Section: New Software and Platforms

The Biochemical Abstract Machine

Participants : François Fages, François-Marie Floch, Thierry Martinez, Sylvain Soliman, Pauline Traynard.

BIOCHAM V3.6

The Biochemical Abstract Machine (BIOCHAM ) is a software environment for modeling and analyzing biochemical reaction systems, making simulations, performing static analyses, specifying behaviors in temporal logic. It is distributed under the GPL license since 2002.

The new features of version v3.6 released in October 2014 include:

• Hybrid boolean-stochastic-continuous models and simulations

• Quantitative temporal logic patterns with dedicated solvers (based on [20] )

• Trace simplifications (based on [19] )

• export_sbml3 added

• curate_model and curate_sbml added (based on [8] )

• Refinements of the types for command arguments (no effect on Biocham models)

• Bug fixes

BIOCHAM-web

BIOCHAM-web is a web service which makes it possible to try BIOCHAM on line without any installation, through a spreadsheet. A new version BIOCHAM-web was released in March 2014 and is kept evolving since.

That web service will evolve to a complete graphical user interface, named BIOCHAM-gui, and will replace the current graphical user interface.

BIOCHAM-parallel

A (non-distributed) parallel version of BIOCHAM is also maintained for our own use on a cluster of 10000 cores at GENCI CINES. This version speeds-up (linearly in the number of processors) the search of parameter values by parallelizing the evaluation of the fitness function (computed by numerical integration) for both the different parameter sets and the different conditions (perturbations, gene knock down or stress).