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(AVIS) Category Cross-Omics>Pathway Analysis/Tools Abstract AVIS is a visualization tool for viewing and sharing intracellular signaling, gene regulation and protein interaction networks. It 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 a web-based visualization of text-based signaling networks with dynamical zooming, panning and linking capabilities. AVIS is also a cross-platform web-based tool that can be used to visualize network maps as embedded objects in any web page. It allows any webpage to render an image from a text file representation of signaling, gene regulatory, or protein interaction networks. Network diagram images can be zoomed and panned within webpages. As the view of the image changes, the view is re-rendered to ensure that all edges in the view are visible and all nodes in the view have readable labels. Labels with links can be displayed as users move the mouse over the nodes. AVIS is designed to be embedded in any webpage to allow users to dynamically view cellular interaction networks without the webpage administrator having the need to have any programming knowledge. AVIS End-User capabilities/features -- The end-user experience is designed to be light-weight and straightforward. A control panel is displayed beneath the image of the network. The control panel contains controls to zoom-in, zoom-out, and pan the image. The “Set Zoom” and “Set Pan” controls allow users to jump directly to a view of choice. For example, the select node option in the Set Pan menu allows the view to be quickly centered on any node. The values entered for the “Pan X” and “Pan Y” is percents of the total span. For instance, setting both these values to 50% will center the view in the middle of the image as it will be set to 50% of the maximum pan. The “Save/Edit” button allows users to download the image of the current view, the entire network map, or edit a textual representation of the network in AVIS format. When the text is modified and the “submit” link is pressed, the network is re-rendered with the changes. AVIS formats used/implementation -- AVIS supports several standard graph representation formats such as Pajek.net and Systems Biology Markup Language (SBML) as well as a simple structured text file format the manufacturer developed called .sig. It also supports a more flexible native AVIS format which allows editing of any graph features, giving users more control over the placement of nodes, colors of nodes and arrows, shapes of nodes and types of arrows as well as more control on setting up hyperlinks. AVIS was implemented for visualization of PathwayGenerator, a tool that displays over 4,000 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. Software Applications which use AVIS for Network Visualization -- Genes2Networks (see G6G Product Number 20425) - 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 the Signal Transduction Knowledge Environment (STKE) - (see G6G Product Number 20246). Node Neighborhood - A simple program that shows all of the first, second, or third neighbors of a specified node in one of three datasets. This is included with the AVIS distribution. Yeast Node Neighborhood - A simple program that shows the entire 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.
Contact manufacturer Manufacturer
Mount Sinai School of Medicine 1425 Madison Avenue, New York 10029 USA Manufacturer's Web Site http://actin.pharm.mssm.edu/AVIS2/ Price Contact manufacturer G6G Product Number 20480 G6G Manufacturer Number 104054 |
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