{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T14:54:46Z","timestamp":1753887286734,"version":"3.41.2"},"reference-count":11,"publisher":"Walter de Gruyter GmbH","issue":"1","license":[{"start":{"date-parts":[[2024,3,1]],"date-time":"2024-03-01T00:00:00Z","timestamp":1709251200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM123032"],"award-info":[{"award-number":["R01GM123032"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000070","name":"National Institute of Biomedical Imaging and Bioengineering","doi-asserted-by":"publisher","award":["P41EB02391"],"award-info":[{"award-number":["P41EB02391"]}],"id":[{"id":"10.13039\/100000070","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>We describe a web-based tool, MakeSBML (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/sys-bio.github.io\/makesbml\/\">https:\/\/sys-bio.github.io\/makesbml\/<\/jats:ext-link>), that provides an installation-free application for creating, editing, and searching the Biomodels repository for SBML-based models. MakeSBML is a client-based web application that translates models expressed in human-readable Antimony to the System Biology Markup Language (SBML) and vice-versa. Since MakeSBML is a web-based application it requires no installation on the user\u2019s part. Currently, MakeSBML is hosted on a GitHub page where the client-based design makes it trivial to move to other hosts. This model for software deployment also reduces maintenance costs since an active server is not required. The SBML modeling language is often used in systems biology research to describe complex biochemical networks and makes reproducing models much easier. However, SBML is designed to be computer-readable, not human-readable. We therefore employ the human-readable Antimony language to make it easy to create and edit SBML models.<\/jats:p>","DOI":"10.1515\/jib-2024-0002","type":"journal-article","created":{"date-parts":[[2024,6,11]],"date-time":"2024-06-11T10:47:41Z","timestamp":1718102861000},"source":"Crossref","is-referenced-by-count":2,"title":["MakeSBML: a tool for converting between Antimony and SBML"],"prefix":"10.1515","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-7187-6306","authenticated-orcid":false,"given":"Bartholomew E.","family":"Jardine","sequence":"first","affiliation":[{"name":"Department of Bioengineering , University of Washington , Box 355061 , Seattle , 98195 , WA , USA"}]},{"given":"Lucian P.","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Bioengineering , University of Washington , Box 355061 , Seattle , 98195 , WA , USA"}]},{"given":"Herbert M.","family":"Sauro","sequence":"additional","affiliation":[{"name":"Department of Bioengineering , University of Washington , Box 355061 , Seattle , 98195 , WA , USA"}]}],"member":"374","published-online":{"date-parts":[[2024,6,11]]},"reference":[{"doi-asserted-by":"crossref","unstructured":"Hucka, M, Finney, A, Sauro, HM, Bolouri, H, Doyle, JC, Kitano, H, The Rest of the SBML Forum, et al.. 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In: Proceedings of the ACM international conference companion on object oriented programming systems languages and applications companion; 2011:301\u201312 pp.","key":"2024112723335218407_j_jib-2024-0002_ref_008","DOI":"10.1145\/2048147.2048224"},{"doi-asserted-by":"crossref","unstructured":"Malik-Sheriff, RS, Glont, M, Nguyen, TVN, Tiwari, K, Roberts, MG, Xavier, A, et al.. BioModels \u2014 15 years of sharing computational models in life science. Nucleic Acids Res 2020;48:D407\u201315. https:\/\/doi.org\/10.1093\/nar\/gkz1055.","key":"2024112723335218407_j_jib-2024-0002_ref_009","DOI":"10.1093\/nar\/gkz1055"},{"doi-asserted-by":"crossref","unstructured":"Bornstein, BJ, Keating, SM, Jouraku, A, Hucka, M. LibSBML: an API library for SBML. Bioinformatics 2008;24:880\u20131. https:\/\/doi.org\/10.1093\/bioinformatics\/btn051.","key":"2024112723335218407_j_jib-2024-0002_ref_010","DOI":"10.1093\/bioinformatics\/btn051"},{"doi-asserted-by":"crossref","unstructured":"Medley, JK, Hellerstein, J, Sauro, HM. libsbmljs \u2013 enabling web-based sbml tools. Biosystems 2020;195:104150. https:\/\/doi.org\/10.1016\/j.biosystems.2020.104150.","key":"2024112723335218407_j_jib-2024-0002_ref_011","DOI":"10.1016\/j.biosystems.2020.104150"}],"container-title":["Journal of Integrative Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2024-0002\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2024-0002\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,27]],"date-time":"2024-11-27T23:34:52Z","timestamp":1732750492000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2024-0002\/html"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,1]]},"references-count":11,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,4,15]]},"published-print":{"date-parts":[[2024,7,31]]}},"alternative-id":["10.1515\/jib-2024-0002"],"URL":"https:\/\/doi.org\/10.1515\/jib-2024-0002","relation":{},"ISSN":["1613-4516"],"issn-type":[{"type":"electronic","value":"1613-4516"}],"subject":[],"published":{"date-parts":[[2024,3,1]]},"article-number":"20240002"}}