HDTenEightyP/NetNews huggingface dataset:
From: RODRIGOL@BIOMED.UIO.NO (Rodrigo Lopez)
Newsgroups: bionet.software
Subject: Re: BLOCKS searches on VAX/VMS and Alpha/OpenVMS
Date: 28 Jan 93 13:19:43 GMT
Organization: NORWEGIAN EMBNET NODE
X-News-Reader: VMS NEWS 1.24

In <Fuchs-270193150431@rainer-mac.embl-heidelberg.de> Fuchs@EMBL-Heidelberg.DE writes:

> 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

I had a small problem with the frequency tables provided with the program 
source: Blocksearch complains about their format. Just edit the files
and remove the  blank line between the comments (lines beggining with '#')
and the table itself.

I wrote a small DCL script that perhaps helps using the program. It can be
fetched by anonymous ftp from biomed.uio.no (129.240.2.38). Look in the
root directory for a DCL file called RUN_BLOCKS.COM. Edit the file to
customize it to your local setup. There is the command 'Fetch' which should
be removed for sites that don't have GCG.

R:)


                             Rodrigo Lopez
          ****************************************************
          * Work:       The Norwegian EMBnet node            *
          *             The Biotechnology Centre of Oslo     *
          * Address:    Gaustadalleen 21, N-0371 Oslo Norway *
          * Telephone:  +47-2-958756                         *
          * Fax:        +47-2-694130                         *
          * Electronic mail addresses (Internet)             *
          * rodrigol@ulrik.uio.no      UNIX                  *
          * rodrigol@biomed.uio.no     VMS                   *
          ****************************************************
Newsgroups: bionet.software
From: wang_dj@syzygy.cs.jhu.edu (David J. Wang)
Subject: Population Analysis SW
Organization: Johns Hopkins Computer Science Department, Baltimore, MD
Date: Thu, 21 Jan 1993 17:02:54 GMT


I am looking for software that would assist with poplution research for 
UNIX machines.  By population research -- I mean software doing data analysis,
statistics, etc, anything ....
Any suggestions would be greatly appreciated.

David Wang

-- 
_______________________________________________________________________________
David J. Wang                                    CAUTION!
wang_dj@server.cs.jhu.edu                SPACE UNDER CONSTRUCTION!
_______________________________________________________________________________
From: einararn@rhi.hi.is (Einar Arnason)
Newsgroups: bionet.software
Subject: re:re:population analysis sw
Date: 24 Jan 93 01:59:41 GMT


ok but what is SAS (special airforce something) and where
does one get it?

Pitur Henry Petersen
Deptm. Biology
University of Iceland
php@lif.hi.is
From: MCCAINKW@DUVM.OCS.DREXEL.EDU (Kate McCain)
Newsgroups: bionet.software
Subject: Re: re:re:population analysis sw
Date: 24 Jan 93 20:22:39 GMT
Distribution: bionet



SAS -- in this context -- is prob. a large set of statistical routines that are
generally available on mainframe computers (though there are likely to be
versions for PC's that may not run as large data sets).  Equivalents are
SPSS (Statistical Package for the Social Sciences) and BMDP.  EAch of these
offers a remarkably full range of descriptive statistical routines, parametric
& non-parametric statistical analyses, multivariate analyses, time series,
LISREL, etc etc etc.  Each has its own "language," data formatting requirements
and so on.  I personally prefer SPSSX (because that was the one I learned first
and because I find SAS command structure more obscure). SAS offers--in addition
to the "standard," supported programs--a very large library of goodies that
they mount but do not support.  These are documented in various obscure [8-)]
manuals; some are of great interest for certain rare applications. Each
package has its own fans. Each will run on various platforms, though perhaps
not be available in the same version, as the upgrades are developed and
distributed. Each has an extensive set of published manuals for novices, power
users, etc.  Many social scientists of my acquaintance are SAS-freaks; many
biologists prefer BMDP.  I have found that the same "functional procedure"
(e.g. principal components analysis) may be implemented differently in the
different packages -- in terms of defaults, bells & whistles, options, etc.
BMDP got a bad rap in the 1970's for poor programming & some statistical
problems. SAS for a long time would only run on IBM's (I understand) --I
believe one can actually still enter fortran code; I think they are more alike
than different now.  That was NOT the case in 1983 when I was doing a
dissertation and needed procedures & features from all three. Very confusing.

There are also some nice standalone statistical packages formicros-- like
SYSTAT -- and dynamic system modelling software -- like Dynamo/StellaII.

Kate McCain                            "bibliometrics R us"
College of Information Studies
Drexel University                      mccainkw@duvm.ocs.drexel.edu
Xref: sparky bionet.software:2559 comp.sys.ibm.pc.hardware:37518
From: ashok@biochemistry.cwru.edu (Ashok Aiyar)
Newsgroups: bionet.software,comp.sys.ibm.pc.hardware
Subject: Re: Correction of RE: PC 80486 ** CORRECTION **
Date: 29 Jan 93 03:21:01 GMT
Distribution: na
Organization: CWRU School of Medicine
NNTP-Posting-Host: axa12-slip.dialin.cwru.edu

In article <C34907EFA03058B2@uclaue.mbi.ucla.edu> DULANEY@UCLAUE.MBI.UCLA.EDU writes:

>    I pulled a couple of magazines off my shelf just to make sure that this 
>is correct. (PC Magazine V11 N17 p115-257 and PC World December 1991 p 148-
>167) Neither was the definative article that I remember reading somewhere 
>but both contain sidebars about the 486SX.  Perhaps Ken was thinking of the 
>Cyrix 486SLC, which is essentially a 386SX (16-bit data path) with a 1K 
>cache and psuedoFPU.  Whoops, this is longer than I intended.  
>     Bottom line. 486SX= 486DX - FPU. 32 bits internally and externally.

Correct.  All CPUs in the *Intel* 486 series, including the 486SX, 486DX, 
486DX2, OverDrive Processor are 32 bits internally and externally.  

The Cyrix 486 SLC is basically a 386SX with a 1K internal cache, and is 
386SX pin compatible -- i.e 16 bit external bus.

The Cyrix 486 DLC is 386DX pin compatible, making it 32 bits internally and 
externally.  Neither Cyrix CPU has an internal FPU.

Cyrix reputedly has double-clocked versions of its 486 processors on the 
cards.

Ashok

Follow-ups to: comp.sys.ibm.pc.hardware
----------------------------------------------------------------------
                              Ashok Aiyar 
                      Department of Biochemistry
                       CWRU School of Medicine
----------------------------------------------------------------------
From: bdyke@DARWIN.SFBR.ORG (Bennett Dyke)
Newsgroups: bionet.software
Subject: Grant management software
Date: 27 Jan 93 19:19:31 GMT
Distribution: bionet

Has anyone experience with grant management software?  I have literature
from Research Information Systems (the folks who produce Reference
Manager) about their Grant Accountant package, but as highly regarded as
this seems to be, there is only an MS-DOS version. Is there a Mac package 
of comparable quality out there?

Many thanx in advance,

Bennett

+----------------------------------------------------------------------------+
|   Bennett Dyke                                                             |
|   Department of Genetics               Internet:  bdyke@darwin.sfbr.org    |
|   Southwest Foundation                    Phone:  (210) 674-1410 Ext 281   |
|   P.O. Box 28147                            Fax:  (210) 670-3317           |
|   San Antonio, TX 78228, USA                                               |
+----------------------------------------------------------------------------+
From: BIONET@FRCGM51.EARN
Newsgroups: bionet.software
Subject: Re: atomic to phipsi
Date: 27 Jan 93 11:41:00 GMT
              from FRCGM51.BITNET (BIONET) by UKACRL.BITNET (Mailer R2.07) with
               BSMTP id 1509; Wed, 27 Jan 93 10: 43:04 GMT
           from DECNET-MAIL by FRCGM51.BITNET with PMDF#10000; Wed, 27 Jan 1993
Distribution: bionet
X-Envelope-To: bio-software@daresbury.ac.uk
Original-To: bio-software@UK.AC.DARESBURY
X-Vms-To: in%"bio-software@daresbury.ac.uk"


 
 
>
> Hi all.  This is a really dumb question, but for the life
> of me I cannot find a routine for converting atomic
> coordinates to phi-psi angles.  Basically, I would like
> something that will accept Brookhaven type coordinates and
> convert them.  Better yet,  maybe Brookhaven has phi-psi
> angles already generated.  I don't know.  If you are familiar
> with this, or know where routines like this exist, I would
> be very grateful.
> Thank you,
> George Johnson
 
        Each PDB release is distributed with a set of ancillary programs.
 One of them is DIHDRL: "complete torsion angles" and another one is FISIPL:
 "PHI/PSI plots on printer". They are written in plain old FORTRAN and,
 therefore, are easily modifiable to meet your particular requirements.
 
        Good luck,
 
   ------------------------------------------------------------
   |  Jean-Loup Risler                |                        |
   | Centre de Genetique Moleculaire  |  risler@frcgm51.bitnet |
   | 91190  Gif sur Yvette  France    |                        |
   -------------------------------------------------------------
From: seb1005@mbfs.bio.cam.ac.uk (Steven Brenner)
Newsgroups: bionet.software
Subject: PDB C++ Class
Summary: Suggestions for what a pdb class should do
Date: 27 Jan 93 23:25:57 GMT
Organization: U. of Cambridge, England

A few weeks ago, I posted to this group to see if anyone had written
any C++ classes to manage data of biological interest, and
PDB/structure data in particular.

Unfortunately, nobody seems to have made a class for dealing with
protein structure data.  Therefore, I'm going to set about it myself.

While I don't guarantee that I'm going to build anything
re-distributable, I hope to make a good-quality reusable class library
for this use.  What I would like are comments on what people would
like to see such a class be able to do.

I would also like pointers to routines to put into the class, such as
the phi/psi program just recently posted.  

Thanks in advance!

-Steve
--
Steven E. Brenner               |  Internet    seb1005@mbfs.bio.cam.ac.uk
Department of Biochemistry      |  JANET       seb1005@uk.ac.cam.bio.mbfs
University of Cambridge         |  Laboratory  +44 223 333671
Tennis Court Road               |  Home        +44 223 314964
Cambridge CB2 1QW, UK           |  Lab Fax     +44 223 333345

-- 
Steven E. Brenner               |  Internet    seb1005@mbfs.bio.cam.ac.uk
Department of Biochemistry      |  JANET       seb1005@uk.ac.cam.bio.mbfs
University of Cambridge         |  Laboratory  +44 223 333671
Tennis Court Road               |  Home        +44 223 314964
Newsgroups: bionet.software
From: gilbertd@chipmunk.bio.indiana.edu (Don Gilbert)
Subject: Re: IUBio Archive down with disk problems
Organization: Biology, Indiana University - Bloomington
Date: Thu, 21 Jan 1993 18:09:46 GMT

IUBio Archive's main archive disk is indeed dead.  It will
be probably on the order of a week at soonest until it can
be replaced.  In the mean time, if I can find time and disk
space on another machine, I will shift the location of
the archive.  Then we will see who used the proper network link,
ftp.bio.indiana.edu, which will soon point to another 
computer.

More later. -- Don
-- 
Don Gilbert                                     gilbert@bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
From: jasper@molbiol.ox.ac.uk
Newsgroups: bionet.software
Subject: RE: GCGMENU using MFTU
Date: 22 Jan 93 22:05:29 GMT
Distribution: bionet
Organization: Oxford University Molecular Biology Data Centre
Nntp-Posting-User: jasper

In article <1993Jan22.140947.13650@gserv1.dl.ac.uk>, gartmann@VMS.MPIIB-FREIBURG.MPG.dbp.de (Christoph Gartmann) writes:
> 
> unfortunately I didn't realize that you need MFTU to decode MFTU on
> fileserv@wkuvx1.bitnet (and then UnZIP). Sorry for that.

Or for those who have ftp :)   Hunter Goatley's fileserver is mirrored in the 
[.macro32.savesets] directory at ftp.spc.edu - loads of cool stuff here.

Since Hunter's connection to the net is through a 9600 baud line it's better,
if you can, to use the ftp option. 

> By the way: as far as I know there are only two programs which are able to
> keep VMS file-attributes when encoding and decoding a file - MFTU and the new
> ZIP. As GCG-menu consists not only of executables but of RMS-datafiles and
> VMS-libraries, the only way to transfer the package properly is through one
> of the archivers mentioned above.

Zip also has great compression ratios and replaces Zoo on that count also.

> +----------------------------------------------------------------------------+
> | 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? -------------+

Jasper Rees
Oxford University Molecular Biology Data Centre
and The Sir William Dunn School of Pathology

jasper@molbiol.ox.ac.uk
From: DULANEY@UCLAUE.MBI.UCLA.EDU
Newsgroups: bionet.software
Subject: Correction of RE: PC 80486 ** CORRECTION **
Date: 29 Jan 93 02:34:00 GMT
Distribution: bionet


    I have one more correction to Ken Fasman's (ken@oscar.welch.jhu.edu) last
posting.  (Edited version below)  Ken is correct in stating that the original 
486SX was cast from the same die as the 486DX; however, he is incorrect in 
stating that the 486SX has a 16 bit data path.  Same die=same interactions 
with the motherboard=same data path.  
    There was actually quite a bit of furor when the 486SX was first announced
about the fact that the 486SX was being sold for less than the 486DX. Since
the 486SX had to undergo the exact same manufacturing process as the 486DX
with the added step of disabling the FPU, how could the SX be cheaper.  (Intel
claims the cost saving comes from not having to test the FPU.)  The original
concept for the Overdrive was to allow the user to insert a full fledged 486DX
into the slot, completely disabling the 486SX. (Incidently making you pay for
the main microprocessor and 8k cache twice.)  Later incarnations, as Ken
states, no longer contain the FPU. (I guess it was cheaper not to add the
extra silicon after all.)  Anyway, sorry about the trivia.  
    I pulled a couple of magazines off my shelf just to make sure that this is
correct. (PC Magazine V11 N17 p115-257 and PC World December 1991 p 148-167) 
Neither was the definative article that I remember reading somewhere but both
contain sidebars about the 486SX.  Perhaps Ken was thinking of the Cyrix
486SLC, which is essentially a 386SX (16-bit data path) with a 1K cache and
psuedoFPU.  Whoops, this is longer than I intended.  
     Bottom line. 486SX= 486DX - FPU. 32 bits internally and externally.

Tom Dulaney
Dulaney@uclaue.mbi.ucla.edu


>This is not quite right!  It turns out that the 486SX had its floating point 
>unit disabled in the original chip, and removed from the die altogether in 
>later versions.  That is, the 486SX has a 32 bit internal data path, a 16 bit 
>external data path, and NO FLOATING POINT COPROCESSOR.
From: chris47@uxb.liv.ac.uk (Chris Brown )
Newsgroups: bionet.software
Subject: Re: Population Analysis SW
Date: 23 Jan 93 11:27:58 GMT
Organization: The University of Liverpool
X-Newsreader: TIN [version 1.1 PL6]

Try SAS
From: mparker@fred.fhcrc.org (Michael Parker)
Newsgroups: bionet.software
Subject: PC Plasmid program
Date: 22 Jan 1993 01:57:23 GMT
Organization: FHCRC
NNTP-Posting-Host: 140.107.60.180

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

Thanks
Newsgroups: bionet.software
From: gartmann@VMS.MPIIB-FREIBURG.MPG.dbp.de (Christoph Gartmann)
Subject: RE: GCGMENU using MFTU
Content-Identifier: 12
Original-To: bio-software@uk.ac.daresbury
Conversion: Prohibited
Distribution: bionet
Date: Fri, 22 Jan 1993 13:08:13 GMT

Cary O'Donnell (odonnell@arcb.afrc.ac.uk) wrote:

> 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.


Hello,

unfortunately I didn't realize that you need MFTU to decode MFTU on
fileserv@wkuvx1.bitnet (and then UnZIP). Sorry for that.

A better solution (and tested by myself):

Send a message to
  FILESERV@WKUVX1.BITNET
containing the line
  SEND FILESERV_TOOLS
When you receive the result (five parts), extract it from VMS-Mail and store
and concatenate all parts in one file (e.g. TOOLS.COM). Finally execute
the procedure
  @TOOLS
This file is a VMS-Share archive and is self-extracting. You'll get executables
for LZDCMP, UnZip and MFTU.

To decode GCGMENU.MFT define a symbol for MFTU
   MFTU :== $disk:[directory]MFTU
Then type
   MFTU DECODE GCGMENU.MFT
and you will retrieve two files, GCG-MENU021.A and README.TXT . Install the
backup saveset GCG-MENU021.A as described in README.TXT using
   @SYS$UPDATE:VMSINSTAL
(You need SYSTEM privileges to do that)

By the way: as far as I know there are only two programs which are able to
keep VMS file-attributes when encoding and decoding a file - MFTU and the new
ZIP. As GCG-menu consists not only of executables but of RMS-datafiles and
VMS-libraries, the only way to transfer the package properly is through one
of the archivers mentioned above.

Sorry for any inconviencies
  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? -------------+
From: NUM239@MBDS.NRC.CA
Newsgroups: bionet.software
Subject: RE: GCGMENU using MFTU
Date: 23 Jan 93 03:09:44 GMT
Distribution: bionet

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

Newsgroups: bionet.software
From: ralf@frege.gmd.de (Ralf Zimmer)
Subject: Wanted: Mac Program visualizing PDB structures
Organization: GMD, Sankt Augustin, Germany
Date: Mon, 25 Jan 1993 09:50:32 GMT

I am looking for an Apple Macintosh program which displays
3D Molecular structures. 
I know of MacMolecule from the University of Arizona 
(Myers/Blanco/Hallick/Jahnke).
I am especially interested in a PDB interface, and I would be happy
if the program allows for scaling, translation and rotation of
3D structures (It would be GREAT if the program includes some
PDB specific editing features ...).

Ralf Zimmer.

---------------------------------------------------------------------
Ralf Zimmer, e-mail: ralf.zimmer@gmd.de, tel: (++49 2241) 14-2818
GMD - German National Research Center for Computer Science
Schloss Birlinghoven, P.O. Box 1316, W-5205 Sankt Augustin 1, Germany
---------------------------------------------------------------------
Newsgroups: bionet.software
From: mlehman@vetmed.wsu.edu (D Matthew Lehman)
Newsgroups: bionet.software
Subject: Re: PC 80486
Date: 27 Jan 93 16:45:22 GMT
Organization: Washington State University
X-Newsreader: TIN [version 1.1 PL8]

Juan P. Abonia (pablo@acsu.buffalo.edu) wrote:
> In article <1993Jan25.170138.10928@welchgate.welch.jhu.edu> ken@oscar.welch.jhu.edu (Ken Fasman) writes:
> >In article <1993Jan25.090410.12066@gserv1.dl.ac.uk>, schnorr@tournesol.versailles.inra.fr (Kirk Schnorr) writes:
> >|> 	We were thinking to get a 486SX based machine since it is the
> >|> cheapest but I do not want to sacrifice a built in  math co-proccessor
> >|> or 32 bit data path it the 486SX is missing these.  Can anyone enlighten
> >|> me?
> >
> >My understanding of the various members of the Intel 80386 and 80486 families 
> >are as follows:
> >
> >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		16 bits		Yes
> >
> >Please note that Intel uses the "SX" designation to denote the narrower 
> >external data path, NOT the presence or absence of a math coprocessor.

> This isn't always true.  The 486SX has a disabled floating point unit.  The
> upgrade chips (Overdrive) for these machines disable the original CPU when they
> are installed (They have an enabled FPU).  I believe that the 486SX retains a
> 32-bit external data path.
> -- 
> J. Pablo Abonia
> University at Buffalo				 BITNET:    pablo@sunybcs.BITNET
> Roswell Park Cancer Institute			 Internet:  pablo@cs.Buffalo.EDU

Nope, it's only a 16 bit path to memory.  The 486SX was really a backwards
design for Intel.  They had so much success with the 386SX they took the 
486DX and crippled it into a 16 bit path and disabled fpu support, hoping
that everyone would buy the 486SX over a 386 machine (AMD had started 
producing 386 clones and Intel was not pleased).  The basic design of
the 486SX is the same as the 486DX.  My opinion on the 486SX is that
a person is better off with a 486DX.  Beware of benchmarks that say the
chips are almost computationally equal, as they probably don't talk into
account memory reads/writes.

--------------------------------------------------------------------------
D. Matthew Lehman                   Internet: mlehman@vcs10.vetmed.wsu.edu
Veterinary Computing Services       Phone:    (509) 335-0101
Bustad 203
Washington State University
Pullman, WA 99163
--------------------------------------------------------------------------
From: mkuittin@messi.uku.fi (Marko Kuittinen)
Newsgroups: bionet.software
Subject: Re: PC 80486
Date: 27 Jan 93 23:46:53 GMT
Organization: University of Kuopio, Finland

Hi,

Does anyone have reference or empiric benchmarks for motherboards 
equipped with Cyrix 486SLC- processor? There is one cheap solution for a
486- system compared to Intel. The question follows: 
what does one give up in kicks for those decreased bucks?

regs,

#=mk=#