Cytoscape full changelog

Improved layout behavior and performance:
Added “selected nodes only” preferred-layout support
Parallelized selected layout calculations for Prefuse Force Directed and BioLayout FR where appropriate
Preserved deterministic behavior when the deterministic layout option is enabled
Improved table copy/paste behavior so multi-cell clipboard operations preserve spreadsheet-style grid structure
Removed redundant “Copy Selected” table context-menu action in favor of normal Copy
Fixed global tables not appearing in the Unassigned Tables panel when added to CyTableManager but not set as current
Fixed task history window listener cleanup and debounce handling after dialog close
Fixed group/session load handling by listening for SessionAboutToBeLoaded instead of SessionLoaded
Added app update notification bell behavior for App Store upgrades, with tests

Fixed a bug where opening a network in Cytoscape from Cytoscape Web incorrectly set the collection name to ?(SUID: ##)
Fixed a bug where styles were corrupted if Show Tasks was opened at any time before invoking close session
Fixed bug where moving a group of nodes fails after reloading in Cytoscape
The “Layout only selected nodes” control in the Layout Settings dialog is now a button labeled Apply to Selected Nodes, making the action more explicit and easier to use

Updates CyNDEx-2 to 2.3.2 to fix inability to download JXBrowser.

Annotations:
Annotations in the form of shapes, images or text can be added to the network canvas. Place annotations in front of or behind the network to create informative visualizations without leaving Cytoscape!
BrewerColor Node and Edge Mappings:
Choose a predefined palette from the Palette picker. These come from published recommendations for choosing colors in scientific and cartographic applications, such as BrewerColors.
Canvas Selection Toggles:
New and improved toggles for node, edge, and annotation selection, making it easy to maintain control over stacked network elements without having to shuffle them around.
Automatic JVM Installation:
For Windows and Mac users, if the Cytoscape installer doesn't find a suitable Java Virtual Machine (JVM) already on your workstation, it will download and install one for you. For Linux users, the Cytoscape installer won't download a JVM -- Java 8 (rev 151 or later) must be on the PATH (ahead of any other JVM) or referenced by the JAVA_HOME

Automatic JVM Installation:
For Windows and Mac users, if the Cytoscape installer doesn't find a suitable Java Virtual Machine (JVM) already on your workstation, it will download and install one for you. For Linux users, the Cytoscape installer won't download a JVM -- Java 8 (rev 151 or later) must be on the PATH (ahead of any other JVM) or referenced by the JAVA_HOME environment variable.

Cytoscape Automation:
Automating Cytoscape operations promotes reproducible science, scaling to large numbers of networks, and participation in larger and more complex workflows. In 3.6, Cytoscape and various apps are callable as services by Python, R and Cytoscape Command scripts.

ID Mapper:
ID mapping is a classic problem in bioinformatics. Now you don't have to use external tools to do the mapping. You can directly call the ID mapping service from the table browser.
Node Layout Tools:
In 3.5, all of the manual node layout tools are consolidated into one panel for tweaking layouts.

The most popular new features include:
Ability to map symbol names by right-clicking on the column name in the data table
Improvements in the File | Export functions
CoSE Layout (for compound nodes)

Cleaner User Interface - improved network and table file importer, new icons for the toolbar, aesthetic and consistency improvements in many dialogues.
Filters can select based on properties of adjacent nodes and can edit selections
Groups can be visualized as compound nodes.
Some of the Cytoscape core features are now released as independent Core Apps. This means you can get more frequent updates for those features.