CytoITMprobe

Provides access to the ITM Probe database for querying and importing related network nodes and their attributes.
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<p>Earlier, we developed a network information flow framework and implemented it as a web application, called <i>ITM Probe</i>. Given a context consisting of one or more user-selected nodes, <i>ITM Probe</i> retrieves other network nodes most related to that context. Although <i>ITM Probe</i> has several desirable features such a requiring neither restriction to subnetwork of interest nor additional and possibly noisy information, it still has a few limitations. For example, users can only query pre-compiled protein interaction networks. Also, manipulating the layout of significant subnetworks is non-trivial. Most importantly, it is difficult to integrate the results of <i>ITM Probe</i> within workflows involving other analysis methods. To resolve these difficulties. we thus developed <i>CytoITMprobe</i>, a <i>Cytoscape</i> plugin.</p><br><p><i>CytoITMprobe</i> provides access to <i>ITM Probe</i> either through a web server or locally. The input, consisting of desired origins and/or destinations of information and a dissipation coefficient, is specified through a query form. The results are shown as a subnetwork of significant nodes and several summary tables. Users can control the composition and appearance of the subnetwork.</p><br><p>Saving results as node and network attributes, <i>CytoITMprobe</i> allows Cytoscape users to manipulate and visualize context-specific information in a manner more flexible than its web predecessor. It also enables seamless integration of <i>ITM Probe</i> results with other <i>Cytoscape</i> plugins having complementary functionality for data analysis.</p>
CYTOSCAPE 2

Version 1.5

Released 12 Mar 2012

Works with Cytoscape 2.7, 2.8

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