Tutorial session 1 Network generation

1. Tutorial session 1Network generation Exploring PPI networks using Cytoscape EMBO Practical Course Session 8 Nadezhda Doncheva and Piet Molenaar

2. Overview • Focus: Network generation • Importing pre-formatted networks • Generating new networks • Visualizing networks • Saving and exporting network data • Concepts • Layouts • Data • Drosophila protein network

3. Let’s start: GUI basics (Demo)

4. Loading networks • Import pre-formatted networks • SIF • GML, XGMML • BioPAX • PSI-MI 1 & 2.5 • SBML Level 2 • Import your own data from a table • Excel file • Delimited text (tab, comma, etc…)

5. Loading networks (Demo)

6. Layouts • Many algorithms available through plugins • Simple: grid, not very informative • Hierarchical: layout data as a tree or hierarchy (works best when there are no loops) • Circular (Radial): arrange nodes around a circle, could use node attributes to govern position, e.g. degree sorted • Force-Directed: simulate edges as springs (nodes repel and edges pull), good for up to 500 nodes • Multi-layer layouts: partition graph, layout each partition and then layout partitions • …

7. Layouts (Demo)

8. Tips & Tricks: Layouts • Use layouts to convey the relationships between the nodes • Layout algorithms may need to be ”tuned” to fit your network (Layouts  Settings ... menu) • Consider laying out portions of your network • Adjust the layout manually • Load network into a drawing program (e.g. Illustrator) and adjust labels

9. Use case: Drosophila Protein network • Although from fly, serves as model for human • Groundbreaking work now done in model systems • What did they do • Bait-Protein interactions • Statistical analysis; highly confident set

10. Use case: Assignment 1.1 • Open the DrosophilaBasicSession.cys file • Test several layouts; which one is informative? http://cytoscape.org/manual/Cytoscape2_8Manual.html#Import Free-Format Table Files http://cytoscape.org/manual/Cytoscape2_8Manual.html#Automatic Layout Algorithms

11. Generating networks • Import network from web services supported by Cytoscape • Pathway commons (only well-studied organisms) • PSICQUIC Universal Client (collection of many public databases) • MiMI (Michigan Molecular Interactions database) • BisoGenet (SysBiomics database) • Generate a network using a Cytoscape plugin • AgilentLiteratureSearch (based on text mining)

12. Generating networks (Demo)

13. Use case; Assignment 1.2 • Try to locate the protein complexes found in the article in the network • Lookup existing interactions for one of the MCM genes in the PathwayCommons webservice http://cytoscape.org/manual/Cytoscape2_8Manual.html#Example #3: Retrieving Pathways and Networks from Pathway Commons

14. Tips & Tricks: Network view • When you open a large network, you will not get a view by default • To improve interactive performance, Cytoscape has the concept of ”Levels of Detail” • Some visual attributes will only be apparent when you zoom in • The level of detail for various attributes can be changed in the preferences • To see what things will look like at full detail: go to View  Show Graphics Details

15. Exporting & saving data • Sessions save pretty much everything: Networks, Properties, Visual styles, Screen sizes • Export networks in different formats: SIF, GML, XGMML, BioPAX, PSI-MI 1 & 2.5 • Publication quality graphics in several formats: PDF, EPS, SVG, PNG, JPEG, and BMP • Export Session to HTML for Web (SessionForWeb plugin)

16. Exporting & saving data (Demo)

17. Tips & Tricks: Memory • Cytoscape uses lots of it • Doesn’t like to let go of it • An occasional restart when working with large networks is a good thing • Destroy views when you don’t need them • Java does not provide a good way to get the memory right at start time • Cytoscape 2.7 and later releases do a much better job at ”guessing” good default memory sizes than previous versions • Increase Cytoscape’s default memory size: http://cytoscape.wodaklab.org/wiki/How_to_increase_memory_for_Cytoscape

18. Tips & Tricks: General • By default, Cytoscape writes it’s logs to the Error Dialog: Help  Error Dialog • Change the ”logger.console” preference in Edit Preferences  Properties... to write it to the console • .cytoscapedirectory • Your defaults and any plugins downloaded from the plugin manager will go here • Sometimes, if things get really messed up, deleting (or renaming) this directory can give you a ”clean slate” • Plugin manager • ”Outdated” doesn’t necessarily mean ”won’t work” • Plugin authors don’t always update their plugins immediately after new releases • Open source; sometimes bugs occur!

19. Use case: Assignment 1.3 • Export the network view as figure • Find out in which format you’d best save your network • Save your session for later use http://cytoscape.org/manual/Cytoscape2_8Manual.html#Supported Network File Formats

20. Cytoscape extended functionality • Cytoscape extends its functionality with plugins • Developed by third parties • Listed at http://apps.cytoscape.org/ • Usually available through the Plugin Manager • Can be downloaded from the plugins’s websites • Cover many diverse areas of application

21. Cytoscape Plugin Manager (Demo)

22. Use case: Assignment 1.4 • Explore available plugins for PPi relevance http://cytoscape.org/manual/Cytoscape2_8Manual.html#Plugins and the Plugin Manager

23. To be continued… • Build, visualize and analyze your own network with Cytoscape • Network generation • Network annotation and visualization • Loading and manipulating attributes • Identifier mapping • Mapping data onto the network • Use visuals to convey data • Network analysis