CytoSQL

CytoSQL version 1.0 is about to be released. Check the last release candidate!

CytoSQL is a Cytoscape plugin that allows users to query (local or external) relational databases using SQL ("Structured Query language") statements, directly from within the Cytoscape interface. It offers advanced features to map retrieved results sets to Cytoscape nodes, edges or their attributes. CytoSQL supports the use of bind variables, that allow the construction of queries with certain Cytoscape variables (selected node or edge attributes) in the SQL WHERE statement.

CytoSQL makes extensive use of the JAVA JDBC database connection driver. The downloadable version supports PostGRESQL, MySQL and SQLLite out of the box, but users can easily add additional drivers to support alternative database systems.

Important: version 1.0 beta is now available! The latest version (1.0 beta) of the plugin is now available from the downloads section of this website, and will become available through the Cytoscape plugin manager when it exceeds its beta status.

Previous version (0.9) is still available from the Cytoscape plugin Manager (Plugins > Manage Plugins) under the category "Network and Attribute I/O".

Check the documentation in the left menu. Tutorials for CytoSQL are also available from the in the downloads zone.

Stay tuned for updates!