BioBLESS - iGEM USTC Software 2015

Quick Guide

• run ./install.sh to install the application
• run ./run.sh to run the application
• open http://localhost:8000/BioBLESS/index.html to enjoy it.

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Structure of the project

• frontend Frontend logic lies here
• backend Backend code locates here
• doc Documents for developers and users

This project is backend/frontend separatable. This means that you can deploy backend and frontend in different places given frontend is capable of connecting to the backend(e.g. You can run backend in a webserver/your pc, and frontend in wherever a html5-friendly webbrowser is supported. Then you can configure the frontend to connect to the backend, this will be easy).

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Backend

Requirements

• python 2.7
• build-essential
• pip
• virtualenv

code structure

• backend Root of django
• backend/BioBLESS Functional codes
• Test cases are in the backend/BioBLESS directory

Dependency

• django for website
• matplotlib for plotting
• networkx for graph
• you could just use pip install -r requirements.txt to install all the dependency.

Install

cd BioBLESS/biocircuit
make
python biogate_gen.py
cd ../..
python manage.py migrate
python manage.py loaddata parts
python manage.py runserver 0.0.0.0:8000

if you would like serve the static file by a nginx/apache server, you could change setting STATIC_ROOT in backend\BioBLESS\settings.py to your nginx document root directory, and run python manage.py collectstatic to copy the static file to your web server directory.

Unit Test

you could run

    python manage.py test BioBLESS

for unit test

Backend code doc

Please install sphinx package for python. For example:

pip install -U Sphinx

you could run

    ./doc_build/gendoc.sh (under *nix/macos)
    doc_build\gendoc.cmd (under windows)

Then you can open doc_build/doc/html/index.html to view the doc

A built doc exists in doc_build/backend_doc.zip, just use it for convenience.

Rest API doc

You can find it in the URI /docs

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Frontend

Browser Requirements: IE 9+, Safari 5.1+, Edge, current Chrome or Firefox.

If you just want to use our software, you do not need to build the source. If you want to make some improvement, or build the frontend documentations, you can see the instructions below.

Dependency

First of all, you need to install nodejs and npm.

For example, ubuntu 14.04 please run below:

# apt-get install nodejs-legacy npm

Libraries (already included in the project)

jQuery-2.1.4 License: MIT

Pixi.js-3.0.7 License: MIT

Unit Test

mocha-2.2.5 License: MIT

chai-3.2.0 License: MIT

Build

You should just execute the following command:

$ npm install
$ npm run build

Documentations

Run it to view the documents:

$ npm run build-doc

Unit Test

$ npm test