Computer Science MSc Vrije Universiteit Amsterdam - Faculteit der Exacte Wetenschappen - M Computer Science

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1 Computer Science MSc Vrije Universiteit Amsterdam M Computer Science Vrije Universiteit Amsterdam M Computer Science I

2 Computer Science is concerned with notions, methods and skills connected to the operation and applications of computers. The technical side of Computer Science includes 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. Vrije Universiteit Amsterdam M Computer Science II

3 Inhoudsopgave Research variant IWT 1 Individuele vakken 1 Optional Courses 1 Minor Bioinformatica 2 Minor BIOINFORMATICA Compulsory optional courses 2 Minor BIOINFORMATICA Compulsory courses 2 Compulsory Courses 2 Compulsory Optional Courses Theoretical Computer Science 3 Compulsory Optional Courses Mathematics 3 Compulsory Optional Courses Programming 4 Compulsory Optional Courses Software Engineering 4 History, philosophy & social aspects of science 4 Research variant HPDC 4 Individuele vakken 5 Optional Courses 5 Minor Bioinformatica 6 Minor BIOINFORMATICA Compulsory optional courses 6 Minor BIOINFORMATICA Compulsory courses 6 Compulsory Courses 6 Compulsory Optional Courses Theoretical Computer Science 7 Compulsory Optional Courses Mathematics 7 Compulsary Optional Courses Software Engineering 8 Compulsory optional courses Programming 8 vervallen XM_CS modules per History, philosophy & social aspects of science 8 Research variant Software Engineering 8 Individuele vakken 9 Optional Courses 9 Minor Bioinformatica 10 Minor BIOINFORMATICA Compulsory optional courses 10 Minor BIOINFORMATICA Compulsory courses 10 Compulsory Courses 11 Compulsory Optional Courses Mathematics 11 Compulsory Optional Courses Theoretical Computer Science 11 History, philosophy & social aspects of science 12 Research variant Multimedia 12 Individuele vakken 12 Keuzevakken 13 Minor Bioinformatica 13 Minor BIOINFORMATICA Compulsory optional courses 13 Minor BIOINFORMATICA Compulsory courses 13 Compulsory Courses 14 Compulsory Optional Courses Mathematics 14 Vrije Universiteit Amsterdam M Computer Science III

4 Verplichte keuze vakken Theoretical Computer Science 15 Compulsory optional courses Software Engineering 15 History, philosophy & social aspects of science 15 Research variant Formal Methods Software Verification 15 Individuele vakken 16 Optional Courses 16 Minor Bioinformatica 17 Minor BIOINFORMATICA Compulsory optional courses 17 Minor BIOINFORMATICA Compulsory courses 17 Compulsory Courses Theoretical Computer Science 18 Compulsory Optional Courses Mathematics 18 Verplichte keuze vakken 18 Compulsory Choise Practical Work 19 Compulsory Optional Courses Software Engineering 19 History, philosophy & social aspects of science 19 Research variant Technical Artificial Intelligence 20 Individuele vakken 20 Optional Courses 20 CSTAI Compulsory Courses 21 Compulsory Optional Courses Mathematics 21 Compulsory Optional Courses Software Engineering 22 Compulsory Optional Courses Theoretical Computer Science 22 History, philosophy & social aspects of science 22 Flexible Master s Programme 23 Vak: Advanced Logic 23 Vak: Advanced Selforganisation 23 Vak: Advances in Computer Architecture 24 Vak: Algorithms in Sequence Analysis 25 Vak: Automated Reasoning in AI 26 Vak: Behaviour Dynamics 27 Vak: Bioinformatics for Translational Medicine 28 Vak: Biosystems Data Analysis 30 Vak: Cluster and Grid Computing 30 Vak: Coding and Cryptography 31 Vak: Computational Finance 32 Vak: Computer and Network Security 32 Vak: Computer Graphics 33 Vak: Computer Networks Practical 34 Vak: Concurrency and Multithreading 35 Vak: Core Logic 35 Vak: Data Mining Techniques 36 Vak: Developing Services for the Cloud 37 Vak: Distributed Algorithms 38 Vak: Distributed Multimedia Systems 39 Vak: Distributed Systems 40 Vrije Universiteit Amsterdam M Computer Science IV

5 Vak: Evolutionary Computing 41 Vak: Experimental Design and Data Analysis 42 Vak: Fundamentals of Bioinformatics 43 Vak: History and Philosophy of the Information Society 44 Vak: Individual Systems Practical 45 Vak: Industrial Internship 45 Vak: Intelligent Web Applications 46 Vak: Internet programming 46 Vak: Knowledge Management and Modeling 47 Vak: Literature Study 47 Vak: Logical Verification 48 Vak: Master Project 49 Vak: Model Theory 50 Vak: Multimedia Authoring 50 Vak: Operating Systems 51 Vak: Operating Systems Practical 51 Vak: Parallel Programming 52 Vak: Parallel Programming Practical 53 Vak: Performance Analysis of Communication Networks 53 Vak: Project Multimedia 54 Vak: Quantum Computing 55 Vak: Scientific Writing in English 55 Vak: Service Oriented Design 57 Vak: Software Architectuur 58 Vak: Software Asset Management 59 Vak: Software Testing 59 Vak: Structural Bioinformatics 61 Vak: Term Rewriting Systems 62 Vak: Theory and Application of MultThreading 63 Vrije Universiteit Amsterdam M Computer Science V

6 Research variant IWT It needs no saying that Internet and World Wide Web play an ever more central role in our society. This specialisation is concerned with largescale computer systems, especially computer networks and the Internet. Important topics are: Internet and Web protocols, distributed systems, network security, development tools for network applications, peertopeer technology, etc. The progamme consists of 120 credits compulsory courses 81 credits (including a Master Project of 36 credits) compulsory choices Software Engineering 6 credits compulsory choices Theoretical computer Science at least 6 credits compulsory choices Mathematics at least 3 credits optional courses Computer Science at least 6 credits optional courses 18 credits 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. Master Coordinator: Dr. S. Voulgaris K room R447 T +31 (0) E spyros.voulgaris@vu.nl Opleidingsdelen: Individuele vakken Optional Courses Compulsory Courses History, philosophy & social aspects of science Individuele vakken Optional Courses Opleidingsdelen: Minor Bioinformatica Advanced Logic Periode X_ Cluster and Grid Computing Period X_ Computer Graphics Period X_ Vrije Universiteit Amsterdam M Computer Science Pagina 1 van 64

7 Distributed Multimedia Systems Minor Bioinformatica Period X_ Evolutionary Computing Period X_ Industrial Internship Ac. Jaar (september) 6.0 X_ Intelligent Web Applications Periode X_ Knowledge Management and Modeling Period X_ Operating Systems Periode X_ Parallel Programming Periode X_ Performance Analysis of Communication Networks Periode X_ Term Rewriting Systems 6.0 X_ Opleidingsdelen: Minor BIOINFORMATICA Compulsory optional courses Minor BIOINFORMATICA Compulsory courses Minor BIOINFORMATICA Compulsory optional courses Biosystems Data Analysis Periode X_ Literature Study Ac. Year (September) 6.0 X_ Structural Bioinformatics Periode X_ Minor BIOINFORMATICA Compulsory courses Algorithms in Sequence Analysis Bioinformatics for Translational Medicine Fundamentals of Bioinformatics Compulsory Courses Periode X_ Periode X_ Periode X_ Vrije Universiteit Amsterdam M Computer Science Pagina 2 van 64

8 Opleidingsdelen: Compulsory Optional Courses Theoretical Computer Science Compulsory Optional Courses Mathematics Compulsory Optional Courses Programming Compulsory Optional Courses Software Engineering Computer and Network Security Period X_ Distributed Systems Period X_ History and Philosophy of the Information Society Periode X_ Internet programming Periode X_ Literature Study Ac. Year (September) 6.0 X_ Master Project Ac. Year (September) 36.0 X_ Scientific Writing in English Ac. Jaar (september), Periode 4, Periode 5, Periode X_ Compulsory Optional Courses Theoretical Computer Science Compulsory choice Theoretical Computer Science at least 6 credits, recommended are the courses below. 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. Concurrency and Multithreading Periode X_ Distributed Algorithms Period X_ Logical Verification Ac. Year (September) 6.0 X_ Compulsory Optional Courses Mathematics Compulsory choice Mathematics at least 3 credits, recommended are the courses below. 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. Vrije Universiteit Amsterdam M Computer Science Pagina 3 van 64

9 Coding and Cryptography Periode X_ Experimental Design and Data Analysis Periode X_ Compulsory Optional Courses Programming Computer Networks Practical Periode X_ Individual Systems Practical Ac. Jaar (september) 6.0 X_ Operating Systems Practical Periode X_ Parallel Programming Practical Periode X_ Compulsory Optional Courses Software Engineering Compulsory choice Computer Science at least 6 credits, recommended are the courses below. 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. Service Oriented Design Periode X_ Software Architectuur Periode X_ Software Asset Management Period X_ Software Testing Period X_ History, philosophy & social aspects of science The choice of one of these elective courses, has to be discussed and agreed upon with the master coordinator or a personal mentor and approved by the Examination Board. Research variant HPDC 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 had led to the term "high Vrije Universiteit Amsterdam M Computer Science Pagina 4 van 64

10 performance distributed computing." The progamme consists of 120 credits compulsory courses 75 credits (including a Master Project of 36 credits) compulsory choices Software Engineering 6 credits compulsory choices Theoretical computer Science at least 6 credits compulsory choices Mathematics at least 3 credits optional courses 30 credits It is possible to fill the optional courses with a Minor Bioinformatics. 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. Master Coordinator: Dr. S. Voulgaris K room R447 T +31 (0) E spyros.voulgaris@vu.nl Opleidingsdelen: Individuele vakken Optional Courses Compulsory Courses vervallen XM_CS modules per History, philosophy & social aspects of science Individuele vakken Optional Courses Opleidingsdelen: Minor Bioinformatica Advanced Logic Periode X_ Advances in Computer Architecture Computer and Network Security Semester X_ Period X_ Computer Graphics Period X_ Distributed Multimedia Systems Period X_ Evolutionary Computing Period X_ Industrial Internship Ac. Jaar (september) 6.0 X_ Vrije Universiteit Amsterdam M Computer Science Pagina 5 van 64

11 Intelligent Web Applications Periode X_ Internet programming Periode X_ Knowledge Management and Modeling Minor Bioinformatica Period X_ Operating Systems Periode X_ Performance Analysis of Communication Networks Periode X_ Term Rewriting Systems 6.0 X_ Opleidingsdelen: Minor BIOINFORMATICA Compulsory optional courses Minor BIOINFORMATICA Compulsory courses Minor BIOINFORMATICA Compulsory optional courses Biosystems Data Analysis Periode X_ Literature Study Ac. Year (September) 6.0 X_ Structural Bioinformatics Periode X_ Minor BIOINFORMATICA Compulsory courses Algorithms in Sequence Analysis Bioinformatics for Translational Medicine Fundamentals of Bioinformatics Compulsory Courses Periode X_ Periode X_ Periode X_ Opleidingsdelen: Compulsory Optional Courses Theoretical Computer Science Compulsory Optional Courses Mathematics Compulsary Optional Courses Software Engineering Vrije Universiteit Amsterdam M Computer Science Pagina 6 van 64

12 Compulsory optional courses Programming Cluster and Grid Computing Period X_ Distributed Systems Period X_ History and Philosophy of the Information Society Periode X_ Literature Study Ac. Year (September) 6.0 X_ Master Project Ac. Year (September) 36.0 X_ Parallel Programming Periode X_ Parallel Programming Practical Scientific Writing in English Periode X_ Ac. Jaar (september), Periode 4, Periode 5, Periode X_ Compulsory Optional Courses Theoretical Computer Science Compulsory choice Theoretical Computer Science at least 6 credits, recommended are the courses below. 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. Concurrency and Multithreading Periode X_ Distributed Algorithms Period X_ Logical Verification Ac. Year (September) 6.0 X_ Compulsory Optional Courses Mathematics Compulsory choice Mathematics at least 3 credits, recommended are the courses below. 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. Coding and Cryptography Periode X_ Vrije Universiteit Amsterdam M Computer Science Pagina 7 van 64

13 Experimental Design and Data Analysis Periode X_ Compulsary Optional Courses Software Engineering Students need to select a total of 6 credits or more from the following list. 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. Service Oriented Design Periode X_ Software Architectuur Periode X_ Software Asset Management Period X_ Software Testing Period X_ Compulsory optional courses Programming Computer Networks Practical vervallen XM_CS modules per Periode X_ Individual Systems Practical Ac. Jaar (september) 6.0 X_ Operating Systems Practical Periode X_ Computational Finance 6.0 X_ History, philosophy & social aspects of science The choice of one of these elective courses, has to be discussed and agreed upon with the master coordinator or a personal mentor and approved by the Examination Board. Research variant Software Engineering Vrije Universiteit Amsterdam M Computer Science Pagina 8 van 64

14 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. 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, serviceorientation and the incorporation of offtheshelf software profoundly influence the field. The progamme consists of 120 credits compulsory courses 90 credits (including a Master Project of 36 credits) compulsory choices Theoretical Computer Science at least 6 credits compulsory choices Mathematics at least 3 credits optional courses 21 credits 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. Master Coordinator: Prof.dr. J.C. van Vliet K room U303 T +31 (0) E jc.van.vliet@few.vu.nl Opleidingsdelen: Individuele vakken Optional Courses Compulsory Courses History, philosophy & social aspects of science Individuele vakken Optional Courses Opleidingsdelen: Minor Bioinformatica Advanced Logic Periode X_ Cluster and Grid Computing Period X_ Computer and Network Security Period X_ Computer Graphics Period X_ Vrije Universiteit Amsterdam M Computer Science Pagina 9 van 64

15 Developing Services for the Cloud Distributed Multimedia Systems Minor Bioinformatica Periode X_ Period X_ Evolutionary Computing Period X_ Industrial Internship Ac. Jaar (september) 6.0 X_ Intelligent Web Applications Periode X_ Internet programming Periode X_ Knowledge Management and Modeling Period X_ Operating Systems Periode X_ Parallel Programming Periode X_ Performance Analysis of Communication Networks Scientific Writing in English Periode X_ Ac. Jaar (september), Periode 4, Periode 5, Periode X_ Software Testing Period X_ Term Rewriting Systems 6.0 X_ Opleidingsdelen: Minor BIOINFORMATICA Compulsory optional courses Minor BIOINFORMATICA Compulsory courses Minor BIOINFORMATICA Compulsory optional courses Biosystems Data Analysis Periode X_ Literature Study Ac. Year (September) 6.0 X_ Structural Bioinformatics Periode X_ Minor BIOINFORMATICA Compulsory courses Algorithms in Sequence Analysis Bioinformatics for Translational Medicine Periode X_ Periode X_ Vrije Universiteit Amsterdam M Computer Science Pagina 10 van 64

16 Fundamentals of Bioinformatics Periode X_ Compulsory Courses Opleidingsdelen: Compulsory Optional Courses Mathematics Compulsory Optional Courses Theoretical Computer Science Distributed Systems Period X_ History and Philosophy of the Information Society Periode X_ Literature Study Ac. Year (September) 6.0 X_ Master Project Ac. Year (September) 36.0 X_ Service Oriented Design Periode X_ Software Architectuur Periode X_ Software Asset Management Period X_ Compulsory Optional Courses Mathematics Compulsory choice Mathematics at least 3 credits, recommended are the courses below. 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. Coding and Cryptography Periode X_ Experimental Design and Data Analysis Periode X_ Compulsory Optional Courses Theoretical Computer Science Compulsory choice Theoretical Computer Science at least 6 credits, recommended are the courses below. 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. Vrije Universiteit Amsterdam M Computer Science Pagina 11 van 64

17 Concurrency and Multithreading Periode X_ Distributed Algorithms Period X_ Logical Verification Ac. Year (September) 6.0 X_ History, philosophy & social aspects of science The choice of one of these elective courses, has to be discussed and agreed upon with the master coordinator or a personal mentor and approved by the Examination Board. Research variant 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, 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. In the specialization Multimedia there is special attention for the use of 3D virtual environments for the disclosure of multimedia information. The progamme consists of 120 credits compulsory courses 87 credits (including a Master Project of 36 credits) compulsory choices Mathematics at least 3 credits compulsory choices Theoretical computer Science at least 6 credits optional courses 27 credits 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. Master Coordinator: Prof.dr. A. Eliens K room T333 T +31 (0) E a.eliens@few.vu.nl Opleidingsdelen: Individuele vakken Keuzevakken Compulsory Courses History, philosophy & social aspects of science Individuele vakken Vrije Universiteit Amsterdam M Computer Science Pagina 12 van 64

18 Keuzevakken Opleidingsdelen: Minor Bioinformatica Advanced Logic Periode X_ Cluster and Grid Computing Period X_ Computer and Network Security Distributed Multimedia Systems Minor Bioinformatica Period X_ Period X_ Evolutionary Computing Period X_ Industrial Internship Ac. Jaar (september) 6.0 X_ Intelligent Web Applications Periode X_ Internet programming Periode X_ Knowledge Management and Modeling Period X_ Operating Systems Periode X_ Parallel Programming Periode X_ Performance Analysis of Communication Networks Periode X_ Opleidingsdelen: Minor BIOINFORMATICA Compulsory optional courses Minor BIOINFORMATICA Compulsory courses Minor BIOINFORMATICA Compulsory optional courses Biosystems Data Analysis Periode X_ Literature Study Ac. Year (September) 6.0 X_ Structural Bioinformatics Periode X_ Vrije Universiteit Amsterdam M Computer Science Pagina 13 van 64

19 Minor BIOINFORMATICA Compulsory courses Algorithms in Sequence Analysis Bioinformatics for Translational Medicine Fundamentals of Bioinformatics Compulsory Courses Periode X_ Periode X_ Periode X_ Opleidingsdelen: Compulsory Optional Courses Mathematics Verplichte keuze vakken Theoretical Computer Science Compulsory optional courses Software Engineering Computer Graphics Period X_ Distributed Systems Period X_ History and Philosophy of the Information Society Periode X_ Literature Study Ac. Year (September) 6.0 X_ Master Project Ac. Year (September) 36.0 X_ Multimedia Authoring Periode X_ Project Multimedia 6.0 X_ Scientific Writing in English Ac. Jaar (september), Periode 4, Periode 5, Periode 6 Compulsory Optional Courses Mathematics 3.0 X_ Software Architectuur Periode X_ Compulsory choice Mathematics at least 3 credits, recommended are the courses below. 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. Vrije Universiteit Amsterdam M Computer Science Pagina 14 van 64

20 Coding and Cryptography Periode X_ Experimental Design and Data Analysis Periode X_ Verplichte keuze vakken Theoretical Computer Science Compulsory choice Theoretical Computer Science at least 6 credits, recommended are the courses below. 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. Concurrency and Multithreading Periode X_ Distributed Algorithms Period X_ Logical Verification Ac. Year (September) 6.0 X_ Term Rewriting Systems 6.0 X_ Compulsory optional courses Software Engineering Service Oriented Design Periode X_ Software Asset Management Period X_ Software Testing Period X_ History, philosophy & social aspects of science The choice of one of these elective courses, has to be discussed and agreed upon with the master coordinator or a personal mentor and approved by the Examination Board. Research variant Formal Methods Software Verification 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 safetycritical 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 Vrije Universiteit Amsterdam M Computer Science Pagina 15 van 64

21 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. Coinduction 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. The progamme consists of 120 credits compulsory courses 63 credits (including a Master Project of 36 credits) compulsory choices Software Engineering 6 credits compulsory choices Theoretical Computer Science at least 6 credits other compulsory choice 6 credits compulsory choices Mathematics at least 3 credits compulsory choices Practical work Computer Science at least 6 credits optional courses 30 credits 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. Master Coordinator: Dr. R.C. de Vrijer K room U341 T +31 (0) E rc.de.vrijer@few.vu.nl Opleidingsdelen: Individuele vakken Optional Courses Compulsory Courses Theoretical Computer Science History, philosophy & social aspects of science Individuele vakken Optional Courses Opleidingsdelen: Minor Bioinformatica Cluster and Grid Computing Period X_ Computer and Network Security Period X_ Vrije Universiteit Amsterdam M Computer Science Pagina 16 van 64

22 Computer Graphics Period X_ Core Logic Periode X_ Distributed Multimedia Systems Minor Bioinformatica Period X_ Evolutionary Computing Period X_ Industrial Internship Ac. Jaar (september) 6.0 X_ Intelligent Web Applications Periode X_ Internet programming Periode X_ Knowledge Management and Modeling Period X_ Model Theory Periode X_ Operating Systems Periode X_ Parallel Programming Periode X_ Performance Analysis of Communication Networks Periode X_ Quantum Computing Semester X_ Theory and Application of MultThreading Period X_ Opleidingsdelen: Minor BIOINFORMATICA Compulsory optional courses Minor BIOINFORMATICA Compulsory courses Minor BIOINFORMATICA Compulsory optional courses Biosystems Data Analysis Periode X_ Literature Study Ac. Year (September) 6.0 X_ Structural Bioinformatics Periode X_ Minor BIOINFORMATICA Compulsory courses Algorithms in Sequence Analysis Bioinformatics for Translational Medicine Periode X_ Periode X_ Vrije Universiteit Amsterdam M Computer Science Pagina 17 van 64

23 Fundamentals of Bioinformatics Periode X_ Compulsory Courses Theoretical Computer Science Opleidingsdelen: Compulsory Optional Courses Mathematics Verplichte keuze vakken Compulsory Choise Practical Work Compulsory Optional Courses Software Engineering Distributed Systems Period X_ History and Philosophy of the Information Society Periode X_ Literature Study Ac. Year (September) 6.0 X_ Master Project Ac. Year (September) 36.0 X_ Scientific Writing in English Ac. Jaar (september), Periode 4, Periode 5, Periode 6 Compulsory Optional Courses Mathematics 3.0 X_ Term Rewriting Systems 6.0 X_ Compulsory choice Mathematics at least 3 credits, recommended are the courses below. 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. Coding and Cryptography Periode X_ Experimental Design and Data Analysis Verplichte keuze vakken Periode X_ Students need to select a total of 6 credits or more from the following list. 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. Vrije Universiteit Amsterdam M Computer Science Pagina 18 van 64

24 Advanced Logic Periode X_ Concurrency and Multithreading Compulsory Choise Practical Work Periode X_ Distributed Algorithms Period X_ Logical Verification Ac. Year (September) 6.0 X_ Compulsory choice Practical Work Computer Science at least 6 credits, recommended are the courses below. 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. Computer Networks Practical Periode X_ Operating Systems Practical Periode X_ Parallel Programming Practical Periode X_ Compulsory Optional Courses Software Engineering Students need to select a total of 6 credits or more from the following list. 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. Service Oriented Design Periode X_ Software Architectuur Periode X_ Software Asset Management Period X_ Software Testing Period X_ History, philosophy & social aspects of science Vrije Universiteit Amsterdam M Computer Science Pagina 19 van 64

25 The choice of one of these elective courses, has to be discussed and agreed upon with the master coordinator or a personal mentor and approved by the Examination Board. Research variant 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. 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. The progamme consists of 120 Ec compulsory courses 81 Ec (including a Master Project of 36 Ec) compulsory choices Software Engineering 6 Ec compulsory choices Mathematics at least 3 Ec compulsory choices Theoretical Computer Science at least 6 Ec optional courses 24 Ec 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. Master Coordinator: dr. M. Hoogendoorn K room T320a T +31 (0) E m.hoogendoorn@few.vu.nl Opleidingsdelen: Individuele vakken Optional Courses CSTAI Compulsory Courses History, philosophy & social aspects of science Individuele vakken Optional Courses Advanced Selforganisation Period X_ Automated Reasoning in AI Period X_ Cluster and Grid Computing Period X_ Vrije Universiteit Amsterdam M Computer Science Pagina 20 van 64

26 Computer and Network Security CSTAI Compulsory Courses Period X_ Computer Graphics Period X_ Data Mining Techniques Period X_ Distributed Multimedia Systems Period X_ Industrial Internship Ac. Jaar (september) 6.0 X_ Internet programming Periode X_ Operating Systems Periode X_ Parallel Programming Periode X_ Performance Analysis of Communication Networks Periode X_ Term Rewriting Systems 6.0 X_ Opleidingsdelen: Compulsory Optional Courses Mathematics Compulsory Optional Courses Software Engineering Compulsory Optional Courses Theoretical Computer Science Behaviour Dynamics Periode X_ Distributed Systems Period X_ Evolutionary Computing Period X_ History and Philosophy of the Information Society Periode X_ Intelligent Web Applications Periode X_ Knowledge Management and Modeling Period X_ Literature Study Ac. Year (September) 6.0 X_ Master Project Ac. Year (September) 36.0 X_ Scientific Writing in English Ac. Jaar (september), Periode 4, Periode 5, Periode 6 Compulsory Optional Courses Mathematics 3.0 X_ Compulsory choice Mathematics at least 3 credits, recommended are the courses below. 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. Vrije Universiteit Amsterdam M Computer Science Pagina 21 van 64

27 Coding and Cryptography Periode X_ Experimental Design and Data Analysis Periode X_ Compulsory Optional Courses Software Engineering Students need to select a total of 6 credits or more from the following list. 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. Service Oriented Design Periode X_ Software Architectuur Periode X_ Software Asset Management Period X_ Software Testing Period X_ Compulsory Optional Courses Theoretical Computer Science Compulsory choice Theoretical Computer Science at least 6 credits, recommended is the course below. 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. Advanced Logic Periode X_ Concurrency and Multithreading Periode X_ Distributed Algorithms Period X_ Logical Verification Ac. Year (September) 6.0 X_ History, philosophy & social aspects of science The choice of one of these elective courses, has to be discussed and agreed upon with the master coordinator or a personal mentor and approved by the Examination Board. Vrije Universiteit Amsterdam M Computer Science Pagina 22 van 64

28 Flexible Master s Programme Advanced Logic Vakcode X_ (405048) Periode Periode 4 Voertaal Engels Faculteit Coördinator dr. R.D.A. Hendriks Docent(en) dr. R.D.A. Hendriks, A. Polonsky Lesmethode(n) Hoorcollege, Werkcollege Doel vak The objective is to obtain a good understanding of modal logic and its use in computer science and artificial intelligence. Inhoud vak A thorough introduction to modal logics, and its applications in computer science and artificial intelligence. We will select some themes from the book Modal Logics for Open Minds, by Johan van Benthem: basic modal logic and possible world semantics, bisimulation and invariance, modal definability, decidability,... In particular we treat the modal logics most relevant to computer science and AI: temporal, dynamic and epistemic logic. Onderwijsvorm Weekly 2 lectures and 1 exercise class, for the duration of 7 weeks. Toetsvorm A written exam and assignments that can make half a point bonus. Literatuur Johan van Benthem, Modal Logics for Open Minds, CSLI Publications Aanbevolen voorkennis The bachelor course Logica en Modelleren (previously Inleiding Logica), or an equivalent introduction to firstorder logic. Doelgroep maiktiia, maitli, maicvar, mcsfmsv Advanced Selforganisation Course code X_ (400434) Period Period 2 Language of tuition English Faculty Coordinator dr. M.C. Schut Vrije Universiteit Amsterdam M Computer Science Pagina 23 van 64

29 Teaching staff Teaching method(s) dr. M.C. Schut Lecture Course objective To understand, simulate and analyse the behaviour and selforganization of complex systems. The student is able to explain, implement and recognize basic principles and properties of such systems. Course content This course is about the understanding of the behavior and selforganization of complex systems: systems in which the interaction of the components is not simply reducible to the properties of the components. The general question the we address is: how should systems of very many independent computational (e.g. robotic or software) agents cooperate in order to process information and achieve their goals, in a way that is efficient, self optimizing, adaptive, and robust in the face of damage or attack? We will look at natural systems that solve some of the same problems that we want to solve, e.g. adaptive path minimization by ants, wasp and termite nest building, army ant raiding, fish schooling and bird flocking, coordinated cooperation in slime molds, synchronized firefly flashing, evolution by natural selection, game theory and the evolution of cooperation. The course includes a practical part in which students implement a simulation of a selforganizing complex system and conduct structured experimental analysis with this simulation. Form of tuition Theory in lectures and practice in labs. Type of assessment Report including description of simulation and experimental analysis. Course reading Schut M.C., Scientific Handbook for Simulation of Collective Intelligence, Available at collectivae. net/. Target group maicis, maiha, maiktiia, maitai, mba, mbad, mcstai, mpdcs Remarks More information available on BlackBoard. This is a project oriented course and therefore students will be expected to have basic programming skills. Advances in Computer Architecture Vakcode X_ (418047) Periode Semester 1 Voertaal Engels Faculteit Inhoud vak The course description is available on: Vrije Universiteit Amsterdam M Computer Science Pagina 24 van 64

30 Doelgroep mcshpdc Overige informatie Opgave via tot 4 weken voor aanvang van het semester is verplicht Course registration at the UVA is compulsory at least 4 weeks before the start of the semester via Algorithms in Sequence Analysis Vakcode X_ (405050) Periode Periode 2 Voertaal Engels Faculteit Coördinator prof. dr. J. Heringa Docent(en) prof. dr. J. Heringa Lesmethode(n) Hoorcollege, Werkcollege Doel vak Have you ever wondered how we can track a gene across 3 billion years of evolution? Sequence alignment can be used to compare genes from humans and bacteria, using a dynamic programming algorithm. Here we focus on algorithms that can be applied to real scientific problems in biology. Students will obtain an in depth knowledge about the theory of sequence analysis methods. Students will also develop understanding and skills to apply the algorithms to protein and DNA sequences. We would like to stress that no biological knowledge is required to enter this course. 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 handson experience in tackling biological problems using sequence analysis algorithms. At the end of the course, the student will be able to implement several of the most important algorithms in sequence analysis. Inhoud vak Theory: Dynamic programming, database searching, pairwise and multiple alignment, probabilistic methods including hidden markov models, pattern matching, entropy measures, evolutionary models, and phylogeny. Practical: Programming own alignment algorithm based on dynamic programming Reverse translation and dynamic programming Homology searching and pattern recognition using biological and disease examples Multiple alignment of biological sequences Entropybased functional residues prediction Programming own implementation of Hidden Markov Models Vrije Universiteit Amsterdam M Computer Science Pagina 25 van 64

31 Onderwijsvorm 13 Lectures: 2 twohour lectures per week 6 computer practicals: two hours per week Toetsvorm The final grade for this course will consist of 50% practical work (see above) and 50% theoretical assessment. The theoretical assessment will be an oral or written exam (depending on number of students). Literatuur Course material on bb.vu.nl Books: Durbin, R., Eddy, S.R., Krogh, A., Mitchison, G.. Biological Sequence Analysis. Cambridge University Press, 1998, 350 pp., ISBN Recommended reading: Marketa Zvelebil and Jeremy O. Baum Understanding Bioinformatics Garland Science 2008 ISBN10: Vereiste voorkennis Bachelor in any science discipline (including medicine). Basic programming skills and an interest in biological problems. Doelgroep maicis, maiha, maiktiia, maitai, mbio, mcsfmsv, mcshpdc, mcsiwt, mcsmm, mcsse, mcstai Overige informatie Signing up via bb.vu.nl is mandatory. The course is taught in English. Automated Reasoning in AI Course code X_ (400389) Period Period 5 Language of tuition English Faculty Coordinator dr. K.S. Schlobach Teaching staff prof. dr. F.A.H. van Harmelen Teaching method(s) Lecture Course objective Since its early days Artificial Intelligence has employed logic as a mean to provide generic solutions for computationally and conceptually difficult practical problems. The aim of the course is to make the students familiar with a number of popular logic based representation and reasoning mechanisms for Artificial Intelligence. Furthermore, students should have the capability to transfer the learned techniques to other problems and to other representation mechanisms. Course content The course will be structured in three modules. In each of these modules a practical problem will be introduced, a logic based Vrije Universiteit Amsterdam M Computer Science Pagina 26 van 64

32 representation proposed, and the basic techniques for automated reasoning in this language studied in a practical, hands on, way. In a nutshell, we plan to cover: propositional Logic for scheduling, and satisfiability checking with Davis Putnam; Allen's interval logic for Planning, with constraint propagation in Temporal Constraint Networks; description logics for classification, with Tableau calculi for subsumption. Form of tuition In period 5 there will be lectures and practical sessions, plus significant time for self study and practical work. In period 6 there will be regular meetings to support for the work on a larger project. Type of assessment 3 practical assignments Course reading Selected scientific papers. Entry requirements Basic knowledge in logic is an advantage, but not required, as is some familiarity with programming. Target group mai Remarks For further information see the AR in AI blackboard site. Behaviour Dynamics Vakcode X_ (400113) Periode Periode 1+2 Voertaal Engels Faculteit Coördinator dr. O. Sharpanskykh Docent(en) prof. dr. J. Treur Lesmethode(n) Hoorcollege Doel vak To learn how to identify, specify and predict different types of behaviour; to understand how externally observable behaviour emerges from internal mechanisms; to be able to construct computational behavioural models and to perform analysis based on these models using software tools Inhoud vak 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 agentbased systems), cognition (e.g., the use of beliefs, desires and intentions, complex reasoning tasks) and organisation theory (e.g., organisational change). The Vrije Universiteit Amsterdam M Computer Science Pagina 27 van 64

33 dynamics of behaviour of such systems is analysed (including verification and validation), modelled and simulated in this course using different techniques and tools. Onderwijsvorm Combinations of lectures, practical assignments, and presentations. Toetsvorm Examination and practical assignments. Both grades should be at least 5. 5 to pass the course. Literatuur Online reader. Vereiste voorkennis Knowledge in mathematical logics (in particular, firstorder predicate logic), logic programming Aanbevolen voorkennis Conceptual modelling skills; knowledge on agentbased systems Bioinformatics for Translational Medicine Vakcode X_ () Periode Periode 5 Voertaal Engels Faculteit Coördinator prof. dr. J. Heringa Docent(en) prof. dr. J. Heringa Lesmethode(n) Hoorcollege, Practicum Doel vak Observations from biological highthroughput experiments will allow us to improve diagnosis and give a personalised treatment plan for patients. However, integrating data from several sources and using this data for predictions is nontrivial. This is a theoretical and practical Bioinformatics course on computational methods for Translational Medicine; we will focus on Bioinformatics algorithms that are used to predict the clinical outcome for patients and analysis methods to obtain deeper understanding of complex diseases, by combining data from various highthroughput experiments such as proteomics, microarrays and nextgeneration sequencing as well as existing biological databases. goals At the end of the course, students will be aware of Bioinformatics methods that are applicable to the area of Translational Medicine. Students should be able to combine these methods to come to a creative solution to get new insights from large scale biological experiments. At the end of the course, students will have handson experience Vrije Universiteit Amsterdam M Computer Science Pagina 28 van 64

34 in handling large biological datasets, and will understand the complexity of the biological data both from highthroughput experiments and existing biological databases. The student will become familiar with a few in depth research topics that lie within the expertise area of several (Bioinformatics) researchers at the VU, UvA and VUMC. Inhoud vak Theory proteomics (mass spectrometry), genomics, gene regulation, signalling, microarray experiments, proteinprotein interactions, and datamining, nextgeneration sequencing, pattern recognition, ontologies, and GRID computing, Petri nets. Practical Assignment biological data clustering (in R) Assignment gene regulation / signalling network modelling using Petri nets. Assignment classification of tumor data Onderwijsvorm 13 Lectures (2 twohour lectures per week) 12 computer practicals (2 twohour sessions per week) Toetsvorm The final grade for this course will consist of 50% practical work (see above) and 50% theoretical assessment. Theoretical assessment: (50%) Oral or written exam (depending on number of course students). As part of the exam a research paper on a Bioinformatics method needs to be analysed in detail. You will be prepared for you exam through exercises and paper discussion during the lectures. Literatuur course material on bb.vu.nl Marketa Zvelebil and Jeremy O. Baum Understanding Bioinformatics Garland Science 2008 ISBN10: Vereiste voorkennis Bachelor in any science discipline (including medicine), or thirdyear BSc students. Basic programming skills (R) and an interest in biological problems. Aanbevolen voorkennis An interest in Biological problems. Doelgroep maicis, maiha, maiktiia, maitai, mbio, mcsfmsv, mcshpdc, mcsiwt, mcsmm, mcsse, mcstai Overige informatie Signing up via bb.vu.nl is mandatory. The course is taught in English. Compulsory course for students in MSc of Bioinformatics. Optional course for students with Bachelor Physics, Chemistry, Vrije Universiteit Amsterdam M Computer Science Pagina 29 van 64