cvsroot is a script to help keep track of multiple sites when using CVS, and in particular the CVSROOT and CVS_RSH environment variables for those sites. It creates a $HOME/.cvsroot file, with shortcut names representing the different CVS sites. The new environment variables appropriate to the site selected will then be set, and a new shell will be spawned to keep the variables. In this way, you do not have to keep setting the environment yourself, and can rely on the script to keep track of things for you.
ProteomeCommons.org IO Framework is a proper Java framework for handling spectra and peak lists. The framework can read and write to a number of different spectra and peak list formats, and it provides a simple, intuitive Java object model for working with spectra or peak lists. All classes support two methods of handling peak list and spectrum data: in-memory or stream. The goal of this framework is to support all the popular MS and MSMS data formats, and to eliminate any time or effort involved in figuring out how to read and write peak list or spectrum files.
SWISH stands for Simple Web Indexing System for Humans. With it you can index directories of files and search the generated indexes. Based on EIT's swish, this is a cleaner-compiling, enhanced version with better docs, better installation and configuration tools, more sample configurations, and a Web page to help manage index rebuilding. SWISH is used with w4ais as a Web-based front end.
EPOR is an extensible package organiser for Unix-like systems. It's written to trace filesystem changes (something being installed) and save this information in a simple text database (this, as any other provided feature, is customisable via the embedded Guile interpreter). Database entries contain information supplied by the command line (package name, version, etc.) and traced by filesystem changes (new directories, files, etc.). This is achieved using the "LD_PRELOAD method''.