Literature DB >> 29316788

SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology.

James Alastair McLaughlin1, Chris J Myers2, Zach Zundel2, Göksel Mısırlı3, Michael Zhang2, Irina Dana Ofiteru4, Angel Goñi-Moreno1, Anil Wipat1.   

Abstract

The SynBioHub repository ( https://synbiohub.org ) is an open-source software project that facilitates the sharing of information about engineered biological systems. SynBioHub provides computational access for software and data integration, and a graphical user interface that enables users to search for and share designs in a Web browser. By connecting to relevant repositories (e.g., the iGEM repository, JBEI ICE, and other instances of SynBioHub), the software allows users to browse, upload, and download data in various standard formats, regardless of their location or representation. SynBioHub also provides a central reference point for other resources to link to, delivering design information in a standardized format using the Synthetic Biology Open Language (SBOL). The adoption and use of SynBioHub, a community-driven effort, has the potential to overcome the reproducibility challenge across laboratories by helping to address the current lack of information about published designs.

Keywords:  SBOL; Synthetic Biology Open Language; data standards; database; repository; sharing; web of registries

Mesh:

Year:  2018        PMID: 29316788     DOI: 10.1021/acssynbio.7b00403

Source DB:  PubMed          Journal:  ACS Synth Biol        ISSN: 2161-5063            Impact factor:   5.110


  21 in total

1.  Setting Up an Automated Biomanufacturing Laboratory.

Authors:  Marilene Pavan
Journal:  Methods Mol Biol       Date:  2021

2.  Standardizing Automated DNA Assembly: Best Practices, Metrics, and Protocols Using Robots.

Authors:  David I Walsh; Marilene Pavan; Luis Ortiz; Scott Wick; Johanna Bobrow; Nicholas J Guido; Sarah Leinicke; Dany Fu; Shreya Pandit; Lucy Qin; Peter A Carr; Douglas Densmore
Journal:  SLAS Technol       Date:  2019-02-15       Impact factor: 3.047

3.  BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks.

Authors:  Paul F Lang; Yassmine Chebaro; Xiaoyue Zheng; John A P Sekar; Bilal Shaikh; Darren A Natale; Jonathan R Karr
Journal:  Genome Biol       Date:  2020-05-18       Impact factor: 13.583

4.  Better research by efficient sharing: evaluation of free management platforms for synthetic biology designs.

Authors:  Uriel Urquiza-García; Tomasz Zieliński; Andrew J Millar
Journal:  Synth Biol (Oxf)       Date:  2019-06-20

Review 5.  Organizing genome engineering for the gigabase scale.

Authors:  Bryan A Bartley; Jacob Beal; Jonathan R Karr; Elizabeth A Strychalski
Journal:  Nat Commun       Date:  2020-02-04       Impact factor: 14.919

6.  BioModels-15 years of sharing computational models in life science.

Authors:  Rahuman S Malik-Sheriff; Mihai Glont; Tung V N Nguyen; Krishna Tiwari; Matthew G Roberts; Ashley Xavier; Manh T Vu; Jinghao Men; Matthieu Maire; Sarubini Kananathan; Emma L Fairbanks; Johannes P Meyer; Chinmay Arankalle; Thawfeek M Varusai; Vincent Knight-Schrijver; Lu Li; Corina Dueñas-Roca; Gaurhari Dass; Sarah M Keating; Young M Park; Nicola Buso; Nicolas Rodriguez; Michael Hucka; Henning Hermjakob
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

Review 7.  Biological Materials: The Next Frontier for Cell-Free Synthetic Biology.

Authors:  Richard J R Kelwick; Alexander J Webb; Paul S Freemont
Journal:  Front Bioeng Biotechnol       Date:  2020-05-12

8.  SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts.

Authors:  Esteban Martínez-García; Angel Goñi-Moreno; Bryan Bartley; James McLaughlin; Lucas Sánchez-Sampedro; Héctor Pascual Del Pozo; Clara Prieto Hernández; Ada Serena Marletta; Davide De Lucrezia; Guzmán Sánchez-Fernández; Sofía Fraile; Víctor de Lorenzo
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

9.  Repository-based plasmid design.

Authors:  Joshua J Timmons; Doug Densmore
Journal:  PLoS One       Date:  2020-01-09       Impact factor: 3.240

10.  Digitalizing heterologous gene expression in Gram-negative bacteria with a portable ON/OFF module.

Authors:  Belén Calles; Ángel Goñi-Moreno; Víctor de Lorenzo
Journal:  Mol Syst Biol       Date:  2019-12       Impact factor: 11.429

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