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Introduction

"He who passively accepts evil is as much involved in it as he who helps to perpetrate it" - Martin Luther King, Jr.

2013 August: Updated snpMatrix 4-digit series and Bioconductor snpStats Bugs. snpMatrix 1.19.0.19 was released in June with performance improvements to the VCF related code.

2013 April Update:snpMatrix 1.19.0.18 introduces the capability of processing VCF files, especially those from the 1000 Genome Project. A new vignette, I/O Suite, VCF (1000 Genome) and HapMap, serves as the tutorial and test suite for the new functionality. There is a new uncertain= option for reading Chiamo data; and leading up to it, fixed another bug in Bioconductor snpStats.

2013 April Update: snpMatrix 4-digit series describes the enhancements/changes not in the 3-digit versions. Bioconductor snpStats Bugs have also been updated.

2012 March Update: There is a whole bunch of Mac OS X builds: CelQuantileNorm, vcftools, samtools, tabix at the moment, more to follow. They are fat binaries (i.e. works on both PowerPC and Intel 32-bit/64-bit Macs) ; snpStats 1.5.5 turned out to be "differently buggy" so there is a snpStats 1.5.5.1, which is also the first R package available as an Mac OS X build. See link above for installation instructions. Bioconductor snpStats Bugs continues to track the HEAD of snpStats development, while Bioconductor snpStats Bugs 1.5.4, Bioconductor snpStats Bugs 1.3.6 tracks the differently buggy ones.

2012 January Update: snpStats - unsupported, less buggy at top level; added less buggy snpStats 1.4.1.1 and 1.5.2.1 . Windows and Android ports of vcftools, tabix, samtools. New Mono 2.10.8.1 linux and windows builds. New "Algorithms and Thailand" vignette, "Tutorial 2007" (File I/O testsuite) vignette. Some new files housed elsewhere at http://htl10.users.sourceforge.net/Languages/. Both Bioconductor snpStats Bugs and Bioconductor snpStats Bugs were updated.

2011 October Update: The "snpStats Bugs" vignette cataloging bugs on Bioc version of snpMatrix and snpStats have been substantially updated, and split into two: current snpStats Bugs and snpStats Bugs 1.3.6 (up to 20th October 2011). Look under file releases for possibly more up-to-date versions of these.

2011 September Update: Illumina Bead Pool Manifest support in both Broccoli and snpMatrix; new "snpStats Bug" vignette, "Regression and Migration" vignette in snpMatrix: all past and present users of either should check their 2-df genotypic results.

2011 August Update: Adding reference to the Android port of the BeanSprout suite. EGT support added to snpMatrix.

2011 May Addition: Animation for Bioinformatics Talk May 2011

"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/GenomeStudio-related knowledge (which eventually became BeanSprout/Bonsai/SpringOnion/Broccoli/CauliFlower/GARLIC), 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 went into Bioconductor in April 2008 and left in 2011. This is now the primary home of snpMatrix; and Rill and Bary are recent and unplanned additions to complement the core software family's functionalities.

As a side-effect of the project, Mono has improved over time. While the process is still non-trivial, it is now possible to run GenomeStudio on x86_64 Linux (my work platform of choice is Fedora 11). Here is a screenshot of a of a typical genotyping project, cnvPartition in progress, cnvPartition on completion with the cnv display, installed module listings, the Illumina Genome Browser. You can see the Fedora Linux Infinity logo in various places.

Here is GenonomeStudio V2009.2 running under Fedora 12:

Here is CarrotCNV in GenonomeStudio V2010.2 running under Fedora 13:

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). Current release can also read and compare cluster definition (*.egt) files and Bead Pool Manifest reading was adding in version 1.9 in September 2011 (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. There is a new R package as of April 2009 from Bioconductor called flowFlowJo. It has a larger and impressive list of (currently rather buggy) features - could be worth looking out for.

Rill - R package to invoking the Illuminus clustering algorithm from within snpMatrix.

CauliFlower is the name for the CNV analysis tool of the BeanSprout/Bonsai/SpringOnion family.

Bary is a derivative of EBI's AYB algorithm for Advanced Base Calling for next-generation machines; unlike AYB, Bary also works on windows, and windows-based mpi-enabled computing clusters, as well as Linux and MacOS X. (that's primarily why it is called 'Bary' and not 'AYB for windows'), It is created to complement GARLIC, the latest member of the BeanSprout/Bonsai/SpringOnion family, which interacts with the Illumina(Solexa) Pipeline/Cassava work-flow. ('Genome Analyser Reflect-Link Interfacing Code', for those who insists on putting meanings to silly vegetable names ; somehow it is appropriate since the family uses the .NET System.Reflection.* namespace quite extensively).

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. Some of them start to run on Android-based devices (smart phones and tablets) in August 2011.


Here is a screenshot for the Bonsai plug-in:


screenshot of Bonsai Report plug-in

Hin-Tak Leung, last updated 2013-04-02

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