karl's bookmarks: Networks

• aiSee — Graph Visualization - Proprietary software.
• ASIAN - Automatic System for Inferring A Network - - "ASIAN is a tool for automatically inferring the relationships between objects from data including redundant information, e.g. expression profile that were measured for a large number of genes in less number of conditions.The tool is constructed in combination of the cluster analysis, the regression analysis, and the graphical Gaussian modeling.Only by inputing your raw data, you can obtain some relationships between objects: the correlation, the grouping, the group number, and the network graph."
• Complexity Workshop
• Cytoscape: Analyzing and Visualizing Biological Network Data
• Gene Network Inference
• Gene Regulation and Metabolism - The MIT Press
• CellDesigner - "CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. "
• Graph9 - "This Graph9 program does clustering based on adjacency matrix. An adjacency matrix representation of a graph is a V-by-V array of Boolean values, with the entry in row v and column w defined to be 1 if there is an edge connecting vertex v and vertex w in the graph, and to be 0 otherwise. "
• Graphviz - Graph visualization software.
• graphviz -- pixelglow - The Macintosh port of the automated graph layout software, featuring a new document-based GUI, export to PDF and many more bitmap formats, full alpha transparency, native font and shapefile support and anti-aliasing.
• International network for socian network analysis
• Neurotree - The Neuroscience Family Tree - "The Neuroscience Family Tree is a free, volunteer-run website designed to help you track your academic genealogy. Our goal is to collect information about the grad-student and post-doc connections between most neuroscientists."
• Networked Life - Course Home Page for CSE 112, Spring 2006
• Pajek - Program for Large Network Analysis
• Software Packages for Graphical Models / Bayesian Networks
• String: functional protein association networks - "STRING is a database of known and predicted protein-protein interactions.The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources: Genomic Context High-throughput Experiments (Conserved) Coexpression Previous Knowledge"
• Study of Self-Organized Networks at Notre Dame
• systems-biology
• The World Color Survey - A dataset which looks very interesting.
• visone - analysis and visualization of social networks
• VisANT: An integrative platform for network/pathway analysis
• VxInsight - Sandia National Laboratories

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