2011/11/30 by Aleksandar Stojmirović, Stojmirović, Aleksandar, Alexander Bliskovsky +4
Biochemistry, Genetics and Molecular Biology · Computer Science · #Bioinformatics and Genomic Networks #Databases (cs.DB) #FOS: Biological sciences #FOS: Computer and information sciences #Genomics and Phylogenetic Studies #Molecular Networks (q-bio.MN) #Protein Structure and Dynamics #Quantitative Methods (q-bio.QM) #cs.DB #q-bio.MN #q-bio.QM
paper · pdf · doi:10.48550/arxiv.1112.0045
16 pages, 6 figures. Version 2
openalex publication_date 2011/11/30 · arxiv created 2012/03/19 · arxiv updated 2012/03/21 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/04
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.