Section: Software
BIOCHAM
Participants : François Fages, Aurélien Rizk, Sylvain Soliman.
The Biochemical Abstract Machine BIOCHAM is a modeling and validation environment for molecular systems biology [30] , under development since 2001, and distributed as open-source since 2003. Current version is v2.8.
BIOCHAM is compatible with the Systems Biology Markup Language (SBML ) and adds precise semantics to biomolecular interaction maps at three abstraction levels:
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the boolean semantics (presence or absence of molecules),
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the differential semantics (concentrations of molecules),
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the stochastic semantics (discrete numbers of molecules).
Based on this formal framework, BIOCHAM features:
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a compositional rule-based language for modeling biochemical systems, allowing patterns for expressing set of rules in a compact form;
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numerical as well as boolean simulators (Rosenbrock's method for the differential semantics, Gillespie's algorithm with tau lipping for the stochastic semantics);
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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;
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automatic search procedures to infer parameter values, initial conditions and even reaction rules from temporal logic properties of the system;
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automatic conservation law detection, through constraint-based structural analysis of the underlying Petri-net.
BIOCHAM was used in synergy with Beta WB and GINsim by the winning team of the Biological Modelling Competition of the Formal Methods in Molecular Biology workshop held in Dagstuhl in Feb. 2009.
BIOCHAM is fully implemented in GNU-Prolog and interfaced to the symbolic model checker NuSMV and to the continuous optimization tool CMAES .
