Contents. 1 Computer Science (MSc) 5

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Computer Science (MSc) 5

1.1 Internet and Web Technology 5

1.1.1 Compulsory courses 5

1.1.2 Compulsory choices Software Engineering 5

1.1.3 Compulsory choice Theoretical Computer Science 5

1.1.4 Compulsory choice Mathematics 6

1.1.5 Optional choices Computer Science 6

1.1.6 Optional courses 6

1.2 High Performance Distributed Computing 6

1.3 Software Engineering 8

1.4 Multimedia 9

1.5 Formal Methods and Software Verification 10

1.5.4 Other compulsory choice 10

1.5.6 Compulsory choice Practical work Computer Science 11

1.5.7 Optional courses Theoretical Computer Science 11

1.6 Technical Artificial Intelligence 11

1.7 Information and Communication Technology (Society oriented variant) 12

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1.7.5 Minor 13

1.8 Computer Science and Communication 13

1.8.1 Computer Science part 13

1.8.2 Communication part 14

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1 Computer Science (MSc)

The information presented here concerns the structure of the MSc programme in Computer Science and detailed course information. More detailed and general information about the master programme - for instance the master coordinators, schedules, etcetera - can be found at the faculty's website

http://www.few.vu.nl/onderwijs/masters/cs/themaster.html Note:

Every programme, including the choice of optional courses, has to be discussed and agreed upon with the master coordinator or a personal mentor and approved by the Examination Board.

1.1 Internet and Web Technology

The Internet and the World Wide Web play an ever more central role in our society. The specialization Internet and Web Technology focuses on large-scale computer systems, especially computer networks and the Internet. Important topics are: Internet and Web protocols, distributed systems, network and computer security, development tools for network applications, peer-to-peer technology and large-scale decentralized solutions in general.

1.1.1 Compulsory courses

Course code

Course name Cr. Period

400161 Parallel Programming 6 1 400107 ICT in a Social Context 4 1 and 2 400130 Distributed Systems 6 2 400052 Network Programming 9 4 and 5 400127 Computer and Network Security 6 4 and 5 400196 Operating Systems Practical 9 4, 5 and 6 400442 Master Project Computer Science 36 Variable 400277 Literature Study 6 Variable

1.1.2 Compulsory choices Software Engineering

1 out of 2 Course code

400378 Advanced Topics in Software Design 6 1 and 2 400170 Software Architecture 6 2 and 3 400439 Software Testing 6 4 and 5 400413 Software Configuration Management 6 4 and 5

1.1.3 Compulsory choice Theoretical Computer Science

at least 6 cp, recommended Course

code

400211 Distributed Algorithms 6 4 and 5 400117 Protocol Validation 6 5 and 6

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1.1.4 Compulsory choice Mathematics

code

400353 Coding and Complexity 6 1 and 2 400178 Probability and Statistics 4 5

1.1.5 Optional choices Computer Science

code

400198 Computer Networks Practical 9 1, 2 and 3 400162 Parallel Programming Practical 6 2 and 3

1.1.6 Optional courses

Other courses from computer science and related fields, in consultation with the individual mentor for a number of cp such that the total Master program must comprise at least 120 cp.

1.2 High Performance Distributed Computing

High performance computing seeks to solve computing problems as fast and as efficiently as possible. The most important approach is to use a (large) number of computers instead of one, and let these computers work together, in parallel. In clusters and grids, the computers are typically distributed across an organization (a university, for example), a country, or even the globe. This has led to the term "high performance distributed computing".

Course code

400161 Parallel Programming 6 1 400107 ICT in a Social Context 4 1 and 2 400130 Distributed Systems 6 2 400162 Parallel Programming Practical 6 2 and 3 400362 Cluster and Grid Computing 6 4 and 5 400196 Operating Systems Practical 9 4, 5 and 6 400442 Master Project Computer Science 36 Variable 400277 Literature Study 6 Variable

400378 Advanced Topics in Software Design 6 1 and 2 400170 Software Architecture 6 2 and 3 400439 Software Testing 6 4 and 5 400413 Software Configuration Management 6 4 and 5

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code

at least 4 cp, recommended (1 out of 2) Course

code

Recommended optional courses

The UvA also provides some recommended courses. The facultary website provides more information on these courses.

Course code

400111 Evolutionary Computing 6 1 and 2 400165 Performance Analysis of Communication

Networks

6 1 and 2

400106 Computer Graphics 6 2 and 3 400052 Network Programming 9 4 and 5 400127 Computer and Network Security 6 4 and 5

Option minor in Bioinformatics Compulsory for this option

Course code

430045 Sequence Analysis 6 2 and 3 430046 DNA Protein Structure-Function Analysis

and Prediction

6 4

430048 Bioinformatic Data Analysis and Tools 6 4 and 5

Compulsory optional course Bioinformatics

Choose one of Course

code

400436 Computational Genomics and Proteomics 6 1 and 2

470622 Intracellular Networks 6 27.10.2008-21.11.2008 430047 Genome Analysis 6 September

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1.3 Software Engineering

Software engineering is often defined 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 role, next to cognitive and managerial aspects. Keywords are evolution and complexity. The field continually evolves, as the type of systems as well as the world at large changes. New developments such as outsourcing, global system development, service-orientation and the incorporation of off-the-shelf software profoundly influence the field.

Course code

400378 Advanced Topics in Software Design 6 1 and 2 400412 Software Asset Management 6 1 and 2 400107 ICT in a Social Context 4 1 and 2 400130 Distributed Systems 6 2 400170 Software Architecture 6 2 and 3 400413 Software Configuration Management 6 4 and 5 400058 Project Informatiekunde 9 4, 5 en 6 400442 Master Project Computer Science 36 Variable 400277 Literature Study 6 Variable

code

400117 Protocol Validation 6 5 and 6

code

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1.4 Multimedia

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, such 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 3D-graphics. In the specialization Multimedia there is special attention for the use of 3D virtual environments for the disclosure of multimedia information.

Course code

400440 Multimedia Authoring 6 1 400107 ICT in a Social Context 4 1 and 2 400441 Intelligent Multimedia Technology 6 2 400130 Distributed Systems 6 2 400170 Software Architecture 6 2 and 3 400106 Computer Graphics 6 2 and 3 400147 Visual Design 6 4 and 5 400555 Programmeren in Prolog 3 5 400442 Master Project Computer Science 36 Variable 400277 Literature Study 6 Variable 400358 Project Multimedia 6 any

code

400115 Logical Verification 6 1 and 2

Other courses from computer science and related fields, in consultation with the individual mentor for a number of cp such that the total Master program must comprise at least 120 cp. A recommended optional course is

Course code

400158 Multimedia Casus 6 2 and 3

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1.5 Formal Methods and Software Verification

The specialization FMSV is concerned with formal methods for the specification and verification of software systems and communication protocols. At the theory side, three disciplines play a central role: term rewriting, process algebra and co-induction. Tools based on process algebra are used for 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. At the more practical side, students are educated in the design and engineering of distributed systems.

Course code

400121 Term Rewriting Systems 6 1 and 2 400107 ICT in a Social Context 4 1 and 2 400115 Logical Verification 6 1 and 2 400130 Distributed Systems 6 2 400442 Master Project Computer Science 36 Variable 400277 Literature Study 6 Variable

400378 Advanced Topics in Software Design 6 1 and 2 400170 Software Architecture 6 2 and 3

at least 6 cp Course code

1.5.4 Other compulsory choice

1 out of 2, recommended are the following two courses. It is also possible to choose the UvA course Quantum Computing.

Course code

400132 Neural Networks 6 1 400127 Computer and Network Security 6 4 and 5

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code

1.5.6 Compulsory choice Practical work Computer Science

code

400052 Network Programming 9 4 and 5

1.5.7 Optional courses Theoretical Computer Science

Recommended are two of the following courses: the UvA courses Automated Reasoning, Recursion Theory, Theory and Application of Multi-Threading, Distributed Programming Methods, Advanced Modal Logic, Lambda Calculus, Model Theory, Game Theory, Kolmogorov Complexity, Core Logic B or the following VU course

Course code

400410 Voortgezette logica 4 4

1.6 Technical Artificial Intelligence

In this specialization the realisation of intelligent computer programs is the central subject. Artificial intelligence uses a great number of techniques from computer science and also plays a part in the development of these techniques, often inspired by human cognition. Analysing, modelling and implementing 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.

Course code

400054 Design of Multi-Agent Systems 6 1 400132 Neural Networks 6 1 400107 ICT in a Social Context 4 1 and 2 400111 Evolutionary Computing 6 1 and 2 400154 Machine Learning 6 2 400130 Distributed Systems 6 2 400555 Programmeren in Prolog 3 5

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400558 Project kennissystemen 6 5 en 6 400442 Master Project Computer Science 36 Variable 400277 Literature Study 6 Variable

code

400115 Logical Verification 6 1 and 2

1.7 Information and Communication Technology (Society oriented variant)

This is a variant of the Software Engineering specialization that is aimed at the education of computer scientists considering a career within companies or

administrative institutions, rather than at being involved with research. Courses with a more applied character dominate in the curriculum and the final project is in the form of an internship in a professional context, typically a company or a government or non-profit organization. The Information and Communication Technology variant provides students with a broad overview of the field of ICT and a minor in at least one related area, such as economics or computer law.

Course code

400107 ICT in a Social Context 4 1 and 2 400125 Knowledge Management and Modeling 6 1 and 2 400412 Software Asset Management 6 1 and 2 400130 Distributed Systems 6 2 400170 Software Architecture 6 2 and 3 400058 Project Informatiekunde 9 4, 5 en 6 400442 Master Project Computer Science 36 Variable 400277 Literature Study 6 Variable

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recommended Course code

400410 Voortgezette logica 4 4

code

1.7.5 Minor

A minor of at least 16 cp compulsory, broadening the view with courses from, e.g., the economical sciences. The minor has to be discussed and agreed upon with the master coordinator or a personal mentor.

1.8 Computer Science and Communication

This specialization is intended for students in Computer Science who want to specialize in communication. The programme consists of two parts: one part is

dedicated to training in Computer Science at the master level, the other is dedicated to communication and is shared with students with other bachelor degrees. It focuses on science communication theory and research as well as on science communication in practice.

The Communication part is taught in Dutch. Course

code

400442 Master Project Computer Science 36 Variable

1.8.1 Computer Science part Compulsory courses

Course code

400107 ICT in a Social Context 4 1 and 2 400130 Distributed Systems 6 2

Compulsory choice 1

One of Course code

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400440 Multimedia Authoring 6 1 400432 Human-Computer Interaction 6 2 and 3

400054 Design of Multi-Agent Systems 6 1 400083 Web-gebaseerde kennisrepresentatie 6 4 400558 Project kennissystemen 6 5 en 6 Compulsory choice 4 One of Course code

400115 Logical Verification 6 1 and 2 400211 Distributed Algorithms 6 4 and 5 400117 Protocol Validation 6 5 and 6

Optional courses

Other courses from computer science and related fields in consultation with the individual mentor for a number of cp such that the total Computer Science part must comprise at least 60 cp.

1.8.2 Communication part Compulsory courses

Communication part: compulsory courses

Also compulsory is a individual research project (21 cp) and a individual thesis (9 cp).

Course code

470582 Qualitative and Quantitative Research Methods

6 01.09.2008-26.09.2008

470587 Science and Communication 6 05.01.2009-30.01.2009

Compulsory choice

At least 12 cp of

Communication part: optional courses At least 12 cp are required. Course

code

470087 Gezondheidscommunicatie 6 01.06.2009-26.06.2009 470562 Interactive Communication 3 13.10.2008-24.10.2008 471026 Museologie en buitenschoolse educatie 6 24.11.2008-19.12.2008 471014 Wetenschapsjournalistiek (science

journalism)

6 27.10.2008-21.11.2008

471007 Interpersoonlijke communicatie 3 29.09.2008-10.10.2008 470572 Communication, Organization and

Management

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2 Exam parts

subject Advanced Topics in Software Design

code 400378

lecturer dr. P. Lago

credits 6

period 1 and 2

aim Learn advanced design techniques applicable to large software systems. Be able to select among them and apply them for a specific system. Be able to document and compare the design decisions.

content The lectures explain the most innovative design techniques. Examples are: service-oriented design, domain design and product line/family engineering, pattern-oriented design, web design, global software development.

The students work in small groups to discuss the different design techniques and how to use them for an assigned software system. They have to develop different representations of the system. Each representation has to emphasize how a certain design technique has been applied, and the pros and cons it brings in the developed solution. Each representation constitutes a design documentation for the software system.

form of tuition Lectures and group work.

literature Material handed out by the lecturer and on Blackboard.

mode of assessment Written reports of the assignment. Teamwork.

entry requirements Basic knowledge on Software Engineering theory and practice.

target audience mCS, 3IMM, mIS, mBMI, mAI

remarks Registration for this course is compulsory in TIS via https://tisvu.vu.nl/tis/menu, two weeks prior to the start.

Further information on this module will be made available on the Blackboard system http://bb.vu.nl.

subject Bioinformatic Data Analysis and Tools

code 430048

coördinatoren prof.dr. J. Heringa; dr.ir. K.A. Feenstra

lecturers prof.dr. J. Heringa; prof.dr. F.A.H. van Harmelen; dr. T. Kielmann; dr.ir. K.A. Feenstra

credits 6

period 4 and 5

aim 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, so to become a creative bioinformatics problem solver and tools creator.

• At the end of the course, students will have hands-on experience in statistical thermodynamics and clustering techniques.

content Theory:

• Microarray and array-CGH data, introduction to statistical

thermodynamics of soft and biological matter, molecular mechanics simulations and sampling, repeat recognition tools and concepts (e.g. transitivity), protein domain prediction concepts and tools, pattern

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recognition (clustering techniques), machine learning techniques, genetic algorithm, ontologies, semantic web, parallel computational techniques and GRID computing

Practical:

• Assignment statistical thermodynamics

• Assignment biological data clustering

form of tuition • 13 Lectures (2 two-hour lectures per week)

• Assignment introductions

• Computer practicals

• Hands-on support

Oral lectures, active participation, on-line assignments, assignment inductions and consultation (one-to-one teaching)

literature • E-course material (slides, assignment material, papers): http://ibi.vu.nl

• Books: Nelson, P., Biological Physics. Energy, Information, Life. W H Freeman & Co., July 2003, 600 pages, ISBN: 0716743728.

mode of assessment Assignment results and oral or written exam (depending on number of course students).

entry requirements A completed course Sequence Analysis and DNA/Protein Structure-Function Analysis and Prediction is a strong advantage. Some experience in

programming is required.

target audience MSc Bioinformatics, 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 Cluster and Grid Computing

code 400362

lecturer dr. T. Kielmann

credits 6

period 4 and 5

aim Students shall both explore the area of Cluster and Grid Computing and develop their skills in critical assessment of scientific literature.

content Both Cluster and Grid computing are areas of rapid technical developments. Many technical developments are still in flux. We investigate resource management and scheduling, remote data access, network and other performance issues, as well as software architecture and programming models for grids.

form of tuition Introductory lecture, followed by a seminar part and practical programming assignments. In the seminar part, students explore topic areas of Cluster and Grid Computing in small groups, present their findings in a presentation session and prepare a report. The practical programming assignments are to be addressed individually.

literature Various research articles as available online.

mode of assessment Both parts contribute 50% to the grade: (i) seminar presentation and report (ii) programming assignments

entry requirements Parallel Programming (code 400161)

target audience mPDCS, mCS-HPDC

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M.Sc. programme in Parallel and Distributed Computer Systems, and to students following the HPDC specialization of the Msc in Computer Science. Registration for the course is required before the first lecture by sending email to the lecturer; first come first serve.

subject Coding and Complexity

code 400353

lecturer dr. E. Wattel

credits 6

period 1 and 2

content During this course the following subjects are considered: Theory of computational complexity, theory of error correcting codes, Compression codes, and cryptograpy. The chapters of these subjects are: NP-completeness, primality tests, Rivest Shamir Adleman public key Crypto systems, Bose Ray-Chaudhury Hoquenghem error correcting codes, convolution codes, Lempel-Ziv data compression.

form of tuition Lectures.

mode of assessment Oral examination.

entry requirements Discrete Mathematics

target audience 3W, mMath, 3Ect, mCS, mPDCS

subject Communication, Organization and Management

code 470572

co-ordinator dr. M.B.M. Zweekhorst

lecturers dr. M.B.M. Zweekhorst; prof.dr. C.J. Hamelink; drs J. Maas; others

credits 6

period 29.09.2008-24.10.2008

aim • To get acquainted with communication theories

• To obtain in-depth understanding on communication from the perspective of sharing and influencing results

• To acquire knowledge on organizational structures and designs

• To get acquainted with important theories on organizational structures (e.g. Mintzberg)

• To acquire insight into different management practices in the health and lifescience sector;

• To obtain insight in motivation methods and conflict management

• To gain insight and to practice leadership

• To improve communication skills

• To practise team management

content Organizations in the health and life science sector are fast changing in part by newly emerging technologies and increasing societal complexity. A growing number of students with a beta degree become managers/professionals in these organizations. During this course students learn how to be effective performers both individually and in teams within organizations. This requires understanding the macro aspects of organizational behavior, which of

necessity involves managerial skills and ways of strategic thinking. Several speakers conduct lecturers on different aspects, such as motivation, managing behavior between people, leadership, communication and developing and changing of organizations. The speakers will explain theories from literature and relate the theories to the experiences from practice. In addition, the

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students become a project manager of a project team (second year course `Biomedisch Beleid en (Kennis)management’ of `Van Gen tot Gewas¿) that has been given the assignment to write a policy advisory report. While being a project manager you are trained and coached by experts. With the other students you discuss your experiences and the coach helps you relate the experiences to theory.

form of tuition Lectures, self study, training workshops project assignment

literature "Management and organizational behaviour", Wendy Bloisi (European edition), McGraw-Hill Education, ISBN 0-07-709945-1

mode of assessment Written exam and assessment of the functioning as a team manager. Note both parts need to be passed

target audience Compulsory course within the Masterprogramme Management, Policy Analysis and entrepreneurship for the health and life sciences (MPA) and the Societal differentiation of Health, Life and Natural Sciences Masters

programmes

remarks Attendance to trainingworkshops and project are compulsory.

subject Computational Genomics and Proteomics

code 400436

lecturer prof.dr. J. Heringa

credits 6

period 1 and 2

aim The course provides an insight into methods and algorithms for genomics and for proteomics data analysis. The course is aimed at students with an exact sciences background. At the end of the course students will be familiar with the basic principles of analysing the human genome and

high-throughput proteomics data.

content The course is structured around the following main topics:

Biology: An introduction to molecular biology and genome biology, lectures explaining principles of biology required for the course. No additional biological knowledge expected!

Sequences: Sequence comparison, searching large amounts of biological data, detecting genes and motifs

Genomes: Sequencing and assembling, genome duplication, rearrangements, evolution, comparative genomics, genome repeats

Proteomics: High-throughput mass spectrometry data, biomarker detection, computational diagnostics

Protein-protein interaction (PPI): interaction networks, mesoscopic modeling, docking

form of tuition Lectures and assignments.

literature Course materials and references are available at the Centre for Integrative Bioinformatics (IBIVU) website: http://www.ibivu.cs.vu.nl/teaching/

mode of assessment Written exam and assignments

entry requirements Writing algorithms in pseudocode; Mathematical skills.

target audience Third and fourth year students of CS, AI, Math, Physics.

remarks The course will only take place if at least 10 students register within the required notice period. The course is taught in English.

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subject Computer and Network Security

code 400127

lecturer dr. A. Mitrokotsa

credits 6

period 4 and 5

aim Introductive and broad course on security. At the end of the course student will be able to understand and apply the basic notion 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 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. Access control mechanisms, web security and wireless security issues will be also covered. Essential part of the course are the lab assignments.

form of tuition Lectures and practical assignments

literature Kaufman, C., Perlman, R., Speciner, M., Network Security: Private Communication in a Public World second edition. Prentice Hall, 2003.

mode of assessment Written exam and practical assignments.

entry requirements None.

target audience 3I, mCS, mPDCS, 3IK, 3AI, mBMI

remarks http://www.few.vu.nl/~kmitrok/net_security.html

subject Computer Graphics

code 400106

credits 6

period 2 and 3

lecturer dr. T. Kielmann

aim 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 techniques for computer graphics and their implications on graphics hardware.

content 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 programming languages C and C++. Topics of the lecture are:

• graphics programming with OpenGL;

• color, input, interaction;

• transformations (translation, rotation, scaling, shear);

• 3-dimensional viewing (projections, perspective);

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• light and shading;

• implementation of a renderer (clipping, anti-aliasing);

• modeling (object hierarchies, scene graphs);

• advanced topics (texture mapping, curves and surfaces).

form of tuition Lectures (in English) and programming assignments.

literature Edward Angel, Interactive Computer Graphics 4th edition. Addison Wesley.

mode of assessment 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.

entry requirements Introduction to programming.

target audience mCS, mPDCS, fourth year (and higher) students of FEW (and other faculties).

remarks The lectures are given in period 2; the programming assignments are continued in period 3.

subject Computer Networks Practical

code 400198

lecturer ir. M.P.H. Huntjens

credits 9

period 1, 2 and 3

aim Practical experience with the contents of the course Computer Networks.

content Two problems over the content of the course Computer Networks.

form of tuition Practical computer work.

literature See course Computer Networks.

mode of assessment Practical computer work.

entry requirements Computer Networks "Computernetwerken" (400487).

target audience mCS, mPDCS

subject Design of Multi-Agent Systems

code 400054

lecturer dr. M. Hoogendoorn

credits 6

period 1

content 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.

form of tuition Combination of lectures and practical assignments.

literature Reader.

mode of assessment On the basis of the homework assignments, practical assignments and a written exam.

entry requirements Kennissystemen (400126) and Logische taal en redeneermethoden (400043).

target audience 3AI, 3I, mCS

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subject Distributed Algorithms

code 400211

lecturer prof.dr. W.J. Fokkink

credits 6

period 4 and 5

aim To obtain a good understanding of concurrency concepts and a large range of distributed algorithms.

content Snapshots, traversal algorithms, termination detection, routing algorithms, deadlock-free packet switching, leader election, minimal spanning trees, anonymous networks, fault tolerance, failure detection, synchronization, mutual exclusion, garbage collection, scheduling.

form of tuition Lectures and exercise classes.

literature • Gerard Tel, Introduction to Distributed Algorithms (2nd edition). Cambridge University Press, 2000.

• Hagit Attiya and Jennifer Welch, Distributed Computing: Fundamentals, Simulations and Advanced Topics (chapter 4). McGraw-Hill, 1998.

• Jane Liu, Real-Time Systems. Prentice Hall, 2000.

mode of assessment Written examen (plus a home exercise sheet that can provide up to 0,5 bonus point).

subject Distributed Systems

code 400130

lecturer prof.dr.ir. M.R. van Steen

credits 6

period 2

aim After taking this course, the student will have gained insight in the design and implementation of modern distributed systems, and notably the trade-offs that need to be considered between making design decisions.

content We discuss the issues concerning the development of middleware systems for large-scale computer networks. Principles that are discussed

include architecture, processes, communication, naming,

synchronization, consistency and replication, fault tolerance, and security. These principles are further explained by means of different paradigms applied to distributed systems: object-based systems, distributed file systems (NFS), Web-based systems, and

coordination-based systems (publish/subscribe systems). 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.

form of tuition Lectures.

literature Tanenbaum, A.S., Steen, M. van, Distributed Systems,Principles and Paradigms 2nd edition. Prentice-Hall, 2007.

mode of assessment Written exam.

entry requirements Computer Networks (Computernetwerken, code 400016).

remarks More information, slides and relevant literature, can be found in Blackboard.

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subject DNA Protein Structure-Function Analysis and Prediction

code 430046

lecturers prof.dr. J. Heringa; dr.ir. K.A. Feenstra

credits 6

period 4

aim 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.

content Theory:

Protein and DNA structure basics, Protein folding and energetics,

experimental structure determination, protein fold families, protein structure databases, protein secondary and tertiary structure prediction, fold prediction, molecular modeling, protein-protein interactions, DNA/RNA

structure/function relationships, DNA/RNA structure prediction

Practical:

• Assignment homology modelling

• Assignment immunocomplex modelling

form of tuition 13 Lectures (2 two-hour lectures per week), Assignment introductions, Computer practicals, Hands-on support.

literature • E-course material: http://ibivu.cs.vu.nl

• Books: Branden, C., Tooze, J., Introduction to Protein Structure, 2nd edition or higher. Garland Science, 1998, 410 pp., ISBN 0815323050.

mode of assessment Assignment results and oral or written exam (depending on number of course students).

entry requirements Bachelor Physics, Chemistry, Mathematics, Computer Science, Biology, Medical Natural Sciences. A completed course Sequence Analysis (430045) is a strong advantage.

target audience Master students Bioinformatics, Students with Bachelor Physics, Chemistry, Mathematics, Computer Science, Biology, Medical Natural Sciences or Medicine, with a strong interest and some basic knowledge in

Bioinformatics.

subject Evolutionary Computing

code 400111

lecturer prof.dr. A.E. Eiben

credits 6

period 1 and 2

aim 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.

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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.

form of tuition Oral lectures and compulsory pogramming assignment.

literature Eiben, A.E., Smith, J.E., Introduction to Evolutionary Computing. Springer, 2003 ISBN 3-540-40184-9.

Slides available from http://www.cs.vu.nl/~gusz/ecbook/ecbook.html.

mode of assessment Written exam and pogramming assignment (weighted average).

target audience mBMI, 3AI, mAI, mCS, mPDCS

subject Genome Analysis

code 430047

coördinator prof.dr. J. Heringa

lecturers prof.dr. J. Heringa; Gastdocenten

credits 6

period September

aim A 1-month practical bioinformatics course about genome analysis. The course provides an introduction to genomics, the biological and algorithmic principles of genome analysis, as well as their practical implications.

Goals:

• At the end of the course, the student will be aware of the major issues, methodology and available algorithms in genome analysis.

• At the end of the course, the student will have hands-on experience in tackling biological problems in genome analysis.

content Theory:

• Genomic databases, Sequence alignment, dynamic programming,

database searching, gene prediction, and further appropriate downstream genomics analysis techniques

Practical:

• Practical assignments (a.o. multiple sequence alignment, homology searching)

• Reading, discussing and presenting seminal genomics papers

form of tuition • One-to-one assignment introductions

• Hands-on support

• Active participation

literature • E-course material, articles and overheads

• Xiong, J., Essential Bioinformatics, Cambridge University Press, 2006, ISBN-13: 978-0521600828.

mode of assessment Assignments, presentation results and oral or written exam.

entry requirements Bachelor course Genomics or equivalent.

target audience Third or fourth year students Computer Science, Mathematics, Chemistry or Physics;

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Master students Bioinformatics, Biomolecular Sciences, Biology and Biomedical Sciences

naam Gezondheidscommunicatie

code 470087

coördinator dr. J.E.W. Broerse

docenten dr M. Adriaanse; Gastdocenten; dr. E.W.M.L. de Vet; dr. J.E.W. Broerse

studiepunten 6

periode 01.06.2009-26.06.2009

doel • Inzicht krijgen in de centrale begrippen rond het communiceren van gezondheidsboodschappen naar de hele samenleving of specifieke doelgroepen

• In staat zijn een planningsmodel toe te passen op een concreet voorbeeld en de valkuilen te onderkennen in de planning van

gezondheidscommunicatie.

• In staat zijn het belang van de analyse van gezondheidsproblemen voor de planning van gezondheidscommunicatie te onderkennen, op te kunnen stellen en de uitkomsten te interpreteren.

• In staat zijn de gereedschappen van de voorlichter en de daarbij passende literatuur te beschrijven en toe te passen op een concreet voorbeeld.

• In staat zijn de uitkomsten van een gedrags- en

omgevingsfactorenanalyse van een gezondheidsprobleem te interpreteren en te verwerken in een plan van aanpak middels

gezondheidscommunicatie.

Niveau 2:Verdieping

inhoud In deze cursus worden de definities, concepten en theorieën rondom gezondheidscommunicatie en gedrag uiteengezet, alsook een aantal

specifieke vormen van (gezondheids)communicatie (persuasief, informatief en educatief), doelgroepen en kanalen (media; zoals TV, posters, etc.). Naast het bieden van een theoretisch kader is deze cursus gericht op de praktische toepasbaarheid. In het kader van een specifiek gezondheidsprobleem maak je met twee/drie medestudenten een probleemanalyse, definieer je de

doelgroep, maak je een gedrags- en omgevingsfactorenanalyse en bedenk je (op basis van de voorgaande analyses) een communicatiestrategie.

werkwijze Hoorcolleges, werkcolleges, (groeps)opdrachten en zelfstudie

literatuur Syllabus en aanvullende literatuur bij de colleges

toetsing • Beoordeling van de opdracht (drie deelopdrachten plus een presentatie): 40 procent van het eindcijfer.

• Schriftelijk tentamen (multiple choice en open vragen): 60 procent van het eindcijfer.

Voor zowel de opdracht, als het tentamen dient een voldoende behaald te worden!

doelgroep Keuze voor derdejaars studenten BSc Algemene

Gezondheidswetenschappen, derdejaars studenten BSc Gezondheid en Leven, en masterstudenten in 1 van de bètaopleidingen in de C-specialisatie (wetenschapscommunicatie).

De cursus wordt ten zeerste aanbevolen voor bachelorstudenten die de masterspecialisatie Preventie en gezondheid willen gaan volgen.

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presenteren en mag maximaal eenmaal afwezig zijn bij de werkcolleges. Maximaal 90 deelnemers.

subject Human-Computer Interaction

code 400432

lecturer dr. L.M. Aroyo

credits 6

period 2 and 3

aim Learn the fundamental concepts of human-computer interaction and user-centered design through hands-on experience in course projects, and

supported by lectures and readings. Learn to evaluate and design useable and effective graphical user interfaces for interactive systems.

content The lectures in this course will discuss and present examples of concepts and methods in the field of human-computer interaction. It will outline general usability challenges associated with existing case studies. It will also cover in detail the most important methods used in requirements gathering, iterative testing of interfaces, and summative evaluation phases of the user-centered design process. Next to the lectures in individual assignment students will be able to practice the use of relevant methods within the context of the the case study systems. Some of the topics covered in the course are: User Needs Analysis, Conceptual Design, Task Analysis, Mockups and Prototypes, Usability Evaluation.

form of tuition Lectures

literature • Tom Brinck, Darren Gergle and Scott Wood (2001). Usability for the Web: Designing Web Sites that Work, ISBN 978-1-55860-658-6

• Lecture notes and study guide in http://bb.vu.nl

mode of assessment 4 assignments and examination

target audience 2IMM, 3AI, 3I, mCS, mIS

subject ICT in a Social Context

code 400107

lecturer drs. W. Rekers

credits 4

period 1 and 2

content This course aims to introduce participants to the social context of ICT. This is done in four parts taught by different lecturers.

• part one, taught by Jan Willem van Doorn deals with ICT in practice. ICT is studied from a commercial point of view. Ethical issues are also

discussed from the point of view of the management of a large software firm;

• in part two, taught by lawyers from the Computer/Law Institute, the legal aspects of ICT are discussed;

• part three, taught by Joop Daalmeijer, journalist, editor in chief and manager, is devoted to a journalistic reflection on some trends in the development of the information society;

• part four, taught by Wijnand Rekers, concerns ethics and professional codes.

form of tuition Lectures (mainly in English).

literature To be announced on the Blackboard page of the course. Digital material will be made available there as well.

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mode of assessment Written exam (in English).

entry requirements None.

target audience mCS, mBMI, mAI, 2IK, 3IMM, mIS.

subject Intelligent Multimedia Technology

code 400441

credits 6

period 2

lecturer dr. A. Eliens

aim The course aims to provide practical and theoretical knowledge about the application of intelligent multimedia technology in the development of component-based multimedia applications

content The course will cover several topics, including:research and development of multimedia and game applications

• rich internet application(s) -- AJAX / Flex 3 SDK

• XML-based multimedia -- X3D/VRML, SVG, SMIL, XIMPEL

• web services for game and multimedia application development

• mashups -- component-based approach to web-based multimedia

The course takes an explorative approach in investigating the potential of the various technologies and services for multimedia and (serious) game

applications. Students are required to take an active role in exploring tools, APIs and SDKs, and are required to present their findings. The course will focus on the practical work of the students, organized in a series of

assignments.

form of tuition Lectures and practicum.

literature online reference material(s)

mode of assessment Essay and practicum assignment(s).

entry requirements Multimedia Authoring, or proficiency with VRML, and preferrably basic knowledge of XML.

target audience mCS-MM, and interested students.

remarks For information see: www.cs.vu.nl/~eliens/imt.

subject Interactive Communication

code 470562

coördinator drs. J.F.H. Kupper

lecturers drs. J.F.H. Kupper; prof.dr. C.J. Hamelink; drs. B.J. Regeer

credits 3

period 13.10.2008-24.10.2008

aim • To acquire insight into the need for different ways of (professional) communication

• To understand the dilemmas and constraints, which have been identified for interactive communication

• To establish and put into practice a framework for analyzing interactive communication

• To practice skills in interactive communication

content Changes in society have resulted in a growing need for (more) interactive communication. Within this course we analyze the change from Public Relations as a one way stream (such as Postbus 51 commercials) to

interactive communication (such as debates, conversations) at three levels. First of all, we assess the changes which have occurred within the societal

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context which reduced the success of the one-way stream. What does the transformation of the industrial society towards the network society mean for communication strategies? And, what limitations are faced by interactive communication at the macro-level (such as lock-in, resilience, institutional tradition). Secondly, what does this mean for communication instruments? For example, what is the difference between one-way and two-way

communication? How do you recognize the difference between a genuine open dialogue and a debate between different points of view? Thirdly, what are the constraints of interactive communication at the individual level? How can you recognize these within conversations and debates? Assessment of the relations and connections between the different levels forms an essential part of the course. Students will gain insight into the relevant theoretical concepts underlying the need for interactive communication.

form of tuition Lecturers, self study, workshops, training workshops and individual assignments.

literature Reader

mode of assessment Assessment is based on individual assignments, a group assignment and active participation. All assignments need to be passed.

target audience Optional course for Master students Management, Policy Analysis and Entrepreneurship in health and life sciences (MPA), Science communication and Societal differentiation of the Health, Life & Natural Sciences.

remarks Attendance of workshops and training workshops is compulsory. For information: [email protected]

naam Interpersoonlijke communicatie

code 471007

coördinator drs. I. Pauw

lecturers drs. I. Pauw; D.T.A. Wols

studiepunten 3

aim Development of:

• insight in interaction processes/ how communication takes place in groups;

• skills for communicating in groups effectively, especially in management roles.

content This course is concerned with gaining insight in interaction patterns that take place in a group. Your own contribution to the communication as a member of a group and your possibilities to fulfill a "leader¿s role" are discussed. We work with the Interpersonal Teacher¿s Behavior Model, which is used in the secondary teacher training program but which is also applicable in other situations. Effects of the `leader¿s` behavior on that of group members are analyzed. Also, `effective¿ behavior will be trained.

form of tuition Seminars and workshops during which theory will be analysed with the help of video images and practice through active training; identifying interaction patterns; training/rehearsing of communication skills.

literature Reader

mode of assessment On the basis of an assignment (e.g. via a video fragment), of which the results will be displayed in the portfolio.

target audience Optional course in the C-differentiations (Science Communication) of most of the two year master programs of FALW and FEW.

period 29.09.2008-10.10.2008

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remarks Course is taught in Dutch. Maximum participants: 20

subject Intracellular Networks

code 470622

co-ordinator dr. K. Krab

lecturers dr. F.J. Bruggeman; prof.dr. H.V. Westerhoff; dr. K. Krab; prof.dr. J. Heringa; dr. J.L. Snoep

credits 6

period 27.10.2008-21.11.2008

aim To train the students to analyse networks of cellular processes in terms of systems properties (System Biology). Integration of knowledge about individual processes and (spatial, temporal and organisational) structure of networks in biological systems.

content Enzyme kinetics; Metabolic and Hierarchical control Analysis; properties of metabolic and signalling networks. Analysis of quantitative kinetic models of such networks ('Silicon cells').

form of tuition Lectures, self-study and computerpractical.

literature Lecture notes (ca. 10 euro)

mode of assessment Written exam and computer assignment.

target audience Masterstudents with a background in Biology, Medical Biology,

Bioinformatics, Physics and Mathematics with an interest in the quantitative analysis of the behaviour of biological systems.

remarks Taught in English

subject Knowledge Management and Modeling

code 400125

lecturers dr. A.C.M. ten Teije; prof.dr. F.A.H. van Harmelen

credits 6

period 1 and 2

content 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. These knowledge models can be used to develop knowledge based systems. 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.

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.

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subject Literature Study

code 400277

lecturer various lecturers (Students should consult their mentor to find a topic and a supervisor.)

credits 6

period Variable

aim Students will learn to:

• conduct autonomously a literature study;

• search and select bibliographic material that is relevant for the chosen topic;

• give a presentation where they explain the research problem and present the state of the art.

content The course consists of carrying out a literature study on a topic chosen in agreement with a supervisor. Students select a topic of their interest that they particularly like, contact a person involved in the relevant research area and discuss with him/her the possibility to carry out a literature study under his/her supervision. Once agreed on the topic the study is carried out in two phases:

• Students autonomously search, select and study relevant related bibliographic material (i.e. papers, reports, books etc.)

• Give a written and/or oral presentation of the topic covered for an audience of computer scientists, for instance by giving a slide show. The exact form of presentation should be discussed and agreed upon with the supervisor. A clear indication of the used sources is an essential element of the presentation.

form of tuition Supervision by a faculty member.

mode of assessment Written and/or oral presentation (in English), exact form to be agreed with the supervisor.

target audience mCS, mAI-TAI

remarks http://www.few.vu.nl/~kmitrok/literature_study2008.html

subject Logical Verification

code 400115

lecturer dr. F. van Raamsdonk

credits 6

period 1 and 2

aim Introduction to type theory and the proof-assistant Coq.

content 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 proof-assistant 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.

form of tuition This is a 13-weeks cours with 4 hours class every week: 2 hours theory and 2 hours practical work.

literature Course notes.

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mode of assessment A written examination plus exercises. It is imperative to have a sufficient mark for the exercises.

entry requirements Inleiding logica (400119).

target audience mCS, mAI, mMath

subject Machine Learning

code 400154

lecturer drs. E.W. Haasdijk

credits 6

period 2

aim 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

• decision tree learning;

• artificial neural networks;

• evaluating hypotheses;

• bayesian learning;

• instance-based learning;

• Genetic Algorithms;

• learning sets of rules;

• reinforcement learning.

form of tuition Lectures with final written examination.

literature Tom Mitchell, Machine Learning. Mc Graw Hill, 1997 ISBN 0-07-042807-7.

mode of assessment Written eximination.

target audience 3BWI, 2AI, mCS

remarks Students are required to sign up for this course at Blackboard and via TIS: https://tis.vu.nl/tis/menu

naam Master Project Computer Science

code 400442

lecturer various lecturers

studiepunten 36

aim The Master Project is the place in the study where scientific and professional skills are trained most extensively. The Master Project will always involve an element of originality or creativity, for example in performing a design task or in contributing to the solution or the analysis of a scientific problem. Other important elements of the Master Project are the cooperation with

professionals and possibly with other students, planning the project, and documenting and presenting the final results.

content The Master project concludes the Master programme. It is either in the form of a graduation project in one of the research groups of the Department of Computer Science, or as an internship in a company. In most cases it will be performed as an individual project but it can be a group project as well. For additional information and rules we refer to the website of Exact Sciences.

There you will also find links to the web pages of the research groups of the Department of Computer Science, with options for master projects.

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form of tuition The Master Project has always to be supervised by a staff member, in the case of an internship in cooperation with a supervisor in the company. Internships proposed by the student him/herself need approval in advance from a member of staff, who will cooperate with supervising the project.

mode of assessment The final grade will be based on the quality of the research, the written thesis and an oral presentation.

target audience mCS

period Variable

remarks You will find useful documentation on all aspects of internships and the Master Project at the website of the Internship Office. This office can give you als advise about internships.

subject Multimedia Authoring

code 400440

docent dr. A. Eliens

credits 6

period 1

aim The course gives a practical introduction to multimedia authoring, in particular the development of 3D web applications.

content In the course an extensive introduction to the use of VRML (Virtual Reality Modeling Language) is given. Topics treated include the construction of 3D objects, positioning of objects in 3D space, material, light and animation. Also the use of images, video and sound to augment the users experience will be treated. Ample attention will be given to the programmatic interface to VRML, including prototypes and scripting, needed for the development of interactive applications.

The assignments include a 3D product demo and an infotainment application.

form of tuition lectures and practicum.

literature Online syllabus.

mode of assessment Practicum assignments.

target audience 2IK-minor MMC, mCS-MM and interested students.

remarks For course information, see www.cs.vu.nl/~eliens/mma For the course material, see www.cs.vu.nl/~eliens/web3d

subject Multimedia Casus

code 400158

lecturer dr. A. Eliens

credits 6

period 2 and 3

content 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