Cytoscape
Cytoscape
3.8.0

0.0

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Cytoscape3.8.0

17 April 2020

Molecular interaction network visualizations.

Overview

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. They may be developed by anyone using the Cytoscape open API based on Java technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store

What's new in Cytoscape

Version 3.8.0:
Faster Renderering:
  • Rendering performance has been increased and optimized for interacting with larger networks. Cytoscape now provides an interactive user experience for networks with as many as 10,000 nodes and 3,000,000 edges
New Panel Options:
  • Your Cytoscape workspace can now be customized for your available screen space with a new workspace panel system. Panels can now be minimized, set to float, or docked in the workspace
Toolbar Customizations:
  • You can now select when items appear in your toolbar, reducing clutter, and giving you quick access to your most used tools
Updated Analyzer App:
  • The Network Analyzer core app has been reworked. The user interface has been improved, and Cytoscape Automation support has been added for accessibility from scripts and analysis workflows
Label Repositioning Tool:
  • Labels can now be quickly and intuitively positioned from within the Network View
CyBrowser JavaFX Update:
  • CyBrowser, Cytoscape's included web browser, has been updated to use JavaFX 13. CyBrowser now has greater compatibility with modern web pages and applications
Java 11 Support:
  • Cytoscape is compatible with Java 11, keeping up to date with the latest Java support. Cytoscape comes bundled with an AdoptOpenJDK JVM
CyNDEx-2 Updates:
  • CyNDEx-2 has been updated with Swing UI support, significantly reducing startup time and increasing stability
CX Support Updates:
  • Support for the CX data exchange format continues to improve, facilitating reliable transfer of network data between Cytoscape desktop and other ecosystem components

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