Provision of DNA Sequencing as a core facility

Steve Steve
Mon Jun 2 08:04:51 EST 1997


In article <5lfhku$54d at net.bio.net>, LHALL at fs1.scg.man.ac.uk wrote:

>                 Dear all,
> 
>                                                                              
                  
I currently run a DNA sequencing core facility at the 
> university of Manchester, England, which utilises an ABI 377.
> 
>         At the moment, I am experiencing some bizarre problems, which I 
think 
> relate to networking : In essence, the collection software is mixing up 
> samples when new sample files are being generated after manual tracking 
> of a gel. In addition, the gel file is jamming and during manual 
> tracking etc. the mac is reporting a number of errors , such as 
> Miscellaneous hardware errors, zero divide errors, chk errors and 
> segment loading errors.
> 
>         I am led to believe that these may stem from having file sharing 
open 
> during collection of sequencing data. In response to these problems, I 
> have wiped the hard disk, scanned for viruses, reloaded the software and 
> even taken the precaution of having the logic board within the 
> collection mac changed.
> 
>         I would like some specific answers on the following questions :
> 
> 1. Should I shut down file sharing, period ,on the collection mac or 
> just during collection itself ?
First, I do work for PE Applied Biosystems as a FS Engineer in So Calif.
File sharing must be turned off during collection. After that it is OK. We
have always reccomended to turn file sharing off during daa collection.
You should turn off the networking software as well. When I install the
377 I create an extension manager set for Sequencing that only turns on
what is needed for the sequencer. You can set another set up for
networking. Just restart the computer using the non-network set and
collect your data. Then restart after the run in network mode. I know many
sites that do fine with file sharing and the network active, but many also
have problems. It seems noise from the net can interfere with the way the
gel file is written during collection and can cause similar problems to
what you see. This was more prevalent with the 373 but has been seen on
the 377 as well.


 
> 2.As a follow on from the above, is it o.k to write sample files over 
> the network form the collection mac,or is it preferable to have a second 
> mac for disrtibuting data ?
This works fine usually. The core facility I ran before I joined PE ABD
xfered the samples over the net after they were generated. This would be
my reccomendation. 
> 3. I have started archiving data to an Iomega jaz drive, although I Am 
> led to believe that these drives in the context of sequence analysis 
> data may cause problems. Is there any truth in this ? Incidentally, when 
> I first tried to install the driver software onto the collection mac it 
> wouldn't have it and subsequently one of the apple talk extensions 
> became jammed. Ever since then I have had problems like gel files 
> jamming etc.
This is news to me. I will check with some in house people and find out.
 
> 4. Has anyone experienced problems with writing gel files over the 
> network ?
I have had problems in the past. It turns out it was the version of Fetch
that we were using for the xfer. It worked with everything except the
files generated by the sequencing software. The latest version of fetch
eliminated that problem.
> 
> 
Hope this helps.
Steve Marsh
PE Applied Biosystems NA 
email: marshsr at ccmail.apldbio.com



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