Cytoscape @version@ 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

Copyright (c) 2001-2014 The Cytoscape Consortium

Introduction

Cytoscape @version@ is the latest version of Cytoscape, building upon the new architecture, developer API and set of user controls established in the 3.x series. If you’re familiar with former versions of Cytoscape, this version will feel completely familiar and you’ll be all set to go. In future releases, we will continue to tweak and improve both the software and the documentation. This manual will be updated to reflect all the latest changes.

This manual describes the installation and use of Cytoscape. For a more thorough understanding of Cytoscape and its ecosystem, we highly recommend reading the **Welcome Letter* accessible on the http://cytoscape.org website.

TOC

• System requirements
• Getting Started
  • Install Java
  • Install Cytoscape
    • Downloading and installing
    • A quick note on upgrading your Cytoscape installation
  • Launch the application
  • Note on Memory Consumption
    • Overall Memory Size for Cytoscape
    • Stack Size
• Command Line Arguments
• Quick Tour of Cytoscape
  • Welcome Screen
  • Basic Features
    • Network Editing
  • The Menus
    • File
    • Edit
    • View
    • Select
    • Layout
    • Apps
  • Note: A list of available Cytoscape apps with descriptions is available online at:
    • Tools
    • Help
  • Network Management
    • Arrange Network Windows
  • The Network Overview Window
• Creating Networks
  • Import Fixed-Format Network Files
    • Load Networks from Local Computer
    • Load Networks from a Remote Computer (URL import)
  • Import Networks from Unformatted Table Files
    • Supported Files
    • Basic Operations
      • Import List of Nodes Without Edges
    • Advanced Options
    • Modify Column Name/Type
  • Import Networks from Public Databases
    • What is a Web Service?
  • Getting Started
  • Example: Retrieving Protein-Protein Interaction Networks from Multiple Databases
    • PSICQUIC Options
  • Create a New Network Manually
    • Adding a Node
    • Adding an Edge
    • Grouping nodes
    • Adding Network Annotations
• Nested Networks
  • Creating Nested Networks
  • Visualization of Nested Networks
  • Programmatically Manipulating Nested Networks
• Supported Network File Formats
  • SIF Format
    • Delimiters
  • NNF
    • Examples
      • Example 1
      • Example 2
      • Example 3
      • Example 4
      • Example 5
  • 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
    • Important Note
• Node and Edge Column Data
  • Import Data Table Files
    • Basic Operation
      • Unassigned Table
  • Legacy Cytoscape Attributes Format
    • Detailed file format (Advanced users)
  • sourceName space openParen edgeType closeParen space targetName
  • sourceName whiteSpace edgeType whiteSpace targetName
    • Newline Feature
    • Advanced Options
      • Annotation File to Table Mapping
      • Aliases
    • Table Panel
      • Column Batch Editor
  • Import Data Table from Public Databases
    • Basic Operation
• 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
    • Cytoscape-specific functions
    • Numeric Functions
    • String Functions
    • Logical/Boolean Functions
    • List Functions
    • Statistical Functions
    • Miscellaneous Functions
  • Pitfalls
  • Useful Tips
  • The Formula Builder
  • A Note for App Writers
• Finding and Filtering Nodes and Edges
  • Search Bar
  • Filters
    • Narrowing Filters
      • Interactive Filter Application Mode
      • Column Filter
      • Degree Filter
      • Topology Filter
      • Grouping and Organizing Filters
    • Chainable Filters
      • Interaction Transformer
    • Working with Narrowing and Chainable Filters
  • The Select Menu
• Navigation and Layout
  • Basic Network Navigation
    • Zoom
    • Pan
  • Other Mouse Behaviors
    • Select
    • Context
    • Node Context Menu
      • Nested Network Node Context Menu
  • Automatic Layout Algorithms
    • Grid Layout
    • Edge-weighted Spring-Embedded Layout
    • Attribute Circle Layout
    • Group Attributes Layout
    • Prefuse Force Directed Layout
  • yFiles Layouts
    • yFiles Organic Layout
    • yFiles Circular Layout
    • yFiles Hierarchical Layout
  • Layout Parameters
  • Edge Bend and Automatic Edge Bundling
  • Manual Layout
    • Rotate
    • Scale
    • Align, Distribute and Stack
  • Node Movement and Placement
• Styles
  • What are Styles?
  • Introduction to the Style interface
  • Introduction to Style
    • List of Node, Edge and Network Properties
    • Available Shapes and Line Styles
    • How Mappings Work
      • Text Passthrough Mapping
        • Examples
  • Custom Graphics
    • Managing Images with the Custom Graphics Manager
    • Using Custom Graphics in Styles
      • Custom Graphics Positions
      • Z-Ordering
    • Saving and Loading Custom Graphics
  • Styles Tutorials
    • Tutorial 1: Create a Basic Style and Set Default Values
    • Tutorial 2: Creating a New Style with a Discrete Mapping
    • Tutorial 3: Creating a New Style with a Continuous Mapping
    • Tutorial 4: How to Use Utilities for Discrete Mapping
    • Tutorial 5: Using Custom Graphics in Styles
    • Tutorial 6: Creating Node Charts
  • Advanced Topics
    • Discrete Mappings
      • Automatic Value Generators
      • Edit Selected Values at Once
      • Property Dependencies
    • Working with Continuous Mapping Editors
      • Range Setting Panel
      • Gradient Editor
      • Continuous-Continuous Editor
      • Continuous-Discrete Editor
  • Managing Styles
    • Saving Styles
      • Style File Formats
    • Importing Styles
• App Manager
  • What are apps?
  • Installing Apps
  • Managing your Installed Apps
• Command Tool
• Merge
  • Merge Networks
    • Basic Operations
      • Advanced Options
  • Merge Tables
• NetworkAnalyzer
  • Network Analysis
    • Analyze Network
    • Analyze Subset of Nodes
    • Batch Analysis
    • Load Network Statistics
    • Plot Parameters
    • Generate Style from Statistics
    • NetworkAnalyzer Settings
  • 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)?
    • Parameters for Controlling LOD
    • Force to Display Detail
• Publish Your Data
  • Publish Your Visualizations
    • As a Session File
    • As a Static Image
      • Known Issues
    • As an Interactive Web Application (New in 3.2.0)
      • Sharing via CyNetShare
      • Generating a Full Web Application
      • Generating a Simple Network View (For Web Application Developers)
      • Customize Export Template (For Web Application Developers)
        • Requirements
        • Full Export Template
        • Simple Export Template
        • Use Your Custom Templates for Export
• Cytoscape.js and Cytoscape
  • What is Cytoscape.js?
    • Examples
    • Differences and Shared Concepts
      • Cytoscape
      • Cytoscape.js
  • Data Exchange between Cytoscape and Cytoscape.js
    • Export Network and Table to Cytoscape.js
      • Important Note about Data Compatibility
    • Export Styles to Cytoscape.js
      • Limitations
      • Cytoscape.js and Cytoscape compatibility charts
    • Import Cytoscape.js data into Cytoscape
  • Build Your Own Web Application with Cytoscape.js
    • Questions?
• Programmatic Access to Cytoscape Features (Scripting)
  • Programmatic Access to Cytoscape Features
  • Topics
  • Background
    • Commands
    • RESTful API
      • 1. REST API for Commands
      • 2. cyREST
• Cytoscape Privacy Policy