{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T18:50:42Z","timestamp":1792090242475,"version":"4.4.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1014207","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:00:00Z","timestamp":1792022400000}}],"reference-count":61,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T00:00:00Z","timestamp":1791763200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute of Health","award":["P41EB023912"],"award-info":[{"award-number":["P41EB023912"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    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\u2019s 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++\u2009library 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\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/sys-bio\/antimony\" xlink:type=\"simple\">https:\/\/github.com\/sys-bio\/antimony<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1014207","type":"journal-article","created":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T17:40:46Z","timestamp":1791826846000},"page":"e1014207","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-2865-6128","authenticated-orcid":true,"given":"Adel","family":"Heydarabadipour","sequence":"first","affiliation":[{"name":"University of Washington","place":["Seattle, Washington, United States of America"],"department":["Department of Bioengineering"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7002-6386","authenticated-orcid":true,"given":"Lucian P.","family":"Smith","sequence":"additional","affiliation":[{"name":"University of Washington","place":["Seattle, Washington, United States of America"],"department":["Department of Bioengineering"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0802-4069","authenticated-orcid":true,"given":"Joseph L.","family":"Hellerstein","sequence":"additional","affiliation":[{"name":"University of Washington","place":["Seattle, Washington, United States of America"],"department":["Department of Bioengineering"]},{"name":"University of Washington","place":["Seattle, Washington, United States of America"],"department":["Paul G. Allen School of Computer Science and Engineering"]},{"name":"University of Washington","place":["Seattle, Washington, United States of America"],"department":["eScience Institute"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3659-6817","authenticated-orcid":true,"given":"Herbert M.","family":"Sauro","sequence":"additional","affiliation":[{"name":"University of Washington","place":["Seattle, Washington, United States of America"],"department":["Department of Bioengineering"]},{"name":"University of Washington","place":["Seattle, Washington, United States of America"],"department":["eScience Institute"]},{"name":"University of Washington","place":["Seattle, Washington, United States of America"],"department":["Molecular Engineering and Sciences Institute"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,10,12]]},"reference":[{"key":"pcbi.1014207.ref001","unstructured":"Pedersen M. Modular languages for systems and synthetic biology [PhD]; 2010."},{"issue":"4","key":"pcbi.1014207.ref002","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models","volume":"19","author":"M Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"pcbi.1014207.ref003","doi-asserted-by":"crossref","first-page":"20200021","DOI":"10.1515\/jib-2020-0021","article-title":"CellML 2.0","volume":"17","author":"M Clerx","year":"2020","journal-title":"J Integr Bioinform"},{"issue":"8","key":"pcbi.1014207.ref004","doi-asserted-by":"crossref","first-page":"1254","DOI":"10.1109\/JPROC.2008.925458","article-title":"CellDesigner 3.5: A versatile modeling tool for biochemical networks","volume":"96","author":"A Funahashi","year":"2008","journal-title":"Proc IEEE"},{"issue":"4","key":"pcbi.1014207.ref005","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1089\/153623103322637670","article-title":"Next generation simulation tools: The Systems Biology Workbench and BioSPICE integration","volume":"7","author":"HM Sauro","year":"2003","journal-title":"OMICS"},{"issue":"24","key":"pcbi.1014207.ref006","doi-asserted-by":"crossref","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","article-title":"COPASI--A complex pathway simulator","volume":"22","author":"S Hoops","year":"2006","journal-title":"Bioinformatics"},{"issue":"6","key":"pcbi.1014207.ref007","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1093\/bioinformatics\/btn051","article-title":"LibSBML: An API library for SBML","volume":"24","author":"BJ Bornstein","year":"2008","journal-title":"Bioinformatics"},{"issue":"4","key":"pcbi.1014207.ref008","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1093\/bioinformatics\/bti046","article-title":"Modelling cellular systems with PySCeS","volume":"21","author":"BG Olivier","year":"2005","journal-title":"Bioinformatics"},{"issue":"21","key":"pcbi.1014207.ref009","doi-asserted-by":"crossref","first-page":"3366","DOI":"10.1093\/bioinformatics\/btw469","article-title":"BioNetGen 2.2: Advances in rule-based modeling","volume":"32","author":"LA Harris","year":"2016","journal-title":"Bioinformatics"},{"issue":"5","key":"pcbi.1014207.ref010","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1013024","article-title":"MobsPy: A programming language for biochemical reaction networks","volume":"21","author":"F Cravo","year":"2025","journal-title":"PLoS Comput Biol"},{"issue":"61","key":"pcbi.1014207.ref011","doi-asserted-by":"crossref","first-page":"3215","DOI":"10.21105\/joss.03215","article-title":"yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML","volume":"6","author":"J Vanhoefer","year":"2021","journal-title":"JOSS"},{"issue":"1","key":"pcbi.1014207.ref012","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1008646","article-title":"PEtab-Interoperable specification of parameter estimation problems in systems biology","volume":"17","author":"L Schmiester","year":"2021","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1014207.ref013","doi-asserted-by":"crossref","unstructured":"Bergmann F, Sauro H. SBW - A modular framework for systems biology. Proceedings of the 2006 Winter Simulation Conference. IEEE; 2006. p. 1637\u201345. https:\/\/doi.org\/10.1109\/wsc.2006.322938","DOI":"10.1109\/WSC.2006.322938"},{"issue":"18","key":"pcbi.1014207.ref014","doi-asserted-by":"crossref","first-page":"2452","DOI":"10.1093\/bioinformatics\/btp401","article-title":"Antimony: A modular model definition language","volume":"25","author":"LP Smith","year":"2009","journal-title":"Bioinformatics"},{"issue":"8","key":"pcbi.1014207.ref015","doi-asserted-by":"crossref","DOI":"10.15252\/msb.20199110","article-title":"SBML Level 3: An extensible format for the exchange and reuse of biological models","volume":"16","author":"SM Keating","year":"2020","journal-title":"Mol Syst Biol"},{"issue":"1","key":"pcbi.1014207.ref016","doi-asserted-by":"crossref","first-page":"20170082","DOI":"10.1515\/jib-2017-0082","article-title":"SBML Level 3 package: Flux balance constraints version 2","volume":"15","author":"BG Olivier","year":"2018","journal-title":"J Integr Bioinform"},{"key":"pcbi.1014207.ref017","doi-asserted-by":"crossref","first-page":"20200018","DOI":"10.1515\/jib-2020-0018","article-title":"Systems biology markup language (SBML) level 3 package: Distributions, version 1, release 1","volume":"17","author":"LP Smith","year":"2020","journal-title":"J Integr Bioinform"},{"issue":"2","key":"pcbi.1014207.ref018","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1515\/jib-2015-267","article-title":"The systems biology markup language (SBML) level 3 package: Layout, version 1 core","volume":"12","author":"R Gauges","year":"2015","journal-title":"J Integr Bioinform"},{"issue":"1","key":"pcbi.1014207.ref019","doi-asserted-by":"crossref","first-page":"20170078","DOI":"10.1515\/jib-2017-0078","article-title":"SBML Level 3 package: Render, version 1, release 1","volume":"15","author":"FT Bergmann","year":"2018","journal-title":"J Integr Bioinform"},{"key":"pcbi.1014207.ref020","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.biosystems.2018.07.006","article-title":"Tellurium: An extensible python-based modeling environment for systems and synthetic biology","volume":"171","author":"K Choi","year":"2018","journal-title":"Biosystems"},{"issue":"1","key":"pcbi.1014207.ref021","doi-asserted-by":"crossref","first-page":"20240002","DOI":"10.1515\/jib-2024-0002","article-title":"MakeSBML: A tool for converting between Antimony and SBML","volume":"21","author":"BE Jardine","year":"2024","journal-title":"J Integr Bioinform"},{"key":"pcbi.1014207.ref022","unstructured":"Sauro H. Iridium; 2026. Available from: https:\/\/github.com\/sys-bio\/IridiumSimulator"},{"key":"pcbi.1014207.ref023","unstructured":"Hellerstein J, Sauro H. Web Iridium; 2026. Available from: https:\/\/sys-bio.github.io\/WebIridium\/"},{"key":"pcbi.1014207.ref024","unstructured":"Sauro H. JARNAC: A system for interactive metabolic analysis. Animating the Cellular Map: Proceedings of the 9th International Meeting on BioThermoKinetics; 2000."},{"key":"pcbi.1014207.ref025","unstructured":"Smith L, Sauro HM. An update to the SBML human-readable antimony language. ArXiv. 2024:arXiv\u20132405."},{"key":"pcbi.1014207.ref026","author":"GNU Project","year":"1985"},{"key":"pcbi.1014207.ref027","doi-asserted-by":"crossref","unstructured":"Heydarabadipour A, Smith L, Hellerstein JL, Sauro HM. SBMLNetwork: A framework for standards-based visualization of biochemical models. bioRxiv. 2025:2025\u201305.","DOI":"10.1101\/2025.05.09.653024"},{"key":"pcbi.1014207.ref028","doi-asserted-by":"crossref","unstructured":"Gao Z, Pan Y, Zhang Y, Chiu K. A high performance schema-specific XML parser. Third IEEE International Conference on e-Science and Grid Computing (e-Science 2007); 2007. p. 245\u201352. https:\/\/doi.org\/10.1109\/e-science.2007.5","DOI":"10.1109\/E-SCIENCE.2007.5"},{"key":"pcbi.1014207.ref029","unstructured":"Beazley DM, et al. Swig: An easy to use tool for integrating scripting languages with C and C. Tcl\/Tk Workshop, vol. 43; 1996. 74 p."},{"key":"pcbi.1014207.ref030","author":"Python","year":"2006"},{"key":"pcbi.1014207.ref031","author":"WebAssembly","year":"2015"},{"key":"pcbi.1014207.ref032","doi-asserted-by":"crossref","unstructured":"Zakai A. Emscripten: an LLVM-to-JavaScript compiler. Proceedings of the ACM International Conference Companion on Object Oriented Programming Systems Languages and Applications Companion; 2011. p. 301\u201312.","DOI":"10.1145\/2048147.2048224"},{"key":"pcbi.1014207.ref033","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkv1031","article-title":"ChEBI in 2016: Improved services and an expanding collection of metabolites","volume":"44","author":"J Hastings","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1014207.ref034","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae909","article-title":"KEGG: Biological systems database as a model of the real world","volume":"53","author":"M Kanehisa","year":"2025","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pcbi.1014207.ref035","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1021\/ci00057a005","article-title":"SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules","volume":"28","author":"D Weininger","year":"1988","journal-title":"J Chem Inf Comput Sci"},{"key":"pcbi.1014207.ref036","article-title":"BioModels-15 years of sharing computational models in life science","volume":"48","author":"RS Malik-Sheriff","year":"2020","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"pcbi.1014207.ref037","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1013239","article-title":"Verification and reproducible curation of the BioModels repository","volume":"21","author":"LP Smith","year":"2025","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1014207.ref038","article-title":"BiGG Models: A platform for integrating, standardizing and sharing genome-scale models","volume":"44","author":"ZA King","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"pcbi.1014207.ref039","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1093\/bioinformatics\/btt641","article-title":"SBML and CellML translation in antimony and JSim","volume":"30","author":"LP Smith","year":"2014","journal-title":"Bioinformatics"},{"key":"pcbi.1014207.ref040","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkr1097","article-title":"Identifiers.org and MIRIAM Registry: Community resources to provide persistent identification","volume":"40","author":"N Juty","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"20","key":"pcbi.1014207.ref041","doi-asserted-by":"crossref","first-page":"9107","DOI":"10.1073\/pnas.88.20.9107","article-title":"A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase","volume":"88","author":"A Goldbeter","year":"1991","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1014207.ref042","article-title":"The gene ontology resource: 20 Years and still GOing strong","volume":"47","author":"Consortium GO","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1014207.ref043","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae1082","article-title":"InterPro: The protein sequence classification resource in 2025","volume":"53","author":"M Blum","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1014207.ref044","unstructured":"Consortium TU. UniProt: The universal protein knowledgebase in 2025. 2025."},{"issue":"11","key":"pcbi.1014207.ref045","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btad658","article-title":"An automated model annotation system (AMAS) for SBML models","volume":"39","author":"W Shin","year":"2023","journal-title":"Bioinformatics"},{"issue":"2","key":"pcbi.1014207.ref046","first-page":"271","article-title":"Systems biology markup language (SBML) level 2 version 5: Structures and facilities for model definitions","volume":"12","author":"M Hucka","year":"2015","journal-title":"J Integr Bioinform"},{"issue":"3","key":"pcbi.1014207.ref047","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1038\/s41596-018-0098-2","article-title":"Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0","volume":"14","author":"L Heirendt","year":"2019","journal-title":"Nat Protoc"},{"issue":"5","key":"pcbi.1014207.ref048","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.0010046","article-title":"Flux balance analysis of mycolic acid pathway: Targets for anti-tubercular drugs","volume":"1","author":"K Raman","year":"2005","journal-title":"PLoS Comput Biol"},{"issue":"8","key":"pcbi.1014207.ref049","article-title":"Escher: A web application for building, sharing, and embedding data-rich visualizations of biological pathways","volume":"11","author":"ZA King","year":"2015","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1014207.ref050","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/s12918-016-0269-0","article-title":"Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: An adaptive network case","volume":"10","author":"Y Boada","year":"2016","journal-title":"BMC Syst Biol"},{"key":"pcbi.1014207.ref051","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.jtbi.2015.01.006","article-title":"Mathematical model of brain tumour with glia-neuron interactions and chemotherapy treatment","volume":"368","author":"KC Iarosz","year":"2015","journal-title":"J Theor Biol"},{"issue":"29","key":"pcbi.1014207.ref052","doi-asserted-by":"crossref","first-page":"16732","DOI":"10.1073\/pnas.2006520117","article-title":"The challenges of modeling and forecasting the spread of COVID-19","volume":"117","author":"AL Bertozzi","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pcbi.1014207.ref053","doi-asserted-by":"crossref","first-page":"20190021","DOI":"10.1515\/jib-2019-0021","article-title":"The systems biology markup language (SBML): Language specification for level 3 version 2 core release 2","volume":"16","author":"M Hucka","year":"2019","journal-title":"J Integr Bioinform"},{"issue":"5","key":"pcbi.1014207.ref054","doi-asserted-by":"crossref","first-page":"1877","DOI":"10.1063\/1.1681288","article-title":"Oscillations in chemical systems. IV. Limit cycle behavior in a model of a real chemical reaction","volume":"60","author":"RJ Field","year":"1974","journal-title":"J Chem Phys"},{"issue":"3","key":"pcbi.1014207.ref055","doi-asserted-by":"crossref","first-page":"20250002","DOI":"10.1098\/rsfs.2025.0002","article-title":"Reproducible Boolean model analyses and simulations with the CoLoMoTo software suite: A tutorial","volume":"15","author":"V No\u00ebl","year":"2025","journal-title":"Interface Focus"},{"key":"pcbi.1014207.ref056","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1186\/1752-0509-7-135","article-title":"SBML qualitative models: A model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools","volume":"7","author":"C Chaouiya","year":"2013","journal-title":"BMC Syst Biol"},{"issue":"1","key":"pcbi.1014207.ref057","doi-asserted-by":"crossref","first-page":"20170077","DOI":"10.1515\/jib-2017-0077","article-title":"SBML Level 3 package: Multistate, multicomponent and multicompartment species, version 1, release 1","volume":"15","author":"F Zhang","year":"2018","journal-title":"J Integr Bioinform"},{"key":"pcbi.1014207.ref058","unstructured":"Krishnan BN, Heydarabadipour A, Sauro H. BioModelsRAG: A biological modeling assistant using RAG (retrieval augmented generation). arXiv [Preprint]. 2026. https:\/\/arxiv.org\/abs\/260122684"},{"issue":"8","key":"pcbi.1014207.ref059","doi-asserted-by":"crossref","first-page":"7296","DOI":"10.3390\/ijms24087296","article-title":"Automatic generation of SBML kinetic models from natural language texts using GPT","volume":"24","author":"K Maeda","year":"2023","journal-title":"Int J Mol Sci"},{"key":"pcbi.1014207.ref060","doi-asserted-by":"crossref","unstructured":"Greugny \u00c9T, Ratto N, Etheve L, Gourlet JB, Cogny F, Monteiro C. Leveraging AI for improved reproducibility of mathematical disease models: Insights from a retinitis pigmentosa case study. bioRxiv. 2024:2024\u201304.","DOI":"10.70534\/HSRC5460"},{"issue":"4","key":"pcbi.1014207.ref061","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/3733719","article-title":"Using (not-so) large language models to generate simulation models in a formal DSL: A study on reaction networks","volume":"35","author":"JN Kreikemeyer","year":"2025","journal-title":"ACM Trans Model Comput Simul"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1014207","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:00:00Z","timestamp":1792022400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1014207","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T17:54:54Z","timestamp":1792086894000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1014207"}},"subtitle":[],"editor":[{"given":"Marc R","family":"Birtwistle","sequence":"first","affiliation":[{"name":"Clemson University","place":["UNITED STATES OF AMERICA"]}],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,10,12]]},"references-count":61,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,10,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1014207","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,12]]}}}