Cytoscape
Cytoscape
3.9.0
0.0
0.0
Cytoscape free download for Mac

Cytoscape

Version 3.9.0

Molecular interaction network visualizations.

Cytoscape 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 version 3.9.0

Updated on Oct 13 2021

Version 3.9.0:
Improvements
  • The network view now supports native resolution on 4K Ultra-HD and Retina displays
  • New visual property for haystack edges A haystack edge is drawn as a straight line from the source node to the target node, randomly placed along some angle from each node’s centre In this manner, many parallel haystack edges make a tight bundle, especially when semi-transparent This makes haystack edges an effective way to visualise graphs with a high number of parallel edges
  • New visual property for edge z-order This allows control over the order in which edges overlap
  • Improved UI for creating and editing Annotations The dialog for editing annotations has been removed and replaced with a tab in the Annotations panel This allows annotations to be edited in a more convenient way that does not block the network view
  • New ability to rotate node labels and annotations
  • The Fit Content action, which zooms and fits the network to the window, will now take node labels into account
  • The network view now supports SVG graphics for node and annotation images
  • Network view rendering speed has been improved
Tables:
  • There is now support for visual styles in the node and edge tables Using a new Table tab in the Style Panel, it is now possible to set style values and style mappings on individual columns in the node and edge tables This includes the ability to customize fonts, colors, row height and table grid lines There is also support for charts such as bar charts and sparklines
  • The node and edge tables have improved copy/paste support It is now much easier to select a set of cells from the node or edge table and copy/paste to an external application This removes the need to export the table to a file in order to insert the data into an application such as Excel
  • The equation builder has been completely redesigned It now supports free-form editing of formulas with syntax highlighting, built-in documentation, and instant feedback when the formula has errors
General:
  • The style selector pop-up in the Style Panel has been enhanced to allow easy searching for styles based on name, and to make it easier to copy, duplicate, and delete styles
  • Color palettes are now universally available in the color picker
  • Improved hotkey mapping
  • Filters can now select or highlight nodes and edges
  • New auto page size option for network view PDF export This allows the dimensions of the exported PDF document to automatically match the dimensions of the network view
For Notebook Writers:
  • There are several new commands for creating and editing network annotations
  • Support for Python (via py4cytoscape) and R (via RCy3) based Cytoscape workflows
  • The Help menu now has a link to automation tutorials
  • Support for Google Colab and GenePattern Notebooks
For App Developers:
  • All of the new table style visual properties are available as API This includes the ability to set the order, visibility and width of columns through API
  • Several existing visual properties that were private and internal to the 2D renderer are now public API
  • There is a new OSGi service API for creating network thumbnail images It is no longer necessary to create a RenderingEngine in order to generate a simple network image thumbnail
  • New Togglable Task Factories, which can be used to create menu items that have checkmarks when enabled

Information

License

Free

Size

288.9 MB

Downloads

463

App requirements

  • Intel 64
  • Mac OS X 10.7.3 or later
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