Literature DB >> 24911500

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

Michal Galdzicki1, Kevin P Clancy2, Ernst Oberortner3, Matthew Pocock4, Jacqueline Y Quinn5, Cesar A Rodriguez5, Nicholas Roehner6, Mandy L Wilson7, Laura Adam7, J Christopher Anderson8, Bryan A Bartley9, Jacob Beal10, Deepak Chandran5, Joanna Chen11, Douglas Densmore3, Drew Endy12, Raik Grünberg13, Jennifer Hallinan4, Nathan J Hillson11, Jeffrey D Johnson14, Allan Kuchinsky15, Matthew Lux7, Goksel Misirli4, Jean Peccoud7, Hector A Plahar11, Evren Sirin16, Guy-Bart Stan17, Alan Villalobos18, Anil Wipat4, John H Gennari1, Chris J Myers19, Herbert M Sauro9.   

Abstract

The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.

Mesh:

Year:  2014        PMID: 24911500     DOI: 10.1038/nbt.2891

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


  33 in total

1.  Developer's and user's guide to Clotho v2.0 A software platform for the creation of synthetic biological systems.

Authors:  Bing Xia; Swapnil Bhatia; Ben Bubenheim; Maisam Dadgar; Douglas Densmore; J Christopher Anderson
Journal:  Methods Enzymol       Date:  2011       Impact factor: 1.600

2.  j5 DNA assembly design automation software.

Authors:  Nathan J Hillson; Rafael D Rosengarten; Jay D Keasling
Journal:  ACS Synth Biol       Date:  2011-12-20       Impact factor: 5.110

3.  Improved tools for biological sequence comparison.

Authors:  W R Pearson; D J Lipman
Journal:  Proc Natl Acad Sci U S A       Date:  1988-04       Impact factor: 11.205

4.  Evolution of the Sequence Ontology terms and relationships.

Authors:  Christopher J Mungall; Colin Batchelor; Karen Eilbeck
Journal:  J Biomed Inform       Date:  2010-03-10       Impact factor: 6.317

5.  Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

Authors:  Timothy S Ham; Zinovii Dmytriv; Hector Plahar; Joanna Chen; Nathan J Hillson; Jay D Keasling
Journal:  Nucleic Acids Res       Date:  2012-06-19       Impact factor: 16.971

6.  The BioPAX community standard for pathway data sharing.

Authors:  Emek Demir; Michael P Cary; Suzanne Paley; Ken Fukuda; Christian Lemer; Imre Vastrik; Guanming Wu; Peter D'Eustachio; Carl Schaefer; Joanne Luciano; Frank Schacherer; Irma Martinez-Flores; Zhenjun Hu; Veronica Jimenez-Jacinto; Geeta Joshi-Tope; Kumaran Kandasamy; Alejandra C Lopez-Fuentes; Huaiyu Mi; Elgar Pichler; Igor Rodchenkov; Andrea Splendiani; Sasha Tkachev; Jeremy Zucker; Gopal Gopinath; Harsha Rajasimha; Ranjani Ramakrishnan; Imran Shah; Mustafa Syed; Nadia Anwar; Ozgün Babur; Michael Blinov; Erik Brauner; Dan Corwin; Sylva Donaldson; Frank Gibbons; Robert Goldberg; Peter Hornbeck; Augustin Luna; Peter Murray-Rust; Eric Neumann; Oliver Ruebenacker; Oliver Reubenacker; Matthias Samwald; Martijn van Iersel; Sarala Wimalaratne; Keith Allen; Burk Braun; Michelle Whirl-Carrillo; Kei-Hoi Cheung; Kam Dahlquist; Andrew Finney; Marc Gillespie; Elizabeth Glass; Li Gong; Robin Haw; Michael Honig; Olivier Hubaut; David Kane; Shiva Krupa; Martina Kutmon; Julie Leonard; Debbie Marks; David Merberg; Victoria Petri; Alex Pico; Dean Ravenscroft; Liya Ren; Nigam Shah; Margot Sunshine; Rebecca Tang; Ryan Whaley; Stan Letovksy; Kenneth H Buetow; Andrey Rzhetsky; Vincent Schachter; Bruno S Sobral; Ugur Dogrusoz; Shannon McWeeney; Mirit Aladjem; Ewan Birney; Julio Collado-Vides; Susumu Goto; Michael Hucka; Nicolas Le Novère; Natalia Maltsev; Akhilesh Pandey; Paul Thomas; Edgar Wingender; Peter D Karp; Chris Sander; Gary D Bader
Journal:  Nat Biotechnol       Date:  2010-09-09       Impact factor: 54.908

7.  Standard biological parts knowledgebase.

Authors:  Michal Galdzicki; Cesar Rodriguez; Deepak Chandran; Herbert M Sauro; John H Gennari
Journal:  PLoS One       Date:  2011-02-24       Impact factor: 3.240

8.  BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.

Authors:  Nicolas Le Novère; Benjamin Bornstein; Alexander Broicher; Mélanie Courtot; Marco Donizelli; Harish Dharuri; Lu Li; Herbert Sauro; Maria Schilstra; Bruce Shapiro; Jacky L Snoep; Michael Hucka
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

9.  Gene Designer: a synthetic biology tool for constructing artificial DNA segments.

Authors:  Alan Villalobos; Jon E Ness; Claes Gustafsson; Jeremy Minshull; Sridhar Govindarajan
Journal:  BMC Bioinformatics       Date:  2006-06-06       Impact factor: 3.169

10.  TinkerCell: modular CAD tool for synthetic biology.

Authors:  Deepak Chandran; Frank T Bergmann; Herbert M Sauro
Journal:  J Biol Eng       Date:  2009-10-29       Impact factor: 4.355

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  66 in total

1.  GMO Genetic Elements Thesaurus (GMO-GET): a controlled vocabulary for the consensus designation of introduced or modified genetic elements in genetically modified organisms.

Authors:  Paulien Adamse; Emilie Dagand; Karen Bohmert-Tatarev; Daniela Wahler; Manoela Miranda; Esther J Kok; Joachim Bendiek
Journal:  BMC Bioinformatics       Date:  2021-02-05       Impact factor: 3.169

2.  Intellectual property issues and synthetic biology standards.

Authors:  Jorge L Contreras; Arti K Rai; Andrew W Torrance
Journal:  Nat Biotechnol       Date:  2015-01       Impact factor: 54.908

3.  Reply to Intellectual property issues and synthetic biology standards.

Authors:  Michal Galdzicki; Linda J Kahl; Drew Endy; Herbert M Sauro
Journal:  Nat Biotechnol       Date:  2015-01       Impact factor: 54.908

Review 4.  Design Automation in Synthetic Biology.

Authors:  Evan Appleton; Curtis Madsen; Nicholas Roehner; Douglas Densmore
Journal:  Cold Spring Harb Perspect Biol       Date:  2017-04-03       Impact factor: 10.005

5.  Open-source, community-driven microfluidics with Metafluidics.

Authors:  David S Kong; Todd A Thorsen; Jonathan Babb; Scott T Wick; Jeremy J Gam; Ron Weiss; Peter A Carr
Journal:  Nat Biotechnol       Date:  2017-06-07       Impact factor: 54.908

Review 6.  The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable.

Authors:  David Nickerson; Koray Atalag; Bernard de Bono; Jörg Geiger; Carole Goble; Susanne Hollmann; Joachim Lonien; Wolfgang Müller; Babette Regierer; Natalie J Stanford; Martin Golebiewski; Peter Hunter
Journal:  Interface Focus       Date:  2016-04-06       Impact factor: 3.906

7.  Living factories of the future.

Authors:  Michael Eisenstein
Journal:  Nature       Date:  2016-03-17       Impact factor: 49.962

Review 8.  Advanced genetic tools enable synthetic biology in the oleaginous microalgae Nannochloropsis sp.

Authors:  Eric Poliner; Eva M Farré; Christoph Benning
Journal:  Plant Cell Rep       Date:  2018-03-06       Impact factor: 4.570

9.  Genetic Engineering of Bee Gut Microbiome Bacteria with a Toolkit for Modular Assembly of Broad-Host-Range Plasmids.

Authors:  Sean P Leonard; Jiri Perutka; J Elijah Powell; Peng Geng; Darby D Richhart; Michelle Byrom; Shaunak Kar; Bryan W Davies; Andrew D Ellington; Nancy A Moran; Jeffrey E Barrick
Journal:  ACS Synth Biol       Date:  2018-04-13       Impact factor: 5.110

10.  Guidelines for Reproducibly Building and Simulating Systems Biology Models.

Authors:  J Kyle Medley; Arthur P Goldberg; Jonathan R Karr
Journal:  IEEE Trans Biomed Eng       Date:  2016-07-18       Impact factor: 4.538

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