HDTenEightyP/NetNews huggingface dataset:
From: DULANEY@UCLAUE.MBI.UCLA.EDU
Newsgroups: bionet.software
Subject: Re: PC 80486
Date: 26 Jan 93 04:50:00 GMT
Distribution: bionet

!!In article <1993Jan25.090410.12066@gserv1.dl.ac.uk>, 
!!schnorr@tournesol.versailles.inra.fr (Kirk Schnorr) writes:
!!|> I was wondering if anyone out there could inform me about the relative

[ much good discussion deleted  to which John Penniston aptly replied]

!Chip		Internal	External	Floating
!Designation	Data Path	Data Path	Point Unit?
!-----------	---------	---------	-----------
!386DX		32 bits		32 bits		No
!386SX		32 bits		16 bits		No
!
!486DX		32 bits		32 bits		Yes
!486SX		32 bits		32 bits		No
!	As you can see, Intel changed the meaning of "SX" between the 386
!and 486 chips.
                               
I'd just like to add a bit more to the pot.
                                                               Run @ 2X
Chip	     Internal   External   Floating     8K Internal     speed   
Designation  Data Path  Data Path  Point Unit?    Cache       internally?
-----------  ---------  ---------  -----------  -----------   ----------
386SX	     32 bits	16 bits	     No             No            No
386DX	     32 bits	32 bits	     No             No            No

486SX	     32 bits	32 bits	     No             Yes           No
486DX	     32 bits	32 bits      Yes            Yes           No
486DX2	     32 bits    32 bits      Yes            Yes           Yes
                                                 ^^^^^^^^^^^^^^^^^^^^^^^
                                                  additional speed boosts

   Does any of this speak to the point of which processor you should buy?  Not 
really.  Most software (90%) is written to run on 16 bit processors.  I think 
windows 3.1 now incorporates a little 32 bit code but not much.  Some of the 
newest windows programs incorporate 32 bit code but again not much.  NO 
software, to my knowledge, have been written that REQUIRE the 486 chip.  A 386 
machine with a 387 math coprocessor is identically functional (as far as
software is concerned, though you might notice a slight speed difference) to a
486 chip. Furthermore, currently very few programs utilize the math
coprocessor portion of the 486, though this may change rapidly. The primary 
advantage of a 486 over a 386 is SPEED.

  SO... what should you do?  As always, the decision boils down to dollars. 
Buy the most powerfull machine you can comfortably afford.  I'd shy from 386SX
but other than that, 32 bits is 32 bits.  You may opt to buy a (slightly)
cheaper 386 but purchase more RAM so you can multitask in Windows more easily 
or you could add a tape drive to facilitate backups.  Certainly, if you can
afford it, you would want to buy a MEGA PC with 80486, 32 MB RAM, 600 MB hard
drive, tape backup, etc, but, for most, the decision is a big balancing act. 
I hope I haven't complicated things too much. :) Just my 2c.

Tom Dulaney
Graduate Student
Molecular Biology Institute
University of California, Los Angeles
From: gartmann@VMS.MPIIB-FREIBURG.MPG.dbp.de (Christoph Gartmann)
Newsgroups: bionet.software
Subject: RE: HELP:GCG-MENU
Date: 25 Jan 93 13:39:14 GMT
Distribution: bionet
Content-Identifier: 12
Original-To: bio-software@uk.ac.daresbury
Conversion: Prohibited

Inna Perlov ("Inna@vms.huji.ac.il") wrote:

>	My system manger have installed GCG-MENU but wasn't able to relink
> GCG-MENU software. He got the "illegal record format" message, it seems that
> it is attempting to link not .obj file.
>  When I try to run MENU now, I get
>       Error accessing MENUE Database! RC= 0000000008
>
> Anyone can help me?

Could it be that you got the UUEncoded version of GCG-menu available on the
EMBL-fileserver? This version cannot be installed because its encoding is not
appropriate. Thus, when decoding the package everything is in Stream_LF format,
even the datbase-files and libraries, which then cannot be read by the program.

You should pick up GCGMENU.MFT instead from the EMBL fileserver. You need a
copy of MFTU to decode this version. Look at earlier postings in this newsgroup
on how to get a copy of MFTU or send me a mail.

To say it again: GCGMENU.UAA on the EMBL fileserver won't work! Take
GCGMENU.MFT instead.

Regards
  Christoph Gartmann

+----------------------------------------------------------------------------+
| Christoph Gartmann          Phone : +49-761-5108-465   Fax: -221           |
| Max-Planck-Institut fuer    PSI   : PSI%02624505016037::GARTMANN           |
| Immunbiologie               X400  : S=gartmann;OU=vms;O=mpiib-freiburg;    |
| Stuebeweg 51                        P=mpg;A=dbp;C=de                       |
| D-7800  Freiburg            RFC   : gartmann@vms.mpiib-freiburg.mpg.dbp.de |
| FRG                           will change to:     gartmann@immunbio.mpg.de |
+------------- Do you know MENUE, the user environment for VMS? -------------+
Newsgroups: bionet.software
Subject: RE: GCGMENU using MFTU
From: macrides@sci.wfeb.edu
Date: 24 Jan 93 20:57:10 EDT
Distribution: bionet
Organization: Worcester Fndn. for Exptl. Biol.

In article <930122220944.b87@MBDS.NRC.CA>, NUM239@MBDS.NRC.CA writes:
> I got the same as you got. I am unable to use MFTU for the same reason.
> I asked for an explanation and never got any answer.
> 
> B. R. Baum

	I put the following in IUBio's incoming directory, for transfer to
the util/vms or molbio/vms directories, so you could access them via gopher as
well as ftp.  Note that most of file handling utilities currently in its
util/vms directory are old (obsolete) versions.

vms_fileutils.uue:
=================
	Executables and HELP modules for the lastest (as of 24-JAN-1993)
versions of MFTU, UNZIP, ZIP, VMSTAR, LZDCMP and LZCOMP for VMS systems are
included here, for convenience, as an EMBL-UUENCODEd, ZIP archive.  You
can use the UNZIP created by the UUDECODEing to break out the ZIP archive.
Then delete that UNZIP (which will be in stream_LF format), and thereafter use
the UNZIP (FIXED 512, Best Try Contiguous format) from the ZIP archive.

	Note that UNZIP may issue warnings about VMS version mismatches during
the breakout.  Ignore them, there's nothing to worry about!

	You can get the sources for these file-handling utilities by email
from FILESERV@WKUVX1.BITNET (send it the message HELP for instructions), or
from its FTP mirror:  ftp.spc.edu (in directories [.MACRO32.SAVESETS...]).

	Install the .EXE's as foreign commands:

$ foo :== $device:[directory]foo.EXE

	Install the system HELP modules with the command:

$ LIBRARY/INSERT/HELP SYS$COMMON:[SYSHLP]HELPLIB.HLB foo.HLP

				Fote

=========================================================================
 Foteos Macrides           Worcester Foundation for Experimental Biology
 MACRIDES@SCI.WFEB.EDU     222 Maple Avenue, Shrewsbury, MA 01545
=========================================================================
Newsgroups: bionet.software
From: harper@convex.csc.FI (Rob Harper)
Subject: Re: ARCHIE and Gopher
Organization: Finnish Academic and Research Network Project - FUNET
Date: Tue, 26 Jan 93 08:21:05 GMT

In <1993Jan25.160416.17288@news.miami.edu> kramer@oj.rsmas.miami.edu (Jack Kramer) writes:

>Is there any way to do an ARCHIE type search to locate things while
>connected to a Gopher hole?

It is possible. I have the following link in our gopher at CSC.

Name=The Ultimate Bionaut software search (ARCHIE)
Type=8
Port=23
Path=archie
Host=archie.funet.fi

which opens up a telnet session to the Finnish Archie. I would suggest
that you choose an archie closer to home if you want to do searches...
and really telnet sessions ARE NOT the best possible way to interact
with Archie... get yourself a client.

If you are only interested in molbio software then you might be interested
in the following options... which are a collection of links I have put 
together... other people have done work (Dan Jacobson, Don gilbert, Dave
Kristofferson), I only make the links. For example Dan earlier posting about
macmimic can be found from the software searches.

                     Wais sources for the Biologist

 -->  1.  Agriculture/
      2.  Journal TOC search <?>
      3.  Materials & Methods search <?>
      4.  Prosite protein database search <?>
      5.  Search Usenet News "sci"-groups (UK) <?>
      6.  Search for Software at EMBL (Mac, Dos, Unix, Vax)/
      7.  Search for Software at Indiana - IUBio (Mac, Dos, Unix, Vax)/
      8.  Search the Biosci/Bionet newsgroups (USA) <?>
      9.  Search the INFO-GCG mailing list (FINLAND) <?>
      10. Search the Protein Data Bank (USA) <?>
      11. Search the WAIS directory of servers (USA) <?>

Rob "knowing where to look is as important as knowing what to look for" Harper


--
 ~ Rob Harper                    ~ E-mail:          harper@convex.csc.fi    
 ~ Finnish State Computer Centre ~ Molbio/software: harper@nic.funet.fi
 ~ P.O. Box 40                   ~ Telephone:       +358 0 457 2076
 ~ SF-02101 Espoo Finland        ~ Fax:             +358 0 457 2302
From: inna@vms.huji.ac.il
Newsgroups: bionet.software
Subject: HELP:GCG-MENU
Date: 17 Jan 93 09:58:00 GMT
Distribution: world
Organization: The Hebrew University of Jerusalem

	My system manger have installed GCG-MENU but wasn't able to relink
GCG-MENU software. He got the "illegal record format" message, it seems that
it is attempting to link not .obj file.
 When I try to run MENU now, I get
       Error accessing MENUE Database! RC= 0000000008

Anyone can help me?
----------------------------------------------------------------------
 Inna Perlov 			   Phone      972-2-584848
 Hebrew University 		   E-Mail    Inna@hujivms.bitnet
 Computation center			     Inna@vms.huji.ac.il
 Givat-Ram 91904 Jerusalem	   FAX	      972-2-527349
 Israel
----------------------------------------------------------------------
From: wito@tansei.cc.u-tokyo.ac.jp ( )
Newsgroups: bionet.software
Subject: [Q]LIGAND
Date: 26 Jan 93 08:07:36 GMT
Organization: Computer Centre, University of Tokyo

Maybe one of FAQ.
We have a plan of binding assay.  For the purpose, we need
some analyis software, maybe LIGAND.
How can I get LIGAND software for IBM/compatibles?
Can I get it by FTP?

Thanks 

Wataru Ito(wito@tansei.cc.u-tokyo.ac.jp)
Fujita Health Univ.
Toyoake,Aichi,Japan
From: huff@mcclb0.med.nyu.edu (Edward J. Huff)
Newsgroups: bionet.software
Subject: Re: How to unsubscribe?
Date: 27 Jan 93 21:43:08 GMT
Followup-To: bionet.software
Distribution: bionet
Organization: NYU Chemistry Dept.

In article <9301270315.AA04422@herald.usask.ca>, MISRA@HERALD.USASK.CA
wrote:
> 
> Can anyone tell me how to UNsubscribe to this mailing list. It's not that I 
> don't think it to be a great newsgroup, but I can pick it up with my 
> newsreader, and not get tons of e-mail.
> 
> Thanks,
> 
> Pearse

From biosci.FAQ (frequently asked questions) file available
by ftp from net.bio.net in directory /pub/BIOSCI and posted regularly.

How do I request or cancel e-mail subscriptions to BIOSCI newsgroups?
---------------------------------------------------------------------

If you have access to USENET news software, then YOU DO NOT NEED AN
E-MAIL SUBSCRIPTION!  Only those people who need to receive postings
by e-mail must request to be added to the mailing lists.  USENET users
can simply read the various bionet newsgroups using their news
software.  If your site has USENET news but does not get the bionet
newsgroups, please request help by sending a message to
biosci@net.bio.net.

For those who need e-mail subscriptions or who want to cancel current
e-mail subscriptions, please send a request to one of the following
addresses.  Please choose the site that serves your location.  Simply
pick the newsgroup(s) from the list above that you wish to subscribe
to and request that your address be added to the chosen mailing lists.
Please use plain English; no special message syntax is required in
your subscription or cancellation request.

Address                               Serving
-------                               -------
biosci@net.bio.net                    The Americas and Pacific Rim
biosci@daresbury.ac.uk                Europe, Africa, and Central Asia

****If you are changing e-mail addresses****, please be sure to send a
message to your appropriate biosci address above and request that your
subscriptions be changed or canceled!!

--
Edward J. Huff   huff@mcclb0.med.nyu.edu   (212)998-8465
Keck Laboratory for Biomolecular Imaging
NYU Chemistry Deptartment, 31 Washington Place, New York NY 10003
Posted from the new Mac NewsWatcher 1.3d5
From: mengland@eniac.seas.upenn.edu (Michael England)
Newsgroups: bionet.software
Subject: Molecular Bioanalysis Software (PC)
Date: 28 Jan 93 23:57:39 GMT
Distribution: usa
Organization: University of Pennsylvania


Is there shareware available for PC's which is analagous to the mac 
programs:
	Strider
	Genedisplay
	Plasmid Draw

This information is for a colleague of mine at Thomas Jefferson University in 
Philadelphia. I am not familiar with this newsgroup and appologize if this
 request is a FAQ.

Mike England
Newsgroups: bionet.software
From: rndy@wimsey.mmid.ualberta.ca (Randy Read)
Subject: PIMA on SGI
Keywords: protein sequence alignment
Reply-To: rndy@wimsey.mmid.ualberta.ca 
Organization: University Of Alberta, Edmonton Canada
Date: Wed, 27 Jan 1993 08:12:24 GMT

I've downloaded Smith & Smith's PIMA (Pattern Induced Multiple Alignment)  
package (MBCRR-Package/pima-1.22.tar.Z on mbcrr.harvard.edu) by ftp as  
suggested in their paper.  Attempts to install the package on either an SGI or  
a NeXT lead to a number of compile-time warnings and fatal errors.  I still  
only speak pidgin C, so I'm hoping that someone with a greater facility with  
the language has sorted this out.

Has anyone out there succeeded in implementing this package on SGI hardware?   
If so, is the revised version available, or is it just a matter of the right  
compiler flags?  I would greatly appreciate any information, either by e-mail  
or posted to this newsgroup.

Randy J. Read
rndy@wimsey.mmid.ualberta.ca
Newsgroups: bionet.software
From: Jeremy John Ahouse <ahouse@hydra.rose.brandeis.edu>
Subject: Re: ClustalV in SeqApp
X-Xxdate: Thu, 21 Jan 93 20: 04:17 GMT
Organization: Center for Complex Systems
X-Useragent: Nuntius v1.1.1d17
Date: Thu, 21 Jan 1993 20:00:53 GMT

In article <1993Jan19.221442.22635@news.cs.brandeis.edu> Jeremy John
Ahouse, ahouse@hydra.rose.brandeis.edu writes:

>OK, I have tried using ClustalV from SeqApp again.  I redownloaded
>the files.   The loaded the sample file, selected some of the aa's
>and then chose the mult alignment option.  At this point, as it was
>the last time, my whole system hung and I dropped into the debugger
>with no way out, except to reboot. > >	Does this work smoothly
for everyone else?

A couple of responses, here and by email, encouraged me to look to
system extensions, after a morning of removing them all and then
adding them back one at a time found that superClock 3.9 (or 4.0.1 as
it turns out) are involved in my system crash...  

I would be interested to hear if this is a common finding.  I really
like this particular extension and am sad to see it go, but just now
multiple alignment is more important.

	by the way the following extensions do not(!) seem to cause 
problems:

!Extensions Manager
!Rival 1.1.9
After Dark
After Dark Files
AppleCD Speed Switch
Color
File Sharing Monitor
General Controls
HAM
HDT LightShow! 1.0
HDT Prober! 1.0
Keyboard
Labels
MacTCP 1.1
Map
Memory
Monitors
Mouse
Network
Serial Switch
Sharing Setup

        	Jeremy John Ahouse
        	Center for Complex Systems and Biology Dept
        	Brandeis University
        	Waltham, MA 02254-9110

        	(617) 736-4954
        	email: ahouse@hydra.rose.brandeis.edu
Newsgroups: bionet.software
From: gilbertd@chipmunk.bio.indiana.edu (Don Gilbert)
Subject: IUBio Archive down with disk problems
Organization: Biology, Indiana University - Bloomington
Date: Thu, 21 Jan 1993 15:47:15 GMT


IUBio archive of biology software and data, at internet address
ftp.bio.indiana.edu, will be closed some of today as I try to
diagnose problems with it's main disk drive.  If the problem is
serious as I suspect, IUBio archive may be closed indefinitely
as the disk is repaired.  

Stay tuned to this channel for further bulletins.

-- Don
-- 
Don Gilbert                                     gilbert@bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
From: anadeem@ampere.alt.graphics.pixutils (Ahmed Nadeem)
Newsgroups: bionet.software
Subject: MRI and CT-SCAN Images For Dogs?
Date: 27 Jan 93 07:23:45 GMT
Distribution: bionet.software
Organization: /home/ampere1/anadeem/.organization

Netters,
      I am currently working on a research project that involves construction 
of realistic, solid or geometric models for dogs.
      Does anyone know where I can get serial section images( MRI, CT-SCAN, 
etc ) for dogs?
                                                       Thanks,
                                                              Ahmed Nadeem
From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs)
Newsgroups: bionet.software
Subject: BLOCKS searches on VAX/VMS and Alpha/OpenVMS
Date: 27 Jan 93 14:08:05 GMT
Followup-To: bionet.software
Organization: EMBL Data Library

A new program, BlockSearch, is available for the analysis of new protein
sequences using site-specific scoring matrices derived from Steven and
Jorja Henikoff's BLOCKS database. The program was developed primarily for
VMS/OpenVMS systems, but is written in ANSI C and should work on other
platforms as well. It reads sequences in a variety of formats, including
SWISS-PROT and GCG. A comparison of a typical-length protein sequence
against BLOCKS release 6 takes about 15-20 CPU secs.

A copy can be obtained from ftp.embl-heidelberg.de
(/pub/software/vax/blksrch.uue) or by email from netserv@embl-heidelberg.de
(get vax_software:blksrch.uue).


Rainer Fuchs
EMBL Data Library
Fuchs@EMBL-Heidelberg.DE
From: mjhf@troi.cc.rochester.edu (Michael James Horsfall)
Newsgroups: bionet.software
Subject: Re: PC Plasmid program
Date: 22 Jan 93 03:11:50 GMT
Organization: University of Rochester - Rochester, New York

In <1jnka3INN9mu@shelley.u.washington.edu> mparker@fred.fhcrc.org (Michael Parker) writes:

>Are there any public domain PC based plasmid drawing programs and where are
>they?

There are one or two available at EMBL. The one I know of is called
PLASMIDG.EXE. It comes uuencoded as PLASMIDG.UAA and PLASMIDG.UAB via
e-mail. You will need EMBL's uudecode program to convert it. Instructions
are as follows:

1. E-mail to NETSERV@EMBL-Heidelberg.DE
   -include the following commands in the body of the text (one command per
    line).

    GET DOS_SOFTWARE:UUEMBL.UUE
    GET DOS_SOFTWARE:PLASMIDG.UAA
    DIR DOS_SOFTWARE

2. Save the messages you receive as PLASMIDG.UAA and PLASMIDG.UAB. You might
have to read them initially, in order to know which is (1/2) and which is
(2/2).

3. Use a generic uudecoder to convert UUEMBL.UUE to UUEMBL.EXE -a
self-extracting compression containing UUE.EXE and UUD.EXE. If you don't
have or can't get a hold of a generic uudecoder read the DOS_SOFTWARE
DIRECTORY message you will receive for instructions.

4. Type UUD PLASMIDG.UAA <Enter> to recombine the two files and convert them
to a self-extracting executable. And your off!!!!! A .DOC file is included.


Michael Horsfall
mjhf@troi.cc.rochester.edu
--
=====================================================Michael James Horsfall
Phone: (716)-275-8703 (Lab)                        Department of Biophysics
Fax: (716)-275-6007                  University of Rochester Medical Centre
E-mail: mjhf@troi.cc.rochester.edu=========================================
From: harper@nic.funet.fi (Rob Harper)
Newsgroups: bionet.software
Subject: MRI And CT-SCAN Images For Dogs? (fwd)
Date: 27 Jan 93 08:30:36 GMT
Organization: Finnish Academic and Research Network Project - FUNET
X-Mailer: ELM [version 2.3 PL11]

This note came to me as moderator of sources. I forward it to software, 
since it is more appropriate there.

-=ROB=-

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% CLIP %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Ahmed Nadeem wrote:

Netters,
        I am currently working on a research project that involves generating
solid or geometric models from MRI images. Part of the procedure will require 
me to possibly perform Thresholding & Edge Detection on my MRI images in order
to find out which pixels lie on boundaries between two different regions. 
Thus, I would like to have an Image Processing Software package that has good 
Edge Detection and Classification ( Segmentation ) modules/routines.  
        I have heard a lot about Khoros ( University Of New Mexico) and 
PV-WAVE (Precision Visuals) and was curious if other professionals or students
had any experience on how good they are for the above purposes. Suggestions 
on other software packages are also much welcome.
                                                       Thanks,
                                                              Ahmed Nadeem
From: MISRA@HERALD.USASK.CA
Newsgroups: bionet.software
Subject: How to unsubscribe?
Date: 27 Jan 93 03:15:59 GMT
Distribution: bionet

Can anyone tell me how to UNsubscribe to this mailing list. It's not that I 
don't think it to be a great newsgroup, but I can pick it up with my 
newsreader, and not get tons of e-mail.

Thanks,

Pearse

Newsgroups: bionet.software
From: rjhoffma@iastate.edu (Richard J. Hoffmann)
Subject: Re: Windows interested people!
Organization: Iowa State University, Ames, IA
Date: Fri, 22 Jan 1993 14:13:09 GMT

In article <1993Jan22.045259.17954@jupiter.sun.csd.unb.ca> dpope@mta.ca writes:
>If your interested in some opinions on various windows software, and
>want my thoughts, just send my a note... maybe we could setup a mail
>windows support group - sounds good to me :)

Or, you could subscribe to comp.os.ms-windows.apps and
comp.os.ms-windows.misc.

Just a thought.

Dick



-- 
Richard J. Hoffmann                Internet: rjhoffma@iastate.edu
Department of Zoology & Genetics     Bitnet: rjhoffma%iastate.edu@isumvs
Iowa State University                 Voice: (515) 294-8075
Ames, Iowa 50011
From: abola@PAE.PDB.BNL.GOV (Enrique E. Abola)
Newsgroups: bionet.software
Subject: phi/psi program
Date: 28 Jan 93 01:39:39 GMT
Distribution: bionet


I have just placed a copy of the program dihdrl.f
on our anonymous ftp account (pdb.pdb.bnl.gov).  This
version works on both SGI and VAX/VMS machines.  A
sample data and output is provided.  The program calculates
PHI/PSI and CHI angles for PDB entries.

The program is in the directory dihdrl.  The filename
is dihdrl.sgi.



-- 
________________________________________________________________                                 
				 | 
enrique e. abola                 |   BITNET:    abola1@bnl
Protein Data Bank                |   INTERNET:  abola1@bnl.gov 
Department of Chemistry          |   (516)-282-4383 
Brookhaven National Laboratory   | 
Upton NY 11973                   |
________________________________________________________________ 

Newsgroups: bionet.software
From: ODONNELL@ARCB.AFRC.AC.UK (Cary O'Donnell)
Subject: GCGMENU using MFTU
Original-To: BIO-SOFT@UK.AC.DARESBURY
Distribution: bionet
Date: Fri, 22 Jan 1993 10:19:00 GMT

Please correct me if I'm plain stupid, but:

I retrieved GCGMENU from the EMBL file server. The original
announcement stated that MFTU was required to decode it.

On decoding the MFTU file from fileserv@wkuvx1.bitnet I get a file called 
MFTU_ZIP.MFTU

What do I use to decode this? It doesn't appear to be UNZIP50P1, because
when I retrieve that & unpack it I get a file UNZIP50P1_ZIP.MFTU.

Can anyone tell me my way out of this ?

 *************************************************************************
 Cary O'Donnell             Tel: (+44) 582 762271 ext 229 
 Scientific Support Group   Fax: (+44) 582 761710
 AFRC Computing Division    
 West Common                JANET    : odonnell@uk.ac.afrc.arcb
 Harpenden                  Internet : odonnell@arcb.afrc.ac.uk
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