词条 | SED-ML |
释义 |
| name = Simulation Experiment Description Markup Language | icon = | iconcaption = | icon_size = | screenshot = | screenshot_size = | caption = |_noextcode = | extension = .xml |_nomimecode = | mime = | type code = | uniform_type = | conforms_to = | magic = | developer = | released = {{start date and age|2011|03|25|df=yes}} | latest_release_version = Level 1 Version 2, Release 1 | latest_release_date = {{start date and age|2013|12|02|df=yes}} | genre = Markup language | container_for = | contained_by = | extended_from = XML | extended_to = | standard = | free = Yes | url = {{URL|sed-ml.org/}} }} The Simulation Experiment Description Markup Language (SED-ML) is a representation format, based on XML, for the encoding and exchange of simulation descriptions on computational models of biological systems. It is a free and open community development project. SED-ML Level 1 Version 1[2], the first version of SED-ML, enables descriptions of time course simulation experiments. StructureThe SED-ML format is built of five major blocks:
More information on the SED-ML structure is available from the SED-ML home page and the reference publication.[4] HistoryThe idea of developing a standard format for simulation experiment encoding was born at the European Bioinformatics Institute (EMBL-EBI). In 2007, Dagmar Waltemath and Nicolas Le Novère started to draft such a format during Dagmar's Marie-Curie funded internship in the Computational Neuroscience group at EMBL-EBI.[5] The SED-ML project was first discussed publicly at the 12th SBML Forum Meeting in 2007, in Long Beach (US). The first version of SED-ML was then presented at the "Super-hackathon "standards and ontologies for Systems Biology"" in Okinawa in 2008. Back then, the language was called MIASE-ML (in accordance with the MIASE guidelines). In Okinawa, many researchers showed a high interest in the format, and discussions were vital. MIASE became the Minimum Information guideline for simulation experiments. MIASE-ML was renamed into "Simulation Experiment Description Markup Language" (SED-ML). Level 1 Version 1 of SED-ML officially appeared in March 2011, but SED-ML was presented, discussed and further specified during several community meetings in the years in between, including the combined "CellML-SBGN-SBO-BioPAX-MIASE workshop" in 2009, or the "2010 SBML-BioModels.net Hackathon". Since then SED-ML has been developed in collaboration with the communities forming the "computational modeling in biology network" COMBINE. Besides dedicated sessions at various meetings, the development of SED-ML benefits from community interactions on the SED-ML-discuss mailing list.[6] SED-ML CommunitySED-ML is part of the COmputational Modeling in Biology Network (COMBINE). Format development is coordinated by an editorial board elected by the community.[7] Discussions take place at SED-ML-discuss.[6] References1. ^1 {{cite news| authors = D. Waltemath, F. T. Bergmann, R. Adams, N. Le Novère| title = Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1| doi = 10.1038/npre.2011.5846.1| year = 2011| journal=Nature Precedings}} [1][2][3][4][5]2. ^1 {{cite news| authors = D. Waltemath, R. Adams, F.T. Bergmann, M. Hucka, F. Kolpakov, A.K. Miller, I.I. Moraru, D. Nickerson, J.L. Snoep, N. Le Novère| title = Reproducible computational biology experiments with SED-ML – The Simulation Experiment Description Markup Language.| journal = BMC Systems Biology |volume=5 |pages=198| doi = 10.1186/1752-0509-5-198| year = 2011}} 3. ^1 {{cite web| url = http://sed-ml.org/about.html| title = Current SED-ML Editors| publisher = SED-ML| accessdate = 6 July 2017| date =}} 4. ^1 2 {{cite web| url = https://groups.google.com/forum/#!forum/sed-ml-discuss| title = SED-ML-discuss Info Page| publisher = SED-ML| accessdate = 6 July 2017| date =}} 5. ^1 {{cite web| url = http://www.ebi.ac.uk/compneur-srv/| title = Computational Systems Neurobiology Group| publisher = EMBL-EBI| accessdate = 24 April 2014| date = 1 October 2012}} }}{{COMBINE}} 2 : XML markup languages|Systems biology |
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