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bioRxiv · 10.64898/2026.09.18.752660

PyKappa: Rule-based modeling in Python

Alpay, B. A.·Lin, A.·Damiani, A. C.·Fontana, W.
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Abstract

Rule-based languages have proven effective for modeling systems of interacting structured entities as typically encountered in chemistry and molecular biology. We present PyKappa, a rule-based modeling package written in Python whose interpreted nature enables interactive simulation and analysis, including by agentic AI. The package seeks to broaden the base of developers by utilizing a widely known programming language and serves as an easy-to-deploy teaching tool. Using PyKappa, we conduct a case study of phase separation.

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Alpay, B. A., Lin, A., Damiani, A. C., Fontana, W.. 2026-09-24. PyKappa: Rule-based modeling in Python. https://doi.org/10.64898/2026.09.18.752660

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