Behaviour Preservation of a Biological Regulatory Network when Embedded into a Larger Network
Fundamenta Informaticae
Graph-Based modeling of biological regulatory networks: introduction of singular states
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Behaviour Preservation of a Biological Regulatory Network when Embedded into a Larger Network
Fundamenta Informaticae
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In the field of biological regulation, models obtainedfrom experimental biology are usually complex networks ofinduction and repression between genes. Due to the developmentof high throughput genomic, it is now necessary totreat large scale networks. The challenge is to automaticallyanalyze their behavior.Here, we propose a formal framework to define this BiologicalRegulatory Networks.Our model is derived from R. Thomas representation, wherea biological regulatory network can be seen as a discretemodel. We propose a formal definition of such representation.We separate the static part (description of the systems)from the dynamic one (we develop two semantics, synchronousor asynchronous, to illustrate our method).A software environment to support this framework is alsodescribed. This software, developed to be used by biologists,can be used to rapidly obtain a prototype describingthe behavior of the system, to product simulations and toautomatize proofs of properties.