NEW — Apropos Database and Annotation Tool

Apropos is an open-source, web-based proteomic and genomic data annotation tool written in Ruby. It is built on top of unique rat/mouse/human annotation database compiled from a variety of databases. With Apropos, you can upload your own gene lists and get annotation reports, view annotation for specific genes/proteins, and search and view KEGG pathways. For more information, visit the Apropos home page.

NEW — GeneIlluminator: PubMed Abstract Disambiguation

GeneIlluminator is a disambiguation methodology for gene nomenclature. The tool assigns biological functions to a gene symbol and its alternative names. If a symbol is ambiguous, GeneIlluminator creates clusters describing in which part of the tree of life a gene symbol unambiguously points to the same gene. When given a species in addition to a gene symbol, GeneIlluminator uses naive bayes classification to predict which cluster this gene belongs to for the given species. Hence GeneIlluminator can be used to enrich query terms unambiguously and effectively for searching the literature, starting solely with a gene symbol and optionally a species of interest. See GeneIlluminator's Web interface.

tYNA: Network Analysis

A tool for analyzing all kinds of networks, including biological, computer, and social ones. Provided functionality includes network management (storage, retrieval, formal conversion), statistics calculation (clustering coefficient, betweenness, eccentricity), network operations (name filtering, statistics filtering), and multiple-network operations (such as computing the intersection and union of networks. The tool is written in Java. Visualization of networks is done with the aid of aiSee. See tYNA's Web interface.

Wgraph: Graph Generation for MediaWikis

Wgraph is a powerful visualization instrument for wikis. It allows users to define graphs on wiki pages using a simple, customizable notation. The graphs are laid out on-the-fly on the server side and the resulting SVG or PNG images are immediately included on the wiki page. Nodes in SVG images can be easily mapped with hyperlinks. Wgraph also provides for easy data mining and visualization of wiki structures such as article dependencies, category intersections etc. See online demo.

PAG/WWW: Static Program Analysis

An easy-to-use system for experimenting with classical data flow analyses. Some analyses are already predefined and there is a variety of example programs, but PAG/WWW also allows specifying custom programs and analyses. The PAG distribution package includes a tool for animating graph sequences with aiSee. See PAG/WWW and PAGanim example graphs.

CoSy: Compiler Development

A highly flexible compiler development system, which allows construction of production-quality performance compilers in a highly efficient manner. aiSee can be used in conjunction with CoSy for graphical representation of your compiler's IR when it is processing an application source file. See example graph.

StackAnalyzer: Stack Usage Analysis

A tool for automatically determining maximum stack usage of tasks in real-time, safety-critical systems. The stack usage analysis results are visualized with aiSee. Stack height differences are shown as annotations in the call graph and control flow graph. See example graph.

Chilibot: Gene/Protein/Keyword Relationship Mining

Chilibot is a software robot that digs into the PubMed database of the U.S. National Library of Medicine to hunt for information regarding the relationships between genes, proteins and keywords of your interest. Chilibot uses aiSee to generate a relationship map for further evaluation by the user. See example graph.

Sphinx-4: An Open Source Speech Recognizer

A state-of-the-art, speaker-independent, continuous speech recognition system written entirely in the Java programming language. It is jointly developed by Carnegie Mellon University, Sun Microsystems Laboratories, Mitsubishi Electric Research Labs, and Hewlett-Packard's Cambridge Research Lab. See example graph.

PubNet: Publication Network Graph Utility

A web-based tool that accepts as input up to two PubMed queries, and returns as output a network graph based on user-specified node and edge selection properties. The visualization is done with the aid of aiSee. See example graph.

Rush Hour Solver

A C++ program that reads a Rush Hour board from a text file, solves it, and produces a GDL file that shows the shortest solution. See example graph.

3LS: A Peer-to-Peer Network Simulator

A 3-level, time-stepped P2P network simulator that uses a central step-clock to simulate the timing. Visualization of the network is done with the aid of aiSee. See example graph.

aiCall: Software Visualization

aiCall automatically calculates a GDL representation of the call graph and the control flow graph of your application code. The graph can then be interactively explored or printed with aiSee, which is included in the aiCall distribution package. Typical graphs contain several thousand nodes and edges and hundreds of nested subgraphs.

aiT: Worst-Case Execution Time Analyzers

Based on the technique of abstract interpretation, aiT WCET Analyzers statically compute tight bounds for the worst-case execution time of tasks in real-time systems. As a part of the aiT package, aiSee supports the visualization of the worst-case program path and the interactive inspection of all pipeline and cache states on arbitrary program points. See example graph.

Apache2GDL: Web Site Visitor Movements Visualization

A Perl script that generates visitor movement graphs from Apache log files, thus helping you find out how people actually browse your site. See example graphs.

SCORtoGDL: Ecosystem Network Analysis

An open source tool written in Visual Basic, which translates SCOR files (numeric description of carbon exchanges in ecosystems) into GDL. See example graph.

Smute: A Programming Language for Processing Structured Data

Unlike general-purpose programming languages such as C, C++, or Java, Smute is a special-purpose programming language especially designed for the implementation of functions processing data. It features high efficiency, modularity, support for large data instances and special support for processing recursively structured data — including built-in functionality for data visualization. See example graph.

MIM: Mixed Interaction Modeling

A tool for graphical modeling applied in many different fields. MIM is designed to help you understand complex multivariate data, by facilitating graphical representations of the dependencies between the variables under study. See example graph.

IRCmap: Visualization of IRC Networks

A collection of open source scripts for visualization of IRC networks. IRCmap retrieves the structure of a network and uses aiSee to visualize it. A web-based demo is available. See example graph.

aiLink: Hypertext Linkage Visualization

aiLink takes a URL as input, gets a copy of the Web page, extracts all hyperlinks, generates a GDL file, and tells aiSee to visualize the linkage graph. The computed layout can then be viewed online using almost any Web browser. aiSee also enables mapping output images with links to Web pages represented by graph nodes, and with javascript node tooltips. See example graph or go directly to our online demo.

GnuMap: Network Visualization

The objective of the GnuMap project is to find an efficient way to create network maps of the gnutella P2P network and to gather statistics without changing the gnutella protocol. GnuMap enables the user to learn more about P2P networks and to keep visual track of how the topology of the network changes over time. Typical graphs contain hundreds or even thousands of nodes and edges. See example graph.

fxviz: An XML Tree Visualizer

fxviz reads an XML document from a file or standard input and produces a GDL representation of the document tree. The graph can then be explored and printed with aiSee. See example graph.