HDTenEightyP/NetNews huggingface dataset:
From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs)
Newsgroups: bionet.software
Subject: Re: Help needed on 3D_Align on EMBL ...
Date: 13 Aug 92 07:18:59 GMT
Followup-To: bionet.software
Distribution: bionet
Organization: EMBL Data Library

In article <9208121139.AA28518@genbank.bio.net>, HYUNERHO@KRSNUCC1.BITNET
wrote:

> Recently EMBL Netserv has set up new directory called
> 3D_ALIGN . And when I just browse there they keep some
> sequences(so large size) and others.
> I guess that might be one of recently highlighted forms
> of Sequence Homology matrix and results.
> BTW how can I view them and do ananlysis on my platforms
> such as Mac or IRIS ?
> Is anybody out there who knows well about them
> and are willing to let me know ?
> Any comments would be appreciated.

From our help file:

The service provided by the EMBL Data Library allows users to download the
files constituting the 3D_ALI database, provided by Stefano Pascarella
and Patrick Argos, EMBL.

Pascarella S., Argos P. (1992) Protein Engineering 5 (1) 121-137
"A data bank merging related protein structures and sequences"

From the 3d_ali.doc file:

General description:
===================
The  3D_ALI databank is a collection of data which merges protein
structural  and sequence information.  Structural  superpositions
amongst  proteins with similar main-chain fold were performed  or
collected from the literature.  Sequences taken from the  protein
primary  structure  databases were associated with  the  multiple
structural  alignments  providing they were at least 50%  or  35%
(alternatively)  homologous  in  residue identity to one  of  the
structural sequences and at least 50% of the structural  sequence
residue  were  alignable.  Such   restrictions  allow  reasonable
confidence   that    the  primary   sequences   share  the   same
conformation of  the  tertiary structural templates,   except  in
the less conserved loop regions.
Multiple structural superpositions were collected for 38 familial
groups  containing  a  total  of  209  tertiary  structures;   45
structures  had no superposable mates and were used  individually
(these figures may vary in future releases). Other information is
also provided as main chain and side chain conformational angles,
secondary structural assignments and the like.
Wedding  the primary and tertiary structural data resulted in  an
8-fold   increase  of  data  bank  sequence  entries  over  those
associated with the known three-dimensional architectures alone.

I don't know about any Mac programs that could utilize this databases, but
there should be Unix software available from the authors. Try to contact 
Argos@EMBL-Heidelberg.DE

Rainer Fuchs
EMBL Data Library
Fuchs@EMBL-Heidelberg.DE
Newsgroups: bionet.software
Subject: Re: OOP and molecular biology
From: robison1@husc10.harvard.edu (Keith Robison)
Date: 14 Aug 92 03:06:40 GMT
Distribution: bionet

Two addenda on the C++ in biology posting:

1) An extensive system of C++ programs for manipulating E.coli genetic
   data is described in:

	DG Shin, C Lee, J Zhang, KE Rudd, and CM Berg.  1992.  CABIOS 8:227-238
	Redesigning, implementing, and integrating Escherichia coli genome
	software tools with an object-oriented database.

2) My rudimentary C++ library is available from golgi.harvard.edu
   in directory ftp/pub/contrib/kertools.  Within are a number
   of libraries for general sequence and GenBank flat-file
   handling.  Programs in the directory include ones for:

	Manipulating data in GenBank flatfile format.
	Translating DNA to protein, including extraction of ORFs
	 to separate sequences and generation of codon usage tables.
	Detecting coiled-coil regions in proteins by the method
  	 of Lupas et al (Science 252:1162-1164).
	Condensing output from NCBI's BLAST
	Detecting repetitive DNA sequence regions by the method of
	 Tautz et al (Nature 322:652-656) [soon - coded but not tested].

These tools and the underlying class library are still in a very fluid
state, but if you send me an E-mail note I will keep you informed as
to updates and changes.  All feedback will be appreciated.


Keith Robison
Harvard University
Program in Biochemistry, Molecular, Cellular, and Developmental Biology

robison@ribo.harvard.edu 


Newsgroups: bionet.software
From: harper@convex.csc.FI (Rob Harper)
Subject: Re: NCBI internet access inquiry
Organization: Finnish Academic and Research Network Project - FUNET
Distribution: bionet
Date: Mon, 17 Aug 92 13:22:03 GMT

In <1992Aug17.124402.22334@gserv1.dl.ac.uk> ES@UK.AC.AFRC.JII writes:

>Could anyone provide us with the internet access number of NCBI?
>The address NCBI.NLM.NIH.GOV being unknown of our computer address 
>database, we can't currently use ftp to that site.

On Unix systems there is a tool called nslookup which you can use
to find out IP numbers if you have the IP address. He is the result.

sun4 /csc/harper 43> nslookup NCBI.NLM.NIH.GOV
Server:  venus.csc.fi
Address:  128.214.46.21

Non-authoritative answer:
Name:    NCBI.NLM.NIH.GOV
Address:  130.14.20.1

RGDS -=ROB=-
--
   Rob Harper                     /   E-mail:          harper@convex.csc.fi    
   Finnish State Computer Centre  /   Molbio/software: harper@nic.funet.fi
   P.O. Box 40, SF-02101 Espoo    /   Telephone:       +358 0 457 2076
   Finland                        /   Fax:             +358 0 457 2302
Newsgroups: bionet.software
From: jhammo@uwovax.uwo.ca (James Hammond)
Subject: sequence analysis program?
Organization: University of Western Ont, London
Date: Wed, 19 Aug 1992 00:55:41 GMT

Could anyone point me to a good, inexpensive (Shareware or Commercial) sequence
analysis program.  My requirements are quite basic -- comparaative sequence
homology, PCR primer design, etc.  y information would be appreciated. .
Thanks. 

________________________________________________________________________________

    James R. Hammond: Department of Pharmacology and Toxicology
                      University of Western Ontario
                      Tel: (519) 661-3780
                      Fax: (519) 661-3797
________________________________________________________________________________
From: JWALKER@EARN.SBBIOVM (jeff Walker)
Newsgroups: bionet.software
Subject: mac screen capture
Date: 14 Aug 92 17:23:02 GMT
Distribution: bionet
Original-To: bio-software <bio-software@UK.AC.DARESBURY>

try command-shift-3 (the command is the butterfly to the left of the space
bar)...this is apples own screen capture utility.  by the way, i saw at the
macworld festival a screen sequence capture utility (cameraman) that uses
quicktime to capture a sequence of screen events (animation, pulling down
menues, mouse tracks, or whatever).
 
JAW
Stony Brook
Newsgroups: bionet.software
From: gonnet@inf.ethz.ch (Gaston Gonnet)
Subject: Scoring matrices
Keywords: Dayhoff, Needleman & Wunsch
Organization: Dept. Informatik, Swiss Federal Institute of Technology (ETH), Zurich, CH
Date: Fri, 14 Aug 1992 19:40:19 GMT

We are developing techniques for comparing the effectiveness
of various scoring matrices used in conjunction with dynamic
programming (Needleman & Wunsch).  We would really appreciate
receiving (preferably by e-mail) matrices that people have
been using with some success.  Any format is acceptable.

We are particularly interested in the deletion penalties
used in conjunction with these matrices.

Also, if any of you know where a repository of this information
may be, please let us know.

In return we promise to post the result of the analysis of
the methods and a short explanation of the methodology used.

Gaston H. Gonnet, Informatik, ETH, Zurich.
From: WGANNON@BOOTES.UNM.EDU
Newsgroups: bionet.software
Subject: noooooo mmoooorrreee
Date: 19 Aug 92 00:28:00 GMT
Distribution: bionet

pleeze unsubscribe me too!  wgannon@unmb.unm.edu
From: cherry@frodo.mgh.harvard.edu (Mike Cherry)
Newsgroups: bionet.software
Subject: Re: Screen capture for Mac
Date: 17 Aug 92 05:22:00 GMT
Organization: Molecular Biology, Massachusetts General Hospital, Boston

In article <1992Aug14.092342.3541@pollux.lu.se>, biogen10@gemini.ldc.lu.se (Bo Servenius) writes...
>Doing some work with the ABI373A dna sequencer I have got
>the need to do screen captures. Anyone knows about a good
>program that could be found over internet for this purpose.

An excellent screen capture program for the Macintosh is FlashIt! which is
available from sumex.stanford.edu. (Look in the info-mac/cp directory for
the BinHex encoded file flash-it-22.hqx). FlashIt! will capture all or any
part of the screen in color or however your monitor is configured to a
PICT file, to the clipboard, or to the printer. The PICT file can be
created with any creater/type you choose. FlashIt! works very well with
System 7, and 6 too.

Mike Cherry
P.S. In another message Bosse asked about NIH Image. NIH Image is a
Macintosh application, and a very good one. 
Newsgroups: bionet.software
From: cup@bones.biochem.ualberta.ca (Chris Upton)
Subject: Re: gcg
Reply-To: cup@bones.biochem.ualberta.ca
Organization: University of Alberta
Date: Fri, 14 Aug 1992 15:25:34 GMT

In article 22836@news.columbia.edu, rs54@cunixf.cc.columbia.edu (Richard Sucgang) writes:
>In article <1992Aug13.231529.26113@Princeton.EDU> lpcasson@phoenix.Princeton.EDU (Lawrence P. Casson) writes:
>>In article <1992Aug2.181655.18486@news.columbia.edu> rs54@cunixf.cc.columbia.edu (Richard Sucgang) writes:
>>>
>>>I have found that a lot of gcg programs can output PostScript. If
>
>>write EPS files.  It writes them okay, producing files with filled data
>>and resource forks.  However, EPS files generated on our UNIX system and
>>FTP'd to the Mac have empty resource forks (SURPRISE, SURPRISE!!).  I
>>assume that this acounts for the inability of MacDraw Pro to display
>>them.  Does anybody know if it's possible to convert these to files that
>>can be used with MacDraw?
>>

I haven't done this for a while, but I was using a MAC and VersaTermPro to connect
to the GCG package. The graphics were popped into a tektronix screen and could be 
saved on the MAC in various formats, some of which must be useful for import
into MacDraw. 
I could check this out if you like,

Cheers,

Chris

---
Chris_Upton@darwin.biochem.ualberta.ca
Biochemistry Department
University of Alberta
Edmonton, AB T6H 2H7
Canada
From: MCCAINKW@DUVM.OCS.DREXEL.EDU (Kate McCainFINED)
Newsgroups: bionet.software
Subject: object-oriented BASIC???
Date: 20 Aug 92 11:04:11 GMT
Distribution: bionet

C++ exists as (apparently) the most visible OOP language.  Can anyone with
a greater range of knowledge than I have tell me if there is an object-
oriented BASIC?

Kate McCain                              "Bibliometrics R Us"
College of Information Studies
Drexel University

BITNET:   MCCAINKW@DUVM
Internet: mccainkw@duvm.ocs.drexel.edu
From: dab@ray.nlm.nih.gov (Dennis Benson)
Newsgroups: bionet.software
Subject: Re: Genbank services?
Date: 18 Aug 92 21:25:26 GMT
Organization: National Library of Medicine
X-Newsreader: Tin 1.1 PL4

Subject: Re: Genbank services?
Newsgroups: bionet.software
Distribution: bionet
X-Newsreader: Tin 1.1 PL4

SBAIRD@ACADVM1.UOTTAWA.CA (Stephen Baird) writes:
: Dear David Kristofferson,
: 	I am a little unclear as to what services Genbank will be
: offering to the public after the end of September. I gather the
: FASTA, BLAST, BLAZE and RETRIEVE e-mail servers will no longer be
: available.  Instead of these servers, researchers will be able to
: use the NCBI BLAST and RETRIEVE e-mail server as well as the
: various FASTA e-mail servers from the University of Houston's
: gene-server, EMBL, and PIR. I don't think BLAZE will be available

Correct, the BLAST and RETRIEVE e-mail servers are now operational at NCBI.
Documentation can be received by sending mail with the word 'help' in
the body of the message to:

blast@ncbi.nlm.nih.gov

retrieve@ncbi.nlm.nih.gov


: to anyone for free anymore.
: 	What about data submission?  Will Genbank still be the main
: North American public repository?  What about the FTP server and
: the Genbank database updates, will this be NCBI's responsibility?

Yes, NCBI is currently offering and will continue to offer anonymous
FTP access to GenBank (full release) and updates.  The host is:
'ncbi.nlm.nih.gov'

The directory is ncbi-genbank.  It contains compressed files of the latest
public release.  A subdirectory, 'daily', contains the cumulative updates
made to the database since the last public release.  Another subdirectory,
'daily-nc' contains non-cumulative updates, i.e., each file contains a
single day's updates.  Currently, the files in 'daily-nc' contain only
NCBI Backbone sequence entries (from the scanned journal literature), but
will eventually be augmented with the daily updates from Los Alamos'
direct submissions.

Dennis Benson
NCBI/NLM
From: wmelchior@NTBTOX.NCTR.FDA.GOV ("Bill Melchior, NCTR/FDA")
Newsgroups: bionet.software
Subject: Re: Object oriented programming
Date: 20 Aug 92 12:31:23 GMT
Reply-To: wmelchior@NTDOC.NCTR.FDA.GOV
Distribution: bionet

My thanks to those who have given descriptions of OOP.  I hope I never
have to try it, but I think I now have some feeling for the kind of thing 
that's going on.  It sounds like it's going to be a major factor in
the future of computation.
________________________________________________________________________________
The opinions stated are mine, not those of NCTR or its sponsoring organizations.

Bill Melchior                                ||   "You have lawyers the way
National Center for Toxicological Research   ||    other people have mice."
Jefferson, AR  72079                         ||
(501) 543-7206                               ||   -Kenneth Duncan, English
                                             ||    Health & Safety Executive,
WMELCHIOR@NTDOC.NCTR.FDA.GOV                 ||    to US regulators
Newsgroups: bionet.software
From: Bo Servenius <biogen10@gemini.ldc.lu.se>
Subject: Re: Images
Organization: Lund University, SWEDEN
X-Useragent: Nuntius v1.1
Date: Fri, 14 Aug 1992 09:40:52 GMT

Subject: Re: Images
From: mangalam
In article <9208140244.AA05710@genbank.bio.net> ,
mangalam@SALK-SC2.SDSC.EDU writes:
>Bart Man (pun?) or Brent, depending on which part of the message you
>believe writes:
>
>>I am looking for an anonymous FTP site that may have color or b&W
scanned
>>images of MRI, PET or CAT, (or anything remotely similar).  Does
anyone
>>know of a site?  I heard that NIH had such a site.
>>
>>please e-mail:  bkronenb@sdcc13.ucsd.edu
>  
>   The directories associated with NIH Image, now in its 1.45
incarnation,
>have at least one series of MRI data (25 slices, I think).  It can
be found
>at alw.nih.gov in /pub/image/images(?) or something close.  If you
need
>others, I can probably dig up at least a few other series.  
>   And while the fingers are still pliable, here's a LOUD PLUG for
NIH
>Image, one of the best image analysis programs available (FOR FREE,
WITH
>SOURCE CODE, WITH A MACRO LANGUAGE, WITH AN ON-LINE AUTHOR, WITH A
READABLE
>MANUAL).   GNUdos to Wayne Rasband for his work.
>
>
>Cheers,
>
>Harry
>
>
>
>Harry Mangalam                                   Vox:(619)
453-4100, x250
>Dept of Biocomputing                                   Fax:(619)
552-1546
>The Salk Institute                            
mangalam@salk-sc2.sdsc.edu
>10010 N Torrey Pines Rd                       
mangalam@salk-sgi.sdsc.edu
>La Jolla CA 92037                                   
mangalam@salk.bitnet
>
Dear NEtters:

Excuse me my ignorance but what hardware system is Images working
with.

yours

BOSSE
Newsgroups: bionet.info-theory
From: hsaiah@ul9000.unil.ch
Subject: URGENT!!! EPA medium formula?
Organization: University of Lausanne CH (Switzerland)
Date: Tue, 18 Aug 1992 15:57:24 GMT

Hello I have a small problem, big for me. Is anyone could help me?
I need URGENTLY the composition of a medium for ecotoxicological test on
      ^^^^^^^^^^^
crustacean.  I lost the formula and I have actually experiments running with
this medium. The book were I could find the formula does'nt exist in
Switzerland.
 I wonder if someone could just look to the original book where is
describe the formula for the  moderately hard synthetic freshwater EPA medium:
                              `^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 (EPA= Environmental Protection Agency)

what I need:
NaHCO3......??  mg/l
MgSO4......??   mg/l
CaCl2.......?? mg/l
KCl..........?? mg/l                (ph = 7,6 +- 02,  Hardness 80-100mg/l CaCO3)

The book is:
--------------------------------------------------------------------------------
Title:         Methods for measuring the acute toxicity of effluents to
                 freshwater and marine organisms / edited by William H. Peltier
                 and Cornelius I. Weber. 3rd ed. Cincinnati, Ohio :
                 Environmental Monitoring and Support Laboratory, Office of
                 Research and Development, U.S. Environmental Protection
                 Agency, 1985.
Description:   xv, 216 p. : ill., forms ; 28 cm.

Doc Numbers:   Govt Doc No.:  EP 1.23/5:600/4-85-013
               Report No.:    EPA/600/4-85/013

Notes:         "March 1985."
               "EPA/600/4-85/013."
               Includes bibliographies.

Subjects:      Water quality bioassay -- United States.
               Water -- Pollution -- United States -- Measurement.

Other entries: Weber, Cornelius I.
               Peltier, William.
               Environmental Monitoring and Support Laboratory, Cincinnati,
                 Ohio.
--------------------------------------------------------------------------------
thanks in advance for your help. Mail directly to me the answer please. 
					bye,        Henni

:::::::::::::::::::::::::::::::::::::::::::::::::
Henni SAIAH , Lausanne University, Switzerland  :
Email:    Hsaiah@ulys.unil.ch	(internet)      :
	  Hsaiah@clsuni51.bitnet  (Bitnet)      :
:::::::::::::::::::::::::::::::::::::::::::::::::
Newsgroups: bionet.info-theory
Subject: Re: What's behind door #3?
From: marder@agri.huji.ac.il
Date: 10 Aug 92 08:28:42 IST
Distribution: world
Organization: The Hebrew University of Jerusalem - Faculty of Agriculture

In article <9701@uqcspe.cs.uq.oz.au>, matthew@cs.uq.oz.au (Matthew McDonald) writes:

>
> 	Code to test this empirically follows. Could you (or someone else)
> explain what's wrong with it?
>
> 	I'm no statistician, but the odds definitely seem 2-to-1 to me ...
>
It's time to concede that 2-to-1 is right.  It becomes even more obvious
with more than 3 garage doors.  One's first reaction is to think
"showmasters usually offer gimmicks, seldom real gain ..."
Credit to the various explanations.  Even more credit to Matthew
for running the "experiment".

                                 '      Jonathan B. Marder
Internet: MARDER@AGRI.HUJI.AC.IL |      Department of Agricultural Botany
Bitnet:   MARDER@HUJIAGRI        | /\/  The Hebrew University of Jerusalem
Phone:    (08 or +9728) 481918   |/  \  Faculty of Agriculture
Fax:      (08 or +9728) 467763   /      P.O.Box 12, Rehovot 76100, ISRAEL
Newsgroups: bionet.info-theory
From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Newsgroups: bionet.info-theory
Subject: A biomolecular photonic transistor?
Summary: Two recent articles on molecular computing machines
Keywords: photonic transisitor molecular logic state storage switching
Date: 16 Aug 92 09:32:52 GMT
Organization: Crop Science Dept., NCSU, Raleigh, NC 27695-7620

This book:

	"Complexity, Entropy and the Physics of Information:
	Proceedings of the Santa Fe Institute Workshop
	entitled, "Complexity, entropy, and the physics of
	information, held may 29 to June 10, 1989."
	Edited by W.H. Zurek, The Advanced Book Program,
		Addison-Wesley, Redwood City, CA., 1991.

has numerous articles of interest to participants of this
group.

An interesting one is:

	"Information Processing at the Molecular Level: Possible
	Realizations and Physical Constraints."
	by WG Teich and G Mahler

This article discusses physical design parameters of molecular
level photonic switching  of logic states....in a way that is not
readily "connectible" to the necessary macrolevel I/O required
in real world devices.

In contrast, this article:

	"The dawn of the Light Transistor: An Optical Computer
	Method Using Interference Fringe Component Regions."

	JN Hait, Circuit Cellar INK (ISSN 0896-8985): The Computer
	Applications Journal  28:40 1992.
	(This magazine is available in stores where you would find
	magazines like Scientific American.)

Hait explains lucidly his U.S. Patent #5,093,802, a method of
constructing and using the logic state storing/switching
capacity of a scaled down Michelson Interferometer with a
fringe mask.  Switching speed would be limited by system 
element spacing and the wavelength of the laser light used. 

This latter method is food-for-thought on how to do it with 
biomolecules rather than with semiconductors.

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
From: kristoff@genbank.bio.net (David Kristofferson)
Newsgroups: bionet.general
Subject: Re: bionette stuff
Date: 18 Aug 1992 19:57:58 GMT
Distribution: bionet
Organization: GenBank Online Service

roy@alanine.phri.nyu.edu (Roy Smith) writes:

>> You are a bit late in piping up.  Unfortunately when the opportunity
>> was announced for discussion on this newsgroup, no one said anything.
>> Discussion ended almost a month ago and voting is also just about over
>> (Sunday the 23rd).

>Maybe I've just been being oblivious, but this is the first I've ever heard
>about it.  Personally, if I opened a topic for discussion and no one said
>anything, I would assume that either 1) the word never got out or 2) nobody
>was interested.

I have sent out other RFD's previously; some generated discussion and
some did not.  There is no reason to believe that anything is wrong
with the bionet.ANNOUNCE distribution (if you were looking for RFD's
here in bionet.general, you will never see *any*).  If no one reacts
to an RFD, it is not an automatic veto of the group.  This has
happened with other groups too, not just on bionette.  Voting occurs
during the voting period, not during the discussion period.

My bet is that summer vacations/travel are probably making people
devote less attention to news than usual.  Everything was done by the
book on this one, and there is no reason to change anything in this
vote.

To make an analogy regarding this proposed group, several people
including myself wrote a letter to Science last year describing all of
the free network services available to biologists.  Science turned it
down with the feeble excuse that "everyone already knows about these
things."  I felt, "If so, why did we, the people closest to the issue,
feel the need to write the letter???!!!"  I humbly submit that if
women scientists feel the need for a group like bionette, then I can't
take quite seriously statements from men that women are already equal.

				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff@genbank.bio.net