Go to Outmoded Bonsai Project page for downloads
The history of the project is largely documented in the news archive and mailing list archive.
Or jump to How to check and patch illuminus for the Chrom X bug.
Or jump to FlowJo data corruption issue.
Or jump to Description of the GenTrain Genotypes.
Or jump to CNV Analysis.
Or jump to Installing R packages.
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A version of snpMatrix 4-digit series and snpStats Bugs and snpStats ISSUES are here, but in general, those in the download area are kept more up to date. There is also a version of snpMatrix's snpStats Compatibility Mode document here.

It has been a while, so here is Illumina BeadStudio under Gnome 3/Fedora 20, and GenomeStudio under Gnome 3/Fedora 20 Linux.

And screenshots of Illumina BeadStudio under Mac OS X 10.9 (Mavericks), and GenomeStudio under Mac OS X 10.9 (Mavericks). I haven't bothered to install everything like I did on Linux, just the gnotyping module.


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

"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), 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:

Here is a screenshot for the Bonsai plug-in:

screenshot of Bonsai Report plug-in

The older long winded version of the main page.

Hin-Tak Leung, last updated 2015-01-19

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