You must have two tables in your MySQL database, id_ec and id_ec_atributo.

To start off, setup your basic dev system environment. Make sure you follow the on-screen instructions

$ sudo apt-get install python-setuptools git-core python-git python-dev libmysqlclient-dev python-mysqldb

Instal virtualenv and setup a clean environment

$ sudo easy_intall virtualenv
$ virtualenv --no-site-packages venv

Install the necessary python packages

$ . venv/bin/activate
$ pip install mysql-python uuid

Time to create the necessary tables for the visualization.

$ mysql -uroot -p <name_of_the_db> < sqlscripts/id_ec_num.sql
$ mysql -uroot -p <name_of_the_db> < sqlscripts/id_ec_atributo_num.sql
$ mysql -uroot -p <name_of_the_db> < sqlscripts/nivel1.sql

Go to the python folder and edit your mysql_local_settings.py to your configuration

$ cp mysql_local_settings.py.template mysql_local_settings.py

You will have to fix the ECs for five proteins in both the id_ec and id_ec_atributo tables. Their indice fields are 809633, 879653, 1005944, 1080973 and 1216344. The EC fields with the values 1.1..- must be changed to 1.1.-.-. Here is one example:

mysql> update biovis.id_ec_atributo set ec_novo = '1.1.-.-' where indice = 1005944;

Time to run the scripts

$ python p1.py
$ python p2.py
$ python p3.py

After running the scripts above, the database will have three new tables, nivel1, id_ec_num and id_ec_atributo_num. Finally, indices must be created for the two latter tables:

$ mysql -uroot -p
mysql> create index i1 on id_ec_num(ver_estudo, prefixo);
mysql> create index i1 on id_ec_atributo_num(ver_estudo, prefixo);
mysql> create index i2 on id_ec_atributo_num(ver_estudo, prefixo, subidas, descidas, ec_ant0, ec_novo0);

The Processing code is located on the prot2 folder, and should run on major operating systems. To download the Processing Sandbox go to http://www.processing.org .

You need to download the SQLibrary by Florian Jenett at this link and follow the instructions on the same website.

You need to configure the file mysql_settings.txt.template to match your database's configuration. Then simply rename the file:

$ cp mysql_settings.txt.template mysql_settings.txt