Section: Software
BIOCHAM, biochemical abstract machine
Participants : François Fages, Steven Gay, Sylvain Soliman.
The Biochemical Abstract Machine BIOCHAM [18] is a modeling environment for systems biology distributed as open-source since 2003. Current version is v3.4, released in October. BIOCHAM uses a compositional rule-based language for modeling biochemical systems, allowing patterns for expressing set of rules in a compact form. This rule-based language is compatible with the Systems Biology Markup Language (SBML ) and is interpreted with three semantics correspnding to three abstraction levels:
Based on this formal framework, BIOCHAM features:
Boolean and numerical simulators (Rosenbrock's method for the differential semantics, Gillespie's algorithm with tau lipping for the stochastic semantics);
a temporal logic language (CTL for qualitative models and LTL(
) with numerical constraints for quantitative models) for formalizing biological properties such as reachability, checkpoints, oscillations or stability, and checking them automatically with model-checking techniques;automatic search procedures to infer parameter values, initial conditions and even reaction rules from temporal logic properties;
automatic detection of invariants, through constraint-based analysis of the underlying Petri net;
an event handler allowing the encoding of hybrid models and formalisms.
BIOCHAM is implemented in GNU-Prolog and interfaced to the symbolic model checker NuSMV and to the continuous optimization tool CMAES developed by the EPI TAO.