Standardization in synthetic biology.

Synthetic Biology is founded on the idea that complex biological systems are built most effectively when the task is divided in abstracted layers and all required components are readily available and well-described. This requires interdisciplinary collaboration at several levels and a common understanding of the functioning of each component. Standardization of the physical composition and the description of each part is required as well as a controlled vocabulary to aid design and ensure interoperability. Here, we describe standardization initiatives from several disciplines, which can contribute to Synthetic Biology. We provide examples of the concerted standardization efforts of the BioBricks Foundation comprising the request for comments (RFC) and the Registry of Standardized Biological parts as well as the international Genetically Engineered Machine (iGEM) competition.

[1]  Adam Arkin,et al.  Setting the standard in synthetic biology , 2008, Nature Biotechnology.

[2]  E. Andrianantoandro,et al.  Synthetic biology: new engineering rules for an emerging discipline , 2006, Molecular systems biology.

[3]  Samik Ghosh,et al.  Consistent design schematics for biological systems: standardization of representation in biological engineering , 2009, Journal of The Royal Society Interface.

[4]  Nigel W. Hardy,et al.  Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations” (MIBBI) workshop , 2010, Standards in genomic sciences.

[5]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[6]  D. Schwarzenbach Acta Crystallographica Section A: Foundations of Crystallography , 2005 .

[7]  D. Endy,et al.  Refinement and standardization of synthetic biological parts and devices , 2008, Nature Biotechnology.

[8]  J. Boyle,et al.  Synthetic Biology: Caught between Property Rights, the Public Domain, and the Commons , 2007, PLoS biology.

[9]  Raik Grünberg,et al.  Fusion Protein (Freiburg) Biobrick assembly standard , 2009 .

[10]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[11]  Patrick Lambrix,et al.  A review of standards for data exchange within systems biology , 2007, Proteomics.

[12]  Chris F. Taylor,et al.  Guidelines for reporting the use of gel electrophoresis in proteomics , 2008, Nature Biotechnology.

[13]  Johann Joets,et al.  Guidelines for reporting the use of gel image informatics in proteomics , 2010, Nature Biotechnology.

[14]  Matthew W. Lux,et al.  Essential information for synthetic DNA sequences , 2011, Nature Biotechnology.

[15]  Chris F. Taylor,et al.  Guidelines for reporting the use of capillary electrophoresis in proteomics , 2010, Nature Biotechnology.

[16]  Raik Grunberg,et al.  BBF RFC 30: Draft of an RDF-based framework for the exchange and integration of Synthetic Biology data , 2009 .

[17]  Daniel Auerbach,et al.  The N-end rule pathway is mediated by a complex of the RING-type Ubr1 and HECT-type Ufd4 ubiquitin ligases , 2010, Nature Cell Biology.

[18]  John Quackenbush,et al.  Data reporting standards: making the things we use better , 2009, Genome Medicine.

[19]  W Szybalski,et al.  Nobel prizes and restriction enzymes. , 1978, Gene.

[20]  Kei-Hoi Cheung,et al.  BioPAX – A community standard for pathway data sharing , 2010, Nature Biotechnology.

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

[22]  Lennart Martens,et al.  The PSI formal document process and its implementation on the PSI website , 2007, Proteomics.

[23]  Peter Woollard,et al.  The minimum information required for reporting a molecular interaction experiment (MIMIx) , 2007, Nature Biotechnology.

[24]  Hamid Mirzaei,et al.  Guidelines for reporting the use of column chromatography in proteomics , 2010, Nature Biotechnology.

[25]  Lennart Martens,et al.  The minimum information about a proteomics experiment (MIAPE) , 2007, Nature Biotechnology.

[26]  H. Sauro,et al.  Standard Biological Parts Knowledgebase , 2011, PloS one.

[27]  Bruno J. Strasser,et al.  GenBank--Natural History in the 21st Century? , 2008, Science.

[28]  Chris F. Taylor,et al.  Guidelines for reporting the use of mass spectrometry in proteomics , 2008, Nature Biotechnology.

[29]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[30]  Thomas Reiss,et al.  Making the most of synthetic biology , 2009, EMBO reports.

[31]  George M Church From systems biology to synthetic biology , 2005, Molecular systems biology.

[32]  Thomas F. Knight,et al.  Idempotent Vector Design for Standard Assembly of Biobricks , 2003 .

[33]  Paul S. Freemont,et al.  Computational design approaches and tools for synthetic biology. , 2011, Integrative biology : quantitative biosciences from nano to macro.

[34]  D. Moher,et al.  CONSORT 2010 statement: Updated guidelines for reporting parallel group randomised trials , 2010, Journal of pharmacology & pharmacotherapeutics.

[35]  Kristian M Müller,et al.  Structural perturbation and compensation by directed evolution at physiological temperature leads to thermostabilization of beta-lactamase. , 2005, Biochemistry.