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. Although ITM Probe has several desirable features such as 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 ITM Probe within workflowsinvolving other analysis methods. To resolve these difficulties. we developed CytoITMprobe, a  Cytoscape plugin. CytoITMprobe  provides access to ITM Probe 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 . Saving results as node and network attributes, CytoITMprobe 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 ITM Probe results with other Cytoscape plugins having complementary functionality for data analysis.
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 results are shown as a subnetwork of significant nodes and several summary tables. Users can control the composition and appearance of the subnetwork and interchange their ITM Probe results with other software tools through tab-delimited files. The main strength of CytoITMprobe is its flexibility. It allows the user to specify as input any Cytoscape network, rather than being restricted to the pre-compiled protein-protein interaction networks available through the ITM Probe web service. Users may supply their own edge weights and directionalities. Consequently, as opposed to ITM Probe web service, CytoITMprobe can be applied to many other domains of network-based research beyond protein-networks . It also enables seamless integration of ITM Probe results with other Cytoscape plugins having complementary functionality for data analysis.
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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. Although ITM Probe has several desirable features such as 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 ITM Probe within workflowsinvolving other analysis methods. To resolve these difficulties.
To provide the Cytoscape users the possibility of integrating ITM Probe into their workflows,
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new
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maintains all the desirable features of ITM Probe and adds additional flexibility not achievable through its web service version. It
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a Cytoscape network, together with the
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. Saving results as node and network attributes, CytoITMprobe allows Cytoscape users to manipulate and visualize context-specific information in a manner more flexible than its web predecessor
and interchange their ITM Probe results with other software tools through tab-delimited files. The main strength of CytoITMprobe is its flexibility. It allows the user to specify as input any Cytoscape network, rather than being restricted to the pre-compiled protein-protein interaction networks available through the ITM Probe web service. Users may supply their own edge weights and directionalities. Consequently, as opposed to ITM Probe web service, CytoITMprobe can be applied to many other domains of network-based research beyond protein-networks