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Bioinformatics Advance Access originally published online on September 12, 2007
Bioinformatics 2007 23(20):2803-2805; doi:10.1093/bioinformatics/btm444
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

AVIS: AJAX viewer of interactive signaling networks

Seth I. Berger , Ravi Iyengar and Avi Ma’ayan *

Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, 1425 Madison Avenue, New York 10029, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Increasing complexity of cell signaling network maps requires sophisticated visualization technologies. Simple web-based visualization tools can allow for improved data presentation and collaboration. Researchers studying cell signaling would benefit from having the ability to embed dynamic cell signaling maps in web pages.

Summary: AVIS is a Google gadget compatible web-based viewer of interactive cell signaling networks. AVIS is an implementation of AJAX (Asynchronous JavaScript with XML) with the usage of the libraries GraphViz, ImageMagic (PerlMagic) and overLib. AVIS provides web-based visualization of text-based signaling networks with dynamical zooming, panning and linking capabilities. AVIS is a cross-platform web-based tool that can be used to visualize network maps as embedded objects in any web page. AVIS was implemented for visualization of PathwayGenerator, a tool that displays over 4000 automatically generated mammalian cell signaling maps; NodeNeighborhood a tool to visualize first and second interacting neighbors of yeast and mammalian proteins; and for Genes2Networks, a tool to connect lists of genes and protein using background protein interaction networks.

Availability: A demo page of AVIS and links to applications and distributions can be found at http://actin.pharm.mssm.edu/AVIS2. Detailed instructions for using and configuring AVIS can be found in the user manual at http://actin.pharm.mssm.edu/AVIS2/manual.pdf

Contact: avi.maayan{at}mssm.edu

Associate Editor: Alfonso valencia

Received on December 5, 2006; revised on July 18, 2007; accepted on August 21, 2007

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