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GeNetDB, contraction of Genetic Network Database, is a bioinformatic platform destined to the study of genetic regulatory networks. It contains in one place the data and the way to study them, providing the user an access to all tools needed for his work
Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.
A Java program to parse chemical names using IUPAC nomenclature. The output can be either a visualisation of the molecule, or in a form for other programs to use (e.g. CML).
Netsim is a mobile ad hoc network simulator targeted at large heterogeneous node configurations. It is written in Java and is easily extensible through its modular concept.
HyperSpider (Java app) collects the link structure of a website. Data import/export from/to database and CSV-files. Export to Graphviz DOT, Resource Description Framework (RDF/DC), XML Topic Maps (XTM), Prolog, HTML. Visualization as hierarchy and map.
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wlandscape is a tool for collecting access point data of public wireless networks ( wlan ) in order to share it with anyone. It also supports gps and visualisation with the help of topographical maps. Visit our homepage for further informations.
idyuts is \"I Dare You to Use This Shell\"; a pre-hibernate approach to replacing an ORM written with jython functors into a pure-Java language command pattern. The \"pipeline codegen artifacts\" are simple IoC templates, and trivial to adapt
JRVFSim (Jarvis) is a simulator of a fluid dynamics phenomenon known as radial viscous fingering. Its main feature consists of taking jordan curves and simulating their evolution subject to various parameters. Includes a partial API for numerical methods
JMAT : Java MATrix tools package.
Provides an easy-to-use class of matrix with MATLAB-like functions and syntax. JMAT also includes plots and histograms in 2D or 3D, an expression parser, and some statistic simulation tools.
OmniGene is a set of reausable components that have been packaged into frameworks. These frameworks are used to produce domain specific services for common bioinformatics tasks including: visualization, database access, and pipeline building.
MathGenius is a graphical tool intended to simplify your work in mathematics. By now it includes a graphical function plotter, a mechanism (still in development) to derive functions, and an equation solver. An extension mechanism will be developed.
QRay is an interactive 3D modelling system in Java. It's built-in real-time raytracing engine implements the Quadric-CSG representation model and the Seed-Fill optimization method, which empower QRay to provide cool WYSIWYG 3D modelling functionalities.
jATLAS is a Java implementation of ATLAS [Architecture and Tools for Linguistic Analysis Systems]. For more information, see http://jatlas.sourceforge.net.
Fractal View is a fractal viewing application used for exploration of common fractal sets. It runs in fullscreen, supports four different fractal sets, has 22 different color palettes, saves in png format, does antialiasing, and zooms in all sets.
Cytoscape is a software platform for computational biology and
bioinformatics, useful for integrating data, and for visualizing and
performing calculations on molecular interaction networks
Pattern recognition software package. It includes several classification and clustering algorithms. It can read data from a
set of images, an ASCII file or a JDBC connection. A small TCP data server with its corresponding JDBC driver is included.