SED-ML

Last updated
Simulation Experiment Description Markup Language
SEDML logo.png
Filename extension
.xml
Initial release25 March 2011;12 years ago (2011-03-25)
Latest release
Level 1 Version 2, Release 1
2 December 2013;10 years ago (2013-12-02)
Type of format Markup language
Extended from XML
Open format?Yes
Website 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. [1] It is a free and open community development project.

Contents

SED-ML Level 1 Version 1, [2] the first version of SED-ML, enables descriptions of time course simulation experiments.

Structure

The SED-ML format is built of five major blocks:

More information on the SED-ML structure is available from the SED-ML home page [1] and the reference publication. [3]

History

The 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. [4]

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. [5]

SED-ML Community

SED-ML is part of the COmputational Modeling in Biology Network (COMBINE). Format development is coordinated by an editorial board elected by the community. [6] Discussions take place at SED-ML-discuss. [5]

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References

  1. 1 2 "Simulation Experiment Description Markup Language". SED-ML. Retrieved 6 July 2017.
  2. ↑ D. Waltemath; F. T. Bergmann; R. Adams; N. Le Novère (2011). "Simulation Experiment Description Markup Language (SED-ML): Level 1 Version 1". Nature Precedings. doi:10.1038/npre.2011.5846.1.
  3. ↑ 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 (2011). "Reproducible computational biology experiments with SED-ML – The Simulation Experiment Description Markup Language". BMC Systems Biology. 5: 198. doi: 10.1186/1752-0509-5-198 . hdl: 20.500.11820/1b2fc55b-d3b0-4e6b-8b60-6614254b020a .
  4. ↑ "Computational Systems Neurobiology Group". EMBL-EBI. 1 October 2012. Retrieved 24 April 2014.
  5. 1 2 "SED-ML-discuss Info Page". SED-ML. Retrieved 6 July 2017.
  6. ↑ "Current SED-ML Editors". SED-ML. Retrieved 6 July 2017.
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