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Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative

Hucka, Michael and Nickerson, David P. and Bader, Gary D. and Bergmann, Frank T. and Cooper, Jonathan and Demir, Emek and Gamy, Alan and Golebiewski, Martin and Myers, Chris J. and Schreiber, Falk and Waltemath, Dagmar and Le Novère, Nicolas (2015) Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative. Frontiers in Bioengineering and Biotechnology, 3 (2). Art. No. 19. ISSN 2296-4185. PMCID PMC4338824. https://resolver.caltech.edu/CaltechAUTHORS:20150317-083603133

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.3389/fbioe.2015.00019DOIArticle
http://journal.frontiersin.org/article/10.3389/fbioe.2015.00019/abstractPublisherArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338824/PubMed CentralArticle
ORCID:
AuthorORCID
Hucka, Michael0000-0001-9105-5960
Nickerson, David P.0000-0003-4667-9779
Bergmann, Frank T.0000-0001-5553-4702
Cooper, Jonathan0000-0001-6009-3542
Myers, Chris J.0000-0002-8762-8444
Waltemath, Dagmar0000-0002-5886-5563
Le Novère, Nicolas0000-0002-6309-7327
Additional Information:© 2015 Hucka, Nickerson, Bader, Bergmann, Cooper, Demir, Garny, Golebiewski, Myers, Schreiber, Waltemath and Le Novère. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Received: 10 November 2014; Accepted: 08 February 2015; Published online: 24 February 2015. Edited by: Steve McKeever, Uppsala University, Sweden. AG would like to thank the Asclepios team at Inria, France, for kindly hosting him. The authors also thank the reviewers for their helpful suggestions. Funding : DN and AG are supported by The Virtual Physiological Rat Project (NIHP50-GM094503). DN is also supported by the Maurice Wilkins Centre for Molecular Biodiversity. JC gratefully acknowledges research support from the “2020 Science” program funded through the EPSRC Cross-Disciplinary Interface Programme (EP/I017909/1) and supported by Microsoft Research. DW is funded through the Junior Research Group SEMS, BMBF e:Bio program, grant no. FKZ0316194. CM and SBOL are supported by the National Science Foundation under Grant Nos. DBI-1356041 and DBI-1355909. FB and MH are supported by NIH grant R01GM070923. FS is supported by BMBF grant FKZ0316181 and ARC grant DP140100077. NN is supported by the BBSRC Signalling Institute Strategic Programme (BBS/E/B/000C0419). Gis supported by the German Federal Ministry for Economic Affairs and Energy (BMWi) through the NormSys project (FKZ01FS14019) and by the German Federal Ministry of Education and Research (BMBF) through the Virtual Liver Network. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the US National Science Foundation or the US National Institutes of Health.
Funders:
Funding AgencyGrant Number
NIHP50-GM094503
Engineering and Physical Sciences Research Council (EPSRC)EP/1017909/1
Microsoft ResearchUNSPECIFIED
Junior Research Group SEMSUNSPECIFIED
Bundesministerium für Bildung und Forschung (BMBF)FKZ0316194
NSFDBI-1356041
NSFDBI-1355909
NIHR01GM070923
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/B/000C0419
Bundesministerium für Wirtschaft und Energie (BMWi)FKZ01FS14019
Subject Keywords:standardization, data sharing, reproducible science, computational modeling, biology, file formats
Issue or Number:2
PubMed Central ID:PMC4338824
Record Number:CaltechAUTHORS:20150317-083603133
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20150317-083603133
Official Citation:Hucka M, Nickerson DP, Bader GD, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D and Le Novère N (2015) Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative. Front. Bioeng. Biotechnol. 3:19. doi: 10.3389/fbioe.2015.00019
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:55828
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:17 Mar 2015 16:24
Last Modified:09 Mar 2020 13:19

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