BIOINFORMATIC TOOLS

AVIS AJAX Viewer for Signaling Networks is a visualization tool for viewing and sharing intracellular signaling, gene regulation and protein interaction networks. AVIS is implemented as an AJAX enabled syndicated Google gadget. It allows any webpage to render an image from a text file representation of signaling, gene regulatory or protein interaction networks.
PubMed Abstract

 

Genes2Networks is tool that can be used to place lists of mammalian genes in the context of a background mammalian signalome and interactome networks. The input to the program is a list of human Entrez Gene gene symbols and background networks in SIG format, while the output includes: (a) all identified interactions for the genes/proteins, (b) a subnetwork connecting the genes/proteins using intermediate components that are used to connect the genes, (c) ranking of the specificity of intermediate components to interact with the list of genes/proteins, and (d) a clustering analysis of the genes/proteins from the seed list based on their distance from one another in network space.
PubMed Abstract

 

MOOSE (Multiscale Object Oriented Simulation Environment) is designed to handle large complex simulations especially in biology. MOOSE spans the range from single molecules to subcellular networks, from single cells to neuronal networks, and to still larger systems. It is backwards-compatible with GENESIS, and forward compatible with Python and XML-based model definition standards like SBML and MorphML.

 

SAVI (Signaling Analysis and Visualization) is a software tool that can be used for statistical analysis and visualization of large-scale biological networks, including intracellular biochemical networks and tissue level cell-to-cell networks. SAVI is a PC-based desktop application which implements standard graph-theory methods to compute the clustering, connectivity distribution, and detection of network motifs, as well as provides means to visualize the network and network motifs. SAVI is capable of generating linkable webpages from network datasets loaded in text format. SAVI can also create networks from lists of gene or protein names.