sequence analysis software

Mike Cherry cherry at frodo.mgh.harvard.edu
Thu Jun 18 18:19:00 EST 1992


In article <18JUN199210443325 at seqvax.caltech.edu>, mathog at seqvax.caltech.edu (David Mathog) writes...
>Here's my two cents on this thread.

I'll add my penny.

>    ....  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.

Then where would all the molecular biology system managers come from, 
computer science? ;-) At least around Boston the majority of people that 
support and manage molecular biology computing are former molecular 
biologist.

>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. 

Yes but as you point out below the cost of the person to support the 
multi-user system can be high, if you can find anyone that you can afford.

>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

I can not add anything on grant approval or disapproval of system
managers. My experience helping several start-up companies or newly formed
departments is that they never see the need for a system manager in their
initial design. These companies are willing to spend lots of money to get
good computers and networks but then think their scientists will be able
to run the systems. Its not that they cannot learn Unix or VMS but its
that once you have a few people working on the computers you then need
someone to answer the questions about program use, printing problems,
networking, setting or installing new software and their updates. Part of
the problem is that it appears difficult to find journeyman system managers
that can give the molecular biologist the type of support that they want. (I
believe thats why so many of the system managers are former wet lab
molecular biologist.) 

After a year or so the trying to do it all themselves most new sites see
that they really do need a computer person and create a new job. However 
for most academic departments that must use grants to support a system 
manager the problem of funding may be a major obstacle.

Mike Cherry
Molecular Biology, Massachusetts General Hospital




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