standards > model/format > DOI:10.25504/FAIRsharing.27tnee
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ready Open Modeling EXchange format

Abbreviation: OMEX


General Information
Open Modeling EXchange format (OMEX), together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), 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.



How to cite this record FAIRsharing.org: OMEX; Open Modeling EXchange format; DOI: https://doi.org/10.25504/FAIRsharing.27tnee; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Dec 08 2021 1:57 p.m.

Publication for citation  COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. Bergmann FT,Adams R,Moodie S,Cooper J,Glont M,Golebiewski M,Hucka M,Laibe C,Miller AK,Nickerson DP,Olivier BG,Rodriguez N,Sauro HM,Scharm M,Soiland-Reyes S,Waltemath D,Yvon F,Le Novere N; BMC Bioinformatics ; 2014; 10.1186/s12859-014-0369-z;


This record is maintained by matthiaskoenig  ORCID

Record added: May 19, 2016, 2:18 p.m.
Record updated: June 22, 2021, 2:54 p.m. by The FAIRsharing Team.

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

Bergmann FT,Adams R,Moodie S,Cooper J,Glont M,Golebiewski M,Hucka M,Laibe C,Miller AK,Nickerson DP,Olivier BG,Rodriguez N,Sauro HM,Scharm M,Soiland-Reyes S,Waltemath D,Yvon F,Le Novere N
BMC Bioinformatics 2014

View Paper (PubMed) View Publication

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Related Databases (2)
BioSimulators
BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects.

BioSimulations
BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help researchers discover published models that might be useful for their research and quickly try them via a simple web-based interface.

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Grant Number(s)

  • 115156 (Innovative Medicines Initiative (IMI), Europe)

  • EP/I017909/1 (Engineering and Physical Sciences Research Council (EPSRC), UK)

  • GM070923 (National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA)

  • NIH P50-GM094503 (The Virtual Physiological Rat Project)