22 February 2005
Cytoscape 2.1 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 2.1 release of Cytoscape includes: major performance improvements for loading, manipulating and managing large networks; new layout and visual attribute operations; support for new external data formats; usability improvements; and bug fixes.
Performance Optimization of Graph Model
Node label color control has been added.
New layout features are available, providing new operations on selected nodes:
A direct cPath Interface is available via a new cPath plug-in.
cPath is a freely available, open-source protein-protein interaction database from Memorial Sloan-Kettering Cancer Center. Using cPath, a researcher can search for specific protein-protein interaction records, inspect matching records, and export them to a third-party database or visualization application, such as Cytoscape. More information about cPath is available at http://www.cbio.mskcc.org/cpath
Support for new data import and export formats has been added:
Headless mode operation is now supported.
Headless mode allows users to now run their own Cytoscape processing/analysis jobs without creating the GUI and user interaction components or requiring user intervention.
New Progress Bar Manager/Threading Control/Task Framework.
Progress Bar and Task control has been added for the following longer-running operations:
Load OperationsA
new Threading/Task Framework and associated GUI components have been
added to the Cytoscape core architecture which allows for visual
feedback and user control for longer-running tasks. A progress bar
API is available for communicating activity and status to users for
operations which formerly blocked the GUI, thereby improving
usability and perceived performance of the application. Many load,
save, and layout operations now utilize the Threading/Task Framework.
On-line Help System
An on-line help system supporting topic-based, indexed, context-sensitive and full-text search is now available. The on-line help system is based on JavaHelp technology, and supports the standard on-line help conventions, including “F1” (function key F1) and Help menu activated help system invocation. Current help content is derived and indexed from the Cytoscape 2.1 User Manual.
The 2.1 release of Cytoscape includes updates to the user and developer documentation. Updated APIs and more complete “JavaDoc”'s capturing new, changed and deprecated APIs introduced by the core changes in the Cytoscape 2.1 release are included for developers and plug-in writers.
Five “core” plug-ins are bundled and distributed with Cytoscape 2.1. 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 |
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 |
Web Search |
yeast-context.jar |
Provides graph object-based general web search functionality; launches Google search against selected node or edge name |
Yeast context-sensitive menu |
yeast-context.jar |
Provides Yeast-specific web search capabilities |
Table 1. Core Plug-ins
The Cytoscape Collaboration © 2005