3700 problems

Phillip San Miguel pmiguel at purdue.edu
Sun Sep 10 11:55:58 EST 2000

Laurence Hall wrote:

> [...]Of late, curious things have been happening with two of our machines :
> In
> particular, the autoloader has been crashing into the electrophoretic
> chamber and damaging the loading tips. This has happened 3 times with one
> 3700 and two times with the other; For each machine, ABI replaced the
> autoloader head twice and recalibrated the offsets................yet the
> problem persists.
> I am imformed by ABI in England that problems of this sort are recognised
> as genuine and seem to correlate with use of the foil piercing module.

    I'm not the best person to answer, but in case no one else does I decided
to respond. We've done about 500 runs on our 3700 in foil piercing mode. During
this time we only had one robot mishap--where the loading robot froze during
loading[1]. Because of this, our service engineer gave us a program that was to
be run before data collection is started called "port off.exe". I was told it
turns off the diagnostic port (whatever that means.)
    No problems of this type since then--but this isn't a large sample size. If
any of the large sequencing groups (I'm thinking MIT, Whitehead here) have
found port off.exe to be the answer to many of the 3700's problems perhaps they
will comment.
    Apparently foil piercing mode was not a recent addition to the 3700--beta
test sites are said to have had early versions of if. Steven Lasky has reported
in this group that autoloader failures were correlated with using foil piercing
on beta-3700. However, presumably there were changes introduced into foil
piercing mode before its field release in version 1.1 of the Data Collection
software. As I note above, we've had more than 500 runs on our machine using
foil piercing on 384-well plates.
    One issue comes to mind with regard to autoloader failures being caused by
foil piercing. The 3700 documentation for doing foil piercing suggests the use
of a certain type of 3M foil tape for foil piercing. However, many labs
probably had already in their possession a roll (or many rolls) of a thicker
grade of foil tape used for plate sealing during alcohol precipitations and
such. If this thicker foil tape were being used, then it might, over time,
damage the auto loader. I had thought that the piercing fangs were simply
unable to pierce this thicker grade of foil--but have recently inadvertantly
discovered that this is not the case. Hence, one could be using this type of
foil tape without immediate negative effects.

> For another of our 3700's, the instrument will sometimes skip the first 96
> well segment of a run; We routinely run 2 384 well plates at a time. In
> addition, we have experienced other glitches such as machine jamming during
> data collection and inability to quite data collection from the program
> itself or from 'task manager'. Our thinking is to reinstall the collection
> software.
> [...]

    The "jamming during data collection" is the signature of the problem that
he "port off.exe" script was designed to fix.
    You don't happen to used run modules with different names on the same
plate, do you? If so, the one that is first in the alphabet will run first[2].
This might give the appearance of the quadrant having been skipped. But this
should be obvious in the run schedule. Also, eventually the run should
happen--just later in the batch. Unless you had the "maximum number of runs per
batch" field in preferences set to less than the number of runs linked.

Phillip San Miguel
Purdue Genomics Core Facility

[1] This mishap allows us to answer a question we never asked: "Can an array be
recovered after sitting longer than 24 hrs with the oven on, the oven door open
with no water covering the caps?" The answer is yes. Following the instructions
of our service engineer, we able to restore the array with no blocked
capillaries and have since performed several hundred runs.

[2] Believe me, this is a feature, not a bug. In fact, this feature can be used
to force the robot to load "nested" quadrants of a 384 well plate. That is, in
the same way a 96-well pipetting device, such as a Hydra, addresses a 384-well
plate, the auto-loader can be instructed to load. Hence you could load a
384-well plate with 96 samples *with a Hydra*  (leaving the other 288 wells
empty, if you like). Why not use a 96-well plate? Well, for one thing, a
384-well plate is cheaper than a 96-well plate.  Also you can force the loading
of 104 samples per run. I frequently run low-throughput samples (finishing
reactions, for instance) along with high-throughput samples in this manner. I
posted a description of this process to this group some time ago. Since then
I've discovered you can schedule runs with big-dyes and drhodamines together.
Because the 3700 employes a virtual filter set it is even possible to schedual
different dye-set reactions in the same run (eg, E and F), should this be


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