BioJava aims to provide a comprehensive set of Java components for the rapid development of applications in Bioinformatics. It contains interfaces for representing Sequences, Features, and other important bioinformatics concepts. It can also read and write sequence data in a variety of common formats and communicate with Ensembl databases and with DAS and BioCorba servers.
Grok is a library of Java components for performing various natural language tasks. These include several preprocessing tasks, chart parsing, a large categorial grammar for English (induced from the Penn treebank), and some knowledge representation components (basic coreference, salience tracking, etc.). The library also has a companion kit which provides a GUI interface to the components, several of which are implementations of interfaces in the Quipu OpenNLP API.
JavaWeather is multithreaded Java code which connects to the NWS servers to download current weather conditions and forecasts from 3,000 observation stations around the US and the world, and provide bean-like access info for Java applications and servlets (not applets). It also includes some temperature utilities.
Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.
JReferences is a program written in Java for managing bibliographic references in the BibTeXML format. Storage is done in a binary file database or, optionally, in a MySQL database. A PHP Web frontend is available. It can input BibTex, RIS, BibTeXML, and DocBook formated references.