There are many different ways to model gene regulatory networkds. One of the possible approaches consists in representing them by generalized chemical reaction systems. These systems can endowed with many different dynamics. So far, we have focused on deterministic (continuous space and time, deterministic determination) and stochastic (continuous time, discrete space, stochastic determination) modeling.
In the deterministic domain, our group designed a new method for performing quasi-steady state approximations. In the stochastic one, we have been working on methods for establishing formulas, giving the evolutions of the statistical moments of the random variables which count molecules.
We developed the MABSys MAPLE package, dedicated to deterministic models. The FreeMABSys project, supported by the French ANR BLANC LEDA project, consists in developing a new, free, version of it. In the stochastic domain, we have been working on a MAPLE package, in collaboration with the BioComputing group.