The Java Algebra System (JAS) is an object oriented, type safe, multi-threaded approach to computer algebra. JAS provides a well designed software library using generic types for algebraic computations implemented in the Java programming language. The library can be used as any other Java software package, or it can be used interactively or interpreted through a Jython or JRuby front end. The focus at the moment is on commutative and solvable polynomials, power-series, multivariate polynomial factorization, Gröbner bases, and applications.
Universal Password Manager (UPM) allows you to store usernames, passwords, URLs, etc. in an encrypted database protected by one master password. Its three strongest features are simplicity (it provides a small number of very strong features with no clutter), the ability to run cross-platform, and database sharing. Rather than having many separate databases (home, work, etc.), database sharing allows you store your database at a remote location (password protected HTTP URL, for example) and then have UPM automatically keep your local database in sync with the remote database.
Ruzzle Solver PRO is an offline solver (aka cheater) for Ruzzle puzzles. It aims to be usable, fast, and easy to extend and improve for both users and developers thanks to a sensible and modular design. It allows you to add, replace, or update the dictionaries and the score tables, thus supporting an arbitrary number of languages.
LabKey Server is open source software that helps scientists manage, analyze, and share complex datasets. It supports tandem mass spectrometry, flow cytometry, assays for neutralizing antibodies, Luminex, observational studies, and secure, Web-based collaboration. The software is modular, configurable, and customizable. It can be installed in your institution on any modern hardware and operating system. It is designed to integrate with your existing systems, instruments, and work flows, and to be readily adapted by skilled programmers to novel methods of inquiry. The project is under active development by a team of professional software engineers and a community of active contributors. New versions are released about four times per year.
The Shepherd Project is a software framework to support capture-mark-recapture (CMR) studies. CMR is a core technique used in the analysis and management of wildlife populations. The Shepherd Project promotes non-invasive "virtual tagging" mark-recapture techniques (e.g., photo-identification via natural coat/skin coloration instead of physical tags attached to animals) to protect both animals and researchers in population studies. The aim of the Shepherd Project is to aid researchers in obtaining and managing CMR data to better understand and manage animal populations. The Shepherd Project is most successfully used as a collaborative, public-facing Web site, allowing members of the research community to collaborate and analyze data "behind the scenes" (with login access) and allowing members of the public to collect data as "citizen scientists" and submit it through submission forms.