Section: New Software and Platforms

HSIM

Participant : Patrick Amar [correspondant] .

Hsim (Hyperstructure Simulator) is a simulation tool for studying the dynamics of biochemical processes in a virtual bacteria. The model is given using a language based on probabilistic rewriting rules that mimics the reactions between biochemical species. Hsim is a stochastic automaton that implements an entity-centered model of objects. This kind of modelling approach is an attractive alternative to differential equations for studying the diffusion and interaction of the many different enzymes and metabolites in cells which may be present in either small or large numbers.

The new version of Hsim includes a Stochastic Simulation Algorithm a la Gillespie that can be used with the same model in a standalone way or in a mixed way with the entity-centered algorithm. This new version offers also the possibility to export the model in SciLab for a ODE integration. Last, Hsim can export the differential equations system, equivalent to the model, to LaTeX for pretty-printing.

This software is freely available at http://www.lri.fr/~pa/Hsim ; A compiled version is available for the Windows, Linux and MacOSX operating systems.