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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:

https://synbiohub.github.io/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 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]

Bug fixes

• Fixed issue with new SO terms
• Fixed issue with allowing 0 days for index update when not activated
• Fixed issue causing lockup with plugin fails

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:

https://synbiohub.github.io/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 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

• Added sequence-based search
• Added support to edit annotations
• Added ability to add/remove members of collections
• Added ability to filter collections by type
• Added Virtuoso health check

Changes

• Refactored submission process code
• Added validation when editing roles and types
• Added ability to change more config options in admin panel
• Browse page now shows other SynBioHub's in Web-of-Registries

Bug fixes

• Fixed miscellaneous API issues
• Made collection icons persistent
• Fixed inconsistency with buttons
• Fixed issue with arrows on pull down menus
• Fixed issue where not all triples were deleted when collection removed

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 sequence-based search
• Additional improvements to the programmatic API support
• Finer grain types on the collection pages and support to filter by these types
• Ability to add and remove members of collections

Changes

• Updated API error messages
• Change to use sbols.org for SBOL terms

Bug fixes

• Fixed several unhandled promise exceptions
• Fixed bug with logo lost on docker restarts
• Fixed bug that caused crash when attachURL has not type selected
• Fixed several bugs in the add/edit/remove fields functionality

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

• Complete refactor of API, making download, edit, make public, and many other endpoints API accessible
• Support for submit plugins
• Support for download plugins

Changes

• Ask for confirmation when removing object from the collection page
• Remove cloneCollection endpoint
• Remove extra search endpoints

Bug fixes

• Fixed bug with share links
• Fixed bug with non-recursive SBOL Collection fetch dropping members
• Fixed bug where incorrect login token caused exception
• Fixed numerous issues with submit via a complete refactor
• Fixed issue where virtuoso being down caused exceptions
• Fixed bug where collection was getting removed when overwritten by an invalid submission

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

• Added support to download GFF3 files

Changes

• Improved labels for GenBank files
• Modified description box size to match size of current description when editing

Bug fixes

• Fixed bug preventing rendering of Experimental Data pages

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

• Added ability to see different log levels on admin page
• Added ability to delete attachments on page where they are added
• Added a fully functional SPARQL interface for admin users
• Substantial redesign of advanced search
• Added ability to jump back to containing collection

Changes

• Show image attachments at top of page for objects without a visualization
• Logs now stored persistently
• Removed plugin result logging
• Added MapsTos into Module list on ModuleDefinition page

Bug fixes

• Fixed bug with image list for mutable fields
• Fixed bug preventing some top-levels from being viewed
• Fixed bug with create collection
• Fixed bug causing hard crash when attachments are missing
• Fixed edit description and added ability to remove
• Removed pencil for edit on public parts

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

• Show all attachment image types
• Ability to edit name
• Ability to edit description
• Ability to add/edit/delete roles and types
• Added support to add attachments that refer to a URL

Changes

• Remove old sbh:topLevel tags on submission
• Send URL of requester to plugins
• Added SPARQL endpoint to documentation
• Allow rendering of objects with links to objects of incorrect type
• Updating logging to have different log levels and to cycle logs

Bug fixes

• Fixed bug with GenBank export losing names
• Fixed broken link in password reset email
• Fixed submit and thus SBH for Java versions > 8
• Fixed backups for docker images

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 all new features of SBOL 2.3
• Added a full SPARQL interface for administrators
• New rotating log files

Changes

• Search results now indicate the type of an object
• Updated to use libSBOLj 2.4.0 and sboljs 2.2

Bug fixes

• Fixed bug with proper handling of plugins that are down
• Fixed an issue that was causing too many open files errors
• Fixed a bug in the git revision footer message
• Fixed some issues in GenBank conversion • Fixed a bug in ICE collection view

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

• Prototype plugin support
• Testing infrastructure

Changes

• New look to the top of the pages
• After submit, open the Collection submitted
• Added search navigation to bottom of search page

Bug fixes

• Fixed bug preventing implementation without built field from rendering
• Color update on theme now updates immediately
• Updating registries now takes immediate effect

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

https://github.com/SynBioHub/synbiohub/issues?q=is%3Aissue+milestone%3A%22SBH+1.4.1%22+is%3Aclosed

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