Artha is a handy thesaurus based on WordNet with distinct features like global hot key look up, passive desktop notification, regular expression based search, etc. Artha may be used as a free open-source replacement/clone to the proprietary WordWeb Pro thesaurus (which is also based on WordNet) on Unix-like and Windows operating systems.
The MirBSD Korn Shell (mksh) is an actively developed successor of pdksh (the Public Domain Korn Shell), aimed at producing a shell good for interactive use, but with the primary focus on scripting. It is intended to be portable to most *nix-like operating systems as long as they're not too obscure. mksh incorporates improvements from OpenBSD and Debian, as well as bugfixes and enhancements developed for the MirOS, FreeWRT, and MidnightBSD projects and Android. The emacs command line editing mode is UTF-8 capable, and Byte Order Marks are ignored in scripts. The shell supports large files, as well as all pdksh and some csh, AT&T ksh, zsh, and GNU bash features, is compatible with the Bourne shell and POSIX (within limits), has no limit on array sizes, and incorporates some other useful builtins and features. While being already fast and small (without losing functionality), flags to make it even smaller can be given at compile time. An interactive shell reads "~/.mkshrc" on startup.
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.
tzls and tzx are commandline utilities for quickly unpacking or listing the contents of various types of common Unix archive files, which may be compressed in any of several ways. The supported compression types are bzip2, gzip, and compress. The supported archive types are tar, cpio, zip, rar, and arj. The tools are implemented as shell scripts, so no compilation is required.
fff and ffl are tools for searching for files and directories from the Unix shell with more integrated "shell-like" behaviour and simpler syntax than find(1), though find(1) is still used to perform the actual searches. In particular, there is no need to quote wildcards, and searches are case-insensitive. Matching results are shown one per line. fff displays full paths, and ffl relative paths. Detailed find(1) options can be appended to the fff/ffl command line if desired. These utilities are based entirely on shell aliases and functions, so no compliation is required.