CytoITMprobe: a network information flow plugin for Cytoscape

BMC Research Notes
Aleksandar StojmirovicYi-Kuo Yu


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


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

❮ Previous
Next ❯


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

❮ Previous
Next ❯

Related Concepts

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Epigenetics Insights from Twin Studies

Find the latest research on epigenetics and twin studies here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.


Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.

Myocardial Stunning

Myocardial stunning is a mechanical dysfunction that persists after reperfusion of previously ischemic tissue in the absence of irreversible damage including myocardial necrosis. Here is the latest research.

Related Papers

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Aleksandar Stojmirovic, Yi-Kuo Yu
Physical Biology
Yoo-Ah KimTeresa M Przytycka
Samad LotiaAlexander R Pico
© 2021 Meta ULC. All rights reserved