Software Applications which use AVIS for Network Visualization

• Genes2Networks: A web-based interface that allows users to provide a seed list of proteins. All nodes that fall on paths of specified length between these seed genes in the selected background network datasets are then included in a displayed subnetwork along with a statistical report.
• AVIS implementation of PathwayGenerator: A web-based interface that allows users to retrieve automatically generated pathways by selecting an extra-cellular ligand node/molecule and selecting a node that belongs to a cellular machine (i.e. transcription factor) as the target node/molecule. The program searches for all possible pathways that can reach the target molecule in the least number of steps. Previous implementations used SAVI to visualize the pathways and presented connection maps similar to the familiar connection maps published on STKE.
• Node Neighborhood: A simple program that shows all the first, second, or third neighbors of a specified node in one of three dataset. This is included with the AVIS distribution.
• Yeast Node Neighborhood: A simple program that shows all the first, second, or third neighbors of a specified node in the yeast biogrid protein interaction network.
• Upload2AVIS: A simple program that allows you to upload and visualize your own network files in sig, avis, net, or SBML format. This is included with the AVIS distribution.
• Adhesome Network Map: AVIS is used to visualize a comprehensive in-silico biochemical network developed from biomedical literature made of known interactions and cellular components composing the focal adhesion complex in mammalian cells. The web site presents a collaborative project between the Geiger Laboratory, Weizmann Institute of Science and the Iyengar Laboratory, Mount Sinai School of Medicine. This project is funded in part by an NIH NanoMedicine Center grant headed by Michael Sheetz from Columbia University. Other support includes GM-54508 from the NIH and Advanced Research Center Grant NYSTAR from New York State to RI.

All questions related to the listed software should be directed to avi.maayan@mssm.edu and seth.berger@mssm.edu.