[Pipet Devel] yum, canned locus (was: from Justin)

J. Steinbachs stein at fmppr.fmnh.org
Wed Jun 16 10:52:12 EDT 1999


I'm new to this list.  I'm not a programmer or developer, but I will be
configuring, installing and (most importantly) maintaining two "spiffy"
computer systems for the evolutionary biologists here at the Field
Museum of Natural History in Chicago.  These folks align small sequences
(1000 base pairs), but they've usually got AT LEAST 50 species (I've
heard rumors that some of the data sets actually contain upwards of 500
species).  Once the alignment is done, they conduct phylogenetic
analyses using Paup*, fastDNAml, etc.

> IMHO, we have to expect that bench scientists are no more computer-savvy than
> the general public.  They will expect Loci to operate, on the surface, like any
> other GUI application.  They'll want to choose File->Open, then select a
> sequence or whatever, and then push a button and get pretty pictures (well,
> something useful anyway :-)  So, we must have lots of pre-canned command-lines
> too.  I'd like the "learning curve" to be low.  Later on, the user can peel away
> the layers of Loci to find an incredibly powerful and flexible system.

This paragraph applies to my users very well.  While there are some who
love a unix prompt and running Paup* "batch" files, most of my users
have *shudder* Macs sitting on their desks.  The grant money for these
spiffy computers also includes some funding for GCG.  With these users
in mind, I would love to get a system up and running focusing on GCG
simply because it would be administratively simple for me and provides
an instant friendly user interface for the novice computer users (mostly

The other system will likely be some sort of Linux Beowulf cluster
without GCG, and for the time being, without a customized friendly user
interface - unless of course Loci comes into fruition soon :)

When I get one or both of these systems, I would be more than happy to
alpha and/or beta test (and I can think of a few users who might be good
guinea pigs for the user front-end).


Jennifer Steinbachs
Computational Biologist
Dept. of Botany
The Field Museum
Chicago, IL 60605-2496

office: 312-665-7810
fax: 312-665-7158
email: stein at fmnh.org

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