It is a common mistake to confuse these two. Here is a quick comparison: Cytoscape.js Cytoscape Desktop JavaScript Library (for web) Standalone Application (Java) User Software Developers Scientists & Researchers Environment Web Browsers (Chrome, Safari, etc.) Windows, Mac, Linux (requires Java) Primary Use Building custom web apps Heavy-duty biological network analysis Installation npm, CDN, or JS file Installer (.exe, .dmg, .sh) Why Choose Cytoscape.js? Cytoscape.js

Access all versions via the cytoscape CDN on jsDelivr . 3. Direct Download from GitHub

Because it is a developer library, there isn't a single ".exe" file. Instead, you "download" it by integrating it into your project using one of the following standard methods: 1. Via Package Managers (Recommended)