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Section: Software

BIOCHAM

Participants : François Fages, Steven Gay, Dragana Jovanovska, Aurélien Rizk, Sylvain Soliman.

The Biochemical Abstract Machine BIOCHAM [29] is a modeling environment for systems biology distributed as open-source since 2003. Current version is v3.3. 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:

  1. the boolean semantics (presence or absence of molecules),

  2. the differential semantics (concentrations of molecules),

  3. the stochastic semantics (discrete numbers of molecules).

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 QFLTL(R) 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 SBGN-compatible reaction graph editor;

  • an event handler allowing the encoding of hybrid models and formalisms [30] .

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.