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J Integr Bioinform. 2018 Mar 19;15(1). pii: /j/jib.2018.15.issue-1/jib-2017-0086/jib-2017-0086.xml. doi: 10.1515/jib-2017-0086.

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

Author information

1
Modelling of Biol. Processes, BioQUANT/COS, Heidelberg University, Heidelberg, Germany.
2
Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
3
Department of Computer Science, University of Oxford, Oxford, UK.
4
Department of Biology, Humboldt University, Berlin, Germany.
5
Department of Cell Biology, University of Connecticut, Connecticut, USA.
6
Auckland Bioengineering Institute, Auckland, New Zealand.
7
Babraham Institute Cambridge, Cambridgeshire, UK.
8
Systems Bioinformatics, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
9
University of Washington, Seattle, WA, USA.
10
University of Rostock, Rostock, Germany.

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

PMID:
29550789
PMCID:
PMC6167040
DOI:
10.1515/jib-2017-0086
[Indexed for MEDLINE]
Free PMC Article

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