Authors
Adel Heydarabadipour, Lucian P Smith, Joseph L Hellerstein, Herbert M Sauro
Published in
PLoS computational biology. Volume 22. Issue 10. Pages e1014207. Oct 12, 2026. Epub Oct 12, 2026.
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.
PMID:
42862848
Bibliographic data and abstract were imported from PubMed on 13 Oct 2026.
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