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A Java API for manipulation of GDSII stream data. It is intended to provide a useful, reusable and platform independant library for CAD/CAE application developers.
This API Requires the Java Backus-Naur Test API (JBNT). You may download it from:
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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.
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).
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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.
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.
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.
qsh is a shell for any operating system. It is coded in java so it inherits the pros and cons of java. It is in a very nascent stage, but all the regular commands work: Directory navigation, file tasks etc.
Catatumbo is a project for developing a SoftPLC based on the IEC 61131 standard. The goal of this project is to provide a solution for industrial control using Java and XML technologies (for cross-platform support).
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
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.
BioNote is a knowledge base that combines unstructured wiki technology with structured annotation to form a collaborative environment. BioNote adds the concepts of page types and semi-structured annotation to extend the unstructured nature of wiki pages
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
BlueDuke is a lightweight Java Bluetooth stack. It is based on the Harald Bluetooth stack from Lund University, Sweden (http://www.control.lth.se/~johane/harald/), but will feature support for various profiles, with SDP and RFCOMM as mandatory goals
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.
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.
JEDI is an academic tool developed to extract formal models (timed automta) from Java source code and annotations, acting as a front-end for several academic analysis tools.
This is a prolog-like programming language based on the fuzzy logic. It includes the class-libraries for fuzzy logic, probability theory and method of resolution, all made in C++. Java releases possible in the future.
Phoenix is an information extraction engine written in java.
Controlled by rules (declared in xml), it extracts information form any XML document (unstructured XHTML/OpenOffice documents). Supports XPath, additional conditions and top-down decomposit
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
brCluster is a class library, written in java, that implements generic clustering algorithms carefully designed to allow its aplication in any kind of data. The algorithms implemented are K-means and Hierarchical Clustering (Simple and Complete Link).
The NEtwork Visualisation Environment is a framework for 3D-visualisation of and interaction with networks, especially communication networks as the internet in both real time and as a simulation tool. Based on JMX/Java3D.