PyKappa is a Python package for interpreted simulation and analysis of rule-based models of the variety specified by the Kappa language. It supports

• programatic construction of systems;

• manipulation of systems mid-simulation, such as by custom graph transformation and tuning parameters via declared variables;

• monitoring the history of observables;

• cached tracking of rule embeddings for algorithmically efficient simulation updates; and

• passing systems to KaSim for faster compiled execution (see here for a speed comparison).

Visit the examples gallery to see how PyKappa can be used to simulate systems of molecular interactions such as polymerization and gene regulation. See the language manual for a detailed description of the Kappa language.

PyKappa is available via pip:

pip install pykappa