Open Modeling EXchange format
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Open Modeling EXchange format
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
OMEX
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
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Open Modeling EXchange format
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
OMEX
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
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Open Modeling EXchange format
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
OMEX
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
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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.
Description
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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.
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
Webpage:
http://co.mbine.org/specifications/omex.version-1Webpage
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http://co.mbine.org/specifications/omex.version-1
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
Publications:
Publications
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COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
PMID: 25494900
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
Publications
More detailed information about this field from each metasource.
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
PMID: 25494900
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
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COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
PubMed citations: 49.
49 articles citing: COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. PMID:35710409
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. PMID:35671510
BioSimulators: a central registry of simulation engines and services for recommending specific tools. PMID:35524558
Whole-genome based strain identification of fowlpox virus directly from cutaneous tissue and propagated virus. PMID:34914770
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032. PMID:34867870
Specifications of standards in systems and synthetic biology: status and developments in 2021. PMID:34674411
A Modular Mathematical Model of Exercise-Induced Changes in Metabolism, Signaling, and Gene Expression in Human Skeletal Muscle. PMID:34638694
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism. PMID:34625561
The Systems Biology Simulation Core Library. PMID:34554191
Relating simulation studies by provenance-Developing a family of Wnt signaling models. PMID:34351901
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. PMID:34188046
libOmexMeta: Enabling semantic annotation of models to support FAIR principles. PMID:34132740
Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target. PMID:34073716
RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats. PMID:34019658
First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. PMID:33918864
PEtab-Interoperable specification of parameter estimation problems in systems biology. PMID:33497393
Best Practices for Making Reproducible Biochemical Models. PMID:32853539
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
Community standards to facilitate development and address challenges in metabolic modeling. PMID:32845080
Towards standardization guidelines for in silico approaches in personalized medicine. PMID:32827396
Publishing reproducible dynamic kinetic models. PMID:32793969
Editorial Reproducibility of Computational Models. PMID:32636531
Specifications of standards in systems and synthetic biology: status and developments in 2020. PMID:32598316
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
Organizing genome engineering for the gigabase scale. PMID:32019919
Guidelines for benchmarking of optimization-based approaches for fitting mathematical models. PMID:31842943
BioModels-15 years of sharing computational models in life science. PMID:31701150
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. PMID:31301675
Closing the gap between formats for storing layout information in systems biology. PMID:31273380
Harmonizing semantic annotations for computational models in biology. PMID:30462164
SemGen: a tool for semantics-based annotation and composition of biosimulation models. PMID:30256901
Tellurium: An extensible python-based modeling environment for systems and synthetic biology. PMID:30053414
Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology. PMID:29906293
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. PMID:29596055
Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PMID:29447151
BioModels: expanding horizons to include more modelling approaches and formats. PMID:29106614
COPASI and its applications in biotechnology. PMID:28655634
MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME. PMID:28190948
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. PMID:28187405
SED-ML web tools: generate, modify and export standard-compliant simulation studies. PMID:28049131
A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. PMID:27830063
COMODI: an ontology to characterise differences in versions of computational models in biology. PMID:27401413
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
The Cardiac Electrophysiology Web Lab. PMID:26789753
Specifications of Standards in Systems and Synthetic Biology. PMID:26528556
Mimoza: web-based semantic zooming and navigation in metabolic networks. PMID:25889977
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. PMID:25759811
Improving collaboration by standardization efforts in systems biology. PMID:25538939
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mathematical model
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
modeling and simulation
metasource: Fairsharing.org
version: 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: Jan 03 2022 7:11 p.m.
Tags
More detailed information about this field from each metasource.
mathematical model
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
modeling and simulation
metasource: Fairsharing.orgversion: 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: Jan 03 2022 7:11 p.m.
mathematical model modeling and simulation
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