This is an implementation of Smith-Waterman algorithm optimized for execution on the Cell platform, developed on Sony Playstation 3 by Witold Rudnicki, Aleksander Jankowski, Aleksander Modzelewski, Aleksander Piątkowski and Adam Zadrożny at Interdisciplinary Centre for Mathematical and Computational Modelling at University of Warsaw.
All software published on this page is covered by GPL2 free software licence.
Note: efficiency of this version is limited by memory resources aviable on single system. In case of PS3 this is low enough to limit serious applications.
There is a development Mercurial repository aviable at http://bioinfo.icm.edu.pl/source/hg/smith-waterman-2
The distributed implementation is in active development and as of there are no releases. The version from repositories may often not work at all until development stabilizes.
The distributed implementation is aviable in two parts, one working on the coordinating node running any 2.6.x Linux kernel, the other intended for Linux running on Cell platform. The software is developed on Sony Playstation 3 and was not tested on Cell blades.
The client part (running on coordinating node) is aviable from Mercurial repository at http://bioinfo.icm.edu.pl/source/hg/w4a, and the server (PS3) part is aviable at http://bioinfo.icm.edu.pl/source/hg/w4ad.
All Cell software needs IBM's Cell SDK for compilation. Packages for Fedora 7 may be found at IBM's download site. Installation instructions are aviable on this page. Some information about installing Fedora 8 on a Playstation may be found on Fedora Project Wiki.
Mercurial may be found at Selenic. It's also aviable in package repositories of most major distributions. To install Mercurial on Fedora 7, type:
# yum install mercurial
To get a working copy of the code repository type:
$ hg clone <repository address> <directory>e.g.
$ hg clone http://bioinfo.icm.edu.pl/source/hg/w4a w4aTo pull changesets from our repository, enter your local clone and type:
$ hg pull $ hg updateTo find out more about Mercurial, go to Mercurial Quick Start
If you wish to contribute you changes, please make sure to configure your name and email in the hgrc file, commit your changes, and type:
$ hg bundle <filename> <upstream repository>and send the resulting file along with any comments to bioinfo@icm.edu.pl.
Smith-waterman-2 and w4ad packages use custom build systems. To install, copy the Makefile.inc.template file to Makefile.inc, edit it to point at the SDK locations and type
$ makeThe is no explicit installation method, but the only output file really needed is sw in smith-waterman-2 and w4ad in w4ad.
The w4a client application uses the standard autotools mechanism. After downloading and entering the source tree, type:
$ ./configure $ make $ su -c "make install"
We invite everyone to test and contribute to the project. Please direct all communication at bioinfo@icm.edu.pl.