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LineageEvolver is a simulation system for molecular evolution. Sequence evolution is simulated using modular processes such as substitutions, gene duplication/death, horizontal gene transfer, and more.
msgnet is a library that implements a simulation framework with visualisation for message passing networks.
This might be useful for teachers and students of distributed systems courses.
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Java3D 3DS FileLoader for platforms supporting JDK1.4 and Java 3D
Highly functional, multiplatform 3DS File format loader
Supports:
Heirarchical animation
Cameras
Point Lights
Directional Lights
Textures
Smooth Groups
and other features
A visual Domain-Specific Language for Data Transformations, which generates programs for non-programmer domain-experts. The generated program will extract data from one source and converts it into a meaningful format defined by the user.
Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.
Kaboum is an advanced java 1.1 applet that offers a user friendly interface to the mapserver cgi program (http://mapserver.gis.umn.edu).
The displayed maps are made from a combination of mapserver output (gif or jpg image) with editable vectors layers.
CRANKS is an Java application that uses the Swing toolkit to provide an interactive environment for the animation and kinematic synthesis of four-bar mechanisms created through a series of geometrical constructions.
Framework for storing and editing Forestry-related XML data, with a specialised graphical interface for each object type. Plug-in API for adding functionality. Coded in Java, uses WebStart for distribution, swing GUI, ~100k lines of code.
neochip is a collection of algorithms for high-density oligonucleotide microarrays. The current version contains heuristic algorithms that attempt to improve the quality of arrays by re-designing their layout (the location of the probes on the chip).
DNAGalaxy is an attempt to produce an open-source bioinformatics software alternative to the expensive DNAStar Lasergene software. Its features currently include Blast and Entrez searching, a frontend to clustal and a sequence editor. It requires java1.5
JSpice is a Java Wrapper (using JNI) for the CSpice library provided by NAIF.
Goal of JSpice is to provide a full portable version of CSpice wich is used to calculate geometricals parameters of spatial mission as Cassini/Huygens.
An ANN design/implementation focused to work with optimally with NEAT (http://www.cs.utexas.edu/users/kstanley/neat.html). Semiann uses a sparse matrix to fill out the nodes, connections, weights, biases and activation functions for an ANN.
ISAS is a configurable computer instruction set architecture simulator, written in Java, that can be used to quickly define, test and measure performance of computer instruction set architectures.
MicroArray Genome Imaging and Clustering Tool (MAGIC tool) is a platform-independant java program for analyzing MicroArray data (.tiff scans & .txt godlists) via graphs and clustering operations (including QT-clustering). http://www.bio.davidson.edu/magic
This is a Open Source Geographic Information System extreamly open for further developpement due to a plug-ins mecanisme. It uses OpenGL for optimizing graphics and can connect to a native server or handle other map software formats
GiANT is a graphical interface for computer algebra systems (OS X/UNIX/Win). Currently GiANT lets the user work with number fields via KASH, but we aim to develop it into a GUI Library to run on top of any CAS and expose any of its functions.
Alan is a Java Implenmentation of a Turing Machine for educational purpose. Features include: - Easy to use GUI - Many example Programs - ReUsable Turing Machine Component