CytoITMprobe: a network information flow plugin for Cytoscape

BMC Research Notes
Aleksandar StojmirovicYi-Kuo Yu

Abstract

Cytoscape is a well-developed flexible platform for visualization, integration and analysis of network data. Apart from the sophisticated graph layout and visualization routines, it hosts numerous user-developed plugins that significantly extend its core functionality. Earlier, we developed a network information flow framework and implemented it as a web application, called ITM Probe. Given a context consisting of one or more user-selected nodes, ITM Probe retrieves other network nodes most related to that context. It requires neither user restriction to subnetwork of interest nor additional and possibly noisy information. However, plugins for Cytoscape with these features do not yet exist. To provide the Cytoscape users the possibility of integrating ITM Probe into their workflows, we developed CytoITMprobe, a new Cytoscape plugin. CytoITMprobe maintains all the desirable features of ITM Probe and adds additional flexibility not achievable through its web service version. It provides access to ITM Probe either through a web server or locally. The input, consisting of a Cytoscape network, together with the desired origins and/or destinations of information and a dissipation coefficient, is specified through a query form. The re...Continue Reading

References

Jan 15, 2003·BMC Bioinformatics·Gary D Bader, Christopher W V Hogue
Oct 20, 2007·Nature Protocols·Melissa S ClineGary D Bader
Nov 8, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Aleksandar Stojmirović, Yi-Kuo Yu
Mar 6, 2008·Molecular Systems Biology·Silpa SuthramTrey Ideker
Jun 9, 2009·PLoS Computational Biology·Patrycja Vasilyev MissiuroHui Ge
Jun 30, 2009·Bioinformatics·Aleksandar Stojmirović, Yi-Kuo Yu
Dec 1, 2009·BMC Systems Biology·Konstantin VoevodskiYu Xia
Dec 15, 2010·Bioinformatics·Michael E SmootTrey Ideker
Feb 1, 2011·Bioinformatics·Michael SmootSteven Maere
May 17, 2011·Physical Biology·Yoo-Ah KimTeresa M Przytycka
Dec 14, 2011·Bioinformatics·Christopher Whelan, Kemal Sönmez
Mar 14, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Aleksandar Stojmirović, Yi-Kuo Yu

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Citations

Apr 3, 2016·Genetics, Selection, Evolution : GSE·Theodosia CharitouDavid J Lynn

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