concurrent cell

ConCell

In the Concurrent Cell (ConCell) project we model biological cells using formal methods and high-performance computing techniques, to gain insights into the underlying biological processes. We want to be able to capture the global behaviour of the system and its emergent properties. Such an approach is called systems biology.

Cells have a lot in common with distributed systems, notably, they are built from separate components that commmunicate with each other and thus influence each other's behaviour. Therefore, we can apply computer science techniques, such as Petri Nets or Process Caluculi, to model them. We adapted the original semantics of Petri Nets to biological modelling, namely we used maximal parallelism to model bounded asynchrony and we bounded capacities of places.

Using this technique we constructed and later successfully verified a model of the C. elegans vulval development, a process in which the worm develops an egg-laying organ called vulva.
Take a look at the C. elegans network and demos showing its execution.

Software (grader) that we developed to run the worm is available.

Project development website (needs log in).

Facts

The project was started in the end of 2007 by three research groups at VU Amsterdam: ConCell logo.