BioSim: A New Qualitative Simulation Environment for Molecular Biology
ISMB '98 Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology
NuSMV 2: An OpenSource Tool for Symbolic Model Checking
CAV '02 Proceedings of the 14th International Conference on Computer Aided Verification
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
RSP '03 Proceedings of the 14th IEEE International Workshop on Rapid System Prototyping (RSP'03)
Modeling and querying biomolecular interaction networks
Theoretical Computer Science - Special issue: Computational systems biology
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In the field of biological regulation, models extracted from experimental works are usually complex networks comprising intertwined feedback circuits. R. Thomas and coworkers introduced a qualitative description of the dynamics of such regulatory networks, called the generalized logical analysis, and used the concept of circuit-characteristic states to identify all steady states and functional circuits. These characteristic states play an essential role on the dynamics of the system, but they are not represented in the state graph. In this paper we present an extension of this formalism in which all singular states including characteristic ones are represented. Consequently, the state graph contains all steady states. Model checking is then able to verify temporal properties concerning singular states. Finally, we prove that this new modeling is coherent with R. Thomas’ modeling since all paths of R. Thomas’ dynamics are represented in the new state graph, which in addition shows the influence of singular states on the dynamics.