PhD Position: Formal Modelling of Cell Behaviour

PhD Position: Formal Modelling of Cell Behaviour

[Wan Fokkink]

PhD Position: Cell Behaviour Analysis with Formal, High-Performance Verification Techniques
===========================================================================================


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.