"Outmoded Bonsai" is an anagram for "mono BeadStudio", and was to be the home of 4 unreleased software at the end of my time at CIMR in spring 2008: the embodiment of my BeadStudio-related knowledge (which eventually became BeanSprout/Bonsai/SpringOnion/Broccoli), the extension of CelQuantileNorm to Affymetrix Chips without mis-match probes, such as the Human 5.0/6.0, the embodiment of my FlowJo-related knowledge (which eventually became RFlowJo), and some unreleased changes to snpMatrix. snpMatrix has since been accepted to Bioconductor in April 2008, so this site mostly just consists of interrim windows builds of the latest code; and Rill is a recent and unplanned addition.
BeanSprout is a cross-platform command-line utility to load Illumina's Genotyping module and thus make some of BeadStudio/GenomeStudio''s functionality available in a display-less non-windows server environment (such as a Linux/Solaris/MacOS X-based computing grid). It also works on MS Windows. It's main use is for reading BeadStudio/GenomeStudio projects.
SpringOnion is a GenTrain-based clustering tool which takes input in WTCCC signals (same as Chiamo), and can cluster data in far larger batches with far lower resources compared to within BeadStudio/GenomeStudio.
Broccoli is a general-purpose miscelleneous file dumper. It was first written to read Illumina's *.idat files (somewhat equivalent to Affymetrix's CEL files). It is only 50 lines long and probably will be merged into BeadSprout (about 700 lines) eventually. Current release can also read and compare cluster definition (*.egt) files. (It is mostly a testing ground for new miscelleneous functionalities that doesn't fit in elsewhere).
The Bonsai plug-in is an
Illumina BeadStudio/GenomeStudio' plug-in to generate custom report in the WTCCC
signal format. This file format is also known
otherwise as:
Bodhi enbles Illumina BeadStudio/GenomeStudio' to write genotypes out as R data (for snpMatrix), in addition to what Bonsai report does. There is no separate installation instruction --- it is simply another choice in the custom report menu once the Bonsai plug-in is installed. (SpringOnion and BeanSprout 4+ onwards also share the ability to write genotypes as R data).
CelQuantileNorm - a suite of programs for preparing Affymetrix data for genotype calling with Chiamo. Current version supports the Human 5.0/6.0 chips.
snpMatrix - R package for
large-scale SNP association studies
RFlowJo - R package of misc useful routines for TreeStar FlowJo users in flowcytometry
Rill - R package to invoking the Illuminus clustering algorithm from within snpMatrix.
I have very little to do with the Mingw cross compiler. I use it for building the windows packages. Binary package of the compiler is hard to come by, and I have inquired and the Mingw people have no intention of providing it, so it is provided as a convenience. There is also the occasional backports of the latest mono packages from the next fedora alpha/beta to current fedora, which the BeanSprout/Bonsai family use.
There is a small patch to build Affymetrix Power Tool with gcc 4.x . It was sent to Affymetrix. If/when they integrate the patch to APT is not up to my decision.
The SGE sshfs integration I wrote is part of the SGE HOWTO documentation, on running jobs on data kept (on a USB connected HD) in a separate network via sshfs. It is duplicated here. Some other slides, etc may appear in the future.
Two of the tools downloadable and listed are unlikely to be released fully in source form: Broccoli - the functionality is to be integrated to something else, and I don't see the point of it; and Rill - the C++ to R bridging code is released, and the R bridging code uses Illuminus as a library. Due to a prior agreement not to re-distribute the source code of Chiamo, I don't think it is approprate to redistribute the substantial adaptation of the Illuminus code as a library either. (People can make up their own mind with running "nm -C" on the binaries. The boost::* and BZ2_* symbols in Chiamo are my contribution between v0.1.0 and 0.1.1, and they are not in Illuminus). As of Rill 1.1.3.1, substantial change has been made to strip the library of any Chiamo inheritence and the library code was released.
All the tools runs on both unix and windows systems (and most of the time, Mac OS X also). SpringOnion works better on windows than on linux, while Rill works better on linux than on windows.
Here is a screenshot for the Bonsai plug-in:
Hin-Tak Leung, last updated 2009-05-03