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COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

Bergmann, Frank T. and Adams, Richard and Moodie, Stuart and Cooper, Jonathan and Glont, Mihai and Golebiewski, Martin and Hucka, Michael and Laibe, Camille and Miller, Andrew K. and Nickerson, David P. and Olivier, Brett G. and Rodriguez, Nicolas and Sauro, Herbert M. and Scharm, Martin and Soiland-Reyes, Stian and Waltemath, Dagmar and Yvon, Florent and Le Novère, Nicolas (2014) COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics, 15 . Art. No. 369. ISSN 1471-2105. PMCID PMC4272562. http://resolver.caltech.edu/CaltechAUTHORS:20150205-152803537

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[img] Archive (ZIP) (COMBINE Archive containing a model of the Repressilator encoded in SBML and the simulation experiment description provided as supporting information for [[9]]) - Supplemental Material
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[img] Archive (ZIP) (COMBINE Archive containing the expanded version of the Recon1.1 model [[61]]) - Supplemental Material
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[img] Archive (ZIP) (COMBINE Archive containing the expanded version of the Recon1.1 model [[61]]) - Supplemental Material
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Abstract

Background: With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result. Results: We describe the Open Modeling EXchange format (OMEX). Together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive, a single file that supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software. Conclusions: The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. We anticipate that the COMBINE Archive will become a significant help for modellers, as the domain moves to larger, more complex experiments such as multi-scale models of organs, digital organisms, and bioengineering.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1186/s12859-014-0369-zDOIArticle
http://link.springer.com/article/10.1186/s12859-014-0369-zPublisherArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4272562/PubMed CentralArticle
ORCID:
AuthorORCID
Hucka, Michael0000-0001-9105-5960
Waltemath, Dagmar0000-0002-5886-5563
Additional Information:© 2014 Bergmann 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/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. 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: 4 July 2014 Accepted: 30 October 2014. Published online: 14 December 2014. SM, MG, CL received funding from the Innovative Medicines Initiative Joint Undertaking (grant agreement no. 115156, DDMoRe). JC was supported through the EPSRC Cross-Disciplinary Interface Programme (grant number EP/I017909/1) and Microsoft Research Ltd. MH and NR were supported by US National Institute of General Medical Sciences (GM070923). DPN is supported by The Virtual Physiological Rat Project (NIH P50-GM094503) and the Maurice Wilkins Centre for Molecular Biodiversity. BO is supported by a ZonMW Zenith grant 40-41009-98-10038. HMS was partly supported by US National Institute of General Medical Sciences (R01GM081070). MS and DW are funded by the German Federal Ministry of Education and Research (e:Bio program SEMS, FKZ 031 6194). SSR was supported by the EU (FP7 RI-283359 and FP7-ICT-2007-6 270192). NR and NLN were supported by the UK Biotechnology and Biological Science Research Council (BBS/E/B/000C0419).
Funders:
Funding AgencyGrant Number
Innovative Medicines Initiative Joint Undertaking115156
Engineering and Physical Sciences Research Council (EPSRC)EP/I017909/1
Microsoft Research LtdUNSPECIFIED
NIHGM070923
NIHP50-GM094503
Maurice Wilkins Centre for Molecular BiodiversityUNSPECIFIED
ZonMW Zenith40-41009-98-10038
NIHR01GM081070
Bundesministerium für Bildung und Forschung (BMBF)031 6194
European UnionFP7 RI-283359
European UnionFP7-ICT-2007-6270192
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/B/000C0419
Subject Keywords:Data format; Archive; Computational modeling; Reproducible research; Reproducible science
PubMed Central ID:PMC4272562
Record Number:CaltechAUTHORS:20150205-152803537
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20150205-152803537
Official Citation:Bergmann FT, Adams R, Moodie S, et al. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics. 2014;15(1):369. doi:10.1186/s12859-014-0369-z.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:54463
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:06 Feb 2015 01:02
Last Modified:19 Oct 2018 18:16

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