Mixed-formalism hierarchical modeling and simulation with BioRica

Alice Garcia 1, 2, * David James Sherman 1, 2
* Auteur correspondant
2 MAGNOME - Models and Algorithms for the Genome
Inria Bordeaux - Sud-Ouest, UB - Université de Bordeaux, CNRS - Centre National de la Recherche Scientifique : UMR5800
Abstract : Background : A recurring challenge for in silico modeling of cell behavior is that experimentally validated models are so focused in scope that it is difficult to repurpose them. Hierarchical modeling is one way of combining specific models into networks. Effective use of hierarchical models requires both formal definition of the semantics of such composition, and efficient simulation tools for exploring the large space of complex behaviors. Objectives : BioRica (Soueidan et al, 2007) is a high-level hierarchical modeling framework integrating discrete and continuous multi-scale dynamics within the same semantics domain. It is an adaptation of the AltaRica formalism (Arnold et al., 2000). It explicitly addresses model reusability, repurposing and other engineering best practices that are necessary for sustainable, incremental development of comprehensive models incorporating individually validated components. The goal of the present work was to make the BioRica framework accessible for a wider audience. Methods : The BioRica approach expresses each existing model (in SBML) as a BioRica node, which are hierarchically composed to build a BioRica system. 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. Results : The system has been implemented as a distributable software package. The BioRica model compiler and associated tools are available from the INRIA, (address to be provided). Discussion : By providing a reliable and functional software tool backed by a rigorous semantics, we hope to advance real adoption of hierarchical modeling by the systems biology community. By providing an understandable and mathematically rigorous semantics, this will make is easier for practicing scientists to build practical and functional models of the systems they are studying, and concentrate their efforts on the system rather than on the tool.
Type de document :
11th International Conference on Systems Biology, Oct 2010, Edimbourg, United Kingdom. pp.P02.446
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Contributeur : Alice Garcia <>
Soumis le : mercredi 27 octobre 2010 - 09:57:41
Dernière modification le : mercredi 9 septembre 2015 - 16:32:31
Document(s) archivé(s) le : vendredi 28 janvier 2011 - 02:34:12


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  • HAL Id : inria-00529669, version 1


Alice Garcia, David James Sherman. Mixed-formalism hierarchical modeling and simulation with BioRica. 11th International Conference on Systems Biology, Oct 2010, Edimbourg, United Kingdom. pp.P02.446. <inria-00529669>



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