CytoSQL - Installation

Installing the SQLConnector plugin in Cytoscape is simple, but to be able to connect to external libraries, the correct JDBC driver should be installed.

Installation with default drivers

CytoSQL is distributed with JDBC drivers for three widely used databases: MySQL, PostgreSQL and SQLite.

If you want to use CytoSQL with these drivers, there are two, very simple ways to install the plugin:

1. Install the plugin though the Cytoscape plugin manager (available under the Network I/O category)
OR
2. Drop the CytoSQL.jar file, available from the downloads section, in the plugin directory of your Cytoscape installation, and restart Cytoscape.

The plugin then becomes available through the plugin menu.

Usage with alternative drivers

The plugin can be extended with alternative database drivers. You need to look up the right JDBC (java) driver for the relevant database. This is often made available by the RDBMS manufacturer. Before starting Cytoscape, you should ensure that the driver is added to the JAVA CLASSPATH.

Although we intend to collect some practical instructions for widely used combinations of OS and database driver on this page, we currently recommend to consult the JDBC driver documentation for your OS.