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

Frontiers in Bioengineering and Biotechnology
Michael HuckaNicolas Le Novère

Abstract

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. COMBINE's aim is to act as a coordinator, facilitator, and resource for different standardization efforts whose domains of use cover related areas of the computational biology space. In this perspective article, we summarize COMBINE, its general organization, and the community standards and other efforts involved in it. Our goals are to help guide readers toward standards that may be suitable for their research activities, as well as to direct interested readers to relevant communities where they can best expect to receive assistance in how to develop interoperable computational models.

References

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Citations

Jan 3, 2016·Journal of Biotechnology·Rafael S CostaSusana Vinga
May 10, 2011·PLoS Computational Biology·Dagmar WaltemathNicolas Le Novère
Jul 13, 2016·Journal of Biomedical Semantics·Martin ScharmOlaf Wolkenhauer
Jun 14, 2016·IEEE Transactions on Bio-medical Engineering·Dagmar Waltemath, Olaf Wolkenhauer
Apr 6, 2016·IEEE Transactions on Bio-medical Engineering·Robert A McDougalWilliam W Lytton
Jun 16, 2016·IEEE Transactions on Bio-medical Engineering·Dagmar WaltemathFalk Schreiber
Jul 19, 2016·IEEE Transactions on Bio-medical Engineering·J Kyle MedleyJonathan R Karr
Dec 4, 2015·PLoS Biology·Jacqueline Y QuinnHerbert M Sauro
Jan 4, 2017·Bioinformatics·Frank T BergmannMartin Scharm
Dec 7, 2016·BMC Bioinformatics·Vasundra TouréCharles Auffray
Mar 30, 2018·Journal of Integrative Bioinformatics·Falk SchreiberDagmar Waltemath
Jan 8, 2019·Journal of Experimental Botany·Andrew J MillarTomasz Zielinski
Nov 22, 2018·Briefings in Bioinformatics·Maxwell Lewis NealDagmar Waltemath
Apr 24, 2015·Journal of Biomedical Semantics·Rebekka AlmRon Henkel
Dec 25, 2015·Molecular Systems Biology·Natalie J StanfordCarole Goble
Jun 18, 2017·Biochemical Society Transactions·Chris J MyersZach Zundel
Apr 6, 2016·BMC Bioinformatics·Nicolas RodriguezNicolas Le Novère
Jul 17, 2016·BMC Systems Biology·Joanna LewisJonathan Cooper
Jul 14, 2019·Journal of Integrative Bioinformatics·Falk SchreiberDagmar Waltemath
Jul 1, 2020·Journal of Integrative Bioinformatics·Dagmar WaltemathChris J Myers
Jul 1, 2020·Journal of Integrative Bioinformatics·Falk SchreiberDagmar Waltemath
Jan 25, 2019·Journal of Biological Engineering·Kealan ExleyRichard Ian Kitney
Feb 6, 2020·Nature Communications·Bryan A BartleyElizabeth A Strychalski
Sep 4, 2015·Journal of Biological Research·Vasileios LapatasMaria Victoria Schneider
Aug 28, 2020·Molecular Systems Biology·Sarah M KeatingUNKNOWN SBML Level 3 Community members
Jul 13, 2018·Frontiers in Neuroinformatics·Nisha A ViswanUpinder S Bhalla
Mar 5, 2021·Network and Systems Medicine·Massimiliano ZaninHarald H H W Schmidt

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Software Mentioned

SBOL
SBGN
SBML
CellML
COMBINE NEtwork
MathML
Physiome
Path2Models
KiSAO
COMBINE

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