Date: Tue, 27 Feb 2001 21:33:42 +0100 (CET) From: marc.vanwoerkom@science-factory.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/25423: Category "biology" is not sufficient Message-ID: <200102272033.f1RKXgj01741@nil.science-factory.com>
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>Number: 25423
>Category: ports
>Synopsis: The "biology" category holds programs from chemistry, physics and bio informatics
>Confidential: no
>Severity: serious
>Priority: medium
>Responsible: freebsd-ports
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Tue Feb 27 12:40:01 PST 2001
>Closed-Date:
>Last-Modified:
>Originator: Marc van Woerkom
>Release: FreeBSD 5.0-CURRENT i386
>Organization:
>Environment:
System: FreeBSD nil.science-factory.com 5.0-CURRENT FreeBSD 5.0-CURRENT #0: Thu Dec 7 18:17:37 CET 2000 mvw@nil.science-factory.com:/usr/obj/usr/src/sys/NIL i386
>Description:
Dear porters,
the present contents of the "biology" category is getting a bit
inappropriate.
IMHO the "biology" category should be accompained by at
least a "chemistry" category and possibly a "physics" category at
some point in the future as well.
Hard thing is, that most stuff fits some inbetween role,
like "physical chemistry" or "biochemistry", and lately the part of
biochemistry that deals with the computational aspects of genetics
has spawned a field called "bioinformatics".
(I studied physics and worked in a "cheminformatics" company and now
in a bio informatics company :)
Let's look what populates "biology" right now, and where I would
rather like to see the stuff:
babel molecular files -> fits chemistry as well
biojava this rather bioinformatics (thus mostly computational genetics, biochemistry) than biology
chemeq -> chemistry
clustalw -> bioinformatics
deft -> chemistry, physics
emboss -> bioinformatics
fasta -> bioinformatics
fasta3 -> bioinformatics
fastdnaml -> bioinformatics, biology
gaussian98 -> chemistry, physics
gperiodic -> chemistry
hmmer -> bioinformatics
kinemage -> chemistry, physics
molden -> chemistry
mopac -> chemistry, physics
nab -> bioinformatics
ncbi-toolkit -> bioinformatics, biology
ortep3 -> physics, chemistry
p5-AcePerl -> bioinformatics
p5-bioperl -> bioinformatics
paml -> bioinformatics
phylip -> bioinformatics, biology
platon -> physics, chemistry
povchem -> chemistry, graphics
psi88 -> physics, chemistry
py-biopython -> bioinformatics
rasmol -> bioinformatics
seaview -> bioinformatics
sim4 -> bioinformatics
tinker -> chemistry, physics
xdrawchem -> chemistry
xmolwt -> chemistry
It must not be this scheme, but I hope I have illustrated,
that just "biology" getting all those ports is not a good
choice. Example I would rather look under "graphics" or "chemistry"
for the "povchem" ray tracer package.
>How-To-Repeat:
>Fix:
Discuss, introduce new categories, fix existing categorization. :-)
Regards,
Marc
>Release-Note:
>Audit-Trail:
>Unformatted:
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