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PreprintCC BYbioRxiv

PyKappa: Rule-based modeling in Python

  • B. A. Alpay1
  • A. Lin
  • A. C. Damiani
  • W. Fontana
  1. 1Harvard Medical School
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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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Cite

BibTeXRIS
BibTeX
@misc{alpay2026pykappa,
  title = {{PyKappa: Rule-based modeling in Python}},
  author = {B. A. Alpay and A. Lin and A. C. Damiani and W. Fontana},
  howpublished = {bioRxiv},
  year = {2026},
  month = sep,
  doi = {10.64898/2026.09.18.752660},
  url = {https://www.biorxiv.org/content/10.64898/2026.09.18.752660v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - PyKappa: Rule-based modeling in Python
AU  - B. A. Alpay
AU  - A. Lin
AU  - A. C. Damiani
AU  - W. Fontana
PY  - 2026
DA  - 2026/09/18
PB  - bioRxiv
DO  - 10.64898/2026.09.18.752660
UR  - https://www.biorxiv.org/content/10.64898/2026.09.18.752660v1
AB  - 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.
ER  -