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Cytoscape Changelog

What's new in Cytoscape 3.10.2

Mar 27, 2024
  • Layout tools exposed in CyREST: rotate and scale
  • SVG export with Japanese locale
  • Lucene wildcard query
  • Many bug fixes

New in Cytoscape 3.10.1 (Aug 31, 2023)

  • Better support for all versions of Java 17 and greater
  • Many bug fixes

New in Cytoscape 3.10.0 (May 12, 2023)

  • Highlights:
  • New selection lasso tool. Hold Ctrl-Shift on Windows/Linux, or Cmd-Shift on Mac, then use the mouse to draw a free-form loop around nodes you wish to select.
  • Edge label rotation allows edge labels to be aligned with the edge slope.
  • Table styles are now part of the Network Style and are applied to the node and edge tables.
  • New App Store panel has replaced the old “App Manager”
  • The search bar is faster and more reliable. There are new types of search queries available such as numeric range queries.
  • Additional Improvements and New Features:
  • The mouse wheel now zooms to the location of the mouse pointer.
  • Shape Annotations now support color gradients.
  • New Visual Properties for node and edge label background color.
  • Network image export is much faster.
  • Edge bundling is faster and uses significantly less memory.
  • New native installer for Mac computers with Apple Silicon.
  • The Image Manager has been streamlined for ease of use.
  • Networks in the Network panel can now be sorted alphabetically.
  • New toolbar button in the edge table can be used to map node table columns into the edge table.
  • For App and Notebook Developers:
  • Cytoscape now uses Java 17
  • JavaFX version upgraded to 18.0.2
  • The OpenCL app has been moved into core. OpenCL support is now part of the Cytoscape API as the ‘cycl-api’ bundle.
  • The TableVisualMappingManager has new API methods for working with table styles.
  • The network view can now be exported using new commands “view export png, view export pdf, view export jpg, etc”. These commands provide additional parameters that can fine tune the results for each format.
  • New LEN() equation function returns the length of a list.
  • String Tunables have a “password” property that causes the text field to be masked.
  • The framework-cytoscape.log file no longer grows forever. Log entries are deleted after 30 days.

New in Cytoscape 3.9.1 (May 12, 2023)

  • Addressing the following issues:
  • Updated log4j dependencies in core to 2.17.1 via pax-logging (1.11.13)
  • Updated log4j dependencies to 2.17.1 in SBMLReader core app
  • Automation: updates to annotation and app-related commands
  • Minor fixes to table equations

New in Cytoscape 3.9.0 (Oct 13, 2021)

  • Network Renderer:
  • 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.

New in Cytoscape 3.8.2 (Oct 30, 2020)

  • Cytoscape 3.8.2 is a Cytoscape Desktop BugFix release, addressing multiple issues.

New in Cytoscape 3.8.1 (Sep 27, 2020)

  • Cytoscape 3.8.1 is a Cytoscape Desktop BugFix release, addressing multiple issues.

New in Cytoscape 3.8.0 (Apr 17, 2020)

  • 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.

New in Cytoscape 3.7.2 (Sep 6, 2019)

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

New in Cytoscape 3.7.0 (Mar 7, 2019)

  • 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 environment variable.
  • Cytoscape Automation:
  • Automating Cytoscape operations promotes reproducible science, scaling to large numbers of networks, and participation in larger and more complex workflows. As of 3.6, Cytoscape and various apps are callable as services by Python, R and Cytoscape Command scripts.
  • NDEx Integration:
  • It is now possible to load networks from an NDEx database directly into Cytoscape (using the Network Search Bar) and to save them directly from Cytoscape (using standard menus). NDEx makes cloud-based sharing and collaboration easy.
  • Network Search Bar:
  • The user interface for loading networks from web-based databases has been dramatically streamlined. Using the new Network Search Bar, you choose the database and enter a query, all from the main Cytoscape network panel. Apps that provide this access include PSICQUIC, NDEx, STRING, STITCH and Pathway Commons.
  • Drag & Drop Support:
  • To load networks and data tables from files, you can simply drag & drop them onto Network Panel / Table Browser.
  • CyBrowser Integration:
  • App developers can create HTML-based material that can appear in a browser-like window within Cytoscape itself, and can access Cytoscape APIs and events.
  • Diffusion:
  • This heat propagation algorithm uses the network topology to deduce a pertinent set of nodes given a seed set. Subnetworks can then be derived for further investigation.
  • Copycat Layout:
  • Use node positions in one network to lay out nodes in another network, thereby simplifying visual network comparison.
  • Animated Tooltips:
  • Toolbar buttons have illustrative tooltip GIFs to show the functionality of the button.
  • Improved Selection Performance:
  • Select large numbers of nodes much more quickly than in previous versions.

New in Cytoscape 3.6.1 (Mar 28, 2018)

  • 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.
  • yFiles Update:
  • 3.6 includes an all new set of yFiles layouts, replacing the older and slower versions. The layouts are more attractive and perform routing with much greater precision.
  • NDEx Integration:
  • It is now possible to load networks from an NDEx database directly into Cytoscape (using the Network Search Bar) and to save them directly from Cytoscape (using standard menus). NDEx makes cloud-based sharing and collaboration easy.
  • Network Search Bar:
  • The user interface for loading networks from web-based databases has been dramatically streamlined. Using the new Network Search Bar, you choose the database and enter a query, all from the main Cytoscape network panel. Apps that provide this access include PSICQUIC, NDEx, STRING, STITCH and Pathway Commons.
  • Starter Panel:
  • When Cytoscape starts, it shows both recent and sample networks in an attractive layout that replaces the older Welcome Dialog. Cytoscape now represents saved networks as thumbnails for faster and easier access. The new sample networks are packaged as modern, immediately useful, and ready-to-load sessions.
  • Drag & Drop Support:
  • To load networks and data tables from files, you can simply drag & drop them onto Network Panel / Table Browser.
  • CyBrowser Integration:
  • App developers can create HTML-based material that can appear in a browser-like window within Cytoscape itself, and can access Cytoscape APIs and events.
  • Diffusion:
  • This heat propagation algorithm uses the network topology to deduce a pertinent set of nodes given a seed set. Subnetworks can then be derived for further investigation.
  • Copycat Layout:
  • Use node positions in one network to lay out nodes in another network, thereby simplifying visual network comparison.
  • Unattended Installation:
  • Bypass the Cytoscape installer user interface when it's convenient to install Cytoscape via a script.
  • Improved Selection Performance:
  • Select large numbers of nodes much more quickly than in previous versions.

New in Cytoscape 3.6.0 (Nov 26, 2017)

  • 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.
  • yFiles Update:
  • 3.6 includes an all new set of yFiles layouts, replacing the older and slower versions. The layouts are more attractive and perform routing with much greater precision.
  • Network Search Bar:
  • The user interface for loading networks from web-based databases has been dramatically streamlined. Using the new Network Search Bar, you choose the database and enter a query, all from the main Cytoscape network panel. Apps that provide this access include PSICQUIC, NDEx, STRING, STITCH and Pathway Commons.
  • Starter Panel:
  • When Cytoscape starts, it shows both recent and sample networks in an attractive layout that replaces the older Welcome Dialog. Cytoscape now represents saved networks as thumbnails for faster and easier access. The new sample networks are packaged as modern, immediately useful, and ready-to-load sessions.
  • Drag & Drop Support:
  • To load networks and data tables from files, you can simply drag & drop them onto Network Panel / Table Browser.
  • CyBrowser Integration:
  • App developers can create HTML-based material that can appear in a browser-like window within Cytoscape itself, and can access Cytoscape APIs and events.
  • Diffusion:
  • This heat propagation algorithm uses the network topology to deduce a pertinent set of nodes given a seed set. Subnetworks can then be derived for further investigation.
  • Copycat Layout:
  • Use node positions in one network to lay out nodes in another network, thereby simplifying visual network comparison.
  • Unattended Installation:
  • Bypass the Cytoscape installer user interface when it's convenient to install Cytoscape via a script.
  • Improved Selection Performance:
  • Select large numbers of nodes much more quickly than in previous versions.

New in Cytoscape 3.5.0 (Mar 29, 2017)

  • 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.
  • Improved Export Dialog:
  • When you export network views to images, you can specify DPI directry to create proper resolution bitmap images.
  • Drag & Drop Support:
  • To load networks and data tables from files, you can simply drag & drop them onto Network Panel / Table Browser.
  • Long Running Remnote Task API:
  • This feature is for App developers. To execute long running remote tasks, such as network analysis or layout using remote computing clusters, app developers can use this API to manage those tasks.
  • Compound Spring Embedder (CoSE) Layout:
  • For grouped nodes rendered as cmpound nodes, you can apply CoSE llgorithm for better result.
  • Faster Row Deletion:
  • Table row deletion is much faster than the previous version.

New in Cytoscape 3.5.0 RC 2 (Feb 15, 2017)

  • 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)
  • Fixed memory leaks and forever-growing .cys files
  • Faster deleteRows()
  • Network import using https is fixed
  • Removing duplicate edges on large networks doesn’t hang
  • Help Citations works with new PubMed

New in Cytoscape 3.5.0 RC 1 (Dec 5, 2016)

  • 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)
  • Fixed memory leaks and forever-growing .cys files
  • Faster deleteRows()

New in Cytoscape 3.4.0 (May 14, 2016)

  • NEW NETWORK VIEW MANAGER:
  • Cytoscape 3.4 has new user interface for browsing networks. You can choose from three view modes:
  • Standard View
  • Grid View
  • Detached View
  • NETWORK PREVENANCE:
  • Parent-child relationships of your networks are visualized as trees on the Network Panel.

New in Cytoscape 3.4.0 Beta (Mar 15, 2016)

  • All new network view management system leverages multiple monitors
  • Startup speed much quicker

New in Cytoscape 3.3.0 (Nov 28, 2015)

  • Highlights:
  • Network Analyzer is more than 1000 times faster
  • Filters can select based on properties of adjacent nodes and can edit selections
  • Improved network and table file importer
  • GPU support for Prefuse layouts
  • Improvements in Group settings & visualization
  • Default network layout is now force directed
  • Aesthetic and consistency improvements in many dialogs
  • Cytoscape core functions are repackaged as apps that can be improved often
  • Cytoscape now detects when new versions of your installed apps are available
  • cyREST is now delivered with Cytoscape
  • Cleaner User Interface:
  • Improved network and table file importer
  • New icons for the toolbar
  • Aesthetic and consistency improvements in many dialogs
  • Improved Filter:
  • Filters can select based on properties of adjacent nodes and can edit selections
  • Improved Group Visualization:
  • Groups can be visualized as compound nodes
  • Core Apps:
  • Some of the Cytoscape core features are now released as independent Core Apps. This means you can get more frequent updates for those features.
  • Bug Fixes:
  • This release includes many bug fixes. Addresses 193 issues relative to v3.2.1.
  • Integrated RESTful API:
  • cyREST is now a part of core distribution as a core app. Both cyREST API and Commands are accessible from same port.
  • Faster Network Analyzer:
  • Network Analyzer is optimized and is up to 1000 times faster than previous version.
  • GPU-Based Layout:
  • Force-directed layout algorithm is optimized via GPU. It is up to 100 times faster than CPU-based layout.

New in Cytoscape 3.2.1 (Feb 13, 2015)

  • Full support for Java 8 and 43 bug and feature fixes, including:
  • Command scripts can be executed from the command line using the –s option
  • Various layouts now honor node selection: improvements for accessing Cytoscape data model and functions via cyREST
  • Lots of cosmetic improvements, and minor fixes for app writers

New in Cytoscape 3.2.0 (Nov 26, 2014)

  • PERFORMANCE:
  • Improved Network Loading Speed:
  • Network loading process is optimized and faster than 3.1.x.
  • Improved Rendering Engine Performance:
  • Rendering engine is optimized especially for large networks. Zoom/pan is more efficient and faster than past 3.x series.
  • Faster Network Merge:
  • Network merge function is parallelized and is much faster for large networks.
  • Improved Startup Speed:
  • Startup process has been optimized and startup time is shorter than 3.1.
  • Chart Editor:
  • Cytoscape 3.2 has a built-in chart editor. You can use node table data as the source of your charts and render them as high-quality vector graphics. It supports standard charts including: bar, box, line, pie, heatmap, and ring. In addition to charts, it supports gradients. It is a part of Visual Style editor and you can save everything in your session file.
  • INTERACTIVE WEB VISUALIZATION:
  • Cytoscape exports your session as Cytoscape.js-based web visualization. You can publish your networks as a complete web application. This feature is for Mac and Linux only. Support for Windows will be available in 3.2.1.
  • IMPROVED COMMAND/TUNABLE API:
  • API for Tunables and Commands are cleaned up and more stable (for developers).

New in Cytoscape 3.2.0 Beta 1 (Sep 18, 2014)

  • Much faster startup
  • Much faster session loading
  • Much faster drawing of large networks
  • Much faster network merge
  • Ability to display a node as a chart
  • Export network as a full web site
  • Safer internal data handling of multi-threaded apps [App Developers]
  • Improved command/tunable API [App Developers]

New in Cytoscape 3.1.1 (May 28, 2014)

  • Major Bug Fixes:
  • #2465: DialogTaskManager/CyTableImpl threw: column already exists ... 'layoutAlgorithm'
  • #2055: JVM SIGSEGV appears on Cytoscape startup/shutdown on Ubuntu 13.04+Oracle Java 7
  • #2511: Mappings sometimes not applied when restoring session
  • #2514: Session saved with equation return type not matching column type results in instability when reloaded
  • #2516: Filters not cleared when starting/loading new session
  • #2548: ConcurrentModificationException When Recreating CyNetworkViews
  • #2653: Command processing using "-S" is broken
  • #2586: Ding deadlock in 3.1.1

New in Cytoscape 3.1.0 (Feb 21, 2014)

  • Improved Welcome Screen
  • Greatly improved Vizmapper
  • JSON format network export
  • Sample personal web site publishing template
  • Import and merge/link of unassigned tables
  • Command line and REST interface
  • Blazing fast filtering
  • Annotation groups
  • Much improved PSICQUIC support
  • App citation listings
  • Updated and improved user documentation
  • Retired over 236 issues since the v3.0.2 release in July

New in Cytoscape 3.1.0 Beta 3 (Jan 29, 2014)

  • Improved Welcome Screen
  • Greatly improved Vizmapper
  • JSON format network export
  • Sample personal web site publishing template (still under development)
  • Import and merge/link of unassigned tables
  • Command line and REST interface
  • Blazing fast filtering
  • Annotation groups
  • Much improved PSICQUIC support
  • App citation listings
  • Updated and improved user documentation

New in Cytoscape 3.1.0 Beta 2 (Dec 3, 2013)

  • Improved Welcome Screen
  • Greatly improved Vizmapper
  • JSON format network export (still under development)
  • Import and merge/link of unassigned tables
  • Command line and REST interface
  • Blazing fast filtering
  • Annotation groups
  • Greatly improved task display
  • Much improved PSICQUIC support
  • App citation listings

New in Cytoscape 3.0.2 (Oct 18, 2013)

  • Many bug fixes

New in Cytoscape 3.0.1 (Apr 23, 2013)

  • Addresses over 100 bugs and issues

New in Cytoscape 3.0.0 (Feb 5, 2013)

  • Updated Welcome Screen:
  • For convenience, Cytoscape shows Welcome Screen at startup timewhich provides easy way to access sample data sets and public databases.
  • Edge Bend Visual Property:
  • Edge Bend is now a standard Visual Property. You can use it as a part of your Visual Style.
  • Edge Bundling:
  • You can bundle edges by automatic Edge Bundling. This feature is useful for dense network views.
  • Network Annotations:
  • You can add notes and simple shapes to background or foreground of network view.
  • Advanced Search Function:
  • From this version, EnhancedSearch plugin is part of core. You can search networks using Lucene syntax.
  • Show All feature in Data Table Browser:
  • By selecting Show All option in Data Table Browser, you can display all network objects in the table. Nodes and edges will be selected when you select associated rows in the table.
  • Network Collection:
  • Cytoscape 3 manages networks based on Network Collection. When you load networks to Cytoscape, you can choose creating a new set of networks or adding them to existing collection.

New in Cytoscape 3.0.0 Beta 1 (Oct 12, 2012)

  • New welcome screen and toolbar for quick access to common actions
  • New Data Table controls to interface with your data
  • Integrated support for graphical annotations in networks
  • Support for independent collections of networks within a single session
  • Advanced network and table import controls
  • Enhanced searching
  • Edge bending and bundling
  • One-click installation of apps from the Cytoscape App Store
  • Improved architecture and API for a more stable experience

New in Cytoscape 2.8.3 (Jul 19, 2012)

  • VizMapper fixes:
  • We fixed a few problems with the VizMapper that were disappearing visual properties and otherwise making the VizMapper difficult to use.
  • Better support for Macs without a 3-button mouse:
  • You can now CMD-click to simulate right clicking on Mac laptops, which allows easier panning of networks. We've also enabled the arrow keys (and shift-arrow) to allow panning.
  • Reorganized plugin categories:
  • Reorganized plugin categories. You should see the new categories in the plugin manager and on the plugin website. This is just a prelude of exciting changes to come!