Cytoscape 2.4 Release Notes

Cytoscape version 2.4 is the latest release of the open source bioinformatics software platform for visualizing general networks, especially for molecular interaction networks. Cytoscape can integrating these networks with any attributes, such as gene expression profiles and other state data.

The 2.4 release of Cytoscape includes the following new features:

Publication quality image generation

  • Node label position adjustment - Node label position can be adjusted through graphical user interface.
  • Automatic Visual Legend generator - Visual legend can be created from VizMapper setting.
  • Node position fine-tuning by arrow keys
  • The ability to override selected VizMap settings - User can override VizMap from network view.

Quick Find Plugin

Quick Find plugin is a simple selection plugin that enables users to quickly find nodes and edges through simple user interface. You can interactively select nodes and edges using attributes.

New Cytoscape Icons

Icons are replaced by new OpenOffice icon set for cleaner look.

Consolidated network import capabilities

  • Import network from remote data sources (through http or ftp) - Users can load local and remote files seamlessly.
  • Default support for popular file formats for intaraction data:

New Ontology Server

New Ontology server will eventually replace BioDataServer. Instead of using special data structure, ontology data is stored in normal CyNetwork data structure. Plugin writers can access this function through CyNetwork API or BioJava Ontology API.

  • Native support for OBO format ontology files - Users can import arbitrary OBO ontology file. Both format version 1.0 and 1.2 are supported.
  • Ability to visualize the ontology tree as a network (DAG) - Since ontology uses CyNetwork data object, users and plugin writers can use Cytoscape's visualization functions for ontology DAGs.
  • Full support for Gene Association files - All data in Gene Association files are imported directly into attributes.

Support for Java SE 5

Cytoscape core uses new features introduced in Java SE 5. Plugin writers can use those features.

Core Plugins:

Seven "core" plugins are bundled and distributed with Cytoscape 2.4. 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.

BioPax Import

biopax.jar

Plugin for importing network files in BioPAX format.

SBML Import

SBMLReader.jar

Plugin for importing network files in SBML format.

PSI-MI Import

psi_mi.jar

Plugin for importing network files in PSI-MI format. Supports PSI-MI version 1.0 and 2.5.

Table Import

TableImport.jar

Plugin for importing network and attribute files from text table and Excel Workbook.

Quick Find

quick_find.jar

Quick Find plugin.