Inhoudsopgave 1 Faculty of Sciences 8



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subject

Caput Infinite Dimensional Topology

code

400333

credits

6

period

1 and 2

lecturer

prof.dr. J. van Mill

content

The aim of this course is to develop homeomorphism theory in topological manifolds modeled on the Hilbert cube Q. Among others things, we prove that Q is topologically homogeneous, that Q is homeomorphic to its own cone, and that separable Hilbert space is topologically homeomorphic to the countable infinite product of lines. If time permits, we will also prove that the product of a "letter T" and Q is homeomorphic to Q.

literature

Mill, J. van, Infinite-dimensional topology: prerequisites and introduction. North-Holland Publishing Company, 1989.

mode of assessment

Oral examination.

entry requirements

Topologie I (400416).

target audience

3W, mMath

remarks

Registration for this course via https://tisvu.vu.nl/tis/menu, two weeks prior to the start. For the course schedules please refer to http://www.few.vu.nl/onderwijs/roosters.




subject

Caput Institutionalising Participatory Approaches in the South

code

470567

lecturer

dr. M.B.M. Zweekhorst (co-ordinator)

credits

3

period

In consultation

aim

  • To develop a detailed understanding of the importance of participation strategies for sustainable development

  • To understand the difficulties that have been identified for institutionalising interactive approaches within existing organisations

  • To obtain insight into different strategies to institutionalize interactive approaches.

  • To acquire knowledge on the learning organisation.

content

During the past three decades participation has become increasingly visible as an issue in development. It is recognized that participation is a key element in poverty eradication and sustainable development. Methodologies to enhance participation are now commonly used in development projects and `participation¿ has become a development orthodoxy. However, it is one thing to acknowledge the effectiveness of participatory approaches, but another to apply these approaches consistently over longer periods of time. This requires institutionalisation of these approaches within the organisations concerned, so as to build the necessary capacity. Most organisations are not well adapted to the application of participatory approaches. Some organisational change is therefore likely to be necessary if participatory approaches are to be institutionalised successfully. In this theoretical course you study in depth scientific literature about various theoretical concepts and practical experiences of institutionalisation processes of interactive approaches that were undertaken by organisations in the South.

form of tuition

This theoretical course comprises self study and three discussion meetings. After a short introduction you study various scientific articles that are then critically analyzed and discussed in a subsequent meeting.

literature

Selected scientific articles.

mode of assessment

Individual assessment though an exam.

target audience

Optional course for Master students Health Sciences, Biology or Biomedical sciences (e.g. diff. International Public Health) Management, Policy Analysis and Entrepreneurship in health and life sciences (MPA), or M-differentiation of the Health, Life and Natural Sciences.

remarks

Minimum number of three students. Basic knowledge on organisation and management is required. For information and application: ciska.heuvelman@falw.vu.nl




subject

Caput Knowledge Integration and (patient) Participation

code

470569

lecturers

dr. J.E.W. Broerse (co-ordinator); dr. J.F. Caron-Flinterman

credits

3

period

In consultation

aim

  • To acquire in-depth understanding of different types of knowledge. and their specific characteristics and values;

  • To acquire detailed knowledge concerning models on knowledge integration and transdisciplinarity, and their key concepts;

  • To acquire the ability to translate from theory to practice with respect to participation strategies.

content

This course increases your theoretical knowledge about different types of knowledge and their respective role in the health and life sciences. The role of these different types of knowledge is changing over the past two decades because of the emergence of a so-called knowledge-based society in which knowledge integration and transdisciplinarity are becoming important concepts. During this 2-weeks course you will read various scientific articles on different visions and models to describe and facilitate knowledge integration. Specific attention is paid to the role and value of `lay¿ knowledge (of patients) for research in the health and life sciences. You will analyse various articles about different practices of patient participation in health research. You will address questions, such as who should participate, when, how and why, in order to realize patient participation in health research in the most effective way.

form of tuition

This theoretical course comprises self study and three discussion meetings. After a short introduction you study various articles that are then critically analysed and discussed in a subsequent meeting.

literature

Selected scientific articles.

mode of assessment

Individual assessment through an exam

target audience

Optional course for Master students Health Sciences, Biomedical Sciences, Management, Policy Analysis and Entrepreneurship in health and life sciences (MPA) or M-differentiation of the Health, Life and Natural Sciences Masters programmes.

remarks

Minimum number of three students.

For information and application: ciska.heuvelman@falw.vu.nl






subject

Caput Optimization of Business Processes

code

400260

credits

6

period

1 and 2

lecturer

prof.dr. G.M. Koole

aim

To learn more about one or two of the subjects of modeling of
business processes, to study and present scientific papers.

content

We deal with a number of application areas of stochastic modeling, such as production logistics, call centers and health care. For each area we present quantitative problems and discuss how they can be solved using mathematical models. We also discuss a number of new models. Several guest lectures are given by people from industry.

form of tuition

Lectures.

literature

Lecture notes (handed out).

mode of assessment

Written examination.

entry requirements

Applied Stochastic Modeling (400392).

target audience

mBMI




subject

Caput Success factors in sustainable innovations by SME's

code

470581

lecturers

prof.dr. E. Masurel (co-ordinator); various lecturers

credits

3

period

In consultation

aim

  • To acquire understanding of specific aspects of sustainable innovations by small and medium-sized enterprises (SMEs) in the health and life sciences.

  • To develop skills to understand the link between theory and practice.

content

In this course the emphasis is on success factors in the process of sustainable innovation by small and medium-sized enterprises (SMEs) in the health and life sciences. With sustainable innovations we mean the introduction of new products, services or processes with relevance in the field of sustainability. The latter is translated into finding a balance between firm performance and the impact their production has on people and the planet. There is already a considerable body of knowledge about the relationship between SMEs and innovation, also some information on sustainable entrepreneurship by SMEs and on sustainable innovations is available. But there is much less known about sustainable innovations by SMEs. Small businesses are not just little big businesses. Therefore, attention will be paid also to qualitative aspects of SMEs: short-term focus, local and regional impact, family businesses etc.

form of tuition

Discussion sessions, in which the lecturer(s) will present the main outcomes of previous research. Field research, based on which the students will present their cases.

literature

Selected scientific articles

mode of assessment

Case presentation and exam

target audience

Optional course for Master students Management, Policy Analysis and Entrepreneurship in health and life sciences (MPA), M-specialisation of the Health, Life & Natural Sciences, Biology, Health sciences, Biomedical Sciences, (e.g. spec. International Public Health).

remarks

Minimum number of three students. For information and application: ciska.heuvelman@falw.vu.nl




subject

Cell Structures and Functions

code

470615

lecturers

various lecturers; dr. J. Luirink (co-ordinator; joen.luirink@falw.vu.nl); prof.dr. B. Oudega; dr. I.M. van Die

credits

6

period

30.10.2006-24.11.2006

aim

The aim of the course is to refresh and deepen the knowledge of the students in a number a selected areas of Molecular Cell Biology. These areas are the complex structures and functions of the living cell and subcellular organelles and compartments, especially membranes, intracellular compartments, membrane proteins, transport processes, protein sorting, trafficking and secretion, vesicle transport, cytoskeleton and cell division. In these specific areas the students will get detailed knowledge and insight in the most recent research data, theories and findings. Also the impact of up-to-date molecular cell biological research on medical sciences, understanding of disease and drug development as well as medical oriented biotechnology will get attention. Furthermore the students will get information on a number of methods and techniques, such as isolation and growth of cells, protein isolation and characterization, proteomics, molecular interaction/crosslinking an visualization of cells and cell components.

form of tuition

In the first part of the course (one week) students will study and discuss in working groups part III (methods) and part IV (internal organization of the cell) of the book: "Molecular Biology of the Cell" (Alberts et al.). Chapter by chapter the students will be guided through the book and questions will be answered.

In the second part of the course (about two weeks) specific topics (protein trafficking, protein insertion into membranes, membrane protein channels, glycosylation and quality control) will be studied and discussed with lecturers and guest researchers. Each lecturer will present lectures and discuss with the students very recent research papers and developments in the specific area of interest. The reviews and papers will be presented in advance in a course syllabus.



The third part (last week) of the course will be used to study and to prepare for the exam. The exam will be an "open slabs" exam.

literature

  • Molecular Biology of the Cell (Alberts, Johnson, Lewis, Raff, Roberts, Walter) Fourth edition. GARLAND SCIENCES.

  • A course syllabus with recent reviews and papers presented by the lecturers and guest researchers.

mode of assessment

A written exam with assay questions in which the syllabus can be used.

entry requirements

A bachelor degree in biology. medical biology, biomedical sciences, biochemistry or in a related undergraduate curriculum. Basic (bachelor) knowledge of cell biology, microbiology, molecular biology and molecular genetics is a good start.

target audience

Masterstudents Biomedical Sciences, Biomolecular Sciences or Biology




subject

CERN Research Project

code

420116

lecturer

dr. E. de Wolf (Phone: +31 (0) 20 592 5123, e-mail: edewolf@science.uva.nl)

credits

6

period

6

aim

The objectives of this project is to learn to work in an international group of physicists and technicians at an accelerator institute. In addition it is important to build a network with possibly future colleagues in particle physics.

content

The CERN summerstudent research project is part of the CERN Summer Student Programme for master students at CERN in Geneva, Switzerland. During two or three months in the summer selected students will work in one of the experimental teams at CERN at their own project. For students of the master programme Particle and Astroparticle Physics this project can be part of their master research project.

form of tuition

Written report.

target audience

mPhys.

remarks

For more information and enrolment contact dr. De Wolf.




subject

CERN Summerstudent Lecture Programme

code

420122

lecturer

dr. E. de Wolf (UvA, phone: +31 (0) 20 592 5123, email: edewolf@science.uva.nl)

credits

3

period

6

aim

The objectives of this course is to learn from the experience from well known particle physicists from around the world the different aspects of experimental particle physics.

content

The lecture programme is part of the CERN Summer Student Programme for master students at CERN, Geneva, Switzerland. In a series of lectures several scientists from around the world share their knowledge about a wide range of topics in the fields of theoretical and experimental particle physics and computing.

form of tuition

Contact the coordinator.

literature

Will be announced.

mode of assessment

Contact the coordinator.

target audience

mPhys. Exclusively for students of the Master's programme Particle and Astroparticle Physics

remarks

For more information and enrolment contact dr. De Wolf.




naam

Chemistry of Life

code

430025

lecturers

dr. M.H. Siderius; dr. J.C. Vos

studiepunten

6

periode

1

aim

An overview of the practical and theoretical aspects of Molecular Biology, Genetics and Biochemistry and their applications in Molecular Medicine wille be given.

content

A general introduction of the important compounds of life and their relevance for various pathological and genetic conditions will be given. The biochemical causes underlying various diseases (e.g. Infectiuous diseases, Cancer and Aging) and strategies to cure disease will be discussed. The focus will be on the human genome and its genetics, expression and regulation. Important cellular and animal model systems used to investigate (pathological and pharmacological) aspects of cell biology will be discussed. Biotechnological production of medically relvant peptides or drugs wille be studied.

form of tuition

  • Lectures

  • Self-study

  • Assignments

literature

Primrose and Twynman, Principles of Gene Manipulation and Genomics, 7th edition. And scientific papers.

mode of assessment

Written examination and assignments.

entry requirements

BIO 1, BIO 2

target audience

MSc Students with Bachelor in Medical Natural Sciences, Chemistry, Pharmaceutical Sciences.

remarks

Application for this course should reach dr. Vos, JC.Vos@few.vu.nl, at least 2 weeks before the starting date of the course.




subject

Clinical Development and Clinical Trials

code

470574

lecturers

prof.dr. E.H.J.H.M. Claassen (co-ordinator); guest lecturers

credits

3

period

13.11.2006-24.11.2006

aim

To acquire knowledge and skills with respect to the understanding of issues and regulation concerning clinical development of pharmaceutical products for human preventive and therapeutic use.

content

In this two-week course a diversity of subjects relevant for clinical trials are presented and discussed. Topics include: Role and objectives of clinical development within the product development programme; Overview of the various clinical development phases; Clinical development strategies and plans; Ethics in clinical research ; Marketing input in clinical research; Regulatory framework and guidelines; Quality assurance in clinical trials; The role of clinical pharmacology in drug development; Drug interactions; pharmacodynamic and metabolic interactions; Role, objectives, aims and design of exploratory, dose ranging and dose finding studies; Objectives, aims and design of confirmatory studies; Health economics in confirmatory trials; Role of biometrics in clinical development; Designs for randomized clinical trials; Safety and efficacy parameters; Quality of life assessments; Clinical project management organization; Planning in clinical development; Budgeting; Clinical trial administration; Role and interaction of clinical development with other disciplines involved in product development.

form of tuition

Lectures and self study

literature

Reader

mode of assessment

Individual assessment through an exam

target audience

Optional course for Master students Management, Policy Analysis and entrepreneurship in health and life sciences (MPA), M-differentiation of the Health, Life & Natural Sciences, Biology, Health sciences, Biomedical Sciences, (e.g. diff. International Public Health).

remarks

For information and application: ciska.heuvelman@falw.vu.nl




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

remarks

Participation in the course is limited; priority is given to students of the 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

credits

6

period

1 and 2

lecturer

dr. E. Wattel

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.

werkwijze

Lectures.

mode of assessment

Oral examination.

entry requirements

Discrete Mathematics (400019).

target audience

3W, mMath, 3Ect, mCS, mPDCS




subject

Coding Theory

code

400448

credits

8

period

1 and 2

target audience

mMath

remarks

This course is part of the joint national master programme in mathematics.
For schedules, course locations and course descriptions see http://www.mastermath.nl.
Registration required via http://www.mastermath.nl.




subject

Cognitive Neuroscience and Neuropsychology

code

813077

credits

6

period

1

lecturer

dr. D.J. Heslenfeld

aim

Provide knowledge of the new, multidisciplinary area of cognitive neuroscience, neuropsychology and neurocognition

content

De course will treat modern techniques and recent data that relate brain functions to cognitive processes. Specific subjects are: perception, motion, control, memory, emotion, consciousness, development. Techniques are: EEG, ERP, MRI, TMS. An important aspect will be how studies of patients with brain lesions help understand cognitive functions.

form of tuition

lectures

literature

to be announced

mode of assessment

tentamination




subject

Combinatorial Optimization

code

64432010

credits

6

contact

24 hours (6 active participation, 18 lecture)

period

4

lecturer

Unknown (Lecturer: dr. J. dos Santos Gromicho)

aim

To acquire an overview of the many combinatorial optimization models that are relevant in Logistics. Learn how to identify those optimization problems and realize the difficulties involved in finding an optimal solution for them. Moreover, acquire a sound knowledge of both exact and heuristic solution techniques for such computationally complex problems.This course is interwoven with the course Case study, Optimization

content

Combinatorial Optimization deals with situations where the best alternative has to be selected out of a finite set. Because the set is finite this may seem trivial. However although being finite, the number of elements may be huge, and it may be far from easy to find the best or even a good solution.

We cover Combinatorial Optimization models, such as the Travelling Salesman Problem, Steiner Trees, Set Covering, etc., which are important for many practical problems related to transportation, telecommunication, production and activity planning.



Foundations of the computational complexity theory will be explained, which shows that most of these problems are too hard to solve optimally in a reasonable time. Therefore, apart from exact methods like Branch & Bound, cutting planes, emphasis will also be given to heuristics. The heuristics will be illustrated on a broad class of practical problems especially from logistic and transportation sectors.

literature

  • Papadimitriou, Christos H., & Steiglitz, Combinatorial Optimization (Algorithms And Complexity), Kenneth Dover Publications, 1999, ISBN 0486402584 paperback   

  • Recommended literature: Zbigniew Michalewicz  & D.B. Fogel,  How To Solve It (Modern Heuristics: Modern Heuristics). Springer-Verlag, 1999, ISBN 3540660615

examination format

oral interim examination
and essay.

entry requirements

Optimazation, period 3.




subject

Combinatorial Stochastic Processes

code

400402

lecturer

dr. A. Gnedin (Phone: +31 (0) 30 253 1726, e-mail: a.v.gnedin@math.uu.nl)

credits

6

period

Semester 1

aim

The course is focused on random combinatorial structures, their asymptotic properties and their connections to stochastic processes with continuous time. The aim of the course is, on one hand, to study approximation techniques for random discrete objects and, on the other hand, to develop combinatorial representations of complex continuous objects (like, e.g., random mass fragmentations) via their discrete counterparts.

content

The course will highlight a number of topics in discrete probability related to enumeration, asymptotics and evolution of random combinatorial structures, such as random permutations, partitions, records and trees. We will also discuss classical and weighted branching processes and their connections to fragmentation phenomena and Brownian motion.

form of tuition

Lectures.

entry requirements

Basic probability.

target audience

mMath, mSFM

remarks

Contact the coordinating lecturer of this course.

No course in 2006/2007.

Location: Utrecht.





subject

Communicatiewetenschappen

code

471006

docenten

dr. J.F. Hoorn; dr. C.M. Koolstra (cursusleider); prof.dr. J.T.J.M. Willems

credits

6

period

04.09.2006-29.09.2006

aim

  • Introduction to basic concepts of communication science;

  • Introduction to communication processes from interpersonal, organizational and social perspectives;

  • Introduction to research methods that are often used in communication science (content analysis, survey and experiment);

  • Learn to describe communication processes in scientific terms in order to use theories and produce elementary predictions.

  • (level indication: 1 (2)

content

We live in a "communication society". According to EU-estimates over half of the working society is involved in one or other form of communication. These people are sometimes called communication workers. In order to communicate in a meaningful way in a communication society, one does not need just communication skills (like writing, speaking and illustrating), but also insight in the mechanisms, patterns, ideas and presumptions that underlie communication processes. What is communication? Which media are important? What is a target group? What is interactive communication? What is the effectiveness of public campaigns?

Naturally, an introduction to communication science is insufficient to train you as a communication scientist; you would need several years of study for that. But basal knowledge of and insight in communication processes is necessary to communicate adequately with communication scientists, for instance when starting a campaign or evaluating it.



form of tuition

A combination of lectures, seminars and home-study.

literature

Severin, W. J. & Tankard, J. W. (2001). Communication theories: Origins methods and uses in the mass media. New York: Longman (5th ed.).

Some recent scientific articles (on Blackboard).



mode of assessment

  • Participation during seminars;

  • A group assignment;

  • A written exam, consisting partly of multiple choice and partly of open questions.

  • The group assignment and the written exam will count equal (50%) for the final mark. Reexamination is possible for each part seperately.

target audience

All Master's students of FALW and FEW, plus 3rd year Bachelor's students Algemene gezondheidswetenschappen.

remarks

The course is taught in Dutch.




subject

Communication, Organization and Management

code

470572

lecturers

dr. M.B.M. Zweekhorst; prof.dr. C.J. Hamelink (co-ordinator); others

credits

6

period

02.10.2006-27.10.2006

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

The world of organizations in the health and life science sector is fast changing in part by quickly evolving technology and increasingly complex societal questions. 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. Next to the theoretical part, the students learn practical skills associated with managerial success, e.g. how to engage in group-based planning. During two weeks the students become a project manager of a project team (second year course `Biomedisch/Biologie Beleid¿ en (Kennis)management, Beheer en beleid¿ Health Sciences) that has been given the assignment to write a policy advisory report.

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: the grades for both parts must at least be sufficient (6)

target audience

Compulsory course within the Masterprogramme Management, Policy Analysis and entrepreneurship for the health and life sciences (MPA) and the M-differentiation of Health, Life and Natural Sciences Masters programmes. Optional course for Master students in Biomedical Sciences, Health Sciences and Biology.

remarks

Attendance is Compulsory. Basic knowledge of Analysis of Governmental Policy . For information and application: ciska.heuvelman@falw.vu.nl




subject

Compiler Construction

code

400105

credits

5

period

4 and 5

lecturer

dr. H. Bos

content

Modern compiler construction is no longer restricted to imperative source languages. This course takes this as a starting point. The course consists of two parts:

  • general structure of compilers, including lexical, syntactical and semantical analysis, code generation techniques and memory management; 

  • compilation of imperative, functional, logical, object-oriented and distributed languages, including code generation and run-time support for each of these paradigms.

The practical work consists of the extension of a compiler for a small language with new features for some of these paradigms, using support tools. See also http://www.cs.vu.nl/~herbertb/courses/coco/.

form of tuition

Lectures.

literature

Grune, D., Bal, H.E., Jacobs, C.J.H., Langendoen, K.G., Modern Compiler Design.John Wiley, 2000.

mode of assessment

Written exam.

entry requirements

 Compulsory for examination participation: Datastructuren, Computerorganisatie. Recommended Principes van Programmeertalen.

target audience

mPDCS, mCS

remarks

As part of the internationalization effort the course will be taught in English.




subject

Complex Analysis

code

400399

lecturer

dr. J.J.O.O. Wiegerinck (Phone: +31 (0) 20 525 5097, e-mail: janwieg@science.uva.nl)

credits

8

period

Semester 1 and 2.

content

This is a topics course: There are some fixed elements, while other topics may vary and may even be adapted to the students needs and wishes while the course is in progress. Fixed are: Normal families and Montel's theorem; Riemann mapping theorem; Product representations; Harmonic and subharmonic functions.
Possible additional topics are: Gamma, zeta and elliptic functions; Potential theory in the complex plane; Theory of Hardy spaces; Holomorphic dynamics in the complex plane; approximation theory; Entire functions of exponential type; Analytic continuation; Picard's theorem.

form of tuition

Reading Course.

literature

Notes: Advanced function theory will be available. Additional literature: books by Conway, Narasimhan, Ahlfors, Garnett, Berenstein en Gay, Duren, Heins, Segal, Boas: an extended list is part of the notes.
For more information consult http://www.science.uva.nl/~janwieg/edu/voorfunc/

mode of assessment

Take home exercises and an additional oral examination.

entry requirements

Elementary Function Theory, Real Analysis, Functional Analysis, Elementary Fourier Analysis.

target audience

mMath

remarks

Registration via http://studieweb.student.uva.nl 4 weeks prior to the start of the course. UvA code: WI405028. Course registration includes registration for the examination. Registration is also possible at the Education Office, phone: 525 7100, e-mail: ondwns@science.uva.nl

Consult the schedules at http://www.student.uva.nl or contact the coordinator.

Location: UvA.





subject

Complex Dynamics

code

400342

coördinator

dr. A.J. Homburg (Phone: +31 (0) 20 525 6282, e-mail: alejan@science.uva.nl)

lecturer

dr. J.J.O.O. Wiegerinck

credits

6

period

Semester 1.

aim

Students will obtain a basic knowledge of complex dynamics in the complex plane.

content

Complex dynamics is the theory of iteration of holomorphic functions. Often the functions are very simple (quadratic polynomials), but the iteration (the dynamics) leads to surprisingly complicated and beautiful results. The course is an introduction to the subject. We will discuss fixed points and conjugations, critical points, periodic components, Julia sets, Fatou sets and their local geometry, properties of the Mandelbrot set.

form of tuition

Seminar; lectures by the participants.

literature

John Milnor, Dynamics in One Complex Variable, Annals of mathematics studies 3rd ed., number 160. Princeton University Press,  2006.

mode of assessment

Through the lectures of the students.

remarks

Registration via http://studieweb.student.uva.nl 4 weeks prior to the start of the course. UvA code: WI404036. Course registration includes registration for the examination. Registration is also possible at the Education Office, phone: 525 7100, e-mail: ondwns@science.uva.nl

Consult the schedules at http://www.student.uva.nl or contact the coordinator.



Location: UvA.




subject

Computational Design and Synthesis of Drugs

code

435673

coördinator

dr. B.C. Oostenbrink

lecturers

dr. I. de Esch; dr. B.C. Oostenbrink

credits

6

period

2

aim

To gain insight and experience in the molecular modeling tools that enable (rational) drug design and planning a route to synthesize the ligand.

content

In the post-genome era, an overwhelming amount of data describing the molecular characteristics of the targets is becoming available. For example, the structure of many proteins is being determined using Xray analysis and NMR techniques. Furthermore, high-throughput screening results in massive amounts of data that reveal the molecular properties of the ligands that are able to have interaction with the drug targets. In this course, several techniques that can help to translate this data into novel ligands will be discussed and demonstrated. Specific topics include crystal structure analysis, the building of homology models, docking of ligands, calculating binding free energy and affinity of ligands for the protein, de novo structure generation, and pharmacophore modelling. These techniques generate ideas for novel compounds. Because a design that cannot be synthesized is by definition a useless design, the synthetic feasibility is a key and integral part of the design process. Therefore, it is important to be able to define a synthetic pathway for the preparation of the designs. In this course, this aspect will be covered by a case study. For a specific design, a versatile and robust synthesis route has to be defined. A thorough literature search, in combination with detailed study of the reactions involved will result in a report that describes the suggested chemistry in detail.

form of tuition

Lectures, tutorials and self study.

mode of assessment

Written examination, preparation of a report.

entry requirements

Knowledge of basic organic chemistry.

target audience

mPhar

remarks

Please contact the coordinator four weeks prior to the start of the course (e-mail: c.oostenbrink@few.vu.nl).

Absent on Wednesday and Thursdaymorning.






subject

Computational Genomics and Proteomics

code

400436

lecturers

dr. E. Marchiori; 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.




subject

Computational Medicinal Chemistry and Toxicology I

code

435671

co-ordinator

dr. B.C. Oostenbrink (phone: 59 87606, room P2.62, c.oostenbrink@few.vu.nl)

lecturer

dr. B.C. Oostenbrink

credits

3

period

4

aim

To get acquainted with the principles and applications of modern molecular modeling and computer assisted drug design in medicinal chemistry.

content

Introduction to the basics of computational medicinal chemistry. The theory and methods of modeling of ligands will be discussed. An introduction to the modeling of proteins will be given. Methods for the automatic retrieval of pharmacophore keys and other relevant features from chemical databases are evaluated. The use of such data, combined with methods for calculating receptor affinity, for structure-based drug design is another topic.

form of tuition

Lectures, tutorials and self-study.

literature

A. R. Leach, Molecular Modelling: principles and applications (ISBN 0-582-38210-6)

mode of assessment

Written or oral examination.

entry requirements

Courses "Computational Chemistry" and "Computational Design and Synthesis of Drugs".

target audience

mPhar

remarks

Please contact the coordinator four weeks prior to the start of the course (e-mail: c.oostenbrink@few.vu.nl).




subject

Computational Medicinal Chemistry and Toxicology II

code

435672

coördinator

dr. B.C. Oostenbrink

lecturer

dr. B.C. Oostenbrink

credits

6

period

4, 5 and 6

aim

Providing theoretical background on biomolecular modeling and computer assisted drug design, and an overview of recent developments, applications and trends.

content

Methods and techniques of molecular modeling, quantum and molecular mechanics, advanced /ab initio/ methods, energy minimization, conformational analysis, molecular interactions, molecular dynamics simulations, free energy calculations. Protein structure prediction, sequence analysis and protein folding. Chemoinformatics: chemical databases and database searching. The use of biomolecular modeling and chemoinformatics for de novo drug design: molecular docking procedures and scoring functions, molecular similarity searching; structure-based de novo design, genetic algorithms; QSAR, multiple linear regression, discriminant analysis, partial least-squares methods and molecular field analysis; simulation methodology, statistical mechanical background of free energy.

form of tuition

Lectures, tutorials and self-study.

literature

Leach, A.R., Molecular Modelling: principles and applications, (ISBN 0582382106), and several recent review articles.

mode of assessment

Written or oral examination.

entry requirements

Courses "Computational Design and Synthesis of Drugs" and "Computational Medicinal Chemistry and Toxicology I".

target audience

mPhar

remarks

Please contact the coordinator four weeks prior to the start of the course (e-mail: c.oostenbrink@few.vu.nl).




subject

Computational Methods

code

420014

lecturer

dr. H.J. Bulten

credits

6

period

4 and 5

aim

  • Acquaintance with popular numerical methods in physics

  • Critical assessment of numerical approaches

  • Hands-on experience with the solution of problems in computational physics

content

  • Function evaluation

  • Determination of zeros and extremal points

  • Solution of coupled linear equations and eigenvalue systems

  • Numerical integration

  • Solution of differential equations

  • Stochastic methods, Monte Carlo

form of tuition

Oral presentation and tutoring of pairs of students working on projects.

literature

Numerical Recipes, Flannery et al. This book is available on line on the web, http://www.nr.com/

mode of assessment

Grading of three papers on different projects.

target audience

mPhys




subject

Computer Algebra

code

400458

credits

8

period

4 and 5

target audience

mMath

remarks

This course is part of the joint national master programme in mathematics.
For schedules, course locations and course descriptions see http://www.mastermath.nl.
Registration required via http://www.mastermath.nl.




subject

Computer and Network Security

code

400127

credits

6

period

4 and 5

lecturer

dr. B. Crispo

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.cs.vu.nl/~crispo/teaching/security.




subject

Computer Graphics

code

400106

credits

6

period

1 and 2

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);

  • 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

This course is given in English.




naam

Computernetwerken

code

400016

studiepunten

5

periode

4 en 5

docent

prof.dr.ir. M.R. van Steen

doel

Het inzichtelijk maken van de architectuur van computernetwerken.

inhoud

De nadruk ligt op het behandelen van de architectuur van communicatieprotocollen, zowel voor hoog- als laagniveau-communicatie. Onderwerpen die aan de orde komen zijn: de fysieke laag, de datalinklaag, de netwerklaag, de transportlaag en de applicatielaag. Voorbeelden die aan de orde komen zijn onder meer het Internet, Internet via de kabel, Bluetooth, en draadloze netwerken. Veel aandacht wordt ook besteed aan beveiligen van netwerken.

werkwijze

Hoorcollege.

literatuur

Tanenbaum, A.S., Computer Networks 4th edition. Prentice-Hall, 1996.

toetsing

Schriftelijk.

doelgroep

2I, 2IK, 3IK

voorkennis

  • Veronderstelde voorkennis voor het college: Datastructuren (400145) en Computerorganisatie (400017).

  • Vereist voor deelname aan het tentamen: Inleiding Computersystemen (400033).

opmerkingen

Actuele informatie over het vak is te vinden op
http://www.cs.vu.nl/cs/cn-ds-os/




subject

Conserv.Princ. in the Num.Treatment of Wave Equations

code

400464

coördinator

dr.ir. J.E. Frank (Phone: +31 (0) 20 592 4096, e-mail: J.E.Frank@cwi.nl)

credits

6

period

Semester 1.

aim

To introduce advanced conservative discretization techniques for hyperbolic and variational/Hamiltonian wave equations. This course surveys a broad selection of numerical methods for such problems, addresses stability theory of finite difference methods, dispersion analysis, backward error analysis, discrete numerical operator theory and discrete differential forms.

content

Wave equations are prevalent in continuum mechanics (fluid dynamics, elastodynamics) and field theory (electromagnetics, optics). Their numerical treatment is challenging because of their lack of inherent dissipation (neutral stability). Preservation of mathematical structure under discretization will play a central role in the discussion. We distinguish between hyperbolic wave equations in conservation law form and dispersive wave equations with variational or Hamiltonian structure, for which conservation laws can be derived from the equations of motion.
Modern numerical discretization techniques attempt to mimic the conservation laws in the discrete approximation, to enhance stability and ensure that the simulated solution is qualitatively correct.
We start with a discussion of conservation laws and their discrete analogs, and how these yield global conservation under appropriate (numerical) boundary conditions. This theory is directly applied to hyperbolic wave equations, for which application of finite volume methods automatically leads to the discrete conservation laws. In the presence of shock waves and discontinuities, this approach must be supplemented with Riemann solvers and monotonicity-preserving time integrators to ensure the conservation of monotonicity of the solution (and prevent spurious numerical oscillations).
For dispersive wave equations, the relevant conservation laws are often not readily evident from the equations of motion, but instead are derived from some underlying structure. Care must be taken to ensure that analogous manipulations can be carried out on the discrete system. For example, discretizations starting from a Hamiltonian structure or utilizing a discrete variational principle. Modified equation analysis is important for understanding the qualitative behavior of numerical methods.
Adaptivity, implementation of numerical boundary conditions, and conservative time integration are additional aspects which must be dealt with.
Specific topics we will cover are: finite volume discretization of conservation laws, Riemann solvers, monotonicity-preserving discretizations, (pseudo-)spectral methods, symplectic and symmetric time integrators, energy-conserving finite difference methods, discrete variational principles, discrete Poisson brackets, numerical dispersion, backward error analysis, stability and boundary conditions, nonuniform meshes and mimetic discretizations/discrete differential forms.

form of tuition

Lectures and instruction.

literature

Lecture notes.

mode of assessment

Based on homework exercises and more involved projects.

entry requirements

Calculus and an understanding of differential equations are necessary. Helpful are: multivariable calculus, linear algebra, ordinary and partial differential equations, numerical analysis, familiarity with Matlab. Please contact the instructor if you are in doubt.

remarks

Registration via http://studieweb.student.uva.nl 4 weeks prior to the start of the course. UvA code: M25. Course registration includes registration for the examination. Registration is also possible at the Education Office, phone: 525 7100, e-mail: ondwns@science.uva.nl

Consult the schedules at http://www.student.uva.nl or contact the coordinator.



Location:UvA




subject

Continuous Optimization

code

400446

credits

6

period

1 and 2

target audience

mMath

remarks

This course is part of the joint national master programme in mathematics.
For schedules, course locations and course descriptions see http://www.mastermath.nl.
Registration required via http://www.mastermath.nl.


subject

Control and System Theory of Positive Systems

code

400348

credits

6

period

4 and 5

lecturers

prof.dr.ir. J.H. van Schuppen; prof.dr. G.J. Olsder; prof.dr. A.C.M. Ran

aim

The aim of the course is to provide an introduction to the basic concepts and results of control and system theory for positive systems. Such systems arise as models of phenomena in biology, economics, and engineering and many of these will be presented in the course. Classes of positive systems covered include linear, bilinear, polynomial, and rational positive systems. The mathematics needed for positive systems differs considerably from that used for finite-dimensional linear systems yet is simpler than for nonlinear systems based on mechanics. The emphasis of the course is on positive linear algebra (with the geometric concept of a polyhedral cone), on realization with decompositions, system reduction, system identification, and on control of positive systems.
The course is very useful for mathematics students interested in models of biological phenomena, for students of economics, for students of certain branches of engineering, and for selected students of physics.

content

  • models from biology, economics, and engineering;

  • positive matrices, polyhedral cones, decompositions,
    spectral theory;

  • positive linear dynamic systems: dynamics,
    stability, monotonicity, realization, decomposition,
    invariant subcones, system reduction, system identification;

  • positive nonlinear dynamic systems: existence solutions, decompositions;

  • control of positive linear systems: reachability,
    stabilization, control-invariant sets, observers,
    output feedback, and dynamic games;

  • control of positive nonlinear systems:
    stability, state feedback, observers, and output feedback.

form of tuition

Lectures.

literature

Lecture notes in combination with references to books.

mode of assessment

Written exam in combination with home work sets.

entry requirements

Differential equations and linear algebra.
It is possible to follow this course without having followed
the course Systems and Control (mMath); knowledge of that course would be beneficial, but is not a requirement.

target audience

mMath; students from engineering, economics, biology,
and physics; international students are also welcome!

remarks

Location is preferably at the Vrije Universiteit in Amsterdam




subject

Control of Stochastic Systems in Continuous-Time

code

400337

lecturer

prof.dr.ir. J.H. van Schuppen

credits

6

period

1 and 2

aim

The aim is to provide an introduction to the  basic concepts and results of control and system theory. for stochastic systems in continuous time.  The motivation for the course is control and signal processing problems  as these arise in engineering, economics, physics, and biology.  The program of the course is:
(1) The concept of a stochastic system, the properties of such systems, and the characterization of the equivalence class of dynamic systems representing observed trajectories.
(2) Online estimation of the state trajectory on the basis  of output signals by methods of filtering theory.
(3) Online control of the stochastic system by feedback solved by methods of control synthesis including dynamic programming.

content

Stochastic systems described by stochastic differential equations are mathematical models for phenomena with irregular fluctuations. Examples from engineering and economics will be used throughout the course. Properties of such stochastic systems will be explored,  such as the existence and properties of an invariant measure.

The optimal stochastic control problem for such  a system is to determine a control law such that  the closed-loop system meets prespecified control objectives.  The dynamic programming approach to optimal stochastic control  problems will be presented because it yields global necessary and  sufficient conditions for optimality.  Examples of optimal stochastic control problems will be treated  such as linear-quadratic-Gaussian systems, Markov chains, and jump process systems. For mathematical finance the portfolio selection problem of Samuelson-Merton and the Black-Scholes equation will be treated.

The filtering problem is to determine the conditional distribution of the state conditioned on the past of the observed process. The Kalman filter and the Benes filter will be treated as examples.

Finally stochastic control problems with partial observations will be discussed in which  there is available for control not the state but only  an observed process related to the state.



form of tuition

Lectures in class; the language of the class is English.

literature

Lecture notes will be distributed during the semester.

mode of assessment

Oral exam in combination with weekly homework sets.

entry requirements

Measure and integration theory.  Stochastic processes in a measure theoretic formulation. Stochastic differential equations.
(At the University of Amsterdam the course `Stochastic Integration' covers the prerequisites of the course.)

target audience

Master level students in mathematics and economics. European students in these subjects visiting the VU are particularly welcome.




subject

Coordination and Organometallic Chemistry

code

435664

lecturers

prof.dr. C.J. Elsevier (Phone: +31 (0) 20 525 5653, e-mail: elsevier@science.uva.nl); dr. B. de Bruin (Phone: +31 (0) 20 525 6437, e-mail: elsevier@science.uva.nl)

credits

6

period

1

aim

The course aims at familiarizing the student with elementary and advanced concepts in molecular inorganic chemistry, with an emphasis on the organometallic chemistry of the transition metals.

content

Concepts comprise thermodynamic and kinetic considerations, bonding in organometallic complexes, sigma- and pi-bonded ligands, fundamental reactions and their mechanism, physical methods, clusters and bioorganometallic compounds.

form of tuition

Lectures

literature

Crabtree, R.H., The Organometallic Chemistry of the Transition Metals, 4th edition, Wiley Interscience, 2005; ISBN 0471662569.

mode of assessment

Written examination.

entry requirements

B.Sc.

target audience

mCh

remarks

Registration for the course: via http://studieweb.student.uva.nl three weeks prior to the start of the course. Examination: one week prior to the examination date. Registration is also possible at the UvA Education Office, phone: 020-5257100/7049. E-mail: ondwns@science.uva.nl (mathematics and physics students). E-mail: svhouten@scienc.uva.nl (chemistry students). For the course schedules please consult the separate UvA schedule guide or phone the Education Office.




subject

CP Violation

code

420114

lecturer

dr. G. Raven (Phone: +31 (0) 20 592 5107, e-mail: Gerhard.Raven@nikhef.nl)

credits

6

period

1 and 2

content

The (tiny) breaking of the discrete symmetry under the combined Charge and Parity operators is responsible for a subtle difference between matter and antimatter. This course will cover the theory of CP violation by examining, in detail, the experimental results on which it is built: from a surprise discovery in 1964, the current state of the art experiments at so-called e+e- B-meson factories, to the discovery potential of the next generation experiments at the Large Hadron Collider.

form of tuition

Lectures and exercises.

literature

Lecture notes.

mode of assessment

To be announced.

entry requirements

Either the course Particle Physics or the course Particles and Fields.

target audience

mPhys.




subject

Critical Percolation, Conformal Invariance and SLE

code

400393

lecturers

F. Camia; J. van den Berg

credits

6

period

4 and 5

content

This course gives, starting practically from scratch, an introduction
to one of the most fascinating developments in modern probability.
This development involves techniques and ideas from
several subfields of mathematics: probability, complex function theory, combinatorics, conformal maps and stochastic calculus.
Some of these techniques are not usually included in the standard mathematics undergraduate program, and  will therefore be introduced during the course.

We say that a system is critical for certain values of its parameters


when a small change in those values causes a drastic change in the
global properties of the system. Such critical behaviour plays an important role in physics, biology and technology (large communication systems). The introduction of the so-called Stochastic Loewner Evolutions (SLE), five years ago by Oded Schramm, has enormously increased our understanding
of a large class of two-dimensional critical systems. An important
example is the percolation model.

After a short, general introduction on critical phenomena, we will treat the percolation model, in particular in two dimensions, including Smirnov's famous proof (2001) of the long-standing conjecture that the large-scale behaviour of 2D percolation is conformally invariant (these notions will be explained in the course).


Next, the necessary conformal mapping theory and stochastic calculus will be introduced, followed by the construction of deterministic and stochastic Loewner evolutions.
Finally, we will explain the connection between critical percolation and SLE and, as an application, we will show how it can be used to compute the so-called critical percolation exponents.

form of tuition

Lectures.

literature

Will be provided by the lecturers.

mode of assessment

Exercises and oral exam.

entry requirements

basic undergraduate probability and (complex) analysis; some
familiarity with Brownian motion and stochastic calculus is helpful.

target audience

mSFM, mMath, mPhys




subject

Data Mining Techniques

code

400108

credits

6

period

4 and 5

lecturer

dr. W.J. Kowalczyk

content

The course will provide a survey of basic data mining techniques and their applications for solving real life problems. After a general introduction to Data Mining we will discuss some "classical" algorithms like Naive Bayes, Decision Trees, Association Rules, etc., and some recently discovered methods like boosting, Support Vector Machines, co-learning. In the second part of the course a number of most successful applications of data mining will be discussed: marketing, fraud detection, text and Web mining, bioinformatics. In addition to lectures there will be an extensive practical part, where students will experiment with various data mining algorithms and data sets. The grade for the course will be based on these practical assignments (i.e., there will be no final examination).

form of tuition

Lectures and compulsory practical work.

literature

Ian H. Witten, Eibe Frank, Data Mining: Practical Machine Learning Tools and Techniques with Java Implementations, Morgan Kaufman, 2000. Additionally, a collection of articles in electronic form.

mode of assessment

Computerpracticum.

entry requirements

Vereist voor deelname aan het tentamen: Kansrekening en Statistiek of Algemene Statistiek. Aanbevolen: Machine Learning.

target audience

mBMI, mCS, mAI




subject

Describing Morphosyntax, MA

code

539618

lecturer

prof.dr. L.J. de Vries

credits

10

contact

28 hours (28 lecture)

period

1 and 2

aim

To learn basic notions and methods of descriptive morphosyntax

content

Students learn how to describe and document the morphosyntax of languages about which little or nothing is known.

literature

Thomas Payne, Analysing Morphosyntax (1997) Cambridge University Press, Cambridge

mode of assessment

Written exam (with access to course book)

target audience

Master's students of Linguistics (Bible translation)

blackboard

Yes

remarks

Registration via TIS obligatory

reqd. subject

500011 : Inleiding algemene taalwetenschap, 1




subject

Design of Experiments and Analysis of Variance

code

400310

credits

2

period

2

lecturers

prof.dr. A.W. van der Vaart; prof.dr. G.C. van der Veer

aim

Learn how to design experiments and analyse the results of these by ANOVA. Not only in theory, also in practice using a statistical package.

content

In order to be able to draw conclusions from experiments or surveys, it is necessary that the design of the study is well chosen. In this course some well known designs (completely randomized, randomized block etc.) and the associated analyses of variance are discussed.

form of tuition

Classes.

literature

Lecture notes and slides that can in due time be found via http://www.math.vu.nl/~aad/courses.html

mode of assessment

Exercises, final project with oral examination.

entry requirements

Descriptive statistics (comparable to third year course "toegepaste statistiek")

target audience

mIS, mCS

remarks

Homework consists of computer exercises, to be handled using the statistical package R (http://www.r-project.org/). Classes are in English.




subject

Design of Multi-Agent Systems

code

400054

credits

6

period

1 and 2

lecturer

dr. V.N. Stebletsova

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

remarks

More information can be found on Blackboard.




subject

Design of Multi-Agent Systems Practical

code

400059

credits

7

period

3 and 4

lecturer

dr. V.N. Stebletsova

aim

After completing the practical course, the student has advanced skills in designing multi-agent systems. He/she has learned to use the most important concepts of agent technology such as beliefs, desires, intentions, goals in practice, and has experience in solving coordination and cooperation problems using agent technology.

content

In two practical assignments the students work in teams to design multi-agentsystems. The assignments differ per year, but always the problems of coordination and cooperation play a central role.

form of tuition

Practical assignments in groups of 2-3 students under supervision of a project-leader.

literature

Reader.

mode of assessment

Assessment is made on the basis of the effectiveness and eloquence of the systems designed as well as on the written report of the design and the design process.

entry requirements

The student has successfully attended the course Design of Multi-Agent Systems (400054).

target audience

3AI, 3I, mCS, mAI-T

remarks

More information can be found on Blackboard.




subject

Designing Research

code

815107

credits

6

period

4

lecturers

dr. J.B. Deijen; dr. S.A. Los

aim

At the end of this course the student should be capable of:

  • choosing an adequate research design for a given problem;

  • selecting an adequate statistical test for a given data set;

  • explaining the basic priniples of testing the null hypothesis, and how these are applied in several statistical tests;

  • telling the major factors that influence power and effect size;

  • independent performance of simple (experimental) research;

  • reporting research in APA format.

content

  • Lectures: review of central statistical principles, including the null hypothesis, significance, power, and effect size; review of various research designs and corresponding statistical analyses.

  • Practical: analysis of standard experimental data in SPSS; reporting on research on a subject of choice.

form of tuition

Lectures: 16 hours, Practical: 28 hours

literature

Greer, B. & Mulhern, G. (2002). Making sense of data and statistics in psychology (first edition). New York: Palgrave.

mode of assessment

  • Lectures: multiple-choice questions about the lectures and book.

  • Practical: reports of experimental work.
    Note: Students should pass both the exam and the practical. The final grade is the mean of the grades of the exam and the practical.

remarks

Attendance during the practical is obligatory.




subject

Discrete Optimization

code

400445

credits

6

period

1 and 2

target audience

mMath

remarks

This course is part of the joint national master programme in mathematics.
For schedules, course locations and course descriptions see http://www.mastermath.nl.
Registration required via http://www.mastermath.nl.




subject

Discrete Structure

code

400457

credits

8

period

4 and 5

target audience

mMath

remarks

This course is part of the joint national master programme in mathematics.
For schedules, course locations and course descriptions see http://www.mastermath.nl.
Registration required via http://www.mastermath.nl.




naam

Discrete wiskunde

code

400019

studiepunten

5

periode

1 en 2

docent

dr. E. Wattel

inhoud

Teltheorie met genererende functies en inclusie/exclusie. Grafentheorie (Euler- en Hamiltongrafen, bomen). Stromen in netwerken met algoritmen, toepassingen in scheduling, grafentheorie, enzovoort. Een eerste inleiding in de coderingstheorie.

werkwijze

Hoorcollege met practicum.

literatuur

Dictaat "Combinatoriek, grafentheorie en getaltheorie" (open universiteit). Nota's "coderingstheorie" worden beschikbaar gesteld.

toetsing

Schriftelijk.

doelgroep

2W, mBMI, 3Ect

voorkennis

Veronderstelde voorkennis: Calculus I (400300), Calculus II (400301), Lineaire Algebra.




subject

Distributed Algorithms

code

400211

credits

6

period

4 and 5

lecturer

prof.dr. W.J. Fokkink

aim

To obtain a good understanding of a large range of distributed algorithms, with an emphasis on algorithms that are of importance for the course Distributed Systems.

content

Transition systems, snapshots, routing algorithms, traversal algorithms, leader election, termination detection, minimal spanning trees, anonymous networks, fault tolerance, failure detection, mutual exclusion, 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).

entry requirements

Data Structures (400145) and Computer Networks (400016)

target audience

3I, 3BI, 3AI, mCS, mPDCS




subject

Distributed Systems

code

400130

credits

6

period

1

lecturer

prof.dr.ir. M.R. van Steen

aim

Provide insight into the design and implementation of modern distributed systems.

content

We discuss the issues concerning the development of middleware systems for large-scale computer networks. Principles that are discussed include communication, processes, naming, consistency and replication, fault tolerance, and security. These principles are further explained by means of different paradigms applied to distributed systems: object-based systems, distributed file systems (NFS), document-based systems (the Web), 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, 2002.

mode of assessment

Written exam.

entry requirements

  • Computer Networks (Computernetwerken, code 400016).

  • Introduction to Computer Systems (Inleiding computersystemen, code 400033).

target audience

mCS, mPDCS

remarks

  • More information, slides and relevant literature, can be found on http://www.cs.vu.nl/cs/cn-ds-os/




subject

Distribution Theory

code

400236

lecturer

prof.dr. T.H. Koornwinder (Phone: +31 (0) 20 525 5297, e-mail: thk@science.uva.nl)

credits

6

period

Semester 2.

aim

The course intends to provide a working knowledge of distribution theory, largely avoiding topological vector spaces, to develop Fourier analysis in the generalized setting of tempered distributions, and to give some tools for applying distribution theory to PDE's.

content

The following subjects will be treated:

  • test functions and distributions 

  • differentiation

  • multiplication by smooth functions 

  • tensor products of distributions 

  • convolution  

  • fundamental solutions 

  • tempered distributions and Fourier transforms

Distributions (or generalized functions) were introduced by the French mathematician Laurent Schwartz in 1945. The theory gives meaning to the (iterated) derivative of a continuous function on R or R^n, even if this function is non-differentiable.
Distributions can be viewed as continuous linear functionals on a space of so-called test functions: the C^infinity functions of compact support. Operations on distributions, like the derivative, can be defined by their dual action on the space of test functions. The distributions form a linear space which contains the linear space of continuous functions, but also the linear space of complex measures, as subspaces. Dirac's delta "function" and its derivatives are famous examples of distributions.
The Fourier transform can be extended to a transform on the space of tempered distributions, a subspace of the space of all distributions. Here the rapidly decreasing C^infinity functions play the role of test functions.
Distributions are nowadays a standard tool in analysis, in the theory of PDE's, and in mathematical physics.

literature

  • Duistermaat, J.J.,  Kolk, J.A.C., Distributions: an Introduction course notes. University of Utrecht; Springer-Verlag, to appear.

  • Friedlander, G. Joshi, M., Introduction to the Theory of Distributions second printing (paperback). Cambridge University Press, 1999.

mode of assessment

Will be announced.

remarks

Registration via http://studieweb.student.uva.nl 4 weeks prior to the start of the course. UvA code: M26. Course registration includes registration for the examination. Registration is also possible at the Education Office, phone: 525 7100, e-mail: ondwns@science.uva.nl

Consult the schedules at http://www.student.uva.nl or contact the coordinator.

Location: UvA.





subject

DNA Protein Structure-Function Analysis and Prediction

code

430046

coördinator

prof.dr. J. Heringa

lecturer

prof.dr. J. Heringa (and other lecturers)

credits

6

period

3

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 and methodology.

  • At the end of the course, the student will have hands-on experience in molecular modeling and studying structure-function relationships.

content

Theory:

Protein folding and energetics, experimental structure determination, protein fold families, protein structure databases, protein secondary structure prediction, fold prediction, molecular modeling, protein-protein interactions, DNA/RNA structure/function, DNA/RNA structure prediction



Practical:

  • Assignment homology modelling

  • Assignment immunocomplex modelling

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

  • Carl Branden & John Tooze, Introduction to Protein Structure, 2nd Edition or higher. Garland Science, ISBN 0815323050, 1998.

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 is a strong advantage.

target audience

Students with Bachelor 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

Drug Toxicity: Basic Concepts and Experimental Approaches

code

435682

lecturer

dr. J.N.M. Commandeur

credits

3

period

4

aim

To get acquainted with basic concepts and experimental approaches in molecular toxicological research.

content

Enzymology of biotransformation enzymes; experimental approaches to identify (iso)enzymes involved in drug metabolism, enzyme kinetics, assessment of the formation of reactive intermediates and reactions with biological macromolecules, in vitro approaches to assess toxicity and genotoxicity of drugs, biochemical mechanisms leading to cell death, introduction to toxicogenomics and proteomics factors determining organ-selectivity of toxicants, genetic toxicology and chemical carcinogenesis.

form of tuition

Lectures and case-studies.

literature

Casarett & Doull's Toxicology, The Basic Science of Poisons, 6th edition, (ISBN 0-07-134721-6).

mode of assessment

Written examination.

entry requirements

Course Molecular Pharmacology and Toxicology of Drugs.

target audience

mPhar

remarks

Please contact the mastercoordinator four weeks prior to the start of the course (e-mail: jnm.commandeur@few.vu.nl).




subject

Drug-Target Analysis

code

435044

lecturers

prof.dr. H. Irth; dr. H. Lingeman

credits

6

period

2

aim

Introduction in the bio-analytical aspects realated to drug discovery focusing on proteomics, genomics and metabolomics, as well as the techniques used for screening and monitoring procedures.

content

An overview of the drug development process will be given dealing with preclinical and clinical development. Followed by the specific roles for bio-analysis in drug development. Aspects like lead optimization, screening for pharmacokinetic properties, absorption, metabobolite stability screening, toxicity screening, ADME studies, metabolite identification and characterization. Most of these aspects will be illustrated with clinical or pharmacokinetic applications and therapeutic drug monitoring and the focus will be on the separation / detection systems used for these applications.

form of tuition

Lectures and tutorials.

literature

Hand-outs (electronically available).

mode of assessment

Written or oral examination.

entry requirements

Basic knowledge of biochemistry, chromatography, electrophoresis and mass spectrometry.

target audience

mCh, mPhar.




subject

Dynamic Energy Budgets

code

470503

lecturer

prof.dr. S.A.L.M. Kooijman (course co-ordinator)

credits

6

period

08.02.2007 - 19.04.2007

content

A quantitative theory for processes of energy uptake and use by organisms is discussed. For more information see http://www.bio.vu.nl/thb/deb/course/deb

form of tuition

Tele-course, form of tuition to be discussed with the course co-ordinator.

literature

See http://www.bio.vu.nl/thb/deb/course/deb

mode of assessment

Software package DEB tool will be used to exercise the practical application of the DEB theory

target audience

Master and PhD students in natural sciences & mathematics

remarks

For more information see http://www.bio.vu.nl/thb/deb/course/deb.




subject

Dynamical Systems

code

400429

credits

8

period

4 and 5

target audience

mMath

remarks

This course is part of the joint national master programme in mathematics.
For schedules, course locations and course descriptions see http://www.mastermath.nl.
Registration required via http://www.mastermath.nl.




subject

E-Business Innovation

code

400110

credits

7

period

1 and 2

lecturers

dr.ing. J. Gordijn; drs. E. Schulten; prof.dr. J.M. Akkermans

aim

To understand and systematically analyze the multi-disciplinary
aspects (strategy, business processes, technology issues,
implementation) involved in innovations with information and
communication technologies (ICT) in networked businesses.

content

We will discuss theories and practical experiences, from different disciplines and industry sectors, covering some important
recent topics in electronic business: 

  • formulation of strategy;

  • design and evaluation of e-business models;

  • organizational readiness;

  • future and perspectives of electronic business.

Key topics will be exercised by small classroom workshops as part of an e-business strategy and implementation project to be carried out by the students.

form of tuition

Combination of lectures, topical workshops and project.

literature

Reader with recent articles and lecture materials.

mode of assessment

On the basis of an e-business project, workshops and a written exam.

entry requirements

Advance knowledge equivalent to Bedrijfsmodellering en requirements engineering (400010) and Software Engineering (400071) is recommended.

target audience

3IK, mIS, mCS, mBMI




naam

Encyclopedie der rechtswetenschap I (B1)

code

200107

studiepunten

8,6

coördinator

mr. J. Zwart (kamer 7A-37, tel. (020) 59 86326)

periode

week 6 - 18

doel

Het vak Encyclopedie der rechtswetenschap I bestaat uit twee onderdelen: Geschiedenis van de rechtsfilosofie (de omvangrijkste component) en Argumentatieleer.
Bij Geschiedenis van de rechtsfilosofie gaat het om kennis van een aantal belangrijke stromingen in het westerse denken over recht en staat. Tevens leert men rechtsfilosofische grondteksten analyseren.
Bij Argumentatieleer gaat het om kennis van de verschillende wijzen van argumentatie, die bij het juridische redeneren relevant zijn, en het kunnen toepassen daarvan op eenvoudige juridische teksten.

inhoud

Aan de hand van een aantal centrale vraagstukken, zoals de Verlichtingswaarden van vrijheid en gelijkheid, de verhouding van recht en moraal en dergelijke, worden de hoofdlijnen van de geschiedenis van het westerse denken over recht en staat geschetst.
In het kader van Argumentatieleer komen de volgende onderwerpen aan de orde: (juridisch) redeneren, logica en recht, tekstanalyse, analyse van (juridische) argumentatie, drogredenen.

werkwijze

Het onderwijs in beide onderdelen van Encyclopedie I wordt verzorgd in de vorm van hoorcolleges en werkcolleges. Bij de werkcolleges, waarin intensief de voorgeschreven stof wordt behandeld, wordt een actieve voorbereiding en deelname van de student verwacht in die zin, dat hij de in de literatuur geformuleerde vragen en opdrachten vooraf schriftelijk moet beantwoorden, respectievelijk uitvoeren.

literatuur

  • Nader op te geven literatuur.

  • Collegestof.

toetsing

Schriftelijk tentamen.




naam

Encyclopedie der rechtswetenschap II (B2/BN2)

code

200206

studiepunten

8,6

coördinator

mr.drs. W.J. Veraart (kamer 7A-35, tel. (020) 5986325)

periode

week 39 - 51

doel

De bedoeling van het vak Encyclopedie der rechtswetenschap II is handvatten aan te reiken, die de studenten helpen (beter) te gaan nadenken over een aantal fundamentele vragen met betrekking tot het recht, inzicht te krijgen in sociaal-maatschappelijke aspecten van het recht en (beter) inzicht te krijgen in normatief-ethische aspecten van het recht.

inhoud

De volgende thema's komen aan de orde:

  • De verhouding tussen recht en moraal.

  • De grondslagen van de democratische rechtsstaat.

  • De grenzen van wetgeving.

  • Rechtsvinding.

  • Sociaal-wetenschappelijke bestudering van het recht.

werkwijze

Het onderwijs zal in de vorm van twee uur hoorcolleges per week gedurende het eerste trimester worden verzorgd. De hoorcolleges dragen een ondersteunend karakter en dienen om de stof waar nodig uit te leggen, aan te vullen en te illustreren. Tevens worden werkcolleges verzorgd waarin artikelen, arresten en stellingen nader worden uitgediept. Tijdens die werkcolleges is er ruimte voor debat.

literatuur

  • G.J. Wiarda, Drie typen van rechtsvinding, Deventer, Tjeenk Willink, 1999 (vierde druk);

  • A. Soeteman, De droom van recht, Utrecht, Lemme 2000/2002;

  • Reader Encyclopedie II 2006-2007 (verkrijbaar in de VU-boekhandel);

  • Syllabus Encyclopedie II 20065-2007 (verkrijgbaar in de VU-boekhandel);

  • Collegestof.

toetsing

Schriftelijk tentamen met open vragen.

voorkennis

Als 6 (zes) van de 10 (tien) vakken van het eerste bachelorjaar Rechtsgeleerdheid en Encylcopedie I zijn behaald.

voorkennisvak

200107 : Encyclopedie der rechtswetenschap I (B1)




subject

Entrepreneurship in Health and Life sciences

code

470575

lecturers

dr. H. Smit; guest lecturers; prof.dr. E. Masurel (co-ordinator)

credits

6

period

27.11.2006-22.12.2006

aim

  • To get acquainted with the various aspects of entrepreneurship

  • To learn to integrate beta knowledge with knowledge of various other scientific fields such as, management, organization, finance, marketing

  • To learn to translate (bio) medical findings and business ideas into commercial value

  • To become updated about the present situation and future developments of the international health- and life sciences based business sector

  • To learn about business ethics and corporate social responsibitly.

  • To learn how to think as an entrepreneur

  • To learn how to start up your own company

  • To get experienced in writing a business plan

  • To learn how to work effectively in a business team

  • To improve your communication as well as management skills

content

During this course you will focus on various dimensions of modern entrepreneurship. You will work on several assignments including the generation of your own business ideas and the analyses of a pharmaceutical company. The main part of the course will be dedicated to "making a business plan for a real startup company in the health and life sciences". You will do this in a business team that will be formed by 4 or 5 students. The creation of this real-case based startup company and the feedback you will get during this process from (former) entrepreneurs and business advisors is aimed to give you a broad overview of the many aspects of entrepreneurship in Health and Life sciences.

Theoretical concepts of the course `Business Management in the health and Life Sciences¿ are applied and deepened and various skills are further practiced. At the end of the course your will present your business plan to an expert panel of investors and other specialists.



form of tuition

Training; Project assignments, workshop.

literature

Reader + Handbook `Starting up¿ ¿ achieving success with professional business planning

mode of assessment

Individual evaluation based on the assignments, personal performance in the business team, and assessment of the content and the presentation of the business plan.

target audience

Optional course for Master students Management, Policy Analysis and entrepreneurship in health and life sciences (MPA), M-differentiation of the Health, Life & Natural Sciences, Biology, Health sciences, Biomedical Sciences.

remarks

Attendance is compulsory. Prior Knowledge: Business Management in Health and Life sciences. For information and application: ciska.heuvelman@falw.vu.nl




subject

Ergodic Theory

code

400263

lecturer

mw.dr. K. Dajani (Kraaikamp-) (Phone: +31 (0) 30 253 1424, e-mail: dajani@math.uu.nl)

credits

6

period

Semester 1

aim

On successful completion of the course the students will be able to understand the basic concepts of measure preserving transformations, invariant measures, recurrence, ergodicity and entropy. This will allow them to describe the asymptotic behaviour of ergodic averages via ergodic theorems, and to understand the structure of the sets of invariant and ergodic measures for continuous transformations.

content

The roots of ergodic theory go back to Boltzmann's ergodic hypothesis concerning the equality of the time mean and the space mean of molecules in a gas, i.e., the long term time average along a single trajectory should equal the average over all trajectories. The hypothesis was quickly shown to be incorrect, and the concept of ergodicity ('weak average independence') was introduced to give necessary and sufficient conditions for the equality of these averages. Nowadays, ergodic theory is known as the probabilistic (or measurable) study of the average behavior of ergodic systems, i.e., systems evolving in time that are in equilibrium and ergodic. The evolution is represented by the repeated application of a single map (in case of discrete time), and by repeated applications of two (or more) commuting maps in case of 'higher dimensional discrete time'. The first major contribution in ergodic theory is the generalization of the strong law of large numbers to stationary and ergodic processes (seen as sequences of measurements on your system). This is known as the Birkhoff ergodic theorem. The second contribution is the introduction of entropy to ergodic theory by Kolmogorov. This notion was borrowed from the notion of entropy in information theory defined by Shannon. Roughly speaking, entropy is a measure of randomness of the system, or the average information acquired under a single application of the underlying map. Entropy can be used to decide whether two ergodic systems are not 'the same' (not isomorphic). With a basic knowledge of measure theory, the notions of measure preserving (stationarity), ergodicity, mixing, isomorphism and entropy will be introduced. Also applications to other fields such as probability theory and number theory will be given.

form of tuition

Lectures.

mode of assessment

Will be announced.

entry requirements

Measure Theoretic Probability.

target audience

mSFM

remarks

Contact the coordinating lecturer of this course.

Location: Utrecht.






naam

Evolutiebiologie

code

470063

docenten

prof.dr. N.M. van Straalen (cursusleider); dr. J.H.C. Cornelissen; dr. D. Roelofs

studiepunten

6

periode

05.02.2007 -02.03.2007

doel

Kennismaking met de principes van de evolutieleer, verwerven van inzicht in de mechanismen van soortvorming, de diversiteit en onderlinge samenhang van bouwplannen van planten en dieren.

Niveau 1.



EindtermenDe student is in staat:

  • de belangrijkste bewijzen voor evolutie te omschrijven;

  • de hoofdtijdperken in de evolutionaire geschiedenis aan te geven;

  • de mechanismen van soortvorming te omschrijven;

  • zelf een fylogenetische reconstructie te kunnen maken;

  • de hoofdgroepen van het planten- en dierenrijk te benoemen;

  • de bouwplannen van algen, mossen, varens en zaadplanten te beschrijven;

  • de bouwplannen van de hoofdgroepen van het dierenrijk te beschrijven;

  • de evolutionaire lijnen binnen de gewervelde dieren aan te geven;

  • de evolutie van de primaten en de mens te omschrijven;

  • met behulp van microscoop en eenvoudig snijmateriaal de externe morfologie van planten te achterhalen;

  • met behulp van microscoop en snijmateriaal de bouwplannen van de hoofdgroepen van het dierenrijk te achterhalen.

inhoud

In de cursus worden de principes van de evolutieleer geïllustreerd, met name de organische aspecten (ontstaan van bouwplannen, onderlinge samenhang en diversiteit binnen het plantenrijk en het dierenrijk).

De stof omvat de volgende onderwerpen:



  • Evidentie voor evolutie;

  • Mechanismen van soortvorming;

  • Invloed van geologische gebeurtenissen op evolutie;

  • Classificatie en systematiek;

  • Fylogenie;

  • Diversiteit van algen, mossen, varens en zaadplanten;

  • Diversiteit van ongewervelde dieren;

  • Bouwplannen van gewervelde dieren, incl. primaten;

  • Evolutie van de mens;

werkwijze

Hoorcolleges (38 uur); computerpractica (8 uur, aanwezigheid verplicht); voorcolleges (8 uur, aanwezigheid verplicht); snijpractica (32 uur, aanwezigheid verplicht); computer-ondersteund leren (20 uur); excursies (12 uur, verplichte deelname); tentamen (2 uur); onbegeleide zelfstudie (40 uur).

literatuur

M.W. Strickberger, Evolution, 3rd Ed., 2000. ISBN 0-7637-1066-0, prijs ongeveer 45 euro en een syllabus, prijs ongeveer 20 euro, inclusief toegang tot het museum Naturalis en Artis.

toetsing

Schriftelijk tentamen en verslag over de plantkunde-, dierkunde- en computerpractica en de excursies.

doelgroep

Verplicht voor eerstejaars bachelorstudenten Biologie.

opmerkingen

Een laboratoriumjas tijdens de snijpractica is verplicht. Snijmaterialen kunnen aangeschaft worden bij het eerste practicum (ongeveer 25 euro).




naam

Evolutionaire genetica

code

470053

docenten

dr. J.M. Kooter (cursusleider); dr. H. Schat; dr. D. Roelofs

studiepunten

6

periode

4.06.2007-29.06.2007

doel

Verwerven van kennis en inzicht in :

  • dynamische karakter van genetisch materiaal en genetische variatie

  • oorzaken genetische variatie op nucleotide, gen, en chromosoom-niveau

  • genoomevolutie bij pro- en eukaryoten

  • vergelijkende genomics

  • evolutionaire gevolgen van sex

  • ecologische en moleculaire oorzaken van soortvorming

  • horizontale DNA overdracht

  • gebruik van genomische databanken bij evolutiestudies

  • modellen van de moleculaire oorsprong van leven op aarde

  • reconstructie van fylogenetische bomen met behulp van het computerprogramma PAUP

  • verschillende vormen van selectie en theoretische onderbouwing

  • manieren waarbij genetische variatie wordt gebruikt om oorzaken van stochastische en deterministische processen af te leiden

  • toepassing van wiskundige regels die bestaan voor het gedrag van allelen van één of twee loci in ideale populaties, en voor genen met een kwantitatief effect

  • de relatie tussen ziekte en evolutie

  • moleculaire evolutie van pathogenen (bacterien, virussen, protozoa)

inhoud

De cursus behandelt:

- Genetische concepten die de basis vormen voor het begrijpen van de evolutietheorie, waaronder moleculaire evolutie, ontstaan van nieuwe genen en functies, genoom organisatie, vergelijkende genomics, soortvorming, humane genoom evolutie, relatie ontwikkeling en evolutie, en hypothesen over het ontstaan van `leven¿,

- Theoretische principes van de populatie genetica, waaronder verschillende vormen van selectie, quantitatieve genetica, drift, en hun toepassingen bij het bestuderen van variatie en evolutie in natuurlijke populaties.

- Fylogenetische reconstructies op basis van DNA sequenties met behulp van een cladistisch computerprogramma



- Toepassing van evolutiebiologie bij analyse en bestrijding van ziekten bij mens, dier, en plant.

werkwijze

  • Hoorcolleges (40 uur)

  • Werkcolleges (verplicht, 20 uur)

  • Literatuurbespreking (verplicht, 9 uur)

  • Computer Practicum (verplicht, 9 uur)

  • Lab. Practicum (verplicht, 8 uur)

  • Zelfstudie

  • Ondersteuning via Blackboard

literatuur

  • Studieboek: 'Evolutionary Analysis', Scott Freeman and Jon C. Herron,  Third Edition, 2004, Pearson, Prentice Hall

  • Syllabus met Onderzoeks- en Reviewartikelen over onderwerpen die niet in het boek worden behandeld

toetsing

Schriftelijk tentamen (0.8) en een literatuurbespreking (0.2). Beide moeten voldoende zijn.

doelgroep

Keuzevak voor derdejaars bachelorstudenten Biologie en Bio-medische Wetenschappen.

voorkennis

Alle vakken uit het eerste jaar en Moleculaire Ontwikkelingsbiologie uit het twee jaar (470038).

opmerkingen

De cursus wordt gegeven door de afdelingen Genetica, Ecologie en Fysiologie van planten, en Dierecologie.




subject

Evolutionary Computing

code

400111

credits

6

period

1

lecturer

prof.dr. A.E. Eiben

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.

content

The course is treating various algorithms based on the Darwinian evolution theory. Driven by natural selection (survival of the fittest), an evolution process is being emulated and solutions for a given problem are being "bred". During this course all "dialects" within evolutionary computing are treated (genetic algorithms, evolutiestrategieën, evolutionary programming, genetic programming, and classifier systems). Applications in optimisation, constraint handling and machine learning are discussed. Specific subjects handled include: various genetic structures (representations), selection techniques, sexual and asexual genetic operators, (self-)adaptivity. If time permits, subjects in Artificial Life and Artificial Societies, and Evolutionary Art will be handled. Hands-on-experience is gained by a compulsory pogramming assignment.

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

Facets of AI

code

400123

credits

8

period

5 and 6

lecturer

dr. V.N. Stebletsova

aim

The main objective of this course is that students learn how to do a litature-study, and present the results in written and oral form. The teachers supply materials to support this learning process.

content

The course provides an overview of important research themes within the area of Artificial Intelligence, eg.,  knowledge representation, types of reasoning (reasoning with uncertainty, meta-reasoning, etc.), use of evolutionary computing techniques, knowledge acquisition, philosophical questions related to AI. During this course each student chooses two subjects, each of which is researched (by acquiring articles) and the results of this research are presented in written (paper) and oral (presentation) form. The students will evaluate the written paper and presentation of their fellow students. Students are required to actively participate in the course; the presence during individual meetings with the instructor and presentations is compalsory.

form of tuition

Combination of lectures, group meeting for presentations and individual meeting  with a supervisor.

literature

Lecture notes and course materials on the Blackboard.

mode of assessment

The grade a student obtains is based on the quality of the written paper, oral presentation and participation in class-room discussions, as well as the evaluations of their fellow students and keeping up with deadlines.

entry requirements

Kennissystemen (400126) or Design of Multi-Agent Systems (400054).

target audience

3AI, mCS

remarks

More information can be found on the Blackboard.


subject

Femtosecond Lasers and Nonlinear Techniques

code

420178

lecturers

dr. K.S.E. Eikema; prof.dr. W.M.G. Ubachs

credits

6

period

4 and 5

content

This course focuses on the physics and techniques of advanced femtosecond (nonlinear) laser spectroscopy. After a review of basic femtosecond laser techniques, the interaction of light with matter in the femtosecond regime will be discussed using Bloch equations and the (nonlinear) wave equation for propagation. This is followed by the concepts of nonlinear processes such as second-harmonic generation, parametric amplification, stimulated Raman scattering, polaritons, photon echos, pump-probe and transient spectroscopy. Also applications of these methods will be discussed. Other topics that will be covered are pulse measurement techniques such as FROG and SPIDER, femtosecond frequency combs, phase-locking, spectrum extension methods such as continuum, THz and X-ray generation and spectral and temporal shaping of pulses, including some of the applications such as coherent control.

literature

Syllabus.

mode of assessment

Written examination.

target audience

mPhys, mCh




subject

Financial Risk Management

code

61332080

credits

6

contact

24 hours (24 lecture)

 

and active participation

period

4

co-ordinator

ir. F.W. van den Berg

aim

This course expands on financial topics covered in the first and second year. While in Financial Management / Corporate Finance the financial function of an industrial or trading corporation is analyzed, we concentrate in this course on Financial Markets and Financial Institutions and how these institutions protect themselves against financial risk (credit, foreign exchange, interest rate, international, operational etc.). The structure of financial markets is also analyzed. Hedging of (financial) risk through various advanced instruments (derivatives et al) is explained. The aim is to prepare students for a (possible) career in the FBI sector: Finance, Banking (commercial and investment) and Insurance, incl. pension funds, investments funds, stock markets, Euronext, DNB, ECB, AFM etc.

content

The following topics, issues and concepts will be dealt with:

  • Determination and management of various financial risks, such as Liquidity risk, Sovereign risk, Insolvency risk, Interest Rate risk, Foreign Exchange risk etc. including concepts as Value-at-Risk, Stress Test, Gap analysis, Immunization, (Modified) Duration, Disintermediation, Securitization

  • Asset Liability Management (at basic level) and (International) Financial Risk Management (incl. application of derivatives such as swaps, options, futures and forwards) to hedge against the volatility of interest rates and exchange rates

  • Credit extension by banks: credit analysis, risk classification, financing need projections, credit classification, pricing, collateral, procedures, covenants, legal lending contracts

  • Financial products: types of loans such as mortgages, revolving credits, term loans; convertible / subordinated bonds, commercial paper, money market instruments, trade credit, preference shares, venture capital, mezzanine financing, warrants

  • Several Financial Scandals which are (partly) the result of insufficient control, such as: Barings - Nick Leeson; junk bonds - Michael Milken; Savings & Loans banks in USA; Wall Street crash '29 - '33; Octobre 1987 crash; LTCM - Long Term Capital Mgt.; problems with Continental Illinois Bank, Penn Square Bank, Bankers Trust Co., BCCI, Herstatt Bank, Credit Lyonais / Slavenburg Bank; insider trading - Ivan Boesky; derivatives problems with Orange County / Procter & Gamble

form of tuition

Lectures, discussions, videos.

literature

Saunders, Anthony & Marcia Millon Cornett, Financial Institutions Management: A Risk Management Approach. 5th edition, McGraw-Hill, 2005/6

examination format

written interim examination

entry requirements

This course is a core course for Business Administration students specializing in Finance, Banking & Insurance (FBI). Students must be familiar with Corporate Finance / Financial Management as covered in the 1st and 2nd year. Pre-master students (from a finance, economics, accounting or equivalent background) must familiarize themselves with this material beforehand. This not a basic finance course, knowledge of financial accounting and corporate finance is a prerequisite.




subject

Financial Time Series

code

400469

coördinator

prof.dr. C.A.J. Klaassen (Phone: +31 (0) 20 525 5010, e-mail: chrisk@science.uva.nl)

credits

6

period

Semester 2

aim

Making students familiar with the basic models for stochastic processes indexed by time with special applications for financial processes.

content

A time series is a sequence of random variables ordered according to an integer index, which is usually referred to as "time". This course is an introduction to the theory of time series, including prediction theory, spectral (=Fourier) theory, and parameter estimation. Among the time series models we discuss the classical ARMA processes, and also the GARCH and stochastic volatility processes, which have become popular models for financial time series. Within the context of nonparametric estimation we also discuss the ergodic theorem and extend the central limit theorem to dependent ("mixing") random variables. The course is a mixture of probability and statistics, with some Hilbert space theory coming in to develop the spectral theory and the prediction problem.

form of tuition

Lectures.

literature

Lecture notes by A.W. van der Vaart: Time Series. An expanded list of literature is in the lecture notes.

mode of assessment

Will be announced.

remarks

Registration via http://studieweb.student.uva.nl 4 weeks prior to the start of the course. UvA code: ST406036. Course registration includes registration for the examination. Registration is also possible at the Education Office, phone: 525 7100, e-mail: ondwns@science.uva.nl

Consult the schedules at http://www.student.uva.nl or contact the coordinator.



Location: UvA.




subject

From Genome to Physiome

code

420127

 

Location: Academic Medical Center, dept. Medical Physics
Thursday, 14-17

lecturer

dr. E.T. van Bavel (e.vanbavel@amc.uva.nl)

credits

6

period

4 and 5

content

Living systems obey the same physical and chemical laws as non- living systems. However, a property of living systems is the degree of complexity: living systems comprise multiple levels of organization and highly multi variate and non-linear structure at each level. The aim of this course is an introduction into the characteristics of this structure. Apart from descriptions at the genome level, we will report on current initiatives towards a complete description of life functions at the protein-level and organ-level.

form of tuition

Practical work.

mode of assessment

Written and oral report.

target audience

mPhys, mCh

remarks

Once in every 2 years.




naam

Functieleer (Experimental Psychology)

code

811003

studiepunten

6

contacturen

168 (15 paper, 3 tentamen, 15 practicum, 24 hoorcollege, 109 zelfstudie, 2 ondersteunend college)

periode

4

docenten

dr. C.N.L. Olivers; prof.dr. J.L. Theeuwes; dr. M. Meeter

doel

Kennismaking met de psychologische functieleer: de studie van algemene menselijke gedragsfuncties, zoals waarnemen, leren, geheugen, taal, beslissen, probleem-oplossen, aandacht en motoriek.

inhoud

In de cursus worden perceptie, aandacht, reactieprocessen en signaaldetectie besproken alsmede hun biologische basis. Ook komen het geheugen, taal, beslissen en probleemoplossen aan de orde.

werkwijze

Hoorcolleges, Blackboardpractica via de computer, schrijven van een paper over de resultaten van een zelfgedaan experiment, responsiecollege. Hoorcolleges: Er zijn in totaal 12 hoorcolleges waarin de stof op hoofdlijnen wordt doorgenomen. Blackboardpractica via de computer: Naast de colleges zijn er 10 practica. Bij elk practicum worden via de computer een aantal vragen over de behandelde stof gesteld en doet de student zelf mee aan een aantal experimenten of demonstraties die representatief zijn voor bepaalde soorten onderzoek (b.v. op het gebied van signaaldetectie, visuele waarneming, taal, geheugen en neurale netwerken). De practica zullen worden gegeven in de computerruimte van FPP. Elke student zal een eigen computer tot zijn/haar beschikking hebben en via een unieke inlognaam inloggen. De student krijgt voor elk behaald practicum een punt. Het totaal aantal punten voor de practica bepaalt 10% van het eindcijfer.

Paper: Tegen het eind van de cursus maakt elke student individueel een kort, paper over een zelfstandig uitgevoerd experiment. Het paper bevat de volgende onderdelen: titel, samenvatting, inleiding, methode, resultaten, discussie en referenties. Het paper wordt zowel op inhoud als op vorm beoordeeld. Het cijfer telt eveneens voor 10% mee bij de bepaling van het eindcijfer. Het paper wordt electronisch ingeleverd via Blackboard.

Responsiecollege: De collegereeks eindigt met een responsiecollege, waarin studenten vragen over de stof aandragen ter voorbereiding van het tentamen.


literatuur

  • Ashcraft, M.H. (2005). Cognition. Upper Saddle River, NY: Prentice Hall.

  • Syllabus Inleiding Functieleer 2006/2007

toetsing

tentamen
paper

Multiple choice tentamen. Het tentamen telt voor 80% mee bij de bepaling van het eindcijfer, 10% wordt bepaald door de punten voor de practica en 10% door het cijfer voor het paper. Het eindcijfer wordt afgerond op gehele getallen.



opmerkingen

Alle studenten volgen in principe alle onderdelen van de cursus (dit geldt ook voor AI studenten). Deelname aan de practica en het paper is verplicht. Dit betekent dat minstens één practicum voldoende gemaakt, en een paper ingeleverd moet zijn, wil het tentamencijfer (vermenigvuldigd met bijbehorend gewicht) toegekend worden. Deelresultaten blijven in principe één jaar geldig. Aan practicum en paper moet tijdens de cursus voldaan worden en kunnen niet worden ingehaald of overgedaan. Eventuele vrijstellingen kunnen schriftelijk aangevraagd worden bij de Examencommissie van de Faculteit Psychologie en Pedagogiek. Verdere details staan in de syllabus.




subject

Function Theory of Several Complex Variables

code

400465

lecturer

dr. J.J.O.O. Wiegerinck (Phone: +31 (0) 20 525 5097, e-mail: janwieg@science.uva.nl)

credits

6

period

Semester 2.

aim

Familiarity with the basic concepts in the theory of analytic functions of several complex variables, as well as with a number of fundamental results of the subject.

content

Analyticity in several variables, domains of convergence of power series (Reinhardt domains), Cauchy-Riemann equations, Hartogs' extension theorem, domains of holomorphy, pseudoconvexity and the Levi problem. Description of zero sets (Weierstrass preparation theorem), holomorphic mappings. Plurisubharmonic functions, L^2 and Kernel methods for solving inhomogeneous Cauchy Riemann equations. Cousin problems and cohomology.

form of tuition

Lectures.

literature

  • Korevaar, J., Wiegerinck, J., Lecture notes several complex variables notes available as .ps or .pdf file.

Additional reading: 

  • Krantz, S., Function Theory of Several Complex Variables. AMS-chelsea, 1992.

  • Hormander, L., Complex Analysis in Several Variables. North Holland, 1973.     

  • Fritzsche, K., Grauert, H., From Holomorphic Functions to Complex Manifolds. Springer, 2002.

mode of assessment

Examination takes part during the course via take home exercises. Students will work on and present exercises, or short papers in the practical sessions.

entry requirements

Analysis courses from the Bachelor Mathematics.

remarks

Registration via http://studieweb.student.uva.nl 4 weeks prior to the start of the course. UvA code: M27. Course registration includes registration for the examination. Registration is also possible at the Education Office, phone: 525 7100, e-mail: ondwns@science.uva.nl

Consult the schedules at http://www.student.uva.nl or contact the coordinator.



Location: UvA.




subject

Functional Analysis

code

400328

credits

8

period

1 and 2

target audience

mMath

remarks

This course is part of the joint national master programme in mathematics.
For schedules, course locations and course descriptions see http://www.mastermath.nl.
Registration required via http://www.mastermath.nl.




naam

Fundamentals of Analytical Sciences

code

435059

coördinator

dr. W.T. Kok

lecturers

dr. W.T. Kok; dr. H. Lingeman

studiepunten

6

periode

3

aim

To give insight in the procedures used in analytical chemistry, from sampling strategies to method validation, and to teach basic statistical techniques required for data interpretation.

content

In this course general aspect of analytical methods, techniques and instrumentation will be treated. The complete analytical procedure, from sampling to data handling and interpretation, will be covered. Parameters to describe the quality of analytical methods (accuracy and precision, sensitivity, selectivity, robustness, etc.) will be defined. Principles of modern analytical instrumentation and data acquisition techniques will be discussed. Attention will also be given to validation procedures and to quality control in analytical laboratories. An important part of the course is devoted to basic statistical techniques as used routinely in laboratories.

form of tuition

Lectures, workgroups and PC-use sessions.

literature

Hand-outs and course syllabus.

mode of assessment

Written examination.

entry requirements

Basic knowledge of analytical chemistry.

target audience

mCh, mPhar.

remarks

Enrolment course: three weeks prior to the start of the course via UvA `studieweb¿: http://studieweb.student.uva.nl (`werkgroepen¿).

Examination: one week prior to the examination date via studieweb (`tentamen¿).



Registration is also possible at the Education Office.




subject

General Relativity

code

420128

lecturer

prof.dr. J. de Boer (UvA, phone: +31 (0) 20 525 5769, e-mail: jdeboer@science.uva.nl
http://staff.science.uva.nl/~jdeboer/gr)

credits

6

period

1 and 2

aim

To familiarize the student with the foundations and applications of general relativity and some basic cosmology.

content

The precise content will be announced later. The course will at least contain an introduction to basic general relativity and the Friedmann-Robertson-Walker cosmological solutions and the Schwarzschild solution for a black hole will certainly also be described.

form of tuition

Lectures and exercise sessions.

literature

Spacetime and Geometry: An Introduction to General Relativity', S. Carroll, Addison Wesley

mode of assessment

Written examination.

entry requirements

Special Relativiy.

target audience

mPhys.

remarks

Registration via http://studieweb.student.uva.nl three weeks prior to the start of the course. Course registration includes registration for the examination. Registration is also possible at the Education Office, phone: 525 7100, e-mail: ondwns@science.uva.nl. For the course schedules consult the separate schedule guide or see http://www.student.uva.nl/




subject

Genome Analysis

code

430047

coördinator

prof.dr. J. Heringa

lecturers

prof.dr. J. Heringa; Gastdocenten

credits

6

period

1

aim

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

content

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. 

Theory:

  • Sequence alignment, dynamic programming, database searching, and further appropriate downstream genomics analysis techniques.

Practical:
A choice between assignments:

  • Phylogenetic profiling of a selected bacterial gene

  • Prediction of function of unknown ORF's in selected viruses or bacteria

  • Function prediction through interpolation of distances from Clusters of Orthologous Groups (COGs)

form of tuition

  • One-to-one assignment introductions

  • Hand-on support

  • If necessary: parts of bachelor course Genomics

literature

  • E-course material and overheads

  • Gibson G and Muse,  A primer of genome science, SV, Sinauer Associates Inc Publishers, 2002, ISBN 0878932348 (pbk).

  • Durbin, R., Eddy, Sean R., e.a.,  biological Sequence Analysis, Cambridge University Press, 350 pp., ISBN 0521629713.

  • Extra: Parts from the book; Claverie & Notrdame, Bioinformatics for Dummies, Wiley Publishing, Inc., 2003, ISBN 0764516965

mode of assessment

Assignment results and oral or written examination (depending on number of course students).

entry requirements

Bachelor course Genomics.

target audience

Third or fourth year students Computer Science, Mathematics, Chemistry or Physics
Masterstudents Biomolecular Sciences, Biology en Bio-Medical Sciences, all with a strong interest in Bioinformatics.

remarks

Active participation is required.
The course will be taught in English (master level) and Dutch (bachelor level).




subject

Genomes and Gene Expression

code

470614

lecturers

dr. J.M. Kooter (coordinator, VU-FALW); guest lecturers

credits

6

period

02.10.2006 - 27.10.2006

aim

To provide students with the latest facts and concepts of the various levels of gene expression regulation in eukaryotes.

content

The following topics will be covered:

Transcriptional regulation:

  • Genome organization: coding versus non-coding sequences

  • Composition and biochemistry of basic transcription machinery

  • Transcription initiation, elongation and termination

  • Regulatory sequences: promoters, enhancers, suppressors, boundaries

  • Application of comparative genomics in identifying cis-acting elements

  • Chromatin structure and histone modifications

  • DNA methylation and epigenetics

  • Nuclear structure and transcription factories

  • Transcription regulation through the cell cycle

  • Transcription regulation through development

  • Regulatory networks

  • Cellular memory: establishing and maintaining differentiation status

  • Non-coding RNAs and control of gene expression

  • Intergenic and antisense transcription

  • Techniques and applications

Post-transcriptional regulation

  • RNA processing, including alternative splicing and its regulation

  • Nucleo-cytoplasmic RNA transport

  • RNA stability and degradation pathways

  • RNA interference (siRNAs and micro-RNAs)

  • Translation regulation

  • RNA-editing

  • Riboswitches

  • Techniques and applications

Analysis of gene expression

  • Human transcriptome

  • Single-gene analyses and techniques

  • Parallel analyses: micro-arrays

Micro-arrays: statistical analysis, data mining, applications

form of tuition

This advanced Master course consists of formal lectures, working groups, literature discussions. We aim for a highly interactive course

literature

  • Book: will be announced

  • Chapters on gene expression regulation from the book: Molecular Biology of the Cell by Alberts et al.

  • Hand-out with Research and Review articles

  • PPT-notes from lectures. 

mode of assessment

Written exam, literature discussion, and participation in working groups

entry requirements

Bachelor Genetics and Molecular Developmental Biology

target audience

Master students: Biomolecular Sciences, Biology and Bio-Medical Sciences




naam

Genomics

code

470076

docenten

dr. J.M. Kooter; prof.dr. M. Verhage (cursusleider, matthijs@cncr.vu.nl); dr A.S. Groffen; prof dr P. Heutink; prof.dr. A.B. Smit; dr. R.J.M. van Spanning

studiepunten

6

periode

04.09.2006-29.09.2006

doel

(A) De hoofddoelen zijn:

  • het verkrijgen van inzicht in de samenstelling en organisatie van het genoom en de benaderingen om dat te analyseren.

  • het analyseren van verschillen en overeenkomsten binnen het genoom en tussen genomen van verschillende individuen of species en het inzichtelijk maken hoe die verschillen en overeenkomsten de basis vormen voor verschillen en overeenkomsten in het funktioneren van cellen en het gedrag van organismen en in het ontstaan van ziekte

  • het verkrijgen van inzicht in hoe genoom-elementen bijdragen tot complexe biologische funkties of het ontstaan van ziektes.

(B) Voor deze hoofddoelen worden de volgende vaardigheden bijgebracht:

  • het gebruiken van de bioinformatica in genoomanalyse, bij het vinden en gebruiken van de verschillende databases voor DNA sequenties, transcriptomics profielen, proteomics en metabolomics en het vergelijken van deze verschillende genoomsequenties,

  • het identificeren van genetische diversiteit en variaties die bijdragen tot het onstaan van ziekte of de kwetsbaarheid hiervoor.

  • het vergelijken van de funktie van orthologe genen in verschillende organismen

(C) Ten slotte heeft de cursus het doel de student te laten kennismaken met een aantal belangrijkse toepassingen en afgeleiden van genoomanalyse:

  • de transcriptomics, de proteomics en de metabolomics, ook voor diagnostische doeleinden

  • methodes om in model organismen in te grijpen in hun genoom, om daarmee de basis van fysiologisch, biotechnologisch en pathologisch functioneren te onderzoeken (tuneable promoters, transgenese, knock-out technologie, RNA-interferentie)

  • de genetische basis van gedrag en gedragsafwijkingen

  • medische toepassingen van genomics (vergelijken zieke en gezonde weefsels, diagnose; uitzicht op therapie, pharmacogenomics)

  • biotechnologische toepassingen van genomics

  • ecologische toepassingen van genomics

  • ethische aspecten aan genomics en genetische modificatie

inhoud

De cursus bestaat uit twee kort 'opfris' colleges afgerond met een toets om een goed ingangsniveau te garanderen. Het hoofdbestanddeel van de cursus zijn 14 modules die elk bestaan uit hoorcolleges en een computerpracticum. Tenslotte is er tijd voor het afronden van opdrachten en voorbereiden van het tentamen.

werkwijze

Hoorcolleges, (computer)werkcolleges, zelfstudie

literatuur

syllabus Genomics

toetsing

Tentamen en ingeleverde werkopdrachten. Het eindcijfer wordt bepaald uit het gewogen gemiddelde van de scores voor het tentamen (60%) en de werkopdrachten (samen 40%) Studenten kunnen alleen slagen nadat zij alle computerpraktica hebben volbracht.

doelgroep

Verplicht voor derdejaars bachelorstudenten Biomedische wetenschappen. Keuze voor derdejaars bachelorstudenten Biologie.

De cursus staat open voor belangstellenden uit andere opleidingen. Studenten uit andere studierichtingen moeten vooraf contact opnemen met de docent en goedkeuring vragen bij de examencommissie van hun eigen opleiding.






naam

Gezondheidscommunicatie

code

470087

docenten

dr M. Adriaanse; Gastdocenten; drs. A.M.C. Plass; drs. J. Veldhuis (coordinator, e-mail: jolanda.veldhuis@falw.vu.nl, tel.: 020 5985583)

studiepunten

6

periode

04.06.2007 - 29.06.2007

doel

Het doel van de cursus is om inzicht te krijgen in het communiceren van gezondheidsboodschappen naar de hele samenleving of specifieke groepen en het ontwikkelen van communicatieve interventies.

Na deze cursus is de student in staat:



  • de volgende begrippen te onderscheiden/definiëren:
    communicatie/voorlichting, voorzieningen en regelgeving, gezondheidsvoorlichting en gezondheidsbevordering.

  • een planningsmodel toe te passen op een concreet voorbeeld en de valkuilen te onderkennen in de planning van gezondheidscommunicatie.

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

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

  • uitkomsten van een gedrags- en omgevingsfactorenanalyse van een gezondheidsprobleem te interpreteren en te verwerken in een plan van aanpak middels gezondheidscommunicatie.

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, en bijbehorende kanalen (media; zoals TV, posters, etc.). Naast het bieden van een theoretisch kader is deze cursus tevens gericht op de praktische toepasbaarheid; o.m. analyse van een specifiek gezondheidsprobleem als onderwerp voor een communicatiecampagne, het definiëren van de doelgroep en het bedenken van een communicatiestrategie/interventie.

werkwijze

Colleges, werkcolleges, gastcolleges, opdrachten, zelfstudie

literatuur

Syllabus en aanvullende literatuur bij de colleges

toetsing

  • Beoordeling van de opdracht bestaande uit drie deelopdrachten plus een presentatie (cijfers voor elk onderdeel vormen gemiddeld cijfer voor opdracht) = 40 procent van eindcijfer cursus

  • Schriftelijk tentamen: multiple choice en open vragen = 60 procent van eindcijfer cursus

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

doelgroep

Keuze voor derdejaars studenten BSc Algemene Gezondheidswetenschappen, premasterstudenten Algemene Gezondheidswetenschappen en masterstudenten in 1 van de bètaopleidingen in de specialisatie (wetenschaps)communicatie.

De cursus wordt ten zeerste aanbevolen voor studenten die de masterspecialisatie Preventie en gezondheid willen gaan volgen, dus met name bestemd voor alle premaster en bachelorstudenten die deze masterspecialisatie willen gaan volgen.



opmerkingen

Aanwezigheidsplicht: iedere student moet bij de opdracht minimaal eenmaal presenteren en mag maximaal eenmaal afwezig zijn bij de werkcolleges
Maximaal aantal deelnemers in de cursus: 60 studenten




subject

Group Theory

code

420025

lecturers

dr. B.L.G. Bakker; dr. D. Boer

credits

6

period

4 and 5

aim

Acquire knowledge about the most important applications of group theory in physics.

content

Symmetry plays an important role in the description of physical systems. Group theory is a way to treat symmetry systematically. After an introduction into the theory of abstract groups, the first half of the lectures will focus mainly on discrete groups and the second half on continuous groups, in particular Lie groups. Both types of groups are widespread in physics and an outline of this will be given. Applications of group theory in physics, in particular quantum mechanics, will be given throughout the course.

form of tuition

Lectures.

literature

Lecture Notes. Other suggested (but not mandatory) literature: Jones H.F., Groups, Representations and Physics ; Institute of Physics Pub.

mode of assessment

Oral examination.

entry requirements

Quantum mechanics and special relativity.

target audience

mPhys

remarks

For students of the Master's programme Theoretical Physics several additional tasks will be required for the examination, due to considerable overlap with the compulsory course Mathematical Methods in Physics.




subject

High Energy Astrophysics

code

420129

lecturers

dr. L.J. van den Horn (UvA, phone: +31 (0) 20 525 5776, e-mail: vdhorn@science.uva.nl); prof.dr. M.B.M. van der Klis

credits

6

period

4 and 5

content

This course is in the form of a seminar with different topics. Of central importance are cosmic X-ray and gamma ray sources, radiation from accelerated particles, and physical processes in and near neutron stars and black holes. The characteristic properties of sources of high energy radiation are discussed and related to the evolution of narrow binaries and the endpoints of stellar evolution.

form of tuition

Seminars.

literature

Lecture notes.

mode of assessment

By individual agreement.

entry requirements

Bachelor level physics/astronomy.

target audience

mPhys.

remarks

Registration via http://studieweb.student.uva.nl four weeks prior to the start of the course. Course registration includes registration for the examination. Registration is also possible at the Education Office, phone: +31 (0)20 5257100, e-mail: ondwns@science.uva.nl. For the course schedules consult the separate schedule guide or see http://www.student.uva.nl/




subject

High-Throughput Screening

code

435047

lecturers

prof.dr. H. Irth; dr. H. Lingeman

credits

6

period

4

aim

In depth study on the bio-analytical aspects related to target- and lead discovery of drugs focusing on proteomics, genomics, metabolomics, high-throughput / high-resolution screening and monitoring of biological effects by using bio-markers.

content

During this course the potential of modern analytical and immunological techniques (e.g., sample preparation, separation, detection, identification) used in target- and lead-discovery will be discussed. The emphasis will be on the treatment of advanced sample preparation techniques (i.e. automation, high-throughput / combinatorial chemistry, miniaturization), advanced separation modes and bio-specific assays and mass-spectrometric methods. The techniques will be discussed in relation with pharmacokinetic studies ¿ the applicability of the various techniques within the different stages of ADME will be discussed. Finally, biological-effect monitoring, for proteomics and genomics, exposure monitoring, pharmacokinetics and plasma / serum analyses will be dealt with.

form of tuition

Lectures and tutorials.

literature

Hand-outs (electronically available).

mode of assessment

Written or oral examination.

entry requirements

Basic knowledge of biochemistry, chromatography, electrophoresis and mass spectrometry.

target audience

mCh, mPhar




subject

Homogeneous Calatysis

code

435668

lecturers

prof.dr. P.W.N.M. van Leeuwen; prof.dr. J.N.H. Reek (Phone: +31 (0) 20 525 46637, e-mail: reek@science.uva.nl); dr. B. de Bruin

credits

6

period

4

aim

To create insight in the wordking principles of homogeneous catalysts and demonstrate the applications in academia and industry.

content

A broad range of important homogeneous catalytic reactions will be
discussed. Emphasis will be on transition metal catalyzed reactions.
Important aspects like mechanistic studies, kinetics, and effects of the nature of the metal ion and ligand structure will be explained. A small selection of processes that are applied industrially are discussed more indepth. The important role of homogeneous catalysis in organic synthesis will be illustrated.

form of tuition

Lectures, blackboard, exercises.

literature

Leeuwen, P.W.N.M. van, Homogeneous Catalysis, Kluwer Academic Publishers, Dordrecht, 2004.
We will also provide recent literature.

mode of assessment

Written examination.

entry requirements

B.Sc.

target audience

mCh

remarks

Registration for the course: via http://studieweb.student.uva.nl
three weeks prior to the start of the course. Examination: one week prior to the examination date.
Registration is also possible at the UvA Education Office, phone: 020-5257100/7049. E-mail: ondwns@science.uva.nl (mathematics and physics students). E-mail: svhouten@scienc.uva.nl (chemistry students). For the course schedules please consult the separate UvA schedule guide or phone the Education Office.




subject

Human Information Processing (Informatieverwerking)

code

815048

credits

6

period

4

lecturer

dr. S.A. Los

aim

At the end of this course students should be capable of:

  • outlining some major theories and controversies in human information processing, in particular relating to the concepts of processing stages, the central bottleneck, and executive control;

  • specifying major methodological approaches to these controversies;

  • deriving experimental predictions from research hypotheses and theories;

  • interpreting results from research in terms of theoretical constructs;

  • discussing interrelations among different theories in human information processing.

content

One or two research articles are covered during each lecture. The emphasis will be on (1) distinguishing the research hypotheses and underlying assumptions; (2) the experimental approach to test the hypotheses and (3) how the data bear on the different hypotheses.

form of tuition

Lectures

literature

A series of journal articles to be specified at the first lecture.

mode of assessment

Open-ended written examination.

remarks

Basic knowledge of experimental methods is assumed.




subject

Human-Computer Interaction

code

400432

credits

6

period

2 and 3

lecturer

drs. A.J. Bongers

aim

Explaining the User-Centered Design process and providing understanding of the interaction between people and information systems. The main goal is to teach students how to design and evaluate interactive systems that are easy to use and able to support people and organizations using them.

content

The usability aspects (cognitive ergonomic aspects) of human-computer interaction are related to both software engineering and to human aspects. This course introduces recent theories, approaches, and sources of Human-Computer Interaction to analyze and design Complex Interactive Systems. Several relevant schools are indicated, theories and techniques are discussed, and tools and applications are illustrated. The course also introduces some relevant basic notions about psychological aspects of computer use, aspects of organisational aspects of the introduction and application of information technology, and the theoretical basis for GTA (Groupware Task Analysis) and DUTCH (Design for Users and Tasks, from Concepts to Handles).

form of tuition

Lectures.

literature

  • Dix, A. e.a., Human-Computer Interaction 3rd edition. London: Prentice Hall, 2004 ISBN 0-130-461091.

  • Lecture notes and study guide on the website www.cs.vu.nl/~mmc/mci

mode of assessment

Written essay and examination.

target audience

2IK, 3AI, 3I, mCS, mIS.




subject

Hydrodynamics of Fluids and Plasmas

code

420132

lecturer

dr. L.J. van den Horn (UvA, phone: +31 (0) 20 525 55776, e-mail: vdhorn@science.uva.nl)

credits

6

period

4 and 5

aim

Knowledge and understanding of the fundamental laws of fluid flow, and their application to a variety of physical and astrophysical situations. Introduction to plasma and radiation hydrodynamics.

content

Conservation laws for ideal and dissipative fluid flow; local flow analysis, Cauchy-Stokes theorem; vorticity and circulation, Kelvin's theorem; potential flow, Bernoulli's law; hydrostatic equilibrium, stability, convection.
Hydrodynamic waves, sound propagation in homogeneous medium and in graviational field; wave damping through viscosity and thermal conduction, damping of acoustic waves through radiative flux; nonlinear phenomena: simple shock waves.
Fundamentals of magnetohydrodynamics, coupling of flow and e.m. field; frozen-in field, theorems of Alfven and Walen; static and stationary configurations: pinch and force-free fields, stability; magneto-acoustic and Alfven waves.
Introduction to radiation hydrodynamics: thermodynamics of radiative systems, radiation intensity, radiative energy density, flux and pressure tensor, energy-momentum conservation; radiation transport, emission/absorption, diffusion, free streaming, flux-limiting.

form of tuition

Lectures and interactive working sessions.

literature

Lecture notes.

mode of assessment

Group and individual assignments.

entry requirements

Bachelor's level Physics/Astronomy, Vector Calculus.

target audience

mPhys.

remarks

Registration via http://studieweb.student.uva.nl three weeks prior to the start of the course. Course registration includes registration for the examination. Registration is also possible at the Education Office, phone: +31 (0)20 5257100, e-mail: ondwns@science.uva.nl. For the course schedules consult the separate schedule guide or see http://www.student.uva.nl/


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