{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,19]],"date-time":"2026-06-19T17:49:45Z","timestamp":1781891385962,"version":"3.54.5"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published\n                      <jats:italic>Minimum Information About a Simulation Experiment<\/jats:italic>\n                      (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is\n                      <jats:italic>Level 1 Version 1<\/jats:italic>\n                      . It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/1752-0509-5-198","type":"journal-article","created":{"date-parts":[[2011,12,15]],"date-time":"2011-12-15T14:26:21Z","timestamp":1323959181000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":209,"title":["Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language"],"prefix":"10.1186","volume":"5","author":[{"given":"Dagmar","family":"Waltemath","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Adams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frank T","family":"Bergmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Hucka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fedor","family":"Kolpakov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew K","family":"Miller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ion I","family":"Moraru","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Nickerson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sven","family":"Sahle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacky L","family":"Snoep","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Le Nov\u00e8re","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2011,12,15]]},"reference":[{"issue":"4","key":"839_CR1","doi-asserted-by":"publisher","first-page":"e1001122","DOI":"10.1371\/journal.pcbi.1001122","volume":"7","author":"D Waltemath","year":"2011","unstructured":"Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin E, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller A, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro H, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Nov\u00e8re N: Minimum Information About a Simulation Experiment (MIASE). PLoS Compututational Biology. 2011, 7 (4): e1001122-10.1371\/journal.pcbi.1001122.","journal-title":"PLoS Compututational Biology"},{"issue":"8","key":"839_CR2","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1038\/nbt.1411","volume":"26","author":"CF Taylor","year":"2008","unstructured":"Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Clark AM, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Nov\u00e8re N, et al, et al.: Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology. 2008, 26 (8): 889-896. 10.1038\/nbt.1411.","journal-title":"Nature Biotechnology"},{"issue":"4","key":"839_CR3","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","volume":"19","author":"M Hucka","year":"2003","unstructured":"Hucka M, Finney A, Sauro H, Bolouri H, Doyle J, Kitano H, Arkin A, Bornstein B, Bray D, Cornish-Bowden A, Cuellar A, Dronov S, Gilles E, Ginkel M, Gor V, Goryanin I, Hedley W, Hodgman T, Hofmeyr JH, Hunter P, Juty N, Kasberger J, Kremling A, Kummer U, Le Nov\u00e8re N, Loew L, Lucio D, Mendes P, Minch E, Mjolsness E, et al, et al.: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003, 19 (4): 524-31. 10.1093\/bioinformatics\/btg015.","journal-title":"Bioinformatics"},{"issue":"12","key":"839_CR4","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1177\/0037549703040939","volume":"79","author":"AA Cuellar","year":"2003","unstructured":"Cuellar AA, Lloyd CM, Nielsen PF, Bullivant DP, Nickerson DP, Hunter PJ: An Overview of CellML 1.1, a Biological Model Description Language. SIMULATION. 2003, 79 (12): 740-747. 10.1177\/0037549703040939.","journal-title":"SIMULATION"},{"issue":"6","key":"839_CR5","doi-asserted-by":"publisher","first-page":"e1000815+","DOI":"10.1371\/journal.pcbi.1000815","volume":"6","author":"P Gleeson","year":"2010","unstructured":"Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, Barnes SR, Dimitrova YD, Silver RA: NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Computational Biology. 2010, 6 (6): e1000815+-","journal-title":"PLoS Computational Biology"},{"key":"839_CR6","volume-title":"BMC Systems Biology","author":"C Laibe","year":"2007","unstructured":"Laibe C, Le Nov\u00e8re N: MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. BMC Systems Biology. 2007, 58:"},{"key":"839_CR7","volume-title":"World Wide Web Consortium","author":"R Ausbrooks","year":"2003","unstructured":"Ausbrooks R, Buswell S, Carlisle D, Dalmas S, Devitt S, Diaz A, Froumentin M, Hunter R, Ion P, Kohlhase M, Miner R, Poppelier N, Smith B, Soiffer N, Sutor R, Watt S: Mathematical Markup Language (MathML) version 2.0. W3C recommendation. World Wide Web Consortium. 2003"},{"key":"839_CR8","volume-title":"XML path language (XPath)","author":"J Clark","year":"1999","unstructured":"Clark J, DeRose S: XML path language (XPath). 1999"},{"key":"839_CR9","doi-asserted-by":"crossref","unstructured":"Courtot M, Juty N, Kn\u00fcpfer C, Waltemath D, Zhukova A, Dr\u00e4ger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell D, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Ro-driguez N, Villeger A, Wilkinson D, Wimalaratne S, Laibe C, Hucka M, Le Nov\u00e8re N: Controlled vocabularies and semantics in Systems Biology. Molecular Systems Biology. 2011, 7 (543):","DOI":"10.1038\/msb.2011.77"},{"issue":"3","key":"839_CR10","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1006\/jtbi.1999.0924","volume":"198","author":"J Leloup","year":"1999","unstructured":"Leloup J, Goldbeter A: Chaos and birhythmicity in a model for circadian oscillations of the PER and TIM proteins in Drosophila. Journal of theoretical biology. 1999, 198 (3): 445-459. 10.1006\/jtbi.1999.0924.","journal-title":"Journal of theoretical biology"},{"issue":"7","key":"839_CR11","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1093\/bioinformatics\/btq069","volume":"26","author":"JO Dada","year":"2010","unstructured":"Dada JO, Spasi\u0107 I, Paton NW, Mendes P: SBRML: a markup language for associating systems biology data with models. Bioinformatics (Oxford, England). 2010, 26 (7): 932-938. 10.1093\/bioinformatics\/btq069.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"suppl 2","key":"839_CR12","doi-asserted-by":"publisher","first-page":"W689","DOI":"10.1093\/nar\/gkq394","volume":"38","author":"J Bhagat","year":"2010","unstructured":"Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble C: BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic acids research. 2010, 38 (suppl 2): W689-","journal-title":"Nucleic acids research"},{"issue":"1895","key":"839_CR13","doi-asserted-by":"publisher","first-page":"1845","DOI":"10.1098\/rsta.2008.0310","volume":"367","author":"DA Beard","year":"2009","unstructured":"Beard DA, Britten R, Cooling MT, Garny A, Halstead MD, Hunter PJ, Lawson J, Lloyd CM, Marsh J, Miller A, Nickerson DP, Nielsen PM, Nomura T, Subramanium S, Wimalaratne SM, Yu T: CellML metadata standards, associated tools and repositories. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences. 2009, 367 (1895): 1845-1867. 10.1098\/rsta.2008.0310.","journal-title":"Philosophical transactions. Series A, Mathematical, physical, and engineering sciences"},{"key":"839_CR14","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1186\/1752-0509-3-34","volume":"3","author":"P Saffrey","year":"2009","unstructured":"Saffrey P, Orton R: Version control of pathway models using XML patches. BMC Sytems Biology. 2009, 3: 34-10.1186\/1752-0509-3-34.","journal-title":"BMC Sytems Biology"},{"issue":"3","key":"839_CR15","doi-asserted-by":"publisher","first-page":"181","DOI":"10.2174\/157016406779475380","volume":"3","author":"F Bergmann","year":"2006","unstructured":"Bergmann F, Vallabhajosyula R, Sauro H: Computational tools for modeling protein networks. Current Proteomics. 2006, 3 (3): 181-197. 10.2174\/157016406779475380.","journal-title":"Current Proteomics"},{"key":"839_CR16","first-page":"1637","volume-title":"WSC '06: Proceedings of the 38th conference on Winter simulation","author":"FT Bergmann","year":"2006","unstructured":"Bergmann FT, Sauro HM: SBW - a modular framework for systems biology. WSC '06: Proceedings of the 38th conference on Winter simulation. 2006, 1637-1645."},{"issue":"21","key":"839_CR17","doi-asserted-by":"publisher","first-page":"2848","DOI":"10.1093\/bioinformatics\/btp457","volume":"25","author":"C Myers","year":"2009","unstructured":"Myers C, Barker N, Jones K, Kuwahara H, Madsen C, Nguyen N: iBioSim: a tool for the analysis and design of genetic circuits. Bioinformatics. 2009, 25 (21): 2848-10.1093\/bioinformatics\/btp457.","journal-title":"Bioinformatics"},{"issue":"24","key":"839_CR18","doi-asserted-by":"publisher","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","volume":"22","author":"S Hoops","year":"2006","unstructured":"Hoops S, Sahle S, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U: COPASI - a COmplex PAthway SImulator. Bioinformatics. 2006, 22 (24): 3067-3074. 10.1093\/bioinformatics\/btl485.","journal-title":"Bioinformatics"},{"issue":"6","key":"839_CR19","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1093\/bioinformatics\/btn051","volume":"24","author":"BJ Bornstein","year":"2008","unstructured":"Bornstein BJ, Keating SM, Jouraku A, Hucka M: LibSBML: an API Library for SBML. Bioinformatics. 2008, 24 (6): 880-881. 10.1093\/bioinformatics\/btn051.","journal-title":"Bioinformatics"},{"key":"839_CR20","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1186\/1471-2105-11-178","volume":"11","author":"A Miller","year":"2010","unstructured":"Miller A, Marsh J, Reeve A, Garny A, Britten R, Halstead M, Cooper J, Nickerson D, Nielsen P: An overview of the CellML API and its implementation. BMC bioinformatics. 2010, 11: 178-10.1186\/1471-2105-11-178.","journal-title":"BMC bioinformatics"},{"issue":"suppl 1","key":"839_CR21","doi-asserted-by":"publisher","first-page":"D689","DOI":"10.1093\/nar\/gkj092","volume":"34","author":"N Le Nov\u00e8re","year":"2006","unstructured":"Le Nov\u00e8re N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M: BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research. 2006, 34 (suppl 1): D689-D691.","journal-title":"Nucleic Acids Research"},{"issue":"13","key":"839_CR22","doi-asserted-by":"publisher","first-page":"2143","DOI":"10.1093\/bioinformatics\/bth200","volume":"20","author":"B Olivier","year":"2004","unstructured":"Olivier B, Snoep J: Web-based kinetic modelling using JWS Online. Bioinformatics. 2004, 20 (13): 2143-10.1093\/bioinformatics\/bth200.","journal-title":"Bioinformatics"},{"key":"839_CR23","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1186\/1471-2105-11-582","volume":"11","author":"P Li","year":"2010","unstructured":"Li P, Dada J, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW: Systematic integration of experimental data and models in systems biology. BMC bioinformatics. 2010, 11: 582-","journal-title":"BMC bioinformatics"},{"key":"839_CR24","volume-title":"Simulation Experiment Description Markup Language (SED-ML): Level 1 Version 1","author":"D Waltemath","year":"2011","unstructured":"Waltemath D, Bergmann FT, Adams R, Le Nov\u00e8re N: Simulation Experiment Description Markup Language (SED-ML): Level 1 Version 1. 2011, [Available from Nature Precedings, http:\/\/dx.doi.org\/10.1038\/npre.2011.5846.1]"},{"issue":"6767","key":"839_CR25","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/35002125","volume":"403","author":"M Elowitz","year":"2000","unstructured":"Elowitz M, Leibler S: A synthetic oscillatory network of transcriptional regulators. Nature. 2000, 403 (6767): 335-338. 10.1038\/35002125.","journal-title":"Nature"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-5-198.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T14:23:14Z","timestamp":1630506194000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-5-198"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,12]]},"references-count":25,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["839"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-5-198","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.721960073.793556793","asserted-by":"object"}]},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,12]]},"assertion":[{"value":"2 September 2011","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 December 2011","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 December 2011","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"198"}}