Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.

Cytoscape is available as a platform-independent open-source Java application, released under the terms of the LGPL. By downloading Cytoscape, you agree that you have read the license agreement that follows and agree to its terms. If you don't agree, do not download Cytoscape.

Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration

Cytoscape 3.0 is the latest version of Cytoscape, which introduces a whole new architecture, developer API and set of user controls. Cytoscape 3.0 represents a major redesign from the ground up, toward the goal of provide a stable, extensible, high-performance platform for network visualization and analysis.

Quick Tour of Cytoscape¶ This chapter describes the basic layout and mechanics of using Cytoscape. If you would prefer to learn by doing, consider starting with the Basic Expression Analysis Tutorial. 4.1. Starter Panel¶ When you start Cytoscape, you can access basic functions from the Starter Panel:

Cytoscape Single Cell Analysis; Cytoscape Futures; Introduction to Cytoscape and Network Biology; Advanced Cytoscape Automation; Intro to RCy3 - Cytoscape Automation; Network Biology - PSPG; Train-the-Trainers; Scientific Visualization: Network Visualization with Cytoscape; Protein-protein Interactions I: Tools and Approaches

There are 4 different ways of creating networks in Cytoscape: Importing pre-existing, fixed-format network files. Importing pre-existing, unformatted text or Excel files. Importing data from from public databases. Creating an empty network and manually adding nodes and edges. 5.1. Import Fixed-Format Network Files¶

Cytoscape 3.10.3 User Manual¶ The Cytoscape User Manual copyright is owned by The Cytoscape Consortium, and is made available under the same GPL license as Cytoscape …

Cytoscape 3.9.1 User Manual¶ The Cytoscape User Manual copyright is owned by The Cytoscape Consortium, and is made available under the same GPL license as Cytoscape itself: LGPL 2.1, the GNU Lesser General Public License, version 2.1, February 1999 available in text at http://www.gnu.org/licenses/lgpl-2.1.html .

Launching Cytoscape¶ Cytoscape is a Java application verified to run on the Linux, Windows, and Mac OS X platforms. Although not officially supported, other UNIX platforms such as Solaris or FreeBSD may run Cytoscape if Java version 8 is available for the platform.