Cytoscape 2.2 Release Notes

Cytoscape 2.2 is the latest release of the open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.

The 2.2 release of Cytoscape includes: Improved node/edge attribute browsing, Cytoscape Graph Editor v1.0, Support for Gene Ontology OBO and gene annotation files, Cytoscape panels (CytoPanels) to ease window management, Independent internal network windows for easy comparison, New GML visual style to manage visual attributes from GML files, Simplified mechanism for saving Visual Styles in between sessions, Many performance improvements, Improved attribute API (CyAttributes), and many bugs fixes.

Cytoscape panels (CytoPanels) to ease window management

CytoPanels are floatable / dockable panels to cut down on the number of pop-up windows within Cytoscape, and create a more unified user experience. Cytoscape 2.2 includes three CytoPanels:

  • CytoPanel 1 (appears on the left). By default, it has Network Tree Browser panel.
  • CytoPanel 2 (appears on the bottom). Node/Edge attribute browser will be shown here.
  • CytoPanel 3 (appears on the right). Mainly for advanced features.

Improved node/edge attribute browsing:

Improved Attribute Browser is on CytoPanel 2. Users can browse, edit, and export attributes in the table.

Cytoscape Graph Editor v1.0

New network files can be created visually by Cytoscape Editor .

Support for Gene Ontology OBO and gene annotation files

Now Cytoscape supports standard ontology and annotation file formats:

Through the new Gene Ontology Server Wizard, users can select those files from GUI.

Independent internal network windows for easy comparison

Ecah network is displayed in a independent window.

Multiple network windows can be displayed in the main panel.

New GML visual style to manage visual attributes from GML files

When a gml file is loaded into Cytoscape, its visual properties will be registered as a new visual style.

Improved mechanism to save users' custom Visual Styles

Visual styles property files (vizmap.props) are saved to the same place they were loaded from.

Improved Attribute API (CyAttributes)

New attribute API (CyAttributes) is now available for plugin developers.

Core Plug-Ins:

Seven "core" plug-ins are bundled and distributed with Cytoscape 2.2. These plug-ins offer fundamental operations of value to many users, and are included in the basic distribution.

Plug-In Name

JAR file

Description

Filter

filter.jar

Provides filtering functionality; adds filter icon, filters menu and filtering dialog box.

Attribute Browser

browser.jar

Provides attribute browser functionality; adds browser menu item under Data.

Cytoscape Editor

CytoscapeEditor.jar

Provides network editor functionality; adds setEditor menu item under File.

yFiles Layouts

yLayouts.jar

Provides yFiles layouts functionality; adds yFiles submenu to layout menu.

Layouts provided:
  - Circular
  - Organic
  - Hierarchic
  - Random
  - MirrorX
  - MirrorY
  - Orthogonal

Align

control.jar

Provides alignment/distribution functionality; adds align menu item to layout menu and align/distribute dialog box.

Hierarchical Layout

HierarchicalLayout.jar

Provides hierarchical layout functionality; adds hierarchical layout menu item to layout menu.

Yeast context-sensitive menu

yeast-context.jar

Provides Yeast-specific web search capabilities.