Andy Law Big Nose Andy.Law at bbsrc.ac.uk
Tue May 30 08:54:33 EST 1995

In article <n.morrison-250595131943 at>,
n.morrison at garvan.unsw.edu.au (Nigel Morrison) wrote:

  > We bought two ABI377 "ABI PRISM" machines for automated genotyping and DNA
  > sequencing.  We were not told that the software GENESCAN for the automated
  > genotyping was not ready for the powermac.  Despite this problem ABI is
  > advertising (in Biosystems Reporter issue 24, February Page 1) that the
  > famous geneticist JOHNTODD of the new Wellcome Trust Center for Human
  > Genetics at the University of Oxford, used the ABI PPRISM to map the
  > polygenes involved in diabetes suceptibility.  John Todd's paper (Nature
  > 371:130-136) was a beautiful example of genetic analysis of complex
  > disorders.  The suggestion that John Todd uses the ABI PRISM (377)
  > certainly influenced our level of comfort in buying these machines. 
  > Quoting the Biosystems Reporter " "We could not have completed this project
  > in the time we did without the ABI PRISM Automated Genotyping Sysem," Todd
  > commented." For future work in mutation detection, it will be invaluable." 
  > The Biosystems reporter also stated that: "Todd's group was able to rapidly
  > (in six months) and accurately screen the entire human genome for
  > micosatellite marker alleles that might be linked to diabetes."  
  >   Now we find that the software is not ready, so how could he have used the
  > ABI PRISM?; or does ABI PRISM now refer to the ABI373 model which is
  > superceded by the ABI 377.  The questions are, what model machine was used
  > for the Nature paper, what computer software is reliable and when will the
  > ABI GENESCAN software be ready?  We are waiting for the software, and it
  > appears that we will be waiting more than the six months it took Todd to
  > finish his project.

As I understand it the situation is as follows:-

*  The GENESCAN software does exist and works on most older models of 
   Mac with an fpu.

*  ABI's software engineers decided to follow Microsoft's example and
   ignore Apple's guidelines when writing the code that wrote the
   gel images to the screen.

*  Apple have changed the way that video memory is mapped to the screen
   (as they always said they would) in order to allow easy use of multi-
   scan monitors and on-the-fly resolution switching. This applies to all
   machines currently in Apple's product line from Performa 475 to 
   PowerMac 8100/110.

*  Software that followed Apple's guidelines still works. Software that
   did not (i.e. GENESCAN etc.) is broken on the new machines.

*  ABI seem unconcerned about this problem (since they probably already
   have your money for the machines) and are being very slow in producing
   a fix for what should be a relatively trivial code fix.

If you can find a Quadra or Centris 650 type machine, then the software
should run on it. These were the last machines made by Apple that used the
old style video architecture. I heard a rumour that ABI had bought up a
stock pile of these machines to cover themselves with this problem, but it
seems that either it was untrue or they have run out.

I reserve the right to be proved wrong over any or all of the above.
Andy Law

( Andy.Law @ bbsrc.ac.uk )
( Big Nose in Edinburgh )

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