Petri Net Representations in Metabolic Pathways
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology
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Many models in Systems Biology are described as Ordinary Differential Equations (ODEs), which allows for numerical integration, bifurcation analyses, parameter sensitivity analyses, etc. Before fixing the kinetics and parameter values however, various analyses can be performed on the structure of the model. This approach has rapidly developed in Systems Biology in the last decade, with for instance, the analyses of structural invariants in Petri net representation [4] model reductions by subgraph epimorphims [2], qualitative attractors in logical dynamics or temporal logic properties by analogy to circuit and program verification. These complementary analysis tools do not rely on kinetic information, but on the structure of the model with reactions.