HDTenEightyP/NetNews huggingface dataset:
From: jkirkbride@ASRR.ARSUSDA.GOV ("JOSEPH H. KIRKBRIDE")
Newsgroups: bionet.software
Subject: Latest version of DELTA software available
Date: 10 Nov 92 19:34:00 GMT
Distribution: bionet

The latest version of the DELTA software system from Michael J. 
Dallwitz, CSIRO Division of Entomology, GPO Box 1700, Canberra ACT 
2601, Australia, telephone +61 6 246 4075, FAX +61 6 246 4000, 
Internet delta@ento.csiro.au, is now available as shareware via 
Internet FTP.  To get the DELTA software and associated databases for 
flowering plants, connect via FTP to HUH.HARVARD.EDU using the id FTP 
and the password FTP.  The DELTA software is now available for three 
different operating systems: 

  /PUB/SOFTWARE/DELTA/MSDOS
    DELTA programs for MS-DOS operating system on IBM-compatible 
      microcomputers.
  /PUB/SOFTWARE/DELTA/OS2
    DELTA programs for OS2 operating system on IBM-compatible microcomputers.
  /PUB/SOFTWARE/DELTA/SUNOS
    DELTA programs for the SUN operating system.
There are two databases available ready use with the DELTA software 
(INTKEY) for identification of organism or querying for information. 
  /PUB/SOFTWARE/DELTA/ANGIO
    Families of flowering plants of th
e world with emphasis on Australia.
  /PUB/SOFTWARE/DELTA/GRASS
    Genera of grasses of the world.
In addition there are a number of shareware programs for MS-DOS stored in:
  /PUB/SOFTWARE/DELTA/GRAHICS
These programs are very useful in preparing graphic images for use 
with the DELTA software. 
 
Joseph H. Kirkbride, Jr.
USDA, Agricultural Research Service
Systematic Botany and Mycology Laboratory
Building 265, BARC-East                          Voice telephone: 301-504-9447
Beltsville, Maryl
and 20705-2350 USA      Internet: JKIRKBRIDE@ASRR.ARSUSDA.GOV
From: bsh@MED.PITT.EDU (Basavaraju Shankarappa)
Newsgroups: bionet.software
Subject: pub domain software for rearranging frag disk
Date: 12 Nov 92 18:22:05 GMT
Distribution: bionet


Hello netters:

	Can any one tell me whether and where I can get a public domain
software for correcting the fragmented disk space.  I was told that
some of the programs that can do the job are COMPRESS,  SPIN-WRITE
DISK OPTIMIZER etc.,  I am looking for a public domain software
that can do the job above programs can do.

	Thank you for considering the request.
Raj Shankarappa
Univ of Pittsburgh
bsh@med.pitt.edu
From: jkirkbride@ASRR.ARSUSDA.GOV ("JOSEPH H. KIRKBRIDE")
Newsgroups: bionet.software
Subject: Latest version of DELTA software available on Internet via FTP
Date: 12 Nov 92 12:02:00 GMT
Distribution: bionet

The latest version of the DELTA software system from Michael J. 
Dallwitz, CSIRO Division of Entomology, GPO Box 1700, Canberra ACT 
2601, Australia, telephone +61 6 246 4075, FAX +61 6 246 4000, 
Internet delta@ento.csiro.au, is now available as shareware via 
Internet FTP.  To get the DELTA software and associated databases for 
flowering plants, connect via FTP to HUH.HARVARD.EDU using the id FTP 
and the password FTP.  The DELTA software is now available for three 
different operating systems: 
  /PUB/SOFTWARE/DELTA/MSDOS
    DELTA programs for MS-DOS operating system on IBM-compatible 
      microcomputers.
  /PUB/SOFTWARE/DELTA/OS2
    DELTA programs for OS2 operating system on IBM-compatible microcomputers.
  /PUB/SOFTWARE/DELTA/SUNOS
    DELTA programs for the SUN operating system.
There are two databases available ready to use with the DELTA software 
(INTKEY) for identification of organism or querying for information. 
  /PUB/SOFTWARE/DELTA/ANGIO
    Families of flowering plants of the world with emphasis on Australia.
  /PUB/SOFTWARE/DELTA/GRASS
    Genera of grasses of the world.
In addition there are a number of shareware programs for MS-DOS stored in:
  /PUB/SOFTWARE/DELTA/GRAHICS
These programs are very useful in preparing graphic images for use 
with the DELTA software. 
 
Joseph H. Kirkbride, Jr.
USDA, Agricultural Research Service
Systematic Botany and Mycology Laboratory
Building 265, BARC-East                          Voice telephone: 301-504-9447
Beltsville, Maryland 20705-2350 USA      Internet: JKIRKBRIDE@ASRR.ARSUSDA.GOV
From: Bo.Servenius@wblab.lu.se (Bo Servenius)
Newsgroups: bionet.software
Subject: The program Amplify for PCR design - where can I find it???
Date: 10 Nov 92 01:22:49 GMT
Organization: Lund University, SWEDEN
X-Useragent: Nuntius v1.1

Dear Netters:

Have heard about a program Amplify for designing of PCR primers.
Is it a freeware/shareware and if so where can I find it for FTP???

yours

BOSSE
From: bwilliam@oyster.smcm.edu (Bill Williams)
Newsgroups: bionet.software
Subject: Re: HELP: .HQX Format for Macs
Date: 13 Nov 92 20:58:05 GMT
Organization: St. Mary's College of Maryland
X-UserAgent: Nuntius v1.1.1d10
X-XXMessage-ID: <A7299013780201D2@williams.smcm.edu>
X-XXDate: Fri, 13 Nov 92 22:02:11 GMT

In article <1992Nov9.190919.12960@cs.mun.ca> Harold Wareham,
harold@odie.cs.mun.ca writes:
>I recently obtainted a Macintosh file in .HQX format from the UIBio
>archives. I need a copy of BinHex 4.0 or Stuffit to uncompress and
>use the thing. Where can I obtain copies of either of these
>programs?

For anyone with a Mac but unfamiliar with the downloading conventions
for Macs, I highly recommending downloading a number of very
informative files (in text format, hence not requiring any fancy
programs) at sumex-aim.stanford.edu in the directory /info-mac/reports.
 I don't have the specific names of the files handy, but looks for
things like FTP-site directories, FTP how-to, etc.  As I recall the
reports are well written and direct.
___________________________________
William E. Williams, bwilliam@oyster.smcm.edu
Divison of Natural Sciences and Mathematics
St. Mary's College of Maryland
St. Mary's City, MD 20686
Newsgroups: bionet.software
From: uvsmr@Msu.oscs.montana.edu (Matt Rognlie)
Subject: Software for PC scanners
Reply-To: uvsmr@Msu.oscs.montana.edu (Matt Rognlie)
Organization: Montana State University
Date: Thu, 12 Nov 1992 20:13:00 GMT

We would like to purchase a flatbed scanner (i.e. HP ScanJet) to use
with a DEC 486.  Is there software available which would allow us to
use the scanner as a densitometer?  We want to scan autoradiograms or
gels, but be able to get density data so that bands can be compared.
Any suggestions on the latest scanner technology would also be 
appreciated.
Thanks for your help.
Matthew Rognlie                  |
Veterinary Molecular Biology     | uvsmr@trex.oscs.montana.edu
Marsh Lab                        | phone: 406-994-6379
Montana State University         |   FAX: 406-994-4303
Bozeman, MT  59717-0360          |
From: kjm@buc.edu.au (Kevin Moore)
Newsgroups: bionet.info-theory
Subject: Re:  Question on entropy at 0K (was Re: Tom's Test Thu Nov  5 17:22:37 EST 1992)
Date: 11 Nov 92 15:27:59 GMT
Distribution: bionet

Actually, if I recall Tom's original article, he looked up the entropy of 
copper in his CRC tables, for which values are tabulated for temperatures
between 1K and 300K in 1K steps. They appear to have been calculated for
standard pressure, for a constant pressure process. (At least as far as I
could make out from the somewhat cryptic introduction) So the thermodynamic
system being described in his table has (T,P) information used to describe
the state. More complicated system information, say, involving the copper
under strain, rather than a uniform pressure, wouldn't be describable using
this entropy.

I never quite understood the relevance of the 0K business, so I didn't
venture a reply to it. We were in the middle of some argument about
anthropomorphism, as I recall.

Cheers,

Kevin.

kjm@eureka.buc.edu.au
From: mroussel@alchemy.chem.utoronto.ca (Marc Roussel)
Newsgroups: bionet.info-theory
Subject: Re: Question on entropy at 0K
Keywords: entropy of Cu
Date: 13 Nov 92 02:37:16 GMT
Organization: Department of Chemistry, University of Toronto

In article <6734@m1.cs.man.ac.uk> mshute@cs.man.ac.uk (Malcolm Shute) writes:
>I was happy with this... but then you mentioned these CRC tables, and I was
>confused... they seem to be tables of absolute static entropy for Copper at
>various temperatures.  I don't understand!
>How can you say: "This 63.5g lump of copper at 1K has 'x' units of entropy"?

     This part is easy to explain.  Let's suppose that we all believe
the third law and, in particular, that the entropy of copper at 0K is 0.
We can calculate the change in entropy of copper due to heating it up
from 0 to whatever temperature we want.  (All we need is the heat
capacity of copper as a function of temperature.  The calculation itself
is straightforward.)  Now since S(Cu,0K) = 0, S(Cu,T) = Delta S(Cu,0K -> T)
since S is a state function and therefore an exact differential.
     In fact, it's even better than that.  Delta S = -d(Delta G)/dT so
if you know the entropy of a few substances and some Delta G's, you can
infer a bunch more S's.  Also, statistical mechanics tells us how to
compute S from spectroscopic data.  Sometimes, entropies will be available 
by more than one method.  Most of the time, they agree.  When they
don't, you can usually trace the difficulty back to the third law and
the assumption that S(0K) = 0.

>Surely the amount of entropy in a substance (like the potential energy) depends
>on how deep you are prepared to look into it...
>This particular lump has 6.024e23 atoms to arrange in an imperfect lattice,
>so there's one source of entropy... the amount of information needed to specify
>that arrangement.
>But... 63.5g of Cu can also be thought of as being a lump of
>(29+29+34.5)*6.023e23
>(i.e. 5.57e25) atomic particles... and they require somewhat more information
>to specify as a structure.
>But... 63.5g of Cu can also be viewed as 1.67e26 quarks...
>But... 63.5g of Cu can also be viewed as n*1.67e26 sub-quark particles which we
>haven't even discoved the existance of yet...!

     To this day, I don't really understand this sort of information
theoretic argument.  I just think of entropy as something we get from
calorimetry :-).

				Marc R. Roussel
                                mroussel@alchemy.chem.utoronto.ca
From: hybl@umbc4.umbc.edu (Dr. Albert Hybl (UMAB-BIOPHYS))
Newsgroups: bionet.info-theory
Subject: What is a "perfect" crystal?
Summary: An example for the Chowder Society
Keywords: Entropy Twinning Disorder
Date: 12 Nov 92 17:15:56 GMT
Organization: Univ. of MD, Baltimore County

In Acta Crystallographica Vol. B27, Part 5 May 1971 pages
977-986, (1971), D Dorset & A Hybl reported "The Crystal Structure
of the 1,3-Diglyceride of 11-Bromoundecanoic Acid."  We
described the disorder in solvent crystallized DBU as "entropy
twinning."  Let me quote the germane section:

(iv) Disorder as entropy twinning
  "Though glycerol possess reflective symmetry in that it can
be superimposed on its mirror image, glycerol does not possess
rotation symmetry.  This rotational asymmetry does not give rise
to optical antipodes, but does allow a distinction to be made
between the two primary hydroxyl groups [GB Ansell & JN Hawthorne
(1964) Phospholipids, p 404-407 Amsterdam: Elsevier] as
shown below:

      CH2OR               CH2OR          (below plane)
      .                   .
      .                   .
   HO-C-H     and       H-C-OH
      .                   .
      .                   .
      CH2OR               CH2OR          (below plane)
  (a)                 (b)

The disorder results from the competitive occupancy for each
site by rotational isomers (a) and (b). 
  "The disorder may be described as a form of entropy twinning.
By analogy to twinning my merohedry, the space group of an
untwinned crystal would be Cc; any of the additional symmetry
elements of the space group C2/c can be used randomly as twin
elements to relate a pair of molecules."


Furthermore, the fatty acid chains in DBU exhibit a 34 degree
helical twist; they are not "perfectly planar" extended-trans
hydrocarbon chains.

Comments from the 0K Corral?
  Is the entropy disordered crystal more "perfect" than the
hypothetical untwinned crystal?  Who or what defines "perfect?"  

=================
PS. For those not familiar with the extreme polymorphic
behavior of lipids, let me suggest that you read:
JT Joseph, A Hybl, & JH Flynn (1978). "Differential Scanning
Calorimetry Studies of some Analogs of the lipid Component of
Biological Membranes," in Chemistry and Physics of Lipids,
Vol. 22 pages 239-243.
Newsgroups: bionet.info-theory
From: ahouse@HYDRA.ROSE.BRANDEIS.EDU
Newsgroups: bionet.info-theory
Subject: Re: Question on entropy at 0K
Date: 10 Nov 92 18:04:06 GMT
Distribution: bionet

>     Now if you cool copper to 0K, it should form a perfect crystal
>PROVIDED THAT YOU COOL IT SUFFICIENTLY SLOWLY.  If you don't, you could
>get any number of imperfections "frozen in" (that is the usual jargon)
>and thus almost any number for the entropy.
>
        . . .

>                                Marc R. Roussel
>                                mroussel@alchemy.chem.utoronto.ca

        Couldn't you also wait long enough (infinite time?) so statistical
fluctuations provide a "perfect" crystal?  Or is the claim here that the
perfect crystal state is completely inaccessible from the "frozen in"
imperfections?

        - jeremy

        	:::::::::::::::::::::::::::::::::::::::::::
        	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
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: Question on entropy at 0K
Keywords: entropy of Cu
Date: 10 Nov 92 18:23:19 GMT
Organization: Frederick Cancer Research and Development Center

In article <6697@m1.cs.man.ac.uk> mshute@cs.man.ac.uk (Malcolm Shute) writes:
>Tom, you're back!

:-)

>I said that I was therefore confused as to what it was that you had consulted
>in your tables on entropy of copper.

Pull out your CRC and look up entropy entries.  You'll see the data there.
Other folks posted answers to the other parts of your question.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: mroussel@alchemy.chem.utoronto.ca (Marc Roussel)
Newsgroups: bionet.info-theory
Subject: Re: Question on entropy at 0K
Date: 13 Nov 92 15:52:21 GMT
Distribution: bionet
Organization: Department of Chemistry, University of Toronto

In article <9211130508.AA26254@eureka.buc.edu.au> kjm@buc.edu.au (Kevin Moore)
writes:
>In article <9211130141.AA00630@net.bio.net>
>mshute@cs.man.ac.uk (Malcolm Shute) writes:
>> So... really, my initial question was "What are these CRC tables able to
>>state"?
>
>The entropy of a perfect crystal at a particular temperature, and standard
>pressure, under a particular model (which doesn't include subatomic
>particles to my knowledge.) 

     No.  The tables are determined experimentally.  If the work is
properly done and we're talking about a crystalline solid, the tabulated
entropy is that of a well-annealed (but likely not perfect) crystal of
high purity at a specific temperature and pressure (usually 298K and
1 atm).

>> A 58.4g lump of NaCl at 0K would then be indistinguishable from a 23g lump
>> of Na lieing beside a 35.4g lump of Cl.  Is this correct?

     They would have the same entropy (0 = 0+0), but entropy is not the
only state function.  The two systems would have different internal
energies, different enthalpies, etc.  They would not be
indistinguishable.

				Marc R. Roussel
                                mroussel@alchemy.chem.utoronto.ca
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: Tom's Test Thu Nov  5 17:22:37 EST 1992
Keywords: test posting, crossed fingers
Date: 5 Nov 92 22:30:18 GMT
Organization: Frederick Cancer Research and Development Center

With any luck this message will FINALLY bother everybody on the chowder group!
This is yet another test to see whether posting is working on this
news group.  Please email me if I contacted you by email before.  Thanks!
  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
Newsgroups: bionet.info-theory
From: mroussel@alchemy.chem.utoronto.ca (Marc Roussel)
Subject: Re: Entropy at 0K
Organization: Department of Chemistry, University of Toronto
Distribution: bionet
Date: Tue, 10 Nov 1992 17:44:01 GMT

In article <9211101510.AA04425@shiva.psu.edu> zauhar@SHIVA.PSU.EDU
(Dr. Randy Zauhar) writes:
>  The entropy of a system is related to the volume of phase space it 
>occupies. A perfect crystal and a disordered structure both occupy the 
>same phase space volume (ignoring zero-point energy) at 0K - namely 
>ZERO. Why then don't they both have the same entropy (what does the
>particular arrangement of atoms have to do with anything?)

     I think I know what you're getting at (in fact I think this is one
of the paradoxes that lead to Q.M. in the first place) but perhaps you
could flesh out the phase space argument to make sure that we are all
talking the same language.  If you would construct the phase space whose
volume has a simple relationship to the entropy and point out this
relationship, we should be able to clear this up quickly.
     The stock answer of course is that the statistical definition of
entropy tells us that, for a microcanonical ensemble, S vanishes only if
the number of microscopic configurations yielding the ensemble energy
reduces to one.  (A minor quibble:  Is a crystal at 0K a member of a
microcanonical ensemble?  I don't know but the only other reasonable
ensemble to which such a crystal could belong, the canonical ensemble,
also has statistics which suggest that S vanishes only if the number of
configurations reduces to 1.  I'm inclined to think that systems at 0K
should really be members of microcanonical ensembles since a canonical ensemble
requires a heat bath and I can't easily conceive of a 0K heat bath.)
The arrangement of the atoms certainly matters in counting the
microscopic configurations.  For an example with both calculations and
experimental results, consult Moore's "Basic Physical Chemistry"
(Prentice-Hall, 1983), pp. 139-140.

				Marc R. Roussel
                                mroussel@alchemy.chem.utoronto.ca
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: On test postings
Date: 6 Nov 92 18:15:57 GMT
Distribution: bionet
Organization: Frederick Cancer Research and Development Center

In article <Nov.6.10.01.29.1992.14207@net.bio.net> shibumi@net.bio.net writes:
>If you need to test whether postings to a bionet. group are working at
>your site, please try to change the 'Distributions' line (which you are
>queried to set) to 'local' or to something like a local domain.  This
>won't help you if you are a mailing list gateway (like IG), but it will
>help cut down on postings going to other sites, and the mailing lists, that
>are of no interest to them.

Sorry.  Normally we would do this.  However, there were several problems.
Postings LOOKED like they had gone out on the net, but they never really left
our site.  This happened to the FAQ sheet.  It took me two weeks to realize
this was happening!  Part of the trouble was here in the news programs, and
part was in the computer which takes our feed, which has been down.  Postings
to misc.test worked (with the bounce back from all those places), but NOT to
bionet.info-theory!  The only way to test was to do it directly and have real
people respond.  Sorry to bother everybody, but you never saw the 3 or so
messages before the one that finally went out!!  BACK TO INFO-THEORY!  Tom
Newsgroups: bionet.info-theory
From: mroussel@alchemy.chem.utoronto.ca (Marc Roussel)
Subject: Re: Question on entropy at 0K
Keywords: Pinheads PseudoScience FlameThrowers Reality-check 
Organization: Department of Chemistry, University of Toronto
Distribution: bionet
Date: Wed, 11 Nov 1992 15:10:07 GMT

In article <1992Nov11.123056.16262@ncsu.edu> samodena@csemail.cropsci.ncsu.edu
(S. A. Modena) writes:
>You are all so @#$%@&#$*@^ stupid!
>
>Entropy is a measure of a DYNAMIC process/system; no dynamics? ==> H(x) = 0!

     That's wrong.  (If you're going to be rude, I reserve the right to
be blunt :-).)  The state functions of classical thermodynamics are
undefined for dynamic processes.  Classical thermodynamics is a theory
of equilibrium states.  The contortions one has to go through to
rigorously extend it to a theory of nonequilibrium states are not
entirely satisfying.
     It is true that we can generally only measure the change of entropy
during a process, but that doesn't mean that the entropy is undefined in
equilibrium states.  Quite the contrary.

				Marc R. Roussel
                                mroussel@alchemy.chem.utoronto.ca
Newsgroups: bionet.info-theory
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Subject: Re: human mind, an ergodic source?
Organization: Frederick Cancer Research and Development Center
Distribution: usa
Date: Thu, 5 Nov 1992 23:45:36 GMT

In article <1992Oct27.164431.5092@athena.mit.edu> makra@athena.mit.edu
(Mohamad A. Akra) writes:

|Does anyone know if there has been any work justifying (or criticizing)
|the modeling of the human mind as an ergodic process? where ergodic
|means, in plain terms, that the model parameters can be estimated from
|observing the output over some time, using the law of large numbers.

That's an interesting thought.  My understanding is that the 'parameters' are
the probabilities of the states.  That is, if a system is ergodic (or fits the
ergodic theorem, help, someone!) then one can follow it over time (infinite!)
and this will tell you the probabilities of states; those will be the same as
if one had set up a series of parallel systems and looked at one instant
(infinite number of parallel systems).  Brownian motion is ergodic (my
understanding, please correct as needed), as one can do this and get the
Gaussian distribution either way.

So if the mind were ergodic, it would mean we couldn't change with time, hence
we couldn't learn!  So the question is whether, excluding learning, one can
look at large numbers of organisms to obtain data about how a single organism
may act (or the other way around).  Curious and interesting.  Sounds like
behavioral population genetics on the fruit fly Drosophila!

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: zauhar@SHIVA.PSU.EDU (Dr. Randy Zauhar)
Newsgroups: bionet.info-theory
Subject: Entropy at 0K
Date: 10 Nov 92 15:10:01 GMT
Distribution: bionet


  Regarding Keith Robison's posting - 

  The entropy of a system is related to the volume of phase space it 
occupies. A perfect crystal and a disordered structure both occupy the 
same phase space volume (ignoring zero-point energy) at 0K - namely 
ZERO. Why then don't they both have the same entropy (what does the
particular arrangement of atoms have to do with anything?)

  Randy Zauhar
  Penn State

Newsgroups: bionet.info-theory