Presenter: Scooter Morris, University of California, San Francisco

Title: Clusters and Groups


Grouping nodes and edges together is a common requirement for biologists dealing with biological networks of various types.  Systems biologists are interested in looking at the proteins in a network that are co-regulated based on expression data or genetically linked based on an epistatic mapping experiment.  Structural biologists might be interested in looking at groups of proteins that act on similar ligands and enzymologists might be interested in looking at groups of proteins based on sequence or structural similarity. All of these uses have two things in common: a mechanism to group nodes and edges together and an algorithm to partition the network into those groups. I will be demonstrating a group of plugins that meet some of those needs:

 *namedSelectionPlugin* - A way to group nodes together using a particular name
 *metaNodePlugin2* - A way to collapse and expand groups
 *groupTool* - A general tool to allow manipulation of groups, their nodes, edges, and viewers
 *clusterMaker* - A new plugin that provides hierarchical, k-means, FORCE, and MCL clustering and the ability to visualize cluster results using TreeView
 *clusterExplorer* - A tool that displays various cluster statistics

I'll demonstrate how these tools can work together to provide a platform for clustering using Cytoscape.

Slides: ClustersAndGroups.ppt

CytoscapeRetreat2008/Scooter (last edited 2009-02-12 01:03:50 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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