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The systems biology format converter

Rodriguez, Nicolas and Pettit, Jean-Baptiste and Dalle Pezze, Piero and Li, Lu and Henry, Arnaud and van Iersel, Martijn P. and Jalowicki, Gael and Kutmon, Martina and Natarajan, Kedar N. and Tolnay, David and Stefan, Melanie I. and Evelo, Chris T. and Le Novère, Nicolas (2016) The systems biology format converter. BMC Bioinformatics, 17 . Art. No. 154. ISSN 1471-2105. PMCID PMC4820913. http://resolver.caltech.edu/CaltechAUTHORS:20160427-140820446

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Abstract

Background: Interoperability between formats is a recurring problem in systems biology research. Many tools have been developed to convert computational models from one format to another. However, they have been developed independently, resulting in redundancy of efforts and lack of synergy. Results: Here we present the System Biology Format Converter (SBFC), which provide a generic framework to potentially convert any format into another. The framework currently includes several converters translating between the following formats: SBML, BioPAX, SBGN-ML, Matlab, Octave, XPP, GPML, Dot, MDL and APM. This software is written in Java and can be used as a standalone executable or web service. Conclusions: The SBFC framework is an evolving software project. Existing converters can be used and improved, and new converters can be easily added, making SBFC useful to both modellers and developers. The source code and documentation of the framework are freely available from the project web site.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1186/s12859-016-1000-2DOIArticle
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1000-2PublisherArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820913/PubMed CentralArticle
Additional Information:© 2016 Rodriguez et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Received: 13 January 2016; Accepted: 23 March 2016; Published: 5 April 2016; The authors declare that they have no competing interests. Authors’ contributions: JBP, NLN, NR, MK and MPI conceived and designed the project; JPB, MK, MPI, NR and PDP implemented the software; in addition LL, AH, GK and KN contributed to some of the included converters. JPB, PDP, NLN and NR wrote the manuscript. All authors read and approved the final manuscript. Fundings: The work was funded by British BBSRC (BB/F010516/1, BBS/E/B/000C0419), EMBL-EBI and US National Institute of Health (GM070923C).
Funders:
Funding AgencyGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)BB/F010516/1
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/B/000C0419
European Molecular Biology Laboratory (EMBL)UNSPECIFIED
NIHGM070923C
European Bioinformatics Institute (EBI)UNSPECIFIED
Subject Keywords:Converter; Format; Systems biology; SBML
PubMed Central ID:PMC4820913
Record Number:CaltechAUTHORS:20160427-140820446
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20160427-140820446
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66515
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:02 May 2016 20:44
Last Modified:02 May 2016 20:44

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