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SB-MASE is aimed at students and researchers in AI, for simulation and control of agents and robots. It uses task based decomposition and the subsumption architecture as its core control mechanisms and includes numerous possibilities for adding plug-ins.
Formicidae is the official simulator and visualizer for the Ant-Wars competitive programming site, written in Java and SISC. The site is hosted at www.ant-wars.net.
This is a toolkit for medical natural language processing (NLP). The core engine is general enough to be used in a variety of text processing domains, though the toolkit includes specific support for medical reports and patient de-identification.
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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.
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).
The Linear Algebra class library for Java provides a full set of tools to programmers who need linear algebra operations to use in their own projects.
Currently the library supports elementary matrix operations.
...It allows you to find, display and inspect clones, which are fragments of duplicated source code resulting from lack of proper reuse. It can be used as a plugin for Eclipse and on the commandline.
Java Randomness Test Suite is a gui application to run randomness tests on random stream resource (file or algorithm). Application can be run in commandline. Includes general statistical tests, NIST and DIEHARD tests.
A command-line program to manipulate annotated genetic sequences (initially in EMBL format). The user supplies a pattern to identify which features or qualifiers to process. These can then be deleted, renamed etc
VKAS uses genetic programming methods to find out the relationship among a set of independent and dependent variable. It is a problem solver software which uses evolutionary computing methods.
When vkas is run, it creates a population of chromosomes at random. This population is then genetically modified and next population is generated. Each population is subjected to fitness calculation and if a suitable answer chromosome is found then vkas stops and the answer is printed. If a...
A service-oriented, single-source, Java integration server with virtual Service Stores(TM) that expose services via web services, HTTP and more. Service Flows provide process automation. Mainframe, database, email, web, soap & ftp adapters are included.
Ober brings the power of the Oberon interface to Java, blending command-line and GUI models. Ancestors are Oberon(http://www.oberon.ethz.ch/), Acme (http://plan9.bell-labs.com/sys/doc/acme/acme.ps) and Wily (http://www.cs.yorku.ca/~oz/wily/index.html).
NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.
The Mechanical Engineering Department at Oregon State University currently has high-resolution x-ray tomography equipment that allows three-dimensional imaging of the interior of objects. Their existing imaging software is commandline based and difficult
A java command-line application where the main goal is to solve any simplex problem. It's a team-work school project. It can be usefull for other students who needs to understand the simplex algorithm.