SynBioHub Plugins

SynBioHub Plugins

Plugins are modular stand-alone additions to SynBioHub. They function in a way that is similar to browser extensions. They can be installed separately from the browser/SynBioHub and provide additional ‘custom’ functionality to the browser/SynBioHub experience despite having a completely separate code base from the browser/SynBioHub. Though, they seem integrated to the user.

Currently there are three types of plugins available:

Submit: Submit plugins are available to use from the submit endpoint. They work by taking in the file that is uploaded in the submit and processing it to return SBOL to the SynBioHub endpoint.

Visual: Visual plugins are available on all ‘endpoint’ pages, for example pages for components, sequences, activities, etc. Visual plugins return html to be displayed on the page.

Download: Download plugins are available on all ‘endpoint’ pages, for example pages for components, sequences, activities, etc. Download plugins return some kind of file which is downloaded by the user.

Contributors

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Jet Mante

Graduate Researcher, Ph.D.

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Zach Zundel

Facebook, Product Engineer

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Isabel Pötzsch

University of Cambridge, Zoology Undergraduate

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