we have upgraded our three 377 recently (5 weeks the first, two weeks the
two others). Here is our current view:
General impression:
- loss of resolution on 96 lane gels
- peaks show a "n+1"-like problem, the peak shape is not symetrical
- the readable sequence starts later, sequences close to the primer are l=
ost
- SA 3.2 is much better than 3.0 and works well with 48 and 64 lane gels
- tracking of 96 lanes always needs manual assistance (which is easier wi=
th
3.2)
- loading of the 0.4 deep slots is easier. It would be good if Abi would
offer combs with 48/64 lanes which fit the step-plates (the 0.4 373 combs
can be used in principal but thats tricky due to the reduced length of th=
e
comb teeth)
>1. Lack of resolution is the main problem.
compared to 48-lane gels we lost 100 to 150 bases prior to the first N
(reload of the same probe). We are collecting the data to show them in th=
e
near future on the net ("bizzare gels" at
http://www.mpiz-koeln.mpg.de/~weisshaa/Adis/Bizzare-Gels.html).
>2. Weak signal: We are now keeping the CCD gain set at 4
seems not to be a problem for us. The 0.4 mm deep slots of 96-well combs
take easily the same amount of probe as those 0.2 48-well combs.
>3. Gel tracking: 64 lanes tracks robustly with the new neural net
>tracker, about 10% of gels need to be manually altered.
>All of the 96 lane gels we have run, have required manual tracking.
Same with us, exept that due to the nature of our probes (DNA from
different users at the MPIZ) there are also problems with 64 lane gels if
we have bad luck with templates.
>4. Our computers are 7300/200 and 7200/120 with 32Mb Ram each
>with virtual memory set to 50Mb. If analysis is set for automatic
>analysis, even if only 64 lanes are being collected, the run pauses at
>5hours into the run with a power fail message. The computer has to be
>restarted and the run continues. These computers are supposed to be the
>bare minimum required to run the 96 lane upgrade. We CANNOT run automati=
c
>analysis, but we can collect data without any problems and dump the data
>to our remote G3s for analysis.Today, we have upgraded memory in both
>collection computers to 96 Mb each and will see if analysis can be
>automatically fired off without any conflicts. The new g3 computers are
>wonderful, running system 8.0, so haven't seen any conflicts there.
Automatic analysis works on our "Data collection Macs" (7200/90 and 2x
7200/120 with MacOS 8.0) with 48MB RAM. We have reduced the system and
other stuff to the absolute minimum. HD size is the problem we have here.
Initial problems with automatic analysis were changes is the configuratio=
n
due to installation of data collection 2.5. Re-Analysis, hand-tracking an=
d
so on is done on "Data analysis Macs" - all G3 with 96 MB RAM and System
8.1. This part of the upgrade in our hands works.
Best regards, Bernd
_____________________________________________________________________
PD Dr. Bernd Weisshaar
MPI f=FCr Z=FCchtungsforschung
Carl-von-Linn=E9-Weg 10
50829 K=F6ln
Germany
Tel. office: +49-221-5062 590 Tel. lab: +49-221-5062 311
Fax: +49-221-5062 313
e-mail: weisshaa@mpiz-koeln.mpg.de
WWW-URL: http://www.mpiz-koeln.mpg.de/~weisshaa/BW-info.html