{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:44:39Z","timestamp":1740185079975,"version":"3.37.3"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2017,1,21]],"date-time":"2017-01-21T00:00:00Z","timestamp":1484956800000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"German Federal Ministry of Education and Research","award":["(FKZ 031 6194)"],"award-info":[{"award-number":["(FKZ 031 6194)"]}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM081070"],"award-info":[{"award-number":["GM081070"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, an online application for creating, editing, simulating and validating SED-ML documents. The Web Tools implement all current SED-ML specifications and, thus, support complex modifications and co-simulation of models in SBML and CellML formats. Ultimately, the Web Tools lower the bar on working with SED-ML documents and help users create valid simulation descriptions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>http:\/\/sysbioapps.dyndns.org\/SED-ML_Web_Tools\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw812","type":"journal-article","created":{"date-parts":[[2016,12,24]],"date-time":"2016-12-24T07:56:19Z","timestamp":1482566179000},"page":"1253-1254","source":"Crossref","is-referenced-by-count":7,"title":["SED-ML web tools: generate, modify and export standard-compliant simulation studies"],"prefix":"10.1093","volume":"33","author":[{"given":"Frank T","family":"Bergmann","sequence":"first","affiliation":[{"name":"COS\/BioQUANT, Heidelberg University, Heidelberg, Germany"}]},{"given":"David","family":"Nickerson","sequence":"additional","affiliation":[{"name":"Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand"}]},{"given":"Dagmar","family":"Waltemath","sequence":"additional","affiliation":[{"name":"Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany"}]},{"given":"Martin","family":"Scharm","sequence":"additional","affiliation":[{"name":"Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany"}]}],"member":"286","published-online":{"date-parts":[[2017,1,10]]},"reference":[{"year":"2011","author":"Bergmann","key":"2023020205014723600_btw812-B1"},{"key":"2023020205014723600_btw812-B2","doi-asserted-by":"crossref","first-page":"369.","DOI":"10.1186\/s12859-014-0369-z","article-title":"COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project","volume":"15","author":"Bergmann","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023020205014723600_btw812-B3","doi-asserted-by":"crossref","first-page":"262.","DOI":"10.1515\/jib-2015-262","article-title":"Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2","volume":"12","author":"Bergmann","year":"2015","journal-title":"J. Integr. Bioinf"},{"year":"2006","author":"Bergmann","key":"2023020205014723600_btw812-B4"},{"key":"2023020205014723600_btw812-B5","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1177\/0037549703040939","article-title":"An overview of CellML 1.1, a biological model description language","volume":"79","author":"Cuellar","year":"2003","journal-title":"Simulation"},{"key":"2023020205014723600_btw812-B6","doi-asserted-by":"crossref","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","article-title":"COPASI \u2013 a complex pathway simulator","volume":"22","author":"Hoops","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020205014723600_btw812-B7","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":"2023020205014723600_btw812-B8","doi-asserted-by":"crossref","first-page":"19.","DOI":"10.3389\/fbioe.2015.00019","article-title":"Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative","volume":"3","author":"Hucka","year":"2015","journal-title":"Front. Bioeng. Biotechnol"},{"year":"2002","author":"Kolpakov","key":"2023020205014723600_btw812-B9"},{"key":"2023020205014723600_btw812-B10","doi-asserted-by":"crossref","first-page":"2143","DOI":"10.1093\/bioinformatics\/bth200","article-title":"Web-based kinetic modelling using JWS Online","volume":"20","author":"Olivier","year":"2004","journal-title":"Bioinformatics"},{"key":"2023020205014723600_btw812-B11","first-page":"054601.","article-title":"Tellurium: a python based modeling and reproducibility platform for systems biology","author":"Sauro","year":"2016","journal-title":"bioRxiv"},{"year":"2014","author":"Scharm","key":"2023020205014723600_btw812-B12"},{"year":"2016","author":"Scharm","key":"2023020205014723600_btw812-B13"},{"year":"2015","author":"Scharm","key":"2023020205014723600_btw812-B14"},{"key":"2023020205014723600_btw812-B15","doi-asserted-by":"crossref","first-page":"198.","DOI":"10.1186\/1752-0509-5-198","article-title":"Reproducible computational biology experiments with SED-ML \u2013 the Simulation Experiment Description Markup Language","volume":"5","author":"Waltemath","year":"2011","journal-title":"BMC Syst. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/8\/1253\/49038337\/bioinformatics_33_8_1253.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/8\/1253\/49038337\/bioinformatics_33_8_1253.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T05:05:30Z","timestamp":1675314330000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/8\/1253\/2881437"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,1,10]]},"references-count":15,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2017,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw812","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2017,4,15]]},"published":{"date-parts":[[2017,1,10]]}}}