HDTenEightyP/NetNews huggingface dataset:
From: acc@asterix.inescn.pt (Antonio Costa)
Subject: Image synthesis package (RTrace version 8.0.0)
Keywords: ray tracing, molecular rendering
Organization: CG & CAD - INESC Norte
Date: Thu, 10 Sep 92 15:36:22 GMT


There is a new version of the RTrace ray-tracing package (8.0.0) at
asterix.inescn.pt [192.35.246.17] in directory pub/RTrace

****************************************

The MAC port is being prepared to be released by Reid Judd 
(reid.judd@east.sun.com) and Greg Ferrar
(gregt@function.mps.ohio-state.edu).
A working version will be available shortly!

****************************************

Enhancements were done since version 7.3.2, mainly:

1. It has no limit on the number of objects to render (there is a
command line option to control it; scenes with up to 1000000 have been
rendered!).
The same applies to light sources and surfaces.

2. It is now possible to produce animation fly-throughs easily. The scene is
read only once and successive images are produced. There are new command
line options to specify it. The fly-throughs may be controlled by the
EYE and LOOK points, the UP vector and the APERTURE angles.
All there is to do is just create a text file with the numbers and give
it to the program...


The support programs 'nff2sff', 'nffclean' and 'nffp2pp' have been
enhanced to support unlimited number of objects, etc.


****************************************

Here goes a short description of current converters from
molecular/chemistry packages to the SCN format.

The package programs are related as below (those marked with * have been
modified)

	        irit2scn
	IRIT -------------|
                          |               NFF (nffclean*, nffp2pp*)
	         sol2scn  |                |
	ACAD11 -----------+                | nff2sff*
                          |                |
	      mol2scn	  v    scn2sff     v	rtrace*
   ALCHEMY  -----------> SCN -----------> SFF ----------> PIC or PPM
			  ^      cpp
	        pdb2scn   |
	PDB --------------|
			  |
	       chem2scn   |
   CHEMICAL --------------|

****************************************

The DOS port of RTrace is in pub/RTrace/PC-386 (rtrac800.arj and
utils800.arj). See the README file.
Requires DJGPP GO32 DOS extender (included), which can be found in
directory pub/PC/djgpp (and in many sites around netland).
There are also demo scenes, manuals and all the source code...

****************************************

Please feel free to get it and use it.
Hope you like it.

Regards,
Antonio Costa.
.........................................................................
     O     O
    /     /                        I N E S C
   | O   |        Antonio Costa        | E-Mail   acc@asterix.inescn.pt
   | |\  |   O                         |          acc@basinger.inescn.pt
   | | \ |  /  O  Comp. Graphics & CAD | DECnet   inescn::a_costa
   | |  \| /  /                        | VAX-Mail +26802001576::a_costa
   | |  /  | |    Largo Mompilher 22   | UUCP     {mcvax,...}!...
   O | |-O | |    4100 Porto PORTUGAL  | Bell     +351+02+321006
    /   \ /   \
   O     O     O          "Let the good times roll..."


Newsgroups: bionet.software
From: parker@cpsc.ucalgary.ca (Jim Parker)
Subject: Computer vision
Organization: University of Calgary Computer Science
Distribution:  World
Date: Fri, 4 Sep 1992 15:16:24 GMT

I am currently working on a book on computer vision, the target audience
being scientists and science students in areas other than computer science.
It concentrates on shape, useful grey level enhancements, and practical
examples. It should be out by next summer (Wiley).

There has been a good deal of interest from individuals working in
biological and medical areas, so I thought I would ask 'what specific
information would you like such a book to include?' The last three chapters
are basically all examples and case studies, and while I have them sketched
I would be happy to add new material if it would make the book more useful.
I am trying to keep the math level reasonable, and am including source
code with the book (diskette + listings).

If you have some special interest, please let me know. Thanks.


	Jim Parker
	Space Information Science Group		(403) 220-6784
	Department of Computer Science		(403) 220-6015
	University of Calgary			(403) 284-4707  [FAX]
	Calgary, Alberta, CANADA	parker@cpsc.ucalgary.ca  [internet]
	T2N-1N4
----------------------------------------------------------------------------
From: BIONET@FRCGM51.EARN
Newsgroups: bionet.software
Subject: Re: HCA Plot
Date: 15 Sep 92 16:08:00 GMT
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"


 
        As mentioned in a recent posting, there is indeed an implementation
of HCA Plot in DNAid. I use it and it works (output in Postscript on a
LaserWriter).
        You can also get commercial programs at the following address:
 
        DORIANE S.A.
        16 rue Julien Poupinet
        78150 Le Chesnay France
 
        Tel: (33-1) 39-63-34-44
 
        Fax: (33-1) 39-55-57-82
 
There is one version for the Mac and one for PC-Windows. The cost for non-
profit organizations is 900 FF (about $180). These programs are quite
recent, I did'nt try them.
 
Hope it helps.
Standard disclaimer .....
 
   ---------------------------------------------------------------
  | J-L. Risler                         |                         |
  | CNRS                                |  Bionet@frcgm51.bitnet  |
  | Centre de Genetique Moleculaire     |  Risler@frcgm51.bitnet  |
  | 91190 Gif sur Yvette   France       |                         |
   ---------------------------------------------------------------
Newsgroups: bionet.software
Subject: Re: REQUEST: INFO ON MEDLARS & TOXNET
From: nholford@ccu1.aukuni.ac.nz (Nick Holford)
Date: Sun, 6 Sep 1992 22:02:12 GMT
Distribution: bionet
Organization: University of Auckland, New Zealand.

ABOLA@PB1.PDB.BNL.GOV writes:


>Get in touch with 

>	MEDLARS Management Section
>	National Library of Medicine
>	Bldg. 38A, Rm 4N421
>	8600 Rockville Pike
>	Bethesda, Maryland 20894

>	(800) 638-8480

>They will send you an information packet describing their databases
>and how to access them.  I have not seen anything about internet access 
>in their literature.   
The Medline section at the NIH can be contacted by mail at:
	Tilley@lhc@nlm.nih.gov
This is a person named Carolyn Tilley ( Phone 301-496-6193).
I understand that the Medline/Medlars group are very encouraging about
Internet access. However, NZ has been granted access via the Dept of 
Health which is currently a roadblock to users here because they are
the official source for local passwords and claim not to have any
to distribute!

> 
> 
>enrique
-- 

Nick Holford, Dept Pharmacology & Clinical Pharmacology
University of Auckland, Auckland, New Zealand
INTERNET: n.holford@aukuni.ac.nz
From: tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman)
Newsgroups: bionet.info-theory
Subject: More wacky theory
Date: 8 Sep 92 20:03:04 GMT
Distribution: bionet
Organization: University of Utah, CompSci Dept

Hello,

  This is a continuation of the philosophy of information (of the wacky
theory).  There have not been any responses on the net system, but I have
gotten some interesting comments in the mail.  Therefore, I am going to
present the theory from a different vantage point, to try to generate more
criticism.

  Information is directly linked to causality.    If I cause something,
I am "informing" the event.  That which is information will cause future
effects.  The information content of the universe at the present
is a reflection of past causal actions.  

Examples:

  An individual consists of many memories and experiences, and each of those
things which influence them in some way "inform" that person.  The culture
as a whole represents a great deal of past experiences and developed 
attitudes, all of which are part of its information.

  Events which propagate themselves forwards through time are information,
and those that do not are lost information.  A piece of DNA represents 
many random mutations, and those which survive are information in the
future.  Events can be remembered by an organism through behavioral
inheritence (for more complex organisms) as it passes on lessons learned
to its offspring.

  The very first events in the universe which propagated themselves forwards
were quantum fluctuations in the original hot plasma.  These created density
inhomogeneities which allowed for (or precipitated) the formation of the
galaxies and star systems.  The universe became more complex because of the
formation of the stars, and these initial informational events have lasted
through to the visible sky today.


  Thus information can be seen as relics of the past- past events that have
propagated forwards through to today.  Quantum events become fossilized
in the dynamics of information flow, and we live in a projection of the past.
Of course, most of the creative activity has not occurred yet, and the
information is likely to rise much higher.  Most of the information being
generated at any point (mutations, bad books, bad ideas) dissolve as they
are forgotten, and unfortunately some "poor quality" information survives
anyway, such as outdated tradition.

  Information is that which informs the future, although someone in the
present can not know what will happen, a person can look backwards and see
the creative acts of the past and actually "measure" it.  This then would
be the informational content of the universe.

 Tommy tom T
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: More wacky theory
Date: 10 Sep 92 18:53:37 GMT
Distribution: bionet
Organization: Frederick Cancer Research and Development Center

In article <6049@m1.cs.man.ac.uk> mshute@cs.man.ac.uk (Malcolm Shute) writes:

>In article <1992Sep8.140304.24664@hellgate.utah.edu>
tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman) writes:

>>  Events which propagate themselves forwards through time are information,
>>and those that do not are lost information.

>So... gaining and losing information come at the same cost? and in fact
>occur simultaneously?  (A flip-flop which is being 'set' at this moment
>is gaining the information of what I want it to store, but is destructively
>overwriting its old contents).

That's an interesting point.  Following the definition I normally use, the
information in a flip-flop will be lost as one supplies energy to it (eg.
priming the molecular machine, flipping a coin into the air).  Then when it is
set to the new state (molecular machine operation, coin lands or is set down),
it gains information.  One doesn't directly overwrite simultaneously.  The gain
is not the same as the loss.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
Newsgroups: bionet.info-theory
From: tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman)
Subject: Re: More wacky theory
Date: 9 Sep 92 17:20:31 MDT
Organization: University of Utah, CompSci Dept
Distribution: bionet

>Ok, since you asked for it, get ready for this pie in the face ... :-)
>
>Numbers.  How do you measure information?

Glad you asked.  The information of a system is equal to the minimal number
of nondetermined events required to reach a specified state.  This does
imply that one knows the initial and final state, and it works out quite
nicely with cellular automata. This is very similar to Kolmogrov's notion
of complexity, although he confined it to sequences of numbers.  If one
were to use this conception of information and apply it to sequences it
would have the same measure as Kolmogrov's.  A universal Turing machine
"attempting" to produce a sequence would first nondeterministically spit
out the Kolmogrov sequence, and then utilize this as its input.  This would
be the minimal number of nondetermined transitions to produce the sequence.

The initial state of the universe is somewhat questionable, but if it was
a space-time singularity then no information came in from before it and it
was a relatively simple place.  It had zero information.  Today's measure
of entire information would only be able to be approximated however.

One might wish to consider the change in information during relative
periods of time (of known states)  For example, if the DNA of forms
could be approximated for various times (such as before the eukaryotic
explosion) then the amount of new knowledge of todays forms could be
measured. (minimal mutations to reach expressed DNA of extant forms)

This is not to say that Shannon's measure is incorrect at all- it has
very useful and accurate applications to channel theory.  However, if one
is attempting to define the information to an entire (ergodic?) system,
Shannon's does not appear to be applicable.  This is an alternative,
although at this point it is still somewhat speculative.
From: madavis@nmsu.edu (Mark Davis)
Subject: Re: More wacky theory
Organization: Computing Research Lab
	<1992Sep9.172031.6002@hellgate.utah.edu> <3877@fcs280s.ncifcrf.gov>
Distribution: bionet
Date: Fri, 11 Sep 1992 21:13:16 GMT


   In article <1992Sep9.172031.6002@hellgate.utah.edu>
   tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman) writes:

   >>Numbers.  How do you measure information?
   >

The Chaitin/Kolmogorov extensions to Shannon's theory illustrate the
value of a complexity measure as a measure of a system's information.

It is admittedly abstracted to generalized machines, but is prolly
a good starting point as it avoids the kind of fuzziness one finds
in most other measures.  The Chaitin formulation involves
subdividing a region of space into small d-diameter spheres, each
of which is sufficiently small that the segment of the system
encompassed by the sphere is representable only by itself (there
is no redundancy in form).  A higher-order map of interactions
between these spheres (formulated again as a Turing machine) is then
added-in.  Voila.  A complexity measure.

One complaint about the Chaitin/Kolmogorov measure is that it gives
bigger numbers when the system is more random (in Chaitin's sense;
not reducable to a simpler representation).  The intuitive notion
about complexity is that a completely uniform material should have
low complexity and a highly disordered material should also have
low complexity.  It is only a tenuous intermediate that should
receive high marks for complexity.  An approach by Hubermann and Hogg
normalizes the measure with a measure of maximum complexity for
a class of same-size systems, thereby providing precisely the
desired spectrum.

Another complaint is that there were several problems in the first
paper on this, which were subsequentally corrected but at a cost
in readability.

mark

--
*************************************************************
***   M. W. Davis,             madavis@NMSU.edu           ***
*************************************************************
***       "Crap and Art still toiling together"           ***
*************************************************************
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: More wacky theory
Date: 10 Sep 92 19:47:48 GMT
Distribution: bionet
Organization: Frederick Cancer Research and Development Center

In article <1992Sep9.172031.6002@hellgate.utah.edu>
tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman) writes:

>>Numbers.  How do you measure information?
>
>Glad you asked.  The information of a system is equal to the minimal number
>of nondetermined events required to reach a specified state.

I don't know what "nondetermined" means.  Please define.

"to reach a specified state" seems to imply that you want some kind of state
function.  So there must be a "before" state and an "after" state.  Or do I
misunderstand?

"minimal number of nondetermined events":  This does not seem to be counting
the number of choices being made in each event.  That is, it is not correlated
with the entropy change needed to construct the object.  The units are not in
bits.  So what are the units?  Can you give an example on a small physical
system?  (Not the whole universe for pete's sake!)  For example, I take 100
coins out and set them down all heads up.  How much information is in (or have
I put into) this system according to your measure?  100?  100 what?  (Not bits,
you've rejected that apparently.)  Suppose I take 100 dice and put them down
all with 1 dot facing up.  How much information is in that system?  100?  600?
Certainly not 100*log_2(6) = 258.5 bits; you've rejected that.

So:  Numbers and discrete small examples please.

Also, how your measure is better than measuring things in bits.  Finally, some
good excuse for the fact that you can't add independent events together to get
the total "information".  (Only Shannon's measure allows that.)

>This is not to say that Shannon's measure is incorrect at all- it has
>very useful and accurate applications to channel theory.  However, if one
>is attempting to define the information to an entire (ergodic?) system,
>Shannon's does not appear to be applicable.  This is an alternative,
>although at this point it is still somewhat speculative.

I don't see WHY you want to know the "information" of a whole system.  If you
get a number, what are you going to DO with it?  Can you predict what it should
be (and so set up a scale)?  Years ago people cooked up a measure of the
"complexity" of a bacterial cell.  Nobody (even me) remembers those papers -
it's useless stuff.  So could you state why you are interested in measuring the
information content of the universe?  ("I need a thesis" is not sufficient!!
:-)

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: tolman%mindblow.cs.utah.edu@cs.utah.edu (Kenneth Tolman)
Subject: Re: More wacky theory
Date: 10 Sep 92 21:50:42 MDT
Organization: University of Utah, CompSci Dept
Distribution: bionet

[some interesting questions which will be addressed at a later point]

>I don't see WHY you want to know the "information" of a whole system.  If you
>get a number, what are you going to DO with it? 
>So could you state why you are interested in measuring the
>information content of the universe?  ("I need a thesis" is not sufficient!)

I began to pursue this question because something is going on in the universe-
life forms have evolved from almost nothing to incredibly complex things,
and now culture is advancing like crazy.  I wanted to know what was going
on, for the PURE SAKE OF KNOWLEDGE.

Now, if the theory is correct, then it has certain implications.  

1. An epistemology of ethics can be constructed, giving foundations to human
   rights. (if you study ethics, it really has no good foundation)

2. It means that our current rate of technological growth is stunted, because
   we are not tapping the informational capabilities of our universe.  Our
   computers are technologically inferior to what is capable of being made.
   The artificial intelligence community would be barking up a dead tree.

As for the actual NUMBER, it means nothing- you are right, who cares about
the number.  What matters is the mechanism- and we can use that mechanism
to our own advantage, and make truly creative and spontaneous machinery.  In
the long run that will pay off with technologies and applications.

Perhaps though- that number will actually be valuable for considering 
sub systems of the larger system (such as messages, transfer RNA, and so on)
But I donnow about that, I've been looking at that seriously and it would
require some major thought.  Too much for a measly masters :)  See, that is
why I am talking about it- so you can figure that part out!

Tom
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: More wacky theory
Date: 9 Sep 92 17:11:27 GMT
Distribution: bionet
Organization: Frederick Cancer Research and Development Center

In article <1992Sep8.140304.24664@hellgate.utah.edu>
tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman) writes:

>  This is a continuation of the philosophy of information (of the wacky
>theory).  There have not been any responses on the net system, but I have
>gotten some interesting comments in the mail.

      ***********************************************************
      * PLEASE FOLKS:  keep the discussion directly on the net! *
      ***********************************************************

> Therefore, I am going to present the theory from a different vantage point,
> to try to generate more criticism.

Ok, since you asked for it, get ready for this pie in the face ... :-)

Numbers.  How do you measure information?

  "...when you can measure what you are speaking about, and express it in
  numbers, you know something about it; but when you cannot measure it, when
  you cannot express it in numbers, your knowledge is of a meagre and
  unsatisfactory kind."

  - William Thompson, Lord  Kelvin

If you cannot answer this, your "theory" is useless.

  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: More wacky theory
Organization: Department of Chemistry, University of Toronto
Distribution: bionet
Date: Thu, 10 Sep 1992 14:46:26 GMT

In article <1992Sep9.212445.16675@hellgate.utah.edu>
tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman) writes:
>>(Human DNA is more complex than Mouse DNA, which is more complex than Amoeba
>>DNA).
>
>Yes, this is true too, probably.  Mighty mouse might be humans..

     This really depends on your definition of complexity, doesn't it?
As I understand it, the DNA of some unicellular organism is incredibly
deviously put together.  By some definition, it might be considered much
more complex than our DNA which appears to have many "wasted"
(noncoding) regions.  (As I understand it, it is also an open question
whether we really have any "junk" DNA.)  That human DNA codes for a
more complex organism than ameboid DNA is of course indisputable.  I'm
pretty sure that there's more of it too.  I'm less than convinced that
it's in any reasonable sense more "complex".

				Marc R. Roussel
                                mroussel@alchemy.chem.utoronto.ca
From: tim@ccwf.cc.utexas.edu
Newsgroups: bionet.general
Subject: Re: bionet.bionette or bionet.women ?
Date: 8 Sep 92 01:42:25 GMT
Organization: The University of Texas at Austin, Austin TX

In article <Sep.2.04.28.40.1992.2324@genbank.bio.net> kristoff@genbank.bio.net (David Kristofferson) writes:

> or break it up into bionet.xxxxxxxxxxxxxx.yyyyyyyyyyyyyy where the x's

I'm afraid y's are totally inappropritate here.  Perhaps we should take a
clue from the International Olympic Committee's cytological purity standard
and just use "bionet.23xx".
Organization: Queen's University at Kingston
Date: Monday, 14 Sep 1992 10:39:55 EDT
From: <STEINBAJ@QUCDN.QueensU.CA>
Newsgroups: bionet.general
Subject: Re: Chaos Theory; a place in biology?

A very good book to read about chaos in physiology in particular is
"From Clocks to Chaos" by Leon Glass and Michael Mackey.  This book
was published around 1988, so the material is already dated, but it does
provide a good description of this type of research in layman's terms.