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Encyclopedia of Computational Neuroscience pp 1–4Cite as

Simulation Experiment Description Markup Language (SED-ML)

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Definition

The Simulation Experiment Description Markup Language is an XML-based exchange format for the encoding of simulation experiments mainly in the field of computational biology. It stores the simulation recipe, including the models used in the experiment, the pre- and post-processing procedures, and the instructions for how to generate the simulation output.

Detailed Description

Overview

The Simulation Experiment Description Markup Language (SED-ML) encodes simulation setups in XML. Thereby it provides a means to exchange simulation descriptions in standard format. SED-ML respects the Minimum Information Guidelines for Simulation Experiments (Minimum Information About a Simulation Experiment, MIASE (Waltemath et al. 2011a)). Following these recommendations, the first version of SED-ML has been published in March 2011 (Waltemath et al. 2011b). It covers the description of time-course simulations and consists of five major building blocks:

  1. 1.

    The Modelentity contains references...

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References

  • Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N (2011a) Minimum information about a simulation experiment (MIASE). PLoS Comput Biol 7(4):e1001122

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Waltemath D, Bergmann FT, Adams R, Le Novère N (2011b) Simulation experiment description markup language (SED-ML): level 1 version 1. http://sed-ml.org/documents/sed-ml-L1V1.pdf. Accessed 28 Sept 2013

  • Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, Miller AK, Moraru II, Nickerson D, Snoep JL, Le Novère N (2011c) Reproducible computational biology experiments with SED-ML: the simulation experiment description markup language. BMC Syst Biol 5:198

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Further Readings

  • Adams RA (2012) SED-ED, a workflow editor for computational biology experiments written in SED-ML. Bioinformatics 28(8):1180–1181

    Article  CAS  PubMed  Google Scholar 

  • Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N (2011) Controlled vocabularies and semantics in systems biology. Nat Mol Syst Biol 7:543

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  • Waltemath D, Henkel R, Winter F, Wolkenhauer O (2013) Reproducibility of model-based results in systems biology. In: Prokop A, Csukas B (eds) Systems biology: integrative biology and simulation tools, vol 1. Springer (in press)

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Author information

Authors and Affiliations

  1. Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany

    Dr. Dagmar Waltemath

  2. EMBL European Bioinformatics Institute & Babraham Institute, Cambridge, CB10 1SD, UK

    Nicolas Le Novère

Authors
  1. Dr. Dagmar Waltemath
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  2. Nicolas Le Novère
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Corresponding author

Correspondence to Dagmar Waltemath .

Editor information

Editors and Affiliations

  1. Atlanta, Georgia, USA

    Dieter Jaeger

  2. Department of Biomedical Engineering, Florida International University, Miami, Florida, USA

    Ranu Jung

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Cite this entry

Waltemath, D., Le Novère, N. (2013). Simulation Experiment Description Markup Language (SED-ML). In: Jaeger, D., Jung, R. (eds) Encyclopedia of Computational Neuroscience. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7320-6_377-6

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  • DOI: https://doi.org/10.1007/978-1-4614-7320-6_377-6

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  • Publisher Name: Springer, New York, NY

  • Online ISBN: 978-1-4614-7320-6

  • eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences

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