Cytoscape 2.3 Release Notes

Cytoscape 2.3 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 2.3 release of Cytoscape includes:

High-performance rendering engine

New rendering engine enables users to draw, navigate, and manipulate huge networks in real time. On modern workstations Cytoscape can render networks with 100,000+ nodes and edges.

Ability to save a session

From this version, Cytoscape's basic data file is .cys (CYtoscape Session) file. This is a zip archive which includes the following data files:

  • cysession.xml - File for saving desktop states
  • Property Files
    • session_vizmap.props - Visual Styles
    • session_cytoscape.props - Preference values
  • Network files in XGMML format - Networks and attributes
With session files users can save everything in the workspace, including networks, attributes, visual styles, properties, and relationships between networks (shown in the Network Panel) into a single .cys file.

Support for network attributes

In addition to node and edge attributes, Cytoscape supports attributes for networks. This includes network metadata in RDF (Resource Description Framework).

An improved command line interface

The new command line simplifies the option specification.

The GraphMerge plugin included by default

GraphMerge plugin is now a core plugin.

Enhanced context or pop-up menus for nodes

The LinkOut plugin provides enhanced mechanism to link nodes to external web resources within Cytoscape.

A rewritten bird's eye view of the network

Rewritten bird's eye view window enables users to browse huge network more efficiently.

Enhanced Undo/Redo support

New Undo manager provides better undo/redo function.

Enhanced Ontology Server Wizard

Enhanced Gene Ontology wizard has more intuitive user interface for importing Gene Ontology data files.

More user-friendly UI for Attribute Browser

Network attribute browser panel is added. Attribute import related functions are attached to new icons on browser.

Greater flexibility in expression data loading

Users can specify key value for mapping expression matrix data.

Ability to rename networks

Network names can be modified from the Network Panel.

Re-organized menu system

Menu items have been re-organized to better match common applications like Firefox and Word.

Core Plugins:

Seven "core" plugins are bundled and distributed with Cytoscape 2.3. These plugins offer fundamental operations of value to many users, and are included in the basic distribution.

Plugin 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.

cPath

cpath.jar

Provides aility to directly query, retrieve and visualize interactions retrieved from the cPath database.

yFiles Layouts

yLayouts.jar

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

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

Linkout

linkout.jar

Provides a right-click menu of hyper links for nodes and edges.

Graph Merge

GraphMerge.jar

Provides ability to merge networks and perform other set operations on networks.

Manual Layout

ManualLayout.jar

Provides align functionality.

Automatic Layout

AutomaticLayout.jar

Provides layout algorithms shown under menu items JGraph Layouts and Cytoscape Layouts. The code for these algorithms is all open source.

Yeast context-sensitive menu

yeast-context.jar

Provides Yeast-specific web search capabilities.