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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

4 Issues per year


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 15, Issue 1

Issues

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)

Frank T. BergmannORCID iD: http://orcid.org/0000-0001-5553-4702 / Jonathan CooperORCID iD: https://orcid.org/0000-0001-6009-3542 / Matthias KönigORCID iD: http://orcid.org/0000-0003-1725-179X / Ion Moraru / David NickersonORCID iD: https://orcid.org/0000-0003-4667-9779 / Nicolas Le NovèreORCID iD: https://orcid.org/0000-0002-6309-7327 / Brett G. OlivierORCID iD: https://orcid.org/0000-0002-5293-5321
  • Modelling of Biol. Processes, BioQUANT/COS, Heidelberg University, Heidelberg, Germany
  • Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
  • Systems Bioinformatics, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
  • orcid.org/0000-0002-5293-5321
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Sven Sahle / Lucian SmithORCID iD: https://orcid.org/0000-0001-7002-6386 / Dagmar WaltemathORCID iD: https://orcid.org/0000-0002-5886-5563
Published Online: 2018-03-19 | DOI: https://doi.org/10.1515/jib-2017-0086

Abstract

The creation of computational simulation experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML) describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of simulation studies among users and software tools. The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format that encodes, for a given simulation experiment, (i) which models to use; (ii) which modifications to apply to models before simulation; (iii) which simulation procedures to run on each model; (iv) how to post-process the data; and (v) how these results should be plotted and reported. SED-ML Level 1 Version 1 (L1V1) implemented support for the encoding of basic time course simulations. SED-ML L1V2 added support for more complex types of simulations, specifically repeated tasks and chained simulation procedures. SED-ML L1V3 extends L1V2 by means to describe which datasets and subsets thereof to use within a simulation experiment.

Keywords: Simulation experiment; computational modeling; reproducibility

About the article

Received: 2017-12-31

Accepted: 2018-02-02

Published Online: 2018-03-19


Citation Information: Journal of Integrative Bioinformatics, Volume 15, Issue 1, 20170086, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2017-0086.

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©2018, Frank T. Bergmann et al., published by De Gruyter, Berlin/Boston. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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