Encyclopedia of Computational Neuroscience

Living Edition
| Editors: Dieter Jaeger, Ranu Jung

Simulation Experiment Description Markup Language (SED-ML)

Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-7320-6_377-6

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...

This is a preview of subscription content, log in to check access.

References

  1. 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):e1001122PubMedCentralPubMedCrossRefGoogle Scholar
  2. 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
  3. 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 5:198PubMedCentralPubMedCrossRefGoogle Scholar

Further Readings

  1. Adams RA (2012) SED-ED, a workflow editor for computational biology experiments written in SED-ML. Bioinformatics 28(8):1180–1181PubMedCrossRefGoogle Scholar
  2. 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 7:543Google Scholar
  3. 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)Google Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.Systems Biology and BioinformaticsUniversity of RostockRostockGermany
  2. 2.EMBL European Bioinformatics Institute & Babraham InstituteCambridgeUK