van wiskundige modellen voor diverse optimaliseringsproblemen. Daarnaast worden de basisideeën besproken van de wiskundige technieken waarmee deze modellen worden doorgerekend. In het college is het gebruik van educatieve software voor het oplossen van de wiskundige optimaliseringsproblemen geïntegreerd. De volgende onderwerpen komen aan de orde: - lineaire programmering (modelformuleringen, simplex algoritme, schaduwprijzen, gevoeligheidsanalyse) ¿ netwerkanalyse (kortste-pad algoritme, mimimumopspannende boom, Steiner probleem) - geheeltallige en combinatorische optimalisering (modelformuleringen, 0-1 variabelen, branch-en -bound methode ) - sequentiele beslissingsproblemen (dynamische optimalisering)vooraadtheorie ( de EOQ-formule, Silver-Meal heuristiek). Hoorcollege: 2 uur per week; practicum: 2 uur per week. H.C. Tijms, Inleiding in de Operationele Analyse, Epsilon , Utrecht, 2002 Via twee deeltentamens aan het einde van periode 1 en periode 2. 1BWI, 1W

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Inleiding in de Psychologie voor AI 811012 4 112 (3 tentamen, 16 hoorcollege, 93 zelfstudie) dr. W. Donk Een eerste kennismaking met het vakgebied psychologie waarbij niet alleen zal worden ingegaan op inhoudelijke aspecten van het vakgebied maar ook op het belang van de verschillende methodologische aspecten die een rol spelen bij het doen van onderzoek binnen de psychologie. Na een inleiding (theorievorming binnen de psychologie, onderzoeksmethoden) komen aan de orde de biologische basis van gedrag, motivatie, leren, sensorische processen, perceptie, geheugen, denken en kennis, en intelligentie. Hoorcolleges Gleitman, H., Fridlund, A.J., & Reisberg, D. (2004). Psychology (6th edition). New York: Norton & Company Inc. tentamen Schriftelijk tentamen met multiple-choice vragen. Inschrijving voor tentamen vanaf 40 werkdagen tot aan de vijfde werkdag voor de dag waarop het tentamen plaatsvindt. Inschrijving tentamen bij het studiesecretariaat van FPP, via het tentameninformatiesysteem "TISVU". hoorcollege zelfstudie Inleiding programmeren I 400150 4 1 en 2 ir. M.P.H. Huntjens Het doel van de cursus is algoritmisch leren denken, gestructureerd leren programmeren en het verwerven van inzicht in de manier waarop computers gebruikt kunnen worden om problemen op te lossen. primitieve types, declaraties, expressies, toekenningsopdracht, keuzeopdrachten, herhalingsopdrachten, methoden, I/O, arrays, classes, instanties van classes (objecten), standaard classes String en Math, ontwerpen maken, twee-dimensionale arrays, meerdere objecten tegelijk gebruiken in een programma. Hoorcollege met een parallel practicum. Een nog nader te bepalen boek dat op het eerste college verkocht zal worden en het dictaat Practicumhandleiding Inleiding Programmeren. Via practicumopgaven. 1I, 1BWI, 1AI, 1IK Geen Inleiding programmeren II 400151 3 4 ir. M.P.H. Huntjens

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zie inleiding programmeren I recursie, lineair search, binary search. hoorcollege zie inleiding programmeren I schriftelijk 1I, 1BWI, 1AI, 1IK Inleiding programmeren I (400150) Inleiding programmeren II practicum 400085 2 4 ir. M.P.H. Huntjens het opdoen van praktijkervaring met de in de colleges Inleiding Programmeren I en II behandelde stof afsluitende opgave over de stof van Inleiding Programmeren I + een opgave over het onderwerp recursie practicum Practicumhandleiding Inleiding Programmeren via practicumopgaven 1I, 1BWI, 1AI, 1IK vereist voor deelname aan het practicum: Inleiding programmeren I (400150).

naam Inleiding wetenschapsfilosofie code 150006 docent dr. J.A. Radder (kamer 13a-32, tel. (020) 44 46689, e-mail [email protected]) studiepunten 6 periode 30.08.2004 - 22.10.2004 doel Het op een inleidend niveau verwerven van kennis van en inzicht in de belangrijkste stromingen en problemen in de hedendaagse wetenschapsfilosofie. Dit impliceert ook kennis en inzicht ten aanzien van de verwevenheid van wetenschap en technologie en de ethische en maatschappelijke vragen die deze oproepen. inhoud De volgende onderwerpen komen aan de orde: • De klassieke wetenschapsfilosofie; • Het historische en sociologische wetenschapsonderzoek; • De problematiek van realisme en reductionisme; • Filosofie van de sociale en menswetenschappen; • De relaties tussen wetenschap en technologie; • Maatschappelijke en ethische vragen rond wetenschap en technologie. werkwijze Hoor- en werkcollege. Per week zijn er zes contacturen. In 2x2 uur worden twee aspecten van het betreffende onderwerp behandeld. De andere twee uur worden besteed aan opdrachten, oefening, video's e.d. literatuur De verplichte literatuur bestaat uit het boek van Gerard de Vries, De ontwikkeling van wetenschap (Groningen: Wolters-Noordhoff, alleen de 3e of hogere druk) en uit de bij de VU-boekhandel verkrijgbare reader Inleiding Wetenschapsfilosofie. Zie voor de volledige literatuurlijst de studiehandleiding.

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toetsing Schriftelijk tentamen over de collegestof en literatuur. Uitvoeren opdrachten tijdens colleges. doelgroep BA1-studenten wijsbegeerte en andere belangstellenden. onderwijs Dit college wordt in het studiejaar 2004/2005 zowel in voltijd als in deeltijd gegeven. Voor de exacte dag(en) en tijd(en) verwijzen wij u naar het rooster. naam Inleiding wijsgerige antropologie code 150005 docent dr. L.D. Derksen (kamer 13a-40, tel. (020) 44 46684, e-mail [email protected]) studiepunten 6 periode 28.03.2005 - 27.05.2005 doel Dit college is bedoeld als een eerste oriëntatie in wijsgerige theorieën over de mens en als een introductie tot theoretische benaderingen van het vak. inhoud In Explaining Consciousness, The Hard Problem zijn artikelen opgenomen die geschreven zijn door vooraanstaande filosofen op het gebied van 'philosophy of mind', waaronder David Chalmers, Daniel Dennett, Patricia Churchland, en Francis Crick. Het hersenen-geest probleem wordt besproken vanuit diverse perspectieven. Het boek bevat benaderingen vanuit de filosofie maar zoekt ook naar antwoorden in vakgebieden zoals neurofysiologie, cognitieve wetenschap en de biologie. werkwijze Hoor- en werkcollege. Probleemgericht college. literatuur Jonathan Shear, red., Explaining Consciousness, The Hard Problem. Cambridge, Massachusetts/London, England, MIT Press, 1997. Paperback editie, 1999. toetsing Schriftelijk tentamen. onderwijs Dit college wordt in het studiejaar 2004/2005 zowel in voltijd als in deeltijd gegeven. Voor de exacte dag(en) en tijd(en) verwijzen wij u naar het rooster. naam Inleiding wijsgerige ethiek code 150007 docent dr. A.C.M. Roothaan (kamer 13a-27, tel. (020) 44 46680, e-mail [email protected]) studiepunten 6 periode 25.10.2004 - 17.12.2004 doel Vertrouwd raken met ethische begrippen en stromingen. Kennis verwerven van hedendaagse stromingen in de ethiek, en van hun wijsgerige inhoud. Door gezamenlijke discussie leren welke standpunten in ethische casussen kunnen worden ingenomen. inhoud Naar aanleiding van casussen uit de gezondheidsethiek worden hedendaagse ethische stromingen onder de loep genomen. Dat wil zeggen: zowel de stromingen die de laatste decennia het beeld van de ethiek hebben bepaald (waarin zelfbeschikking van mondige mensen het uitgangspunt is en waarin gezocht wordt naar principes voor het maken van goede keuzen), alsook stromingen die zoeken naar aanvullingen hierop, om meer recht te doen aan de situatie van zogenaamde 'wilsonbekwamen' en om zicht te krijgen op de relaties met anderen en op de persoonlijke levensloop, die mede de context van morele keuzen bepalen. Veel aandacht zal besteed worden aan de wijsgerige wortels van deze stromingen, zoals de filosofie van Kant, maar ook 20e eeuwse wijsgerige stromingen zoals fenomenologie, hermeneutiek 170

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en existentialisme. werkwijze Hoor- en werkcollege. literatuur • Reader met teksten; • G. Widdershoven, Ethiek in de kliniek, Boom, 2000. toetsing Schriftelijk tentamen. onderwijs Dit college wordt in het studiejaar 2004/2005 zowel in voltijd als in deeltijd gegeven. Voor de exacte dag(en) en tijd(en) verwijzen wij u naar het rooster. subject code credits period lecturers aim content

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Integrative Bioinformatics and Genomics 430049 6 5 prof.dr. H.V. Westerhoff; dr. B.M. Bakker; dr. J.L. Snoep A 1-month intensive course providing an introduction to cell biological networks. Theory: The course gives an introduction to the behavior of intracellular networks, including metabolic pathways, signal transduction chains, gene expression pathways and their hierarchical organization. Metabolic and Hierarchical Control Analysis, Biological Non Equilibrium Thermodynamics, Genetic Network Analysis, Elementary Mode Analysis, Flux (Balance Analysis) will be explained and practiced. The levels of genomics (genome, transcriptome, proteome, metabolome and function) and their interrelationships will be clarified, both theoretically and experimentally. Practical: • inspection experiments performing flux and metabolite; measurements and subsequent regulation analysis; inspection experiments; designing network targeted inhibitors of parasites; flux analysis on the basis of a set of computer data; control analysis on the basis of earlier experimental results; • extra assignment integrative bioinformatics for bioinformatics master students (1 ECTS) Lectures Tutorials/discussions of book material, lecture notes Web-courses (www.siliconcell.net ) Computer practicals Lab-inspection work: Students follow and assist an experienced postdoc/Ph D student performing a key experiment. Data evaluation and interpretation on site. Reader (10 euro) E-course material: http://www.bio.vu.nl/hwconf/teaching/Mathbiochemie/; www.siliconcell.net Books: Chapters from:Understanding the Control of Metabolism (Fell, D) Portland Press; Metabolic Engineering in the Postgenomic Era (Kohlodenko & Westerhoff, Editors), Horizon Bioscience; Thermodynamics and Control of Biological Free-energy transduction (Westerhoff and Van Dam), Elsevier Written exam Bachelor Physics, Chemistry, Mathematics, Informatics, Biology, Medical Natural Sciences, or equivalent;

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target audience Students with Bachelor Physics, Chemistry, Mathematics, Biology, Medical Biology with a strong interest in the interface between these disciplines and bioinformatics remarks The course is taught in the English language and involves extensive direct contact with the professors and associate professors. subject code credits period lecturers aim

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Intelligent Interactive Distributed Systems 400152 8 2 and 3 dr. F.M.T. Brazier; dr. B.J. Overeinder; dr. N.J.E. Wijngaards The aim of this course is twofold. The first aim is to acquire knowledge and insight in conceptual design of knowledge intensive systems in multi-agent environments. The second aim is to acquire skills in the following areas: analysing and modelling complex domains and complex tasks in general;analysing and modelling multi-agent environments in particular, analysis of recent relevant literature; writing reports; presenting results. In this course the main focus is on analysing, modelling and implementing realistic, interactive, intelligent, distributed systems. A realistic example domain involving trading agents is explored in the course and (mostly) implemented. A combination of lectures, meetings and practical work. To be announced during the course (notably articles). On the basis of exercises. The courses Distributed Systems (400130) and BusinessMOdelling and Requirements Engineering (400010) are recommended for Computer Science students. The courses Design of Multi-agent systems (400054) and Behavioural Dynamics (400113) aanbevolen are recommended for Artificial Intelligence students. mCS, mAI Attendance of lectures/meetings is obligatory; pre-registration is obligatory for this course.

Intelligent Web Applications I 400153 8 1 and 2 prof.dr. F.A.H. van Harmelen; dr. H. Stuckenschmidt under discussion How to intelligently utilize huge, rich and shared web resources and services taking into account heterogeneity of sources, user preferences and mobility. content The World-Wide Web today is a huge network of information resources which was built in order to broadcast information for human users. Consequently, most of the information on the Web is designed to be suitable for human consumption: The structuring principles are weak, many different kinds of information co-exist, and most of the information is represented as free text. With the increasing size of the web and the availability of new technologies such as mobile applications or smart devices, there is a strong

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need for making the information on the World Wide Web accessible to computer programs which search, filter, convert, interpret, and summarize the information for the benefit of the user. The Semantic Web is a synonym for a World Wide Web whose accessibility is similar to a deductive database where programs can perform well-defined operations on well-defined data or even derive new information from existing data. This course addresses methods to create and use such a Semantic Web. It extends and complements the "Web-based Knowledge Representation" course by. I. deepening the understanding of the formal foundations of knowledge representation and reasoning on the web A) Semantics of web languages B) Reasoning in Semantic Web LanguagesII. investigating typical application scenarios concerned with the use of distributed and heterogeneous information on the web C) Information Extraction D) Information Integration E) Information Access Intensive lectures (in English) 3 times per week in the first 3 weeks, and a practical assignment in the following weeks Set of research paper. Web-based Knowledge representation (required). Knowledge Based Systems (preferred). mAI Interpersoonlijke communicatie 471007 drs. J.H. Zloch; drs. I. Pauw 3 01.11.2004 - 12.11.2004 Ontwikkelen van: • inzicht in interactieprocessen/het verloop van de communicatie in een groep; • vaardigheden met betrekking tot het goed kunnen communiceren in een groep, in het bijzonder in een leidinggevende rol. In deze module gaat het om het zicht krijgen op interactiepatronen die zich afspelen in een groep. Je eigen communicatieaandeel als groepslid en je mogelijkheden een 'leidersrol' te vervullen komen aan de orde. Er wordt gewerkt aan de hand van het Model Interpersoonlijk Leraarsgedrag, dat wordt gebruikt in de lerarenopleiding maar dat ook bruikbaar is in andere situaties. Effecten die gedragingen van de 'leider' hebben op de leden van de groep worden geanalyseerd. Daarnaast wordt 'effectief' gedrag getraind. Werkcolleges/workshops waarin videobeelden worden geanalyseerd; herkennen van interactiepatronen; training/oefenen van gedragsvaardigheden. • F. Oomkes: communicatieleer, ISBN 9053525378 • Artikelen die in de bijeenkomsten worden uitgereikt Op basis opdracht (bijvoorbeeld via videofragment), waarvan de resultaten in het portfolio zichtbaar worden gemaakt.

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voorkennis Geen. subject code co-ordinators lecturers credits period aim content

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Introduction to Bio-Complexity 430050 prof.dr. S.M. van der Vies; prof.dr. C.F. Schmidt prof.dr. S.M. van der Vies; prof.dr. C.F. Schmidt; dr. R.J. Wijngaarden; guests 6 1 To gain an understanding of the fundamental properties of complex systems with an emphasis on biology and the typical scientific approaches that are used for research on complex systems Complexity is the rule rather than the exception in biology, society economics and many other areas. The scientific study of complex systems, be they ocean currents or molecules, neurons in the brain or bits within a computer, requires new approaches to quantitatively describe the collective behaviour of many basic but strongly interacting units. Basic concepts of complexity will be discussed and specific examples will be considered, with a focus on biological systems. We will browse through Nature from small- to large-scale phenomena, from the (self)organisation of atoms into biological macromolecules, proteins into extensive functional structures in cells, and cells into organisms. Pattern formation will be a recurring theme, visible in simple non-equilibrium chemical reactions, in the shapes of bacterial colonies or the stripes of zebras. • Lectures • Tutorials/discussions of book material, lecture notes • Self-study Review papers and syllabus, books will be recommended for additional reading written examination Bachelor Medical Natural Sciences, Physics, Chemistry, (Medical) Biology or Pharmaceutical Sciences MSc Students with Bachelor in Medical Natural Sciences, Physics, Chemistry, (Mecial) Biology, Pharmaceutical Sciences with an interest in the interface between Physics, Chemistry and Biology Applications should be directed to Prof. van der Vies (phone. 47548, E-mail: [email protected]) or Prof. Schmidt (phone: 47972, E-mail: [email protected]) at the latest two weeks before the starting date of the course.

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Kansrekening en Statistiek 400178 4 5 Dit college is gericht op onderdelen van de kansrekening en statistiek, die een rol spelen in de informatica en de kunstmatige intelligentie (bijvoorbeeld bij software-reliability en expertsystemen). De eerste helft van de stof geeft

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werkwijze literatuur toetsing doelgroep docenten voorkennis naam code studiepunten contacturen periode docent doel inhoud werkwijze literatuur toetsing opmerkingen onderwijs

een inleiding in de kansrekening, in de tweede helft komt de statistiek aan de orde. Een werkcollege biedt gelegenheid beter te leren omgaan met de begrippen. Hoorcollege met werkcollege. We gebruiken het boek "Mathematical Statistics and Data Analysis" van John A. Rice Schriftelijk. mCS Onbekend Calculus Kennisrepresentatie 815050 6 168 (3 tentamen, 18 hoorcollege, 147 zelfstudie) 4 en 5 dr. E.A. Das-Smaal Verdieping van kennis en inzicht op dit gebied. Centraal staat de vraag naar het karakter van mentale representaties. Zowel de statische, lange termijn kennisbasis, als de dynamische, voor tijdelijk gebruik geconstrueerde representaties komen aan de orde. Hoorcollege Reader tentamen Tentamen met open vragen. In het jaar 05/06 wordt het vak niet gegeven, in het jaar 06/07 wordt het vak in periode 1 en 2 geroosterd. hoorcollege zelfstudie

Kennissystemen 400126 4 4 dr. M. Klein Het ontwikkelen van kennissystemen wordt in dit college behandeld als een activiteit op twee niveaus: het ¿symboolniveau¿ en het ¿kennisniveau¿. Op het symboolniveau gaat het om de representaties die kunnen worden gebruikt om verschillende soorten kennis te representeren en ermee te redeneren. Het college behandelt de representatie en het redeneren over tijd en ruimte en het redeneren met onzekere of onvolledige kennis. Op het kennisniveau wordt een analyse gemaakt van de verschillende soorten taken die door een kennissysteem kunnen worden uitgevoerd en van het soort kennis die voor een bepaalde taak benodigd is. Voorbeelden die in het college ter sprake komen zijn classificatie, configuratie en diagnose. Voor elk van deze taken zullen de relevante kennistypen worden besproken, evenals een aantal praktische systemen. werkwijze Hoorcollege en opdrachten. literatuur Mark Stefik, Introduction to Knowledge Systems, Morgan Kaufmann Publishers, 1995.

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toetsing Schriftelijk. doelgroep 2BWI, 3I, 1AI, 3MMC opmerkingen • De praktische vaardigheden van het bouwen van een kennissysteem komen aan de orde in Project Kennissystemen (400201), 7 sp - Teletop en http://www.cs.vu.nl/vakgroepen/ai/education/courses/ks/ • Zie ook blackboard pagina. naam code studiepunten docent inhoud

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Keuzemodulen 990004 4 Diverse Docenten Het Onderwijscentrum VU biedt keuzemodulen aan. Eén van de mogelijkheden is één of meer van de door het instituut aangeboden keuzemodulen te volgen. De dio kan er echter ook voor kiezen om een bepaald aspect van een schoolvak of een aspect van het leerproces van leerlingen of van het coachen van leerlingen nader te bestuderen. Door het Onderwijscentrum VU worden onder andere de volgende keuzemodulen aangeboden: • Docent in Europa • Lesgeven in het HBO • Excursie Gent • Petje af • Lesgeven in het VMBO Binnen de clusters en vakken worden keuzemodulen aangeboden als: • Veldwerkweek • Klassieke Culturele Vorming (KCV) • Culturele en Kunstzinnige Vorming (CKV) Wordt bij aanvang van de cursus bekend gemaakt. opdracht In het voorjaar worden het definitieve aanbod van keuzemodulen bekend gemaakt. De inschrijving voor de modulen vindt dan plaats. werkcollege werkcolleges vinden plaats op maandag

Knowledge Management and Modeling 400125 6 1 and 2 prof.dr. J.M. Akkermans; dr. A.T. Schreiber Knowledge management is a relatively new discipline which has as its aim the efficiency improvement of the production factor "knowledge" and of the related business processes (knowledge creation, distribution, application and maintenance). The course "Knowledge Management and Modeling" is concerned with the organizational aspects of knowledge management, as well as the question how knowledge can be described with the support of modern information-modeling techniques. The notion of pattern-based knowledge modeling is a key issue in the knowledge management process. Students carry out a knowledge-management project in small project groups in a problem domain and organization of choice. form of tuition Lectures, assignments, group project. subject code credits period lecturers content

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literature Schreiber, Akkermans, Anjewierden, de Hoog, Shadbolt, van de Velde, Wielinga: Knowledge Engineering & Management. The MIT Press, Cambridge MA, 2000, ISBN 0-262-19300-0. mode of assessment Assignment, project reports, self evaluation. target audience mIS Kwaliteitszorg van de informatievoorziening 400195 5 1 en 2 B. Derksen (hoofddocent. e-mail: [email protected]); J.J. Wintraecken (e-mail: [email protected] e-mail: [email protected]); G. Brilleman (e-mail: [email protected]) inhoud Het vak beoogt: • de student bewust te maken van een veranderende gebruikersattitude wat betreft de informatievoorziening; • de student methodes te leren om structureel de kwaliteit van de informatievoorziening te onderzoeken en te verbeteren. • De student bekent te maken met de praktijksituatie Steeds meer professionele organisaties die zich bezighouden met de informatievoorziening gaan over tot certificering van hun producten en hun dienstverleningsproces. De kwaliteitsbeoordeling neemt een steeds belangrijkere rol in voor de informatievoorziening. Evaluatie, assessment, kwaliteitsbeheersing, kwaliteitsborging en integrale kwaliteitszorg zijn echter nog geen "levende" termen. Dit college beoogt daarin verandering aan te brengen. De leerstof wordt behandeld in 10 hoorcolleges waarin de volgende onderwerpen aan de orde komen: 1 Kwaliteit en kwaliteitszorg 2 Kwaliteitsinspectie, kwaliteitsbeheersing, kwaliteitsborging en integrale kwaliteitszorg 3 De infrastructuur van de informatievoorziening en de levenscyclus ervan 4 De kwaliteit van de informatievoorziening 5 Kwaliteitszorg van de informatievoorziening Het accent van het vak ligt bij het in de praktijk toepassen van de in de colleges aangeleerde theorie, begrippen, principes en instrumenten. werkwijze De hoorcolleges worden gegeven aan de hand van overheadsheets, waarvan de kopieën aan de student ter beschikking worden gesteld. De in de hoorcolleges verkregen kennis dient te worden aangescherpt en aangevuld door het bestuderen van door de docent uit te reiken studieteksten. De opdrachtteams De studenten dienen zich te organiseren in opdrachtteams. Het aantal te vormen teams en het aantal studenten per team is afhankelijk van het aantal inschrijvingen voor het vak en wordt tijdens een van de colleges meegedeeld. De teams dienen de volgende opdrachten uit te voeren: • het uitwerken van een aantal cases die tijdens de colleges worden aangereikt en het presenteren van de uitwerkingen; • het uitvoeren van een opdracht na afloop van de hoorcolleges. toetsing De mondelinge toets

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De kennis van en het inzicht in de tijdens de colleges gepresenteerde en in de reader weergegeven stof, wordt tijdens een mondelinge toets geverifieerd. De toetsen vinden plaats op nog nader vast te stellen tijdstippen De opdracht Ten tijde van de colleges dient door ieder team een opdracht te worden uitgevoerd. Dit kan een opdracht bij een externe organisatie (buiten de Universiteit) zijn, of een interne opdracht binnen de Universiteit. De docent maakt de opdrachten tijdens een van de colleges bekend. De teams dienen uiterlijk tijdens het zesde college aan de docent bekend te maken welke opdrachten zij kiezen. Hierbij geldt het principe "wie het eerst komt, het eerst maalt". Van iedere opdracht dient een verslag te worden gemaakt en een presentatie te worden verzorgd. De presentaties worden gegeven tijdens een "terugkomdag". In de mate van het mogelijke zijn de opdrachtgevers van de externe opdrachten bij de presentaties aanwezig. Het verslag dient uiterlijk een werkweek voorafgaand aan de presentatie bij de docent en, voor externe opdrachten, bij de externe opdrachtgever te zijn ingeleverd. Bij vragen, onduidelijkheden, problemen en dergelijke bij de uitvoering van de opdracht dient de teamleider contact op te nemen met de docent. Bij de eindpresentatie dient, waar mogelijk, gebruik te worden gemaakt van de theorie, de termen, de begrippen en de instrumenten uit de hoorcolleges en de verplichte literatuur. De eindpresentatie dient goed gedocumenteerd en op zichzelf leesbaar te zijn. De eindpresentatie mag niet langer dan dertig minuten duren (na verloop van dertig minuten zal de docent de presentatie afbreken). De voor het verslag en de presentatie te maken kosten zijn voor rekening van de studenten. doelgroep 3BI naam Let alg: Taalgebruikstheorie code 500013 docenten dr. R.J.U. Boogaart; vacature; dr. J. Noordegraaf; drs. M.C.G. Schasfoort; prof.dr. W.P.M.S. Spooren; dr. D.M.F. Torck studiepunten 5 contacturen 28 (28 college) periode 4 doel Door kennis te maken met wetenschappelijke benaderingen van taalgebruik ontwikkel je inzicht in hoe mensen zich talig gedragen. Je leert hoe je je tegenover je eigen taalgebruik en dat van anderen analytisch en kritisch op kunt stellen. Je zult je er daarbij van bewust worden dat waarden en normen voor taalgedrag in je eigen sociale omgeving sterk kunnen verschillen van de waarden en normen in andere maatschappelijke verbanden. inhoud Je maakt kennis met opvattingen over en inzichten in taalgebruik. De centrale gedachte is dat taalgebruikers hun taalgebruik - en daardoor hun taal - afstemmen op hun gesprekspartners: taalgebruik komt in interactie tot stand. Het college zal inzicht geven in wat taalgebruikers doen, in de wijze waarop ze handelen en in de vraag waarom ze doen wat ze doen. Je maakt kennis met begrippen die van belang zijn voor verdere studies in de 178

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taalkunde en taalbeheersing en voor het onderwijs in de taalvaardigheid. Verder maak je kennis met methodes om taalgebruik te onderzoeken. Daarvoor moet je onder andere gespreksmateriaal verzamelen en een analyse maken van enkele taalgebruiksaspecten. Er zijn zeven hoorcolleges van twee uur en zeven werkcolleges van twee uur. Theo Janssen (ed.), Taal in gebruik. Een inleiding in de taalwetenschap, Den Haag: Sdu Uitgevers, 2002 Een schriftelijk tentamen in de laatste week van de collegeperiode (1/2 van het cijfer); een individueel werkstukdossier (1/2 van het cijfer). Het dossier bevat een uitwerking van verschillende opdrachten die op de blackboardsite te vinden zijn. Ze kunnen in de collegevrije weken in juni gemaakt worden. Zowel voor het tentamen als voor het werkstukdossier moet een voldoende behaald worden. Verplicht voor 1e jaars studenten CIW en Nederlands. Naar keuze voor studenten die geïnteresseerd zijn in menselijke communicatie. • Het vak maakt deel uit van de mini-minor Taalgebruikstheorie/Vlootschouw taalbeheersing. • Het vak maakt deel uit van de minor Algemene taalwetenschap, inl./Taalgebruikstheorie • Inschrijven verplicht via TISVU Ja college Lex: Het relationele lexicon 540150 dr. H.D. van der Vliet 5 14 (14 werkcollege) 4 Inzicht krijgen in verschillende mogelijkheden van representatie van de betekenis van woorden en woordgroepen. We gaan aan de hand van artikelen na op welke manieren de betekenis van woorden gerepresenteerd kan worden en wat de voor- en de nadelen van de verschillende opvattingen en werkwijzen zijn. Daarbij zal de nadruk liggen op relationele beschrijvingsmodellen. Werkcollege, met referaten. Studenten presenteren en bediscussiëren de artikelen. Wordt op de eerste bijeenkomst bekendgemaakt Werkstuk en opdrachten Masterstudenten Taalwetenschap-Lexicologie en Terminologie, studenten AI Inschrijven verplicht via TISVU werkcollege 540115: Lex: Het computationele lexicon 540117: Lex: Lexicale semantiek 1 Lex: Lexicale semantiek 1 540117 dr. H.D. van der Vliet 5 28 (28 college)

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periode 1 doel De bedoeling van dit college is de studenten wegwijs te maken in theorieën met betrekking tot woordbetekenis. De nadruk ligt daarbij op de Cognitieve Semantiek. Er wordt ook nagegaan in hoeverre binnen de lexicografische praktijk met de desbetreffende theorie rekening zou moeten worden gehouden. inhoud Behandeling van verschillende stromingen in de lexicale semantiek, van de historisch- filologische aanpak via de structurele, de generatieve, de logische tot en met de cognitieve benadering. literatuur Een verzameling artikelen, waaronder enige hoofdstukken uit Cognitieve Linguistics, Craft and Cruse, Camebridge Univ.Press, 2004 toetsing Take-home tentamen doelgroep 2e jaars studenten Taalwetenschap; studenten met een talenstudie opmerkingen • Lexicale semantiek 1 en 2 (540118) kunnen als minor gevolgd worden • Inschrijven verplicht via TISVU onderwijs college naam code docent studiepunten contacturen periode doel inhoud toetsing doelgroep opmerkingen onderwijs voorkennisvak naam code docent studiepunten contacturen periode doel inhoud

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Lex: Lexicale semantiek 2 540118 dr. H.D. van der Vliet 5 14 (14 college) 2 Voortzetting en uitdieping Lexicale semantiek 1 Een overzicht van de stand van zaken in het onderzoek rond de lexicale semantiek. De nadruk ligt daarbij op de betekenis van werkwoorden. Take-home tentamen 2e jaars studenten Taalwetenschap; studenten met een talenstudie • Lexicale semantiek 1 en 2 kunnen als minor gevolgd worden • Inschrijven verplicht via TISVU college 540117: Lex: Lexicale semantiek 1 Lex: Terminologie, inleiding 540114 dr. H.D. van der Vliet 5 28 (28 hoorcollege) 5 Kennismaking met het vakgebied terminologie. Dit college is een inleiding in het vakgebied Terminologie. Dit vakgebied wordt gedefinieerd en gesitueerd ten opzichte van de Lexicologie, de Linguïstiek, Vertaalwetenschappen en andere verwante disciplines. Er wordt een overzicht gegeven van ontwikkelingen in theorie en praktijk, met name de situaties waarin termen gebruikt worden en de functie die zij er vervullen. Verder wordt een aantal basisbegrippen geïntroduceerd zoals term, vaktaal, concept, conceptsysteem, waarmee de specifieke eigenschappen van termen ten opzichte van de algemene woordenschat worden belicht. Tot slot worden methoden voor terminologiebeschrijving besproken en is er aandacht voor het vertalen van termen.

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Hoorcollege met verwerkingsopdrachten Wordt op het eerste college bekendgemaakt Schriftelijk tentamen, einde periode 5 2e jaars studenten Taalwetenschap - Lexicologie; studenten met een talenstudie opmerkingen Inschrijven verplicht via TISVU onderwijs hoorcollege subject code credits period lecturer aim content


Logical Verification: Applied Logic 400115 6 1 and 2 dr. F. van Raamsdonk introduction to type theory and the proof-assistant Coq A proof-assistant is used to check the correctness of a specification of a program or the proof of a theorem. The course is concerned with the proofassistant Coq which is based on typed lambda calculus. In the practical work, we learn to use Coq. One of the exercises is concerned with the correctness proof of the specification of a sorting algorithm, from which a functional program is extracted. In the course, we focus on the Curry-Howard-De Bruijn isomphism between proofs on the one hand and lambda-terms (which can be seen as functional programs) on the other hand. This is the basis of proof-assistants like Coq. We study various typed lambda calculi and the corresponding logics. This is a 13-weeks cours with 4 hours class every week: 2 hours theory and 2 hours practical work. Course notes. A written examination plus exercises. It is imperative to have a "pass" for the exercises. Inleiding logica (400119) mCS, mAI, mMath

Logische taal en redeneermethoden 400043 5 1 en 2 dr. M.L.J. van de Vel Het gelijktrekken van wiskundige voorkennis, het opdoen van ervaring met precieze en meer geformaliseerde logische en wiskundige taal, en het leren analyseren en opbouwen van correcte redeneermethoden. inhoud Er worden nadere omschrijvingen en notaties gegeven voor basistechnieken met betrekking tot verzamelingsoperaties, relaties en functies, en de logische opbouw van uitspraken. Verder worden de principes achter een aantal argumentatie- en redeneermethoden besproken, waaronder ook inductie. Er wordt met veel voorbeelden geoefend, zowel in een formele context als in meer praktische contexten. Dit oefenen omvat het zelf leren formuleren van een redenering in een correcte taal en in het aaneenschakelen van correcte redeneerstappen bij het oplossen van een gegeven probleem. werkwijze Hoor-/werkcollege.


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literatuur Collegedictaat. toetsing Schriftelijke toets en ingeleverde huiswerkopgaven. doelgroep 1I, 1AI, 1IK naam code studiepunten contacturen periode docent doel

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Logistics 61331060 6 28 (16 hoorcollege, 12 casecollege) 4 prof.dr. A.R. van Goor • Het kennisnemen van de logistieke concepten die gebruikt kunnen worden bij een logistieke doorlichting van productie-, handels- en distributiebedrijven. • Het kunnen werken met een aantal logistieke instrumenten. A. Logistiek concept van inkoop, productie, fysieke distributie en reverse logistics • logistieke terminologie en kosten; • concurrentiestrategie en logistiek; • raakvlakken met marketing, inkoop en ICT • integraal logistiek concept; • vraagvoorspelling en voorraadbeheer; • inkooplogistiek en E-procurement • produktielogistiek, MRP, JIT, en OPT. • reverse logistics B. Distributielogistiek • fysieke distributie en productiekarakteristieken; • vestigingsplaatskeuze en materials handling; • economic trade off management; • DRP I en DRP II • traffic management en EDI; • Supply Chain Management • Contract logistics/ logistieke dienstverlening. wordt later bekend gemaakt schriftelijk tentamen weging 70% Cases weging 30%. hoorcollege casecollege

Machine Learning 400154 6 1 and 2 dr. M.A. Keijzer The course Machine Learning (ML) surveys methods of acquiring and/or modifying theories from observations. content Learning is one of the fundamental attributes of intelligence, and ML is currently the most active area of research in AI. The main topics covered in the course are: - Concept Learning and the General-to-Specific Ordering -

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Decision Tree Learning - Artificial Neural Networks - Evaluating Hypotheses - Bayesian Learning - Instance-Based Learning - Genetic Algorithms - Learning Sets of Rules - Reinforcement Learning Lectures with parallel assingments Machine Learning , TomMitchell, Mc Graw Hill, 1997 ISBN 0-07-042807-7 Assignments None 3BWI, 2AI, 3AI, mCS This course is given in English. Look at: http://www.cs.vu.nl/~elena/ml.html Management en organisatie 1.1 60111030 3 30 (24 hoorcollege, 6 activerende werkvormen) 1 drs. G.P. Melker; M.J. Visser • Het ontwikkelen van je theoretische kennis op het gebied van strategisch management en besluitvorming; • Het ontwikkelen van vaardigheden om relevante informatie te verzamelen en te analyseren met betrekking tot actuele cases; • Het ontwikkelen van je schriftelijke rapportagevaardigheden en je presentatie-vaardigheden In dit vak staat het interne en externe functioneren van een bedrijf in de markt en de maatschappij centraal. De organisatie wordt gezien als een samenwerkingsverband van belanghebbenden gericht op het realiseren van specifieke organisatiedoelen (marktpositie, winst, maatschappelijke verantwoordelijkheid et cetera). Binnen het vak wordt ingegaan op strategisch management, strategieformulering, besluitvorming en denkrichtingen binnen het vakgebied van management en organisatie. Tijdens de activerende werkvormen word je in de gelegenheid gesteld om de aangereikte theorie toe te passen met behulp van actuele cases. Dit kunnen recente krantenartikelen zijn of andersoortige voorbeelden uit de praktijk. De activerende werkvormen hebben dan ook een hoog praktijkgehalte • Keuning, D., & Eppink, D.J. (2004). Management & Organisatie. Theorie en Toepassing. Houten: Educatieve Partners Nederland; hoofdstukken 1, 2 en 7 en appendix 1 • Keuning, D., & Eppink, D.J. (2004). Werkboek Management & Organisatie. Houten: Educatieve Partners Nederland • Keuning, D. (2004). Management & Organisatie. 33 Cases. Houten: Educatieve Partners Nederland • Hagel III, J., & Singer, M. (1999). Unbundling the corporation. Harvard Business Review, maart-april, p. 133 - 141 • Zie verder de studiewijzer van blok 1.1 schriftelijk tentamen Tijdens de activerende werkvorm zullen de studenten werken aan een praktijkcase waarmee de studenten reeds een indruk krijgen op welke wijze de aangereikte leerstof kan worden toepast binnen organisaties. Ook in blok 2.1 en 2.4 zal het vak Management & Organisatie worden verzorgd. De complexiteit van de cases neemt naarmate de blokken vorderen steeds verder toe. Uiteindelijk ben je in staat om de verschillende inzichten en concepten

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op het gebied van management en organisatie te integreren en om de aangereikte theorie te vertalen in praktisch toepasbare oplossingen. Bij het oplossen van cases zal gebruik worden gemaakt van de `casemethodiek-invijf-stappen¿. onderwijs hoorcollege activerende werkvormen zelfstudie 66 uur naam code studiepunten periode

Master Project Artificial Intelligence 400285 30 4, 5 en 6

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Master Project Business Mathematics and Informatics 400286 37 4, 5 en 6

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Master Project Information Sciences 400284 30 4, 5 en 6

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Mathematical System Theory 400180 6 4 and 5 drs. A.N. Vardy; dr. A.C.M. Ran Vele verschijnselen worden gekenmerkt door een dynamische ontwikkeling waarbij we geïnteresseerd zijn in een input/outputgedrag. Voorbeelden zijn bijvoorbeeld te vinden in de natuur (denk aan mechanica, biologie, ecologie), in de techniek (luchten ruimtevaart, werktuigbouwkunde) en ook in de economie (macro-economische ontwikkelingen, conjunctuurbewegingen, trend- en seizoeninvloeden in vraag en aanbod, productiesystemen). Systeemtheorie houdt zich bezig met de modelvorming, schatting en regeling van dynamische verschijnselen. In het college worden de volgende onderwerpen behandeld: modellen en representaties (lineaire systemen, input-output, toestand, overdrachtsfunctie, stochastische systemen, spectrum), regeling (stabiliseren, terugkoppeling, poolplaatsing, dynamisch programmeren, het LQprobleem), en identificatie (spectraalanalyse, maximale aannemelijkheid, Kalman- filter, modelreductie). Toepassingen liggen op het gebied van optimale besluitvorming en voorspellen. Er is een hoorcollege van twee uur per week. Verder is er een vragenuur voor het bijbehorende computerpracticum, dat een verplicht onderdeel van de cursus is. Hierbij wordt gebruik gemaakt van het pakket Matlab. C. Heij, M.A. Kaashoek en A.C.M. Ran: Lineaire Systemen (collegedictaat). Via computerpracticum. 3W, mBMI, mMath - Veronderstelde voorkennis: Lineaire Algebra (400042) en Algemene Statistiek (400004). - Vereist voor deelname aan het tentamen: Wiskundige

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Analyse II (400088) of Analyse BWI I (400005) en Lineaire Algebra (400042). subject code credits period lecturer aim

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Modeling of Business Processes 400157 6 1 and 2 prof.dr. G.M. Koole The goals of this course is to obtain insight in mathematical modelling and the way it's used in practice, to get acquainted with a number of application domain where mathematical modeling is used, and to explore some stochastic solution methods. This course consists of three parts: - An overview of mathematical modelling, including aspects such as the economic context, the modelling itself, the choice of solution method, decision support systems, and the role of the applied mathematician in the whole solution process. - A discussion of solution techniques from operations research and applied probability. Some queueing models are dealt with in detail. - An overview of the use of models in several application domains: call centers, reliability, yield management, production scheduling, supply chain planning, field service, etc. Parts 2 and 3 are integrated. In addition, some guest lectures are given by consultants from Dutch companies. Lectures. Lecture notes (available electronically). Weekly assignments and written exam. Stochastische Methoden (400074) or equivalent. mMath, mBMI and exchange students. • Lectures are in English. • Registration for this course via https://tisvu.vu.nl/HTM/TISVULogin.htm, one week prior to the start. For the course schedules please refer to http://www.few.vu.nl/onderwijs/roosters.

Molecular Biology 430056 J.C. Vos J.C. Vos; guests 6 4 To gain knowledge and insight into the practical and theoretical aspects of recombinant DNA technology and its applications with a special emphasis on site-directed mutagenesis and gene expression. content Theoretical focus will be on the analysis of genetic variation and the analysis of gene expression by virtue of e.g. Northern blotting, reverse transcription PCR, and differential screening. Also, the use of reporter genes constructs for the study of promoters, in vivo transposon mutagenesis and in vitro DNA mutagenesis will be covered. A part of the course will be devoted to


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acquiring practical expertise with some of the molecular biological techniques. • Lectures • Self-study • Work at the bench 'From Genes to Genomes; Concepts and Applications of DNA Technology'by Jeremy Dale en Malcolm von Schantz, Wiley Europe, ISBN: 0-471- 49782- and scientific papers. written examination Prior experience in gene cloning and content of the course Principles in Molecular Biochemistry (MSc MNS-MBC programme). MSc Students with Bachelor in Medical Natural Sciences, Chemistry, Physics, Pharmaceutical Sciences or (Medical) Biology. Application for this course should reach Dr. Vos (tel 47569, [email protected]) at least 2 weeks before the starting date of the course. Molecular Pharmacology and Toxicology of Drugs 435674 dr. M.J. Smit (tel. 4447572, [email protected]) dr. J.N.M. Commandeur; dr. R.A. Bakker; dr. M.J. Smit 6 2 To obtain knowledge of fundamental principles and aspects of drug action within the field of molecular pharmacology and toxicology. Most drugs display their pharmacological actions following the interactions with receptor proteins. As for the molecular pharmacological aspects the mechanisms by which these drugs act with respect to their therapeutic application will be studied. Aspects of modern technologies, such as highthroughput screening and pharmacogenomics, within the process of drug discovery and target finding will be addressed. The following aspects will be studied for molecular toxicology: role of ADME-Tox in drug development; pharmacokinetics; factors determining bioavailability and distribution of drugs; enzymology of drug metabolising enzymes; biotransformation reactions of drugs; molecular basis of drug-drug interactions and interindividual differences of drug action; molecular and biochemical mechanisms underlying toxicity and carcinogenicity. Lectures, tutorials and self-study. Rang, Dale and Ritter - Pharmacology 5th edition (ISBN 0-443-07145-4) and Casarett & Doull's Essentials of Toxicology (ISBN 0-07-138914-8). Written examination. Knowledge of basic principles of drug action. mPhar Please contact the mastercoordinator four weeks prior to the start of the course (e-mail: [email protected]). Morphology 539170 prof.dr. G.E. Booij 10 28 hours (28 lecture)

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period 4 and 5 aim To provide an overview of current issues in morphological theory, with focus on the position of morphology in the grammar, and the interaction between morphology, phonology, syntax, and semantics. content Program: the following topics will be dealt with: syntagmatic versus paradigmatic approaches to morphology; morphological typology, theoretical models (distributed morphology, realizational morphology, construction grammar), similarities and differences between morphology and syntax, morphology and syntactic valency, morphology and constructional idioms, the interface between morphology and phonology. form of tuition Interactive lectures literature • Geert Booij (2004), The Grammar of Words, Oxford: OUP • Andrew Spencer (1991), Morphological Theory, Oxford: Blackwell, ch. 5-8 • Ray Jackendoff (2002), Foundations of Language, Oxford: OUP, Chapters 5-8 • Some recent articles on morphological topics (to be selected) mode of assessment Each student will have to do a presentation of a chapter from the reading list. At the end of the seminar, each student has to write an essay on a morphological topic; which makes clear the student understands the literature discussed in the seminar. target audience 3rd year students Linguistics remarks Registration via TISVU obligatory class lecture naam code studiepunten periode docent inhoud

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Multimedia Authoring I -- Web3D/VRML 400050 6 1 dr. A. Eliens In deze cursus wordt een praktische inleiding gegeven tot Web3D, en meer specifiek tot het gebruik van de Virtual Reality Modeling Language (VRML). Aan de orde komen de constructie van 3D objecten, deplaatsing van objecten in 3D ruimte, materiaal en belichting, alsook animatie en interactie. Tevens zal ingegaan worden op het gebruik van graphics, audio en video voor de bekleding van 3D virtuele werelden. Ook wordt de programmatische interface tot VRML behandeld, met name prototypes en scripts. De opdrachten omvatten een 3D product demo en een infotainment applicatie. hoorcollege en simultaan practicum Online syllabus. mondeling of schriftelijk tentamen, practicum opdracht 2MMC, mCS, en overige belangstellenden Multimedia Authoring II -- Virtual Environments 400051 6 2 dr. A. Eliens; dr. Z. Huang

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inhoud The subject of the course is virtual environments. The theoretical part treats research aspects and applications of virtual environments. The focus of this course is on the application of intelligent agent technology in the development of virtual environments, for example programming the behavior of avatars and the creation of information services. In the practical part, students will gain experience with the 'intelligent multimedia platform', which offers a combination of logic programming and Web3D, as well as with the design and realization of a virtual environment using this technology. werkwijze lectures/practicum literatuur Syllabus. toetsing essay and practicum assignment doelgroep 3MMC, mCS, and interested students voorkennis Multimedia Authoring I, or proficiency with VRML subject code credits period lecturers content

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Multimedia Design Casus 400158 6 2 and 3 dr. A. Eliens; dr. G.C. van der Veer; dr. J.F. Hoorn The assignment in the multimedia casus is to develop a virtual environment for some cultural or governemental institute or company. The practicum takes the form a stage, in which external supervision plays an important role. In the multimedia casus, techniques learned in previous courses (see the resources) will applied to create the application. At the start of the course the actual assignment will be determined. Examples of possible assignments are: the development of a virtual exposition hall for the Dutch Royal Museum of the Arts, a virtual city square, which gives information about both the present and the past, a virtual shop, with online buying facilities, or an online broker, which offers facilities for inspecting houses. Practicum/stage. online studyguide assignment Multimedia Authoring I -- Web3D/VRML (400050) and Multimedia Authoring II -- Virtual Environments (400051) 3MMC Museologie en buitenschoolse educatie 471026 drs I. van Veen; drs. B.J. Regeer; dr. P.J.A. van Mensch 6 29.11.2004 - 24.12.2004 Eindtermen na afloop van de module hebben de studenten: • inzicht in de rol die musea, bezoekerscentra en tentoonstellingen (kunnen) spelen bij het populariseren van wetenschappelijke informatie, zowel nationaal als internationaal;

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inzicht in de rol die musea kunnen spelen bij het maatschappelijk debat over natuurwetenschappen. • kennis van theorie en praktijk van educatie naast educatie op school; zoals bijvoorbeeld educatie in musea, op televisie, via de radio, debatteren, spellen of gedrukte informatie, maar ook volwasseneneducatie. na afloop van de module kennen de studenten: • de globale geschiedenis en ontwikkeling van musea in de 20e en 21e eeuw. na afloop van de module kunnen de studenten: • natuurwetenschappelijke musea, bezoekerscentra en tentoonstellingen kritisch beoordelen; • een bezoekersonderzoek opzetten, uitvoeren en beoordelen; • een tentoonstellingsplan maken en beoordelen. werkwijze Hoor- en werkcolleges, excursies. literatuur • Reader wordt bij college verstrekt; • Museumjaarkaarten voor de studenten (zelf aanschaffen). toetsing Aan de hand van praktijkopdrachten •

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Network Programming 400052 9 5 and 6 dr.ir. G.E.O. Pierre Let the student get familiar with the development of network applications. The course discusses a number of programming facilities for the development of network applications. Attention is paid to designing and implementing applications with threads, sockets, RMI/RPC, CGI/BIN, servlets, PHP. In addition, attention is paid to security and modern enabling technologies like peer-to-peer systems. Lectures combined with lab assignments. Internetworking with TCP/IP, Vol. III: Client-Server Programming and Applications, Linux/Posix Sockets Version, by Douglas E. Comer and David Stevens, Prentice Hall, 2001, ISBN 0-13-032071-4. Lab assignments plus an exam - Introduction to Computersystems (400033). - knowledge of C - (preferred:) Computer Networks, Distributed Systems. mCS

Network Security 400127 6 4 and 5 dr. B. Crispo Introductive and broad course on security. At the end of the course students will be able to understand and apply the basic notions of cryptography, understand the most common protocols, mechanisms and security architectures, in particular the ones related to network security. content The course covers a wide spectrum of security issues. It starts by introducing the fundamental cryptographic techniques and

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algorithms used today. Then it addressed the issues raised by the design of security protocols and in particular authentication protocols. Specific examples of the most significant protocols (Needham-Schroeder, X.509, SSL IPSec) will be thoroughly discussed. Trust infrastructures needed for those protocols to run and the main key management problems solved by those infrastructures will be then analyzed. The course presents an example of such infrastructure based on symmetric-key that is Kerberos and some example of infrastructures based on public-key will be presented, in particular PGP and X.509. Some important aspects tightly related to network security such as firewall, worms, mobile code, and intrusion detection will be also covered. In the last part of the course access control mechanisms and web security issues will be also explained. Lectures To be determined. Written exam None 3I, mCS, 3BI, 3AI, mBMI Neural Networks 400132 6 5 dr. E. Marchiori Introduce the student to the most popular neural network models and their applications. The course provides an introduction to the basic neural networks architectures and learning algorithms. The following main topics are covered: single layer perceptrons, LMS algorithm, multilayer perceptrons, radial-basis function networks, support vector machines, self-organizing maps, discrete Hopfield model, brainstate- in-a-box model. Moreover, typical applications of neural networks are discussed. Lectures. Slides available during the course. No obligatory text book. See http://www.cs.vu.nl/¿elena/nn.html for suggested text books. Assignments. None 3AI, 3I, 3BWI, mCS, mBMI Lectures in English. Neural models of cognitive processes 815051 6 158 (2 deeltentamen, 10 werkcollege, 4 practicum, 16 hoorcollege, 126 zelfstudie) 1 en 2 dr. M. Meeter Kennismaking met de basisprincipes van Neurale Netwerken en hun toepassing binnen de cognitieve psychologie In het eerste gedeelte van de cursus worden de volgende onderwerpen behandeld: McCulloch-Pitts neuronen, perceptrons, feedforward netwerken,

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opmerkingen onderwijs


form of tuition literature mode of assessment entry requirements target audience subject code credits period adviser lecturer content

recurrente netwerken, Hopfield netwerken, zelf organiserende netwerken en leerregels, waaronder error back-propagation. Daarna worden door middel van referaten verschillende toepassingen van neurale netwerken besproken binnen de cognitieve psychologie, bijvoorbeeld op het gebied van aandacht, geheugen en taal. werkcolleges met groepsreferaten en een kort practicum m.b.t. error backpropagation. Boek (wordt nader bekend gemaakt) en syllabus. deeltentamen 2 deeltentamens van elk 2 uur deeltentamen 2 deeltentamens van elk 2 uur Twee deeltentamens met open vragen, en presentatie. Het vak wordt in 2004/2005 niet gegeven, maar wel in 2005/2006. hoorcollege werkcollege practicum zelfstudie Object-Oriented Software Development 400137 4 1 and 2 dr. R. Laemmel The course gives a survey of the most important notions in object-oriented software development. Concepts such as data abstraction, encapsulation, inheritance and polymorphism play a central role. Moreover, object-oriented design and analysis techniques will be discussed, and the application of these concepts in the development of frameworks and reusable software. Also subjects such as design patterns, components, refactoring, aspect-oriented programming, distributed object technology and software architecture will be covered. Lectures. There is a separate practical work for 9 cp. A. Eliëns, Principles of object-oriented software development., AddisonWesley 2000. ISBN 0-201-39856-7. Essay. Java or C++. 3I, mCS, 3BI, mBMI, mAI Object-Oriented Software Development Practical 400164 9 5 and 6 dr. A. Eliens (for multimedia-related assignments) dr. R. Laemmel The practical OOSD gives students the opportunity to gain experience with object-oriented analysis, design and implementation. In fact, the practical is not restricted to "pure" OO technologies such as Java and .NET, but coverage of advanced technology such as adaptive, aspect-oriented and generative programming is intended as well. The typical project will start from some

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piece of technology, an application domain, and a concrete goal. It will then work out this project at the levels of requirements, design and implementation. See http://www.cs.vu.nl/~ralf/oo Documentation and realization. Java or C++. 3I, mCS, 3BI, mBMI, mAI Ondernemerschap I 470558 drs. E.H.P.M. Claassen; Gastdocenten 3 01.11.2004 - 12.11.2004 • Inzicht verwerven in diverse aspecten van ondernemerschap; • Het creëren van een kansrijk businessconcept. In deze cursus zal je aan de hand van reele casestudy een innovatief businessplan toetsen op haalbaarheid, met de intentie het businessconcept daadwerkelijk te realiseren. Deskundigen uit de praktijk zullen hierin fungeren als jouw businesscoach. De cursus wordt gegeven in de vorm van gastcolleges en workshops waarbij telkens een aspect van het ondernemen aan de orde komt. de colleges combineren state of the art business concepten, vertaald naar de behoefte van startende ondernemingen, met praktische tips van ondernemers die al verder op weg zijn. Daarnaast zijn er interactieve en doelgerichte workshops over waardering van bedrijfstechnologie, het vaststellen en realiseren van 'milestones', het inschatten van faal- en slaagkansen, het binnenhalen van eerste ronde financiering en andere onderwerpen die cruciaal zijn bij het realiseren van een businessplan. Gastcolleges en workshops onder begeleiding van ervaren businesscoaches. In kleine groepjes zullen de studenten een businessplan toetsen op haalbaarheid. Reader. Aanschaf van de reader is tijdens het eerste college. Prijs ongeveer 15 euro. Individuele toetsing door middel van een mondeling tentamen. Onderdeel van de M-variant van de algemene Masters Biologie, Biomedische wetenschappen en van de Bèta brede Masters. Verplichte cursus in de Master Beleid, management en ondernemerschap voor natuur en levenswetenschappers. Inlichtingen en aanmelden via [email protected]. geen Ondernemerschap II 470559 prof.dr. J.F.G. Bunders-Aelen 9 10.01.2005 - 18.02.2005 • Kennismaken met de diverse aspecten die bij het opstarten van een (biomedisch) bedrijf een rol spelen; • Leren integreren van beta-kennis met kennis uit andere vakgebieden zoals management en organisatiekunde, financiële administratie, marketing, octrooirecht etc.;

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Het opdoen van ervaring met zowel het schrijven van een businessplan als een interdisciplinair onderzoeksrapport; • Experimenteren met communicatieve- en managementvaardigheden, zoals vergaderen, organiseren, mondelinge en schriftelijke presentatie en taakverdeling. Deze cursus volgt op Ondernemerschap I. Onder begeleiding ga je in een groep met ongeveer 7 medestudenten een fictief, eigen (biomedisch) bedrijfje vormgeven. Hiervoor moet naast een businessplan ook een interdisciplinair onderzoeksrapport opgesteld worden, waarin de keuzes van het businessplan onderbouwd worden. Het businessplan zal gepresenteerd worden aan een panel van investeerders en andere deskundigen. Zelfwerkzaamheid onder begeleiding van coaches. In kleine groepjes zullen de studenten een businessplan en een interdisciplinair onderzoeksrapport maken. Tevens vindt een aantal vaardigheidstrainingen plaats. Syllabus. Aanschaf van de syllabus is tijdens het eerste college. Prijs ongeveer 15 euro Individuele beoordeling aan de hand van het individuele werk, het functioneren in de onderwijsgroep en een afgeleide van de groepsbeoordeling op basis van het gemaakte businessplan en het onderzoeksrapport. Onderdeel van de M-variant van de algemene Masters Biologie, Biomedische wetenschappen en van de Bèta brede Masters. Keuzecursus in de Master Beleid, management en ondernemerschap voor natuur- en levenswetenschappers. Inlichtingen en aanmelden via [email protected]. Inleiding beleidswetenschappen, Inleiding organisatie & management en Ondernemerschap I. Andere studierichtingen in overleg. •

inhoud


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Onderzoeksmethoden I voor AI: Dataverzamelingstechnieken 812025 6 vacature (coördinator); dr. F.A. Goossens; dr. C. Bruinsma; dr. J.R.P.B. de Mey i) Kennis van standaard dataverzamelingtechnieken en onderzoeksopzet. ii) Kennis van belangrijkste typen validiteit In deze cursus worden de technieken behandeld waarmee een theoretische of diagnostische vraagstelling kan worden geoperationaliseerd in een concrete onderzoeksopzet. Het verzamelen van testresultaten, observaties en interviews, vormt een belangrijk onderdeel van psychologisch en pedagogische onderzoek en de werkzaamheden van praktisch werkzame psychologen en pedagogen. Het accent in dit studieonderdeel ligt op de methodologische principes die ten grondslag liggen aan de onderzoeksopzet, de constructie en het gebruik van psychologische tests, vragenlijsten, systematische observatie en interviews als methode van gegevensverzameling. Hoorcollege Wordt nader bekend gemaakt Multiple-choice-tentamens. Inschrijving voor tentamen vanaf 40 werkdagen tot aan de vijfde werkdag voor de dag waarop het tentamen plaatsvindt. Inschrijving tentamen bij het studiesecretariaat van FPP, via het tentameninformatiesysteem "TISVU".

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Onderzoeksmethoden II-A: Data-analysetechnieken 812005 12 5 en 6 dr. S.E. Huismans (coordinator) Uitbreiding van kennis van statistiek en deze kennis leren toepassen in de onderzoekssituatie: 1. Uitvoeren statistische toetsen met SPSS 2. Uitbreiden kennis statistiek met name op het gebied van lineaire modellen 3. Leren gebruiken van Factoranalyse voor de ontwikkeling van meetinstrumenten 4. Toepassen van klassieke testtheorie De cursus bevat 8 modules (ieder module is 40 uur), onderwerpen: Omgaan met SPSS. Beschrijving van data. Uitvoeren t-toetsen APA normen. Chikwadraattoetsen. Variantieanalyse met één factor. Regressieanalyse. (enkelvoudig) Regressieanalyse. (Multipel). Correlatierekening. Toepassing regressieanalyse. SPSS (Vergelijken van modellen, Variantieanalyse met meer factoren, Covariantie-analyse) Factoranalyse en Schaalanalyse. Nonparametrische statistiek. Robuuste schatters. • Prakticumgroepen van maximaal 25 studenten, tweemaal twee uur per module • Colleges twee maal twee uur per module van 40 uur. • Toetsen op Blackboard. • Schriftelijk tentamen. • Wonnacott, Th.H. en Wonnacott, R.J., Introductory Statistics. (Hoofdstuk 10 t/m 17) • Green, S.B. en Salkind, N.J., Using SPSS for Windows (analysing and understanding data) (Les 15 t/ 26, 35 t/m 44) • Aanvullingen op Blackboard actieve deelname werkstuk tentamen presentatie Statistiek A of B Dit studieonderdeel is pas behaald als behalve een voldoende voor het tentamen ook een voldoende is behaald voor de aan dit onderdeel gekoppelde opdracht in het kader van het tutoraat. Regelingen voor inschrijving practica bij Onderzoeksmethoden II-A: dataanalysetechnieken • Alleen studenten die statistiek in het eerste jaar hebben afgerond kunnen zich inschrijven voor de practica van deze cursus. Studenten, die zich hebben ingeschreven voor het herkansingstentamen Statistiek A in maart, kunnen zich voorwaardelijk inschrijven. Deze voorwaardelijke inschrijving wordt alleen definitief bij het behalen van het hertentamen. • Studenten dienen zich minimaal twee weken voor het eerste college van dit onderdeel in te schrijven. Wie niet aan deze voorwaarden voldoet,

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wordt uitgesloten van de practica. Bij overschrijding van het door de faculteit te bepalen maximale aantal worden die studenten op een wachtlijst geplaatst. • Studenten die zich inschrijven voor de practicumgroepen en deze niet of niet in zijn geheel volgen, worden het volgende studiejaar aan het eind van de wachtlijst geplaatst. • Verzoeken om deel te nemen aan specifieke practicumgroepen dienen schriftelijk en met redenen omkleed minimaal drie weken voor het eerste college van dit onderdeel ingediend te zijn bij de coördinator van dit studieonderdeel. Verzoeken ingediend na die datum worden niet in behandeling genomen. onderwijs hoorcollege werkgroep practicum •


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Ontology Engineering 400292 3 6 dr. A.T. Schreiber Ontologies are nowadays used in computer science a means to share common concepts between information systems, This course is focused on theory, methods, and tools for constructing and/or extending ontologies for this purpose. Teaching subjects typically center around engineering principles, e.g. for subtype hierarchies (backbone identification, viewpoints, dimensions, constraint specification), part-of structures (types of part-of relations, representation of part-of relations), and default knowledge. Also, the mapping and/or integration of different ontologies is discussed. The course contains examples of how ontologies are used in practice. The assignments focus on real-life examples of ontologies currently in use in web applications. Lectures, assignments Reader Assignments, self evaluation mIS

Optimization of Business Processes 400260 6 5 prof.dr. G.M. Koole To learn more about one or two of the subjects of modeling of business processes, and to learn to study and present scientific papers. content During this course we study papers on one or two subjects from modeling of business processes. Possible subjects are production scheduling, inventory management, call centers, yield management, etc. We also visit once or twice a company. form of tuition Every student presents twice a paper and writes a report about it. Every student also implements an algorithm presented by another student. literature None subject code credits period lecturer aim

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mode of assessment presentations and papers entry requirements Modeling of Business Processes target audience mBMI remarks • presence is compulsory • Registration for this course via https://tisvu.vu.nl/HTM/TISVULogin.htm, one week prior to the start. For the course schedules please refer to http://www.few.vu.nl/onderwijs/roosters. Opzetten van Onderzoek 813023 6 3 dr. H. Kelderman (coördinator) Voorbereiding op de B-these In het kader van het tutoraat vindt in het B1 en B2 onderwijs plaats in de schrijf-, beoordeling-, uitvoerings- en presentatievaardigheden. In de vakken Algemene Methodologie, Statistiek, Onderzoeksmethoden I en II vindt het onderwijs in de standaard methodologie, statistiek en data-analyse plaats. Het B3 vak Opzetten van Onderzoek (OvO, 6 studiepunten) is het laatste methodenvak voor de B-these. Het vak is bedoeld als profielspecifieke voorbereiding op de B-these. Enerzijds worden profielspecifieke onderzoekstechnieken en statistische methoden e.d. behandeld, anderzijds moet door de studenten, vanuit een gegeven vraagstelling, een onderzoeksvoorstel voor de B-these worden gemaakt. De volgende onderwerpen komen in ieder geval aan bod. 1. Onderzoeksvormen binnen het profiel 2. Statistische methoden binnen het profiel 3. Planning en werkwijze bij het schrijven van de B-these. 4. Ethiek van onderzoek 5. Literatuuronderzoek op het gebied van de onderzoeksvraag. 6. Operationaliseren van de onderzoeksvraag in een onderzoekbare vraagstelling 7. Het kiezen/construeren van meetinstrumenten die kunnen leiden tot de beantwoording van de vraagstelling. 8. Het kiezen van statistische en/of andere methoden van dataanalyse. 9. Het pretesten van het onderzoeksontwerp en/of analyse methode. 10. Het schrijven van een concept APA inleiding en methode sectie. 11. Mondelinge presentatie van het onderzoeksvoorstel. werkwijze Hoor- en werkcolleges, practicum. Op de hoorcolleges wordt de benodigde theorie behandeld. De werkcolleges sluiten aan op de hoorcolleges er worden oefeningen een aantal oefeningen doorgewerkt. In het practicum bereidt men zich in groepjes van 3-5 personen voor op de B-these. Het practicum sluit bij voorkeur aan bij onderzoek binnen de afdeling van het profiel. Bij de aanvang van het practicum wordt een korte tekst over de onderzoeksvraag en een aantal sleutelreferenties aangeboden. literatuur Wordt nader bekend gemaakt. In ieder geval Publication manual of the American Psychological Association. toetsing - Schriftelijk tentamen over de collegestof. - Uitgewerkt voorstel voor de B-these en presentatie. Het voorstel wordt

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beoordeeld op, uitvoerbaarheid, kritische massa, theoretisch en/of praktisch belang, literatuur overzicht (omvang, relevantie, up-to-date, organisatie van het materiaal), hypothesen (ondersteuning door de literatuur), onderzoeksopzet (consistent met hypotheses, statistische conclusie validiteit i.h.b power, constructvaliditeit van de manipulatie en/of meting, interne/externe validiteit van het ontwerp), data-analyse (toetsen consistent met hypothesen, aannamen realistisch) , toepassing van de APA stijl (juiste redactie, stijl en typografie). entreevoorwaarden Onderzoeksmethoden I en II. opmerkingen • Aanwezigheid is verplicht • Voor de verschillende bachelortrajecten gelden de volgende vakcodes van Opzetten van Onderzoek: (813056) Klinische Psychologie, (813068) Sociale Psychologie, (813061) Ontwikkelingspsychologie, (813065) Biologische Psychologie, (813058) A & O Psychologie, (813066) Cognitieve Psychologie en (813067) Klinische Neuropsychologie. Meer gedetailleerde informatie over Opzetten van Onderzoek kan worden • verkregen bij de afdeling. voorkennisvakken 812015: Onderzoeksmethoden I: Dataverzamelingstechnieken (Research Methods I: Data collection) 812005: Onderzoeksmethoden II-A: Data-analysetechnieken (entreevoorwaarde) naam code docent studiepunten periode doel inhoud


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Organisatietheorie (bacheloropleiding) 703000 drs. S.B. Ybema 6 5e en 6e: dinsdagmorgen en donderdagmiddag Het verkrijgen van kennis en inzicht in theorieën, begrippen en benaderingen op het gebied van het sociaal-wetenschappelijk denken over organisaties. Dit blok geeft een algemeen historisch overzicht van de hoofdstromen in de organisatietheorie en de voornaamste theorieëen en theoretici binnen elke stroming en biedt daarnaast inzicht in specifieke onderwerpen aan de hand van de praktijkvoorbeelden en theoretische verdieping. De bedoeling is dat de student leert vanuit uiteenlopende invalshoeken en naar verschillende aspecten van organisaties te kijken. Hoorcollege. • Ybema, S. (red.) Reader Organisatietheorie (met klassieke teksten, praktijkvoorbeelden en toelichting op thema's en opdrachten). Verkrijgbaar bij de VU-boekhandel. • Nadere literatuur wordt via het collegerooster bekend gemaakt. Schriftelijk tentamen. Organisational Dynamics 400188 6 3 dr. M.C. Schut To understand, simulate and analyse models of organisations and the dynamics of organisational structure. The student is able to explain organisational dynamics from both internal and external viewpoints.

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content This course is on the simulation and analysis of organisations and their dynamics. In this respect, an organisation is a social or computational structure for achieving controlled performance in pursuit of collective goals. We study the dynamics within existing organisations as well as the dynamics and evolution of organisational structure itself. Computational organisation models specify the dynamics of information, personnel, decision responsibilities, tasks, and resources that are distributed georgraphically and temporally. We consider organisations as complex, dynamic, adaptive and evolving systems. A case study example of such a system, as discussed in the course, involves the traditional economic market. The analysis of organisational structure is explained from internal (managerial) as well as external (market) perspectives. Regarding the latter, evolution is discussed as a mechanism that drives organisational change from the outside. In the course, aspects of the courses on self organising systems and organisation theory are placed in the context of organisation dynamics. form of tuition Theory in lectures and practice in labs literature Reader mode of assessment Written exam and submitted assignments target audience mAI (organisational dynamics and self organisation), mBMI, mIS, mCS remarks More information available on BlackBoard naam Parallel Computing code 400304 studiepunten 6 subject code credits period lecturer content

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Parallel Programming Practical 400162 6 1 and 2 prof.dr.ir. H.E. Bal With this practicum, several parallel programs have to be written, using different programming environments, including Java and MPI. The programs must be tested on a parallel machine of the faculty (see http://www.cs.vu.nl/das2) and the performance (speedups) of the programs must be measured, analyzed, and, whenever necessary, optimized. A brief report must be written that explains the approach and discusses the measurements. Practical computer work. Practical computer work. Knowledge about the first part of the class Parallel Programming is recommended (introduction into parallel programming, MPI, and Java). 3I, mCS, mPhys. Parallel programming 400161 6 1 and 2 prof.dr.ir. H.E. Bal This lecture discusses how programs can be written that run in parallel on a large number of processors, with the goal of reducing execution time. The

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class has a brief introduction into parallel computing systems (architectures). The focus of the class, however, is on programming methods, languages, and applications. Both traditional techniques (like message passing) and more advanced techniques (like parallel object-oriented languages and Tuple Space) will be discussed. In addition, attention is paid to implementation aspects of several languages. Finally, several parallel applications are discussed, including N-body simulations and game tree search. The class fits well with existing research projects within the department of Computing Systems. It is a good basis for M.Sc. projects in the area of parallel programming, which use the parallel computing systems of the department. Class with separate practicum (6 cp.). To be announced. Written exam. mCS Perceptie 815047 6 178 (3 tentamen, 18 hoorcollege, 157 zelfstudie) 1 dr. C.N.L. Olivers Kennismaking met de fundamentele principes van waarneming. Een overzicht wordt gegeven van de fysiologische, psychofysische en cognitieve benadering van de visuele, auditieve en somatosensorische waarneming. Hoorcolleges. Goldstein, E.B. (2002). Sensation and perception. 6th edition. London: Brooks/Cole Publishing Company. tentamen Schriftelijk tentamen Wordt in 2004/2005 wel gegeven, maar in 2005/2006 niet. hoorcollege zelfstudie

Performance Analysis of Communication Networks 400165 6 1 and 2 dr. T. Kielmann; prof.dr. R.D. van der Mei Knowledge: The student will acquire basic knowledge of (1) quantitative models for predicting and analyzing the performance of communication networks, (2) traffic models, (3) traffic management techniques, and (4) performance evaluation and approximation techniques. Skills: The student will gain experience in the development and analysis of performance models and will learn how to tackle practical performance problems arising in the telecommunications industry. content Over the past few years the use of communication services (WWW, mobile voice, mobile Internet access, PC banking, teleshopping) has experienced tremendous growth. Consequently, communication networks are expected to handle large amounts of (digital) information, and in many situations the


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available amounts of transmission or processing capacity is a limiting factor. A key factor for the commercial success of communication services in the competitive telecommunications market is the ability to deliver a high and predictable Quality of Service (QoS) level to the customers (in terms of performance measures such as response times, throughput and availability) in a cost-effective manner. Typical questions that will addressed during the course are • What does the traffic in the network look like? • How do we deal with traffic problems in the network? • How can we predict the performance of a service in the network?, and • How many customers can a given network handle without significant performance degradation? This type of questions can be tackled by developing and analyzing quantitative performance models. In addition to the basic theory of performance models for communication networks, the application of the theory to solve practical problems will play a central role. The course is 2 hours per week. Practical home work assignments will be distributed bi-weekly Reader On the basis of both the homework assignments and a written exam Basic knowledge of stochastics and computer networks mBMI, mCS Pharmacodynamics of Drug Action 435686 drs. R.A. Bakker (tel. 4447588, [email protected]) dr. M.J. Smit; drs. R.A. Bakker 3 4 To get acquainted with basic concepts and experimental approaches in molecular pharmacology. This course comprises the study of the fundamental principles and aspects of receptor structure and function related to the research topics within the section of Medicinal Chemistry (Drug discovery and target finding/ Drug design and synthesis). Molecular mechanisms by which drugs act will be studied, focusing on ligand-receptor interactions, intracellular signaling pathways activated by these receptors and the role of these receptors in (patho)physiology. Modern pharmacological concepts such as including constitutive receptor activity and receptor assays will be addressed as well. Assignment and self-study. Assignment based on selected review and research papers and Rang, Dale and Ritter - Pharmacology 5th edition (ISBN 0-443-07145-4) Written report. Knowledge of the basic principles of drug-action. mPhar Please contact the coordinator four weeks prior to the start of the course (email: [email protected]).

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Docent Taalcentrum VU 3 07.02.2005 - 8.02.2005 Na afloop van de module hebben de studenten: • inzicht in de specifieke aard van Engelse bètawetenschappelijke teksten; • inzicht in interculturele aspecten bij het gebruik van de Engelse taal. Na afloop van de module kennen de studenten: • de opbouw van een Engelstalige tekst en de verschillende stijlkenmerken van Engelse teksten; • de verschillen tussen de Nederlandse en de Engelse schrijftaalconventies. Na afloop van de module kunnen de studenten: • korte pakkende stukjes in het Engels schrijven over bètawetenschappelijke onderwerpen en daarbij jargon vermijden; • een Engelstalig persbericht, samenvatting of brochure schrijven en redigeren • een Engelstalige sollicitatiebrief schrijven. De cursus is opgebouwd uit verschillende blokken. Elk blok wordt afgesloten met een schrijfopdracht. In deze blokken komen o.a. aan bod: • algemene tekstopbouw: wat is de functie van de tekst, welke boodschap wil je overbrengen? • Popular science writing versus Academic writing: wat zijn de verschillen? • Taalvariatie en taalvergelijking: wat zijn de verschillen tussen een Nederlandse en Engelse tekst. En ook: behandeling van de diverse valkuilen als het gaat om het schrijven van een Engelse tekst. • Interculturele verschillen: schrijven voor een internationale doelgroep: schrijven voor native en non-native speakers; taalverschillen binnen Europa. De werkwijze is wisselend: theorie en praktijk wisselen elkaar af. De werkcolleges worden zoveel mogelijk verzorgd in het computerlab van de faculteit Letteren. De daar geïnstalleerde software biedt bijvoorbeeld de mogelijkheid voor 2 studenten om samen aan een tekst te werken. Tijdens de werkcolleges werkt men in groepen van maximaal 12-15 studenten. De syllabus die behoort bij deze cursus is af te halen bij het TaalcentrumVU, in de week voorafgaand aan de cursus. Ten minste 4 schrijfopdrachten Deelnemers moeten de cursus Wetenschapsjournalistiek hebben gevolgd.

Practicum Ontwerp van multi-agent systemen 400059 7 4 dr. C.M. Jonker Het hoofddoel van het practicum is practische ervaring opdoen in het modelleren en ontwerpen van complexe, op kennis gebaseerde, multiagentsystemen door het maken van een duidelijke en precieze documentatie van het ontwerp en het plannen van een project. Bij dit laatste hoort uiteraard ook het halen van de daarbij horende deadlines. inhoud Het hoofddoel kan opgesplitst worden in de volgende subdoelen: * Het leren analyseren van problemen en kennis, en deze in een


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compositioneel, op kennis gebaseerd multi-agentsysteem modelleren. * Het leren maken van een overzichtelijk en adequaat conceptueel ontwerp. * Het leren maken van een gedetailleerd ontwerp, gebaseerd op het conceptuele ontwerp. * Het leren schrijven van een goede rationale bij het ontwerp. Hierin staan alle ideeën achter het ontwerp en ook alle ontwerpkeuzes uitgelegd. * Het leren testen van een prototype van een systeem, herkennen van fouten en hiaten en het reviseren van de ontwerpen (conceptueel en gedetailleerd). * Het leren plannen van een project zodat de deadlines gehaald worden. Om deze doelen te verwezenlijken moeten er twee agentsystemen ontwikkeld worden gedurende dit practicum. De agent-architectuur speelt hierbij een belangrijke rol. De belangrijkste agent-specifieke eigenschappen zoals behandeld tijdens het hoorcollege Ontwerp van Multi-agentsystemen moeten nu in systemen verwezenlijkt worden. De huidige opgaven betreffen het ontwerpen van een agent voor het besturen van een chemisch proces en het ontwerpen van een multi-agentsysteem voor ofwel onderhandelende agenten ofwel cooperatieve agenten. De studenten werken in principe samen in groepen van drie. Elke groep wordt intensief begeleid door een student-assistent die de rol van projectleider vervult. De syllabus van het college Ontwerp van Multi-agentsystemen, practicumhandleiding (te vinden via http://www.cs.vu.nl/~ovm). Documentatie en systeemspecificaties voor beide opdrachten worden beoordeeld (criteria zijn te vinden via http://www.cs.vu.nl/~ovm). 3AI, mCS, mAI-T De theoretische kennis waarop deze practische ervaring gefundeerd wordt is behandeld in het hoorcollege Ontwerp van Multi-agentsystemen. Er wordt vanuit gegaan dat de deelnemers aan het practicum vertrouwd zijn met deze stof. Praktijk 1 en 2 990002 30 Op school geeft de docent in opleiding minimaal 120 lessen en maakt minimaal 250 klassencontacturen. Minimaal 40 lesuren worden gegeven in bovenbouwklassen havo/vwo. 30.08.2004 - 31.08.2005 Praktijkervaring opdoen op school vormt de kern van de opleiding. In overleg met de begeleider op school en op de opleiding voert de docent in opleiding stageopdrachten op school uit en verwerkt deze in het portfolio. stageverslag De praktijkervaring wordt door de schoolbegeleider en door de instituutsbegeleider beoordeeld. Opdrachten in het kader van praktijkervaring worden opgenomen in het portfolio. Er zijn twee begeleiders: één vanuit de school en één vanuit de opleiding. stage (30.08.2004 - 31.08.2005) De praktijkervaring wordt opgedaan op een school voor Voortgezet Onderwijs.

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Praktijkonderzoek 990003 8 Ongeveer 15 Diverse docenten • Zicht krijgen hoe door systematisch onderzoeken van onderwijssituaties inzicht verkregen kan worden leerprocessen van leerlingen. • Opdoen van ervaring met het voorbereiden uitvoeren en rapporteren van onderzoek van onderwijssituaties. Bij het praktijkonderzoek diept de dio één of meer vraagstukken uit de (eigen) onderwijspraktijk uit. Hij doet dat door het opzetten, uitvoeren en evalueren van een op de onderwijspraktijk gericht onderzoek waarbij op één of enkele scholen empirisch materiaal wordt verzameld rond de meesterproef. Elke dio maakt in het kader van vakdidactiek een meesterproef. In het praktijkonderzoek wordt het leereffect (van een of meer aspecten) van de meesterproef onderzocht. Dit onderzoek mondt uit in een (voor)onderzoekverslag, een peer review en een onderzoeksartikel. Op de onderwijsresearchdag van het Onderwijscentrum VU worden enkele praktijkonderzoeken van dio's gepresenteerd en bediscussieerd. Aan het begin van de opleiding worden doel, planning en beoordeling van het praktijkonderzoek uitgelegd en ontvangen de dio's een handleiding met daarin onder meer een beoordelingschecklist en literatuursuggesties op het gebied van methoden en technieken van onderzoek. Er worden drie werkcolleges georganiseerd ter ondersteuning. Dio's worden uitgedaagd met hun praktijkonderzoek aan te sluiten bij onderzoek dat wordt verricht door medewerkers van het Onderwijscentrum VU en zoveel mogelijk gemeenschappelijke thema¿s op te pakken. Literatuurverkenning, probleemstelling, onderzoeksvraag en onderzoeksdesign dienen door de instituutsbegeleiders goedgekeurd te worden alvorens de dio verder kan gaan met de dataverzamelingsfase en de data verwerkingsfase. Gedurende deze fasen zijn de instituutsbegeleiders beschikbaar voor individuele hulp. Aan de hand van concepten van het onderzoeksverslag reflecteert de dio met zijn instituutsbegeleider op de analyse van de onderzoeksgegevens in het licht van de literatuur. Vervolgens wordt het definitieve onderzoeksartikel geschreven. • Baarda, D.B. et al. (1998) Kwalitatief onderzoek. Basisboek. Houten: EPN. ISBN: 90-207-2485-1. • Oost, H. & Markenhof, A. (2002) Een onderzoek voorbereiden. Baarn: HB. ISBN: 90-5574-376-3. • Oost, H. (2002) Een onderzoek uitvoeren. Baarn: HB. ISBN: 90-5574373-9. • Oost, H. (2002) Een onderzoek rapporteren. Baarn: HB. ISBN: 90-5574-374-7. • (Voor)onderzoeksverslag • Peer review over (voor)onderzoeksverslag • onderzoeksartikel voor vaktijdschrift voor leraren Het onderzoek wordt uitgevoerd rond de meesterproef en bevat een

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Principles of Biophysics 430051 prof.dr. C.F. Schmidt; dr. J.P. Dekker prof.dr. C.F. Schmidt; dr. J.P. Dekker 6 1 To gain knowledge of the basic concepts of biophysics and the application of physics to biology, with a view to increase the understanding of biological systems. Physics is an exact science in the sense that it tries to explain phenomena observed in the world around us by as simple as possible laws in mathematical form. Physics has been extremely successful in its endeavor from describing the structure of atoms, via understanding how electrons behave in a semiconductor, to unraveling the history and structure of the universe. There is a general consensus in science that the quantitative physics approach will eventually also be applicable to phenomena that are not yet understood. Many such problems exist and they are often characterized by a high degree of complexity, systems with many parts interacting in complicated ways, which defeat the standard tools of simplification and generalization. Most biological systems fall into this category, and a phenomenon such as consciousness is certainly far from being scientifically understood. In this course we will provide an overview of important physical concepts used in the biophysics. We will start with an general background (statistical thermodynamics, distributions, random walks, diffusion, viscosity, thermal conduction, etc.). Other important topics will include: semi-flexible biopolymers, conformational dynamics, hydrodynamics, chemical reaction rates, enzyme kinetics, biological membranes, biological energy, excitable membranes and nerve signals. • Tutorials/discussions of book material, lecture notes. • Self-study. R. Cotteril, Biophysics - An Introduction (2002, Wiley): ISBN 0471485381 Bachelor in Medical Natural Sciences, Physics, Chemistry, (Medical) Biology or Pharmaceutical Sciences MSc Students with Bachelor in Medical Natural Sciences, Physics, Chemistry, Biology with an interest in the interface between these disciplines. Application for this course should reach Prof. Schmidt (tel 47972, [email protected]) or Dr. Dekker (tel. 47931, E-mail: [email protected]) at least 2 weeks before the starting date of the course. Principles of Molecular Biochemistry 430052 J.C. Vos J.C. Vos; dr. H. van Heerikhuizen 6 1 To acquire basic knowledge of DNA, RNA and proteins in the context of the living cell.

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content The flow of genetic information from gene DNA via RNA to proteins will be discussed and the molecular details of the biochemical processes that are involved i.e. transciption, translation and protein synthesis. The basic structure and function of DNA, RNA and proteins will be discussed as well as a number of cellular processes such as DNA replication, RNA splicing, protein transport and degradation, metabolism, signal transduction, stress response, cell-cell communication. As part of the course some "routine" biochemical and molecular biological techniques will be performed, such as polymerase chain reaction, gene cloning and enzyme purification. form of tuition • Tutorials/discussions of book material, lecture notes • Self-study literature Depending on the background knowledge of the student one of the folowing books will be used: `From Genes to Genomes; Concepts and Applications of DNA Technology' by Jeremy Dale en Malcolm von Schantz, Wiley Europe, ISBN: 0-471- 49782 or "Essential Cell Biology, Second Edition" by Bruce Alberts et al., ISBN: 081533480X examination format written examination entry requirements Bachelor in Medical Natural Sciences, Physics, Chemistry, (Medical) Biology or Pharmaceutical Sciences target audience MSc Students with Bachelor in Physics or (Medical) Biology remarks Application for this course should reach Dr. Vos (tel 47569, [email protected]) at least 2 weeks before the starting date of the course subject code co-ordinator docenten credits period aim content

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Principles of Molecular Medicine 430063 prof.dr. N.P.E. Vermeulen (tel. 4447590; e-mail:[email protected]) dr. H. Lingeman; prof.dr. N.P.E. Vermeulen; prof.dr. R. Leurs 6 1 General introduction into and deepening of knowledge of concepts, mechanisms and recent developments in pharmaceutical sciences, with emphasis on medicinal chemistry. A general introduction will be given to the process of drug discovery, drug design, drug development and drug safety assessment. Subsequently, potential drug targets, mechanisms of drug actions (including drugreceptor/enzyme interactions and dose-response relations), drug disposition (including pharmaco-/toxicokinetics) and drug toxicity will be discussed. Using various drug classes, relationships between chemical structures and biological activities will be derived and illustrated. Finally, various modern developments and tools will be illustrated by recent applications in the field of drug research, with emphasis on molecular pharmacology, molecular toxicology and bioanalytical chemistry. Lectures and tutorials. Introduction to Medicinal Chemistry, 2nd edition by G.L. Patrick (Oxford University Press, ISBN 0-19-850533-7) and Casarett & Doull¿s Essentials of Toxicology (ISBN 0-07-138914-8). Written examination

entry requirements Basic knowledge of (pharmaco)chemistry or related fields remarks Please contact the secretary four weeks prior to the start of the course (e-

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Principles of Pharmaceutical Scienses / Pharmacochemistry 435675 prof.dr. N.P.E. Vermeulen (tel. 4447590, [email protected]) prof.dr. R. Leurs; prof.dr. N.P.E. Vermeulen 6 1 General introduction into and deepening of knowledge of concepts, mechanisms and recent developments in pharmaceutical sciences, with emphasis on medicinal chemistry. A general introduction will be given to the process of drug discovery, drug design, drug development and drug safety assessment. Subsequently, potential drug targets, mechanisms of drug actions (including drugreceptor/enzyme interactions and dose-response relations), drug disposition (including pharmaco-/toxicokinetics) and drug toxicity will be discussed. Using various drug classes, relationships between chemical structures and biological activities will be derived and illustrated. Finally, various modern developments and tools will be illustrated by recent applications in the field of drug research, medicinal chemistry and toxicology. Lectures and tutorials. Introduction to Medicinal Chemistry, 2nd edition by G.L. Patrick (Oxford University Press, ISBN 0-19-850533-7) and Casarett & Doull's Essentials of Toxicology (ISBN 0-07-138914-8). Written examination. Basic knowledge of (pharmaco) chemistry or related fields. mPhar Please contact the secretary four weeks prior to the start of the course (email: [email protected]). Programmeren in Prolog 400270 4 5 dr. A.C.M. ten Teije De cursus programmeren in Prolog bestaat uit colleges en een begeleid praktikum. Een introductie wordt gegeven van de declaratieve programmertaal Prolog. Aandacht wordt geschonken aan het ontwerp en het implementeren van kennisrepresentatie formalismes, zoekstrategieen, kennissystemen en natuurlijke taal verwerking. De cursus programmeren in Prolog is een vereiste voor het deelnemen aan "Project AI". Colleges en verplicht practicum. I. Bratko, PROLOG programming for Artificial Intelligence, 3rd edition, Addison- Wesley, 2001. J. Wielemaker, SWI-Prolog Reference Manual. Tentamen & practicum Het eindcijfer is het gemiddelde van het practicumcijfer en het tentamencijfer, onder de voorwaarde dat beide onderdelen (practicum en tentamen) voldoende zijn. 1AI, 3I, mCS Zie ook blackboard pagina

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Project AI 400293 6 6 dr. Z. Huang Dit project gaat verder in op het programmeren van AI technieken met behulp van Prolog. Speciale aandacht wordt besteed aan de toepassing van kennisrepresentatie en zoektechnieken op het gebied van kennis-gebaseerde systemen, automatisch leren of taalkundige toepassingen. Studenten besteden vier volledige weken aan de opdrachten. Practicum + spreekuren. Luger, G.F , Artificial Intelligence, 4th edition 2002, Pearson Education Limited Bratko, I. PROLOG programming for Artificial Intelligence, 3rd edition 2001, Addison-Wesley. Ingeleverde opdrachten. 1AI (verplicht) 3IN (keuze) zie ook blackboard pagina Programmeren in Prolog (400168). Project ISO 400058 9 4, 5 en 6 prof.dr.ir. J.L. Top Het doel van ISO is de student inzicht te geven in de problematiek rond het uitvoeren van een extern informatiseringsproject. Het gaat hierbij om het ontwerpen of analyseren van informatiesystemen voor een klant, in teamverband en volgens een planning. De student leert omgaan met de onzekere en onvoorspelbare factoren in een realistische setting. De in de studie opgedane kennis en vaardigheden met betrekking tot systeemontwikkeling worden in het practicum zoveel mogelijk geïntegreerd en in praktijk gebracht door middel van het uitvoeren van een informatiseringsproject voor een bedrijf met een werkelijk probleem. Het project doet echter ook een beroep op de inventiviteit, creativiteit, zelfstandigheid en collegialiteit van de student. Het uiteindelijke resultaat voor de klant is een ontwerp van een mogelijk informatiesysteem of een gedetailleerde informatieanalyse. Het projectteam legt een volledig projecttraject af in de vorm van een contractfase, een uitvoeringsfase en een individuele evaluatiefase. Het is niet de bedoeling dat er gedurende het practicum een systeem daadwerkelijk wordt geïmplementeerd. Communicatie binnen het projectteam, met de opdrachtgever en met de stuurgroep (vanuit de VU) is een cruciaal aspect van dit vak. • De deelnemers werken in projectgroepen van 6-8 personen. De teams worden samengesteld door de ISO-begeleiding. Elk team benoemt haar eigen projectmanagement en regelt alle projectbijeenkomsten. • Deelnemers voor dit project moeten zich uiterlijk 7 januari 2005 inschrijven via TISVU. Collegedictaat. Het practicum wordt beoordeeld door de klant (bruikbaarheid van het

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resultaat), door een stuurgroep vanuit de universiteit (proces en methode) en door de practicumbegeleiding (op basis van een persoonlijke evaluatie). doelgroep 3I, 3BI voorkennis Vereist voor deelname aan het practicum: Software Engineering (400071), Databases (400018), Bedrijfsmodellering en Requirements Engineering (400010, theorie en practicum). naam code studiepunten periode docent inhoud

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Project Kennissystemen 400201 7 5 en 6 dr. A.C.M. ten Teije Het doel van Project Kennissystemen is ervaring opdoen in het ontwerpen en realiseren van een kennissysteem. In Project Kennissystemen kun je veel van de kennis die je hebt opgedaan tijdens het vak Kennissystemen praktisch toepassen. In dit practicum wordt gebruik gemaakt van de programmeeromgeving Jess (Java Expert System Shell). Er zijn twee soorten opdrachten. A-opgaven: in deze opdrachten leer je de basis van Jess die je nodig hebt bij het maken van de B-opgave. B-opgave: voor de B-opgaven ontwerpen en realiseren jullie een bruikbaar kennissysteem. Jullie bepalen zelf het domein en de taak en zoeken een of meer kennissen in jullie omgeving die als experts kunnen fungeren voor jullie systeem. Dit practicum wordt gedaan in groepen van twee studenten. bijeenkomsten en spreekuren Mark Stefik, Introduction to knowledge systems, Morgan Kaufmann Publishers, 1995 ingeleverde opdrachten en verslag 2AI (verplicht), mCS Zie ook blackboard pagina. Kennissystemen (400126) Project Optimalisation of Business Processes 400213 6 3 prof.dr. G.M. Koole To acquire skills related to Decision Support Systems, and to learn to apply relevant scientific knowledge. Project optimization of business processes concerns the construction and/or design of (part of) a decision support system that: - is designed and built in a scientifically sound way; - can be used in practice. The use will be tested through contacts with companies. Students work in groups. The DSS will be implemented in Excel; getting acquinted with Visual Basic for Applications (the macro language of Excel) is part of the project and will be graded separately. None Individual test for VBA, individual grade for participation in group project

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entry requirements Modeling of Business Processes (400157) target audience Compulsory for mBMI naam code studiepunten periode docent inhoud


doelgroep opmerkingen voorkennis

Project Software Engineering 400067 8 5 en 6 dr. P. Lago Het doel van het SE project is de theorie opgedaan in het SE college toe te passen in een zo¿n realistisch mogelijke praktijksituatie. Het project bestaat uit het construeren van een groot programma in teamverband volgens de RAD (Rapid Application Development) methode. Zoveel mogelijk aspecten van projectmatig werken en software engineering zullen hierbij aan de orde komen, waaronder het opstellen van een projectplan, requirements engineering, design, implementatie en testen, maar ook het samenwerken in een team. Het uitvoeren van een project in teamverband (4 à 5 personen) met een 'progress report' presentatie van 15 minuten. H. van Vliet, Software Engineering, Principles and Practice, 2nd edition, John Wiley, 2000; Martin Fowler, UML Distilled, 3rd edition, Addison Wesley, 2003. Een team wordt beoordeeld op samenwerking (10%), kwaliteit van de documentatie (25%), kwaliteit van de opgeleverde producten (25%), de consistentie van de documentatie en het eindproduct (10%), projectpresentatie (10%) en een individuele evaluatie (20%). 2I, 2BI, 2MMC, 2BWI, 3AI Tijdens de eerste drie weken van dit practicum (week 14 t/m 16), wordt er 2 uur college gegeven Vereiste voorkennis: Practicum Datastructuren (400140).

Protocol Validation 400117 6 5 and 6 prof.dr. W.J. Fokkink; dr. R.C. de Vrijer Learning to use formal techniques for specification, and validation of communication protocols. content This course is concerned with specification of protocols: formulation of desired properties, and verification of these properties. Interesting properties of a specification are: ¿something bad will never happen¿ (safety), and: ¿something good will eventually happen¿ (liveness). The following three topics will be treated: - Input/output automata: a formalism used for specificatio and verification of (asynchronous) concurrent and distributed discrete systems. I/O automata are used for specification of (e.g.) communication protocols, concurrent data base systems, and network resource allocation algorithms. - (micro) Common Representation Language (muCRL): a specification language based on process algebra combined with abstract data types. This formal system can be used for specification of parallel, communicating processes with data. - Model-checking: a method for formal verification of concurrent finite-state systems. In the practicum we


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will use a tool for automated verification of the required properties of a specification. Lectures with practical work. During the practical work a muCRL-tool and a modelchecker will be used for validation of protocols discussed during lectures. I/O automaten: N.A. Lynch, Distributed Algorithms, Morgan Kaufmann Publishers, San Mateo, CA, 1996. Chapter 8. S.J. Garland, N.A. Lynch, M. Vaziri, IOA: A language for Specifying, Programming, and Validating Distributed Systems (draft), MIT Laboratory for Computer Science, September 1997. Dictaat: muCRLen Model checking.. Schriftelijk, aangevuld met practicumopgaven. Het tentamencijfer wordt berekend volgens de formule C = (2T + P)/3 waar T het cijfer van het tentamen aangeeft en P het gemiddelde cijfer van de practicumopgaven. Voor het tentamen dient tenminste een 5.0 gehaald te worden. Inleiding Logica (400119), Datastructuren (400145) 3I, 3BI, 3AI, mCS This course will not be given this year. Qualitative Research Methods for the Information Sciences 400290 3 3 prof.dr. J.M. Akkermans (contact); drs.ing. J. Gordijn This course helps prepare students who want to embark on their (Master) research. The course provides an overview and assessment of different scientific research methods, needed in a multi-disciplinary approach to Information Systems and how they function in an organizational context. Major topics are: - developing the research questions you want to answer; - planning your research; - qualitative research methods (e.g. interview, case study, action research, ethnography); - quantitative research methods (e.g. survey, questionnaire, statistical data analysis); - IS research methods (e.g. modelling, prototyping, simulation, scenario analysis); - aspects of theory formation; - how do you (and others) know that your research results are valid?; - research report writing. In group sessions, we will critically review existing samples of research (papers, articles, MSc theses) against criteria of scientific argumentation, validity, soundness, completeness. Reader with recent articles, plus textbook: Pervez Ghauro and Kjell Gronhaug, Research Methods in Business Studies, 2nd ed, Prentice Hall, Essex UK, 2002 Classroom presentation and written review essay Bachelor-level IK, IN or AI mIS, mCS, mAI A useful reference point is the document that specifies the procedure and

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criteria for Master research (see study guide). subject code co-ordinator lecturers credits period aim content

form of tuition literature mode of assessment entry requirements target audience remarks naam code studiepunten docent periode doel


Receptor Structure and Function 435680 dr. M.J. Smit (tel 47572; e-mail: [email protected]) dr. M.J. Smit; dr. R.A. Bakker; prof.dr. R. Leurs 6 4, 5 and 6 To obtain extensive knowledge of the molecular aspects of drug targets and their interaction with ligands. This course comprises a more elaborate study of fundamental principles and aspects of receptor structure and function within the field of Molecular Pharmacology. In depth insight in molecular mechanisms by which most important groups of drugs act will be provided, focusing on ligand-receptor interactions and intracellular signalling pathways activated by these receptors. Modern pharmacological concepts such as e.g. constitutive receptor activity, receptor regulation and dimerization will be addressed. Lectures, tutorials and self-study. Textbook Receptor Pharmacology - second edition - edited by J.C. Foreman and T. Johansen (ISBN 0- 8493-1029-6), selected primary (original research papers) and secondary (review papers) literature. Oral or written examination. Course on Pharmacodynamics of Drug Action. mPhar Please contact the coordinator four weeks prior to the start of the course (email: [email protected]). Rechtzoeken (B2/BN2) 200201 2.9 drs. A.J. Wolthuis (kamer 7A-37, tel. (020) 444 6326) Rechtzoeken wordt doorgaans tweemaal per jaar gegeven: direct na de zomervakantie en direct na de kerstvakantie. Let goed op de collegeroosters voor de precieze datum. Rechtzoeken is een vaardighedenvak. U oefent in dit vak de vaardigheden vinden, samenvatten, argumenteren, schrijven, spreken en¿niet te vergeten¿samenwerken, door met een collega-student een werkstuk te schrijven en een presentatie te houden. Recht zoeken kent per gelegenheid één hoorcollege waar uitgelegd wordt wat van de studenten wordt verwacht. Op dat hoorcollege worden bovendien de opdrachten uitgedeeld. Syllabus Rechtzoeken 2004-2005 (verkrijgbaar bij de VU-boekhandel). hoorcollege Rechtzoeken kent per gelegenheid één hoorcollege. Op dit college legt de docent de opdrachten uit voordat hij ze uitdeelt. werkstuk en presentatie Het werkstuk moet twee weken na het uitdelen worden ingeleverd bij het studie-informatiepunt. Wanneer u een onvoldoende voor het werkstuk hebt behaald, komt u niet in aanmerking voor het houden van een presentatie. De docent neemt contact met u op wanneer u een onvoldoende voor het

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werkstuk hebt behaald. (Geen bericht is goed bericht.) opmerkingen inschrijving U dient zich samen met een collega-student voor het vak in te schrijven op een lijst die op de balie van het studie-informatiepunt (5A-13) ligt. Het is verstandig u al vóór de vakantie in te schrijven voor de cursus die direct na de vakantie van start gaat. U schrijft zich automatisch in voor een presentatiedatum. Schrijf uw naam onder een presentatiedatum die u schikt. Noteer uw inschrijfnummer en de presentatiedatum. voorkennisvak 200109: Project (B1) Scientific Visualisation 400114 4 1 and 2 This lecture consists of the first half (about Scientific Visualization) of the lecture "Natuurkundige Informatica 1" (Division of Physics and Astronomy), extended with extra practical assignments for computer science students. form of tuition Class with integrated computer practicum. target audience mCS subject code credits period content


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Sequence Analysis 430045 6 2 prof.dr. J. Heringa; dr. J. Kleinjung A theoretical and practical bioinformatics course about biological sequence analysis. The course provides an introduction to the algorithmic and biological principles of sequence analysis, as well as practical implications. Goals: • At the end of the course, the student will be aware of the major issues, methodology and available algorithms in sequence analysis. • At the end of the course, the student will have hands-on experience in tackling biological problems in sequence analysis. Theory: • Dynamic programming, database searching, pairwise and multiple alignment, probabilistic methods, pattern matching, evolutionary models, and phylogeny. Practical: • Assignment programming own alignment software based on dynamic programming • Assignment homology searching and pattern recognition using biological and disease examples • Assignment multiple alignment of biological sequences 13 Lectures (2 two-hour lectures per week) Assignment introductions, Computer practicals, Hands-on support E-course material: http://ibivu.cs.vu.nl Books: Richard Durbin, Sean R Eddy, Anders Krogh, Graeme Mitchison (1998). Biological Sequence Analysis. Cambridge University Press, 350 pp., ISBN 0521629713. Assignment results and oral or written exam (depending on number of course

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students) entry requirements Bachelor Physics, Chemistry, Mathematics, Computer Science, Biology, Medical Natural Sciences. Some experience in programming is required. target audience Students with Bachelor Physics, Chemistry, Mathematics, Computer Science, Biology, or Medical Natural Sciences, with a strong interest in Bioinformatics remarks The course is taught in English subject code credits period lecturer aim content

mode of assessment entry requirements target audience subject code credits period lecturers aim content


Simulation 400214 5 1 and 2 prof.dr. G.M. Koole To acquire practical skills and advanced knowledge about simulation. In this course we deal with several advanced subjects related to simulation: verification and validation, the regenerative method, modeling formalisms, optimization, etc. The programming assignments are done using Cristal Ball and a tool for discrete-event simulation. Programming assignments and written exercises Stochastic Methods (400074) mBMI Software Architecture 400170 6 2 and 3 prof.dr. J.C. van Vliet; dr. P. Lago Get acquainted with the field of software and information architecture. Understand the drivers behind architectural decisions. Be able to develop and reason about an architecture of a non-trivial system. Students work in groups to develop an architecture for a fictitious system. They have to develop different representations (called views) of the architecture. These different representations emphasize different concerns of people that have a stake in the system. Each group will also be asked to assess ("test") the architecture of another group for certain quality attributes. Group work with a number of assignments Len Bass et al, Software Architecture in Practice (second edition), AddisonWesley, 2003 Written reports of the assignments, presentation, exam Sofware Engineering. mCS, mIS

Statistic and Probability Seminar 400135 4 dr. M.C.M. de Gunst; dr.ir. G. Jongbloed; prof.dr. R.W.J. Meester; prof.dr. A.W. van der Vaart period not fixed content The subject will be chosen in consultation with the students. Possibilities

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include bootstrap methods, statistics for point processes, survival analysis, statistics for genetics, hidden Markov models, Markov chain Monte Carlo methods. Participants will present chapters from books or articles. The style will be informal. Presentation and global understanding will be the main focus. This seminar is meant specifically for students; one or more docents will guide the seminar. None. General Statistics (400004). Interested students are requested to contact one of the docents ample time before they wish to start. 3W, mMath Registration for this course via https://tisvu.vu.nl/HTM/TISVULogin.htm, one week prior to the start. For the course schedules please refer to http://www.few.vu.nl/onderwijs/roosters. Statistical Genetics 400296 6 prof.dr. A.W. van der Vaart Spring Probability and statistics play an important role in genetics. The mechanism of "meiosis", the forming of sperm or egg cells, is thought to be probabilistic in nature, as is the process of mating in large populations. The relationship between "genotypes" (DNA-sequence) and "phenotypes" (observable traits or diseases) can be modelled by probability distributions. The analysis of genetic determinants is based on random samples from a population, often biased, and various statistical methods are necessary to analyse such data. This course provides an introduction to stochastic models and methods used in genetics, directed at students in mathematics. We do assume a good working knowledge of probability and statistics (e.g. likelihood and Bayes inference, asymptotics, testing), but do not assume prior knowledge of genetics. In particular, the jargon in this description will be explained. Statistical genetics is a classical branch of applied probability and statistics, which has recently gained much new interest, due to the signicifant breakthroughs in genetics, both experimentally and theoretically. With modern techniques and significantly increased data it is hoped to link diseases and other traits to genes (pieces of DNA) that can be precisely located on the genome in an unprecedented manner. This course incorporates parts of many different areas of statistics. Of course we start with Mendel¿s laws of "segregation", which stipulate that each parent passes a randomly chosen gene on to his/her offspring from each pair of genes, independently across genes. The latter independence was later found out to be untrue, and replaced by "linkage models", which stipulate positive dependence between genes sitting close together on the genome. The most popular model is based on a Poisson process model for "crossovers" during meiosis. The resulting models combined with "penetrance models" (conditional distributions for phenotypes given genotopyes) allow to write likelihoods for the observed phenotypes in families (or "pedigrees"), and thus to estimate the dependence of phenotypic traits on genetic factors. Because a full likelihood analysis requires the specification of many probability

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densities and is computationally intensive, other methods with the same aim are based on reduced data, in particular "IBD" (identity by descent) status. "Association" studies are based on the idea that, under a random mating assumption, a population should tend to equilibrium, with deviations in pairs of genes (possibly)in a random sample of individuals indicating that these genes are close together on the genome. Finally, "biometric analysis" is directed at decomposing phenotypic variation into genetic and environmental parts. Lecture Notes. Pak Sham: Statistics in Human Genetics. Kenneth Lange: Mathematical and Statistical Methods for Genetic Analysis. Elizabeth Thompson: Statistical Inference from Genetic Data on Pedigrees. At least two courses in probability and two courses in statistics + general mathematical training. mMath • See http://www.math.vu.nl/sto/onderwijs/statisticalgenetics/ • This course is part of the master class in Stochastics in Molecular Biology and Genetics. See http://mri.math.uu.nl/pagina/vervolg_education_master.html • Registration for this course via https://tisvu.vu.nl/HTM/TISVULogin.htm, one week prior to the start. For the course schedules please refer to http://www.few.vu.nl/onderwijs/roosters. Statistical Models 400171 4 1 and 2 dr. M.C.M. de Gunst Introduction to several frequently used statistical models and their application. Linear models, analysis of variance, generalized linear models, non-linear models, time series. Course of lectures as well as data analysis exercises with the computer (Splus). Lecture notes and S-plus manual. Written exam plus exercises. Prerequisite: Algemene Statistiek (400004), Statistische Data Analyse (400073). Prerequisite for participation in written exam: sufficient mark for the exercises. mMath, mBMI Stochastic Processes for Finance 400352 Unknown 6 5 Financial institutions trade in risk, and it is therefore essential to measure and control such risks. Financial instuments such as options, swaps, forwards, caps and floors, etc. play an important role in risk management, and to

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handle them one needs to be able to price them. This course gives an introduction to the mathematical tools and theory behind risk management. A "stochastic process" is a collection of random variables, indexed by a set T. In financial applications the elements of T model time, and T is the set of natural numbers (discrete time), or an interval in the positive real line. "Martingales" are processes whose increments over an interval in the future have zero expectation given knowledge of the past history of the process. They play an important role in financial calculus, because the price of an option (on a stock or an interest rate) can be expressed as an expectation under a so-called martingale measure. In this course we develop this theory in discrete and continuous time, with an emphasis on the second. Most models for financial processes in continuous time are based on a special Gaussian process, called Brownian motion. We discuss some properties of this process and introduce "stochastic integras" with Brownian motion as the integrator. Financial processes can next be modelled as solutions to "stochastic differential equations". After developing these mathematical tools we turn to finance by applying the concepts and results to the pricing of derivative instruments, by studying models for the "term structure of interest rates", and to risk measurement and management. Foremost, we develop the theory of no-arbitrage pricing of derivatives, which are basic tools for risk management. Lecture notes. Alison Etheridge: Financial Calculus. Martin Baxter and Andrew Rennie: Financial Calculus: an Introduction to Derivatives Pricing. Introductory probability theory and statistics, analysis. 3BWI, mBMI website: http://www.math.vu.nl/sto/onderwijs/RMT/ Dit vak is bijna een must voor een stage bij een financiele instelling. Synthetic Approaches in Medicinal Chemistry I 435689 dr. I. de Esch (tel. 4447841, G343a, [email protected]) 3 4 To obtain knowledge of fundamental aspects of reactivity, reaction mechanisms and stereochemistry in organic chemistry. This course comprises in detail the fundamental aspects of organic chemistry. Important mechanisms are discussed with nucleophilic and electrophilic substitutions, additions, eliminations, and hydrolyses as examples. It will be illustrated how reaction rates depend on reaction circumstances and structural modifications. In addition, chirality and enantioselective synthesis will be discussed. The synthesis of various well-known drugs will be discussed to exemplify these topics. Tutorials, lectures, self-study, problem solving sessions. F.A. Carey and R.J. Sundberg, Advanced Organic Chemistry, Part A Oral or written examination. Course Drug Design and Synthesis mPhar Please contact the mastercoordinator four weeks prior to the start of the

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course (e-mail: [email protected]). subject code lecturer credits period aim content

form of tuition literature mode of assessment entry requirements target audience remarks subject code co-ordinator lecturers credits period aim content


Synthetic Approaches in Medicinal Chemistry II 435685 dr. I. de Esch (room G343a, tel. 4447841, [email protected]) 6 4, 5 and 6 To obtain detailed knowledge of important reactions and synthesis strategies. This course will focus on some of the most important and generally used reactions for organic synthesis. These include, among others, alkylation of nucleophilic carbon intermediates, nucleophilic substitutions, electrophilic additions to carbon-carbon multiple bonds, reductions, oxidations, cycloadditions, aromatic substitution reactions, rearrangements and reactions involving transition metals. Lectures, tutorials and self-study. F.A. Carey and R.J. Sundberg, Advanced Organic Chemistry, Parts B Oral or written examination. Course Drug Design and Synthesis. mPhar Please contact the coordinator six weeks prior to the start of the course (email: [email protected]). Techniques in Molecular Biophysics 430055 dr.ir. E.J.G. Peterman dr.ir. E.J.G. Peterman; dr. J.T.M. Kennis; guests 6 3 To gain knowledge and hands-on experience in modern, widely-used techniques in molecular and cellular biophysics. Theory: Modern research in molecular and cellular biophysics takes advantage of a variety of advanced physical techniques. Subject of this course are: optical spectroscopy (absorption, fluorescence, vibrational spectroscopy, polarization, time-resolved), optical microscopy (confocal microscopy, phase contrast, single-molecule fluorescence), optical trapping, scanning-force microscopy, and NMR. These techniques will be discussed both on the fundamental physical level as on the application level. Practicals: Important parts of the course are lab classes to provide hands-on experience with the techniques and instrumentation. The course is an integral combination of lectures (16 hours) and lab classes (96 hours) • Tutorials/discussions of book material, lecture notes • Laboratory work • Self-study. Notes/handouts from the lecturers. Written exam. Bachelor Medical Natural Sciences, Physics, Chemistry, Pharmaceutical or (Medical) Biology. Some knowlegde of biophysics is an advantage.

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target audience MSc Students with Bachelor in Medical Natural Sciences, Physics, Chemistry, Pharmaceutical Sciences or (Medical) Biology. remarks Application for this course should reach Dr. Peterman (tel 47576, E-mail [email protected]) by the 1st of December 2004. subject code credits period lecturer content

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Term Rewriting Systems 400121 6 4 and 5 prof.dr. J.W. Klop Term rewriting systems (TRSs) provide for a natural formalism for specifying rules of computation and investigating their properties. TRSs are of basic importance for functional programming and for the implementation of abstract data types. Applications can also be found in theorem proving, proof checking and logic programming. Some topics that will be covered in the course are: - Abstract Reduction Systems - Critical pairs and Knuth-Bendix completion - Orthogonality and reduction strategies - Termination (rpo's, monotone algebras) - Combinatory logic - Decidability issues - Infinitary rewriting Lectures and practice sessions. Will be provided Written examination. Compulsory: Inleiding logica. Advised: Algebraische specificaties, Inleiding theoretische informatica. mCS (also an elective course for mAI, mMath) (once every two years, not in 2004) Text Interface Design 400287 3 1 dr. J.F. Hoorn To make students acquainted with the design of text for computer dialogs, help files, manuals, and interactive multimedia. Language processing by users in writing and speech Sentence and text grammar Text structuring Stylistic devices (Non)linear story lines Computer dialogs in writing and speech Help and manuals Interactive multimedia (instruction, persuasion, entertainment, art) Classes Reader Text Interface Design Exercises and project Information Representation

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target audience mIS and mCS remarks Subscription compulsory for students of Information Science and Computer Science via TISVU as well as the bureau of education within the to be announced period. naam code docent studiepunten contacturen periode doel inhoud

werkwijze literatuur toetsing opmerkingen onderwijs

Thema: Aandacht in het brein 812001 dr. D.J. Heslenfeld 6 168 (20 werkcollege, 8 practicum, 140 zelfstudie) 5 en 6 Kennismaking met het moderne onderzoek naar de mechanismen van aandacht in onze hersenen. Aandacht bepaalt in belangrijke mate wat wij waarnemen en waarop wij reageren. Bij het moderne onderzoek naar aandacht spelen de neurale mechanismen een steeds centralere rol. Men probeert erachter te komen welke hersenstructuren aandacht besturen en op welke hersenstructuren aandacht vervolgens inwerkt. In deze cursus wordt een inleiding gegeven op dit moderne "neuro-cognitieve" onderzoek naar aandacht en daaraan gerelateerde functies. Deelnemers zullen kennis maken met actuele theorieën en recente data over de mechanismen van aandacht in onze hersenen. Moderne beeldvormende technieken van de hersenen in actie (zoals EEG en fMRI) zullen worden besproken en live gedemonstreerd. Deelnemers zullen zelf zowel proefleider als proefpersoon zijn bij lopend onderzoek naar de neurale basis van verschillende vormen van aandacht. Werkcolleges, presentaties en practica. Onder voorbehoud: Parasuraman, R. (2000). The Attentive Brain. Boston: MIT Press. Paper Maximaal aantal deelnemers: 16. Aanwezigheid bij de bijeenkomsten is verplicht. practicum zelfstudie werkcollege

Toegepaste Cognitieve Psychologie 813001 6 168 (3 tentamen, 42 presentatie, 5 practicum, 18 hoorcollege, 100 zelfstudie) 5 prof.dr. J.L. Theeuwes Kennismaking met hoe cognitieve psychologie in de praktijk kan worden toegepast bij het oplossen van alledaagse problemen. inhoud In de cursus komen een aantal centrale thema's in de toegepaste cognitieve psychologie aan de orde. Onderzoek in de toegepaste cognitieve psychologie wordt ook wel ergonomie of Human Factors onderzoek genoemd. Aan de hand van een aantal case studies wordt geleerd hoe je praktijk problemen kan omzetten inn concrete en onderzoekbare vraagstellingen. Er komen 4 thema's aan de orde: verkeer, stress en werkbelasting, bewegwijzering en juridisch beslisonderzoek. De cursus wordt afgesloten met een excursie naar het

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belangrijkste human factors laboratorium TNO Technische Menskunde in Soesterberg. Hoorcollege en werkcollege, eigen onderzoek opzetten, excursie naar TNO. Reader. tentamen presentatie Tentamen met open vragen. Presentatie van eigen onderzoek wordt meegenomen bij de bepaling van het eindcijfer. hoorcollege practicum zelfstudie Toegepaste analyse: financiele wiskunde 400076 6 4 en 5 prof.dr. M. van Veldhuizen Dit college geeft een inleiding in de wiskunde die binnen de financiële wiskunde gebruikt wordt. Aan de orde komen de volgende onderwerpen: • inleiding theorie van opties; • de binomiale methode; • inleiding differentiaalvergelijkingen; • de warmtevergelijking; • de Black-Scholes formule met toepassingen; • inleiding numerieke methoden, de benadering van de prijs van een (amerikaanse) optie. Hoorcollege (2 uur per week) met werkcollege (2 uur per week) en in te leveren huiswerkopgaven. P. Wilmott, S. Howison, J. Dewynne, The Mathematics of Financial Derivatives, A student introduction, Cambridge Unversity Press, 1995. Opgaven 3W, 3BWI, 3Ect • Het is mogelijk een aanvulling op het vak te doen door een specifiek onderwerp uit de theorie van de partiële differentiaalvergelijkingen of van de financiële wiskunde uit te werken. • het vak is ook in de masteropleiding toegestaan Vereist voor deelname aan het tentamen: Calculus (400013).

Topics in Anthroplogical Linguistics 539602 prof.dr. L.J. de Vries; prof.dr. W.L.M. Wetzels 5 14 hours (14 lecture) 5 Students learn how the basic concepts and methods are applied in research in the field of anthropological linguistics. content The following topics are discussed: 1) The linguistic and cultural typology of expletive nouns; 2) Orality and literacy; Primary oral languages; Linguistic, cultural and cognitive effects of writing; 3) Kinship terminology; 4)

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Counting and numeral systems. form of tuition Interactive lectures literature • W.A. Foley (1997). Anthropological Linguistics. Blackwell, chapters 5, 6, 13, and 21 • G.J. Van Enk & L.J. de Vries (1997). The Korowai of Irian Jaya. Their language in its cultural context. Oxford University Press, pp. 132-135, and chapter 4 (Kinship) • L.J. de Vries (1993). 'Clause combining in oral Trans-New Guinea languages'. In: TEXT, International Journal for the Study of Discourse 13: 481-502 • L.J. de Vries (1995). 'Spirits and friends: expletive nouns in Korowai of Irian Jaya'. In: Tales of a concave world. Liber Amicorum Bert Voorhoeve, ed. by C. Baak, M. Bakker and D. van der Mey, 178-188. Leiden: Department of Languages and Cultures of South-East Asia and Oceania of the Leiden University • L.J. de Vries (1995). 'Numeral systems of the Awyu language family of Irian Jaya'. In: Journal of the Royal Institute of Linguistics and Anthropology, BKI 150-III, 540-567 • L.J. de Vries (2003). New Guinea communities without writing and views of primary orality. Anthropos. Journal of Anthropology and Linguistics. mode of assessment Short paper entry requirements MPhil course 'Introduction to Anthropological Linguistics' target audience Master's students Linguistics (Bible Translation), MPhil students Linguistics remarks Registration via TISVU obligatory class lecture subject code credits period lecturer aim content

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User Interface Design 400081 4 1 and 2 dr. G.C. van der Veer To apply the theory of user centered design in a design team for a "real" client, and to experience actual use of multiple design techniques and tools The design of user interfaces and interactive systems requires insight in cognitive ergonomic aspects of system use and of task situation. The course provides hands on experience in applying design techniques and tools. Methods include task analysis, specification of the functionality and interface, scenario-based design, dialogue styles, formal representations, prototyping and evaluation techniques. The students will work in design teams to develop a real life design of an interactive system for groupware. There will be about 10 plenary sessions, and practical work will be done in subgroups, guided by consults from the teacher. Material and literature pointers can be found at http://www.cs.vu.nl/~mmc/uid Group design presentation and documentation. Human-Computer Interaction. Without passing that class, students cannot participate in User Interface Design.

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target audience 3I, mCS, 3AI, 3BI, 3MMC naam code studiepunten docent periode inhoud

literatuur toetsing blackboard onderwijs

Vakdidactiek 1 en 2 990000 30 Diverse docenten 30.08.2004 - 31.08.2005 De vakdidactiek houdt zich bezig met de inhoud van het schoolvak en met het lesgeven in het schoolvak. Er is aandacht voor vakspecifieke kennis, vaardigheden en inzichten en voor het schoolvak relevante ICT-toepassingen. In het vakdidactiekprogramma vindt eveneens een vertaling plaats van algemeen didactische thema's naar het vak. Een belangrijk onderdeel van de vakdidactiek is de meesterproef: in de derde fase ontwerpt de docent in opleiding als meesterproef onderwijsmateriaal volgens een aantal richtlijnen. Een meesterproef kan bestaan uit praktische opdrachten, trainingsmodules, een speciaal lessenpakket, een plan voor een excursie, etc. De docent in opleiding laat hiermee zien dat hij zelfstandig vanuit zijn eigen kennis en inzicht t.a.v. onderwijs, vak en maatschappij een uitgewerkt plan kan ontwerpen dat leerlingen in staat stelt op een bepaald gebied leerervaring op te doen. De meesterproef wordt uitgetest in de onderwijspraktijk en geëvalueerd. De vakdidacticus beoordeelt de meesterproef in het kader van het portfolio. Reader kan bij aanvang van de cursus aangeschaft worden. opdracht opdrachten worden opgenomen in het portfolio Ja werkcollege (30.08.2004 - 31.08.2005) op maandag

Verdieping Informatietechnologie voor juristen (M) 201542 9 prof.mr. A. Oskamp (kamer 5A-27, tel. (020) 444 6215); mr. A.R. Lodder (kamer 5A-27, tel. (020) 444 6215) periode week 6 - 15 doel Het behandelen van de mogelijkheden van informatietechnologie voor juristen (internet, databanken, kennissystemen), zowel vanuit een praktische als theoretische invalshoek. De centrale vraag is hoe informatietechnologie gebruikt kan worden door en voor juristen en welke voorwaarden aan dat gebruik vanuit juridische perspectief moeten worden gesteld. inhoud In de rechtspraktijk zijn vele toepassingen van informatietechnologie (IT) te vinden. Het OM wordt geadviseerd door een computerprogramma bij het bepalen van de straf (www.om.nl/bos), belastingaangifte kan via internet en stemmen nog (net) niet. Veel informatie is elektronisch te raadplegen, zoals jurisprudentie via www.rechtspraak.nl en kamerstukken via www.overheid.nl. Door deze verdergaande invoering van informatietechnologie in de rechtspraktijk is het voor juristen niet mogelijk optimaal te functioneren zonder althans enige kennis van informatietechnologie en vooral van de mogelijkheden en beperkingen daarvan voor de rechtspraktijk. Daarom is het volgen van de

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voorkennis onderwijs voorkennisvak

verdieping informatietechnologie voor juristen een voorwaarde om goed beslagen ten ijs de huidige informatiemaatschappij te betreden. Alleen dan kan de jurist op efficiënte, en niet minder belangrijk, kritische wijze gebruik maken van informatietechnologie. Aan de hand van het boek Informatietechnologie voor Juristen en een reader zullen de mogelijkheden en beperkingen van informatietechnologie binnen het recht worden behandeld. Ook zal worden ingegaan op nieuwe ontwikkelingen zoals elektronische dossiers bij de rechtbank en de inzet van intelligent agents daarbij en het oplossen van geschillen, zowel gerechtelijke als buiten de rechter om, via internet. Naast een tentamen, dient er ook een zelf gekozen rechtsterrein te worden geanalyseerd met het oog op een mogelijke IT-toepassing. Werkgroepen met practicum. A. Oskamp & A.R. Lodder (red.), Informatietechnologie voor Juristen, Kluwer, Deventer 2002, 2de druk. De deelnemers maken gedurende de collegeperiode een aantal schriftelijke opdrachten. Aan het eind van de collegeperiode maken zij een eindwerkstuk dat zij aan hun medecursisten presenteren en verdedigen. Het eindcijfer wordt bepaald op basis van de schriftelijke werkstukken. Er is ook een afsluitend tentamen. Deelname aan het verdiepingsvak is alleen mogelijk als de bacheloropleiding Nederlands recht en het voorsorteertraject IT en recht met goed gevolg is afgelegd. algemeen (week 6 - 15) 200367: IT en recht (B3/M) (En een voorsorteervak naar keuze.)

Web-gebaseerde kennisrepresentatie 400083 6 4 en 5 prof.dr. F.A.H. van Harmelen Doel van dit college is om de student kennis te laten maken met de mogelijkheden voor kennis-representatie technieken op het World Wide Web, en de technieken die daarvoor momenteel ontwikkeld worden. inhoud Het WWW biedt grote mogelijkheden voor het gebruik van bestaande en nieuwe kennisrepresentatie technieken. Een belangrijk doel hierbij is het omvormen van het huidige Web (pagina's die voor menselijke lezers bedoeld zijn) tot een Web waarin kennis expliciet is gemodelleerd, zodat deze ook voor machinaal gebruik geschikt is. Dit zal een belangrijke stap zijn naar de verwezenlijking van intelligentere zoek-machines, informatie-filters, adaptieve Web-sites, etc. In dit college behandelen we een aantal technieken die aan de basis van deze nieuwe generatie van het Web zullen staan: modelleer technieken (bijv. ontologieen), standaar web-technieken zoals XML) en kennisrepresenatie talen voor gebruik op het Web (RDF,OWL). Het college bespreekt ook een aantal toepassingsscenario's, zoals ecommerce, zoeken en navigeren, en format-onafhankelijk publiceren. werkwijze Intensief hoorcollege (3x per week) in de eerste 3 weken, met bijbehorend practicum in de weken daarna. In het practicum zal een toepassing worden gerealiseerd met voornoemde markup talen en systemen. literatuur A Semantic Web Primer, G. Antoniou & F. Van Harmelen, MIT Press, ISBN


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0-262-01210-3. doelgroep 2AI, 2BI, 3MMC, keuzevak voor I, BWI voorkennis Kennissystemen (gewenst). naam code docenten studiepunten periode doel

inhoud


opmerkingen voorkennis

Wetenschap, technologie en samenleving studies 470553 drs. M.B.M. Zweekhorst (coördinator); drs J.F. Caron Flinterman 3 15.11.2004 - 26.11.2004 • Kennismaking met filosofische en sociaal-wetenschappelijke theorieën over wetenschap- en technologieontwikkeling; • Inzicht verwerven in verschillende vormen van Technology Assessment; • Inzicht verwerven in interactieve methoden van sturing van wetenschap en technologie. De volgende onderwerpen zullen worden behandeld: • De hoofdlijnen van wetenschap, technologie en maatschappijstudies (WTS) en de wetenschapsleer, de opkomst van het (sociaal-) constructivisme en de democratisering van technologie-ontwikkeling; • De ontwikkeling van Constructive Technology Assessment; • Basisprincipes en het gebruik van een interactieve vorm van Technology Assessment. Zelfstudie en werkcolleges. Reader. Aanschaf van de reader is tijdens het eerste college. Prijs ongeveer 20 euro. Individuele toetsing door middel van tentamen. Onderdeel van de C/E- en M-variant van de algemene Masters Biologie, Biomedische wetenschappen en van de Bèta-brede Masters. Verplichte cursus in de Master Beleid, Management en Ondernemerschap voor natuur en levenswetenschappers. Inlichtingen en aanmelden via [email protected] Geen

Wetenschapsjournalistiek 471014 dr. J.T.J.M. Willems; drs. L. Linsen 6 04.10.2004 - 29.10.2004 • Inzicht verwerven in het proces van het populariseren van de betawetenschappen, met name het begrijpelijk en toegankelijk maken van wetenschappelijke informatie via de journalistiek; • Trainen in het zelf populair wetenschappelijk schrijven voor dagen weekbladen; • Trainen in het schrijven van enkele bijzondere genres zoals interviews, boekrecensies en opinie-artikelen. inhoud Deze module bestaat uit ochtenden waarin de diverse praktische en theoretische aspecten van het journalistiek schrijven over wetenschap (en technologie) aan de orde komen. Dat zijn bij voorbeeld schrijftechniek, interviewen en illustreren resp. de werking van de media, ethische aspecten en communicatiebarrières tussen onderzoekers en journalisten. Deze aspecten worden besproken tijdens werkcolleges (na zelfstudie), aan de


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werkwijze toetsing doelgroep opmerkingen voorkennis

hand van casussen (pgo) en met gastsprekers. De middagen zijn gereserveerd voor het schrijven van tenminste zes populair-wetenschappelijke artikelen. Dat doe je in groepjes van twee (of eventueel drie) studenten. De werkstukken (persberichten, artikelen en interviews) worden in de groep besproken. Het laatste artikel dient in principe geschikt te zijn voor publicatie in een dag- of weekblad (zoals Trouw of Natuurwetenschap & Techniek) (Werk-)colleges over de theorie en over de praktijk van de schrijvende journalistiek, vaardigheidstrainingen en huiswerk (in groepjes), zowel op het terrein van het zelf schrijven als op het beoordelen van andermans artikelen. Journalistiek schrijven, Donkers, H en J. Willems (red.), Coutinho, Bussum, 2002 (tweede druk). Je wordt beoordeeld op basis van je laatste werkstuk: een populairwetenschappelijk artikel voor een dagblad of tijdschrift. Deze module omvat veel huiswerk. Een deel daarvan past in de tijd van het studieprogramma, maar waarschijnlijk zul je ook daarbuiten tijd en energie moet zoeken om de geplande artikelen te schrijven. Zelforganiserende systemen 400090 5 1 en 2 dr. M.C. Schut De doelstelling van het college is het verwerven van basiskennis betreffende zelf organiserende systemen en emergentieverschijnselen. In deze cursus beschouwen we complexe systemen waar geordend gedrag spontaan optreedt. Typerend voor zulke systemen is dat ze bestaan uit vele simpele en interacterende componenten. Het gedrag van het systeem als geheel komt voort uit de interactie van de componenten. Deze systemen worden zelforganiserende systemen genoemd en er zijn tal van voorbeelden van dit soort systemen zoals zwermen vogels, ecologische systemen in de natuur, de vrije markt economie en sociaal gedrag van groepen mensen. Een deel van de cursus zal worden besteed aan het bestuderen van zogenaamde insectgebaseerde systemen zoals het vergaren van b.v. voedsel, het organiseren van het nest, het verdelen van de werklast en het gezamenlijk transporteren van objecten. Daarnaast zal er een aantal principes en mechanismen worden besproken die de ondergrond vormen voor de verschillende aspecten van zelforganisatie. Deze mechanismen en principes zullen duidelijk worden aan de hand van bestudering van computersimulaties van zelforganiserende systemen. In de cursus wordt intensief gebruik gemaakt van praktische voorbeelden en de bestudering van computersimulaties. Hoorcollege, gedurende 8 weken, 2 uur per week; practicum, gedurende 8 weken, 2 uur per week; werkcollege, 1 uur per week, waarin de opdrachten worden nabesproken. Werkstuk. 1AI; Keuzevak voor studenten uit andere richtingen. Meer informatie beschikbaar op BlackBoard Geen.

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Index Cancellation of interim examination or practical, 25 Education office, 16 Exemptions, 25 International relations, 16 Literature thesis, 26 Pr and information, 16 Publication of results of interim examinations, 25 Registering for interim examinations, 24 Registration of course results, 25 Right to inspection, 25 The validity of course results, 25

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Contents. Inhoudsopgave 5

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