Free 1.1.0 software for linux

SMA software consists of a small collection of programs that perform different tests for association between genotypes at a single marker and a binary disease status.

Bky is a minimalistic, distributed Version Control System/Source Code Management tool. Bky uses rsync as a backend to store revisions as complete trees, optimizing the size by storing unchanged files as hard links.
Main features:
Distributed
- The repository is not stored in a central server as in CVS or Subversion, but as a subdirectory inside your working directory, like Arch, Darcs or Linus Torvalds git. Developers communicate via patches.
Cheap branches
- Just copy your tree to another directory and youve started a new branch.
- Old history is easily pruned Legacy revisions can just be deleted or moved to another place with your usual filesystem tools.
Safety
- Any given revision under the repository is a directory with all your files that can be used, copied or stored as-is.
Repository is easily manipulable
- As every revision is stored as plain files, you can delete, add or modify files, or update the commit message without interfering.
No need for special commands to put files under version control
- Just create a file in your working directory and it will automatically be version-controlled. Uninteresting files as object files, libraries or other generated files are automatically ignored. Also, there is support for .cvsignore files.
Small dependencies
- Bky is a shell script. It needs rsync, diff and the usual Unix basic tools. You also need a filesystem that support hard and symbolic links. Thats it. Its just a version control system.
Enhancements:
- This release includes a script to convert a bky repository into a git one.

PHK is a PHP-oriented package system. PHKs purpose is to package a library or an application, in order to distribute and run it as a single file. As an introduction, you may think of it as a PHP-oriented jar, with a lot of additional features.
Main features:
- No runtime software : as it was said above, there is no runtime software to install before using a PHK archive, as it contains its own runtime code. Any installed PHP (version 5.1.0 or more) is ready to include/execute a PHK archive without any modification.
- Supports libraries, applications, plugins : a PHK archive can contain a library or an application (an application is a library with an entry point). PHK archives can also be used as plugins.
- Unlimited number of subfiles : a PHK archive can contain an unlimited number of subfiles and directories. A subfile can contain up 2 Gbytes of binary data. The total size of a PHK archive is limited to 2Gbytes. Every subfile can be, on a file by file basis, compressed (gzip or bz2), and/or filtered through php_strip_whitespace() (for PHP source).
- Standard locations for package information : PHK provides standard locations for administrative informations like packages name, author, license, copyright, etc. PHK also allows to specify an icon file and an URL. All these inforamtion are displayed in webinfo mode.
- Webinfo mode : in webinfo mode, the PHK archive behaves like a small web site, allowing the user to display every information about the archive, and the content of every subfile. This mode is a standard feature of every PHK archive.
- Mount/umount user scripts : the package author can specify a mount_script. This subfile will be called every time the PHK archive is mounted. In the same manner, an umount_script can be specified.
- Built-in CLI commands : several built-in CLI commands are available. These commands are the equivalent, in CLI mode, of the webinfo mode. They allow to display every information about the PHK archives structure and content.
- Meta-packages : PHK supports meta-packages, allowing a PHK archive to be incorporated as a subfile inside another PHK archive, along with other regular files. This feature is useful for unit tests (see the Zend Framework demonstration packages for an example) or to build meta-libraries (incorporating several librairies, but without mixing them together). These sub-PHK archives can be automatically mounted when the main package is mounted.
- Web path protection : In a PHK archive, the subfiles are protected from incorrect or unauthorized access from the web. The legitimate entry points are explicitely identified, making the package easier to secure. From the web, it is impossible to display or to call a subfile if it is not explicitely enabled by an option. Among other benefits, it allows to suppress the usual empty index.htm files in every directories !
- CRC checksum : A PHK archive includes a CRC checksum mechanism. Depending on the packages options, this checksum can be verified every time the package is mounted, or on users request.
- Digital signatures : A PHK package can be digitally signed (using a digital certificate). This feature allows users to verify that their package comes from a source they trust.

Ahoy provides an efficient, decentralized service discovery protocol for MANETs.

Ahoy is an efficient, decentralized service discovery protocol, designed for mobile ad-hoc networks (MANETs). Based on attenuated Bloom filters, it has a low impact on the network and allows services up to a configurable distance (measured in hops) to be discovered.

The protocol is described in full detail in the report Ahoy: A Proximity-Based Discovery Protocol. The report and implementation where developed as part of my Master of Science work at the University of Twente.

Pyne is an offline newsreader/emailer written in Python using the GTK+ toolkit. I started it because I wasnt happy with the graphical newsreaders available for linux. Of course, a few months later Pan and Knode started to kick arse... oh well.
Pyne 0.6.9 is for gtk1.2, and is a bit old and therefore crappy (it follows). Pyne 1.0.0 is shiny and new and for gtk2.0, and therefore great. Pyne 1.1.0 contains fixes and new features for gtk2.4+ (and mailbox formats are unchanged from 1.0.x, so you can use the two versions interchangably).
Pyne is free software and may be distributed under the terms of the GPL, etc...
Main features:
- Offline, threaded news reading and posting.
- Well... the posting is online actually but that cant be avoided. queued outgoing stuff anyway.
- SMTP sending and POP3 and IMAP4 collection of mail.
- Attachments and all that stuff.
- Simple mail/news filtering.
- Optional expiry of mail as well as news. Useful for mailing lists.
- hmm... nice graphical interface. im really scraping the barrel here...
- (Partial) support for MH mailboxes.
- Import and export unix mailbox format.
- External parsing of html messages (lynx -dump)

dclog is a logging library for C and C++. It supports the concept of log levels, configurable logfile timestamps, and a configurable prefix to log messages.

Installation:

1. From source:

make all
make install (as root)

2. Gentoo users:

emerge -vp dclog
emerge dclog

csoap is a SOAP client/server library in pure C.

csoap is a fast and easy way to embed a SOAP client or a SOAP server into an application written in C. It is built on top of libxml2 and supports SSL and HTTP Basic authentication.

Howto use aclocal/auto(conf,make) in your libsoap projects

1. Copy the file libcsoap.m4 to `aclocal --print-ac-dir`
2. Add the following lines to your configure.in (or configure.ac):
dnl AM_PATH_CSOAP([MINIMUM-VERSION, [ACTION-IF-FOUND [,ACTION-IF-NOT-FOUND]]])
AM_PATH_CSOAP(1.0.4)
CFLAGS="$CFLAGS $CSOAP_CFLAGS"
LDFLAGS="$LDFLAGS $CSOAP_LIBS"

Thanks to Heiko Ronsdorf

PHAMLs primary initial goal of the PHAML project was to produce a parallel version of MGGHAT. This has subsequently been extended to include additional capabilities. The target architecture is distributed memory multiprocessors, such as Beowolf-type PC clusters.
MGGHAT is a sequential program for the solution of 2D elliptic partial differential equations using low or high order finite elements, adaptive mesh refinement based on newest node bisection of triangles, and multigrid. All aspects of the method are based on the hierarchical basis functions.
Adaptive refinement, multigrid and parallel computing have each been shown to be effective means of vastly reducing the time required to solve differential equations. However, effectively combining all three techniques is not easy and is the subject of current research. PHAML is an attempt to solve this problem.
Enhancements:
- Native conjugate gradients and GMRES solvers were added, along with support for DRUM and ZOLTAN_FILE in partition methods. -
- The tests have been modified to run in parallel, and assorted bugs have been fixed.