Section: Software

BioRica: Multi-scale Stochastic Modeling

Participants : David James Sherman [correspondant] , Rodrigo Assar Cuevas, Alice Garcia.

BioRica is a high-level modeling framework integrating discrete and continuous multi-scale dynamics within the same semantics field. A model in BioRica node is hierarchically composed of nodes, which may be existing models. Individual nodes can be of two types:

  • Discrete nodes are composed of states, and transitions described by constrained events, which can be non deterministic. This captures a range of existing discrete formalisms (Petri nets, finite automata, etc.). Stochastic behavior can be added by associating the likelihood that an event fires when activated. Markov chains or Markov decision processes can be concisely described. Timed behavior is added by defining the delay between an event's activation and the moment that its transition occurs.

  • Continuous nodes are described by ODE systems, potentially a hybrid system whose internal state flows continuously while having discrete jumps.

The system has been implemented as a distributable software package

The BioRica compiler reads a specification for hierarchical model and compiles it into an executable simulator. The modeling language is a stochastic extension to the AltaRica Dataflow language, inspired by work of Antoine Rauzy. Input parsers for SBML 2 version 4 are curently being validated. The compiled code uses the Python runtime environment and can be run stand-alone on most systems [36] .

For more information see biorica.gforge.inria.fr , the BioRica Gforge web site. BioRica was developed as an Inria Technology Development Action (ADT).