README.md

SynBio is just a S-Din away!

SYSU-Software

Introduction

Welcome to S-Din! This is the most powerful Search engine and Design platform for inspiration with network analysis in Synthetic Biology ever.

S-Din (/sdɪn/, verb) your keyword to:

• Search for projects, parts and papers in Synthetic biology

• Get inspired from infomations provided by our software. Don't worry, our powerful algorithms will provide you the best infomations, rapidly and accurately.

• Design your circuits. With our design tool, you are enabled to integrate collected circuits and parts. Don't know what to add? Recommendation based on interaction prediction may give you a hand.

• Finished your design? Simulate it in a single click! After simulation, plasmid generator may help in lab validation.

SynBio is just a S-Din away!

Requirements

S-Din requires a web browser and a single click: http://sdin.sysusoftware.info. S-Din it right now!

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To setup a server, follow this:

Installation

Before installation

To install S-Din, firstly, you should make sure the following requirements are satisfied:

• Python >= 3.5 :

  Run python3 --version in a command line to check it.

• MySQL >= 5.7 :

  Installation differs from different operating systems. Follow your OS's official guide or MySQL official website to install it. Run mysql --version to check installation.

  Also make sure that character sets are set to UTF-8. You can follow our guide to set it.

Installation

• Clone

  Clone the repository like git clone https://github.com/igemsoftware2017/SYSU-Software-2017

• Setting MySQL root account

  To set up MySQL users used by S-Din, we need your MySQL root account. Add SYSU-Software-2017/tools/config.json like:

  {	
      "mysql_root_account": "root", 
      "mysql_root_password": "123456"
  }

• Install

  The main installation process is packed into scripts. Run setup.sh (Setup.bat for Windows) for installation. Since the powerful S-Din have enormous data, it may take several minutes to initialize the database. After a cup of coffee, just simply runserver.sh (runserver.bat for Windows) to launch the server. So easy!

Used library

Backend

• Python 3: https://www.python.org/
• Django: https://www.djangoproject.com/
• xlrd: https://github.com/python-excel/xlrd
• Requests: http://docs.python-requests.org/en/master/
• MySQL: https://www.mysql.com/cn/
• mysqlclient-python: https://github.com/PyMySQL/mysqlclient-python
• PyMySQL: https://pypi.python.org/pypi/PyMySQL

Algorithm

• NumPy: http://www.numpy.org/
• SciPy: https://www.scipy.org/
• gensim: https://radimrehurek.com/gensim/
• scikit-learn: http://scikit-learn.org/stable/

Frontend

• Semantic UI: https://semantic-ui.com/
• jQuery: https://jquery.com/
• jQuery UI: http://jqueryui.com/
• jQuery Mousewheel: https://github.com/jquery/jquery-mousewheel
• jsPlumb: https://jsplumbtoolkit.com/
• Chart.js: http://www.chartjs.org/
• D3.js: https://d3js.org/
• AngularJS: https://angularjs.org/
• Angular Plasmid: http://angularplasmid.vixis.com/
• html2canvas: https://html2canvas.hertzen.com/

About

Proudly brought to you by SYSU-Software. Licensed under MIT License.