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Cytoscape Changelog

What's new in Cytoscape 3.10.1

Mar 27, 2024
  • Maintenance Release:
  • 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 3.9.0 (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 3.8.1 (Sep 25, 2020)

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

New in Cytoscape 3.7.2 (Sep 5, 2019)

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

New in Cytoscape 3.7.1 (Sep 5, 2019)

  • Hotfix for exporting group annotations in network as png

New in Cytoscape 3.7.0 (Oct 23, 2018)

  • 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 (Jul 18, 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 27, 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 RC1 (Dec 8, 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 (Dec 8, 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 3.3.0 (Dec 2, 2015)

  • 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.
  • This release includes many bug fixes. Addresses 193 issues relative to v3.2.1
  • cyREST is now a part of core distribution as a core app. Both cyREST API and Commands are accessible from same port.
  • Network Analyzer is optimized and is up to 1000 times faster than previous version.
  • 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)

  • Command scripts can be executed from the command line using the –s option
  • On Cytoscape/Windows, the HTML5 exporter now generates valid web sites
  • 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 3.1.1 (May 28, 2014)

  • 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 (Apr 2, 2014)

  • New Style Editor:
  • Cytoscape 3.1.0 has a new Visual Style editor. It is more intuitive, and easy to use
  • New Filter:
  • New Filter is much faster than the last version. User interface is also updated for handling more complex queries in real time.
  • Export to JSON:
  • Cytoscape 3.1.0 can export networks, tables, and Visual Styles into cytoscape.js compatible JSON format. This means you can use network visualizations created with Cytoscape in web browsers. (Try it in the window below.)
  • Commands and Its REST API:
  • Basic Cytoscape functions, such as Layout, or export to files, can be accessed through Cytoscape Commands. You can automate your workflow by writing simple Command files. Commands are accessible from REST API.
  • Updated Welcome Screen:
  • New Welcome Screen with more preset data sets.
  • Updated Remote Database Client:
  • New remote data access client (PSICQUIC Client) is faster, and more stable. It supports new MITAB 2.7 table columns.

New in Cytoscape 3.0.0 (Feb 5, 2013)

  • Updated Welcome Screen:
  • For convenience, Cytoscape shows Welcome Screen at startup time which 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 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:
  • We've 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!

New in Cytoscape 2.8.2 (Mar 8, 2012)

  • Bug Fixes
  • This is mainly a bug fix release. We hope the changes will make the Cytoscape user experience more pleasant and consistent.
  • Improved Memory Allocation
  • We have improved the memory detection and allocation process that occurs when Cytoscape is first installed and launched. The process attempts to optimize memory settings based on your hardware. The new process avoids system crashes that were occurring with 2.8.1.
  • New Gradient Editor
  • We've overhauled the user interfaces controlling the mapping of continuous values to visual styles, like Node Size and Node Color, to provide more intuitive and consistent controls.
  • Well-Behaved CytoPanels
  • We revamped the behavior of CytoPanels so that each plugins preferred panel size will be automatically fit when the user switches to them. A global minimum size is set for all panels so that users can manually resize no matter which panel they are viewing.
  • Error Console Feature
  • If your Cytoscape session starts acting funny, go to Help > Error Console. You can now Save the console output as a single html file and attach it to your helpdesk and discussion list posts.