"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:
Hin-Tak Leung, last updated 2014-06-15