Abstract
Petri nets are directed, weighted bipartite graphs that have successfully been applied to the systems biology of metabolic and signal transduction pathways in modeling both stochastic (discrete) and deterministic (continuous) processes. Here we exemplify how molecular mechanisms, biochemical or genetic, can be consistently respresented in the form of place/transition Petri nets. We then describe the application of Petri nets to the reconstruction of molecular and genetic networks from experimental data and their power to represent biological processes with arbitrary degree of resolution of the subprocesses at the cellular and the molecular level. Petri nets are executable formal language models that permit the unambiguous visualization of regulatory mechanisms, and they can be used to encode the results of mathematical algorithms for the reconstruction of causal interaction networks from experimental time series data.
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