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Simulation Experiment Description Markup Language (SED-ML)

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Encyclopedia of Computational Neuroscience

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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

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  • 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

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  • Courtot M, Juty N, KnĂĽpfer 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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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

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