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. 2014 Dec 14;15(1):369.
doi: 10.1186/s12859-014-0369-z.

COMBINE Archive and OMEX Format: One File to Share All Information to Reproduce a Modeling Project

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Free PMC article

COMBINE Archive and OMEX Format: One File to Share All Information to Reproduce a Modeling Project

Frank T Bergmann et al. BMC Bioinformatics. .
Free PMC article

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.

Figures

Figure 1
Figure 1
Schematic representation of the structure of a COMBINE Archive, a (possibly encrypted) zipped version of an archive containing descriptions of models, simulations, graphical representations, metadata and other sources of information.
Figure 2
Figure 2
Example of manifest file describing 5 files: the manifest itself, an SBML file with the structure of the model, a SED-ML file with the description of a simulation, a PDF version of the article describing the modeling and simulation experience, and an RDF file containing metadata about the archive. In this specific archive, the SED-ML file should be read first, which is indicated by the master attribute set to “true” on the file simulation.xml.
Figure 3
Figure 3
Example of a metadata file bringing additional information about the archive itself (identified by the relative path “.”): a short description of what the archive is about, details about its creator, and dates of creation and last modification.

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References

    1. Mesirov JP. Computer science: accessible reproducible research. Science. 2010;327:415–416. doi: 10.1126/science.1179653. - DOI - PMC - PubMed
    1. Sandve GK, Nekrutenko A, Taylor J, Hovig E. Ten simple rules for reproducible computational research. PLoS Comput Biol. 2013;9:e1003285. doi: 10.1371/journal.pcbi.1003285. - DOI - PMC - PubMed
    1. Hucka M, Bolouri H, Finney A, Sauro HM, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, et al. The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003;19:524–531. doi: 10.1093/bioinformatics/btg015. - DOI - PubMed
    1. Hedley WJ, Nelson MR, Bullivant DP, Nielsen PF. A short introduction to CellML. Phil Trans Roy Soc London Series A. 2001;359:1073–1089. doi: 10.1098/rsta.2001.0817. - DOI
    1. Goddard NH, Hucka M, Howell F, Cornelis H, Shankar K, Beeman D. Towards NeuroML: model description methods for collaborative modelling in neuroscience. Phil Trans Roy Soc London Series B. 2001;356:1209–1228. doi: 10.1098/rstb.2001.0910. - DOI - PMC - PubMed

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