In rules-based modeling, units that undergo transformations such as proteins, small molecules, protein complexes, etc are termed species. The interactions among these species are then represented using structured objects that describe the interactions between the species and constitute what we describe as rules. The specific details of how species and rules are specified can vary across different rules-based modeling approaches. In PySB we have chosen to ascribe to the approaches found in BioNetGen and Kappa, but other approaches are certainly possible for advanced users interested in modifying the source codbe. Each rule, describing the interaction between species or sets of species must be assigned a set of parameters associated with the nature of the rule. Given that BioNetGen and Kappa both describe interactions using a mass-action kinetics formalism, the parameters will necessarily consist of reaction rates. In what follows we describe how a model can be instantiated in PySB, how species and rules are specified, and how to run a simple simulation.
PySB uses the rules languages grammar of BioNetGen and Kappa almost verbatim with the differences being mostly synctactic. This has been done on purpose to keep compatibility with these languages and leverage their available simulating tools. We invited interested users to explore the BioNetGen Tutorial or the Introduction to Kappa Syntax pages for further information. Understanding of any of these languages will make working with PySB rules a very straightforward exercise for the user.