BioDiVinE: A Framework for Parallel Analysis of Biological Models
Ji\v{r}\'i Barnat (Masaryk University), Lubo\v{s} Brim (Masaryk, University), Ivana \v{C}ern\'a (Masaryk University), Sven Dra\v{z}an (Masaryk, University), Jana Fabrikov\'a (Masaryk University), Jan L\'an\'ik (Masaryk, University), David \v{S}afr\'anek (Masaryk University)
TL;DR
BioDiVinE is a new parallel analysis framework for biological models based on chemical reactions, using model checking techniques on finite abstractions of differential equations to facilitate analysis.
Contribution
It introduces a novel tool that enables parallel analysis of biological models through finite discrete abstraction and model checking techniques.
Findings
Demonstrated effectiveness via a case study.
Provides parallel algorithms for biological model analysis.
Transforms chemical reactions into multi-affine differential equations.
Abstract
In this paper a novel tool BioDiVinEfor parallel analysis of biological models is presented. The tool allows analysis of biological models specified in terms of a set of chemical reactions. Chemical reactions are transformed into a system of multi-affine differential equations. BioDiVinE employs techniques for finite discrete abstraction of the continuous state space. At that level, parallel analysis algorithms based on model checking are provided. In the paper, the key tool features are described and their application is demonstrated by means of a case study.
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