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MJ research DNA Sequencer(Basestation)

James VanEe jiv2 at cornell.edu
Wed Dec 13 13:10:12 EST 2000

Hi Jeremy,
   What format are the sample files in?  If it's proprietary, that's 
bad.  If it's SCF, I would argue that it's preferable to ABIF.
  If anyone has a conversion utility to move SCF data to ABIF I would 
be very excited though. I'm familiar on a high level with the 
internal structure of the formats (SCF is open, ABIF is all reverse 
engineered) but I'm not in a position to do any programming for this 
   I'm also interested in a freeware SCF trace browser/editor for the 
macintosh.  I haven't looked at the java implementations recently, 
but I had a devil of a time with them in the past (probably OS/JVM 
problems more than shoddy programming) so I couldn't recommend them 
to core customers.

>*** Data files are not in ABI format(Later version will have this
>    option).
>*** Gel display before tracking is only one expanded view.
>    It is not a good representation of the data.
>*** Trim is all 96 samples and not individually.
>*** Staggered loading is not a option but can be done by loading
>    even sample first(w/ even sample sheet) and then restarting the
>    run to load the odd(w/ odd sample sheet).  In the end, the correct
>    sample sheet is re-installed.
>*** There is an external heating/cooling system.  I.e. water bath at 40'c.
>*** Maintenance looks low.   A H2O bottle and a tray of 10X are the
>    only thing to clean after the run.
>*** Its seems that there is no text files produced.  Files format
>    can be used with any editor.
>*** It runs on a PC. It ahs a CD burner.
>Kudos to MJ Research, Guoshan Tsen, and Christopher Abbot.
>Jeremy Medalle
>Lab Coordinator
>The Rockefeller University
>1240 York Ave
>Box 105
>NY, NY 10021

James VanEe                              Phone: (607) 254-4862
BioResource Center
Computing Facilty
170/171 Biotech Bldg                       Fax: (607) 254-4847
Cornell University
Ithaca, NY 14853                 www: http://brcweb.bio.cornell.edu


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