eQuilibrator

eQuilibrator is a biochemical thermodynamics calculator website. The website enables calculation of reaction and compound energies through an intuitive free-text interface. The current online version of eQuilibrator can be found at: http://equilibrator.weizmann.ac.il/

If you are looking for the back-end library used to estimate standard Gibbs free energies DOI: 10.1371/journal.pcbi.1003098, you can find it in the following GitHub repository: Component Contribution

eQuilibrator is written in Python using the Django framework. It was developed primarily on Ubuntu 16.04 64-bit and is easiest to develop and set up on that operating system. Setup instructions below are really only for Ubuntu users.

Dependencies

• python 2.7
• mysql-server (5.7.16)
• python-glpk
• glpk-tools
• (optional) Indigo Toolkit (https://github.com/ggasoftware/indigo) Python PyPI:
• Django (1.10.4)
• django-extensions (1.7.5)
• django-haystack (2.5.1)
• glpk (0.4.52)
• matplotlib (1.5.3)
• MySQL-python (1.2.5)
• nltk (3.2.1)
• numpy (1.11.3)
• pandas (0.19.1)
• pip (9.0.1)
• PuLP (1.6.1)
• pyparsing (2.1.10)
• scipy (0.18.1)
• seaborn (0.7.1)
• tablib (0.11.3)
• Solr (3.6.2)
• xlrd (1.0.0)

Install binary dependencies on Ubuntu

sudo apt install mysql-server libmysqlclient-dev python-pip python-dev 
sudo apt install solr-common libglpk-dev glpk-utils

Install missing Python dependencies from PyPI

sudo pip install -r requirements.txt

Create MySQL database and user for Django

sudo mysql --user=root mysql -p
mysql> CREATE USER '<MYSQLUSR>'@'localhost' IDENTIFIED BY '<MYSQLPWD>';
mysql> GRANT ALL PRIVILEGES ON *.* TO '<MYSQLUSR>'@'localhost';
mysql> CREATE DATABASE <MYSQLDB>;
mysql> exit;

Configure Solr

sudo cp solr/schema.xml /etc/solr/conf/
sudo /etc/init.d/tomcat7 restart

• Replace the appropriate database name (<MYSQLDB>), username (<MYSQLUSR>) and password (<MYSQLPWD>) in settings.py.
• Run python manage.py migrate --run-syncdb to build database schema.
• Run python db_load_from_sqldump.py to load the data into the database.
• (optional) instead of db_load_from_sqldump, you can use db_load_from_raw_files which will take much longer (2 hours).

Running the Development Server on a Remote Host

sudo python manage.py runserver 0.0.0.0:80

Will run the development server on port 80 and allow external IPs to access the server. This is very useful for debugging differences between your local and remote environments.

Setting up Apache + Django eQuilibrator

• For running eQuilibrator on a web server that can be accessed safely from the internet.

sudo apt install apache2 libapache2-mod-wsgi links
git clone https://github.com/eladnoor/equilibrator.git
cd equilibrator
chmod 666 gibbs.log
sudo cp ~/equilibrator/apache/default.conf /etc/apache2/sites-available/000-default.conf
sudo a2enmod wsgi
sudo apache2ctl restart