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

Waltemath, Dagmar and Adams, Richard and Bergmann, Frank T. and Hucka, Michael and Kolpakov, Fedor and Miller, Andrew K. and Moraru, Ion I. and Nickerson, David and Sahle, Sven and Snoep, Jacky L. and Le Novère, Nicolas (2011) Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. BMC Systems Biology, 5 . Art. No. 198. ISSN 1752-0509. PMCID PMC3292844. https://resolver.caltech.edu/CaltechAUTHORS:20120417-151008602

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1186/1752-0509-5-198DOIArticle
http://www.biomedcentral.com/1752-0509/5/198PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3292844/PubMed CentralArticle
ORCID:
AuthorORCID
Waltemath, Dagmar0000-0002-5886-5563
Hucka, Michael0000-0001-9105-5960
Additional Information:© 2011 Waltemath et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 2 September 2011; Accepted: 15 December 2011; Published: 15 December 2011. The authors thank the whole community of computational systems biology and in particular the members of the network “Computational Modeling in Biology” (COMBINE) for providing requirements and comments. DW received funding for this work from the Marie Curie program and the DFG research training school dIEM oSiRiS (grant 1387/1). AKM was funded partly by the VPH-Share Project and partly by the Maurice Wilkins Centre For Molecular Biodiscovery. RA is grateful for funding by the BBSRC grant BB/D019621/1. IIM was funded by the NIH grants P41-RR013186 and U54-RR022232. MH was funded by the NIH NIGMS grant GM070923. FTB was funded by the NIH/NIGMS grant GM081070. Authors’ contributions: DW and NL initiated the project. All authors participated in the discussions leading to the structure of SED-ML. DW, RA, FB and NL developed the first specification of the language. All authors participated to and approved the final manuscript’s preparation.
Funders:
Funding AgencyGrant Number
Marie Curie FellowshipUNSPECIFIED
Deutsche Forschungsgemeinschaft (DFG)1387/1
VPH-Share ProjectUNSPECIFIED
Maurice Wilkins Centre For Molecular BiodiscoveryUNSPECIFIED
Biotechnology and Biological Sciences Research Council (BBSRC)BB/D019621/1
NIHP41-RR013186
NIHU54-RR022232
NIHGM070923
NIH GM081070
PubMed Central ID:PMC3292844
Record Number:CaltechAUTHORS:20120417-151008602
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20120417-151008602
Official Citation:Waltemath D, Adams R, Bergmann FT, et al. Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. BMC Systems Biology. 2011;5:198. doi:10.1186/1752-0509-5-198.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:30145
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:17 Apr 2012 23:04
Last Modified:03 Oct 2019 03:47

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