Introduction

Cytoscape is an open-source community software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular state information for visualization and analysis. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. A software “Core” provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular state information; and to link the network to databases of functional annotations. The Core is extensible through a plug-in architecture, allowing rapid development of additional computational analyses and features. The central organizing metaphor of Cytoscape is a network (graph), with genes, proteins, and molecules represented as nodes and interactions represented as links, i.e. edges, between nodes.

Development Cytoscape is a collaborative project between the Institute for Systems Biology (Dr. Leroy Hood), the University of California San Diego (Dr. Trey Ideker), Memorial Sloan-Kettering Cancer Center (Dr. Chris Sander) and the Institut Pasteur (Dr. Benno Schwikowski).

Visit http://www.cytoscape.org for more information.

License Cytoscape is protected under the GNU LGPL (Lesser General Public License). The License is included as an appendix to this manual, but can also be found online: http://www.gnu.org/copyleft/lesser.txt Cytoscape also includes a number of other open source libraries, which are detailed in [#acknowledgements Acknowledgements] below.

What’s New in 2.3

Cytoscape version 2.3. contains several new features, plus improvements to the performance and usability of the software. These include:

• A much faster rendering engine. Cytoscape can now render at interactive speed graphs with over 100,000 nodes and edges.
• The ability to save a session. You can now save all of your work in Cytoscape to a single file. When re-opened, this file will return Cytoscape to the state in which you left it including all networks, attributes, and properties.
• A node grouping plugin. This will allow one node to contain and display subnetworks.
• Enhanced Undo/Redo support.
• An enhanced attribute browser.
• An enhanced Ontology Server Wizard.
• An improved command line interface.
• The ability to rename networks.

• The GraphMerge plugin included by default.

• Enhanced context or pop-up menus for nodes.
• Many performance improvements and bug fixes.
• A rewritten "bird's eye view" of the network that is enabled by default.
• The ability to load expression data according to node attribute (such as a commercial probeset identifier) instead of ndoe ID.

Are you an experienced Cytoscape user? If so, you should definitely read the following sections because important parts of Cytoscape have changed and what used to work, may no longer work as you expect!!!

• [#properties Properties (cytoscape.props and vizmap.props) handling.]
• [#renderer Rendering Engine.]
• [#command_line_args Command line arguments.]
• [#menus The menu system.]
• [#navigation Network Panel Navigation.]

Launching Cytoscape

Cytoscape is a Java application that runs on Linux, Windows, and Mac OS X.

System requirements: The system requirements for Cytoscape depend on the size of the networks the user wants to load, view and manipulate. We recommend a recent computer (1GHz CPU or higher) with a high-end graphics card and at least 512MB of free physical RAM. Cytoscape expects a minimum screen resolution of 1024x768.

There are a number of options for downloading and installing Cytoscape:

• For Windows and Linux platforms, one-step installation is available via InstallAnywhere. For one-step installation, go to http://www.cytoscape.org, click Download Cytoscape, and follow the on-screen instructions.

• For Mac OS X, we provide an alternative installation, available as a .dmg.zip file. When installed via this method, Cytoscape functions as a regular Mac application, and can be accessed via your Applications folder.
• Finally, you can download and install a compressed archive distribution. Instructions for this option are provided below.

(1) Download and unpack the distribution. Cytoscape is distributed as a compressed archive (tar.gz or zip) containing the following files and directories:

cytoscape.jar   Main Cytoscape application (Java archive)
cytoscape.props User-configurable properties and preferences
vizmap.props    User-configurable visual mapping preferences
cytoscape.sh    Script to run Cytoscape from command line (Linux, Mac OS X)
cytoscape.bat   Script to run Cytoscape (Windows)
LICENSE.txt     Cytoscape GNU LGPL License
Cytoscape2_3Manual.pdf  Cytoscape 2.3 Manual (the document you are reading now)
sampleData/
  galFiltered.gml       Sample molecular interaction network file *
  galFiltered.sif       Identical network in Simple Interaction Format *
  galExpData.pvals      Sample gene expression matrix file *
  galFiltered.cys       Sample session file created from datasets above *
  BINDyeast.sif Network of all yeast protein-protein interactions in the 
                          BIND database as of Nov, 2005 **
  BINDhuman.sif Network of all human protein-protein interactions in the 
                            BIND database as of Nov, 2005 **
  yeastHighQuality.sif  Sample molecular interaction network file ***
annotation/     Directory containing Gene Ontology database entries (currently 
                      for yeast only). Info in this directory is used to associate gene names 
                      with synonyms as well as process, function, and cellular location data.
plugins/        Directory containing cytoscape PlugIns, in .jar format.
* From Ideker et al, Science 292:929 (2001)
** Obtained from data hosted at 
     http://www.blueprint.org/bind/bind_downloads.html
** From von Mering et al, Nature, 417:399 (2002) and Lee et al, 
     Science 298:799 (2002)

(2) If necessary, install Java. If not already installed on your computer, download and install the Java 2 Runtime Environment, version 1.4.2 or higher. It can be found at:

http://java.sun.com/j2se/1.4.2/download.html

(3) Launch the application by running "cytoscape.sh" from the command line (Linux or Mac OS X) or double-clicking "cytoscape.bat" (Windows). Alternatively, you can pass the .jar file to Java directly using the command "java -Xmx512M -jar cytoscape.jar -p plugins". The -Xmx512M flag tells java to allocate more memory for Cytoscape and the -p plugins option tells cytoscape to load all of the plugins in the plugins directory. Loading the plugins is important because many key features like layouts, filters and the attribute browser are included with Cytoscape as plugins in the plugins directory. See the Command Line chapter for more detail. In Windows, it is also possible to directly double-click the .jar file to launch it. However, this does not allow specification of command-line arguments (such as the location of the plugin directory). On Mac OS X, users who downloaded the Mac OS X version of Cytoscape, can double-click on the Cytoscape icon to start Cytoscape. Either double-clicking or dragging onto the Cytoscape application icon any .sif or .gml file will load that file into Cytoscape.

Cytoscape Window When you succeed in launching Cytoscape, a window will appear that looks like this:

attachment:cytoscape_startup.png