BioDesigner Dolphin - IGEM HFUT Software 2017

System Introduction

In iGEM, competitors always have a hard time finding helpful information. However, with the help of BioDesigner Dolphin now, competitors do not have to worry about the problem mentioned above and they just need to type what they are looking for into the searching box of BioDesigner, then the results will be exhibited as expected. What’s more, BioDesigner also integrates a design panel in which competitors can design their own biobricks conveniently. To further spark their inspiration, we also provide the recommended biobricks for users. Users can also find a gene relationship shown in a big relationship map in BioDesigner which can help to find relationships among genes quickly and easily. Chemical compounds and relationships among them can also be retrieved using BioDesigner. Papers and diseases related to these compounds are also presented. We sincerely hope BioDesigner Dolphin can help iGEMers and synthetic biologists.

Structure of the project

• biosearch: Wiki search function
• 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 3
• Java version "1.8.0_20" or later
• pip 1.5.6 or later
• MySQL 5.6.20 or later
• Mongodb 3.2.10 or later

Pachage Requires

• Django
• elasticsearch
• mysql-python
• Pillow
• pymongo

You can install the software in these two way

1. Install by docker

• Make sure that you have installed docker:

    If you do not have docker or docker-compose, please go to https://www.docker.com/ this page and install them first.
  

• Run it.

• Run a new container:

    download the docker
    cd docker
    sudo docker-compose up --build
  

• Enter http://127.0.0.1 in a browser to see the application running.

2. Run the source code cloned from github

• 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 install

    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