At a glance
A living view of where effort is going. Items move from Later toward Now as work matures; dates firm up as releases approach. Colour marks the track.
Shipping
Released or in active development
Cytoscape 3.10.4 — bug fixes for Web interoperability, layout settings, and session stability.
Cytoscape Web live at web.cytoscape.org — in-browser visualization, styling, and NDEx-backed workspaces.
Mature graph library on npm — weekly patch and monthly feature releases keep turnaround fast.
Up next
Targeted for the coming release cycle
Cytoscape 3.11 (Oct 2026) — Java 25 support and an upgraded REST framework for CyREST.
Web ↔ notebook interoperability and tighter Open in Cytoscape round-tripping.
Release v1.1.0 (Aug 2026) — App API v1.0 and image export support.
Ongoing v3 API refinements and rendering performance, tracked in the GitHub milestones.
Exploring
Direction set, scope still forming
Expanding the Web App ecosystem; deprecate the raw Module Federation store once the new API lands.
Deeper, near-costless NDEx integration as the natural home for networks and workspaces.
Additional rendering engines (e.g. Cell View) and broader automation support in the browser.
Growing first- and third-party extension ecosystem — layouts, UI, and integrations.
Cytoscape Desktop
The full-featured workhorse
Desktop remains the deepest environment for network biology — mature apps, large-network capacity, and full automation. Near-term work modernizes the runtime and tightens the bridge to the browser.
Planned themes & features
- Java 25 support
- Upgraded REST framework for CyREST
- Service App support
Current release: 3.10.4 (Sep 2025). A preliminary feature list is published ahead of each release and frozen ten days before — see Process.
Longer-term vision
Core & Core Apps
A lean Core handles reading, displaying, and writing networks; biology-aware Core Apps ship alongside it but update independently via the App Store — so features and fixes reach users without waiting for a full release.
Cytoscape Automation
A Commands interface for user-style actions and a Functions interface for programmatic network manipulation, both exposed over CyREST — making reproducible, scriptable workflows first-class.
NDEx integration
Loading and saving networks through NDEx as the default, with fast, near-costless sampling so exploration stays on-task and sharing is seamless.
Large language models & agentic AI
A longer-term direction is to integrate Cytoscape Desktop with large language models and broaden support for agentic AI use cases. By publishing skill files tailored to different AI vendors, the project aims to let assistants and autonomous agents drive Cytoscape through its automation interfaces — turning plain-language goals into reproducible, auditable network analyses.
Cytoscape Web
Network biology in the browser
Cytoscape Web brings visualization, data-driven styling, and collaborative workflows to any modern browser — no installation. It synchronizes an in-memory data store to the browser's IndexedDB and persists work through NDEx. As a newer tool it is still growing toward Desktop's depth, while pioneering capabilities of its own.
What's live now
- In-browser visualization with data-driven visual styles
- NDEx integration for network & workspace storage
- Import of CX2 and CSV; export to common image formats
- Open in Cytoscape hand-off to Desktop (requires 3.10+)
- Multiple rendering engines, including Cell View
Where it's heading
A bug-fix release, v1.0.8, will ship first, ahead of the v1.1.0 feature release.
App API v1.0 & image support
Version 1.1.0 targets the first stable release of the App API (v1.0) — the recommended way to build Web apps — alongside image export support. The new API will eventually deprecate the current raw-store approach.
Desktop ↔ Web feature comparison
The two tools are complementary. Desktop leads on analysis depth, apps, and sessions; Web leads on access, workspaces, and hierarchical/Cell views. This mirrors the official Functionality Support Matrix maintained in the Cytoscape Web wiki — capabilities evolve each release.
| Functionality | Desktop | Web |
|---|---|---|
| Network Visualization | Full | Full |
| Visual Styles | Full | Full |
| Table Editing | Full | Full |
| Undo / Redo | Full | Full |
| Access to External Databases | Full | Partial |
| Import | Full | Partial |
| Export | Full | Partial |
| Layout | Full | Partial |
| Layout Tools | Full | Partial |
| Filters | Full | Partial |
| Element Selection | Full | Partial |
| Network Editing & Operation | Full | Partial |
| Annotations | Full | Partial |
| App interface 1 | Full | Partial |
| Analysis Tools | Full | — |
| Network Analyzer | Full | — |
| App Store | Full | — |
| Element Group | Full | — |
| Session | Full | — |
| Hierarchical Network & Cell View | — | Full |
| Workspace | — | Full |
1 Both versions support external apps but use different app frameworks; the Cytoscape Web app interface is currently in public testing.
Cytoscape.js
The open-source graph library
Cytoscape.js is the developer-facing foundation of the platform — a dependency-free JavaScript library for modelling, analysing, and visualising networks. It can be embedded in web apps, websites, and servers, and underpins a wide range of third-party network viewers across research and industry.
What it offers
- Graph-theory model plus an optional interactive canvas renderer
- One-line setup: cytoscape({ elements, container })
- Runs in all modern browsers, or headless under Node.js
- Pure JS, no dependencies — works with npm, Webpack, ES modules, or plain script tags
- Extensible via first- and third-party extensions (layouts, UI, integrations)
- MIT-licensed core and first-party extensions
Where it's heading
Stable, with steady momentum
The version 3 API is mature; future work is planned openly through GitHub milestones. The weekly/monthly release rhythm gives contributors a fast feedback loop for both first- and third-party changes.
Foundation for the web ecosystem
As the rendering and analysis layer behind many browser-based network tools, ongoing performance and API refinement benefits the whole community — including tools that complement Cytoscape Web.
Shared ecosystem
Some work spans both products. These shared foundations are what make Desktop and Web feel like one platform rather than two tools.
Automation & interoperability
CyREST plus the Python and R client libraries let users drive Cytoscape from Jupyter and RStudio, building reproducible, scriptable workflows that scale beyond keyboard and mouse.
NDEx network commons
NDEx is becoming the shared home for networks and workspaces — the connective tissue that lets a network move freely between Web, Desktop, and the wider cyberinfrastructure.
App Store & Collections
The App Store remains the hub for community-built functionality, with Collections bundling the apps a given workflow needs. The new Web App API extends this model into the browser.
Community & outreach
Documentation, tutorials, and an active developer community keep the platform learnable and extensible. Contributions to the roadmap are welcome through the community channels.
Release process & policies
Cytoscape Desktop ships on a predictable cadence with milestone builds and frozen APIs along the way. Cytoscape Web, as a browser app, releases continuously, and Cytoscape.js ships weekly patch and monthly feature releases via npm. The policies below govern the Desktop cycle.
Desktop release cadence & policies P1–P11
A new Desktop version ships roughly every six months (~April 15 and ~November 15), with Core App updates to the App Store as needed.
High-risk Core features must land eight weeks before release, or they carry over to the next cycle.
Other features must land in the Core five weeks before release.
Reviewed bug fixes may land up to ten days before release.
External APIs (including CyREST) are frozen, documented, and preliminarily implemented eight weeks before release; a developer release is published.
Milestone builds are made available eight weeks, five weeks, and ten days before release — plus extra builds when needed.
Milestone and nightly builds are published via the developer Download page.
Emerging API definitions (or links to them) are posted on the developer Download page.
A preliminary feature list is published five months out, updated periodically, and frozen ten days before release.
Functionality is exercised heavily through external scripting (e.g. Python-driven tests) via Cytoscape Automation.
New Core App nominations are accepted until eight weeks before release; Core developers may accept them until five weeks before. Core Apps follow the same Q/A process as Core code.
Release history
Two decades of releases, kept tucked away so the roadmap stays forward-looking. Expand a track to browse the record.
Cytoscape Desktop — recent releases 3.x
Earlier milestones: 3.2 (2014) · 3.1 (2014) · 2.8 (2010) · 2.7 (2010) · 2.5 (2007) · 2.0 (2004) · 1.0 (2003) · 0.8 (Jul 2002, first release). Full version-by-version notes are available on request.
Cytoscape Web — releases 1.x
As a continuously deployed browser application, Cytoscape Web does not follow the six-month Desktop cadence; the reference build at web.cytoscape.org always reflects the latest release.
Cytoscape.js — releases 3.x
Future versions are planned openly in the GitHub issue tracker's milestones. The library follows its own rapid npm cadence, independent of the Desktop and Web schedules.