Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

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TitleReproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.
Publication TypeJournal Article
Year of Publication2011
AuthorsWaltemath, D, Adams, R, Bergmann, FT, Hucka, M, Kolpakov, F, Miller, AK, Moraru, II, Nickerson, D, Sahle, S, Snoep, JL, Le Novère, N
JournalBMC Syst Biol
Volume5
Pagination198
Date Published2011
ISSN1752-0509
KeywordsComputational Biology, Computer Simulation, Programming Languages, Reproducibility of Results, Software
Abstract

<p><b>BACKGROUND: </b>The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools.</p><p><b>RESULTS: </b>In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions.</p><p><b>CONCLUSIONS: </b>With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.</p>

DOI10.1186/1752-0509-5-198
Alternate JournalBMC Syst Biol
PubMed ID22172142
PubMed Central IDPMC3292844
Grant ListBB/D019621/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
GM070923 / GM / NIGMS NIH HHS / United States
GM081070 / GM / NIGMS NIH HHS / United States
P41-RR013186 / RR / NCRR NIH HHS / United States
R01 GM070923 / GM / NIGMS NIH HHS / United States
U54-RR022232 / RR / NCRR NIH HHS / United States