Open Modeling EXchange format
Abbreviation: OMEX
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
Knowledge Domains
User-defined Tags
How to cite this record FAIRsharing.org: OMEX; Open Modeling EXchange format; DOI: https://doi.org/10.25504/FAIRsharing.27tnee; Last edited: Feb. 14, 2020, 5:07 p.m.; Last accessed: Apr 17 2021 7:22 p.m.
Record added: May 19, 2016, 2:18 p.m.
Record updated:
Feb. 10, 2020, 9:19 a.m. by The FAIRsharing Team.
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 |
No XSD schemas defined
Conditions of Use
Applies to: Data use- Public domain
Data Access
COMBINE Archive Specification | http://co.mbine.org/specifications/omex.version-1.pdf |
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
Reporting Guidelines
Terminology Artifacts
No semantic standards defined
Models and Formats
Identifier Schemas
No identifier schema standards defined
Metrics
No metrics standards defined
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.
This record is not implemented by any policy.
Record Maintainer
Funds
Innovative Medicines Initiative (IMI), Europe (Consortium)
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)