HDTenEightyP/NetNews huggingface dataset:
From: kristoff@net.bio.net (David Kristofferson)
Newsgroups: bionet.molbio.genbank
Subject: Re: Internet Commercialization
Date: 8 Jan 93 19:06:20 GMT
Distribution: bionet
Organization: BIOSCI International Newsgroups for Biology

ES@JII.AFRC.AC.UK writes:

>So, do you imply and really think that there is no public research and 
>education (and therefore educators and researchers) 'beyond the U.S.' ?

>Eric Schoonejans.edu.public.free.world

>es @ jii.afrc.ac.uk
> 
>es @ versailles.inra.fr

You mean science really exists outside of our borders??!!  Mon dieu!!
What a revelation!! 8-) 8-)

Of course, I don't mean this.  Each country has their own government
agency or private company or whatever that provides them with network
services.  I don't know the details, but I doubt that the U.S.
National Science Foundation plays a large role in providing network
services in Europe.  I would hazard a guess that each country
currently is already satisfying their own needs, that international
agreements and joint payments for international connectivity are
already in place, and that by "beyond the U.S. research and education
community" this *domestic* document was probably refering to U.S.
commercial companies and potential home users being able to look
forward to fees for Internet access.  If others can shed more light on
this topic however, please feel free to do so.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net
From: kristoff@NET.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.molbio.genbank
Subject: Re: This is a question to bionet.software, commercial issue.
Date: 8 Jan 93 02:41:06 GMT
Distribution: bionet


Mike,

	It appeared from my reading of the announcement that the
phrase

"may charge users beyond the U.S. research and education community."

came up repeatedly.  This still implies to me that the network will be
free to educators and researchers.  There already are commercial
companies providing many of the network services.

Dave
From: kristoff@NET.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.molbio.genbank
Subject: Re: BLAZE survey
Date: 8 Jan 93 02:07:55 GMT
Distribution: bionet

> Hi,
> 
> First, I do not wish this to turn into a flame war, I guess the dreaded
> British humour does not always commute.... I guess I had forgotten that :( 

Neither do I, so I am going to keep this relatively short and only
answer the main question that you posed.  We can agree to differ
without rancor on some of the other issues.

> Are you saying you actually read this message and decided it was OK, or just
> that he asked if it would be OK to post in the general area of this material.
> The latter is what is implied I think. I can't believe you read and sanctioned
> this rubbish. 

I did not read the entire list of comments, and I am not saying that I
thought that the posting was a *definitive* resolution of the relative
merits of the three programs.  I also don't think that Rich Stamm nor
anyone else here or at Maspar felt that way either (but they can
comment for themselves on this if they wish).  However, there was a
belief that readers would be interested nonetheless in seeing users'
survey responses on the issue.  Obviously there is a financial motive
on the part of the companies, but the flip side is that they are
providing a service which several researchers apparently found to be
useful.

While not scientific data, I can not agree that the survey is total
rubbish.  A lot of tips that people pass back and forth in the halls
on experimental methods have not much more in the way of supporting
evidence than "personal experience" and yet their colleagues often act
on these suggestions just to see if they will work.

My personal comment to people on the Blaze team before the posting was
that the posting was O.K. to do since a question was posed on the
issue, but that the scientific comparison should come first followed
by these comments if they really wanted to be effective.  The authors
of the paper were not in a position to post the results yet
unfortunately.  I hope that they will do so when they are ready.  As
you may or may not be aware, one of our (IG's) previous search
programs has been written up in CABIOS, and I hope that the new
results with BLAZE will also make it through the gauntlet (although I
wouldn't be surprised if the fact that it's commercial software may
complicate the review).

> other programs, etc etc etc. which is what was asked for. This really doesn't
> stand up as a survey, the results of which should be a valuable contribution
> to the audience. 

Most people do not take the time to write extensive replies to
surveys.  What you see is what we got.  I understand your concerns
about this not being a complete answer to the question, but, as I said
above, hopefully there will be more substantial stuff to come.  As to
the value of the comments made in the survey, people will obviously
have differing opinions on this depending upon how it affects them.

Dave
Newsgroups: bionet.molbio.genbank
From: MCKMICP@YaleVM.YCC.Yale.Edu (Michael McKenna)
Subject: Re: BLAZE survey
Organization: Yale University
Date: Fri, 08 Jan 93 02:01:00 EST

 
In article <1993Jan7.191621.1@vax.path.ox.ac.uk>
jasper@vax.path.ox.ac.uk writes:
 
>>> Will the *real* Michael McKenna please stand up?   :)
>
>well it *was* a joke....
 
stuff deleted
 
>barely relevant, but I obviously am happy that he exists.
 
me too!
 
As the original poster (I do exist) I have to admit that I was seeking
the kind of qualitative information that was posted in the BLAZE survey.
Since the survey clearly originated from MasPar, I didn't interpret the
post as a manipulative advertisement.
 
Having read some of the literature that compares various algorithms,
the articles tend to sort into two classes:
 
     1) Theoretically based papers discussing the various mathematical
        merits of one algorithm versus another. The authors are likely to
        have an investment in their favorite tool, and it's not always clear
        (to me) how the math translates to the real world
 
     2) Very general papers which look at two or three sequences and
        draw conclusions about algorithm strengths from a limited database.
 
It seems to me that all the algorithms have their unique strengths and
weaknesses- and this is going to be strongly sequence dependent. That
is why I made the original post, in an attempt to discern the relative
strengths of the programs for different applications.
 
Phil Stamm's post from MasPar was interesting in that it derived from
many sources and had different reponses. It is tainted somewhat by the
commercial connection, but more, I thought, by the unwieldiness of the survey
results.
 
Dave Kristofferson e-mailed me and mentioned a summary that Doug Brutlag had
written; does anyone have a copy of this file or any other comparative
reference for that matter.
 
I never thought I'd see a flame-war in bionet.molbio.genbank!
 
Michael McKenna  MCKMICP@YaleVM.YCC.Yale.edu
I do exist-- really...
From: kristoff@NET.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.molbio.genbank
Subject: Re: BLAZE survey
Date: 5 Jan 93 19:20:59 GMT
Distribution: bionet

> 
> Thanks for your views Dave, I guess it's a pretty sticky wicket
> (excuse the cricket term).
> Certainly it's not too much of a sacrifice if companies are denied
> advertizing on USENET to keep things under control.
> 
> Cheers,
>    Chris
> 

NSF is concerned that allowing the posting of commercial jobs will
waste bandwidth that is intended for research purposes.  My feeling is
that science is going to suffer far more damage if scientists can't
find jobs, and this is a great medium to bring people together.  I
have made numerous attempts without success to contact Steve Wolff
over the last three months (he is a very busy guy apparently and
hasn't answered e-mail or phone messages).  I am going to try offering
a compromise position which limits the size of the posting, e.g., to
job title and one line description plus contact address, and see if
this flies.

Dave
From: jasper@vax.path.ox.ac.uk
Newsgroups: bionet.molbio.genbank
Subject: Re: BLAZE survey
Date: 5 Jan 93 17:34:23 GMT
Distribution: bionet
Organization: Oxford University Molecular Biology Data Centre
Nntp-Posting-User: jasper

In article <9301050203.AA16211@argosy.MasPar.COM>, stamm@MasPar.COM 
(Richard Stamm) writes:
> This posting is in response to Michael McKenna who writes:
> 
>> ...I grew kind of fond of the BLAZE server at IG during the short period
>> it was available (for free). And does anybody have any comments regarding the
>> _practical_ advantages of the various search strategies- ie FASTA, BLAST,
>> BLAZE.

Will the *real* Michael McKenna please stand up?   :)

> I recently compiled the responses of a survey taken of all users
> of the GenBank BLAZE server.   We will post a tally and summary of 
> all the responses shortly.  What I am posting here is a listing of 
> the qualitative comments contained in the responses -- that is, 
> comments where the person had actually used the server and took 
> the trouble to write down something other than "yes", "no", or 
> "couldn't tell".  We felt that some of these qualitative comments 
> reveal the kind of information that Michael asks for.

Then instead of the  

>> _practical_ advantages of the various search strategies- ie FASTA, BLAST,
>> BLAZE.                      

requested, there was attached an apparently everlasting string of unascribed, 
unsubstantiated, unscientific nonsense, of the level normally seen in the 
less imaginative television advertisements for products such as soap powder, 
breakfast cereals or dog food.

> A scientific comparison of the various search methods is in also
> in preperation.  

Fine, write it up, submit it for publication in a peer reviewed journal, and
if it is accepted then we can all read it. 
 
> Rich Stamm 
> stamm@maspar.com
               ^^^ !!! 

I think this is unadulterated advertising of the lowest form, this is a
service for which you are expected to PAY, it is not longer free, and as such
this posting is way out of line for UseNet. 

Of course if Dave K thinks it's OK, then I withdraw the above unconditionally 
and apologise. 

regards,   jasper


Jasper Rees
Oxford University Molecular Biology Data Centre
and The Sir William Dunn School of Pathology
Oxford University
United Kingdom

jasper@vax.path.ox.ac.uk
Newsgroups: bionet.molbio.genbank
From: danj@welchgate.welch.jhu.edu (Dan Jacobson)
Subject: Re: (none)
Organization: Johns Hopkins Univ. Welch Medical Library
Distribution: bionet
Date: Mon, 4 Jan 1993 19:22:06 GMT

In article <01GT4AS1XBYS90MT93@vax.csc.cuhk.hk> S911896@VAX.CSC.CUHK.HK writes:
>Dear Sirs,
>
>I want to contact Keiko Ozato of lab of developmental and molecular immunity, national institute of child health and human development, National Institute of Health, Bethesda, MD 20892. I shall have a discussion about his/her published
>paper. Please give me his/her e mail address.
>

I couldn't come up with an email address off-hand but I did find a phone
number.

Dr. Ozato Keiko   (301) 496-9184 


Best of luck,

Dan Jacobson

danj@welchgate.welch.jhu.edu
  
Newsgroups: bionet.molbio.genbank
From: cup@bones.biochem.ualberta.ca (Chris Upton)
Subject: Re: BLAZE survey
Reply-To: cup@bones.biochem.ualberta.ca
Organization: Biochem U 0f A
Distribution: na
Date: Tue, 5 Jan 1993 16:45:59 GMT

A question about the posting of this MasPar "ADVERTISEMENT".....
Don't get me wrong, I'm very interested in the BLAZE survey, but
how come ABI isn't allowed to put job adverts on USENET when this
 this product information/adveristement is allowed? 
I would have thought the ABI job info was more beneficial to the 
readers than ABI.
I guess it's a close call. Any other views?

---
Chris_Upton@darwin.biochem.ualberta.ca
Biochemistry Department
University of Alberta
Edmonton, AB T6H 2H7
Canada
From: ES@JII.AFRC.AC.UK
Newsgroups: bionet.molbio.genbank
Subject: Internet Commercialization
Date: 8 Jan 93 13:01:00 GMT
Distribution: bionet
Original-To: GENBANKB@UK.AC.DARESBURY

Adieu veaux, vaches, cochons, couvees, ftp sites, databases, blaze, electronic
communication.....

Message-Id: <9318024906.MIN-LFKAa11523.bionet-news@uk.ac.daresbury>
kristoff@NET.BIO.NET (Dave Kristofferson)

writes:

>Mike,
>
>	It appeared from my reading of the announcement that the
>phrase
>
>"may charge users beyond the U.S. research and education community."
>
>came up repeatedly.  This still implies to me that the network will be
>free to educators and researchers.  There already are commercial
>companies providing many of the network services.
>
>Dave
>

So, do you imply and really think that there is no public research and 
education (and therefore educators and researchers) 'beyond the U.S.' ?

Eric Schoonejans.edu.public.free.world

es @ jii.afrc.ac.uk
 
es @ versailles.inra.fr
Xref: sparky bionet.molbio.genbank:626 bionet.software:2396
From: bell-peter@yale.edu (vineland expatriate)
Newsgroups: bionet.molbio.genbank,bionet.software
Subject: Re: This is a question to bionet.software, commercial issue.
Date: 7 Jan 1993 23:19:01 -0500
Organization: Yale University Science & Engineering UNIX(tm), New Haven, CT 06520-2158
NNTP-Posting-Host: minerva.cis.yale.edu

<information about commercial bids for managing inet services deleted>

Is this post what it appears to be?  In particular, the language about 
"fees for use by users outside the US research and education community?"  
That sounds a lot like it will start costing money for folks outside the 
US to maintain net feeds in the not-distant-at-all future, over and above the 
current costs--that they will be being billed for the services of the 
contractors, as will .com and some .mil sites, and ultimately .edu sites 
as well, right?

Or, better yet, does it mean that the contractors can begin selling out email
addresses to cover costs, generating electronic junk mail?  

Any comments on this?  Or is there a newsgroup I ought to just go read to hear
more about this?

just wondering,

Peter
From: danj@welchgate.welch.jhu.edu (Dan Jacobson)
Subject: Re: (none)
Organization: Johns Hopkins Univ. Welch Medical Library
Distribution: bionet
Date: Tue, 5 Jan 1993 15:49:40 GMT

In article <01GT62T3HFX48WW3VJ@vax.csc.cuhk.hk> S911896@VAX.CSC.CUHK.HK writes:
>Dear nectters,
>
>If you know the e mail address of Dr. Young-ping Hwung of Dept of 
>Pharmacology, Stanford University. Please let me know.
>
>Best regards.
>
>Qiu Yaowu
>The Chinese University of Hong Kong.
>

I think the following is what you're looking for.
This type of question is better suited for the bionet.users.addreses
(Bionaut) group.


        elaine6.stanford.edu
        Login name: hwung                       In real life: Young-Ping Hwung
        Directory: /s14/h/hwung                 Shell: /bin/tcsh
        Never logged in.
        New mail received Mon Jan  4 10:20:58 1993;
          unread since Tue Dec 22 11:49:32 1992
        Project: Sorry, I don't have a project description yet.
        No Plan.

"Never logged in" so I suspect that this is a mailserver which 'pops'
it over to there Mac or PC.   


Best of luck,

Dan Jacobson

danj@welchgate.welch.jhu.edu
From: POSTMASTER@NBRF.GEORGETOWN.EDU
Newsgroups: bionet.molbio.proteins
Subject: Announcement of PIR Service Interruption
Date: 4 Jan 93 19:32:43 GMT
Distribution: bionet


            Announcement of Temporary Interruption of Access to
                   The Protein Identification Resource

The National Biomedical Research Foundation will (once again) be attempting
to repair a hardware problem on Tuesday 5 January.  From 12:00 EST Tuesday 5
January through about 17:00 EST Wednesday 6 January it will not be possible
for users to access the Protein Identification Resource Network Server.  The
On-line System is currently unavailable but should be back up when the system
is restored.

We regret any inconvenience this temporary loss of service will cause.
------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Information Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMAST@GUNBRF.BITNET
                                 POSTMASTER@NBRF.GEORGETOWN.EDU
Newsgroups: bionet.molbio.proteins
From: zsha@iastate.edu (Zhengyu Sha)
Subject: Re: protein transportation
Organization: Iowa State University, Ames IA
Date: Tue, 12 Jan 1993 21:31:26 GMT

In <1iuvuiINNf0k@terminator.rs.itd.umich.edu> Mark A. Saper <saper@elmo.biop.umich.edu> write:

>I know about the periplasmic transport proteins ... these all have leader
>sequences.  Is the protein that you are working with known to not have a
>leader sequence?

I have cloned and seqed a catalase gene which I purified the enzyme from periplasmic fraction from B.abortus which is a gram-negative bacterium. N-terminal amino acid sequence of the purified enzyme show no cleavable leader sequence. The a.a. sequence predicted by the nuceotide seq. also did not show any signal-like sequences. I checked the a.a. sequence of the periplasmic catalase of E.coli HP I(Biochem.Biophys.Res.Comm. 154:392-397) in the gene bank and could not find a leader sequence too. A recent mini




review in J.B. said membrane and periplasmic bacterial proteins used the uniformal secretion mechanism. In  contrast, some of the extracellular proteins use self-promoted extracellular secretion mechanisms. I wonder if anyone has any idea?
From: Mark A. Saper <saper@elmo.biop.umich.edu>
Newsgroups: bionet.molbio.proteins
Subject: Re: protein transportation
Date: 12 Jan 1993 17:42:42 GMT
Organization: Biophysics Research Div., Univ. of Michigan
Distribution: world
NNTP-Posting-Host: elmo.biop.umich.edu
X-UserAgent: Nuntius v1.1

In article <zsha.726286172@sanger.bb.iastate.edu> Zhengyu Sha,
zsha@iastate.edu writes:
>Could somenetter tell me how a periplasmic protein without a leader
sequence is 

I know about the periplasmic transport proteins ... these all have leader
sequences.  Is the protein that you are working with known to not have a
leader sequence?
From: ramin@brain.bchs.uh.edu (ramin homayouni)
Newsgroups: bionet.molbio.proteins
Subject: Electrospray tandem mass spec for protein sequencing
Date: 7 Jan 1993 01:31:52 GMT
Organization: University of Houston
NNTP-Posting-Host: brain.bchs.uh.edu

Hello netters,
I have recently heard from a colleague that protein sequences may be determined  
by using electrospray tandem mass spectroscopy.  My knowledge in this field is  
extremely poor. So I'm wondering if anyone would suggest some references which  
review this technique and discuss the pros and cons of using this technique in  
comparison with traditional methods of protein sequencing. 
Also, does anyone know of a service which will sequence a protein using  
electrospray tandem mass spec?

ANY input on this topic will be greatly appreciated.

Thank you in advance.

Please reply to : Ramin@brain.bchs.uh.edu
Newsgroups: bionet.molbio.proteins
From: vjongene@isrec-sun1.unil.ch (Victor Jongeneel)
Subject: Re: (none)
Organization: University of Lausanne CH (Switzerland)
X-Newsreader: TIN [version 1.1 PL8]
Distribution: bionet
Date: Mon, 4 Jan 1993 07:08:58 GMT

S911896@VAX.CSC.CUHK.HK wrote:
: Dear nectters,

: If you know what are the transcriptional factors of GCN4, steroid binding 
: protein gene, or other growth regulatory factor genes, please let me known
: as soon as possible. I am doing related analyses.

: Thank you for your great helps.

: Sincerely,

: Qiu Yaowu
: Chinese university of Hong Kong


The primary sequences of most known transcription factors, and much
detailed information about them, are documented in David Ghosh's
Transcription Factor Database (TFD).  The database and its
documentation are available by anonymous ftp from ncbi.nlm.nih.gov in
/repository/TFD.

This should answer both of your questions (and much more).

Good luck!

--

C. Victor JONGENEEL                      vjongene@isrec-sun1.unil.ch
Ludwig Institute for Cancer Research
Chemin des Boveresses 155                       FAX: +41-21-653-4474
CH-1066 EPALINGES                               Tel: +41-21-316-5994
Switzerland                 "Where the cows moo and the people vote"
From: masure@ROCKVAX.ROCKEFELLER.EDU
Newsgroups: bionet.molbio.proteins
Subject: (none)
Date: 9 Jan 93 04:31:53 GMT
Distribution: bionet

help
Newsgroups: bionet.molbio.proteins
From: news@magnus.acs.ohio-state.edu
Subject: help
Organization: The Ohio State University
Distribution: usa
Date: Wed, 6 Jan 1993 13:40:49 GMT

This article was probably generated by a buggy news reader.
From: POSTMASTER@NBRF.GEORGETOWN.EDU
Newsgroups: bionet.molbio.proteins
Subject: Announcement of PIR Technical Development News
Date: 8 Jan 93 17:54:21 GMT
Distribution: bionet


                Announcement of the Protein Information Resource
                           Technical Development News

We have on-going efforts to standardize the PIR databases, improving their
parsability and compliance with CODATA and other format standards.  During
the next year the combined staffs of the PIR-International will be imposing
and enforcing many new rules and requirements on the distributed versions of
the database.  Some of these rules and requirements may affect the currently
existing software designed to read the PIR databases in "NBRF format".
Notification of the broader aspects of these changes will be placed in our
newsletters and in announcements posted on the BioSci Newsgroups PROTEINS and
BIONEWS.  However, some people may wish to be informed about the technical
aspects of these changes before they appear in a database release.  For that
reason we will be setting up an electronic mailing list to inform software
developers and others interested in the technical aspects of these database
changes.

If you would be interested in being placed on this mailing list, please send
a brief electronic mail note to me at one of the network addresses below.
------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Information Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMAST@GUNBRF.BITNET
                                 POSTMASTER@NBRF.Georgetown.Edu
Newsgroups: bionet.molbio.proteins
From: ldruhan@magnus.acs.ohio-state.edu (Lawrence J Druhan)
Subject: help
Keywords: help
Organization: The Ohio State University
Distribution: oh
Date: Wed, 6 Jan 1993 17:35:36 GMT

help - I want to use cassette mutagenesis to create a point mutation but the 
base that must be changed is in the overhang region of one of the restriction 
sites the cassette will use.  There is still 3 bases that can base pair.  Will 
this work?   Please reply via e-mail.
Thanks in advance -
Lawrence Druhan
druhan.1@osu.edu
From: zsha@iastate.edu (Zhengyu Sha)
Subject: protein transportation
Organization: Iowa State University, Ames IA
Date: Wed, 6 Jan 1993 02:09:32 GMT

Could somenetter tell me how a periplasmic protein without a leader sequence is transported across the inner membrane in bacteria. I am specifically interested in the Catalase HP I in the E.coli but the mechanisms involving other proteins  are helpful too.
Newsgroups: bionet.molbio.gene-linkage
From: roger@kean.ucs.mun.ca
Subject: PEDIGREE/DRAW software
Organization: Memorial University. St.John's Nfld, Canada
Date: Tue, 12 Jan 1993 13:40:57 GMT

	I have heard rumours of a new version of PEDIGREE/DRAW software for 
(guess what?) drawing pedigrees on a Mac. We have version 4.3 (Sept 1991); 
is there a later version, or a version for an IBM-PC running OS/2 
or Windows NT?
-- 
Roger C. Green,	Faculty of Medicine                      Phone: (709)737-6884
Memorial University , St. John's, Newfoundland.          FAX  : (709)737-7010