CytoSQL - Download

NEWEST VERSION 1.0 beta (revision 7):

-- update june 29, 2010 --

Version 1.0 beta (revision 7) is now available from this website. As soon as we are sure it is bug-free, we will make it available through the Cytoscape plugin manager. Nevertheless it is already fully operational and should work as expected. If you want to have the latest features available, we recommend you to download and manually install this version.

New features:
- new advanced query favorites and history manager with support for searching through past queries
- Syntax highlighting (with updated dictionary)
- help link starts up default browser, even in Linux verions
- Autocompletion (use ctrl shift - some known user interface bugs are currently being fixed, but you can always turn of this feature)
- Several bug fixes.

Changes to previous release candidates:
- verified to work with Cytoscape 2.7
- some problems with non-scrollable results set when using sqlite are fixed.

Known issues with this version:
- autocompletion box often positioned incorrectly (you can turn it of if this behaviour is disturbing your work)

Updated documentation regarding the new functions is being completed.

-> -> Download CytoSQL 1.0. beta (rev 7)
-> -> Download the Source code (from rev 5) under a LGPL license.

To install it, make sure to uninstall any previous versions (you can do this with the plugin manager), and then drop the downloaded jar file in the plugins folder of your Cytoscape installation.

Main new features of version 1.0:
- common database drivers predefined in database specification window, to facilitate entering new connections
- preview the results of a query before importing them.
- improved layout reflecting the plugin workflow
- any results column can be source or target node, instead of only the first ones.

Previous changes: Revision 1 changes:
- interface typo's fixed
- more clear column mapping dialog messages in expand network mode
- progress bar in all modes

Previous changes: Revision 2 changes:
- under some circumstances, a new user had a problem editing and storing database connection info. This was fixed.

Previous changes: Revision 3 changes:
- references to errors during import were not always properly removed from memory, and then repeated when new errors were encountered. This was fixed.

Previous changes: Revision 4 changes:
- Added experimental syntax highlighting and autocompletion.
- Fixed bug when using postgresql
- Fixed null value bug

Previous changes: Revision 5 changes:
- several minor bug fixes
- syntax highlighting restricted to lowercase


Current documentation mainly reflects version 0.9. Nevertheless most documentation remains valid for the new version, except that version 1.0 offers significantly more flexibility and has a somewhat changed layout. The latest updates to handle any discrepancies between version 0.9 and 1.0 are currently being applied.


Version 0.9 of the CytoSQL plugin is still available and supported. You do not have to download it here: instead we recommend that you use the Cytoscape plugin manager (Under Cytoscape > Plugins > Plugin Manager) to install it directly with this tool. The plugin can be found in the under the category "Network and attribute I/O".

You can also download it from the plugins page on the Cytoscape website.

In case you have problems with the Cytoscape plugin library, you can download the plugin here and install it manually (by dropping the jar file in the plugins folder of your Cytoscape installation):

-> Download CytoSQL 0.9

We try to continuously improve CytoSQL. If you have comments or questions, or if you found a bug, please let us knos: kris DOT laukens At Thank you!

A tutorial is also available:

-> CytoSQL tutorial