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PhD student position Cell Behaviour Analysis with formal verification techniques, Computer Science, Amsterdam (The Netherlands)

PhD Position: Cell Behaviour Analysis with Formal, High-Performance
Verification Techniques
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At the Department of Computer Science at the Vrije Universiteit (VU) in
Amsterdam, a PhD position for four years is available on a research project
devoted to

  Cell Behaviour Analysis with Formal, High-Performance Verification
Techniques

Starting date of this PhD position: as soon as possible.


The project -----------

The goal of the project is to describe biological cells, compartments
(organelles) and molecules (e.g., DNA and proteins) by formal interaction
patterns/models. These models describe cells and their components as
independent, communicating entities.

Using the formal models, the aim will be to derive fundamentally new
insights in cellular behaviour that go beyond the current formalisations in
terms of ordinary differential equations. The PhD student will investigate
the requirements for a formal framework to model the biologically relevant
aspects of cellular behaviour, and define a minimal set of interacting cells
and cellular components.

At the same time the simulation of cellular behaviour involves modeled
entities of high complexity, heterogeneity and variability. This poses new
challenges to and promises new insights in the execution and verification
environment of the formal interaction models. A second PhD student (this
position is already taken!) will for this purpose work on developing the
formal framework to model cell behaviour, and parallel verification
algorithms.

The two PhD students will collaborate on the verification of formal models
of cells. The DAS3 cluster (see http://www.cs.vu.nl/das3/) will be used for
running experiments. In addition, the Ibis01 cluster is available for
running specialized Bioinformatics analyses.

For more detailed information on the project, see

  http://www.cs.vu.nl/~wanf/cell-project.pdf


Research groups ---------------

This project is a collaboration between three research groups at the VU:
Parallel Computing (Henri Bal), Bioinformatics (Jaap Heringa), and
Theoretical Computer Science (Wan Fokkink).

For more information on the involved research groups, see

  http://www.cs.vu.nl/en/sec/cs/
  http://www.ibi.vu.nl/
  http://www.cs.vu.nl/~tcs


Qualifications
--------------

Candidates should have completed their studies in Computer Science,
Bioinformatics or a closely related area. Strong experience in computer
science is essential. Experience with biological systems, distributed
systems, a good theoretical background, and an open attitude to applications
are considered advantages. You should enjoy working in an interdisciplinary
and internationally oriented research environment. Communicative skills and
the ability to work in a team are important.


Information and application
---------------------------

For further information about these positions please contact either:

  Prof.dr. Wan Fokkink   wanf@cs.vu.nl     tel. +31 (0)20 5987735
  Prof.dr. Jaap Heringa  heringa@cs.vu.nl  tel. +31 (0)20 5987649

You are invited to send an application by email to the above email addresses
no later than July 16, 2007. Your application should consist of a cover
letter, a curriculum vitae (including detailed information regarding your
academic degree), and the names and addresses of two references.