Cytoscape User Manual Release 3.5.0 The Cytoscape Consortium Mar 27, 2017 Contents 1 Introduction 3 2 Launching Cytoscape 5 2.1 System Requirements..........................................5 2.2 Getting Started..............................................5 3 Command Line Arguments 9 4 Quick Tour of Cytoscape 11 4.1 Welcome Screen............................................. 11 4.2 Basic Features.............................................. 12 4.3 The Menus................................................ 15 4.4 Network Management.......................................... 20 4.5 The View Navigator........................................... 23 5 Creating Networks 25 5.1 Import Fixed-Format Network Files................................... 25 5.2 Import Networks from Unformatted Table Files............................. 26 5.3 Import Networks from Public Databases................................ 31 5.4 Getting Started.............................................. 32 5.5 Example: Retrieving Protein-Protein Interaction Networks from Multiple Databases......... 32 5.6 Create a New Network or Edit One Manually.............................. 35 6 Nested Networks 39 6.1 Creating Nested Networks........................................ 39 6.2 Visualization of Nested Networks.................................... 39 7 Supported Network File Formats 41 7.1 SIF Format................................................ 41 7.2 NNF................................................... 43 7.3 GML Format............................................... 47 7.4 XGMML Format............................................. 47 7.5 SBML (Systems Biology Markup Language) Format.......................... 48 7.6 BioPAX (Biological PAthways eXchange) Format........................... 48 7.7 PSI-MI Format.............................................. 48 7.8 GraphML................................................. 48 7.9 Delimited Text Table and Excel Workbook............................... 48 i 7.10 Cytoscape.js JSON............................................ 49 8 Node and Edge Column Data 55 8.1 Import Data Table Files......................................... 55 8.2 Legacy Cytoscape Attributes Format.................................. 57 8.3 Import Data Table from Public Databases................................ 60 8.4 Mapping Identifiers........................................... 62 9 Ontology and Annotation Import 65 9.1 Ontology and Annotation File Format.................................. 66 9.2 Default List of Ontologies........................................ 66 9.3 Gene Association File.......................................... 66 9.4 Import Ontology and Annotation.................................... 67 10 Column Data Functions and Equations 69 10.1 Column Formulas............................................ 69 10.2 The Formula Builder........................................... 72 10.3 A Note for App Writers......................................... 73 11 Finding and Filtering Nodes and Edges 75 11.1 Search Bar................................................ 75 11.2 Filters................................................... 76 11.3 The Select Menu............................................. 83 12 Navigation and Layout 85 12.1 Basic Network Navigation........................................ 85 12.2 Other Mouse Behaviors......................................... 86 12.3 Automatic Layout Algorithms...................................... 87 12.4 yFiles Layouts.............................................. 94 12.5 Layout Parameters............................................ 98 12.6 Edge Bend and Automatic Edge Bundling................................ 99 12.7 Manual Layout.............................................. 102 12.8 Node Layout Tools............................................ 102 13 Styles 105 13.1 What are Styles?............................................. 105 13.2 Introduction to the Style Interface.................................... 112 13.3 Introduction to Style........................................... 114 13.4 Images, Charts and Gradients...................................... 117 13.5 Styles Tutorials.............................................. 124 13.6 Advanced Topics............................................. 152 13.7 Managing Styles............................................. 158 14 App Manager 161 14.1 What are Apps?............................................. 161 14.2 Installing Apps.............................................. 161 14.3 Managing your Installed Apps...................................... 163 15 Command Tool 165 16 Merge 167 16.1 Merge Networks............................................. 167 16.2 Merge Tables............................................... 168 17 NetworkAnalyzer 169 17.1 Network Analysis............................................ 169 ii 17.2 Subnetwork Creation........................................... 173 17.3 NetworkAnalyzerDemo: Computation and Visualization of Topological Parameters and Centrality Measures for Biological Networks.................................... 174 18 Cytoscape Preferences 177 18.1 Managing Properties........................................... 177 18.2 Managing Bookmarks.......................................... 179 18.3 Managing Proxy Servers......................................... 180 18.4 Managing Group Settings........................................ 181 18.5 Managing OpenCL Settings....................................... 183 19 Linkout 185 19.1 Adding and Removing Links....................................... 186 20 Panels 189 20.1 Basic Usage............................................... 191 21 Rendering Engine 193 21.1 What is Level of Detail (LOD)?..................................... 193 22 Export Your Data 195 22.1 Raw Data Export............................................. 195 22.2 Exporting for Publication........................................ 197 23 Cytoscape and OpenCL (Computing on the GPU) 209 23.1 What it is for?.............................................. 209 23.2 Setup & Configuration.......................................... 209 23.3 OpenCL/GPU Troubleshooting..................................... 210 24 Cytoscape.js and Cytoscape 211 24.1 What is Cytoscape.js?.......................................... 211 24.2 Data Exchange between Cytoscape and Cytoscape.js.......................... 214 24.3 Export Styles to Cytoscape.js...................................... 215 24.4 Build Your Own Web Application with Cytoscape.js.......................... 215 25 Programmatic Access to Cytoscape Features (Scripting) 217 25.1 Programmatic Access to Cytoscape Features.............................. 217 25.2 Topics................................................... 217 25.3 Background................................................ 217 26 Cytoscape Privacy Policy 223 27 Basic Expression Analysis Tutorial 225 27.1 Loading Network............................................. 225 27.2 Loading Expression Data........................................ 226 27.3 Visualizing Expression Data....................................... 228 iii iv Cytoscape User Manual, Release 3.5.0 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) 2001-2017 The Cytoscape Consortium Table of Contents Contents 1 Cytoscape User Manual, Release 3.5.0 2 Contents CHAPTER 1 Introduction This version of Cytoscape builds upon the new 3.x architecture, developer API and set of user controls established. 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. If you would prefer to learn by doing, consider starting with the Basic Expression Analysis Tutorial chapter. 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. 3 Cytoscape User Manual, Release 3.5.0 4 Chapter 1. Introduction CHAPTER 2 Launching Cytoscape Cytoscape is a Java application verified to run on the Linux, Windows, and Mac OS X platforms. Although not officially supported, other UNIX platforms such as Solaris or FreeBSD may run Cytoscape if Java version 8 or later is available for the platform. System Requirements The system requirements for Cytoscape depend on the size of the networks you want to load, view and manipulate. Note that as of Cytoscape v3.2, networks are loaded faster and in less memory than with previous versions. While this is good news, networks created on v3.2 on a given memory configuration (e.g., 1GB) may not be loadable by prior Cytoscape versions on the same memory configuration. Specific system requirements, limitations, and configuration options apply to each platform, as described in the Release Notes available on the http://cytoscape.org website. Getting Started Install Java Cytoscape requires Java 8 or later. • While Cytoscape versions prior to v3.2 run on Java 6, Oracle and other JVM suppliers have dropped Java 6 support. Consequently, Cytoscape v3.2 and later don’t support Java 6 either. With v3.3, we have also dropped support for Java 7 for the same reason. • We recommend a 64 bit Java