Skip to content


Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
This branch is 3 commits behind bowen1993:master.

Latest commit


Git stats


Failed to load latest commit information.
Latest commit message
Commit time


Build Status

Coverage Status

Synthetic Biology Design toolkit

Installation Guide


  • We're going to assume that you have installed Python 2 and MySQL 5.x and git on your computer.

####Download source code from github

git clone

git checkout master

Install Django

  1. Install pip

    For Unbuntu/Mint Users:

    apt-get install python-pip

    Or you can get standalone pip installer.

  2. Install Django using pip

    For users who has installed pip

    pip install django==1.7.6

    Or you can install Django manually.

    Tip: Know more information on install Django at

3.Install additional mysql & python dev lib

sudo apt-get install python-dev libmysqlclient-dev    

Set up BioDesigner

  1. Open BioDesigner/
  2. Edit your database configuration at line 67.

Set up Database

  1. To connect MySQL in Python, we need install mysql-python first. You can install it using pip:

    pip install mysql-python

    Tip: If you get error message like this: EnvironmentError: mysql_config not found.


  2. Create database named biodesigner in MySQL.

  3. Database import

	cd /path/to/the/app
	sudo mysql -e 'CREATE DATABASE biodesigner'
	python syncdb --noinput
	sudo mysql -e 'source xxx.sql' -u username --password=password biodesigner;

Install Additional Package


	pip install pillow
  1. Install Elasticsearch

    For Ubuntu/Mint Users: Elasticsearch is running on Java, if you don't have a JRE on your machine, please install one.

    For example, We use OpenJDK7:

    apt-get install openjdk-7-jre

    Download and install the Public Signing Key

    wget -qO - | sudo apt-key add -

    Add the following to your /etc/apt/sources.list to enable the repository

    deb stable main

    Run apt-get update and the repository is ready for use. You can install it with :

    apt-get install elasticsearch

    For RHEL/CentOS Users: Download and install the Public Signing Key

    rpm --import

    Add the following in your /etc/yum.repos.d/ directory in a file named (for example) elasticsearch.repo

    name=Elasticsearch repository for 1.3.x packages

    And your repository is ready for use. You can install it with :

    yum install elasticsearch

    Install Elasticsearch bind for python:

    pip install elasticsearch

Start Server

  1. If you want to use this application on a production site, use Apache with mod_wsgi.

    Tip: Get more information at

  2. If you just want to experiment with this application, just use following command:

    python runserver

    If you will get following output,

    May 14, 2014 - 04:50:57
    Django version 1.6.4, using settings 'BioDesigner.settings'
    Starting development server at
    Quit the server with CONTROL-C.

    The application is deployed successfully. And you can use the application by visit in web browser.


SynBio Design tool







No releases published


No packages published


  • CSS 58.1%
  • JavaScript 19.2%
  • Python 18.7%
  • HTML 4.0%