{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Harvard Medical School"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "B. A. Alpay"
    },
    {
      "name": "A. Lin"
    },
    {
      "name": "A. C. Damiani"
    },
    {
      "name": "W. Fontana"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/9vkajaykfksa7.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.18.752660",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.18.752660v1.full",
  "id": "9vkajaykfksa7",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.18.752660v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "systems biology"
    ],
    [
      "openalex",
      "1312|Gene Regulatory Network Analysis"
    ]
  ],
  "openalex": "W7214146083",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.18.752660v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-18",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/9vkajaykfksa7.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:24:26Z",
      "native_id": "10.64898/2026.09.18.752660",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.18.752660v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:systems biology",
      "subfield": "systems-synthetic"
    }
  ],
  "title": "PyKappa: Rule-based modeling in Python",
  "title_text": "PyKappa: Rule-based modeling in Python",
  "type": "preprint",
  "updated_at": "2026-10-30T12:24:26Z",
  "url": "https://research.draconitic.com/paper/9vkajaykfksa7",
  "venue": "bioRxiv",
  "versions": []
}