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Peer-reviewedCC BYPLOS Computational Biology

Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages

  • Adel Heydarabadipour1
  • Lucian P Smith1
  • Joseph L Hellerstein1,2,3
  • Herbert M Sauro1,3,4
4 affiliations
  1. 1Department of Bioengineering, University of Washington, Seattle, Washington, United States of America.
  2. 2Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America.
  3. 3eScience Institute, University of Washington, Seattle, Washington, United States of America.
  4. 4Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, United States of America.
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Abstract

Antimony is a human-readable language for defining and sharing models developed by the systems biology community. It enables scientists to describe biochemical networks with a simple syntax, while supporting seamless conversion to and from the Systems Biology Markup Language (SBML) community standard. Since Antimony’s original release, both SBML and modeling practices have evolved significantly, creating a need to update Antimony to maintain its standards compliance and practical relevance. In this paper, we introduce Antimony 3, a comprehensive update that formalizes its cumulative improvements and extends its support for SBML Level 3 Core and Flux Balance Constraints (FBC), Distributions, Layout, and Render packages. Antimony 3 enables model specifications that combine kinetic reactions with flux balance analysis, represent uncertainty using probability distributions, add biological context through annotations, and define publication-ready visualizations, all within a unified plain-text format. Antimony 3 is delivered as a lightweight C/C++ library with a stable C API. It is available through official bindings for Python, Julia, and JavaScript/WebAssembly, as well as a cross-platform desktop GUI, which enables straightforward use across scripting environments, desktop applications, and browser-based tools. Antimony 3 is released as open-source software under the BSD 3-Clause License and is available at https://github.com/sys-bio/antimony. Author summary: Biological models are typically stored in standardized formats that ensure compatibility across different software tools, but these formats rely on verbose, machine-readable syntax that is difficult for humans to write or inspect directly. Antimony addresses this challenge by providing an intuitive, text-based language for defining biological models that can be automatically converted to and from the Systems Biology Markup Language (SBML). Since Antimony’s original release in 2009, the SBML standard and common modeling workflows have expanded significantly. We developed Antimony 3 to support these advances, enabling researchers to write a single human-readable text file that defines reaction networks, constraint-based objectives, uncertainty in parameters and initial conditions, semantic annotations linking to biological databases, and model diagrams. Antimony 3 is provided as open-source software with broad support across computational environments, making it accessible to researchers in a wide range of workflows.

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Cite

BibTeXRIS
BibTeX
@article{heydarabadipour2026antimony,
  title = {{Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages}},
  author = {Adel Heydarabadipour and Lucian P Smith and Joseph L Hellerstein and Herbert M Sauro},
  journal = {PLOS Computational Biology},
  year = {2026},
  month = oct,
  doi = {10.1371/journal.pcbi.1014207},
  url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1014207},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages
AU  - Adel Heydarabadipour
AU  - Lucian P Smith
AU  - Joseph L Hellerstein
AU  - Herbert M Sauro
PY  - 2026
DA  - 2026/10/12
JO  - PLOS Computational Biology
DO  - 10.1371/journal.pcbi.1014207
UR  - https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1014207
AB  - Antimony is a human-readable language for defining and sharing models developed by the systems biology community. It enables scientists to describe biochemical networks with a simple syntax, while supporting seamless conversion to and from the Systems Biology Markup Language (SBML) community standard. Since Antimony’s original release, both SBML and modeling practices have evolved significantly, creating a need to update Antimony to maintain its standards compliance and practical relevance. In this paper, we introduce Antimony 3, a comprehensive update that formalizes its cumulative improvements and extends its support for SBML Level 3 Core and Flux Balance Constraints (FBC), Distributions, Layout, and Render packages. Antimony 3 enables model specifications that combine kinetic reactions with flux balance analysis, represent uncertainty using probability distributions, add biological context through annotations, and define publication-ready visualizations, all within a unified plain-text format. Antimony 3 is delivered as a lightweight C/C++ library with a stable C API. It is available through official bindings for Python, Julia, and JavaScript/WebAssembly, as well as a cross-platform desktop GUI, which enables straightforward use across scripting environments, desktop applications, and browser-based tools. Antimony 3 is released as open-source software under the BSD 3-Clause License and is available at https://github.com/sys-bio/antimony. Author summary: Biological models are typically stored in standardized formats that ensure compatibility across different software tools, but these formats rely on verbose, machine-readable syntax that is difficult for humans to write or inspect directly. Antimony addresses this challenge by providing an intuitive, text-based language for defining biological models that can be automatically converted to and from the Systems Biology Markup Language (SBML). Since Antimony’s original release in 2009, the SBML standard and common modeling workflows have expanded significantly. We developed Antimony 3 to support these advances, enabling researchers to write a single human-readable text file that defines reaction networks, constraint-based objectives, uncertainty in parameters and initial conditions, semantic annotations linking to biological databases, and model diagrams. Antimony 3 is provided as open-source software with broad support across computational environments, making it accessible to researchers in a wide range of workflows.
SN  - 1553-7358
SN  - 1553-734X
ER  -