HDTenEightyP/NetNews huggingface dataset:
From: lear@yeager.corp.sgi.com (Eliot Lear)
Newsgroups: bionet.molbio.bio-matrix
Subject: Re: Beyond GenBank
Date: 28 Dec 92 23:42:03 GMT
Distribution: bionet

Hello Jim,

``How shall we feed the information to the masses?''

Thanks for your note of 22 Dec 92 on the status of GenBank.  I am
interested in how your database will be updated at different sites on
the Internet.  As you are aware, IntelliGenetics made these updates
available in at least three ways: [1] nightly updates in flat file
GenBank format, [2] nightly updates over USENET which were
incorporated by a program written by Ross Smith and Roy Smith, and [3]
through LANL's portable DB update format (as I recall you received
these updates).

What are NCBI's plans in this area?  I understand that you are using
ASN.1 to exchange transactions.  But how will this affect me if I want
to keep my database synched with yours?  I am confident that you guys
back there have thought about this problem long and hard.

Is there a white paper I can grab on this stuff?

Thanks,

Eliot Lear
[lear@sgi.com]
From: Davison@UH.EDU (Dan Davison)
Newsgroups: bionet.molbio.bio-matrix
Subject: Biomatrix Society and newsgroup status
Date: 30 Dec 92 22:41:24 GMT
Distribution: bionet

brianf@dna.uvm.edu (Brain Foley) writes:
>>Why are all these people not using bionet.molbio.bio-matrix to discuss
>>their latest exciting topics?  Is there a journal of bio-information
>>that I should be reading instead?  Is CABIOS really all that there is?

David Kristofferson replied:
> Perhaps Dan Davison can comment on this but I am getting the distinct
> impression that BIOMATRIX is a dead organization (I'm referring to the
> society, not just the newsgroup).  They tried to collect dues a while
> back and I am not sure if anyone responded.

Neither am I.  The general problem is that we have not recruited new
people into the organization.  "Older" members of the Biomatrix
Society are drifting off into other areas; for instance, the person
who was supposed to do the last newsletter "vanished" off the net.

Much of the effort that went into the Biomatrix Society has gone into
the IS/MB group, with the upcoming workshop and summer school.  It may
be that the Biomatrix effort needs to fold into it; at the moment, the
Biomatrix Society is a co-sponsor (see below).

The bio-matrix newsgroup can be used exactly as Brian proposes, and
I've noticed a few related messages in the last few weeks.  To start
the new year, I will post the Biomatrix message as a way to start
discussion.

There are projects ongoing:

-"Engines of Discovery: A Biomatrix Primer" ed. by Robert Bolender and
Dan Davison is in the "almost contract" stage with a University Press.
When a contract is finished it will be announced here.

-The Biomatrix Society is one of the sponsors of the Intelligent
Systems in Molecular Biology (IS/MB) meeting coming up this summer.
We may also be a co-sponsor of the summer school in 1994. 

-We are trying to put together a meeting in 1994 as an add-on to the
Genes and Machines west coast meeting, but it is way, way too soon to
say whether that will actually happen

-The newsletter will come out when we get either (1) another editor;
or (2) regular columnists to contribute to the newsletter.  Much as I
would like to be able to carry the load myself, I can't.


Comments are welcome and can be directed to me or to the newsgroup
(bionet.molbio.bio-matrix or biomatrix@net.bio.net(?))

Happy holidaze, y'all...


dan

-- 
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77204-5934/davison@uh.edu/DAVISON@UHOU

-----RIP Isaac Asimov 1920-1992     I'll miss him --------------------

Disclaimer: As always, I speak only for myself, and, usually, only to
myself.
From: cherry@OPAL.MGH.HARVARD.EDU
Newsgroups: bionet.molbio.bio-matrix
Subject: Re: The Biomatrix: what it is
Date: 3 Jan 93 20:52:52 GMT
Reply-To: cherry@OPAL.MGH.HARVARD.EDU
Distribution: bionet
Organization: Molecular Biology - Mass Gen Hospital

In article <1i7efsINN1hh@menudo.uh.edu>, davison@menudo.uh.edu (Dan Davison) writes:
>	The Matrix subsitutes reasoning by analogy for reasoning
>from first principles.  The proposal is to combine biological
>knowledge in three ways; (1) collect data into databases, and have the
>agencies that fund research get serious about the proper disposition
>of the knowledge they've been funding (such as requiring, as a
>condition of grant funding, any resulting data to be submitted to
>GenBank for nucleotide information; PIR for protein information; and
>Brookhaven for x-ray crystallographic information).

Is there any funding available for providing the resources that are
required that can contain the "knowledge they've been funding"? I
guess more to the point do the funding agencies share the view that
they should make these requirements, they would then have to fund the
databases and the personal required to organize the information. I can
think of projects funded by NIH, DOE and USDA to provide databases for
small specific sets of biological information. To my knowledge these
projects with the exception of GDB are pretty small funding
commitments. Funding for biology is obviously limited and there are
quite a few special interests which have strong lobbies for money.
However I am increasing puzzled by the small mandate for improved
information systems to allow biological knownledge to become
electronic. Can someone share some insight about policy within the
various funding agencies, or is it all moot until the Clinton
administration gets setup. I would also be interested in what the EC
is planning in this area.

Finally, what is the timeframe considered by the BioMatrix group.  Is
the BioMatrix another Xanadu project? Is this an endeavor that is
waiting for significance technology advancements in software
development or are there many active projects currently being pursued
with the Matrix as a goal. I'm well aware of many "database" efforts
but see these generally just trying to get a hold on sequence
information, I'm simplifying quite alot here, but my impression is
that their goals are far that proposed for the BioMatrix.

Mike Cherry
Newsgroups: bionet.molbio.bio-matrix
From: dbd@THEORY.BCHS.UH.EDU (Dan Davison)
Newsgroups: bionet.molbio.bio-matrix
Subject: New Journal: Computational Biology: The Journal of Computational Cell Biology
Date: 22 Dec 92 21:50:07 GMT
Distribution: bionet

Feel free to contact me or D. Kingsbury about this announcement.

dan davison
----------------------------------------------------------------------------

Announcing an important new quarterly peer-review journal.

March 1993

COMPUTATIONAL BIOLOGY

The Journal of Computational Molecular Cell Biology

Editors

Daniel B. Davison, Ph.D.   David T. Kingsbury, Ph.D. Thomas Marr, Ph.D.
University of Houston	   Johns Hopkins University  Cold Springs Harbor Labs
                           School of Medicine

Goals: First, to provide a forum for communication of scientific and 
technical issues  associated with the analysis, management, and 
visualization of cellular information at the molecular level.  
COMPUTATIONAL BIOLOGY will accept papers on: algorithms, 
genomics; mathematical modeling and simulation of biological 
processes; new methods for sequence analysis, including, for example, 
parallel methods; design and implementation of biological databases; 
biological expert system design and use; reasoning by analogy; 
hypothesis formation and testing by machine; and, information 
theory.

Second, is the communication of significant biological problems 
to investigators traditionally outside of biology, but otherwise 
in appropriate areas of science and technology.  This will be accomplished 
by soliciting mini-reviews in diverse areas, and by providing a forum 
for the informal exchange of theories and experimental approaches.

The growth of molecular cell biology has created large amounts of 
complex data, and challenges to data handling, data analysis, and 
interpretation.  The mounting volume and richness of data require 
quantitative and multidisciplinary approaches for analysis and 
interpretation.

For submission of manuscripts send three copies to: David T. Kingsbury, 
The Welch Laboratory, The Johns Hopkins University School of 
Medicine, 1830 East Monument, 3rd Floor, Baltimore, MD 21205-2100.  
Phone: (410) 995-9705. E-mail: dkingsbu@library.welch.jhu.edu.

Subscription rate:  Volume 1 quarterly 1993.
Publisher: Mary Ann Leibert, Inc.
From: PARSONS_A@snd01.pcr.co.uk
Newsgroups: bionet.molbio.bio-matrix
Subject: Quick Jiffy's for GCG or Ig
Date: 23 Dec 92 10:13:51 GMT
Distribution: bionet
Original-To: BIOMATRX <BIOMATRX@UK.AC.DARESBURY>

Greetings BIONAUTS, Internetters, NetFolk, GCG/Ig Consultants,

I have just downloaded the AIDS database produced by Gerald D. Myers and Kersti
McInnes from the NCBI data repository.  After unpacking I have now ended up
with a directory structure as below.  I want to convert these sequences to a
GCG and Ig data library.  Both these packages have the tools to handle the
GenBank and PIR formatted entries but I was wondering if anyone had written a
quick jiffy just to pick out the sequences and ignore the alignments and
supporting info (I dont want to reinvent the wheel).  Also could anyone tell me
the difference between a file with no extensiona and a .NF extension file diffs
would suggest only changes in the annotation and not the sequence. 

Many  ADVthanksANCE - and a Merry Chritmas and a Peaceful New Year!

Tony Parsons  - Pfizer Central Research (UK) <<parsons_@snd01.pcr.co.uk>>


=========================  AIDS DB subdirectory structure  ===================
[.DATABASE]---+
              |
              |--[.NUC_A]------+--[.AGM]
              |                |--[.HIV_1]---------[.HFL]
              |                |                |
              |                |                +--[.NUC_CONS]
              |                |--[.HIV_2]
              |                |--[.MND]
              |                |--[.RELATED]
              |                +--[.SIV]
              +--[.PRO_A]------+--[.AGM]
                               |--[.HIV_1]---------[.HFL]
                               |                |
                               |                +--[.PRO_CONS]
                               |--[.HIV_2]
                               |--[.MND]
                               |--[.RELATED]
                               +--[.SIV]
From: bishop@MAP.MARC.USDA.GOV
Newsgroups: bionet.molbio.methds-reagnts
Subject: Pulsed Field Electrophoresis
Date: 22 Dec 92 14:09:24 GMT
Distribution: bionet

We are interested in purchasing equipment for pulsed field electrophoresis.
What kind of units are other researchers using?  Which ones are good and
which ones should be avoided?  What considerations must be made when
purchasing an apparatus?  Any suggestions on which one to purchase would be
greatly appreciated.  Thanks.
Michael D. Bishop
%USMARC-ARS
PO Box 166
Clay Center, NE 68933
(402)762-4367
From: bchs1b@Elroy.UH.EDU (Michael Benedik)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: ? How to destroy DNA chemically (to reuse DNA columns)
Date: 28 Dec 1992 16:44:27 GMT
Organization: University of Houston
Reply-To: bchs1b@Elroy.UH.EDU
NNTP-Posting-Host: elroy.uh.edu

In article <1haupeINNjfh@usenet.INS.CWRU.Edu>, bl275@cleveland.Freenet.Edu (Dan Diaz) writes:
>
>In a previous article, djt2@po.CWRU.Edu (Dennis J. Templeton) says:
>>
>>You have a point, but our use here will consume ca $6000 per year.  Here's
>>a comparison: would you throw away 10 FPLC columns a year at $600 each to
>>sleep better at night?  maybe you or some would.  This is a variation of
>>the "kit mentality" theme discussed here several times.  I think there are
>>valid arguments on both sides of the discussion.
>
>If you are spending these amounts of cash on columns then its time for you
>to forget prepacked columns altogether and buy youself some resin, pack
>your own columns, and sleep better at night.
>-- 
>Dizzy Dan         ddiaz@cwru.bitnet      bl275@cleveland.freenet.edu
>Department of Molecular Genetics - Albert Einstein College of Medicine
>"My opinions are my own, and they should be yours as well"

I think a lot of people would be happy to pack these columns themselves,
but the question is with what???

----------------------------------------------------------------------
 Michael Benedik				INTERNET: Benedik@uh.edu
 Dept. of Biochemical & Biophysical Sciences	
 University of Houston				BITNET: Benedik@uhou
-----------------------------------------------------------------------
From: txt15@po.CWRU.Edu (Tao Tao)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: MEDLINE
Date: 27 Dec 1992 02:35:51 GMT
Organization: Case Western Reserve University, Cleveland, Ohio (USA)
NNTP-Posting-Host: slc12.ins.cwru.edu


I would be interested in having this piece of info too, so pleae repost it
to the net.  T.I.A.

Tao
-- 
p
Newsgroups: bionet.molbio.methds-reagnts
Subject: supercoiled DNA migration in agrose ?
From: chai_z@wehi.edu.au
Date: 23 Dec 92 11:11:36 +1000
Organization: Walter & Eliza Hall Institute


Hi,

	Several batches of M13 RF DNA of mine have been cut by EcoRI or SmaI,
etc. and then electrophoresized in agrose gel. Uncut DNA (supercoiled) of some
batches migrated faster than the cut one (linear), while the others slower.
Most likely, some batches of my DNA were nicked (open circular). Could any one
tell me the correct agrose pattern of supercoiled, open circular and linear DNA?
or tell me where to refer to?

Thanks in advance.


Zhonglin Chai 
Newsgroups: bionet.molbio.methds-reagnts
From: belas@comb1.comb.umd.edu (BOB AT COMB)
Subject: Plant RNA Isolation Methods
News-Software: VAX/VMS VNEWS 1.41    
Organization: University of Maryland, Center of Marine Biotechnology
Date: Mon, 28 Dec 1992 14:42:00 GMT

	I have need of a method of isolating and purified total RNA from cells
with lots of polysaccharides which co-purify with RNA (when using routine
protocols.)  Although the cells I am working with are bacterial, I would like
to try one of the plant RNA protocols on these cells.  My reasoning is that
since many of the protocols for plant cells are especially designed to deal
with such polysaccharides, I might stand a better chance at isolating RNA
from my bacteria.  I would appreciate any suggestions and references to
such protocols that deal with extraction of RNA from high polysaccharide 
backgrounds.  Thanks.

	Bob


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~    "By tomorrow, a pot smoker will forget he ever read this message."     ~~
~~		(From the Baltimore City Police, 12/92)                      ~~
~~                                                                           ~~	
~~                     Bob (Belas@mbimail.umd.edu)                           ~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
From: ming@ZEUS.AHABS.WISC.EDU ("Ding Ming")
Newsgroups: bionet.molbio.methds-reagnts
Subject: gene synthesis
Date: 21 Dec 92 16:13:29 GMT
Reply-To: ming@zeus.ahabs.wisc.edu
Distribution: bionet
Organization: Animal Health & Biomedical Sciences

Hi,

I isolated a protein recently and got the sequence by protein 
sequencing. Now I want synthesize the gene for this protein which 
only has 35 amino acids and send someone to have it expressed in 
E.coli. The problem now I am facing is which codon I should use for 
expression in E.coli. e.g., shall I use CUU, or CUG, or CUC etc. for 
lysine? Can someone give me a guid or just the references which I 
can look for by myself?

Thanks in advance.

-=ding=-



~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ 
    Ding Ming                     
    (608)265-3544                   ming@calshp.cals.wisc.edu
    Sweet Protein Section           ming@zeus.ahabs.wisc.edu
    Taste Research Lab               
    Department of Animal Health & Biomedical Sciences    
    University of Wisconsin-Madison, 1655 Linden Dr., Madison, WI53706      
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ 
    Office Location: A215 Babcock Hall   HomePhone: 233-2159      
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
From: sbhattac@crc.ac.uk (Dr. S. Bhattacharya)
Newsgroups: bionet.molbio.methds-reagnts
Subject: T-Tracking etc.
Date: 23 Dec 92 19:04:24 GMT
Distribution: bionet
Original-To: methods@uk.ac.daresbury

One way to estimate the gaps between the bands on a T-track
is to run a M13 control sequence using a standard eg universal primer
alongside.

Shoumo Bhattacharya
From: harper@convex.csc.FI (Rob Harper)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: Database search...
Date: 1 Jan 93 14:22:44 GMT
Distribution: bionet
Organization: Finnish Academic and Research Network Project - FUNET

In <9301010746.AA15358@net.bio.net> DTANG@VM1.SI.USHERB.CA (Denis Tang) writes:



>      I am looking for places where I can do FASTA or BLAST searches for
>proteins (is there another place than FASTA@EMBL-HEIDELBERG?).  Also, how can
>I get the PIR sequence numbered P1;S20314 

If you have the mailfasta script you can do FASTA seaches in JAPAN and BLAST
searches from NCBI. There are quite a few scripts floating about for unix and
vms that take the ache out of submitting mail for searches. The one I have
running on our system is mailfasta from Thon De Boer. It is essential. Anyone
with a unixbox should have it. It does so much.

I have sent you the file. I retrieved it via gopher from Dan Davison's 
gopher hole. If you do not have gopher on your system then use a public
access gopher. You will not regret it. Gopher is opening up the network
in ways that you would not have dreamed possible one year ago. You need it.
 
RGDS -=ROB=-
--
 ~ Rob Harper                    ~ E-mail:          harper@convex.csc.fi    
 ~ Finnish State Computer Centre ~ Molbio/software: harper@nic.funet.fi
 ~ P.O. Box 40                   ~ Telephone:       +358 0 457 2076
 ~ SF-02101 Espoo Finland        ~ Fax:             +358 0 457 2302
From: kristoff@net.bio.net (David Kristofferson)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: MEDLINE
Date: 27 Dec 92 16:17:13 GMT
Organization: BIOSCI International Newsgroups for Biology

gat44@iastate.edu (Gabriel Trueba) writes:


> A few months ago there was a posting indicating how to obtain
>access to MEDLINE for free. I would appreciate if somebody can
>send this information.

>G. Trueba
>gat44@iastate.edu
>|

Here are the articles in question.  These could be retrieved using
either WAIS or gopher as explained in the FAQ.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net


From bionet.molbio.methds-reagnts Sun Dec 27 08:12:32 1992
From: leonfdo@CCWF.CC.UTEXAS.EDU (@ccwf.cc.utexas.edu, Leon F. Garcia)
Newsgroups: bionet.molbio.methds-reagnts
Subject: MEDLINE
Date: 7 Nov 92 19:43:45 GMT
Distribution: bionet

This may be common knowledge, or it may have been asked before, but I don't\
know how to access, if possible, MEDLINE via gopher or telnet (preferably for
free). I would if somebody out there knows how to do this please let me know

thanks.

Leon F. Garcia
Univ. of Texas, Austin
leonfdo@ccwf.cc.utexas.edu

From bionet.molbio.methds-reagnts Sun Dec 27 08:12:52 1992
From: axa12@po.cwru.edu (Ashok Aiyar)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: MEDLINE
Date: 7 Nov 92 22:19:32 GMT
Distribution: bionet
Organization: CWRU School of Medicine
NNTP-Posting-Host: axa12-slip.dialin.cwru.edu

In article <49462.leonfdo@ccwf.cc.utexas.edu> leonfdo@CCWF.CC.UTEXAS.EDU (@ccwf.cc.utexas.edu, Leon F. Garcia) writes:

>This may be common knowledge, or it may have been asked before, but I don't\
>know how to access, if possible, MEDLINE via gopher or telnet (preferably for
>free). I would if somebody out there knows how to do this please let me know

MEDLINE can be accessed over the Internet (via Telnet) but I do not believe 
that access is free (at least we still pay for it).  For those who are 
interested, the NLM MedLine "search" software works fine over SLIP 
connections.  I just got it working about 10 minutes back.  The trick is to 
use the ETHERSLIP packet driver and not the SLIP8250 driver (on DOS 
machines).

Ashok
----------------------------------------------------------------------
                             Ashok Aiyar
                     Department of Biochemistry
                         CWRU Medical School
                          axa12@po.cwru.edu
----------------------------------------------------------------------

From bionet.molbio.methds-reagnts Sun Dec 27 08:13:13 1992
From: axa12@po.cwru.edu (Ashok Aiyar)
Newsgroups: bionet.molbio.methds-reagnts
Subject: Re: MEDLINE
Summary: Grateful Med works over TCP/IP and SLIP connections
Keywords: Grateful Med, Internet, TCPIP
Date: 8 Nov 92 00:06:44 GMT
Distribution: bionet
Organization: CWRU School of Medicine
NNTP-Posting-Host: axa12-slip.dialin.cwru.edu

In article <axa12.41.721174772@po.cwru.edu> axa12@po.cwru.edu (Ashok Aiyar) writes:

>>This may be common knowledge, or it may have been asked before, but I don't
>>know how to access, if possible, MEDLINE via gopher or telnet (preferably 
>>for free). I would if somebody out there knows how to do this please let 
>>me know 
>
>MEDLINE can be accessed over the Internet (via Telnet) but I do not believe 
>that access is free (at least we still pay for it).  For those who are 
>interested, the NLM MedLine "search" software works fine over SLIP 
>connections.  I just got it working about 10 minutes back.  The trick is to 
>use the ETHERSLIP packet driver and not the SLIP8250 driver (on DOS 
>machines).

To clarify myself -- by Medline "search" software, I am specifically 
referring to Grateful Med 6.0

Ashok
----------------------------------------------------------------------
                             Ashok Aiyar
                     Department of Biochemistry
                         CWRU Medical School
                          axa12@po.cwru.edu
----------------------------------------------------------------------