Cytoscape_3/UserManual

Revision History
Revision 82012-12-21 13:11:32PietMolenaar
Changed title of the 'Node and Edge attributes' section to 'Node and Edge data'
Revision 72012-09-20 17:38:40samad
Revision 62012-07-11 23:21:53RozaGhamari
Revision 52012-06-12 16:51:16KeiichiroOno
Revision 42012-05-17 18:35:01PengLiangWang
Revision 32012-05-17 18:17:55PengLiangWang
Revision 22012-02-17 20:40:45MikeSmoot
Revision 12012-02-17 20:35:55MikeSmoot

Table of Contents

Cytoscape 3.0.0 User Manual
Introduction
Launching Cytoscape
System requirements
Getting Started
Quick Tour of Cytoscape
The Menus
Network Management
The Network Overview Window
Cytoscape Preferences
Managing Properties
Managing Bookmarks
Managing Proxy Servers
Managing Group View
Creating Networks
Import Fixed-Format Network Files
Import Unformatted Table Files
Import Networks from Public Databases
Edit a New Network
Supported Network File Formats
SIF Format
NNF
GML Format
XGMML Format
SBML (Systems Biology Markup Language) Format
BioPAX (Biological PAthways eXchange) Format
PSI-MI Format
GraphML
Delimited Text Table and Excel Workbook
Node and Edge Data
Table data
Ontologies
Attribute Functions and Equations
Attribute Formulas
Introduction
Operators
Supported Functions
Pitfalls
Useful Tips
The Formula Builder
A Note for App Writers
Navigation and Layout
Basic Network Navigation
Other Mouse Behaviors
Automatic Layout Algorithms
Edge Bend and Automatic Edge Bundling
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
Custom Graphics Manager
Visual Styles Tutorials
Advanced Topics
Managing Visual Styles
Bypassing Visual Styles
Visual Property Dependencies
Finding and Filtering Nodes and Edges
Enhanced Search
Filters
The Select Menu
Editing Networks
Adding Node
Adding Edge
CytoPanels
What are CytoPanels?
Basic Usage
Rendering Engine
What is Level of Detail (LOD)?
Linkout
Adding or Removing Links
App Manager
What are apps?
Installing Apps
Managing your Installed Apps

Header and copyright information here.