CytoITMprobe: a network information flow plugin for Cytoscape

TL;DR

CytoITMprobe is a flexible Cytoscape plugin that integrates the ITM Probe network information flow analysis, allowing users to analyze custom networks with enhanced control and integration capabilities.

Contribution

It introduces a Cytoscape plugin that extends ITM Probe's functionality, enabling analysis of user-defined networks with customizable parameters and seamless integration.

Findings

Supports local and web server access to ITM Probe

Allows input of custom networks with edge weights and directions

Enables integration with other Cytoscape plugins

Abstract

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.