#BioDesigner Coral - IGEM HFUT Software 2016

Synthetic Biology Design toolkit

##System Introduction

For biologists, it is quite frustrating to find suitable BioBricks and collect useful genetic information in large volumes of literature. Now with BioDesigner Coral, biologists can search BioBricks, design with the help of recommendations and obtain genetic information of BioBricks in a more comprehensive way. It can analyze user’s design, then give recommendations about parts they may need. Through analysis of massive literature, we find useful information about genes, BioBricks, and the relations between genes. All genetic information will be exhibited in a network graph through visualization method to help users understand and use them better. Clicking on the nodes in the network, which represent genes or BioBricks, users can obtain relatively accurate information about related genes, corresponding protein, and relevant literature. We hope BioDesigner Coral can relieve the arduous work in labs and give inspirations to synthetic biologists.

##Structure of the project

• accounts: User information management, such as register, login and so on.
• geneRelationship: Functions related to gene.
• projectManage: Functions related to project. such as create a new project, delete a project, create a new device and so on.
• system: Show the relationships bettween parts or compounds by visualization.
• static: source files of front-end.
• utils: Some tool functions.
• data: Some data used in the system.

##System Environments Requires

• Python 2(Python 3 is not supported)
• Java version "1.8.0_20" or later
• pip 1.5.6 or later
• MySQL 5.6.20 or later

##Pachage Requires

• Django
• elasticsearch
• mysql-python
• Pillow

##Install

Django install:

pip install Django==$DJANGO_VERSION

Mysql-python install:

pip install MySQL-python

Elasticsearch install & run:

wget https://download.elastic.co/elasticsearch/elasticsearch/elasticsearch-1.7.2.zip
unzip elasticsearch-1.7.2.zip
./elasticsearch-1.7.2/bin/elasticsearch -d

Pillow

pip install pillow

Database import

mysql -e 'CREATE DATABASE biodesigner'
python manage.py syncdb --noinput
mysql -e 'source xxx.sql' -u username --password=password biodesigner;

sql source file can downloads from github

Run server

python manage.py runserver