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

Frank T Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K Miller, David P Nickerson, Brett G Olivier, Nicolas Rodriguez (+6 others)
2014 BMC Bioinformatics  
Conclusions: The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file.  ...  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  ...  The COMBINE Archive permits researchers to share all the documents describing a model and associated simulations in a single file.  ... 
doi:10.1186/s12859-014-0369-z pmid:25494900 pmcid:PMC4272562 fatcat:3dqofrgqz5f2dlivtikejgyonu

One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project [article]

Frank T. Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro (+4 others)
2014 arXiv   pre-print
Conclusions: The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file.  ...  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  ...  The COMBINE Archive permits researchers to share all the documents describing a model and associated simulations in a single file.  ... 
arXiv:1407.4992v2 fatcat:x2pn25x6rvdznfzgc7hlhip7aq

COMBINE Archive Specification Version 1

Frank T Bergmann, Nicolas Rodriguez, Nicolas Le Novère
2015 Journal of Integrative Bioinformatics  
The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file.  ...  The Open Modeling EXchange format (OMEX) supports the exchange of all the information necessary for a modeling and simulation experiment in biology.  ...  The Open Modeling EXchange format (OMEX) supports the exchange of all the information necessary for a modeling and simulation experiment in biology.  ... 
doi:10.2390/biecoll-jib-2015-261 pmid:26528559 fatcat:hpqz5ix5enenljdh2mywiym2wu

COMBINE Archive Specification Version 1

Frank T. Bergmann, Nicolas Rodriguez, Nicolas Le Novère
2015 Journal of Integrative Bioinformatics  
These constitute various separate components required to reproduce a given published scientific result.The Open Modeling EXchange format (OMEX) supports the exchange of all the information necessary for  ...  The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file.  ...  The Open Modeling EXchange format (OMEX) supports the exchange of all the information necessary for a modeling and simulation experiment in biology.  ... 
doi:10.1515/jib-2015-261 fatcat:735lll2xlfa5zbvm7eoruv2n6y

A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos

Martin Scharm, Dagmar Waltemath
2016 F1000Research  
Bergmann FT, Adams R, Moodie S, et al.: COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics. 2014; 15(1): 369.  ...  COMBINE archives are standardised containers for data files related to a simulation study in computational biology.  ...  Acknowledgements We would like to thank Vasundra Touré for her help with creating the SBGN-compliant visualisations of the model and Matthias König for running and testing the archive in Tellurium.  ... 
doi:10.12688/f1000research.9379.1 pmid:27830063 pmcid:PMC5082596 fatcat:mrrmaxj7w5fqtp3hwneheihynq

OMEX metadata specification (version 1.2)

John H. Gennari, Matthias König, Goksel Misirli, Maxwell L. Neal, David P. Nickerson, Dagmar Waltemath
2021 Journal of Integrative Bioinformatics  
Modeling and EXchange (OMEX)-formatted archives.  ...  A standardized approach to annotating computational biomedical models and their associated files can facilitate model reuse and reproducibility among research groups, enhance search and retrieval of models  ...  Author contributions All authors (editors) have accepted responsibility for the entire content of this manuscript and approved of its submission.  ... 
doi:10.1515/jib-2021-0020 pmid:34668356 pmcid:PMC8560343 fatcat:2rzioyl35vhb7aswcj4yarcr2q

Open modeling and exchange (OMEX) metadata specification version 1.0

Maxwell L Neal, John H Gennari, Dagmar Waltemath, David P Nickerson, Matthias König
2020 Journal of Integrative Bioinformatics  
Modeling and EXchange (OMEX)-formatted archives.  ...  A standardized approach to annotating computational biomedical models and their associated files can facilitate model reuse and reproducibility among research groups, enhance search and retrieval of models  ...  Separation of annotations from models and data We recommend using separate RDF files to store all annotations associated with model and simulation protocol files within a COMBINE archive.  ... 
doi:10.1515/jib-2020-0020 pmid:32589606 fatcat:onmkf5jptjhihjcml25fxgbrsm

runBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats [article]

Bilal Shaikh, Gnaneswara Marupilla, Mike Wilson, Michael L Blinov, Ion I Moraru, Jonathan R Karr
2021 bioRxiv   pre-print
One promising way to achieve more predictive models is to combine submodels of multiple subsystems.  ...  To make these resources easier to use, we developed runBioSimulations (https://run.biosimulations.org), a single web application for executing a broad range of models. runBioSimulations leverages community  ...  Standardized simulation project (Simulation, reports & plots) SED-ML, COMBINE, OMEX a. Standardized models e.g., BGNL, SBML, SBML-fbc e.  ... 
doi:10.1101/2021.03.05.433787 fatcat:n4tcznroxvgcrjswpc4wb26tuy

Specifications of standards in systems and synthetic biology: status and developments in 2021

Falk Schreiber, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath
2021 Journal of Integrative Bioinformatics  
This document can also be consulted to identify the latest specifications of all COMBINE standards.  ...  OMEX Metadata specification Version 1.2.  ...  Acknowledgements: We thank all members of the COMBINE initiative for their help. DPN is supported by the National Institutes of Health [P41EB023912].  ... 
doi:10.1515/jib-2021-0026 pmid:34674411 pmcid:PMC8573232 fatcat:abs7qckeyfdeddd4x5z6g54ape

Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology

J. Kyle Medley, Kiri Choi, Matthias König, Lucian Smith, Stanley Gu, Joseph Hellerstein, Stuart C. Sealfon, Herbert M. Sauro, Andreas Prlic
2018 PLoS Computational Biology  
by 1) providing a notebook environment which allows models, Python code, and narrative to be intermixed, 2) supporting the COMBINE archive format during model development for capturing model information  ...  in an exchangeable format and 3) enabling users to easily simulate and edit public COMBINE-compliant models from public repositories to facilitate studying model dynamics, variants and test cases.  ...  Acknowledgments The authors wish to thank Frank Bergmann and Chris Myers for their help and guidance in diagnosing and fixing interoperability problems.  ... 
doi:10.1371/journal.pcbi.1006220 pmid:29906293 pmcid:PMC6021116 fatcat:oezetminsbcy3db42nbqfxocu4

SynBiopython: an open-source software library for Synthetic Biology

Jing Wui Yeoh, Neil Swainston, Peter Vegh, Valentin Zulkower, Pablo Carbonell, Maciej B Holowko, Gopal Peddinti, Chueh Loo Poh
2021 Synthetic Biology  
A number of tools will be integrated and developed that we envisage will become the obvious starting point for software development projects within biofoundries globally.  ...  In this paper, we present the first attempt at creating a standardised, open-source Python package.  ...  The Genbabel module was thus extended to provide the capability of generating SBML files and other formats related to modeling, such as SED-ML (14) and COMBINE archives in Open Modeling EXchange (OMEX  ... 
doi:10.1093/synbio/ysab001 fatcat:qmdjsahytzfahfm3bppcwjboyu

Tellurium Notebooks - An Environment for Dynamical Model Development, Reproducibility, and Reuse [article]

Kyle Medley, Kiri Choi, Matthias Konig, Lucian Smith, Stanley Gu, Joseph Hellerstein, Stuart Sealfon, Herbert M Sauro
2017 bioRxiv   pre-print
To address this problem, we have developed Tellurium Notebook, a software system that facilitates building reproducible dynamical models and reusing models by 1) supporting the COMBINE archive format during  ...  model development for capturing model information in an exchangeable format and 2) enabling users to easily simulate and edit public COMBINE-compliant models from public repositories to facilitate studying  ...  Using Tellurium to reproduce model variants in [36] and repackage as a COMBINE archive.  ... 
doi:10.1101/239004 fatcat:glirpeylszecln4q5jn6vgnrvm

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

Dagmar Waltemath, Martin Golebiewski, Michael L Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M Keating, Matthias König, Olga Krebs, Rahuman S Malik-Sheriff, David Nickerson (+7 others)
2020 Journal of Integrative Bioinformatics  
This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019.  ...  The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences.  ...  While a COMBINE Archive bundles all files related to a simulation study in a single package, other options for providing reproducible studies include Docker containers that ship the description of the  ... 
doi:10.1515/jib-2020-0005 pmid:32598315 pmcid:PMC7756615 fatcat:aza4gvbc7ja7lcpnxmldibfobm

Improving Collaboration by Standardization Efforts in Systems Biology

Andreas Dräger, Bernhard Ø. Palsson
2014 Frontiers in Bioengineering and Biotechnology  
Sufficient annotation and metadata of models, experiments, and other data enhance the reproducibility of biomedical ontologies; ODE, ordinary differential equation; OMEX, open modeling exchange format;  ...  , archive, as well as to rank models, and to describe execution and the outcomes of simulation experiments.  ...  Funding : This work was funded by a Marie Curie International Outgoing Fellowship within the European Commission's 7th Framework Program for Research and Technological Development (project AMBiCon, grant  ... 
doi:10.3389/fbioe.2014.00061 pmid:25538939 pmcid:PMC4259112 fatcat:yvsizmtklreanfa6oybwaifccm

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

Michael Hucka, David P. Nickerson, Gary D. Bader, Frank T. Bergmann, Jonathan Cooper, Emek Demir, Alan Garny, Martin Golebiewski, Chris J. Myers, Falk Schreiber, Dagmar Waltemath, Nicolas Le Novère
2015 Frontiers in Bioengineering and Biotechnology  
The Computational Modeling in Biology Network (COMBINE) is a consortium of groups involved in the development of open community standards and formats used in computational modeling in biology.  ...  Novère N (2015) Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative. Front. Bioeng. Biotechnol.  ...  This has already yielded benefits: we have recently developed the COMBINE archive, a format that fills the need for a simple, consistent way of bundling multiple files related to a modeling project 7 ;  ... 
doi:10.3389/fbioe.2015.00019 pmid:25759811 pmcid:PMC4338824 fatcat:xvaol22uj5cgdgwxwpiegluemi
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