Summary

After the Cytoscape retreat held in San Diego in 2005, it became obvious that Cytoscape needs to support metanodes. A metanode is a graph node that contains a subgraph. There are many different ways of modeling and visualizing metanodes, depending on the biological application in question.

The objective is to:

• Clearly identify the biological applications for metanodes
• Clearly define what type of metanode visualization and modeling is needed for each one of these applications
• Come up with a project plan to implement these different ways of visualizing/modeling metanodes

This RFC is a forum for discussing each one of these points.

Iliana Avila developed a Cytoscape plugin that implements one possible way of modeling and visualizing metanodes. This plugin can be used as a concept plugin, so that everyone involved has a clearer idea of what is a metanode, and how it can be used. It is by no means the final implementation of metanodes. See "Concept Plugin" section in this Wiki to learn how to obtain plugin.

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Biological Applications and their MetaNode Needs

Please add your biological application, and a possible metanode solution.

1. Biomodules

• Biological application: Group proteins in a graph of protein-protein interactions that have a collective function in the cell ([http://www.genome.org/cgi/content/abstract/14/3/380]) in order to discern higher levels of organization in the biological network

• Metanode solution: A group of proteins can be visualized by a single node that has visual and topological characteristics that reflect the underlying group of proteins. For example, the size of the node is proportional to the number of proteins it represents, its connections to other proteins reflect connections from its inside proteins to other proteins, its color represents the average expression levels of its members for a certain condition, etc. See the image in [http://labs.systemsbiology.net/galitski/projs/biomodules/index.html]

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Implementation Strategy

Concept Plugin

CVS

Login anonymously into CVS and checkout csplugins:

1. cvs -d :pserver:anonymous@bordeaux.ucsd.edu:/cvsdir5 login

2. cvs -d :pserver:anonymous@bordeaux.ucsd.edu:/cvsdir5 co cytoscape

3. cvs -d :pserver:anonymous@bordeaux.ucsd.edu:/cvsdir5 logout

The plugin is located in: /csplugins/isb/iavila/metaNodeViewer. Edit the build.xml file if necessary to point to the correct Cytoscape path (works with latest Cytoscape version). Type: ant run

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