title: COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
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.
authors.affiliation: Modelling of Biological Processes, BioQUANT/COS, University of Heidelberg, INF 267, Heidelberg, 69120, Germany. fbergman@caltech.edu.
authors.forename: Frank T
authors.initials: FT
authors.lastname: Bergmann
authors.affiliation: ResearchSpace, 24 Fountainhall Road, Edinburgh, EH9 2LW, UK. ra22597@gmail.com.
authors.forename: Richard
authors.initials: R
authors.lastname: Adams
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. stuart.moodie@eightpillars.uk.com.|Current affiliation: Eight Pillars Ltd, 19 Redford Walk, Edinburgh, EH13 0AG, UK. stuart.moodie@eightpillars.uk.com.
authors.forename: Stuart
authors.initials: S
authors.lastname: Moodie
authors.affiliation: Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford, OX1 3QD, UK. jonathan.cooper@cs.ox.ac.uk.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Cooper
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. mglont@ebi.ac.uk.
authors.forename: Mihai
authors.initials: M
authors.lastname: Glont
authors.affiliation: HITS gGmbH, Schloss-Wolfsbrunnenweg 35, D-69118, Heidelberg, Germany. martin.golebiewski@h-its.org.
authors.forename: Martin
authors.initials: M
authors.lastname: Golebiewski
authors.affiliation: Computing and Mathematical sciences, California Institute of Technology, Pasadena, CA, 91125, USA. mhucka@caltech.edu.
authors.forename: Michael
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authors.lastname: Hucka
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. laibe@ebi.ac.uk.
authors.forename: Camille
authors.initials: C
authors.lastname: Laibe
authors.affiliation: Auckland Bioengineering Institute, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand. ak.miller@auckland.ac.nz.
authors.forename: Andrew K
authors.initials: AK
authors.lastname: Miller
authors.affiliation: Auckland Bioengineering Institute, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand. david.nickerson@gmail.com.
authors.forename: David P
authors.initials: DP
authors.lastname: Nickerson
authors.affiliation: Systems Bioinformatics, VU University Amsterdam, Amsterdam, 1081 HV, The Netherlands. b.g.olivier@vu.nl.
authors.forename: Brett G
authors.initials: BG
authors.lastname: Olivier
authors.affiliation: Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK. nicolas.rodriguez@babraham.ac.uk.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Rodriguez
authors.affiliation: Department of Bioengineering, University of Washington, Seattle, 98195, WA, USA. hsauro@u.washington.edu.
authors.forename: Herbert M
authors.initials: HM
authors.lastname: Sauro
authors.affiliation: Systems Biology and Bioinformatics, University of Rostock, Ulmenstrasse 69, Rostock, 18057, Germany. martin.scharm@uni-rostock.de.
authors.forename: Martin
authors.initials: M
authors.lastname: Scharm
authors.affiliation: School of Computer Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK. soiland-reyes@cs.manchester.ac.uk.
authors.forename: Stian
authors.initials: S
authors.lastname: Soiland-Reyes
authors.affiliation: Systems Biology and Bioinformatics, University of Rostock, Ulmenstrasse 69, Rostock, 18057, Germany. dagmar.waltemath@uni-rostock.de.
authors.forename: Dagmar
authors.initials: D
authors.lastname: Waltemath
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. florent@ebi.ac.uk.
authors.forename: Florent
authors.initials: F
authors.lastname: Yvon
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. lenov@babraham.ac.uk.|Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK. lenov@babraham.ac.uk.
authors.forename: Nicolas
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mesh_terms: D001109:Archives; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030561:Databases, Nucleic Acid; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D012984:Software