From marc.vanwoerkom@science-factory.com  Tue Feb 27 12:35:04 2001
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Date: Tue, 27 Feb 2001 21:33:42 +0100 (CET)
From: marc.vanwoerkom@science-factory.com
To: FreeBSD-gnats-submit@freebsd.org
Subject: Category "biology" is not sufficient

>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:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Tue Feb 27 12:40:01 PST 2001
>Closed-Date:    Wed Apr 25 01:22:20 PDT 2001
>Last-Modified:  Wed Apr 25 01:24:36 PDT 2001
>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:

From: Will Andrews <will@physics.purdue.edu>
To: marc.vanwoerkom@science-factory.com
Cc: FreeBSD-gnats-submit@FreeBSD.ORG
Subject: Re: ports/25423: Category "biology" is not sufficient
Date: Tue, 27 Feb 2001 16:42:00 -0500

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 On Tue, Feb 27, 2001 at 09:33:42PM +0100, marc.vanwoerkom@science-factory.c=
 om wrote:
 >         the present contents of the "biology" category is getting a bit=
 =20
 >         inappropriate.
 [.. discussion snipped ..]
 
 Bah.  Another bikeshed.  What I'd prefer to see is a "science" category
 for physical sciences like physics, chemistry, and biology.  Stuff like
 "mathematical sciences" can be better attributed to the "math" category.
 And so on...
 
 --=20
 wca
 
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From: "Matthew Emmerton" <matt@gsicomp.on.ca>
To: <marc.vanwoerkom@science-factory.com>,
	<FreeBSD-gnats-submit@FreeBSD.ORG>
Cc:  
Subject: Re: ports/25423: Category "biology" is not sufficient
Date: Tue, 27 Feb 2001 22:59:35 -0500

 >         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.
 
 Why not just rename 'biology' to 'science'?
 
 --
 Matt Emmerton
 

From: Kris Kennaway <kris@obsecurity.org>
To: marc.vanwoerkom@science-factory.com
Cc: FreeBSD-gnats-submit@freebsd.org, asami@FreeBSD.org
Subject: Re: ports/25423: Category "biology" is not sufficient
Date: Sat, 3 Mar 2001 19:52:47 -0800

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 On Tue, Feb 27, 2001 at 09:33:42PM +0100, marc.vanwoerkom@science-factory.c=
 om wrote:
 >=20
 > >Number:         25423
 > >Category:       ports
 > >Synopsis:       The "biology" category holds programs from chemistry, ph=
 ysics and bio informatics
 > >Confidential:   no
 > >Severity:       serious
 > >Priority:       medium
 > >Responsible:    freebsd-ports
 > >State:          open
 > >Quarter:       =20
 > >Keywords:      =20
 > >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
 >=20
 >=20
 > =09
 > >Description:
 >=20
 > 	Dear porters,=20
 >=20
 >         the present contents of the "biology" category is getting a bit=
 =20
 >         inappropriate.
 >=20
 >         IMHO the "biology" category should be accompained by at=20
 >         least a "chemistry" category and possibly a "physics" category at
 >         some point in the future as well.
 
 I've lost count of the number of times this has come up, but for some
 reason Satoshi has never got around to actually creating the new
 science category.  Satoshi?
 
 Kris
 
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 --EuxKj2iCbKjpUGkD--
State-Changed-From-To: open->analyzed 
State-Changed-By: sada 
State-Changed-When: Wed Apr 18 00:41:10 PDT 2001 
State-Changed-Why:  
Have some replies. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=25423 
State-Changed-From-To: analyzed->closed 
State-Changed-By: dougb 
State-Changed-When: Wed Apr 25 01:22:20 PDT 2001 
State-Changed-Why:  

Motion is occurring on this, and the science category is now 
in existence. Further discussion should take place on freebsd-ports, 
where this topic should have originated in the first place. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=25423 
>Unformatted:
