The BioRica project
BioRica is a high-level modeling framework integrating discrete and continuous multi-scale dynamics within the same semantics field. The co-existence of continuous and discrete dynamics is assured by a pre-computation of the continuous parts of the model. Once computed, these parts of the model act as components that can be queried for the function value, but also modified, therefore accounting for any trajectory modification induced by discrete parts of the model. To achieve this we extensively rely on methods for solving and simulation of continuous systems by numerical algorithms. Discrete nodes in the model act as controllers.
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.
BioRica is developped by the INRIA team MAGNOME, for questions or requests contact Alice Garcia or David Sherman.