Paris/biocham

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[http://contraintes.inria.fr/BIOCHAM/ BIOCHAM] is a programming environment for modeling biochemical systems, making simulations and querying the model in temporal logic.

In its current version BIOCHAM is composed of :

  • a rule-based language for modeling biochemical systems,
  • a simple simulator (either boolean or numerical),
  • a powerful query language based on temporal logic, CTL or LTL with arithmetic constraints over reals, for querying the temporal properties of the model,
  • an interface to the NuSMV model checker for evaluating CTL queries,
  • a machine learning system for correcting/completing a model, either by changing rules w.r.t. a CTL specification or by estimating parameters w.r.t. an LTL specification.
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