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 micro array (Applied Biosystems) manufacturer 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 undersigned 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, undersigned 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, undersigned 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, undersigned wrote
Hello, that would be good. My phone number seems to be +xx xx xx xx
8 May 2007, undersigned 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. Why is vendor lockin always of a lower quality than leaving people to freely choose what they need and feel is the most appropriate in a certain situation ? If they make a scanner they should not force me to use their retarted nomenclature.