Fig. 5

Implementing the ATM/P53/NF- κB pathway model from [31] using Snoopy’s hybrid simulator. Circles (places) represent species, squares (transitions) represent reactions, and arcs denote connections between the two node types. More information about these notations can be found in [11, 21]. Coloured circles represent discrete species, while the uncoloured ones represent continuous species. Similarly, coloured squares represent stochastic reactions, while uncoloured ones denote continuous reactions. Solid black arcs represent connections that consume molecules when the corresponding reaction fires, while dashed coloured ones just permit the use of substrates for defining reaction rates. Grey nodes are logical places that are repeated to simplify the network layout. Please note, inhibitor arcs (arc with small circles) enforce the number of genes to be at most two [31]. The complete Snoopy file is provided in the Additional file 2: S2.