{
  "abstract": "Agent-based modeling is a powerful approach for understanding cellular systems. Yet, many existing frameworks treat cell-level and population behaviors separately, overlooking their interplay. We present AgentBasedModeling.jl, a Julia package for simulating stochastic, continuous-time agent-based models that integrate intracellular processes with population dynamics. In our stochastic framework, agents evolve according to general continuous-time jump-diffusion dynamics and interact via continuous-rate jump processes. It supports flexible specification of the underlying measure-valued process of intracellular reaction networks and cell growth, capturing events such as cell division, death, intercellular communication, and environmental interactions. We demonstrate the use of the package by validating it on models of stochastic gene expression in growing cells and providing new insights into cell-cell communication and stochastic phage infection. Our tool provides a flexible and efficient platform for exploring how single-cell stochasticity drives emergent population-level behaviors in structured biological systems.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Mathematics, Imperial College London, London, United Kingdom"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Paul Piho"
    },
    {
      "affs": [
        0
      ],
      "name": "Philipp Thomas",
      "orcid": "0000-0003-4919-8452"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/be01rjfyrtq7w.bib",
  "cited_by": 1,
  "doi": "10.1371/journal.pcbi.1014366",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13722299/",
  "id": "be01rjfyrtq7w",
  "issns": [
    "1553-734X",
    "1553-7358"
  ],
  "landing_url": "https://doi.org/10.1371/journal.pcbi.1014366",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Agent-Based Modeling"
    ],
    [
      "heading",
      "Algorithms"
    ],
    [
      "heading",
      "Applied Mathematics"
    ],
    [
      "heading",
      "Bacteriophages"
    ],
    [
      "heading",
      "Biochemical Simulations"
    ],
    [
      "heading",
      "Biochemistry"
    ],
    [
      "heading",
      "Biology and Life Sciences"
    ],
    [
      "heading",
      "Cell Biology"
    ],
    [
      "heading",
      "Cell Cycle and Cell Division"
    ],
    [
      "heading",
      "Cell Processes"
    ],
    [
      "heading",
      "Computational Biology"
    ],
    [
      "heading",
      "Computer and Information Sciences"
    ],
    [
      "heading",
      "Drug Interactions"
    ],
    [
      "heading",
      "Gene Expression"
    ],
    [
      "heading",
      "Genetics"
    ],
    [
      "heading",
      "Mathematics"
    ],
    [
      "heading",
      "Medicine and Health Sciences"
    ],
    [
      "heading",
      "Organisms"
    ],
    [
      "heading",
      "Pharmacology"
    ],
    [
      "heading",
      "Physical Sciences"
    ],
    [
      "heading",
      "Population Biology"
    ],
    [
      "heading",
      "Population Dynamics"
    ],
    [
      "heading",
      "Research and Analysis Methods"
    ],
    [
      "heading",
      "Simulation and Modeling"
    ],
    [
      "heading",
      "Software"
    ],
    [
      "heading",
      "Systems Science"
    ],
    [
      "heading",
      "Viruses"
    ],
    [
      "openalex",
      "1312|Gene Regulatory Network Analysis"
    ]
  ],
  "openalex": "W4403883061",
  "pdf_url": "https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1014366&type=printable",
  "pmcid": "PMC13722299",
  "pmid": "42525710",
  "published": "2026-07-29",
  "publisher": "PLOS",
  "ris": "https://research.draconitic.com/paper/be01rjfyrtq7w.ris",
  "sources": [
    {
      "first_seen": "2026-11-03T12:22:50Z",
      "native_id": "PMC13722299",
      "source": "pmc",
      "url": "https://doi.org/10.1371/journal.pcbi.1014366"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "heading:Gene Expression",
      "subfield": "molecular-biology"
    },
    {
      "field": "biology",
      "origin": "heading:Computational Biology",
      "subfield": "bioinformatics"
    },
    {
      "field": "biology",
      "origin": "heading:Cell Biology",
      "subfield": "cell-biology"
    },
    {
      "field": "biology",
      "origin": "heading:Genetics",
      "subfield": "genetics-genomics"
    },
    {
      "field": "mathematics",
      "origin": "heading:Mathematics",
      "subfield": "general"
    }
  ],
  "title": "AgentBasedModeling.jl: A tool for stochastic simulation of structured population dynamics",
  "title_text": "AgentBasedModeling.jl: A tool for stochastic simulation of structured population dynamics",
  "type": "peer-reviewed",
  "updated_at": "2026-11-03T12:22:50Z",
  "url": "https://research.draconitic.com/paper/be01rjfyrtq7w",
  "venue": "PLOS Computational Biology",
  "versions": []
}