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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan

CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

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Volume 12, Issue 2


Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2

Frank T. Bergmann / Jonathan Cooper
  • Corresponding author
  • Department of Computer Science, University of Oxford, Oxford, United Kingdom of Great Britain and Northern Ireland
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  • Other articles by this author:
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/ Nicolas Le Novère
  • The Babraham Institute, Cambridge, United Kingdom of Great Britain and Northern Ireland
  • EMBL European Bioinformatics Institute, Cambridge, United Kingdom of Great Britain and Northern Ireland
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/ David Nickerson / Dagmar Waltemath
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2015-262


The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the structure of models is not sufficient to enable the reproduction of simulation results. One also needs to describe the procedures the models are subjected to, as recommended by the Minimum Information About a Simulation Experiment (MIASE) guidelines.

This document presents Level 1 Version 2 of the Simulation Experiment Description Markup Language (SED-ML), a computer-readable format for encoding simulation and analysis experiments to apply to computational models. SED-ML files are encoded in the Extensible Markup Language (XML) and can be used in conjunction with any XML-based model encoding format, such as CellML or SBML. A SED-ML file includes details of which models to use, how to modify them prior to executing a simulation, which simulation and analysis procedures to apply, which results to extract and how to present them. Level 1 Version 2 extends the format by allowing the encoding of repeated and chained procedures.

About the article

Published Online: 2016-10-18

Published in Print: 2015-06-01

Citation Information: Journal of Integrative Bioinformatics, Volume 12, Issue 2, Pages 119–212, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2015-262.

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© 2015 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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