• VisualAp A visual framework for building application and systems based on visual components, VisualAp can be used in order to perform audio processing, image processing, text and other process-driven emulation.

• Zephyr - A script-based measurement automation program / development framework.

• genvlin - genvlin offers you easy plotting and data manipulating
• Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.
• Sockeye is a standalone Java client that lets you assemble, visualize and work with complex comparative genomics datasets in an interactive 3D graphical workspace.
• Apollo Genome Annotation and Curation Tool
• Argo Genome Browser is the Broad Institute's production tool for visualizing and manually annotating whole genomes.
• Integrated Genome Browser (IGB, pronounced ig-bee) is an application intended for visualization and exploration of genomes and corresponding annotations from multiple data sources.
• Gene ViTo: GeneViTo^? is a JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction.
• VISTA Genome Browser
• CGView - Circular Genome Viewer - is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web.
• cMap Comparative Mapping
• yEd is a graph, diagram, and network creator and editor which offers supreme automatic layout capabilities and network analysis features.

• JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological pairwise local sequence alignment.

• JAligner - An open source Java implementation of biological sequence alignment algorithms. Presently, the package provides a clean and efficient implementation of the Smith-Waterman algorithm with Gotoh's improvement for pairwise alignment with affine gap penalty. JAligner can be used through command line, user interface using Java Web Start, and programmatic APIs.

• JAS3 - A scientific data analysis application

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ScienceApps

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• JChemPaint - JChemPaint KRA00 is an editor for 2D molecular structures. JChemPaint is intended to be complementary to Jmol, a visualisation and analysis tool for 3D molecular structures, started by Dan Gezelter at Notre Dame University, initator of the Open Science Project. and, like JChemPaint, developed by an international team of opensource programmers.
• JMol - Jmol is a free, open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. Jmol is a collaboratively developed visualization and measurement tool for scientists and educators. New features being added on an ongoing basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.
• Simbrain - SIMBRAIN is a freeware tool for building, runnning, and analyzing neural-networks (computer simulations of brain circuitry). Simbrain aims to be as visual and easy-to-use as possible. Also unique are its integrated "world component" and its representation of the network's activation space. Simbrain is written in Java and runs on Windows, Mac OS X, and Linux.
• NanoCAD - A freeware nanotech design system including source code.
• The Chemistry Development Kit - The CDK classes are Java utitility classes for ChemoInformatics^? and Computational chemistry, written in Java. They are developed constantly developed parallel to other projects that make use of them. They are a complete re-write of the CompChem^? classes that were the basis of JChemPaint, a Java Editor for 2D chemical structures, and of JMDraw, a Java package for the graphical layout of 2D chemical structures.
• NeoBio is a library of bioinformatics algorithms implemented in Java.
• JOELib - A Java based computational chemistry (cheminformatics) library.
• JAligner is a Java implementation of biological sequence alignment algorithms.
• JSci - A science API for Java. The aim is to encapsulate scientific methods/principles in the most natural way possible. As such they should greatly aid the development of scientific based software.
• AstroVirgil - With AstroVirgil you can analyze data from the space-based Chandra X-ray telescope. You can study supernovas, black holes and the center of galaxies.
• JAMA is a basic linear algebra package for Java. It provides user-level classes for constructing and manipulating real, dense matrices. It is meant to provide sufficient functionality for routine problems, packaged in a way that is natural and understandable to non-experts.
• Debrief - Welcome to the home page for Debrief, the Open Source application used by navies and companies around the world for the analysis and reporting of maritime exercises. Debrief 2003 has been produced by the Maritime Warfare Centre, in Portsmouth UK, to support the analysis and reporting of maritime tactical exercises.
• Significant Figures - A Java number class for figuring out how many significant figures each of the numbers in a calculation has and displaying the result appropriately.
• GeoVirgil is a free mapping program that automatically downloads and displays data from the Planetary Data Archive at NASA's Jet Propulsion Lab. With it, you can explore the solar system using the very same data that scientists use.
• GeoTools is the leading open source Java library for developing OpenGIS solutions.
• B is a Java-based, on-line biomolecular modeling package. It should be useful in generating initial structures of biopolymers and small organic molecules. Simple force-field energy minimizations can be carried out in addition to simulated annealing with molecular dynamics.
• BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating sequences, file parsers, DAS client and server suport, access to BioSQL^? and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.
• VisAD is a Java component library for interactive and collaborative visualization and analysis of numerical data. The name VisAD^? is an acronym for "Visualization for Algorithm Development".
• ptplot is a 2D data plotter and histogram tool implemented in Java. Ptplot can be used as a standalone applet or application, or it can be embedded in your own applet or application.
• HartMath is an experimental computer algebra system written in Java. It is available free under GNU public license.
• Java CML Filter Library (JCFL) - The Chemical Markup Language (CML) is a XML application for storing and transporting chemical information. The first official release of CML was in spring 1999. Egon Willighagen wrote import and export filters in the Java programming language soon after. These Java classes are now avaiable under GPL license.
• Graph Class Library

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