BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts
Fig 5
A model of the lac operon compiled using BioCRNpyler specifications with 141 species and 271 reactions using ∼50 lines of code.
A. A Mixture contains a set of Components and Mechanisms. The Component classes used for each element of the model are shown in brackets. The colored circles show how Components correspond to compiled CRN species in panel C. B. A schematic of the lac operon and the three looped and one open conformation it can take. Each conformation contains a combinatoric number of states based upon the accessible binding sites: R are lac repressor binding sites; C is the activator c-CRP binding site; P is the promoter; and Z, Y, A are the three lac genes. The conformations are placed over clusters of identically colored species corresponding to that conformation in the compiled CRN. C. A graph representation of the compiled CRN. Each circle is a unique chemical species. Square boxes show how chemical species interact via reactions generated by specific Mechanisms. D. Simulated output of the model.