Cytoscape_3/UserManual

Revision History
Revision 342014-09-24 19:35:29KeiichiroOno
Revision 332014-02-03 20:27:53KristinaHanspers
Added privacy policy
Revision 322014-01-22 23:52:54KristinaHanspers
included section for annotation import
Revision 312014-01-06 22:17:22KristinaHanspers
removed annotations
Revision 302014-01-06 22:15:41KristinaHanspers
commented out Annotations section
Revision 292013-12-17 22:31:05KristinaHanspers
cleaned up sections list
Revision 282013-12-17 21:35:01KristinaHanspers
Revision 272013-12-17 19:18:51KristinaHanspers
Revision 262013-12-17 19:06:52KristinaHanspers
Revision 252013-12-16 22:36:56KristinaHanspers
Added list entry for network analyzer
Revision 242013-12-14 00:29:16KristinaHanspers
Revision 232013-12-14 00:22:31KristinaHanspers
Revision 222013-12-13 23:52:35KristinaHanspers
Revision 212013-12-12 00:20:22KristinaHanspers
Changed the order of sections
Revision 202013-12-11 23:49:53KristinaHanspers
removed "Editing networks" section, now part of creating networks
Revision 192013-12-11 22:07:15KristinaHanspers
Changed order of sections
Revision 182013-12-11 17:36:46KeiichiroOno
Revision 172013-12-11 01:01:49KristinaHanspers
Revision 162013-12-10 23:53:57KristinaHanspers
removed extra horizontal break
Revision 152013-12-10 23:39:51KristinaHanspers
removed horizontal breaks between unused sections
Revision 142013-12-10 19:26:14KristinaHanspers
Revision 132013-12-04 23:40:22KristinaHanspers
Revision 122013-12-04 23:21:30KristinaHanspers
added command tool section
Revision 112013-11-26 22:12:22KristinaHanspers
Added horizontal rules between major sections
Revision 102013-11-26 01:22:53KeiichiroOno
Revision 92013-11-20 22:30:16KristinaHanspers
changing form visual styles to styles
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 3.2.0 User Manual
Introduction
Launching Cytoscape
System requirements
Getting Started
Command Line Arguments
Quick Tour of Cytoscape
Welcome Screen
Basic Features
The Menus
Network Management
The Network Overview Window
Creating Networks
Import Fixed-Format Network Files
Import Networks from Unformatted Table Files
Import Networks from Public Databases
Getting Started
Example: Retrieving Protein-Protein Interaction Networks from Multiple Databases
Create a New Network Manually
Nested Networks
Creating Nested Networks
Visualization of Nested Networks
Programmatically Manipulating Nested Networks
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
Cytoscape.js JSON
Node and Edge Column Data
Import Data Table Files
Legacy Cytoscape Attributes Format
Import Data Table from Public Databases
Ontology and Annotation Import
Ontology and Annotation File Format
Default List of Ontologies
Gene Association File
Import Ontology and Annotation
Column Data Functions and Equations
Column Formulas
Introduction
Operators
Supported Functions
Pitfalls
Useful Tips
The Formula Builder
A Note for App Writers
Finding and Filtering Nodes and Edges
Search Bar
Filters
The Select Menu
Navigation and Layout
Basic Network Navigation
Other Mouse Behaviors
Automatic Layout Algorithms
yFiles Layouts
Layout Parameters
Edge Bend and Automatic Edge Bundling
Manual Layout
Node Movement and Placement
Styles
What are Styles?
Introduction to the Style interface
Introduction to Style
Custom Graphics
Styles Tutorials
Advanced Topics
Managing Styles
App Manager
What are apps?
Installing Apps
Managing your Installed Apps
Command Tool
Merge
Merge Networks
Merge Tables
NetworkAnalyzer
Network Analysis
Subnetwork Creation
Cytoscape Preferences
Managing Properties
Managing Bookmarks
Managing Proxy Servers
Managing Group View
Linkout
Adding and Removing Links
Panels
What are Panels?
Basic Usage
Rendering Engine
What is Level of Detail (LOD)?
Publish Your Data
Publish Your Visualizations
Cytoscape.js and Cytoscape
What is Cytoscape.js?
Data Exchange between Cytoscape and Cytoscape.js
Build Your Own Web Application with Cytoscape.js
Scripting
Scripting Feature is Deprecated!
Scripting in Cytoscape 3
Run Cytoscape from Command Line
Experimental: Adding Other JSR 223 Compatible Scripting Engines
Cytoscape Privacy Policy

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.

Copyright (c) 2001-2014 The Cytoscape Consortium