HDTenEightyP/NetNews huggingface dataset:
From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert)
Subject: Re: 3D RNA Editor wanted
Organization: Biology, Indiana University - Bloomington
Date: Thu, 8 Oct 1992 01:38:40 GMT

You and others with interests in 3D RNA drawings may want to look
at the Macintosh RNA 3D toolkit that Jim Brown here put together
for his work.  These are a selection of RNA building blocks
drawn with the Mac application Swivel 3D, which is a general Mac
3D drawing program.  

You ask for "tetraloops, stacks, helices, bends, pseudoknots" and
I seem to recall that this collection includes those.

Here is the brief description of these drawing tools:

3D RNA toolkit is a "toolkit" of RNA pencil-type structures in
Swivel 3D format.  These files can be used to construct 3D models
of RNAs either from known structures (e.g. tRNA) or to test potential
tertiary models.

from James W. Brown, jwbrown@bio.indiana.edu

You can pick these up by anonymous ftp to ftp.bio.indiana.edu,
currently in folder Incoming/ as rna-3d-tools.hqx ( a 1.9 megabyte file).


-- 
Don Gilbert                                     gilbert@bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
From: coyne@uctvax.uct.ac.za
Newsgroups: bionet.software
Subject: subscribe
Date: 6 Oct 92 11:12:28 +0200
Organization: University of Cape Town

subscribe bionet.software
From: bdyke@DARWIN.SFBR.ORG (Bennett Dyke)
Newsgroups: bionet.software
Subject: NIH Guide
Date: 7 Oct 92 15:19:51 GMT
Distribution: bionet

Does anybody know of a script that will organize, extract, format, etc.
the electronic version of the NIH Guide?  Thanx in advance...

Bennett


-- 
+----------------------------------------------------------------------------+
|   Bennett Dyke                                                             |
|   Department of Genetics               Internet:  bdyke@darwin.sfbr.org    |
|   Southwest Foundation                    Phone:  (512) 674-1410 Ext 281   |
|   P.O. Box 28147                            Fax:  (512) 670-3317           |
|   San Antonio, TX 78228, USA                                               |
+----------------------------------------------------------------------------+
From: bolt@wpi.WPI.EDU (Brandon Scott Coley)
Newsgroups: bionet.software
Subject: Use of Computers in Biology
Date: 13 Oct 1992 14:29:32 GMT
Organization: Worcester Polytechnic Institute
NNTP-Posting-Host: wpi.wpi.edu

I know its probably a hassle, but I could use some help.  Raymond Briggs and 
myself (Brandon Coley) are busy at work on an Interactive Qualifying Project
here at Worcester Polytechnic Institute on how Computers are used in Biology.
Basically, we want to cover:  How they are used, if it is NECESSARY that they
be used, and how they can be made better.  

We would appreciate a brief (I don't want to waste too much of your time)
e-mailing on whats systems you use, how often you use them, what the problems
are, etc., if it wouldn't be too much trouble.

Thanks for reading this and even more thanks if you reply...

-Bolt-
bolt@wpi.wpi.edu
From: klier@iscsvax.uni.edu
Newsgroups: bionet.software
Subject: Image analysis software wanted\
Date: 9 Oct 92 10:37:49 -0500
Organization: University of Northern Iowa

Can someone point me at a good image analysis software package for 
an IBM 386 compatible system (we have a frame grabber board)-- currently
running Jandel's Java.  We'd like to shift to a dynamic image analysis
from still frames.  NIH had a Mac-compatible package a few years back--
anything comparable for the IBM?  And preferably ultra-low cost? (Like
free???)

Thanks!   

Kay Klier   Biology Dept  UNI      in%klier@iscsvax.uni.edu
From: szinser@mzdmza.zdv.uni-mainz.de
Subject: compressing routine
Reply-To: szinser@mzdmza.zdv.uni-mainz.de
Organization: Johannes-Gutenberg Univ. Mainz
Date: Tue, 13 Oct 1992 10:08:37 GMT

Hello, 
can somebody tell me, where to get file-compressing programs with
source-code. (Fortran, C, Basic, Assembler).
Or, how to get a compressing program for Versa-DOS.
Thanks in advance!!!
Sylvi


Sylvia Zinser,
Inst. F. Molek. Biophysik,                            
Jakob-Welder-Weg 26
W6500 Mainz
Germany
Phone: 0049+6131-393568
Email:SZINSER@MZDMZA.ZDV.UNI-MAINZ.DE
From: rybicki@uctvax.uct.ac.za
Newsgroups: bionet.software
Subject: RE: GCG7 to Paup translation? (A)
Date: 7 Oct 92 14:56:40 GMT
Distribution: bionet
Organization: University of Cape Town

In article <921004201058.13c@MBDS.NRC.CA>, NUM239@MBDS.NRC.CA writes:
> Hi:
> Do you know of such a program that will do the same on IBM compatibles
> or on the VAX?

If you have generated a GCG .msf file using PileUp, it is already in the
interleave format - meaning all you have to do is take out all info preceding
and following the multiple sequence alignment matrix, and put in the headers
and tails required for PAUP (different for old MS-DOS and new Mac versions).  I
use EVE on the VAX, or MS-WORD on PC.  Same goes for CLustal alignment files
from PC or VAX - and you can also output CLUSTAL in PIR format which means you
don't have to interleave if you don't want to - just take out extraneous
features in the title line for each sequence.
 _________________________________________________________________________
|                                 |                                       |
|  Ed Rybicki                     |    Now you've got the hang of it      |
|  Dept Microbiology              | There's nothing you can't do with it  |
|  University of Cape Town        |         If you're very into it        |
|  PB Rondebosch 7700             |         You can't go wrong....        |
|  South Africa                   |                                       |
|  fax 27 21 650 4023             |              - Mad John               |
|  ed@micro.uct.ac.za             | (Ogden's Nut-Gone Flake, Small Faces) |
|_________________________________|_______________________________________|
Newsgroups: bionet.software
From: zxmkr08@mailserv.zdv.uni-tuebingen.de (Cornelius Krasel)
Subject: Re: Sequence film scanning systems?
Organization: Comp. Center (ZDV) U of Tuebingen, FRG
Date: Sun, 11 Oct 1992 17:47:39 GMT

Some weeks ago I asked for sequence film scanning systems. The replies
I got were all (without exception) rather discouraging. It seems that
the main problem is the identifying of bands on the autoradiographs.
For that reason we now have decided to spend the money on a graphic
tablet made by Hitachi (sold by Pharmacia, at least here in Germany)
and try to get it running with MacVector (we had a look at the 1.0
demo of DNasis and found it rather terrific; the guy from Pharmacia
told us something that Version 2.0 should come out RSN, but
anyways...).

Thank you for your responses (my colleagues were rather impressed :-).

--Cornelius.
--
/* Cornelius Krasel, Department of Physiological Chemistry, U Tuebingen    */ 
/* email: krasel@mailserv.zdv.uni-tuebingen.de (Internet)                  */
/*        krasel@chemie.uni-tuebingen.dbp.de (WIN/X400)                    */
/* "People are DNA's way of making more DNA." (anonymous)                  */
From: HRWood@cup.portal.com (Harold R Wood)
Newsgroups: bionet.software
Subject: Re: stereo-viewer source
Date: Sat, 10 Oct 92 17:36:29 PDT
Organization: The Portal System (TM)

It is possible, with a little practice, to see sterio without a
viewer.  By superimposing the two images by "kinda crossing
your eyes" you can see the sterio effect.  This is a useful tech.
to learn if you regularly need to see sterios, no good if you
are demonstrating to a class.
I have used the technique with sterio X-rays, sterio aerial maps,
and sterio protein configurations.
Rick Wood
From: spl@pitstop.ucsd.edu (Steve Lamont)
Newsgroups: bionet.software
Subject: Re: compressing routine
Date: 14 Oct 1992 13:30:51 GMT
Organization: University of Calif., San Diego/Microscopy and Imaging Resource
NNTP-Posting-Host: pitstop.ucsd.edu

In article <XDW7V4O@minnie.zdv.uni-mainz.de> szinser@mzdmza.zdv.uni-mainz.de writes:
>can somebody tell me, where to get file-compressing programs with
>source-code. (Fortran, C, Basic, Assembler).
>Or, how to get a compressing program for Versa-DOS.

The standard Unix compress utility, in C language source code form, is
available at many FTP sites around the world.  For instance, in your
"neck of the woods," faui80.informatik.uni-erlangen.de, ftp.denet.dk,
and dsrbg2.informatik.tu-muenchen.de.  It's also at most of the
standard US FTP sites.

							spl




-- 
Steve Lamont, SciViGuy -- (619) 534-7968 -- spl@szechuan.ucsd.edu
UCSD Microscopy and Imaging Resource/UCSD Med School/La Jolla, CA 92093-0608
"Twit twit twit/Jug jug jug jug jug jug/So rudely forc'd./Tereu"
                - T. S. Eliot, "The Waste Land," III. The Fire Sermon
From: francis@monod.Biol.McGill.CA (Francis Ouellette)
Newsgroups: bionet.software
Subject: Re: What Genomes have been Sequenced?
Date: 12 Oct 92 15:31:46 GMT
Distribution: bionet
Organization: McGill University

Jean-Loup Risler (BIONET@FRCGM51.EARN) e'crit: 

>1) The "landmark paper" on Yeast Chromosome III appeared in NATURE, vol. 357
>   pp. 38-46 and not in Science. I'm not quite sure whether the cited
>   number of authors (>100) was ironical or not. If so, why (I'm not a co-
>   author)?

147 authors from 35 labs in Europe.  If I was one of those labs, I sure
would want my name on it.  This papers, and others in the near future to
come from Europe shows one way to do a mini-mega sequencing project.
Many (in the human and C. elegans) project have made fun of the Yeast
project but the Nature paper has silenced many, and it works!  We can
sequence a small genome (14,000,000 bp +/-) by "conventional" cloning and
sequencing methods.  They will not be able to do this for the human genome
project ... they will need new technology.

>2) Keith Robison has forgotten *Bacillus subtilis* in his review of partly

Keith also mentions 3 yeast chromosome on their way to completion ...  it
is more like 4 ...   I, II, III (finished) and XI.

>3) About a former posting: in yeast chromosome III, there are 182
>   open reading frames longer than 300 bp (thus coding for proteins longer

and there are probably more, and some of the already identified ones may
be bogus.  Many carreers are spent on a single gene ... so more than 180
for CHIII and more than a thousand (2000?) for the yeast genome will keep
many many people very busy.  The task of genome sequencing is very
altruistic (well, I think it is ;-).  We are producing data which will be
used (and corrected!) by thousands of scientist worldwide, and not just
yeast biologists.

>That more than 50% of the ORFs in ChrIII do not resemble anything
>previously known is one great information afforded by its sequencing.
>Remember also that yeast is a small eukaryotic organism, whose genome
>contains introns and exons, and that reverse genetic experiments are easy
>with yeast. The choice of this organism for a collaborative project was not
>done by chance...

I think you meant very few introns here (?) ...   and yes, not much
"chance" in choosing yeast here ... if I can quote somebody from my yeast
mailling list (yes, yes, it is comming folks ;-) ...

 "Yeast is Best"

regards to all

francis

(PS maybe this should move from bionet.software to bionet.general?)
(PPS salut Jean-Loup!)


--
| B.F. Francis Ouellette  
| manager, yeast chromosome I project
| dept of biology, McGill university, Montreal, Qc, Canada
| francis@monod.biol.mcgill.ca
Newsgroups: bionet.software
From: James Petts <pettsj@visigoth.demon.co.uk>
Subject: Multiple Alignment S/W for Mac
Organization: No Affiliation
Date: Mon, 5 Oct 1992 13:35:37 GMT
X-Useragent: Nuntius v1.1

Is there anything like MACAW for the Mac available on the net???

James Petts

********************************************************************
* "We use the classical theory on Mondays, Wednesdays and Fridays, *   
*  and the quantum theory on Tuesdays, Thursdays and Saturdays."   *
************************************** Wm. Bragg *******************
From: robison1@husc10.harvard.edu (Keith Robison)
Newsgroups: bionet.software
Subject: Re: What Genomes have been Sequenced?
Date: 13 Oct 92 03:47:42 GMT
Distribution: bionet

gsbs1022@UTSPH.SPH.UTH.TMC.EDU (Zharkikh Andrey) writes:

>Note added in proof:

>Jean-Loup Risler at BIONET@FRCGM51.EARN wrote:

>>3) About a former posting: in yeast chromosome III, there are 182
>>   open reading frames longer than 300 bp (thus coding for proteins longer
>>   than 100 aa). Some of them correspond to already known genes, and 145
>>   ORFs are novel (see the Nature paper). Note that these figures are
>>   consistent with a study of the chrIII transcripts, hence most of these
>>   ORFs are actually translated.
>...
>>That more than 50% of the ORFs in ChrIII do not resemble anything
>>previously known is one great information afforded by its sequencing.

>As Monte Carlo simulation shows, about 24 of these ORF are expected
>to be found by chance (in a random sequence of length 300,000 with
>the same base frequencies as in yeast III chromosome: A=0.31, T=0.30,
>G=0.19, and C=0.20).

>Andrey.

	Curiosity: in the ChrIII paper, the claim was made that
ORFs of >100 amino acids "have 0.2% probability of occurring by
chance in S.cerevisiae DNA." Is this consisistent with the above
estimate?

Reference ginven (I haven't looked it up yet)
	Sharp & Crowe.  Yeast (1991) 7:657-678.

Keith Robison
Harvard University
Department of Cellular & Developmental Biology
Department of Genetics / HHMI

robison@ribo.harvard.edu
From: RROXBY@MAINE.MAINE.EDU (Robert Roxby)
Newsgroups: bionet.software
Subject: UUUDECODING files from EMBL
Date: 14 Oct 92 01:53:01 GMT
Organization: University of Maine System

I am having a problem decoding files obtained from EMBL.
They are supposed to be uuencoded, but when I try to
decode them, I get a message "ERROR:  no begin line".
EMBL gave me some advice about using a Pascal decoder,
but I don't have it, whatever it is.  Thanks for any
suggestions.  (It is a four part file: fn.uua, fn.uub,
etc.  Is that part of the problem?)
Newsgroups: bionet.software
From: BIONET@FRCGM51.EARN
Subject: Re: What Genomes have been Sequenced?
X-Envelope-To: bio-software@daresbury.ac.uk
Original-To: bio-software@UK.AC.DARESBURY
Distribution: bionet
Date: Sun, 11 Oct 1992 15:34:00 GMT
X-Vms-To: IN%"bio-software@daresbury.ac.uk"

 
 
1) The "landmark paper" on Yeast Chromosome III appeared in NATURE, vol. 357
   pp. 38-46 and not in Science. I'm not quite sure whether the cited
   number of authors (>100) was ironical or not. If so, why (I'm not a co-
   author)?
 
2) Keith Robison has forgotten *Bacillus subtilis* in his review of partly
   but well under way sequenced genomes (no sweat, this is not my favourite
   organism).
 
3) About a former posting: in yeast chromosome III, there are 182
   open reading frames longer than 300 bp (thus coding for proteins longer
   than 100 aa). Some of them correspond to already known genes, and 145
   ORFs are novel (see the Nature paper). Note that these figures are
   consistent with a study of the chrIII transcripts, hence most of these
   ORFs are actually translated. My point is that an ORF or a gene is not
   weird or strange if one gets no phenotype upon its disruption:
        a) not getting a phenotype *in your laboratory conditions* does not
           mean that the gene is useless!
        b) it is quite possible that these genes may be duplicated,
           triplicated, etc... on other chromosomes. Disrupting one copy
           will make no harm.
 
That more than 50% of the ORFs in ChrIII do not resemble anything
previously known is one great information afforded by its sequencing.
Remember also that yeast is a small eukaryotic organism, whose genome
contains introns and exons, and that reverse genetic experiments are easy
with yeast. The choice of this organism for a collaborative project was not
done by chance...
 
   ---------------------------------------------------------------
  | Jean-Loup Risler                    |                         |
  | CNRS                                |                         |
  | Centre de Genetique Moleculaire     |  Risler@frcgm51.bitnet  |
  | 91190 Gif sur Yvette   France       |                         |
   ---------------------------------------------------------------
Newsgroups: bionet.info-theory
Subject: Re: AND gate puzzle for you
From: srghkja@zephyr.dsir.govt.nz (Dr Ken Aldous)
Date: 8 Oct 92 13:40:17
Distribution: bionet
Organization: Dept. of Scientific and Industrial Research, NZ.


How much information is lost depends entirely upon the definition of
your measure of information.   It therefore follows that all the answers 
are correct, or can be made correct by adjusting the definition.  
If you define your measure before you do the calculation, it
is a trivial matter to determine which is correct.  Not defining one's
terms until the argument is over (or better still, not defining them at all
if you can get away with it) is a useful trick, much used, for example,
in economics.

Ken Aldous
Newsgroups: bionet.info-theory
From: tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman)
Subject: AND gate puzzle for you
Date: 6 Oct 92 23:35:08 MDT
Organization: University of Utah, CompSci Dept
Distribution: bionet

Here is a riddle.... I will give information theoretic analysis of three
different famous people, and you tell me who you agree with, or if none
say what you think.  The riddle is so easy, you can't miss it!  Except, I
am not sure of the answer at all either.  The identities of the analyzers
will be kept secret to prevent biasing your own analysis.  Here it is:

An AND gate loses information... but how much?  An AND gate has a map like
this:

A  B   X
--------
0  0   0     top three states have equivalent outputs!      
0  1   0
1  0   0
1  1   1     bottom state is unique

(for all of them, assume equally likely probability of the four incoming
states {0,0}, {0,1}, {1,0}, {1,1})

Analysis 1:  
  The entropy of the beginning state is given by - Sum(pi log pi) and
the same for the end state.  The beginning state thus has an entropy of 2,
and the end state an entropy of 0.81126, so the loss of info is 1.189 bits.

Analysis 2:
  The information change is ln 2 units, no matter what the input values
were.  (Figure that out for yourself, it is not clear if ln is 
in base 2 or not)

Analysis 3:
 The computation loses zero bits if the output was 1, whereas it requires
2 bits to describe its previous state if it has an output of 0.  Thus,
1/4 of the time it loses zero information, and 3/4 of the time it loses
2 bits.  The overall average information loss then is 1.5 bits.


Discussion of extremes:

  The AND gate certainly loses information, so the information loss is greater
than 0.  However, it does not lose all of its information, which is clearly
2 bits to start out.  Therefore, the information loss is somewhere greater
than 0, and less then 2.  

Newsgroups: bionet.info-theory
From: tolman%asylum.cs.utah.edu@cs.utah.edu (Kenneth Tolman)
Subject: Re: AND gate puzzle for you
Date: 8 Oct 92 15:58:13 MDT
Organization: University of Utah, CompSci Dept
Distribution: bionet

>What about the following argument: 
>
>The AND gate gains information: Without AND gate, you
>only know the probabilities of inputs A and B separately
>(say 1/2 each). After combining them with an AND gate, you
>also know the combined probability P(A=1 & B=1). You
>gained information (by doing a calculation through the
>AND gate) if you look at the inputs and the outputs
>(assuming the AND gate to be idealized and reflecting at
>the output always the value A & B  instantaneously).

This is an interesting analysis!  I do not agree with it, but it feels
correct in a way, for why would we undertake computation unless we were
given new information?  What would be the point of computation unless it
told us something we did not know?  If computation lost information at
every gate, what the heck would we be doing?

Here we are brushing against a puzzle of information theory... is information
something merely physical, or is there something about the mental involved?
I believe that it is both- there actually is an intrinsic information to
our universe, but for any particular individual they have a different
measure of their own knowledge.  These two aspects are normally merged
in discussions, which prevents one from distinguishing them.

One could even use the halting argument to demonstrate information... (not)


Newsgroups: bionet.info-theory
From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Subject: Adaptive Complexity
Summary: Perhaps it is more of the current same
Keywords: entropy  complexity  adaptivity
Organization: Crop Science Dept., NCSU, Raleigh, NC 27695-7620
Date: Fri, 9 Oct 1992 23:41:42 GMT

The following relayed item is self-explanitory.  Since it will be
in the next building, you may be a book report, if it's good.

    ------------------Cut Here-----------------

>From: marshall@marshall.cs.unc.edu (Jonathan A. Marshall)
>Newsgroups: triangle.talks
>Subject: NCSU Physics talk: Gell-Mann
>Message-ID: <16222@borg.cs.unc.edu>
>Date: 9 Oct 92 16:23:49 GMT



                           L. H. Thomas Lecture

                           Dr. MURRAY GELL-MANN
         Robert Andrews Millikan Professor of Theoretical Physics
                    California Institute of Technology

                   4:00 p.m., Monday, October 19, 1992

                       Auditorium, 222 Dabney Hall
                 North Carolina State University, Raleigh

          "SIMPLICITY, COMPLEXITY, AND COMPLEX ADAPTIVE SYSTEMS"

What makes one landscape or one work of art more complex than another?
Are there different kinds of complexity?  How is complexity related to
information?  Is the fundamental description of the universe simple?  If
so, why does the world around us appear so complex?  How much of that
apparent complexity is genuine?  What level of complexity is required for
a system to be able to learn or adapt?  Are there general principles that
characterize complex adaptive systems?  The new sciences of complexity
have begun to deal with such questions.

--------------------------------------------------------------------------
From: Prof. Marjorie Klenin (919)515-7457 <nwil@ncsumvs.bitnet>
      Physics, Box 8202, NCSU, Raleigh NC 27695-8202
--------------------------------------------------------------------------

    -----------------Cut Here------------------

If the lecture is good, I'll smile.  If it's bad, I'll ask him for his
estimate of the amount of information an ant needs to differentiate
the real Mount Blanc from an ersatz Mount Blanc.  :^)

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.
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
         

Newsgroups: bionet.info-theory