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. Author manuscript; available in PMC: 2017 May 15.
Published in final edited form as: J Integr Bioinform. 2015 Sep 4;12(2):258. doi: 10.2390/biecoll-jib-2015-258

Specifications of Standards in Systems and Synthetic Biology

Falk Schreiber 1,*, Gary D Bader 2, Martin Golebiewski 3, Michael Hucka 4, Benjamin Kormeier 5, Nicolas Le Novère 6, Chris Myers 7, David Nickerson 8, Björn Sommer 9, Dagmar Waltemath 10, Stephan Weise 11
PMCID: PMC5431569  NIHMSID: NIHMS859655  PMID: 26528556

Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic benefits, such as making information exchange, production, and services more efficient. However, novel, innovative areas often either lack proper standards, or documents about standards in these areas are not available from a centralised platform or formal body (such as the International Standardisation Organisation).

Systems and synthetic biology is a relatively novel area, and it is only in the last decade that the standardisation of data, information, and models related to systems and synthetic biology has become a community-wide effort. Several open standards have been established and are under continuous development as a community initiative. COMBINE, the ‘COmputational Modeling in BIology’ NEtwork [1] has been established as an umbrella initiative to coordinate and promote the development of the various community standards and formats for computational models. There are yearly two meeting, HARMONY (Hackathons on Resources for Modeling in Biology), Hackathon-type meetings with a focus on development of the support for standards, and COMBINE forums, workshop-style events with oral presentations, discussion, poster, and breakout sessions for further developing the standards. For more information see http://co.mbine.org/.

So far the different standards were published and made accessible through the standards’ web-pages or preprint services. The aim of this special issue is to provide a single, easily accessible and citable platform for the publication of standards in systems and synthetic biology. This special issue is intended to serve as a central access point to standards and related initiatives in systems and synthetic biology, it will be published annually to provide an opportunity for standard development groups to communicate updated specifications.

COMBINE standards covered in this special issue are:

  • CellML [2] to store and exchange computer-based mathematical models in a modular and reusable manner. In addition, the specification for the CellML Metadata Framework is provided.

  • COMBINE Archive Specification [3] to support the exchange of information necessary for a modeling and simulation experiment in biology. It is a zip-compressed container that includes a manifest file, an optional metadata file, and the files describing the model.

  • SED-ML [4] (the Simulation Experiment Description Markup Language) to describe the procedures to analyse and simulate models, including model identification, pre-processing, simulation setup, post-processing of simulation result and presentation thereof.

  • SBGN [5] (the Systems Biology Graphical Notation) to graphically represent processes and networks studied in systems biology. The specifications of the three SBGN languages SBGN Process Description, SBGN Entity Relationship, and SBGN Activity Flow are provided, and these languages allow the representation of different aspects of biological systems at different levels of detail as graphical maps.

  • SBML [6] (Systems Biology Markup Language) to represent and exchange computational models in systems biology such as models of metabolism, signal transduction and gene regulation. In addition to the specifications for SBML Level 2 and the core of Level 3, this issue includes the specifications for the following extensions to Level 3 (known as “packages” in SBML): Flux Balance Constraints, Hierarchical Model Composition, Qualitative Models, and Layout.1

  • SBOL [7] (Synthetic Biology Open Language) to exchange data about synthetic biology designs including both structural information, such as hierarchically annotated DNA, RNA, and protein sequences for design components, and behavioral information, such as the interactions between these components.

No doubt, standards are necessary to ensure exchange, interpretation and reproducibility of scientific results. Access to their definitions is equally important. We hope that this special issue will help to increase the adoption and use of standards in systems and synthetic biology, and thereby support the exchange, distribution, and archiving of models.

Footnotes

1

SBML “packages” are extensions to SBML Level 3 only.

GB, MG, MH, NLN, CM, DN, FS and DW are COMBINE coordinators; BS, BK, SW and FS compiled the special issue.

Contact the COMBINE coordinators under combine-coord@googlegroups.com

References

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