ADIVSe - Annotation Dynamics Visualization
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ADVISe

We introduce an interactive visualization called ADVISe, which tackles the problem of visualizing evolutions in enzyme annotations across several releases of the UniProt/SwissProt database. More specifically, we visualize the dynamics of Enzyme Commission numbers (EC numbers), which are a numerical and hierarchical classification scheme for enzymes based on the chemical reactions they catalyze.

Configuration

Database

ADVISe uses data stored in a MySQL database. Please set up your environment according to instructions of the MySQL website.

You must then download the database dump of our project, untar the file and apply it to your database:

$ tar xvfj ADVISe.tar.bz2
$ mysql -u <your_username> -p <database_to_be_used> < ADVISe.sql

Processing

The Processing code is located on the Processing/ADVISe folder, and should run on major operating systems. To download the Processing Sandbox go to the website.

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

The template file mysql_settings.txt.template should be used to tell the program how to access your database:

$ cp mysql_settings.txt.template mysql_settings.txt

After that, simply edit it to match your database configuration

License

Released under the MIT License.