Basic cellular model in our simulation framework. (A) A "triplet": capturing the processes of transcription, translation, and post-translational modification. (B) Example of a gene regulatory and biochemical network in an organism where environmental signals (e.g. oxygen, temperature) regulate the expression of certain genes/proteins. The value at each node of the graph corresponds to the number of molecules of a given molecular species. Red/blue arrows denote positive/negative regulation and their corresponding weights.