Cytoscape_3/UserManual Revision History Revision 8 2012-12-21 13:11:32 PietMolenaar Changed title of the 'Node and Edge attributes' section to 'Node and Edge data' Revision 7 2012-09-20 17:38:40 samad Revision 6 2012-07-11 23:21:53 RozaGhamari Revision 5 2012-06-12 16:51:16 KeiichiroOno Revision 4 2012-05-17 18:35:01 PengLiangWang Revision 3 2012-05-17 18:17:55 PengLiangWang Revision 2 2012-02-17 20:40:45 MikeSmoot Revision 1 2012-02-17 20:35:55 MikeSmoot Table of Contents Cytoscape 3.0.1 User Manual ................................................................................................. 2 Introduction ........................................................................................................................ 3 Launching Cytoscape ........................................................................................................... 3 System requirements .................................................................................................... 3 Getting Started ............................................................................................................ 4 Quick Tour of Cytoscape ....................................................................................................... 7 The Menus ............................................................................................................... 10 Network Management ................................................................................................. 14 The Network Overview Window ................................................................................... 17 Command Line Arguments .................................................................................................. 18 Cytoscape Preferences ........................................................................................................ 19 Managing Properties ................................................................................................... 19 Managing Bookmarks ................................................................................................. 21 Managing Proxy Servers ............................................................................................. 22 Managing Group View ................................................................................................ 23 Creating Networks ............................................................................................................. 23 Import Fixed-Format Network Files ............................................................................... 24 Import Unformatted Table Files .................................................................................... 25 Import Networks from Public Databases ......................................................................... 29 Create a New Network Manually .................................................................................. 35 Supported Network File Formats ........................................................................................... 35 SIF Format ............................................................................................................... 35 NNF ........................................................................................................................ 37 GML Format ............................................................................................................. 42 XGMML Format ....................................................................................................... 42 SBML (Systems Biology Markup Language) Format ........................................................ 43 BioPAX (Biological PAthways eXchange) Format ............................................................ 43 PSI-MI Format .......................................................................................................... 43 GraphML ................................................................................................................. 43 Delimited Text Table and Excel Workbook ...................................................................... 43 Node and Edge Data ........................................................................................................... 43 Table data ................................................................................................................. 44 Ontologies ................................................................................................................ 49 Attribute Functions and Equations ......................................................................................... 54 Attribute Formulas ..................................................................................................... 54 Introduction .............................................................................................................. 54 1 Cytoscape_3/UserManual Operators ................................................................................................................. 54 Supported Functions ................................................................................................... 55 Pitfalls ..................................................................................................................... 57 Useful Tips ............................................................................................................... 57 The Formula Builder .................................................................................................. 57 A Note for App Writers ............................................................................................... 58 Navigation and Layout ........................................................................................................ 58 Basic Network Navigation ........................................................................................... 58 Other Mouse Behaviors ............................................................................................... 59 Automatic Layout Algorithms ...................................................................................... 60 Edge Bend and Automatic Edge Bundling ...................................................................... 70 Manual Layout .......................................................................................................... 72 Node Movement and Placement .................................................................................... 78 Visual Styles ..................................................................................................................... 78 What is a Visual Style? ................................................................................................ 78 Introduction to the VizMapper User Interface .................................................................. 83 Introduction to Visual Styles ........................................................................................ 85 Visual Attributes, Graph Attributes and Visual Mappers ..................................................... 88 Custom Graphics Manager ........................................................................................... 95 Visual Styles Tutorials ................................................................................................ 99 Advanced Topics ...................................................................................................... 115 Managing Visual Styles ............................................................................................. 120 Bypassing Visual Styles ............................................................................................. 121 Visual Property Dependencies .................................................................................... 121 Finding and Filtering Nodes and Edges ................................................................................. 123 Enhanced Search ...................................................................................................... 123 Filters .................................................................................................................... 123 The Select Menu ...................................................................................................... 128 Editing Networks ............................................................................................................. 129 Adding Node ........................................................................................................... 129 Adding Edge ........................................................................................................... 129 CytoPanels ...................................................................................................................... 130 What are CytoPanels? ............................................................................................... 130 Basic Usage ............................................................................................................ 131 Rendering Engine ............................................................................................................. 132 What is Level of Detail (LOD)? .................................................................................. 132 Linkout .......................................................................................................................... 133 Adding or Removing Links .......................................................................................