Year: 2026
Type: preprint
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 [email protected]
Institutions: Harvard University, Center for Systems Biology
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funder: John Templeton Foundation
OpenAlex ID: W7214146083