{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T05:16:39Z","timestamp":1722921399130},"reference-count":12,"publisher":"Walter de Gruyter GmbH","issue":"1","license":[{"start":{"date-parts":[[2018,3,19]],"date-time":"2018-03-19T00:00:00Z","timestamp":1521417600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,19]]},"abstract":"Abstract<\/jats:title>The creation of computational simulation experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML) describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of simulation studies among users and software tools. The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format that encodes, for a given simulation experiment, (i) which models to use; (ii) which modifications to apply to models before simulation; (iii) which simulation procedures to run on each model; (iv) how to post-process the data; and (v) how these results should be plotted and reported. SED-ML Level 1 Version 1 (L1V1) implemented support for the encoding of basic time course simulations. SED-ML L1V2 added support for more complex types of simulations, specifically repeated tasks and chained simulation procedures. SED-ML L1V3 extends L1V2 by means to describe which datasets and subsets thereof to use within a simulation experiment.<\/jats:p>","DOI":"10.1515\/jib-2017-0086","type":"journal-article","created":{"date-parts":[[2018,3,24]],"date-time":"2018-03-24T23:44:39Z","timestamp":1521935079000},"source":"Crossref","is-referenced-by-count":18,"title":["Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)"],"prefix":"10.1515","volume":"15","author":[{"given":"Frank T.","family":"Bergmann","sequence":"first","affiliation":[{"name":"Modelling of Biol. Processes, BioQUANT\/COS, Heidelberg University, Heidelberg, Germany"},{"name":"Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA"}]},{"given":"Jonathan","family":"Cooper","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Oxford, Oxford, UK"}]},{"given":"Matthias","family":"K\u00f6nig","sequence":"additional","affiliation":[{"name":"Department of Biology, Humboldt University, Berlin, Germany"}]},{"given":"Ion","family":"Moraru","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, University of Connecticut, Connecticut, USA"}]},{"given":"David","family":"Nickerson","sequence":"additional","affiliation":[{"name":"Auckland Bioengineering Institute, Auckland, New Zealand"}]},{"given":"Nicolas","family":"Le Nov\u00e8re","sequence":"additional","affiliation":[{"name":"Babraham Institute Cambridge, Cambridgeshire, UK"}]},{"given":"Brett G.","family":"Olivier","sequence":"additional","affiliation":[{"name":"Modelling of Biol. Processes, BioQUANT\/COS, Heidelberg University, Heidelberg, Germany"},{"name":"Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA"},{"name":"Systems Bioinformatics, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands"}]},{"given":"Sven","family":"Sahle","sequence":"additional","affiliation":[{"name":"Modelling of Biol. Processes, BioQUANT\/COS, Heidelberg University, Heidelberg, Germany"}]},{"given":"Lucian","family":"Smith","sequence":"additional","affiliation":[{"name":"University of Washington, Seattle, WA, USA"}]},{"given":"Dagmar","family":"Waltemath","sequence":"additional","affiliation":[{"name":"University of Rostock, Rostock, Germany"}]}],"member":"374","reference":[{"key":"ref71","first-page":"79","article-title":"An overview of CellML a biological model description language","volume":"8","author":"Cuellar","year":"2003","journal-title":"Simulation"},{"key":"ref121","article-title":"The Systems Biology Markup Language Language Specification for Level Version Core Release Candidate","author":"Hucka","year":"2010","journal-title":"Nature Precedings"},{"key":"ref131","first-page":"524","article-title":"The systems biology markup language a medium for representation and exchange of biochemical network models re BioModels Database : a free centralized database of curated , published quantitative kinetic models of biochemical and cellular systems issue","volume":"14","author":"Hucka","year":"2003","journal-title":"Bioinformatics Nucleic Acids Res Database"},{"key":"ref81","first-page":"403","article-title":"A synthetic oscillatory network of transcriptional regulators","volume":"9","author":"Elowitz","year":"2000","journal-title":"Nature"},{"key":"ref111","first-page":"298","article-title":"The I\u03baB \u03baB signaling module : temporal control and selective gene activation","author":"Hoffmann","year":"2002","journal-title":"Science"},{"key":"ref61","article-title":"pfer ger re Controlled vocabularies and semantics in Systems Biology","volume":"7","author":"Courtot","year":"2011","journal-title":"Mol Sys Biol"},{"key":"ref151","article-title":"re BioModels Database : An enhanced curated and annotated resource for published quantitative kinetic models","volume":"17","author":"Li","year":"2010","journal-title":"BMC Systems Biology"},{"key":"ref171","article-title":"re Minimum Information About a Simulation Experiment MI","volume":"19","author":"Waltemath","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"ref01","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1186\/s12859-014-0369-z","article-title":"re COMBINE archive and OMEX format : one file to share all information to reproduce a modeling project","volume":"1","author":"Bergmann","year":"2014","journal-title":"BMC bioinformatics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1093\/bioinformatics\/btw812","article-title":"SED - ML web tools : generate modify and export standard - compliant simulation studies","volume":"33","author":"Bergmann","year":"2017","journal-title":"Bioinformatics"},{"key":"ref101","first-page":"356","article-title":"Towards NeuroML : Model Description Methods for Collaborative Modeling in Neuroscience Phil Trans series","author":"Goddard","year":"2001","journal-title":"Royal Society"},{"key":"ref141","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1177\/074873099129000948","article-title":"Limit cycle models for circadian rhythms based on transcriptional regulation in drosophila and neurospora","volume":"16","author":"Leloup","year":"1999","journal-title":"Journal of Biological Rhythms"}],"container-title":["Journal of Integrative Bioinformatics"],"original-title":[],"link":[{"URL":"https:\/\/www.degruyter.com\/view\/journals\/jib\/15\/1\/article-20170086.xml","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2017-0086\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T19:38:31Z","timestamp":1693597111000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2017-0086\/html"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,3,19]]},"references-count":12,"journal-issue":{"issue":"1"},"URL":"https:\/\/doi.org\/10.1515\/jib-2017-0086","relation":{},"ISSN":["1613-4516"],"issn-type":[{"value":"1613-4516","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,3,19]]}}}