SynBioHub

SynBioHub

The SynBioHub repository 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.

Additionally, SynBioHub can be used to publish a library of synthetic parts and designs as a service, to share designs with collaborators, and to store designs of biological systems locally. Data in SynBioHub can be accessed via the HTTP API, Java API, or Python API where it can then be integrated into CAD tools for building genetic designs. SynBioHub contains an interface for users to upload new biological data to the database, to visualize DNA parts, to perform queries to access desired parts, and to download SBOL, GenBank, FASTA, etc.

Contributors

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Jet Mante

Graduate Researcher, Ph.D.

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Ben Hatch

Undergraduate Researcher

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Eric Yu

Undergraduate Researcher

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James Scholz

Undergraduate Researcher

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Curtis Madsen

Sandia National Laboratories, R&D S&E, Computer Science

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Meher Samineni

REI, Software Engineer

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Zach Zundel

Facebook, Product Engineer

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Oliver Flatt

University of Utah, Undergraduate Researcher

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Prubhtej Singh

Guru Gobind Singh Indraprastha University, Junior Year Student and NRNB

Publications

  • Synthetic biology open language (SBOL) version 3.0.0
  • Synthetic biology open language visual (SBOL visual) version 2.2
  • Extending SynBioHub’s Functionality with Plugins
  • SBOL Visual 2 Ontology
  • The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering
  • Asynchronous Genetic Design
  • Improving Authentication and Authorization on SynBioHub
  • SBOLExplorer: Data Infrastructure and Data Mining for Genetic Design Repositories
  • A Computational Workflow for the Automated Generation of Models of Genetic Designs
  • pySBOL: A Python Package for Genetic Design Automation and Standardization
  • SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information
  • Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL)
  • Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019
  • Synthetic Biology Open Language (SBOL) Version 2.3
  • Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1
  • SBOLExplorer: Data Infrastructure and Data Mining for Genetic Design Repositories
  • Software Compliance Testing for Workflows Using the Synthetic Biology Open Language
  • sboljs: Bringing the Synthetic Biology Open Language to the Web Browser
  • Synthetic Biology Open Language (SBOL) Version 2.2.0
  • SBOLDesigner: A Hierarchical Genetic Design Editor
  • Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0
  • SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology
  • A Validator and Converter for the Synthetic Biology Open Language
  • SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design
  • SBOLme: a Repository of SBOL Parts for Metabolic Engineering
  • A standard-enabled workflow for synthetic biology
  • Synthetic Biology Open Language (SBOL) Version 2.1.0
  • A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language
  • Sharing Structure and Function in Biological Design with SBOL 2.0
  • SBOL Visual: A Graphical Language for Genetic Designs
  • libSBOLj 2.0: A Java Library to Support SBOL 2.0
  • Synthetic Biology Open Language (SBOL) Version 2.0.0
  • Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language
  • Computational Synthetic Biology: Progress and the Road Ahead
  • Technology mapping of genetic circuit designs
  • The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology
  • A Methodology to Annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language