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BMC Bioinformatics. 2014 Dec 14;15:369. doi: 10.1186/s12859-014-0369-z.

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

Author information

1
Modelling of Biological Processes, BioQUANT/COS, University of Heidelberg, INF 267, Heidelberg, 69120, Germany. fbergman@caltech.edu.
2
ResearchSpace, 24 Fountainhall Road, Edinburgh, EH9 2LW, UK. ra22597@gmail.com.
3
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. stuart.moodie@eightpillars.uk.com.
4
Current affiliation: Eight Pillars Ltd, 19 Redford Walk, Edinburgh, EH13 0AG, UK. stuart.moodie@eightpillars.uk.com.
5
Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford, OX1 3QD, UK. jonathan.cooper@cs.ox.ac.uk.
6
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. mglont@ebi.ac.uk.
7
HITS gGmbH, Schloss-Wolfsbrunnenweg 35, D-69118, Heidelberg, Germany. martin.golebiewski@h-its.org.
8
Computing and Mathematical sciences, California Institute of Technology, Pasadena, CA, 91125, USA. mhucka@caltech.edu.
9
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. laibe@ebi.ac.uk.
10
Auckland Bioengineering Institute, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand. ak.miller@auckland.ac.nz.
11
Auckland Bioengineering Institute, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand. david.nickerson@gmail.com.
12
Systems Bioinformatics, VU University Amsterdam, Amsterdam, 1081 HV, The Netherlands. b.g.olivier@vu.nl.
13
Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK. nicolas.rodriguez@babraham.ac.uk.
14
Department of Bioengineering, University of Washington, Seattle, 98195, WA, USA. hsauro@u.washington.edu.
15
Systems Biology and Bioinformatics, University of Rostock, Ulmenstrasse 69, Rostock, 18057, Germany. martin.scharm@uni-rostock.de.
16
School of Computer Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK. soiland-reyes@cs.manchester.ac.uk.
17
Systems Biology and Bioinformatics, University of Rostock, Ulmenstrasse 69, Rostock, 18057, Germany. dagmar.waltemath@uni-rostock.de.
18
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. florent@ebi.ac.uk.
19
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. lenov@babraham.ac.uk.
20
Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK. lenov@babraham.ac.uk.

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.

PMID:
25494900
PMCID:
PMC4272562
DOI:
10.1186/s12859-014-0369-z
[Indexed for MEDLINE]
Free PMC Article

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