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Curated Papers > High-impact authoritative literature on "Synthetic Biology"

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

Literature Information ​

DOI10.1038/nbt.2891
PMID24911500
JournalNature biotechnology
Impact Factor41.7
JCR QuartileQ1
Publication Year2014
Times Cited89
KeywordsSynthetic Biology Open Language, data standard, design exchange
Literature TypeJournal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S.
ISSN1087-0156
Pages545-50
Issue32(6)
AuthorsMichal Galdzicki, Kevin P Clancy, Ernst Oberortner, Matthew Pocock, Jacqueline Y Quinn, Cesar A Rodriguez, Nicholas Roehner, Mandy L Wilson, Laura Adam, J Christopher Anderson, Bryan A Bartley, Jacob Beal, Deepak Chandran, Joanna Chen, Douglas Densmore, Drew Endy, Raik Grünberg, Jennifer Hallinan, Nathan J Hillson, Jeffrey D Johnson, Allan Kuchinsky, Matthew Lux, Goksel Misirli, Jean Peccoud, Hector A Plahar, Evren Sirin, Guy-Bart Stan, Alan Villalobos, Anil Wipat, John H Gennari, Chris J Myers, Herbert M Sauro

TL;DR ​

This study introduces the Synthetic Biology Open Language (SBOL), a community-driven data standard designed to facilitate the exchange of synthetic biology designs among researchers, software tools, and commercial providers. The implementation of SBOL as an XML/RDF serialization has already demonstrated its effectiveness in enhancing information exchange, highlighting its potential to advance synthetic biology from a research field to a more structured engineering discipline.

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Synthetic Biology Open Language · data standard · design exchange

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.

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Primary Questions Addressed ​

  1. How does SBOL facilitate collaboration between academic and industrial partners in synthetic biology?
  2. What specific capabilities are expected to be added to SBOL as synthetic biology continues to evolve?
  3. In what ways can SBOL improve the re-use of validated designs in synthetic biology projects?
  4. How do the XML/RDF serialization formats used in SBOL enhance interoperability among different software tools?
  5. What challenges have been encountered in the adoption of SBOL within the synthetic biology community?

Key Findings ​

1. Research Background and Purpose ​

Synthetic biology is rapidly transitioning from a primarily research-focused discipline to a robust engineering practice. A significant challenge in this transition is the need for effective communication and reuse of validated designs. The lack of standardized methods for sharing biological designs hampers collaboration and innovation within the community. The primary purpose of this study is to introduce the Synthetic Biology Open Language (SBOL), a proposed community standard aimed at facilitating the exchange of synthetic biology designs among researchers, software tools, and commercial providers. By establishing a formalized format for design representation, SBOL seeks to enhance interoperability and support the ongoing evolution of synthetic biology practices.

2. Main Methods and Findings ​

The authors detail the development and implementation of SBOL as an XML/RDF serialization, which is designed to standardize how synthetic biology designs are communicated. The SBOL Developers Group has created software libraries and specification documentation to assist developers in incorporating SBOL into their applications. Early successes include demonstrations showcasing SBOL's effectiveness in facilitating information exchange across diverse software tools and repositories, involving both academic and commercial partners. The collaborative nature of the SBOL initiative allows for its adaptation and refinement in response to the changing landscape of synthetic biology.

3. Core Conclusions ​

The introduction of SBOL marks a significant step towards standardizing communication within the synthetic biology community. By providing a formalized, community-driven framework for design representation, SBOL not only enhances the capacity for design reuse but also streamlines collaboration across different platforms and stakeholders. The successful early implementations of SBOL demonstrate its potential to bridge gaps between various software tools and research entities, reinforcing its role as a vital resource for the synthetic biology field.

4. Research Significance and Impact ​

The significance of this research lies in its potential to transform the practice of synthetic biology into a more cohesive engineering discipline. By facilitating the sharing of validated designs, SBOL promotes collaboration and accelerates innovation, ultimately leading to more efficient and reliable synthetic biology applications. As the standard evolves with the field, it will likely address specific needs across various aspects of the synthetic biology workflow, thereby enhancing the overall productivity and effectiveness of the community. The establishment of SBOL may also inspire similar initiatives in other scientific domains, fostering a culture of standardization and interoperability that drives progress in scientific research and engineering as a whole.

References ​

  1. TinkerCell: modular CAD tool for synthetic biology. - Deepak Chandran;Frank T Bergmann;Herbert M Sauro - Journal of biological engineering (2009)
  2. CellML: its future, present and past. - Catherine M Lloyd;Matt D B Halstead;Poul F Nielsen - Progress in biophysics and molecular biology (2004)
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Literatures Citing This Work ​

  1. Parts & pools: a framework for modular design of synthetic gene circuits. - Mario Andrea Marchisio - Frontiers in bioengineering and biotechnology (2014)
  2. SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities. - Esteban Martínez-García;Tomás Aparicio;Angel Goñi-Moreno;Sofía Fraile;Víctor de Lorenzo - Nucleic acids research (2015)
  3. BioModels: ten-year anniversary. - Vijayalakshmi Chelliah;Nick Juty;Ishan Ajmera;Raza Ali;Marine Dumousseau;Mihai Glont;Michael Hucka;Gaël Jalowicki;Sarah Keating;Vincent Knight-Schrijver;Audald Lloret-Villas;Kedar Nath Natarajan;Jean-Baptiste Pettit;Nicolas Rodriguez;Michael Schubert;Sarala M Wimalaratne;Yangyang Zhao;Henning Hermjakob;Nicolas Le Novère;Camille Laibe - Nucleic acids research (2015)
  4. Community-driven development for computational biology at Sprints, Hackathons and Codefests. - Steffen Möller;Enis Afgan;Michael Banck;Raoul J P Bonnal;Timothy Booth;John Chilton;Peter J A Cock;Markus Gumbel;Nomi Harris;Richard Holland;Matúš Kalaš;László Kaján;Eri Kibukawa;David R Powel;Pjotr Prins;Jacqueline Quinn;Olivier Sallou;Francesco Strozzi;Torsten Seemann;Clare Sloggett;Stian Soiland-Reyes;William Spooner;Sascha Steinbiss;Andreas Tille;Anthony J Travis;Roman Guimera;Toshiaki Katayama;Brad A Chapman - BMC bioinformatics (2014)
  5. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. - Frank T Bergmann;Richard Adams;Stuart Moodie;Jonathan Cooper;Mihai Glont;Martin Golebiewski;Michael Hucka;Camille Laibe;Andrew K Miller;David P Nickerson;Brett G Olivier;Nicolas Rodriguez;Herbert M Sauro;Martin Scharm;Stian Soiland-Reyes;Dagmar Waltemath;Florent Yvon;Nicolas Le Novère - BMC bioinformatics (2014)
  6. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. - Andrew Currin;Neil Swainston;Philip J Day;Douglas B Kell - Chemical Society reviews (2015)
  7. Developments in the tools and methodologies of synthetic biology. - Richard Kelwick;James T MacDonald;Alexander J Webb;Paul Freemont - Frontiers in bioengineering and biotechnology (2014)
  8. Improving collaboration by standardization efforts in systems biology. - Andreas Dräger;Bernhard Ø Palsson - Frontiers in bioengineering and biotechnology (2014)
  9. Intellectual property issues and synthetic biology standards. - Jorge L Contreras;Arti K Rai;Andrew W Torrance - Nature biotechnology (2015)
  10. Reply to Intellectual property issues and synthetic biology standards. - Michal Galdzicki;Linda J Kahl;Drew Endy;Herbert M Sauro - Nature biotechnology (2015)

... (79 more literatures)

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