Exact Sciences Master Guide2005/2006

Biomolecular Sciences - Systems Biology (topmaster variant)

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Biomolecular Sciences - Systems Biology (topmaster variant)

  1. General Aspects

The topmasters program Biomolecular Sciences is a masters program for students with a research-oriented profile. It trains students with Bsc ranging from biomedical sciences and biology to chemistry, physics, mathematics and engineering, for a master's degree at the interface between these disciplines.


The top masters program Systems Biology focuses on the issue of how a functioning living cell arises from the collaboration of inanimate molecules and herewith depends more on fundamental biophysics, biochemistry and biomathematics.

This program is organized by institutes in the Biocenter Amsterdam, and at present involves collaboration between  groups at the Faculties of Earth and Life Sciences (FALW) and of Exact Sciences (FEW) of the Vrije Universiteit. In the near future also groups from the University of Amsterdam (Faculty of Science), the National Research Institute for Mathematics and Computer Science (CWI) and the Institute for Atomic and Molecular Physics (AMOLF) will be involved in the program.

The science area of the masters program Systems Biology is explicitly trans- and interdisciplinary.  Students will come from various bachelor curricula from inside and outside the European Union.  Influx from mathematics, informatics, physics, chemistry, biochemistry, biophysics, biology, medical biology, and biomedical sciences is aimed for.  The diversity of the influx of students will be cultivated in order to come to a scientific melting pot from which the students learn to help each other by intensive collaboration. 

More information can be found at the websites: www.falw.vu.nl and www.systembiology.net/topmaster, or be obtained from the coordinator dr. K. Krab (e-mail: systemsbiology@falw.vu.nl) or the director prof. dr. H.V. Westerhoff (e-mail: hans.westerhoff@falw.vu.nl).

Address: Department of Molecular Cell Physiology, Vrije Universiteit, De Boelelaan 1085, NL-1081 HV Amsterdam, The Netherlands.

E-mail (addresses see above): please mention 'top master' on the subject line.

Phone: +31 (0) 20 59 87228. Fax: +31 (0) 0 59 87229.

Visiting address: Sciences building Vrije Universiteit, room M2.36.

      1. Aim of the programme

The aim of the program is to prepare students for an internationally oriented research career in the field of systems biology (e.g. leading to a PhD thesis). These students will have a solid background in the many disciplines that interact in the field of systems biology, and will have the knowledge, skills and insight required to operate as an independent professional within that field. In addition, they will have developed a critical attitude towards research, including the ethical and socially relevant aspects of science.
      1. Admission

The program admits students with bachelors from the disciplines biomedical sciences, biology, chemistry, physics, mathematics, engineering, and bio­chemistry. The entry criteria are threefold; (i) proven excellence in the bachelor phase in one of the above disciplines, (ii) potential excellence at the level of the other disciplines, to be proven in the first month of the masters program (i.e. in its portal phase), and (iii) proven profound motivation for scientific top research. 

(i) will be verified on the basis of a diploma of (a) the Vrije Universiteit Amsterdam bachelors of Biology, Medical Biology, Medical Natural Sciences, Chemistry, Physics and Astronomy, Mathematics or Pharmaceutical sciences with an average grade exceeding 7, (b) a bachelor of the University of Amsterdam, or Hogeschool Windesheim in Biology, Biomedical sciences, Chemistry or Mathematics and Natural sciences with an average grade of 7 or higher, (c) a bachelor program of one of the five international sister schools with comparable grades, (d) a comparable bachelor from another European institution for higher education (University or Higher Technical School [HBO]), in any of the above disciplines with an average grade of 8 or higher or equivalent, (e) any education that is demonstrably equivalent to any of the above, (f) a successful entry exam. The entry exam will be facilitated through an individual preparatory phase, in which the capabilities of the prospective student will be assessed and necessary study material will be suggested.

Verification of criteria (ii) and (iii) will be accomplished by the exam at the end of the portal phase of the masters program, in which potential excellence in all mentioned basic disciplines should be demonstrated by the student.  Failing this second criterion the student may switch to one of the basic masters curricula of the Vrije Universiteit (in particular to that of the basic variant of the Masters Biomolecular Sciences, to Medical Natural Sciences or to Biomedical sciences) or of the University of Amsterdam.

The exam committee may allow the student access to the top masters program before having completed the bachelor exam, provided that at least 150 cp of the bachelor curriculum have been completed successfully, and that the bachelor is completed within a year.

      1. Final Attainment Levels

The qualified master:

  • has knowledge about terminology, state of the art of theory and research topics in the biomolecular discipline of specialization

  • can apply this knowledge in the design of research and in solving emerging problems

  • has the ability to use the principles from the different disciplines (such as mathematics, physics, chemistry and biochemistry) to tackle biomolecular problems

  • has insight in the place of molecular cell biology and biomolecular sciences in biology, biomedical science and science in general

  • has familiarity with general scientific journal such as Nature, Science or PNAS, and international journals in the fields of biochemistry, molecular biology and cell biology.

  • has insight in the scientific and social relevance of current research in biomolecular sciences

  • can design and execute experiments in the different fields and analyze the results

  • is able to note down and report on the results of these experiments

  • can collaborate with other researchers from the same and other disciplines

  • has sufficient knowledge of mathematical and statistical methods applicable to the field

  • has command of the use of computer software relevant for the field

  • has command of advanced research techniques and laboratory procedures

  • is able to acquire independently biological or medical biological information, (with emphasis on biomolecular and cell biological aspects) and can analyze, summarize and critically evaluate this information

  • can select and order information, distinguish between major and minor points, and recognize connections.

  • can think multidisciplinary

  • can analyze and evaluate independently and critically planning, execution and results of research

  • can design and write research plans

  • can report orally and in written form on research

  • can apply scientific knowledge on issues in society

  • contributes to scientific discussions about plans, results and consequences of research

  • can evaluate his or her own functioning, both by reflection and in discussions with others

  • can reflect on ethical aspects of research and applications of research and on implications in decision making.


In addition to these, the qualified top master:

  • has proven excellence as researcher in the quantitative life sciences and systems biology

  • has proven understanding of physical chemical and organizational principles of life

  • has proven expertise with the modern experimental, conceptual and modeling methods for the Biomolecular sciences and Systems Biology

  • has insight in the most important biomathematical, biophysical, biochemical, biological, and biomedical topics of the moment, and in how these can be approached

  • has an unique and excellent profile at the interface between the exact sciences and the life sciences

  • will participate in a local and international network of young life scientists with an interest in Systems Biology.
      1. Programme

The top master program aims for the integration of the training of students with diverse backgrounds to a well-defined set of abilities for the interdisci­plinary area Systems Biology. Accordingly, the program is in principle homo­geneous and all its elements are defined (i.e. compulsory). Because the backgrounds are diverse it is possible that some of the courses overlap for some of the students with courses they followed in their earlier studies. In these cases, in consultation with the exam committee an alternative may be chosen from what is available and of sufficient quality in the Biocenter Amsterdam.


The curriculum (2 year, 120 cp) consists of the following elements:

  • Portal course (6 cp)

  • Central course: molecules integrating into living systems (45 cp)

  • General course (9 cp)

  • Current topics (3 cp)

  • Orientation research project (9 cp)

  • International research project (48 cp)

Details of the courses

Portal course: entry course of mathematics and physics for the biologist and medical student, and biology for the physics / chemistry / mathematics bachelor (Krab, 6 cp)


Central course: from molecules through integration to life (45 cp).

This central course contains the following elements:

  • Ab initio modelling of biological systems (Westerhoff,  6 cp)

  • Sequence analysis (Heringa, 6 cp)

  • Molecular cell physiology and function (Bakker, 6 cp)

  • Biological fluorescence (Bollen, 6 cp)

  • System identification of dynamic systems (Van Schuppen, 6 cp)

  • Intracellular networks (Krab, 6 cp)

  • Physics of biological systems (Van Grondelle, 6 cp)

  • Philosophy of systems biology (Boogerd, 3 cp)

General course: A number of components are compulsory for all Master students of FALW-VU Master programs.  These comprise three courses:

  • History of Life Sciences (3 cp)

  • Ethics (3 cp)

  • Scientific writing in English (3 cp)


Current topics: A series of lectures on systems biology (international lecturers, 3 cp)


International research project: The top master program includes one research exchange project carried out in two laboratories (one being part of the Biocenter Amsterdam and the other in one of the collaborating International Centers of Excellence in the field of systems biology). The project will encompass both aspects of systems biology: practical work in the laboratory, and modelling. In preparation for this project, the student will do a literature survey on the subject of the project.


For more information contact: dr. K. Krab, klaas.krab@falw.vu.nl, Faculteit der Aard- en Levenswetenschappen, Moleculaire Celfysiologie, Kamer G-226F.

    1. Society oriented variant (M-variant)

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

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

      1. General

Due to the growing complexity of technological and medical issues and the interaction with society, organisations working in this sector have a growing and urgent need for academic professionals in the natural and life sciences, who have knowledge of policy management and entrepreneurship. The M-variant offers students with a bachelor degree in the natural and life sciences the chance to combine a specialization in this field with a specialization in research, communication or education.
      1. Programme

The programme of the M-variant is equal to the first year of the master programme Management Policy- Analysis and entrepreneurship (MPA) (for a detailed description of the programme see the description of the master programme MPA). The programme of the M-variant consists of 60 cp (15 cp compulsory courses; 15 cp optional courses and 30 cp internship)  The course language is English, unless all students participating in the course speak Dutch, the course language will be Dutch. The program coordinator is: dr. M.B.M. Zweekhorst. Address: Faculty of Earth and Life Sciences, department Biology and Society, De Boelelaan 1087, room A0.62, phone: +31 (0) 20 59 87033, e-mail marjolein.zweekhorst@falw.vu.nl

M-variant compulsory courses

Course code

Course name




Communication, Organization and Management




Analysis of Governmental Policy


05.09.05 ¿ 30.09.05


Business Management in Health and Life Sciences


31.10.05 ¿ 11.11.05

M-variant optional courses

Recommended courses

Course code

Course name




Interpersoonlijke communicatie




Policy Research Project


09.01.2006 ¿ 03.02.2006


Interactive Communication




Clinical Development and Clinical Trials


14.11.05 - 25.11.05


Interactive Health Technology Assessment


14.11.05 - 25.11.05


Entrepreneurship in Health and Life sciences




Caput Criteria for Corporate Social Responsibility


31.10.05 - 11.11.05


Caput Success Factors in Sustainable Innovations


In consultation

    1. Communication variant (C-variant)

      1. General

This variant is intended for students with a BSc degree in any of the beta-studies who want to specialize in communication. The programme focuses on science communication theory and research as well as on science communication in practice. This includes science journalism as well as museology, the use of internet for science communication and health communication.


The variant is coordinated by prof. dr. Jaap Willems. Adress: Faculty of Earth and Life Sciences, Dept. of Science Communication, De Boelelaan 1087, room B0.29, e-mail jaap.willems@falw.vu.nl.


Teaching in this variant is mainly in Dutch.

      1. Programme

For a specialization degree it is required to spend 60 cp on Science Communication items. Three courses, one internship or research project and a thesis are compulsory. The rest of the programme can be filled in with optional courses. In research projects students will focus on an aspect of science communication, while in internships students will work on a project at a trainee post in a museum, editorial office of a newspaper etc. There they will also do a small research project. The thesis consists of a study of literature on an aspect of science communication.

C-variant compulsory courses

Also a individual Internship/research project (21 sp) and a individual Thesis (9 sp)

Course code

Course name






03.10.05 - 28.10.05




05.09.2005 - 30.09.2005


WTC onderzoek


31.10.05 - 25.11.05

C-variant optional courses

Course code

Course name




Interpersoonlijke communicatie




Museologie en buitenschoolse educatie


09.01.2006 - 03.02.2006


Interactive Communication






13.03.2006 - 07.04.2006


Wetenschapscommunicatie via internet


28.11.05 - 23.12.05

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