Biologists use diagrams to represent complex systems of interaction between molecular species. These graphical notations encompass two types of information: interactions (e.g. protein complexation, modification, binding to a gene, etc.) and regulations (of an interaction or a transcription). Based on these structures, mathematical models can be developed by equipping such molecular interaction networks with kinetic expressions leading to quantitative models of mainly two kinds: ordinary differential equations for a continuous interpretation of the kinetics and continuous-time Markov chains for a stochastic interpretation of the kinetics.Since 2002, we investigate the transposition of programming concepts and tools to the analysis of living processes at the cellular level.
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