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

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 at cs.vu.nl tel. +31 (0)20 5987735 Prof.dr. Jaap Heringa heringa at 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.