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] (http://wiki.synbiohub.org/wiki/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:
- Add the Comsode source repository to your package manager
- Add the Comsode repository
echo 'deb http://packages.comsode.eu/debian jessie main' >> /etc/apt/sources.list - Download the Comsode GPG key for package verification
wget http://packages.comsode.eu/key/odn.gpg.key - Add the Comsode key to your keyring
apt-key add odn.gpg.key
- Add the Comsode repository
- Set up the Node.js repository
- Download the Node setup script
curl -sL https://deb.nodesource.com/setup_6.x | sudo -E bash - - Update your package repositories
apt update
- Download the Node setup script
- Install the necessary packages
apt install default-jdk maven raptor2-utils nodejs virtuoso-opensource jq build-essential python - Clone the SynBioHub repository
git clone https://github.com/SynBioHub/synbiohub - Change to the SynBioHub directory
cd synbiohub - Build the Java components with Maven
cd java && mvn compile - Return to the root directory and install the Node dependencies with NPM
cd ../ && npm install - Start the SynBioHub process
npm start