Cytoscape 2.1 Features

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 Improvements

Optimization and Run-Time Performance Improvements

Performance Optimization of Graph Model

New Features and Functionality

VizMapper

Node label color control has been added.

Graph Model and Operations

New layout features are available, providing new operations on selected nodes:

External Data Support

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:

Usability Improvements

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 Operations Save Operations Layout

A 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.

Documentation

Technical Documentation

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.

Core Plug-Ins

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