{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T04:27:48Z","timestamp":1778646468124,"version":"3.51.4"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,28]],"date-time":"2016-10-28T00:00:00Z","timestamp":1477612800000},"content-version":"vor","delay-in-days":262,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: MATLAB is popular in biological research for creating and simulating models that use ordinary differential equations (ODEs). However, sharing or using these models outside of MATLAB is often problematic. A community standard such as Systems Biology Markup Language (SBML) can serve as a neutral exchange format, but translating models from MATLAB to SBML can be challenging\u2014especially for legacy models not written with translation in mind. We developed MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) to help. MOCCASIN can convert ODE-based MATLAB models of biochemical reaction networks into the SBML format.<\/jats:p>\n               <jats:p>Availability and implementation: MOCCASIN is available under the terms of the LGPL 2.1 license (http:\/\/www.gnu.org\/licenses\/lgpl-2.1.html). Source code, binaries and test cases can be freely obtained from https:\/\/github.com\/sbmlteam\/moccasin.<\/jats:p>\n               <jats:p>Contact: mhucka@caltech.edu<\/jats:p>\n               <jats:p>Supplementary information: More information is available at https:\/\/github.com\/sbmlteam\/moccasin.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw056","type":"journal-article","created":{"date-parts":[[2016,2,15]],"date-time":"2016-02-15T01:09:07Z","timestamp":1455498547000},"page":"1905-1906","source":"Crossref","is-referenced-by-count":17,"title":["MOCCASIN: converting MATLAB ODE models to SBML"],"prefix":"10.1093","volume":"32","author":[{"given":"Harold F.","family":"G\u00f3mez","sequence":"first","affiliation":[{"name":"1 Department of Biosystems Science and Engineering, ETH Z\u00fcrich, Basel CH 4058, Switzerland,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Hucka","sequence":"additional","affiliation":[{"name":"2 Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah M.","family":"Keating","sequence":"additional","affiliation":[{"name":"3 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, UK and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"German","family":"Nudelman","sequence":"additional","affiliation":[{"name":"4 Department of Neurology, Icahn School of Medicine at Mount Sinai, Mount Sinai Medical Center and School of Medicine, New York, NY 10029, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dagmar","family":"Iber","sequence":"additional","affiliation":[{"name":"1 Department of Biosystems Science and Engineering, ETH Z\u00fcrich, Basel CH 4058, Switzerland,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stuart C.","family":"Sealfon","sequence":"additional","affiliation":[{"name":"4 Department of Neurology, Icahn School of Medicine at Mount Sinai, Mount Sinai Medical Center and School of Medicine, New York, NY 10029, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,2,9]]},"reference":[{"key":"2023020112311902100_btw056-B1","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1093\/bioinformatics\/btn051","article-title":"LibSBML: an API Library for SBML","volume":"24","author":"Bornstein","year":"2008","journal-title":"Bioinformatics"},{"key":"2023020112311902100_btw056-B2","first-page":"99","article-title":"Kind analysis for MATLAB","volume-title":"ACM SIGPLAN Notices \u2013 OOPSLA \u201811","author":"Doherty","year":"2011"},{"key":"2023020112311902100_btw056-B3","doi-asserted-by":"crossref","DOI":"10.1137\/1.9780898718195","volume-title":"Simulating, Analyzing, and Animating Dynamical Systems: A Guide to XPPAUT for Researchers and Students","author":"Ermentrout","year":"2002"},{"key":"2023020112311902100_btw056-B4","first-page":"514","article-title":"Inferring reaction systems from ordinary differential equations","volume":"22","author":"Fages","year":"2015","journal-title":"Theor. 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