Cytoscape is a powerful software program developed by Cytoscape Consortium in order to fulfill the needs of biology students or accomplished researchers of digging deep into this field, either by doing complex molecular interaction networks or by integrating them with state data and annotations.
As you enter the program, you get in contact with a modern and enjoyable interface, one that has well-organized sections and tabs, and nicely crafted button icons. Though the software has a pretty neat GUI, it requires important system memory in order to enjoy its features at full capacity.
Also, it would've been nice to have some skin themes to choose from or some advanced appearance options.
Its features are various and can be used in different fields such as biology, social science or complex network analysis.
With Cytoscape you can establish visual mapping across integrated datasets, project functional annotations or perform advanced modeling using Cytoscape Apps.
Moreover, you can assemble social networks from tables and forms, calculate network statistics, or use tools like R or NetworkX for in-depth analysis. Other features included are an option to find clusters by various types of algorithms, or the possibility to find the shortest path.
All in all, Cytoscape is a comprehensive research tool, one that it's intended to be used by professionals, or by skilled students. The program is constantly improved and updated in order to give users a flawless experience.
v3.0 [Feb 6, 2013]
3.x is the whole new version of Cytoscape with modular architecture. It is designed for long-term maintainability and eventually it replaces 2.x series. New major features, including new user interfaces, headless (command-line) distribution, and multiple rendering engine support, will be released for this version. Currently, Cytoscape community is in the middle of transition from 2.x to 3.x. Core and third party App developers are working hard to port as much as 2.x features and Apps to 3.x series.
cytoscape.js is a successor of Cytoscape Web. cytoscape.js is a JavaScript library for network visualization, NOT a complete web application. It shares some design-level concepts with Desktop (Java) version of Cytoscape, but code base is completely independent. It is designed to be a building block for complex data visualization web applications for the HTML5 era.
