1. Copyright OpenHelix. No use or reproduction without express written consent1

2. Cytoscape Cytoscape: visualizing molecular interaction networks and biological pathways Materials prepared by: Cynthia Foote, Ph.D. www.openhelix.com Updated: Q3 2009 Version 1.0_0709

3. Copyright OpenHelix. No use or reproduction without express written consent3 Cytoscape Agenda Introduction and Credits Cytoscape Basics Obtain Network Data Viewing Network Save or Export Network Plugins Summary Exercises Cytoscape: http://cytoscape.org/http://cytoscape.org/

4. Copyright OpenHelix. No use or reproduction without express written consent4 Cytoscape Introduction Customize network visualization Graph layout tools Load file or input data from IntAct or Pathway Commons databases Navigate large networks Filtering tools for network Plugin capability TP53 Interaction Network (obtained from http://cytoscape.org/screenshots.php)

5. Copyright OpenHelix. No use or reproduction without express written consent5 Cytoscape Data Model Creates networks from nodes and edges Built-in features, but customizable by users Node: Represents a protein, gene or molecule Edge or Link: Represents an interaction

6. Copyright OpenHelix. No use or reproduction without express written consent6 Cytoscape Homepage Main Tool Bar Quick Links Latest Version Introduction Cytoscape: http://cytoscape.org/http://cytoscape.org/ Community

7. Copyright OpenHelix. No use or reproduction without express written consent7 Credits Development team consists of consortium of academic and commercial members Scientific Advisory Board Directors Developers Advisory Board Past Contributors

8. Copyright OpenHelix. No use or reproduction without express written consent8 Collaborations Academic and Corporate Collaborators

9. Copyright OpenHelix. No use or reproduction without express written consent9 Publications and Documentation Am Assoc Cancer Res Educ Book 2005: 12-16 Nature Protocols 2007;2(10):2366-82

10. Copyright OpenHelix. No use or reproduction without express written consent10 Cytoscape Agenda Introduction and Credits Cytoscape Basics Obtain Network Data Viewing Network Save or Export Network Plugins Summary Exercises Cytoscape: http://cytoscape.org/http://cytoscape.org/

11. Copyright OpenHelix. No use or reproduction without express written consent11 Download Cytoscape Must install Java (http://java.sun.com/j avase/downloads/in dex.jsp.)http://java.sun.com/j avase/downloads/in dex.jsp Download from homepage current version Cytoscape help desk available

12. Download Process Download the current version (previous versions are available too) Later access it from your programs list or create an icon for your desktop Copyright OpenHelix. No use or reproduction without express written consent12

13. Copyright OpenHelix. No use or reproduction without express written consent13 Cytoscape User Interface Network Graph Panel Results Panel Data Panel Tool Panel Control Panel Main Tool Bar

14. Copyright OpenHelix. No use or reproduction without express written consent14 Main Menu Bar File: Import & Export Files, Open, Save, Exit Edit: Undo, Redo, Create or Destroy View, Destroy Network, Delete Nodes and Edges, Set Preferences View: Hide panels, Open VizMapper, Arrange Network Windows

15. Copyright OpenHelix. No use or reproduction without express written consent15 Main Menu Bar Select: Select nodes or edges Layout: change network layout, select algorithm for layout Plugins: manage plugins, merge networks Help: help contents, contact help desk

16. Copyright OpenHelix. No use or reproduction without express written consent16 Menu Bar Icons Zoom out Zoom in Zoom selected region Zoom to default size Help Open VizMapper Use Filters Open session file Save current session Search Box Search Parameters

17. Load a Sample Pathway To start using Cytoscape we’ll load a sample Access Import  Network from web services…. Import window offers search and selections Copyright OpenHelix. No use or reproduction without express written consent17

18. Copyright OpenHelix. No use or reproduction without express written consent18 Cytopanels Click Float Icon Click Float Icon Click Float Icon Float panels to maximize graphic area

19. Copyright OpenHelix. No use or reproduction without express written consent19 Network Graph Panel Click items on the panel to select and move

20. Layouts to Re-organize Graphics Choose from various layouts. Grid  organic here Copyright OpenHelix. No use or reproduction without express written consent20

21. Copyright OpenHelix. No use or reproduction without express written consent21 Control Panel Lists Networks Loaded In Cytoscape Network Overview Pane Tabs Network Tree Viewer

22. Copyright OpenHelix. No use or reproduction without express written consent22 VizMapper Tab Use VizMapper to create, edit or switch between visual styles for your network Defaults Visual Mapping Browser

23. Copyright OpenHelix. No use or reproduction without express written consent23 Editor Tab Use Editor tab to create new network or add nodes or edges to existing network

24. Copyright OpenHelix. No use or reproduction without express written consent24 Add A Node and Edge

25. Copyright OpenHelix. No use or reproduction without express written consent25 Filters Filters tab allows selection of nodes or edges by specified properties Create new filter wizards Must click “Apply” to have filter applied to network Select Click

26. Copyright OpenHelix. No use or reproduction without express written consent26 Tool Panel Tool Panel lets you Rotate, Scale or Align and Distribute the network

27. Copyright OpenHelix. No use or reproduction without express written consent27 Data Panel Displays attribute data for nodes, edges and network Select Attributes Create New Attributes Delete Attributes Attribute Batch Editor Import Attributes from File Import Expression Matrix Data

28. Copyright OpenHelix. No use or reproduction without express written consent28 Results Panel Node Name, Type, Species Pathway Commons Associated Links

29. Copyright OpenHelix. No use or reproduction without express written consent29 Cytoscape Agenda Introduction and Credits Cytoscape Basics Obtain Network Data Viewing Network Save or Export Network Plugins Summary Exercises Cytoscape: http://cytoscape.org/http://cytoscape.org/

30. Import Network from Web Services Import with easy steps: search, select, load Copyright OpenHelix. No use or reproduction without express written consent30 Click

31. Copyright OpenHelix. No use or reproduction without express written consent31 BAX Search Results Click here Click

32. Copyright OpenHelix. No use or reproduction without express written consent32 Import Multiple File Types File Types.sif.noa and.eda.gml.xgmml SBML BioPAX PSI-MI 1 and 2.5 Click here Click to Import Click here Click to Import

33. Copyright OpenHelix. No use or reproduction without express written consent33 Import Network from Table file:/C:/Users/Cindy/Documents/Openhelix2009/TestNetwork.xls Click here Click Import

34. Copyright OpenHelix. No use or reproduction without express written consent34 Cytoscape Agenda Introduction and Credits Downloading Cytoscape Obtain Network Data Viewing Network Save or Export Network Plugins Summary Exercises Cytoscape: http://cytoscape.org/http://cytoscape.org/

35. Copyright OpenHelix. No use or reproduction without express written consent35 Choose Layout Default import layout is the Grid layout.

36. Copyright OpenHelix. No use or reproduction without express written consent36 Quick Guide to Layouts Cytoscape layouts fully integrated with Settings panel. yFiles Circular- emphasize group and tree structures. Hierarchical-representation of direction or flow. Organic- shows clustered structure of network. Random Mirror X Mirror Y Orthogonal Cytoscape Grid- simple square grid. Force Directed- based on “Force Directed” paradigm. Spring Embedded- based on concept of nodes separated with springs that repel or attract. Attribute Circle- useful for small networks, nodes grouped by attributes. Group Attributes- nodes grouped in multiple circles based on attributes. Inverted Self-Organizing Map Layout Degree Sorted Circle Edge-weighted Force Directed Layout JGraph Circle Simulated Annealing Radial Tree GEM MOEN Sugiyama Tree Spring Embedded

37. 37 Basic Navigation Uses a zoomable user interface which allows zooming and panning for navigation Copyright OpenHelix. No use or reproduction without express written consent Click and drag box Restore to original sizing

38. Copyright OpenHelix. No use or reproduction without express written consent38 Network Visualization Use VizMapper to change visualization of the entire network Defaults Create a style Browser Visual Style

39. Copyright OpenHelix. No use or reproduction without express written consent39 Visual Mapping Bypass Use right click pop up window, select Visual Mapping Bypass to change individual nodes or edges 80

40. Copyright OpenHelix. No use or reproduction without express written consent40 Cytoscape Agenda Introduction and Credits Downloading Cytoscape Obtain Network Data Viewing Network Save or Export Network Plugins Summary Exercises Cytoscape: http://cytoscape.org/http://cytoscape.org/

41. Copyright OpenHelix. No use or reproduction without express written consent41 Saving Data Save a Cytoscape Session file (.cys) File  Save as… Re-load later with File  Open open save

42. Copyright OpenHelix. No use or reproduction without express written consent42 Export Network or Images Cytoscape exports SIF, GML, XGMML and PSI-MI formats Export attributes or properties separately Can export image file formats including JPEG, PNG, PDF

43. Copyright OpenHelix. No use or reproduction without express written consent43 Cytoscape Agenda Introduction and Credits Downloading Cytoscape Obtain Network Data Viewing Network Save or Export Network Plugins Summary Exercises Cytoscape: http://cytoscape.org/http://cytoscape.org/

44. Copyright OpenHelix. No use or reproduction without express written consent44 Cytoscape Plugins Organized into 7 Sections

45. Copyright OpenHelix. No use or reproduction without express written consent45 Plugin Manager Allows quick and easy access to Plugins Run plugins from the Plugin drop down menu Currently Installed Available For Install

46. Copyright OpenHelix. No use or reproduction without express written consent46 Agilent Literature Search Click

47. Copyright OpenHelix. No use or reproduction without express written consent47 Agilent Literature Search TP53 BRCA Cancer Malignant Delete Search Start Search Stop Search

48. Copyright OpenHelix. No use or reproduction without express written consent48 Cytoscape Agenda Introduction and Credits Downloading Cytoscape Obtain Network Data Viewing Network Save or Export Network Plugins Summary Exercises Cytoscape: http://cytoscape.org/http://cytoscape.org/

49. Copyright OpenHelix. No use or reproduction without express written consent49 Cytoscape User Interface Main Tool Bar Control Panel Network Graph Panel Results Panel Data Panel

50. Copyright OpenHelix. No use or reproduction without express written consent50 Import Attributes and Expression Import Selected Attributes into Network for use with Filters and Layout Import Expression data into Network

51. Copyright OpenHelix. No use or reproduction without express written consent51 Plugins

52. Copyright OpenHelix. No use or reproduction without express written consent52 Medical Relevance

53. Cytoscape: Join the community Provides Additional Materials Check the news Join the mailing lists Copyright OpenHelix. No use or reproduction without express written consent53

54. Copyright OpenHelix. No use or reproduction without express written consent54 Cytoscape Agenda Introduction and Credits Downloading Cytoscape Obtain Network Data Viewing Network Save or Export Network Plugins Summary Exercises Cytoscape: http://cytoscape.org/http://cytoscape.org/

55. Copyright OpenHelix. No use or reproduction without express written consent55