title: Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative.
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.
authors.affiliation: Computing and Mathematical Sciences, California Institute of Technology , Pasadena, CA , USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Hucka
authors.affiliation: Auckland Bioengineering Institute, University of Auckland , Auckland , New Zealand.
authors.forename: David P
authors.initials: DP
authors.lastname: Nickerson
authors.affiliation: The Donnelly Centre, University of Toronto , Toronto, ON , Canada.
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bader
authors.affiliation: Computing and Mathematical Sciences, California Institute of Technology , Pasadena, CA , USA ; BioQuant/Centre for Organismal Studies (COS), University of Heidelberg , Heidelberg , Germany.
authors.forename: Frank T
authors.initials: FT
authors.lastname: Bergmann
authors.affiliation: Department of Computer Science, University of Oxford , Oxford , UK.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Cooper
authors.affiliation: Computational Biology, Memorial Sloan-Kettering Cancer Center , New York, NY , USA.
authors.forename: Emek
authors.initials: E
authors.lastname: Demir
authors.affiliation: Auckland Bioengineering Institute, University of Auckland , Auckland , New Zealand.
authors.forename: Alan
authors.initials: A
authors.lastname: Garny
authors.affiliation: Scientific Databases and Visualization, Heidelberg Institute for Theoretical Studies (HITS) , Heidelberg , Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Golebiewski
authors.affiliation: Department of Electrical and Computer Engineering, University of Utah , Salt Lake City, UT , USA.
authors.forename: Chris J
authors.initials: CJ
authors.lastname: Myers
authors.affiliation: Faculty of Information Technology, Monash University , Melbourne, VIC , Australia ; Institute of Computer Science, University Halle-Wittenberg , Halle , Germany.
authors.forename: Falk
authors.initials: F
authors.lastname: Schreiber
authors.affiliation: Department of Systems Biology and Bioinformatics, University of Rostock , Rostock , Germany.
authors.forename: Dagmar
authors.initials: D
authors.lastname: Waltemath
authors.affiliation: Babraham Institute , Cambridge , UK ; European Molecular Biology Laboratory-European Bioinformatics Institute , Cambridge , UK.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Le Novère
keywords: biology; computational modeling; data sharing; file formats; reproducible science; standardization