IsaacLuo/synbiohub

Web application enabling users and software to browse, upload, and share synthetic biology designs

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 16.04) or macOS
• A JDK
• Apache Maven
• node.js >= 6.10
• OpenLink Virtuoso 7.x.x
• rapper (apt install raptor2-utils)
• jq (apt install jq)

Ubuntu 16.04:

1. Add the Comsode source repository to your package manager
   1. Add the Comsode repository echo 'deb http://packages.comsode.eu/debian jessie main' >> /etc/apt/sources.list
   2. Download the Comsode GPG key for package verification wget http://packages.comsode.eu/key/odn.gpg.key
   3. Add the Comsode key to your keyring apt-key add odn.gpg.key
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 virtuoso-opensource jq build-essential python
4. Clone the SynBioHub repository git clone https://github.com/SynBioHub/synbiohub
5. Change to the SynBioHub directory cd synbiohub
6. Build the Java components with Maven cd java && mvn package
7. Return to the root directory and install the Node dependencies with NPM cd ../ && npm install
8. Update the necessary libraries twice npm update && npm update
9. Install nodemon and forever with npm install nodemon && npm install forever
10. Start virtuoso process virtuoso-t +configfile /etc/virtuoso-opensource-7/virtuoso.ini -f
11. Start the SynBioHub process npm start or npm run-script dev