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@3ach 3ach released this 22 Jan 18:45
· 1550 commits to master since this release
v1.4.0
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Learn about vigilant mode.

SynBioHub is a design repository for people designing biological constructs. It enables DNA and protein designs to be uploaded and shared. SynBioHub also facilitates searching for information about existing useful parts and designs by combining data from a variety of sources. Finally, it has a programmatic interface that allows applications to connect to SynBioHub via a RESTful API to enable third-party software to search, fetch, and submit parts and other design information.

The easiest install method is using Docker, instructions here:

http://wiki.synbiohub.org/wiki/Installation

It is also possible to run on Mac and Linux systems without using Docker. Instructions can be found on the repository README here:

https://github.com/SynBioHub/synbiohub

If you have an instance of SynBioHub running on your machine and would like to make it publicly accessible using the web, we recommend using nginx. Instructions for deploying on nginx can be found here:

http://wiki.synbiohub.org/wiki/NGINX_configuration_instructions

Finally, if you do create a publically accessible instance of SynBioHub, we would like to hear from you, so we may add it to our web-of-registries. Please email:

[email protected]

New features

  • Support for SBOL 2.2 including Combinatorial Derivations, Implementations, and Attachments
  • All data encoded in SBOL are now rendered on the page, and every SBOL class has its own page format
  • SBOLExplorer search engine support to improve quality of search results
  • API support for a non-recursive fetch for large SBOL constructs
  • Administrative access to log files
  • Prototype VisBOL support for rendering Modules

Changes

  • Significant refactoring of SBOL rendering code
  • Changes to submission code significantly speeds up submission of new data
  • Moved from monolithic Docker image to micro-service model
  • Rendering of large constructs no longer requires a complete recursive fetch
  • Spoofing can now be configured after setup for debug purposes
  • Confirmation now requested when removing collections
  • Restriction of the use of FROM in SPARQL queries to only public graph and logged in user graph

Bug fixes

  • Docker persistency changes
  • Works with latest release of libSBOLj that contains numerous bug fixes
  • An issue with rendering on first start has been resolved
  • Resolved numerous roundtrip bugs
  • Fixed bug when paging through uses of a construct
  • Several issues when overwriting or adding to an existing collection

A complete list of the issues addressed can be found here:

https://github.com/SynBioHub/synbiohub/milestone/7?closed=1

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