Kappybara

Kappybara is a Python package that provides a simulator of and interpreted interface to rule-based models of the variety specified by the Kappa language. Supported are

• programatic construction of systems from Kappa strings,

• on-the-fly manipulation of systems such as adding and removing agents and editing rules,

• monitoring of the history of observables,

• cached tracking of rule embeddings for algorithmically efficient simulation updates,

• optional transfer to KaSim for faster compiled execution.

Visit the examples gallery to see how Kappybara 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.

Kappybara is available via pip:

pip install kappybara