New Features in Cytoscape 2.8.0

Custom Graphics

We've added the ability to associate images and other custom graphics with nodes. Images can be loaded manually with our image browser or specified as URLs in attributes. Programmers may also use the CyCustomGraphics interface to create images dynamically within plugins. To connect these images to nodes, the VizMapper provides visual properties that allow up to nine images to be mapped independently onto nodes. Users can control both the size and placement of the image with respect to the node.


We've had many requests over the years to provide spreadsheet like functionality in the attribute browser, and now we have! Cells in the attribute browser now accept a subset of Excel-like functions which dynamically compute values as attributes. We've provided an equation editor to help users understand the functions that are available as well as how to properly specify the arguments to a command. Equations are not meant for heavy data analysis, but rather as a simple way to manipulate attribute values within Cytoscape.

Network Analyzer

Mario Albrecht and his team at the Max-Planck Institute for Informatics have graciously provided their Network Analyzer plugin to Cytoscape as a core plugin. This means that Cytoscape now has a full suite of network analysis and graphing routines available right out of the box!

Bug Fixes

We've fixed many bugs in the latest version of Cytoscape. We hope the changes will make the Cytoscape user experience more pleasant and consisten.

Updates in Cytoscape 2.8.1

Bug Fixes

Updates in Cytoscape 2.8.2

Bug Fixes

This is mainly a bug fix release. We hope the changes will make the Cytoscape user experience more pleasant and consistent.

Improved Memory Allocation

We have improved the memory detection and allocation process that occurs when Cytoscape is first installed and launched. The process attempts to optimize memory settings based on your hardware. The new process avoids system crashes that were occurring with 2.8.1.

New Gradient Editor

We've overhauled the user interfaces controlling the mapping of continuous values to visual styles, like Node Size and Node Color, to provide more intuitive and consistent controls.

Well-Behaved CytoPanels

We revamped the behavior of CytoPanels so that each plugins preferred panel size will be automatically fit when the user switches to them. A global minimum size is set for all panels so that users can manually resize no matter which panel they are viewing.

Error Console Feature

If your Cytoscape session starts acting funny, go to Help > Error Console. You can now Save the console output as a single html file and attach it to your helpdesk and discussion list posts.