Sunday, June 26, 2005


Some websites for Networks Analysis and Plot



Graph Visualization
Graph visualization is a way of representing structural information as
diagrams of abstract graphs and networks. Automatic graph drawing has many
important applications in software engineering, database and web design,
networking, and in visual interfaces for many other domains.
Graphviz is open source graph visualization software. It has several main
graph layout programs. See the gallery for some sample layouts. It also has
web and interactive graphical interfaces, and auxiliary tools, libraries, and
language bindings.


GLEE is a .NET tool for graph layout and viewing. It has been developed in Microsoft Research by Lev Nachmanson. GLEE is built on principles of the Sugiyama scheme; it produces so called layered, or hierarchical, layouts. This kind of a layout naturally applies to graphs with some flow of information. The graph could represent a control flow graph of a program, a state machine, a C++ class hierarchy, etc. Please see samples of layouts of such graphs below.


QuickGraph, Graph Data Structures And Algorithms for .Net
QuickGraph 2.0 provides generic directed graph datastructures and algorithms for .Net 2.0. QuickGraph comes with algorithms such as depth first seach, breath first search, shortest path, network flow etc... QuickGraph supports GLEE and Graphviz to render the graphs.

(One of my favorites)


Networks / Pajek
Program forLarge Network Analysis


GUESS is an exploratory data analysis and visualization tool for graphs and
networks. The system contains a domain-specific embedded language called
Gython (an extension of Python, or more specifically Jython) which supports
the operators and syntactic sugar necessary for working on graph structures
in an intuitive manner. An interactive interpreter binds the text that you
type in the interpreter to the objects being visualized for more useful
integration. GUESS also offers a visualization front end that supports the
export of static images and dynamic movies.


InfoVis CyberInfrastructure
This web site provides access to a comprehehsive set of software packages
easing the exploration, modification, comparison, and extension of data
mining and information visualization algorithms. Diverse software packages
were bundled into learning modules. Access to a large-scale data repository,
extensive compute resources, and a growing set of references are provided as
well. It is our hope that the community will adopt this resource to foster
Information Visualization education and research.


Network Workbench: A Large-Scale Network Analysis, Modeling and Visualization
Toolkit for Biomedical, Social Science and Physics Research.

This project will design, evaluate, and operate a unique distributed, shared
resources environment for large-scale network analysis, modeling, and
visualization, named Network Workbench (NWB). The envisioned data-code-computi
ng resources environment will provide a one-stop online portal for
researchers, educators, and practitioners interested in the study of
biomedical, social and behavioral science, physics, and other networks.


The Boost Graph Library (BGL)
Graphs are mathematical abstractions that are useful for solving many types
of problems in computer science. Consequently, these abstractions must also
be represented in computer programs. A standardized generic interface for
traversing graphs is of utmost importance to encourage reuse of graph
algorithms and data structures. Part of the Boost Graph Library is a generic
interface that allows access to a graph's structure, but hides the details of
the implementation. This is an ``open'' interface in the sense that any graph
library that implements this interface will be interoperable with the BGL
generic algorithms and with other algorithms that also use this interface.
The BGL provides some general purpose graph classes that conform to this
interface, but they are not meant to be the ``only'' graph classes; there
certainly will be other graph classes that are better for certain situations.
We believe that the main contribution of the The BGL is the formulation of
this interface.


The Parallel Boost Graph Library
A Generic C++ Library for High-Performance Parallel and Distributed Graph
The Parallel BGL builds on the Boost Graph Library (BGL), offering similar
data structures, algorithms, and syntax for distributed, parallel computation
that the BGL offers for sequential programs. The Parallel BGL is intended
primarily as a research platform, to facilitate both experimentation with and
comparison of parallel graph algorithms and to provide solid implementations
for solving large-scale graph problems in other application areas.


LaNet-vi provides images of large scale networks on a two-dimensional layout. The algorithm is based on the k-core decomposition. A complete description of the algorithm and the visualization layout can be found in our article: k-core decomposition: a tool for the visualization of large scale networks.


Otter is a historical CAIDA tool used for visualizing arbitrary network data that can be expressed as a set of nodes, links or paths. Otter was developed to handle visualization tasks for a wide variety of Internet data, including data sets on topology, workload, performance, and routing. Otter is in maintenance rather than development mode.


Metabolic network toolbox for MATLAB


Network Monitoring Tools


Java Universal Network/Graph Framework

NetDraw is a program for drawing networks. It uses (or will use) several different algorithms for laying out nodes in 2-dimensional space (3D will come later). Netdraw reads UCINET system files, UCINET DL text files, and Pajek text files (.net, .clu and .vec). It can save data to Pajek and to Mage. It can save diagrams as EMF, WMF, BMP and JPG files. It can also print directly from the program at high resolution (much better than printing document containing embedded graphics).


An open software system for the advanced statistical analysis of social networks


Cytoscape: Analyzing and Visualizing Network Data
for bioinformatic only

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