Tutorial session 1
Network generation
Exploring PPI networks using Cytoscape
EMBO Practical Course Session 8
Nadezhda Doncheva and Piet Molenaar
Overview
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Focus: Network generation
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Importing pre-formatted networks
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Generating new networks
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Visualizing networks
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Saving and exporting network data
Concepts
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Data
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Layouts
Drosophila protein network
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Let’s start: GUI basics (Demo)
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Loading networks
Import pre-formatted networks
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SIF
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GML, XGMML
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BioPAX
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PSI-MI 1 & 2.5
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SBML Level 2
Import your own data from a table
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Excel file
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Delimited text (tab, comma, etc…)
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Loading networks (Demo)
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Layouts
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Many algorithms available through plugins
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Simple: grid, not very informative
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Hierarchical: layout data as a tree or hierarchy (works best
when there are no loops)
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Circular (Radial): arrange nodes around a circle, could use
node attributes to govern position, e.g. degree sorted
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Force-Directed: simulate edges as springs (nodes repel and
edges pull), good for up to 500 nodes
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Multi-layer layouts: partition graph, layout each partition and
then layout partitions
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…
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Layouts (Demo)
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Tips & Tricks: Layouts
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Use layouts to convey the relationships between the
nodes
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Layout algorithms may need to be ”tuned” to fit your
network (Layouts  Settings ... menu)
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Consider laying out portions of your network
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Adjust the layout manually
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Load network into a drawing program (e.g. Illustrator)
and adjust labels
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Use case: Drosophila Protein network
Although from fly, serves as model for human
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Groundbreaking work now done in model systems
What did they do
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Bait-Protein interactions
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Statistical analysis; highly confident set
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Use case: Assignment 1.1
1.
Open the DrosophilaBasicSession.cys file
2.
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
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Generating networks
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Import network from web services supported by
Cytoscape
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Pathway commons (only well-studied organisms)
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PSICQUIC Universal Client (collection of many public
databases)
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MiMI (Michigan Molecular Interactions database)
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BisoGenet (SysBiomics database)
Generate a network using a Cytoscape plugin
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AgilentLiteratureSearch (based on text mining)
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Generating networks (Demo)
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Use case; Assignment 1.2
1.
Try to locate the protein complexes found in the article
in the network
2.
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
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Tips & Tricks: Network view
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When you open a large network, you will not get a view
by default
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To improve interactive performance, Cytoscape has the
concept of ”Levels of Detail”
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Some visual attributes will only be apparent when you zoom in
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The level of detail for various attributes can be changed in the
preferences
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To see what things will look like at full detail: go to View 
Show Graphics Details
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Exporting & saving data
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Sessions save pretty much everything: Networks,
Properties,Visual styles, Screen sizes
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Export networks in different formats: SIF, GML, XGMML,
BioPAX, PSI-MI 1 & 2.5
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Publication quality graphics in several formats: PDF, EPS,
SVG, PNG, JPEG, and BMP
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Export Session to HTML for Web (SessionForWeb
plugin)
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Exporting & saving data (Demo)
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Tips & Tricks: Memory
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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_memor
y_for_Cytoscape
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Tips & Tricks: General
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By default, Cytoscape writes it’s logs to the Error Dialog: Help 
Error Dialog
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Change the ”logger.console” preference in Edit  Preferences 
Properties... to write it to the console
.cytoscape directory
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Your defaults and any plugins downloaded from the plugin manager will
go here
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Sometimes, if things get really messed up, deleting (or renaming) this
directory can give you a ”clean slate”
Plugin manager
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”Outdated” doesn’t necessarily mean ”won’t work”
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Plugin authors don’t always update their plugins immediately after new
releases
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Open source; sometimes bugs occur!
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Use case: Assignment 1.3
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Export the network view as figure
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Find out in which format you’d best save your network
3.
Save your session for later use
http://cytoscape.org/manual/Cytoscape2_8Manual.html#Supported Network File
Formats
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Cytoscape extended functionality
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Cytoscape extends its functionality
with plugins
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Developed by third parties
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Listed at http://apps.cytoscape.org/
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Usually available through the Plugin
Manager
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Can be downloaded from the
plugins’s websites
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Cover many diverse areas of
application
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Cytoscape Plugin Manager (Demo)
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Use case: Assignment 1.4
1.
Explore available plugins for PPi relevance
http://cytoscape.org/manual/Cytoscape2_8Manual.html#Plugins and the Plugin Manager
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To be continued…
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Build, visualize and analyze your own network with
Cytoscape
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Network generation
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Network annotation and visualization
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Loading and manipulating attributes
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Identifier mapping
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Mapping data onto the network
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Use visuals to convey data
Network analysis
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