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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.

Homepage http://co.mbine.org/specifications/omex.version-1

Countries that developed this resource European Union , Germany , Netherlands , New Zealand , United Kingdom , United States

Created in 2014

Taxonomic range

All

Knowledge Domains

Subjects

User-defined Tags

Data sharing

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.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.27tnee' by 'The FAIRsharing Team' at 14:55, 22 Jun 2021 (approved):

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			forum|https://groups.google.com/forum/?hl=en-GB#!forum/combine-archive
			forum|https://groups.google.com/forum/?hl=en-GB#!forum/combine-support
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			forum|https://groups.google.com/forum/?hl=en-GB#!forum/combine-archive
			forum|https://groups.google.com/forum/?hl=en-GB#!forum/combine-support
			tess training|https://tess.elixir-europe.org/materials/runbiosimulations-tutorial-and-help
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			COMBINE Archive Specification, data access, http://co.mbine.org/specifications/omex.version-1.pdf
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			COMBINE Archive Specification, data release, http://co.mbine.org/specifications/omex.version-1.pdf
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			COMBINE Archive Specification, data release, http://co.mbine.org/specifications/omex.version-1.pdf
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Edits to 'https://fairsharing.org/FAIRsharing.27tnee' by 'The FAIRsharing Team' at 09:19, 10 Feb 2020 (approved):

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Edits to 'https://fairsharing.org/FAIRsharing.27tnee' by 'The FAIRsharing Team' at 09:17, 10 Feb 2020 (approved):

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In Collections

ISO/CD 20691 Collection - DRAFT

Systems Medicine

Support

General

forum	OMEX format discussion
forum	Report problems with the website

Additional Information

Contact

Nicolas Le Novère

External Links

Bioportal	http://bioportal.bioontology.org/ontologies/OMEX
OBO	http://obofoundry.org/ontology/omex.html

TeSS training resources

runBioSimulations tutorial and help

Tools

No tools defined

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Data Release

COMBINE Archive Specification

http://co.mbine.org/specifications/omex.version-1.pdf

Publications

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

Related Standards

Reporting Guidelines

Terminology Artifacts

No semantic standards defined

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

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.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by matthiaskoenig ORCID

Funds

Innovative Medicines Initiative (IMI), Europe (Consortium)
The Virtual Physiological Rat Project
Engineering and Physical Sciences Research Council (EPSRC), UK (Government body)
National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA (Government body)

Maintains

COmputational Modeling in BIology NEtwork (COMBINE) (Consortium)

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)

Open Modeling EXchange format

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