HDTenEightyP/NetNews huggingface dataset:
From: rbm8p@Virginia.EDU (Rick MacDonald)
Newsgroups: bionet.software
Subject: Phi-Psi code incorrect. Apologies. Correction to follow.
Date: 26 Jan 93 21:07:57 GMT
Organization: University of Virginia
Originator: rbm8p@darwin.clas.Virginia.EDU


Dopey me --- I sent out an old bit of code without checking it.
The output of the version of sifi.c that I recently posted is
not correct.  Those interested can obtain corrected versions
by e-mail.

rbm8p@virginia.edu
Newsgroups: bionet.software
From: ken@oscar.welch.jhu.edu (Ken Fasman)
Subject: Re: PC 80486
Followup-To: bionet.software
Keywords: microcomputer microprocessor Intel 486
Organization: Genome Data Base, Johns Hopkins School of Medicine
Date: Mon, 25 Jan 1993 17:01:38 GMT

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
|> differences between the various flavors of 486 CPU chips in PC
|> computers.  We are about to buy a new system for data aquisition and
|> proccessing for our HPLC to replace our slow and failing HP Vectra 286.
|> 	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.

Intel has also introduced 486DX2 chips, which operate internally at double 
their external clock speed.  For example, the 50 MHz 486DX2 runs internally 
at 50 MHz and externally (memory, local bus video, etc.) at 25 MHz.

IBM has introduced the 386SLC and 486SLC chips, which I believe operate at 
lower power consumption and have other minor performance enhancements, but I 
have not seen actual confirmation of this, so please check on it.

Intel is also getting ready to introduce 486 chips which consume less power, 
using a 3.3 Volt input.  I do not know the official designation of these chips.

I hope this helps a little bit.  :-)

Ken Fasman
Deputy Director of Informatics
Genome Data Base
Johns Hopkins University School of Medicine
2024 E. Monument St.
Baltimore MD  21205

ken@library.welch.jhu.edu
Newsgroups: bionet.software
From: lims01.lerc.nasa.gov (William Tsarones)
Subject: Medical Practice Mgt. Software
Followup-To: bionet.software
Organization: NASA/LeRC
Date: Fri, 22 Jan 1993 14:56:47 GMT

I need help trying to locate any information on medical practice management
software for Macintosh--the type used to run a doctor's office. I've never
seen anything on the Mac for this but have heard it exists.

Any information, even if it's nothing more than where to get information on
Mac software for vertical markets, would be greatly appreciated.

Thanks in advance.


Bill Tsarones
sctsar@lims01.lerc.nasa.gov
From: gozani@VP3.MED.HARVARD.EDU (Shai Gozani)
Newsgroups: bionet.software
Subject: Protein structure templates
Date: 21 Jan 93 23:56:55 GMT
Distribution: bionet



Does anybody know of software that creates 3D profiles that
allows one to match an amino acid sequence against a protein
structure.  I am specifically interested in the method
published by Eisenberg and coworkers at UCLA (Luthy et al. in
Nature vol. 356, 1992 and Bowie et al. in Science vol. 253, 1991).

Thanks for any help.

Shai Gozani
Dept. BCMP
Harvard Medical School
gozani@vp3.med.harvard.edu

Newsgroups: bionet.software
From: dpope@mta.ca
Subject: Windows 3.1 Mail List
Reply-To: dpope@mta.ca
Organization: Mount Allison U, Sackville, N.B. Canada 
Date: Tue, 26 Jan 1993 01:51:03 GMT

To whom it may concern,

Last week I started a mailing group for people interested in discussing
various Windows Apps.  Well my list is growing and I plan on mailing
some of my opinions on Word Processors very soon.  So please, if you
having sent me your address - do so.  I hope this helps some of you
to get an unbiased opinion of some Windows software and to help you also
to solve some basic Windows problems.  My intent also is to give you people
some handy tricks that will make Windows more convince for your usage.
I am also hoping that you will email me your Windows problems even if you
found a solution - this might expand everyone's knowledge of Windows.
There are other news groups of this sort, but it is very large and it
really a slow process to use these groups.  I hope this makes learning
about Windows a bit more fun.  Once again thanks for your interest.

			Mount Allison University, Canada
				D.P.
Newsgroups: bionet.software
From: geojohn@casbah.acns.nwu.edu (George Johnson)
Subject: atomic to phipsi
Organization: Northwestern University, Evanston Illinois.
Date: Tue, 26 Jan 1993 01:23:42 GMT

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
geojohn@casbah.acns.nwu.edu
tt@immuno.esam.nwu.edu
tt@ttwu.esam.nwu.edu
gjohnson@ncbi.nlm.nih.gov
From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs)
Newsgroups: bionet.software
Subject: Yeaststrains HyperCard stack update
Date: 28 Jan 93 13:01:34 GMT
Followup-To: bionet.software
Organization: EMBL Data Library

The author of the HyperCard stack "yeaststrains" asked me to post this
announcement, because many servers have a corrupted version of it:

This Hypercard 2 stack is designed for scientists working with yeast (S.
cerevisiae) and having more than a few strains. The stack is devised for a
storage format of 10x10 strains per box. A version designed for boxes of
8x8  is also available and can be asked for via e-mail.

Besides some bug-fixes from vers. 1.0, vers. 1.2 is several times faster
displaying the individual strains. Those of you who have already built a
strain collection using vers. 1.0 or 1.1 of my stack can e-mail me for an
updater, which installs the 1.2  improvements without messing up the
strains already in the collection.
Attention: A version 1.0 has been posted on a number of servers while
the accompanying README file described it as version 1.2. You should check
the version of your collection in the info field in the Finder.

For each strain, mutant alleles are entered by choosing from a list,
alternative strain names, origin, plasmids and other commentary can be
stored in addition. Diploid  strains can be entered by RmatingS. Strains
can be extracted quickly by searching for the presence or absence of
mutant alleles, or for other criteria. Search results can be printed or
exported as text files.

For German yeast researchers: Eine deutsche Version (nur 10x10-Format)
kann per e-mail bei mir angefordert werden.
kaifr@mailserv.zdv.uni-tuebingen.de


Note: copies can be obtained from EMBL's ftp server
(ftp.embl-heidelberg.de) in /ftp/software/mac, or by sending the command
"get mac_software:yeaststrains.hqx" to netserv@embl-heidelberg.de.
Newsgroups: bionet.software
From: dpope@mta.ca
Subject: Windows interested people!
Reply-To: dpope@mta.ca
Organization: Mount Allison U, Sackville, N.B. Canada 
Date: Fri, 22 Jan 1993 04:52:59 GMT

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 :)

                             D.P.
Newsgroups: bionet.software
From: ajt@rri.sari.ac.uk (Tony Travis)
Subject: Re: Computerized lab notebook?
Original-To: bio-software@uk.ac.daresbury
Reply-To: ajt@rri.sari.ac.uk
Organization: Rowett Research Institute
Distribution: bionet
Date: Fri, 22 Jan 1993 17:50:04 GMT

In article <93122162041.MIN-LDGBa29809.bionet-news@uk.ac.daresbury> you wrote:
: [...lab notebook stuff]
: 3.  No one has mentioned published encrypted summary data.  Somewhere
: I read about (but have not personally seen) services which take any
: data file and produce from a large file a small "signature" which
: is published in the classified section of a microfilmed newspaper.
: Experts will testify that it is essentially impossible to produce
: a file which matches the signature and is not the original.  

Am I totally misunderstanding what you say, or are you just describing
the function of CRC's ??  The combination a file's length in bytes and
its 32-bit CRC (cyclic redundancy check) is virtually unique and serves
to validate many software packages.  This, in essence, is no different
to validating experimental records as original.

: What is needed to make computerized lab notebooks feasible
: is a similar service on the internet (maybe BioSci could offer it)
: where "signature" files could be publically posted and permantly
: archived in such a way that they could not be modified without
: the cooperation of many people (and no one could be certain that
: someone else didn't keep another copy somewhere).  E.G. create
: a newsgroup for these files, and let anyone who wants to archive
: it.

What is needed to make data accessible is ISDN!!

The whole thrust of new developments is NOT to cart your precious data
around the world with you, but to make access to it via wide-bandwidth
communications channels feasable.  What you need is a WORM at work as a
data repository and an ISDN link on your portable in order to get at it
from home or wherever you are working.

My hope is that this will all be affordable - otherwise we will have no
progress.  I'm not saying that the 'Newton' or 'Active Book' are the
answer either.  The essence of what I am saying is that the
communication channel itself is the expensive bottleneck.  The
significance of systems like ISDN is that it is *designed* for digital
communication not adapted for it.

Many people (myself included) dialup via voice lines with ~2400 baud
connections to get at their data.  This is obviously a severe
limitation but I have a *vast* array of information available in
comparison to what I could carry around on a portable.  What *I* want
is an ISDN link so that files on the network are available to me as if
they were stored locally on the PC at home.  This is quite practical
now (if a little expensive).

	Tony.
--
Dr. A.J.Travis,                       |  Tony Travis
Rowett Research Institute,            |  JANET: <ajt@uk.ac.sari.rri>
Greenburn Road, Bucksburn,            |  other: <ajt@rri.sari.ac.uk>
Aberdeen, AB2 9SB. UK.                |  phone: 0224-712751
From: rluethy@ulrec2.unil.ch (Roland Luethy)
Subject: Re: Protein structure templates
Organization: University of Lausanne CH (Switzerland)
X-Newsreader: TIN [version 1.1 PL8]
Distribution: bionet
Date: Fri, 22 Jan 1993 08:24:40 GMT

Shai Gozani (gozani@VP3.MED.HARVARD.EDU) wrote:


: Does anybody know of software that creates 3D profiles that
: allows one to match an amino acid sequence against a protein
: structure.  I am specifically interested in the method
: published by Eisenberg and coworkers at UCLA (Luthy et al. in
: Nature vol. 356, 1992 and Bowie et al. in Science vol. 253, 1991).

: Thanks for any help.

: Shai Gozani
: Dept. BCMP
: Harvard Medical School
: gozani@vp3.med.harvard.edu

  Noncommercial users can get the 3D profile programs from Professor David
Eisenberg. Send email to his secretary: KAHLER@UCLAUE.MBI.UCLA.EDU to
get a software license. 

  Best Regards

 Roland Luethy

 Swiss Institute for Experimental Cancer Research
 1066 Epalinges
 Switzerland
From: brent@kite.imgen.bcm.tmc.edu (Brent Wiese)
Newsgroups: bionet.software
Subject: Re: PIMA on SGI
Keywords: protein sequence alignment
Date: 28 Jan 93 17:10:45 GMT
Organization: Baylor College of Medicine, Houston, Tx
NNTP-Posting-Host: kite.imgen.bcm.tmc.edu
Originator: brent@kite.imgen.bcm.tmc.edu


In article <1993Jan27.081224.21491@kakwa.ucs.ualberta.ca>, rndy@wimsey.mmid.ualberta.ca (Randy Read) writes:
> 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

     Yes, your errors can be resolved by a compiler setting.  Since the
code is not ansi but rather K&R C you should tell the compiler this.
The easiest way to do this would be to run ...

	setenv SGI_CC -cckr

... and then run the install.sh file.  Additionally you will want to make
as slight modification to the file make-cluster.sh .  Line number 258 of
make-cluster.sh should read ...

----------------------------------------------------------------
awk '{print NR,$0}' tmp-cluster.$$ | extract-cluster-loci | awk '{print $2}' |
----------------------------------------------------------------

... instead of ...

----------------------------------------------------------------
cat -n tmp-cluster.$$ | extract-cluster-loci | awk '{print $2}' |
----------------------------------------------------------------

     I don't have access to a NeXT system right now so I don't know how
you can tell the C compiler on your NeXT system to expect K&R C, or if
that is even possible.  If you don't have anybody around there that knows
how to tell the NeXT C compiler this, let me know and I will see what I can
do.  Please contact brent@bcm.tmc.edu or rsmith@bcm.tmc.edu if you are
having any further difficulties.

Thanks,
  Brent
-- 
Brent Wiese				Phone:	   713-798-6034
Institute for Molecular Genetics	Fax:	   713-798-5386
Baylor College of Medicine		Internet:  brent@bcm.tmc.edu
Houston, TX 77030  USA
From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Newsgroups: bionet.info-theory
Subject: Re: Animate Nature and Noise
Date: 28 Jan 93 00:27:44 GMT
Distribution: bionet
Organization: Crop Science Dept., NCSU, Raleigh, NC 27695-7620

In article <Pine.3.03.9301271426.J14804-b100000@spock.creare.com> gda@creare.com (Gray Abbott) writes:
>
>
>On 27 Jan 1993, Venkatesh Murthy wrote:
>
>> is interested.  He claims that in a lot of sensory systems, the coding
>> is close to being maximally efficient given the noise and the statistics
>> of naturally occurring stimuli. 
>
>This is what I always heard.  The fully dark-adapted eye in humans can
>detect a single photon; if the ear were more sensitive, it would hear
>Brownian motion, etc.  (I don't have ready references for either of these;
>they were widely accepted beliefs when I was working in perception.)

Well, Gray, I'm supposing that when one puts a large sea shell to the
ear, that roar of the ocean one hears is either Brownian motion or the
noise of blood cells being pumped through the capillaries within the 
ear.  :^)

Steve
---
+------------------------------------------------------------------+
|     In person:  Steve Modena     AB4EL                           |
|     On phone:   (919) 515-5328                                   |
|     At e-mail:  nmodena@unity.ncsu.edu                           | 
|                 samodena@csemail.cropsci.ncsu.edu                |
|                 [ either email address is read each day ]        |
|     By snail:   Crop Sci Dept, Box 7620, NCSU, Raleigh, NC 27695 |
+------------------------------------------------------------------+
         Lighten UP!  It's just a computer doing that to you.    (c)
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: Animate Nature and Noise
Keywords: info theory isothermal noise physical limit receptors
Date: 28 Jan 93 00:45:12 GMT
Organization: Frederick Cancer Research and Development Center

In article <1993Jan27.062112.13859@ncsu.edu>
samodena@csemail.cropsci.ncsu.edu (S. A. Modena) writes:
 
>Animate Nature Operates at or below the Ambient Noise Level
(etc) 
 
That is very interesting!  :-)

Why did you give the summary "Isothermal-ism is a dead end idea"?  One would
EXPECT systems to operate close to the noise, from the theory of molecular
machines!!

|nine bees run through the procedure, the median threshold was 250 
|nanoTelsa (nT, 0.6% of the background field in Hawaii), whereas 

Does anybody have any idea what the magnitudes of the energies
this must correspond to for moving a small particle?

| The fraction of spontaneous events that are generated by spontaneous 
|activation of the G protein is not clear, but for our purposes we 
|can make the worst case assumption that all spontaneous events 
|are due to G protein.  This gives an upper limit on the rate 
|constant for apparent spontaneous nulceotide exchange on G 
|proteins as follows: if there is one spontaneous event per second 
|in a cell with 10^8 G proteins--there are 10^9 rhodopsin 
|molecules per cell and ~ 0.1 G protein/rhodopsin--the apparent 
|rate constant for spontaneous activation of G protein is 10^-
|8/sec.  Remarkably this number is more than three orders of 
|magnitude lower than the the rate of spontaneous nucleotide 
|exchange  measured biochemically for the vertebrate photoreceptor 
|G protein (2 x 10^-5/s).

What exactly is the spontanious nucleotide exchange that they were referring
to?  Is that the rate that GTP exchanges with hot GTP, or is it the rate that
GTP breaks down to GDP?  If it is the former, then I don't understand what the
problem is, as that would not cause an activation.  Also, if it is rhodopsin
which is causing the activation, and that is at 10^-5/s, then there is no
puzzle.  Further, a single activation of rhodopsin have a 100,000 fold greater
effect than G protein (since one rhodopsin activates 100,000 G proteins).  If
one G protein were to activate, perhaps it couldn't trigger an event at all!

|"APPENDIX: Thermal Fluctuations in Concentration
|...  delta-E = 0.5 ( kT/n) delta-n^2  where n = # of molecules

Steve, why did you include this one?

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Newsgroups: bionet.info-theory
Subject: Re: Animate Nature and Noise
Keywords: info theory isothermal noise physical limit receptors
Date: 28 Jan 93 00:23:35 GMT
Organization: Crop Science Dept., NCSU, Raleigh, NC 27695-7620

In article <1k6igvINNeg0@shelley.u.washington.edu> venk@stein.u.washington.edu (Venkatesh Murthy) writes:
>
>
>This subject is quite fascinating.  Much of the ideas that Steve Block
>talks about in that nice little review were presented in another review
>by Bill Bialek in 1987:
>
>Bialek, W.  1987.  Physical limits to sensation and perception.
>Annual Reviews in Biophysics and Biophysical Chemistry. 16:455-478.

Yes, that review is EXCELLENT and every Shannonesque biological information
theorist ought to read it several times.  :^)  What facinates me is
that these researchers never once mention Shannon and information
theory......which I find refreshing because they work at it formulating
pretty much the *same* questions that Shannon must have as he (mentally)
worked out the paradox that a signal could be well below the ambient noise
level, yet be faithfully received....that encoding schemes, mindful of the
statictical distributions of sources of interference, are more powerful
than high signal power....that intuitive guesses about the limit of natural
systems usually quite wrong (in the old sense that resolution limit of
a receptor array was limited by the physical dimensions of the array
elements)......of course, Shannon actually wrote about 'a theory of
communications...in the presence of noise'...and not about information
theory. 

BTW, current trends in DSP (digital signal processing), especially
statistical analysis of random, non-periodic signals, looks like
it will illuminate the kind of work Block, Bialek and the other
sensory people are doing....and probably link in quite will with
neural nets and fuzzy logic.

>
>Bialek's review is good, as is Block's.
>
>I didn't intend this posting to be so fragmentary.  Mostly it was to
>try and get people to start posting stuff again.  Things have been
>uncomfortably quiet lately :-)

Well, my above thoughts are fragmentary also.  :^)  But I see that my
posting brought out a couple of lurkers and it's nice to see that
others admire this sensory stuff too....

>
>-Venki Murthy
>venk@u.washington.edu

Steve
---
+------------------------------------------------------------------+
|     In person:  Steve Modena     AB4EL                           |
|     On phone:   (919) 515-5328                                   |
|     At e-mail:  nmodena@unity.ncsu.edu                           | 
|                 samodena@csemail.cropsci.ncsu.edu                |
|                 [ either email address is read each day ]        |
|     By snail:   Crop Sci Dept, Box 7620, NCSU, Raleigh, NC 27695 |
+------------------------------------------------------------------+
         Lighten UP!  It's just a computer doing that to you.    (c)
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
From: gda@creare.com (Gray Abbott)
Newsgroups: bionet.info-theory
Subject: Re: Animate Nature and Noise
Date: 27 Jan 93 19:12:28 GMT
Distribution: bionet



On 27 Jan 1993, Venkatesh Murthy wrote:

> This subject is quite fascinating.  Much of the ideas that Steve Block
> talks about in that nice little review were presented in another review
> by Bill Bialek in 1987:
> ...

> is interested.  He claims that in a lot of sensory systems, the coding
> is close to being maximally efficient given the noise and the statistics
> of naturally occurring stimuli. 

This is what I always heard.  The fully dark-adapted eye in humans can
detect a single photon; if the ear were more sensitive, it would hear
Brownian motion, etc.  (I don't have ready references for either of these;
they were widely accepted beliefs when I was working in perception.)

The hair cells in the ear are really amazing, as they can detect
displacements much smaller than their physical dimensions (smaller than
most atoms).  The theory I heard (several years ago) was that when the
stereocillia bundle was moved, the shearing of the fibers against their
neighbors opened ion conduction gates; small displacement could cause a
significant shear.  That seemed plausible, but I haven't read the
literature in a few years...