sequence analysis software

David Mathog mathog at seqvax.caltech.edu
Thu Jun 18 13:44:00 EST 1992

Here's my two cents on this thread.

1.  If you're setting up any kind of sequence analysis center keep in 
    mind that the hardware costs are usually negligible compared to the labor 
    costs.  The only time when this is not true is when system management 
    is by slave labor (ie, grad students).  Personally, I think that 
    the various granting agencies, and certainly the universities should
    outright forbid that practice, but I'm not holding my breath.

2.  Software costs can be pretty misleading.  "Single seat" 
    software (like on a PC or Mac) is usually very expensive when you 
    do any sort of cost/user analysis.  For this reason, GCG is a great
    bargain at 3000/year (especially with > 100 users) compared to the PC
    and Mac options.  This also shows up in service contracts and the like 
    - it's cheaper to maintain a couple of Vaxes or Unix boxes than an army
    of PCs. 

    "Free" software is not without costs - maintenance on this stuff can be
    quite a pain or a breeze, depending entirely on the whims of the 
    program's author.  Sometimes you can get bugs fixed and documentation,
    other times, no.

3.  One system manager usually costs less than N "part time" computer
    honchos distributed at one/lab.  However, there is a strong tendency to
    budget for the latter and not the former.  There is an even stronger
    tendency (apparently among granting agencies) to approve money for 
    hardware but not for labor.  On this last point I'd like some feedback:
    it's been reported to me that this gets lined out on grants, but I've
    no personal experience with it.

David Mathog
mathog at seqvax.caltech.edu
manager, sequence analysis facility, biology division, Caltech

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