{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:44:44Z","timestamp":1753875884310,"version":"3.41.2"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T00:00:00Z","timestamp":1702512000000},"content-version":"vor","delay-in-days":13,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation award","doi-asserted-by":"crossref","award":["CMMI-1933453"],"award-info":[{"award-number":["CMMI-1933453"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NIBIB of the National Institutes of Health"},{"DOI":"10.13039\/100001906","name":"Washington Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001906","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Data Science Environments project award from the Gordon and Betty Moore Foundation","award":["2013-10-29"],"award-info":[{"award-number":["2013-10-29"]}]},{"DOI":"10.13039\/100000879","name":"Alfred P. Sloan Foundation","doi-asserted-by":"publisher","award":["3835"],"award-info":[{"award-number":["3835"]}],"id":[{"id":"10.13039\/100000879","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University of Washington eScience Institute"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Developing biochemical models in systems biology is a complex, knowledge-intensive activity. Some modelers (especially novices) benefit from model development tools with a graphical user interface. However, as with the development of complex software, text-based representations of models provide many benefits for advanced model development. At present, the tools for text-based model development are limited, typically just a textual editor that provides features such as copy, paste, find, and replace. Since these tools are not \u201cmodel aware,\u201d they do not provide features for: (i) model building such as autocompletion of species names; (ii) model analysis such as hover messages that provide information about chemical species; and (iii) model translation to convert between model representations. We refer to these as BAT features.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present VSCode-Antimony, a tool for building, analyzing, and translating models written in the Antimony modeling language, a human readable representation of Systems Biology Markup Language (SBML) models. VSCode-Antimony is a source editor, a tool with language-aware features. For example, there is autocompletion of variable names to assist with model building, hover messages that aid in model analysis, and translation between XML and Antimony representations of SBML models. These features result from making VSCode-Antimony model-aware by incorporating several sophisticated capabilities: analysis of the Antimony grammar (e.g. to identify model symbols and their types); a query system for accessing knowledge sources for chemical species and reactions; and automatic conversion between different model representations (e.g. between Antimony and SBML).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>VSCode-Antimony is available as an open source extension in the VSCode Marketplace https:\/\/marketplace.visualstudio.com\/items?itemName=stevem.vscode-antimony. Source code can be found at https:\/\/github.com\/sys-bio\/vscode-antimony.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad753","type":"journal-article","created":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T00:11:42Z","timestamp":1702512702000},"source":"Crossref","is-referenced-by-count":0,"title":["VSCode-Antimony: a source editor for building, analyzing, and translating antimony models"],"prefix":"10.1093","volume":"39","author":[{"given":"Steve","family":"Ma","sequence":"first","affiliation":[{"name":"NVIDIA Corporation , Redmond, WA 98052, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Longxuan","family":"Fan","sequence":"additional","affiliation":[{"name":"Department of Mathematics, University of Washington , Seattle, WA 98195, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sai Anish","family":"Konanki","sequence":"additional","affiliation":[{"name":"Allen School of Computer Science, University of Washington , Seattle, WA 98195, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eva","family":"Liu","sequence":"additional","affiliation":[{"name":"Allen School of Computer Science, University of Washington , Seattle, WA 98195, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8254-4957","authenticated-orcid":false,"given":"John H","family":"Gennari","sequence":"additional","affiliation":[{"name":"Biomedical and Health Informatics, University of Washington , Seattle, WA 98195, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lucian P","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of Washington , Seattle, WA 98195, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0802-4069","authenticated-orcid":false,"given":"Joseph L","family":"Hellerstein","sequence":"additional","affiliation":[{"name":"eScience Institute, University of Washington , Seattle, WA 98195, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3659-6817","authenticated-orcid":false,"given":"Herbert M","family":"Sauro","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of Washington , Seattle, WA 98195, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,12,14]]},"reference":[{"key":"2023122813172829300_btad753-B1","doi-asserted-by":"crossref","first-page":"D693","DOI":"10.1093\/nar\/gkab1016","article-title":"Rhea, the reaction knowledgebase in 2022","volume":"50","author":"Bansal","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023122813172829300_btad753-B2","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1091\/mbc.6.10.1367","article-title":"Computer analysis of the binding reactions leading to a transmembrane receptor-linked multiprotein complex involved in bacterial chemotaxis","volume":"6","author":"Bray","year":"1995","journal-title":"Mol Biol Cell"},{"volume-title":"Learning GNU Emacs, 3rd edn","year":"2005","author":"Cameron","key":"2023122813172829300_btad753-B3"},{"key":"2023122813172829300_btad753-B4","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":"Choi","year":"2018","journal-title":"Biosystems"},{"key":"2023122813172829300_btad753-B5","doi-asserted-by":"crossref","first-page":"D344","DOI":"10.1093\/nar\/gkm791","article-title":"Chebi: a database and ontology for chemical entities of biological interest","volume":"36","author":"Degtyarenko","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023122813172829300_btad753-B6","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1007\/s004220050302","article-title":"A kinetic mechanism for nicotinic acetylcholine receptors based on multiple allosteric transitions","volume":"75","author":"Edelstein","year":"1996","journal-title":"Biol Cybern"},{"article-title":"Hands-on visual studio 2022","year":"2022","author":"Garcia","key":"2023122813172829300_btad753-B7"},{"key":"2023122813172829300_btad753-B9","doi-asserted-by":"crossref","first-page":"2245","DOI":"10.1093\/bioinformatics\/btn425","article-title":"Detection of stoichiometric inconsistencies in biomolecular models","volume":"24","author":"Gevorgyan","year":"2008","journal-title":"Bioinformatics"},{"key":"2023122813172829300_btad753-B10","doi-asserted-by":"crossref","first-page":"e1008208","DOI":"10.1371\/journal.pcbi.1008208","article-title":"Masspy: building, simulating, and visualizing dynamic biological models in python using mass action kinetics","volume":"17","author":"Haiman","year":"2021","journal-title":"PLoS Comput Biol"},{"key":"2023122813172829300_btad753-B11","doi-asserted-by":"crossref","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","article-title":"Copasi, a complex pathway simulator","volume":"22","author":"Hoops","year":"2006","journal-title":"Bioinformatics"},{"key":"2023122813172829300_btad753-B12","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":"Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"2023122813172829300_btad753-B13","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/s41587-020-0446-y","article-title":"Memote for standardized genome-scale metabolic model testing","volume":"38","author":"Lieven","year":"2020","journal-title":"Nat Biotechnol"},{"volume-title":"Mastering Sublime Text","year":"2013","author":"Peleg","key":"2023122813172829300_btad753-B14"},{"volume-title":"Learning the vi and Vim Editors","year":"2008","author":"Robbins","key":"2023122813172829300_btad753-B15"},{"key":"2023122813172829300_btad753-B16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-8-79","article-title":"Sbmleditor: effective creation of models in the systems biology markup language (sbml)","volume":"8","author":"Rodriguez","year":"2007","journal-title":"BMC Bioinformatics"},{"year":"2015","author":"Sarkar","key":"2023122813172829300_btad753-B17"},{"key":"2023122813172829300_btad753-B18","doi-asserted-by":"crossref","first-page":"2452","DOI":"10.1093\/bioinformatics\/btp401","article-title":"Antimony: a modular model definition language","volume":"25","author":"Smith","year":"2009","journal-title":"Bioinformatics"},{"volume-title":"Learning RStudio for R statistical Computing","year":"2023","author":"van der Lo","key":"2023122813172829300_btad753-B19"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad753\/54450291\/btad753.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/12\/btad753\/54915060\/btad753.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/12\/btad753\/54915060\/btad753.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,28]],"date-time":"2023-12-28T13:17:57Z","timestamp":1703769477000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad753\/7473373"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,12,1]]},"references-count":18,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2023,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad753","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2023,12,1]]},"published":{"date-parts":[[2023,12,1]]},"article-number":"btad753"}}