FLOSSmole (formerly OSSmole) is a set of tools for gathering metrics and publishing analyses about development of free/libre/open source projects. UPDATE: Our data is now released to Google Code. Please see our new home page at http://flossmole.org
PepT-IDE is a protein analysis tool that is used for multiple sequence alignment, 3D visualization and displaying protein contact maps for protein sequences and structures. It also has feedback communication between the different views of the protein.
NickelsWebtranslator is a simple web-based application for internationalization of java-based projects. Properties files can easily be translated by a remote and widespread group of translaters (utf8-encoding). Python web application with mysql backend.
Parapin makes it easy to write code under Linux that controls individual pins on a PC parallel port. This kind of control is very useful for electronics projects that use the parallel port as a generic digital I/O interface (instead of as a printer port)
WDBearManager is a program that enables the user to store the information found inside the WDB files from World of Warcraft (Blizzard) in a relational database (MySQL and HSQL supported). WDB files build the client cache. Forum: www.wdbmanager.de.gg
JLink lets users author flow charts based on ISO 5807 and IBM standards. Developers can use JLink to add flowcharts to applications, serve a flow chart over the web in PDF or PNG, or dynamically create a flowchart with Javascript, Python or Ruby scripts
Sadly JFCUnit is no longer supported but idea is neat and with a few more improvements it can be even more useful tool for regression testing.
JFCUnit-2 will have distributed testing, SWT support, JUnit independent and lots of other improvements.
Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.
GUESS, or the Graph Exploration System, is a system and language for visualizing and manipulating graph structures and creating new visualization applications.
adVM aims to provide a flexible engine for creating adventure games. The new version is written in java and uses ADL (see http://www.hcesperer.org/adl/) as the scripting language.
NetWhistler is SNMP monitoring software that offers integrated fault and performance management functionality. This Java program auto-detects networks and presents them on graphical maps, which reflect host status. Mila NNM is a pyQT fork of Netwhistler.
PARs is a bioinformatics tool for the analysis of cis-regulatory DNA sequences. Composed of two parts: a suite of sequence analysis algorithms for predicting cis-binding sites in DNA sequences and a GUI for visualisation and exploration of the results.
DrPangloss is a python implementation of a three operator genetic algorithm, complete with a javaswing GUI for running the GA and visualising performance, generation by generation