SynBioHub is a Web-based repository for synthetic biology, enabling users to browse, upload, and share synthetic biology designs.

To learn more about the SynBioHub, including installation instructions and documentation, visit the SynBioHub wiki.

To access a sample instance of SynBioHub containing enriched Bacillus subtilis data, features from the Escherichia coli genome, and the complete iGEM Registry of Standard Biological Parts, visit synbiohub.org. To access a bleeding-edge version of SynBioHub, visit dev.synbiohub.org.

Installation

The recommended way to install SynBioHub is via the Docker image. See Installation for more information.

Manual Installation

SynBioHub has both JavaScript (node.js) and Java components.

Prequisites:

Linux (only tested with Ubuntu 18.04.01) or macOS

• If you're using macOS, first install homebrew

A JDK

OS	Command
Ubuntu	apt install default-jdk
Mac	brew install openjdk

Apache Maven

OS	Command
Ubuntu	apt install maven
Mac	brew install maven

node.js >= 11.0.0

OS	Command/Link
Ubuntu	visit https://nodejs.org/en/
Mac	brew install node

OpenLink Virtuoso 7.x.x

OS	Command/Link
Ubuntu	visit https://github.com/openlink/virtuoso-opensource
Mac	brew install virtuoso

rapper

OS	Command
Ubuntu	apt install raptor2-utils
Mac	brew install raptor

jq

OS	Command
Ubuntu	apt install jq
Mac	brew install jq

Ubuntu 18.04.01

1. Install Virtuoso 7 from source at https://github.com/openlink/virtuoso-opensource

• Switch to the branch stable/7 before installing.
• Follow the README on installing virtuoso from source. This involves installing all the dependencies and running build commands.
• Currently, Virtuoso does not support versions of OpenSSL 1.1.0 and above, or versions of OpenSSL below 1.0.0. When installing the dependency, build from a binary between those versions from https://www.openssl.org/source/.

2. Set up the Node.js repository
   1. Download the Node setup script curl -sL https://deb.nodesource.com/setup_6.x | sudo -E bash -
   2. Update your package repositories apt update
3. Install the necessary packages apt install default-jdk maven raptor2-utils nodejs jq build-essential python
4. Start virtuoso process virtuoso-t +configfile /usr/local/virtuoso-opensource/var/lib/virtuoso/db/virtuoso.ini -f

MacOS

1. Install the necessary packages brew install openjdk maven node virtuoso raptor jq python
2. Start virtuoso process
   1. cd /usr/local/Cellar/virtuoso/7.2.5.1_1/var/lib/virtuoso/db
      • The command above is based on where the virtuoso.ini file is located. Your installation might be located somewhere different than /usr/local/Cellar/virtuoso/7.2.5.1_1/var/lib/virtuoso/db, or the version might be different (7.2.5.1_1 might be 7.3.6.1_1 or any other version number).
      • If you're having trouble finding the location of the virtuoso.ini file, run sudo find / -name virtuoso.ini. Press the control and c keys simultaneously to quit the search.
   2. virtuoso-t -f

Both Systems

1. Clone the SynBioHub repository git clone https://github.com/SynBioHub/synbiohub
2. Change to the SynBioHub directory cd synbiohub
3. Build the Java components with Maven cd java && mvn package
4. Return to the root directory and install the Node dependencies with yarn cd ../ && yarn install Make sure that yarn is being used, not 'cmdtest'.
5. Install nodemon and forever with npm install nodemon -g && npm install forever -g
6. Add SPARQL update rights to the dba user in virtuoso.

• Visit localhost:8890, click conductor on the left hand side, and login with user name dba and password dba.
• Visit system admin -> user accounts in the menu at the top.
• Find the accound labled dba and edit.
  Add SPARQL_UPDATE to roles using the menu at the bottom.
• If no dba account exists, add one, then add update rights.

7. Start the SynBioHub process npm start or npm run-script dev

Publishing

The repository is set up to prohibit commits directly to the master branch. Commits must be made in another branch, and then a GitHub PR used to merge them into master. GitHub PRs must be approved by at least one other developer before they can be merged into master. Additionally, they must pass Travis checks, which build a Docker image and run the SBOLTestSuite and SynBioHub integration tests against it. Each time a PR is merged into master, the Travis checks are re-run on the master branch, and if they succeed the resulting image is pushed by Travis to DockerHub under the tag snapshot-standalone.

Publishing a release

Releases are published automatically using GitHub Actions. There is an action which fires on release publication. It publishes an image to Docker Hub under the $VERSION-standalone tag, and updates the synbiohub-docker master branch to point to this version. More information available here.