Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017

Abstract Standards are essential to the advancement of Systems and Synthetic Biology. COMBINE provides a formal body and a centralised platform to help develop and disseminate relevant standards and related resources. The regular special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards by providing unified, easily citable access. This paper provides an overview of existing COMBINE standards and presents developments of the last year.

[1]  Michael L. Hines,et al.  NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail , 2010, PLoS Comput. Biol..

[2]  Gary D Bader,et al.  BioPAX – A community standard for pathway data sharing , 2010, Nature Biotechnology.

[3]  Nicolas Le Novère,et al.  Identifiers.org and MIRIAM Registry: community resources to provide persistent identification , 2011, Nucleic Acids Res..

[4]  Carole Goble,et al.  The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable , 2016, Interface Focus.

[5]  Gary D. Bader,et al.  A brief history of COMBINE , 2017, 2017 Winter Simulation Conference (WSC).

[6]  Fengkai Zhang,et al.  SBML Level 3 package: Multistate, Multicomponent and Multicompartment Species, Version 1, Release 1 , 2018, J. Integr. Bioinform..

[7]  Allan Kuchinsky,et al.  The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology , 2014, Nature Biotechnology.

[8]  Chris J. Myers,et al.  The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core , 2018, J. Integr. Bioinform..

[9]  Aurélien Naldi,et al.  The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1 , 2015, J. Integr. Bioinform..

[10]  Gary D. Bader,et al.  Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative , 2015, Front. Bioeng. Biotechnol..

[11]  Gary D. Bader,et al.  Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016 , 2016, J. Integr. Bioinform..

[12]  Sven Sahle,et al.  The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core , 2015, J. Integr. Bioinform..

[13]  Nicolas Le Novère,et al.  COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project , 2014, BMC Bioinformatics.

[14]  Peter J. Hunter,et al.  The CellML 1.1 Specification , 2015, J. Integr. Bioinform..

[15]  Chris J. Myers,et al.  Toward community standards and software for whole-cell modeling , 2016, IEEE Transactions on Biomedical Engineering.

[16]  Sven Sahle,et al.  SBML Level 3 package: Render, Version 1, Release 1 , 2018, J. Integr. Bioinform..

[17]  Frank T. Bergmann,et al.  SBML Level 3 Package: Flux Balance Constraints version 2 , 2018, J. Integr. Bioinform..

[18]  Sarala M. Wimalaratne,et al.  The Systems Biology Graphical Notation , 2009, Nature Biotechnology.

[19]  Nicolas Le Novère,et al.  Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2 , 2015, Journal of integrative bioinformatics.

[20]  Chris J. Myers,et al.  Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE) , 2011, Standards in Genomic Sciences.

[21]  Carole Goble,et al.  The evolution of standards and data management practices in systems biology , 2015, Molecular systems biology.

[22]  Dagmar Waltemath,et al.  A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos , 2016, F1000Research.

[23]  Nicolas Le Novère,et al.  Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3 , 2011, J. Integr. Bioinform..

[24]  Peter J. Hunter,et al.  The CellML Metadata Framework 2.0 Specification , 2015, J. Integr. Bioinform..

[25]  Jacky L. Snoep,et al.  Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language , 2011, BMC Systems Biology.

[26]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[27]  Nicolas Le Novère,et al.  COMBINE Archive Specification Version 1 , 2015, J. Integr. Bioinform..

[28]  Michel Dumontier,et al.  Controlled vocabularies and semantics in systems biology , 2011, Molecular systems biology.

[29]  Gary D. Bader,et al.  Specifications of Standards in Systems and Synthetic Biology , 2015, J. Integr. Bioinform..

[30]  Robert C. Cannon,et al.  LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2 , 2014, Front. Neuroinform..

[31]  Jacob Beal,et al.  Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0 , 2018, J. Integr. Bioinform..

[32]  Peter J. Hunter,et al.  An Overview of CellML 1.1, a Biological Model Description Language , 2003, Simul..

[33]  Chris J. Myers,et al.  The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2 , 2018, J. Integr. Bioinform..

[34]  Dagmar Waltemath,et al.  Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3) , 2015, J. Integr. Bioinform..

[35]  Yukiko Matsuoka,et al.  Software support for SBGN maps: SBGN-ML and LibSBGN , 2012, Bioinform..

[36]  Zhen Zhang,et al.  Synthetic Biology Open Language (SBOL) Version 2.2.0 , 2018, J. Integr. Bioinform..

[37]  Michael Hucka,et al.  SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3 , 2015, Journal of integrative bioinformatics.

[38]  David D Evans,et al.  Major U.S. Cities Using National Standard Fire Hydrants, One Century After the Great Baltimore Fire. | NIST , 2004 .

[39]  Nicolas Le Novère,et al.  Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2 , 2015, J. Integr. Bioinform..

[40]  Michael Hucka,et al.  SBML Level 3 package: Groups, Version 1 Release 1 , 2016, J. Integr. Bioinform..