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

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Show simple item record Waltemath, Dagmar Adams, Richard Bergmann, Frank T. Hucka, Michael Kolpakov, Fedor Miller, Andrew K. Moraru, Ion I. Nickerson, David Sahle, Sven Snoep, Jacky L. Le Novere, Nicolas 2012-04-12T13:00:47Z 2012-04-12T13:00:47Z 2011-12
dc.identifier.citation Waltemath, D. et al. 2011. Reproducible computational biology experiments with SED-ML -The Simulation Experiment Description Markup Language. BMC Systems Biology, 5(1):198. en_ZA
dc.identifier.other 10.1186/1752-0509-5-198
dc.description The original publication is available at en_ZA
dc.description.abstract Background: 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. Results 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. Conclusions 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. en_ZA
dc.format.extent 10 p. : col. ill.
dc.language.iso en_ZA en_ZA
dc.publisher BioMed Central en_ZA
dc.subject Simulation Experiment Description Markup Language en_ZA
dc.subject Computational biology en_ZA
dc.subject Biological research en_ZA
dc.subject SED-ML encodes en_ZA
dc.subject Biology -- Data processing en_ZA
dc.subject Simulation methods en_ZA
dc.title Reproducible computational biology experiments with SED-ML -The Simulation Experiment Description Markup Language en_ZA
dc.type Article en_ZA 2012-03-03T16:02:41Z
dc.description.version Publishers version en_ZA
dc.rights.holder Waltemath et al.; licensee BioMed Central Ltd. en_ZA
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