Cytoscape_3/UserManual Revision History Revision 35 2015-06-22 17:59:53 KeiichiroOno Revision 34 2014-09-24 19:35:29 KeiichiroOno Revision 33 2014-02-03 20:27:53 KristinaHanspers Added privacy policy Revision 32 2014-01-22 23:52:54 KristinaHanspers included section for annotation import Revision 31 2014-01-06 22:17:22 KristinaHanspers removed annotations Revision 30 2014-01-06 22:15:41 KristinaHanspers commented out Annotations section Revision 29 2013-12-17 22:31:05 KristinaHanspers cleaned up sections list Revision 28 2013-12-17 21:35:01 KristinaHanspers Revision 27 2013-12-17 19:18:51 KristinaHanspers Revision 26 2013-12-17 19:06:52 KristinaHanspers Revision 25 2013-12-16 22:36:56 KristinaHanspers Added list entry for network analyzer Revision 24 2013-12-14 00:29:16 KristinaHanspers Revision 23 2013-12-14 00:22:31 KristinaHanspers Revision 22 2013-12-13 23:52:35 KristinaHanspers Revision 21 2013-12-12 00:20:22 KristinaHanspers Changed the order of sections Revision 20 2013-12-11 23:49:53 KristinaHanspers removed "Editing networks" section, now part of creating networks Revision 19 2013-12-11 22:07:15 KristinaHanspers Changed order of sections Revision 18 2013-12-11 17:36:46 KeiichiroOno Revision 17 2013-12-11 01:01:49 KristinaHanspers Revision 16 2013-12-10 23:53:57 KristinaHanspers removed extra horizontal break Revision 15 2013-12-10 23:39:51 KristinaHanspers removed horizontal breaks between unused sections Revision 14 2013-12-10 19:26:14 KristinaHanspers Revision 13 2013-12-04 23:40:22 KristinaHanspers Revision 12 2013-12-04 23:21:30 KristinaHanspers added command tool section Revision 11 2013-11-26 22:12:22 KristinaHanspers Added horizontal rules between major sections Revision 10 2013-11-26 01:22:53 KeiichiroOno Revision 9 2013-11-20 22:30:16 KristinaHanspers changing form visual styles to styles 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 1 Cytoscape_3/UserManual Table of Contents Cytoscape 3.3.0 User Manual ................................................................................................. 4 Introduction ........................................................................................................................ 4 Launching Cytoscape ........................................................................................................... 4 System requirements .................................................................................................... 4 Getting Started ............................................................................................................ 5 Command Line Arguments .................................................................................................... 8 Quick Tour of Cytoscape ....................................................................................................... 9 Welcome Screen .......................................................................................................... 9 Basic Features ........................................................................................................... 10 The Menus ............................................................................................................... 12 Network Management ................................................................................................. 16 The Network Overview Window ................................................................................... 18 Creating Networks ............................................................................................................. 19 Import Fixed-Format Network Files ............................................................................... 19 Import Networks from Unformatted Table Files ............................................................... 20 Import Networks from Public Databases ......................................................................... 25 Getting Started .......................................................................................................... 26 Example: Retrieving Protein-Protein Interaction Networks from Multiple Databases ............... 26 Create a New Network Manually .................................................................................. 28 Nested Networks ............................................................................................................... 31 Creating Nested Networks ........................................................................................... 31 Visualization of Nested Networks ................................................................................. 31 Programmatically Manipulating Nested Networks ............................................................ 32 Supported Network File Formats ........................................................................................... 32 SIF Format ............................................................................................................... 33 NNF ........................................................................................................................ 34 GML Format ............................................................................................................. 39 XGMML Format ....................................................................................................... 39 SBML (Systems Biology Markup Language) Format ........................................................ 39 BioPAX (Biological PAthways eXchange) Format ............................................................ 39 PSI-MI Format .......................................................................................................... 40 GraphML ................................................................................................................. 40 Delimited Text Table and Excel Workbook ...................................................................... 40 Cytoscape.js JSON ..................................................................................................... 40 Node and Edge Column Data ............................................................................................... 45 Import Data Table Files ............................................................................................... 45 Legacy Cytoscape Attributes Format .............................................................................. 47 Import Data Table from Public Databases ....................................................................... 51 Ontology and Annotation Import ........................................................................................... 53 Ontology and Annotation File Format ............................................................................ 53 Default List of Ontologies ........................................................................................... 53 Gene Association File ................................................................................................. 54 Import Ontology and Annotation ................................................................................... 55 Column Data Functions and Equations ................................................................................... 56 Column Formulas ...................................................................................................... 56 Introduction .............................................................................................................. 56 Operators ................................................................................................................. 57 Supported Functions ................................................................................................... 57 Pitfalls ..................................................................................................................... 59 Useful Tips ............................................................................................................... 60 The Formula Builder .................................................................................................. 60 2 Cytoscape_3/UserManual A Note for App Writers ............................................................................................... 61 Finding and Filtering Nodes and Edges .................................................................................. 61 Search Bar ................................................................................................................ 61 Filters ...................................................................................................................... 62 The Select Menu ........................................................................................................ 68 Navigation and Layout ........................................................................................................ 68 Basic Network Navigation ........................................................................................... 68 Other Mouse Behaviors ............................................................................................... 69 Automatic Layout Algorithms .....................................................................................