PyKappa: Rule-based modeling in Python

Abstract

Summary 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. Availability The official PyKappa website is https://pykappa.org, where code fo the phase separation analysis can also be found. The PyKappa source code is hosted at https://github.com/berkalpay/pykappa. Contact berk_alpay@g.harvard.edu