Cytoscape User Manual


Table of Contents

Cytoscape 2.5.1 User Manual
Introduction
Development
License
What’s New in 2.5
Launching Cytoscape
System requirements
Getting Started
Quick Tour of Cytoscape
The Menus
Network Management
The Network Overview Window
Command Line Arguments
Cytoscape Preferences
Managing Properties
Managing Bookmarks
Managing Proxy Servers
Creating Networks
Import Fixed-Format Network Files
Import Free-Format Table Files
Edit a New Network
Supported Network File Formats
SIF Format
GML Format
XGMML Format
SBML (Systems Biology Markup Language) Format
BioPAX (Biological PAthways eXchange) Format
PSI-MI Format
Delimited Text Table and Excel Workbook
Node Naming Issues in Cytoscape
Node and Edge Attributes
Cytoscape Attribute File Format
Import Attribute Table Files
Loading Gene Expression (Attribute Matrix) Data
Data File Format
General Procedure
Worked Example
Detailed file format (Advanced users)
Navigation and Layout
Basic Network Navigation
Other Mouse Behaviors
Automatic Layout Algorithms
Layout Parameters
Manual Layout
Node Movement and Placement
Visual Styles
What is a Visual Style?
Introduction to the VizMapper User Interface
Introduction to Visual Styles
Visual Attributes, Graph Attributes and Visual Mappers
Visual Styles Tutorials
Advanced Topics
Managing Visual Styles
Bypassing Visual Styles
Finding and Filtering Nodes and Edges
QuickFind
Filters
Using New Filters
Using Old Filters
The Select Menu
Editing Networks
Plugins and the Plugin Manager
The Plugin Manager
Get New Plugins
Delete Existing Plugins
Update Existing Plugins
Download Plugins from a Custom Site
CytoPanels
What are CytoPanels?
Basic Usage
Rendering Engine
What is Level of Detail (LOD)?
Annotation
Ontology and Annotation File Format
Node Name Mapping
Import Ontology and Annotation
Custom Annotation Files for Ontologies Other than GO (for Advanced Users)
Linkout
Adding or Removing Links
Acknowledgements
Appendix A: Old Annotation Server Format
Building your own annotation files
Load Data into Cytoscape
Getting and Reformatting GO Data
Python script examples
Appendix B: GNU Lesser General Public License
Appendix C: Increasing memory for Cytoscape
How to increase memory for Cytoscape
Changing memory allocations on Windows, Mac, and Linux machines

Cytoscape 2.5.1 User Manual

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This document is licensed under the Creative Commons license, 2006

Authors: The Cytoscape Collaboration

The Cytoscape project is an ongoing collaboration between:

Table 1. 

University of California at San Diego

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Institute for Systems Biology

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Memorial Sloan-Kettering Cancer Center

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Institut Pasteur

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Agilent Technologies

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University of California at San Francisco

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Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.