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topics:bib:nikolaeva2011a

Visualization of highly interacting modules in large networks.

Category:Bioinformatics
Supervisor:Elena Nikolaeva
Year:2011
Abstract:Visualization of the large networks helps to reduce the complexity of network analysis. In bioinformatics one of the popular web tool to analyze networks is Graphweb, which is developed in BIIT group. GraphWeb (http://biit.cs.ut.ee/graphweb/) integrates data for constructing different types of graphs, and discovers sub-graphs (modules) using a variety of popular graph mining algorithms. These modules are related but are currently displayed as separate sub-graphs. The task of this project is to add functionality to GraphWeb for integration and visualization of the sub-graphs together. In addition you need to provide interactive interface to browse between modules and allow additional features to be visualized.
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Tasks

  • Use GraphWeb tool to identify sub-graphs from a given large network for eg., a protein-protein interaction data.
  • Visualize the interacting modules using force-directed techniques.
  • Implement additional functionalities as described in the abstract.

Literature

  • Di Battista G, Eades P, Tamassia R, Tollis IG. 1999. Graph drawing: algorithms for the visualization of graphs. New Jersey: Prentice Hall
  • T. M. J. Fruchterman and E. M. Reingold, 1991, “Graph Drawing by Force-Directed Placement”, Software-Practice & Experience, vol. 21, no. 11, pp. 1129-1164.
  • Jüri Reimand, Laur Tooming, Hedi Peterson, Priit Adler and Jaak Vilo 2008 GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. Nucleic Acids Res. 36:452-459.
topics/bib/nikolaeva2011a.txt · Last modified: 2011/10/19 18:20 by balaji