SpectralNET – an application for spectral graph analysis and visualization

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SpectralNET – an application for spectral graph analysis and visualization

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Title: SpectralNET – an application for spectral graph analysis and visualization
Author: Forman, Joshua J; Clemons, Paul A; Schreiber, Stuart L.; Haggarty, Stephen John

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Citation: Forman, Joshua J., Paul A. Clemons, Stuart L. Schreiber, and Stephen J. Haggarty. 2005. SpectralNET – an application for spectral graph analysis and visualization. BMC Bioinformatics 6:260.
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Abstract: Background: Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices) and interactions (edges) that can carry different weights. SpectralNET is a flexible application for analyzing and visualizing these biological and chemical networks. Results: Available both as a standalone .NET executable and as an ASP.NET web application, SpectralNET was designed specifically with the analysis of graph-theoretic metrics in mind, a computational task not easily accessible using currently available applications. Users can choose either to upload a network for analysis using a variety of input formats, or to have SpectralNET generate an idealized random network for comparison to a real-world dataset. Whichever graph-generation method is used, SpectralNET displays detailed information about each connected component of the graph, including graphs of degree distribution, clustering coefficient by degree, and average distance by degree. In addition, extensive information about the selected vertex is shown, including degree, clustering coefficient, various distance metrics, and the corresponding components of the adjacency, Laplacian, and normalized Laplacian eigenvectors. SpectralNET also displays several graph visualizations, including a linear dimensionality reduction for uploaded datasets (Principal Components Analysis) and a non-linear dimensionality reduction that provides an elegant view of global graph structure (Laplacian eigenvectors). Conclusion: SpectralNET provides an easily accessible means of analyzing graph-theoretic metrics for data modeling and dimensionality reduction. SpectralNET is publicly available as both a .NET application and an ASP.NET web application from . Source code is available upon request.
Published Version: http://dx.doi.org/10.1186/1471-2105-6-260
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1276787/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:4453986

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  • FAS Scholarly Articles [6929]
    Peer reviewed scholarly articles from the Faculty of Arts and Sciences of Harvard University
 
 

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