Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
QPDF is a C++ library and set of programs that inspect and manipulate the structure of PDF files. It can encrypt and linearize files, expose the internals of a PDF file, and do many other operations useful to end users and PDF developers.
Collectl is a light-weight performance monitoring tool capable of reporting interactively as well as logging to disk. It reports statistics on cpu, disk, infiniband, lustre, memory, network, nfs, process, quadrics, slabs and more in easy to read format.
GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.
Iconset for KDE constructed from rad-e8.com icons as well as originals.
HTML::Index - Perl modules for creating and searching an index of HTML files
GNU make compatible but reliable and simpler build tool
Makepp, a build program which has a number of features that allow for reliable builds and simpler build files, is a drop-in replacement for GNU make. It supports almost all of the syntax that GNU make supports, and can be used with makefiles produced by utilities such as automake. It is called makepp (or make++) because it was designed with special support for C++, which has since been extended to other languages like Swig or embedded SQL. Some features that makepp adds to make are: greatly improved handling of builds that involve multiple makefiles (recursive make is no longer necessary); automatic scanning for include files; rebuild triggered if build command changes; checksum-based signature methods for reliable builds, smart enough to ignore whitespace or comment changes; extensibility through Perl programming (within your makefile); repositories (automatically importing files from another tree); build caches (not recompiling identically what a user of the same cache already did
FLib is a collection of high-quality Java classes and GUI components.
C compiler and dev kit for the z80 with assembly language libraries.
Z88DK is a complete Z80 / Z180 development kit that includes C compiler, assembler, linker, a tool for generating executables in a number of formats, and miscellaneous other tools. Over 50 machines are directly supported out of the box including standalone Z80 and Z180 embedded systems. Z88DK's extensive assembly language libraries give it significant performance advantages over other Z80 C Compilers. Building software for standalone or generic Z80 systems: https://www.z88dk.org/wiki/doku.php?id=libnew:target_embedded Visit us at github for the current version with bugfixes and new features: https://github.com/z88dk/z88dk
FTE is a text editor geared toward the programmer. Syntax highlighting for over 20 languages, plus configurability for many more, makes this a lightweight but versatile editor for any programmer.
This Database Test Suite aims to create database workload test kits used to simulate heavy user loads for OLTP, Decision Support, and e-commerce database transactions. These test kits can also be used to gather performance results for Linux and other
Binary Perl Distribution
Binary perl distribution with pre-built modules for Wx, DBD::Pg and DBD::mysql.
A Perl script that, given the output of the Firefox extension Live HTTP Headers, will replay the script using Test::WWW::Mechanize.
Expect.pm is a perl implementation of the popular Expect extension for Tcl/Tk by Don Libes. You'll also find the IO::Tty and IO::Stty Perl modules here.
Building a small bundle for MacOS X 10.2 in order to support menu extras in the same way they were supported in MacOS X 10.1
Jetty is an open-source project providing a HTTP server, HTTP client and javax.servlet container. The latest releases of Jetty are hosted from http://jetty.codehaus.org and http://eclipse.org/jetty.
eTktab edits 4/5/6/7 string ASCII tablature. Features: 30 fretboard positions available via single keypress, lyrics, expression marks, etc.
innotop is a powerful monitor for MySQL queries and status information. It is now hosted at http://code.google.com/p/innotop.
Social Networking PHP Script
Big social networks put plenty of websites out of business - anyone can create a group, say, on Facebook, and it's much easier than to build and support whole website. Now we want to get web-masters back into the game, arming them with the same functionality major social networks have. The Micro is the simplest GRA4-powered Social Network. It can run on any PHP hosting (including free ones), and does not even require a database server. Demo: http://micro.ucq.me/gra4/activity Free hosting with auto-installer: http://ucq.me After single 2-minute-long installation your website will have social features likes, friends, groups, blogs, messaging, activity stream, market, events and much more. Wiki: http://en.wiki.gra4.com/Category:Webmaster_guide Before you install the Micro, please make sure you are installing the newest version: http://gra4.com/file/group/97/all
VCore is a hosting control interface developed for Linux hosts.
A linker for MSDOS and MSWindows.
Checkbot is a tool to verify links on a set of HTML pages. Checkbot can check a single document, or a set of documents on one or more servers. Checkbot creates a report which summarizes all links which caused some kind of warning or error.
Fragistics is a Quake3 statistics program. It generates several webpages containing statistics about the games played from the games.log generated by a Quake3:Arena server.
Slirp is a SLIP/PPP link emulator. Clients think it's a normal connection! The Slirp Maintance Project is what it says: keep Slirp up and running! (Primary Developer needed!)
Run your own photo website. Camera Life is PHP software you can run to show your photos on your own website. Camera Life is easy to setup and customize if want to blend it in with the rest of your site.