Exact Sciences Master Guide2005/2006

Final-projects and Training on the job

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Final-projects and Training on the job

  1. Programme

Each Master programme is finished with a graduation project or internship. This can be an individual project as well as a group project. Information about graduation projects and internships can be found on the Internet pages of the AI divisions and on http://www.cs.vu.nl/ai/msc-projects/index-en.html. Internships proposed by the student him/herself need approval in advance from a member of staff, who will also be involved with supervising the project.


Concerning graduation projects, the following rules are important:

  • The size of the graduation projects is as such that with adequate foreknowledge and complete study, the project can be finished within 6 months.

  • Students can in principle only start their graduation project if they have completed all other exam parts. In case one part must still be completed, approval of the project leader is required to start the project. In case more than one part must be completed, explicit approval of the board of exam is required.

  • The student participates in the KIM (Kunstmatige Intelligentie Meeting). In some cases, the amount of participation may be determined by the lecturer. More information can be found on http://www.cs.vu.nl/ai/kim-en.html.

  • Upon project completion, a meeting will be held with all involved in the project, in which a short evaluation will be made and a judgement will be made under responsibility of the lecturer. When the final judgement is that the student work is not sufficient, a supplement will be required from the student.


The rules for graduation internships are similar to those for graduation projects. For details, please contact the study advisor.

    1. Optional courses outside the department

      1. Programme

The student is advised to also consider following courses at other universities to get a programme that best fits his/her interests. Specific topics offered at other universities are, for example, image processing, cryptography, sensor informatics, data & knowledge modelling, computer graphics, embedded systems, robotics.

Before entering a course, the student needs to register at that university for the study that offers that course. The student needs his/her VU-collegekaart for that registration. Example universities that offer interesting courses for an AI-student are the University of Amsterdam (UvA), Utrecht University, University of Nijmegen, Leiden University, University of Groningen, University of Maastricht. The student is advised to consult the study guides and web pages of these universities to get a better insight in the kind of courses offered.

    1. Educational possibilities after the Master

      1. Programme

The AI Master programmes provide an excellent basis for a Ph. D. study in Artificial Intelligence or other research areas, such as Computer Science, and Cognitive Science.


Each year the faculty offers a number of Ph. D. student positions. Graduate students with execellent grades are invited to apply for one of these positions. A Ph.D. student position is normally awarded for 4 years, during which time the Ph.D. student is expected to finish his Ph.D. thesis. Ph. D. Students are supervised by a full professor, whereas daily supervision is sometimes performed by another member of the scientific staff. Aside from his/her research task (which includes following specialised courses and seminars), the Ph. D. student is also expected to contribute to the education of others. All Ph. D. Students are registered with SIKS, i.e., the Dutch research school for Information and Knowledge Systems, http://www.siks.nl. SIKS guarantees an excellent training programme for the Ph. D. student and a high level of research attainment with respect to the accepted Ph. D. theses.


The Department of Artificial Intelligence of the Faculty of Sciences offers Ph.D. student positions in one of the following areas:

  • Knowledge technology and knowledge representation; (prof. dr. F. van Harmelen, fah.van.harmelen@few.vu.nl).

  • Agent systems and their dynamics, also offering interesting cooperation opportunities on cognitive science, biology and organisation theory; (prof. dr. J. Treur, j.treur@few.vu.nl).

  • Computational intelligence; (prof. dr. G. Eiben, ae.eiben@few.vu.nl).

Students interested in a Ph.D. student position can contact either the persons mentioned or study advisor  dr.V. Stebletsova (vn.stebletsova@few.vu.nl).
      1. Training as a researcher

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

  1. Master Bioinformatics

    1. The domain of the Master

Research in Bioinformatics in its broadest definition concerns the analysis of informational processes within living systems with the help of computers. To do this succesfully, Bioinformatics actively uses and integrates contributions from areas such as Mathematics, Computer Science, Chemistry, Medicine and Biology. Bioinformatics has recently become one of the keywords in the life sciences as well as in Biotechnological and Pharmaceutical industries. Although in essence the field exists for over two decades and bioinformatics techniques developed over the years have come of age, the field has gained major prominence relatively recently, owing mostly to the world-wide human genome projects and subsequent structural and functional genomics initiatives. While the complete human genome sequence has been obtained at relatively little cost of around two billion Euros, the current investments in for example proteomics industries amount to orders of magnitude more. Also other genomic technologies, aimed at gaining insight in human physiological functioning such as microarray (gene chip) technology, have attracted multi-billion Euro investments both in industry and academia. Currently, many new small/medium enterprises (SMEs) and large international biotechnological and pharmaceutical companies are actively recruiting bioinformaticians, but experience hardship in doing so due to the lack of individuals with proper training. Similar problems are encountered at national academic centres in The Netherlands, particularly in microarray centres. As the interpretation of the data coming from all the above large-scale projects is crucially depending on the application and creation of new bioinformatics techniques, it is clear that a broad based and integrative master's curriculum in bioinformatics at the Vrije Universiteit is timely.


It is possible to study for a Master's degree at the Vrije Universiteit as of September 2003. The international Bioinformatics Master study takes 2 years and is organised by the Integrative Bioinformatics Institute VU (IBIVU), a multidisciplinary centre within the Vrije Universiteit in which three faculties (Faculty of Sciences; Faculty of Earth and Life Sciences; and the Faculty of Psychology) and the VU Medical Centre take part. To prepare for the Bioinformatics master course, various Bachelor programmes at the Vrije Universiteit offer integral courses in Bioinformatics, such as Medical  Natural Sciences and Biomolecular Sciences. These Bachelor programmes (taking 3 years) are dedicated to providing the student with a broad and thorough basis in each of their areas of study, which is indispensable for starting the Bioinformatics Master programme. The Bioinformatics Master's provides the student with an opportunity to deepen his/her knowledge of the various aspects of Bioinformatics, while the student has ample possibility to specialise in one or a few areas of choice.  It is expected that the breadth and flexibility of the masters programme resulting from the multi-disciplinary setup of the Integrative Bioinformatics Institute as well as the emphasis on creating bioinformatics tools from the strong embedding in the Informatics department (e.g. AI, Computer Systems) will be attractive for students.


The Bioinformatics Master studies are currently organised by the Faculty of Sciences and the Faculty of Earth and Life Sciences. The latest information can always be found at: http://www.cs.vu.nl/~ibivu/teaching/.


Depending on the individual furnishing of his/her Master programme, the student can attend lectures in other faculties and centres, for example Biology or the Centre for Neurogenomics and Cognitive Research (CNCR). Graduation projects can vary from practical to rather fundamental, depending on the preferences and capacities of the students. Students can also go to companies, research institutes or universities either in The Netherlands or abroad.


Study advice is open to all. Advisor prof. dr. Jaap Heringa can be contacted at all times. Furthermore, the website http://www.cs.vu.nl/~ibivu/teaching/ contains information regarding the international Bioinformatics Master programme.

      1. Objectives

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

After graduation the master in Bioinformatics is expected to be critical in a scientific manner, to be aware of the societal aspects of bioinformatics research, and to possess knowledge, experience, and insights regarding the following:

  • As mentioned earlier, Bioinformatics research is now firmly positioned in the scientific limelight, and is generating substantial -and sometimes unrealistic- expectation. Students should be able to recognise good and bad research.

  • Bioinformatics research is often used early on in cost intensive bio-medical development cycles (e.g. to define leads in drug discovery): errors can be costly.

  • Bioinformatics research interfaces many other scientific disciplines. Students should have knowledge concerning all neighbouring disciplines, and also have an ability to deal with incomplete knowledge and mental pictures, while still being able to ask appropriate research questions.

  • Paraphrasing the classical statement of the eminent geneticist Theodosious Dobzhansky: "Nothing in Biology makes sense except in the light of evolution" would give for bioinformatics research: "Nothing in bioinformatics makes sense except in the light of Biology". Biology is the science area of complexity and inconsistency, where mathematical and physical concepts seem to derail frequently. Students should be trained to deal with these complexities.

  • Bioinformatics methods often have to be devised with an ill-defined standard of truth (e.g. multiple alignment, sequence database searching).

  • Many mathematical concepts and novel computational techniques are being implemented in bioinformatics techniques at a rapid pace. To be able to place these innovations, students should have a sound knowledge of statistics, modelling techniques and formalisms, and multivariate statistics. Examples of new concepts are novel machine learning techniques (e.g. recent implementations of Support Vector Machines in bioinformatics methods), parallel and distributed (Grid) computing, etc.

  • Bioinformatics research requires skills to use and understand many different computational methods.

  • Bioinformatics research often involves development of novel methods and/or databases. Students should be confident in programming using different computer languages.

  • Bioinformatics techniques and databases are mostly available via the Internet. Students need web-related computational skills.

  • Quoting another eminent molecular biologist Sydney Brenner "Bioinformatics research ranges from book-keeping to real art". Students need to develop the skills and mentality to allow this full range of activities.


The graduate is further expected to be capable of:

  • practical application of the learned both alone as well as in a team;

  • clear oral and written presentation of the results of his/her work;

  • making good use of the literature and other knowledge sources relating to Bioinformatics.
    1. Requirements for the Master

Since bioinformatics is an inherently multi-disciplinary field, prospective students can be expected from many walks of life, although particular interest in the Bioinformatics masters is expected from bachelors (or equivalent) in Computer Science, Mathematics, Physics, Chemistry, Biology, Medical Natural Sciences, Pharmaceutical Sciences and Medicine.


The programme is open to students who have a Bachelor, Drs or Master diploma obtained at a Dutch institute or foreign university of quality recognised by the Vrije Universiteit. The prospective student should have a thorough interest and experience in biomolecular and computational sciences. Some experience in programming is required.


The programme is also open to students with other diplomas from universities or other research/teaching institutions they deem equivalent. These are kindly invited to contact us if interested in following the international Master's programme in Bioinformatics at the Centre for Integrative Bioinformatics VU.

    1. Master programme

Future perspective:

Employment prospects are excellent and appear relatively independent from economic conditions. Arguably, there is currently no other field in the Life Sciences with such positive job opportunities.



The full Master's programme in Bioinformatics takes two years and is worth 120 credits (within the European Community Course Credit Transfer System). As a rule, the student will take approximately nine months of courses (45 credits) and complete fifteen months of practical training (75 credits). It is also possible to take individual sections of the programme, leading to degree component certificates at Master's level. Unless otherwise stated, the tuition is in English.


The classes consist of:


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

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