A Communication with Applied Biosystems
Werner Van Belle, 17 May 2007
It is widely known that there
is some tension in the scientific
community between Celeras genome project and the more open state funded
genome project. Up to now I never stood still about this but recently
it came to my attention that a particular microarray (Applied
Biosystems) fabricant actually tries to force this issue. The Applied
Biosystems 1700 scanner I'm talking about is the one at Tromsø's
university and my experience with AB on this matter is less than
optimal. The first major problem I encountered was that the output of
the machine produced a large collection of hCG or mCG genes, none of
them which follow standard annotations. The only database able to
actually understand these genes is the pantherDB, but that database is
not the one I would prefer. I would rather have an annotation that
actually uses standard nomenclature (NCBI, swissprot for instance). So,
after trying to get my hands on more information with this respect I
figured out that the AB software should be able to export these columns
as well. Good. So I tried to export all columns. Well, it didn't work.
The machine plainly refuses to export everything that I wanted. After
48hour of 'export in progress' not a single byte was written to the
export-file.
Of course, I contacted Applied Biosystems regarding this issue. Below
is the transcript.
12 April 2007 Werner Van Belle wrote
Hello, exporting the standard collection of columns works. However, as
soon as
I try to include all the gene-related attributes, I find that the
process hangs. Is it correct that to assume that the machine requires
an Internet connection ? (It doesn't have one at the moment).
17 April 2007 Even O. for Applied Biosystems Technical Support wrote
You do not need an Internet connection for this step. However,
depending on the number of arrays to be exported the export process can
become very slow or even freeze if you include all the columns. Try
with less columns (they only need SIGNAL, S/N, FLAGS, eventually
coordinates and).
18 April 2007, WVB wrote
Hello, In order to export all necessary information from 7 arrays, I
waited for more than 48 hours ! Since you are aware of the problem I
can only comment that your solution ('just wait') is completely
unacceptable. Even from a programmatic point of view there is no
reason at all why an export should take such a prohibitively long time.
We are prepared to install new versions of the software, or to talk
about better solutions than the one you propose. If you want I can have
a look at the software together with the developers.
18 April 2007, Even O. wrote
I am sorry if I have given you the impression of "just wait". That was
not the meaning at all! I have taken this problem up with my network
group, and I will respond to you as soon as possible. Ok?
18 April 2007, 3 hours later, Even O. wrote
Hi again, exporting 7 arrays should not take that much time. I will
contact service and let them check the status of the Oracle database.
I'm really sorry for your problems with the exporting time. We will
have this fixed as soon as possible.
27 April 2007, WVB wrote:
Hello, do you already have a solution for this export problem ?
27 April 2007, Even O. wrote
I have taken this problem up with my network group. Can you send me
your phone number so I can call you?
2 May 2007, Werner wrote
Hello, that would be good. My phone number seems to be +xx xx xx xx
8 May 2007, Werner wrote
Hello, I still didn't get a phone call regarding the mentioned issues.
Please contact me either by email (preferably) or if necessary by
phone: +xxxxxxxx would be my phone number,
Of course, a call never came, which
basically makes the AB1700 system too difficult to use.
