HDTenEightyP/NetNews huggingface dataset:
From: samx@vax5.cit.cornell.edu
Newsgroups: bionet.software
Subject: Mac plasmid programs?
Date: 5 Jan 93 11:43:33 EST
Distribution: bionet
Organization: Cornell University

Is anyone aware of Mac programs for keeping records of plasmid constructs?
Such program would hopefully also draw graphic maps of the plasmids,
and keep sequence information.  Thanks!
	-Scott Monsma
	 Boyce Thompson Institute
	 607/254-1369
From: yuan@phoenix.Princeton.EDU (Jeffrey Yuan)
Subject: Has anyone had any experience with DNA Parrot on the Mac?
Originator: news@nimaster
Organization: Princeton University
Date: Fri, 8 Jan 1993 21:50:19 GMT

As the subject header states, I am interested in finding out about
DNA Parrot for the Macintosh.  Apparently, this product is a 
digitizer, but its mode of operation is different than the sonic
digitizers.  Has anyone had any experiences with this.  I will
post any comments that I receive back onto the net.  

******************************************************************
Jeffrey Yuan, Ph.D.
Department of Molecular Biology                                    
Lewis Thomas Laboratory
Princeton University
Princeton, NJ 08544

phone: 609-258-2886     email: yuan@phoenix.princeton.edu or
                               jyuan@quaking.princeton.edu
******************************************************************
From: BOTSALT@VM.UOGUELPH.CA (david salt)
Newsgroups: bionet.software
Subject: what the hell is a gopher?
Date: 11 Jan 93 17:49:15 GMT
Distribution: bionet

A simple question from a wanna-be bionaut.
What the hell is a gopher and/or gopher hole?
Sorry if you have already received this I was not sure if I sent it out.
David Salt (botsalt@vm.uoguelph.ca)
Newsgroups: bionet.software
From: mvalvano@uwovax.uwo.ca
Subject: Re: want pkunpak program
Organization: University of Western Ont, London
Distribution: bionet
Date: Thu, 7 Jan 1993 17:20:18 GMT

In article <00966206.44C22B60.14459@TIGGER.STCLOUD.MSUS.EDU>, q00023@TIGGER.STCLOUD.MSUS.EDU writes:
> Dear netters,
> 	I am looking for PKUNPAK program for de-arcing a program. Also I
> amlooking for some useful list of biotechnoloy softwares. Could anyone can send
> me the program and the list?
> 
> Thanks in advance,
> Gabriel Cheung

There is a long list of available MSDOS programs at Simtel 20. You can access
them (and retrieve them) by ftp at oak.oakland.edu in the  /pub/msdos
subdirectory. Good luck.
-- 
Miguel A. Valvano, Department of Microbiology and Immunology
University of Western Ontario, London, Ontario N6A 5C1, Canada
TEL (519) 661-3996; FAX (519) 661-3499.
Internet Address: mvalvano@uwo.ca
From: smith@mcclb0.med.nyu.edu
Newsgroups: bionet.software
Subject: ENTREZ under VMS and Ultrix anywhere??
Date: 9 Jan 93 19:00:52 GMT
Organization: NYU Medical Center, New York, NY 10016, USA

Is there anywhere where we could get the latest ENTREZ software ported to VAX
/VMS and Motif?  And also Ultrix and Motif...  We have it all up and running 
nicely on our Macs and Win-3.1 PCs: we want to conver all the bases....

Thanks!
 
+----------------------------------------------------------------------------+
|Ross Smith,  Research Computing Resource, Department of Cell Biology, NYU-MC|
|E-Mail:  SMITH@NYUMED.BITNET (BITNET),   SMITH@MCCLB0.MED.NYU.EDU (Internet)|
+----------------------------------------------------------------------------+
Newsgroups: bionet.software
From: saparici@crc.ac.uk (Dr. S.A.J.R. Aparicio)
Subject: Re: Experiences with Entrez under UNIX?
Reply-To: saparici@crc.ac.uk (Dr. S.A.J.R. Aparicio)
Organization: University of Cambridge, Department of Medicine
Date: Fri, 8 Jan 1993 00:22:52 GMT


I would echo the response of cherry@opal.mgh.harv

I maintain entrez on a Sparc cluster with no real troubles.



Sam Aparicio
MRC Molecular Genetics Unit
Cambridge UK
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Subject: belated message!
Organization: Frederick Cancer Research and Development Center
Date: Wed, 6 Jan 1993 18:53:33 GMT

atggagcgacgttattgtcaccgaatttccacaatggcttcagcaaacgatgcgcacgca
cccccttataacgagtggtacgaggcaaga

#include <stdio.h>
#define O (b=b?b-1:(p++,5),*p&1<<b)
#define o O?O
char*p,j=2,b,c;e(n){for(p="|'8I0>+@{=#_P0-]PV.]F>TM!YK'?? |T\"Z8}aE<&D-!:-T'\"\
O<~cG5$,<2'#;/UI.0{d^HV6817-2F95-T7X|c^/1XB]*)3WHG0/0}dN>G RMZB.12.P] ~hM^J\\[\
<R^ (7;)R9A78{gU!:N)E5OPUR><29A6|e&9V;E[Q:,S1.P] }eES.$Z):B.*O+$G_ ~fWU8)75?I#\
75?WHN0{jE=]<V*1]JI#5VK)R9A6~J5X9X#69/+VX4 =S%!X-[)OE #1XRZ\"?~%^-#Dz&M\\RST|%\
G66*~&^HV0> {%^-8_P}%N>FO(}'M^JQ=z&U!:O(J{%&9G4|%ERO(~(WU8)G4{'E=]^G4",b=n;*p++
<122||--b;);c=*p;while(--c>31&&c!=79)putchar(44+(o?o?o?-34:68:O?60:74:O?64:o?o?
2:54:O?23:63:77:O?55:o?76:15:35:-12:o?61:O?56:65:O?66:53:o?o?O?75:58:0:70:57:o?
71:o?73:1:67:O?72:59));c>32?e(n-1):0;}main(){while(++j<15)e(1),e(13+j),e(15),e(
j-(j<4));}

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: robison1@husc10.harvard.edu (Keith Robison)
Newsgroups: bionet.info-theory
Subject: Re: belated message!
Date: 7 Jan 93 04:43:54 GMT

I thought you were a Pascal programmer!?!  -- and who taught 
you how to write readable C code (I thought it was impossible :-)


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

robison@biosun.harvard.edu 
Newsgroups: bionet.info-theory
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Subject: new paper out
Keywords: splice
Organization: Frederick Cancer Research and Development Center
Distribution: bionet
Date: Fri, 8 Jan 1993 23:07:40 GMT

@article{Stephens.Schneider.Splice,
author = "R. M. Stephens
  and T. D. Schneider",
title = "Features of spliceosome evolution and function
inferred from an analysis of the information at human splice sites",
journal = "J. Mol. Biol.",
volume = "228",
pages = "1124-1136",
year = "1992"}

enjoy!

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: p_stampoul@fennel.cc.uwa.oz.au
Newsgroups: bionet.info-theory
Subject: Sabbatical and Research
Date: 8 Jan 93 23:19:39 +0800
Organization: University of Western Australia
NNTP-Posting-Host: fennel.wt.uwa.edu.au

PhD student looking for university in south of England
to spend a one year sabbatical at. No funds required.
Also looking for persons interested in publishing/research
jointly with in the area of application of GA's to Policy
Analysis.
Please respond by e-mail or to:
L. D. Chambers
140 Treasure Road
Queens Park
Western Australia 6107.


THANKS.
From: kristoff@NET.BIO.NET (David Kristofferson)
Newsgroups: bionet.info-theory
Subject: BIOSCI/bionet Frequently Asked Questions
Date: 5 Jan 93 10:00:05 GMT
Distribution: bionet


New users of BIOSCI/bionet may want to read the "Frequently Asked
Questions" or "FAQ" sheets for BIOSCI.  There are two FAQ sheets for
the newsgroup system.  FAQ I describes the general purpose and uses of
the BIOSCI/bionet newsgroups.  FAQ II provides details on how to
participate in these forums.  Both of these FAQs are available for
anonymous FTP from net.bio.net [134.172.2.69] in
pub/BIOSCI/biosci1.FAQ and pub/BIOSCI/biosci2.FAQ.  They may also be
requested by sending e-mail to biosci@net.bio.net (use plain English
for your request).  The FAQs are also posted on the first of each
month to the newsgroup BIONEWS/bionet.announce immediately following
the posting of the BIOSCI information sheet.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net
From: MCCAINKW@DUVM.OCS.DREXEL.EDU (Kate McCain)
Newsgroups: bionet.info-theory
Subject: creationist infosci
Date: 8 Jan 93 21:32:00 GMT
Distribution: bionet

According to Robert Sheaffer's column in the latest *Skeptical Inquirer*
(17(Winter 1993):138-140, there is a creationist biologist named Richard
Lumsden -- associated with the Institute for Creation Research -- who is
"busily demonstrating via information theory that 'the information required
for genomic growth must have been implanted in the organism by creation at the
beginning' and not be a process of evolution."

Do any netters here know of his work? [I will search the standard databases
on DIALOG but just thought I'd ask through informal channels as well.]

Kate McCain                        Die Gedankenexperimente sind frei!!
College of Information Studies
Drexel University
Philadelphia, PA 19104

mccainkw@duvm.ocs.drexel.edu
Newsgroups: bionet.info-theory
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Subject: Re: belated message!
Organization: Frederick Cancer Research and Development Center
Date: Fri, 8 Jan 1993 02:30:35 GMT

In article <robison1.726381834@husc.harvard.edu>
robison1@husc10.harvard.edu (Keith Robison) writes:
>I thought you were a Pascal programmer!?!  -- and who taught 
>you how to write readable C code (I thought it was impossible :-)

credits:

The program is from Eric Snyder (eesnyder@beagle.Colorado.EDU) - I don't
know if he wrote it or got it from somewhere else.
The sequence was posted recently on another bionet group - sorry, I've lost the
reference!  (It should be easy to find in the archive if anybody wants.)

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: p_stampoul@fennel.cc.uwa.oz.au
Newsgroups: bionet.info-theory
Subject: Collaboration and Sabbatical
Date: 8 Jan 93 23:03:00 +0800
Organization: University of Western Australia
NNTP-Posting-Host: fennel.wt.uwa.edu.au

Australian/English PhD student working in the
application of GA's to policy analysis looking
for a place (univ) in the south of England to 
spend a one year, all paid, sabbatical. Would also
like to collaborate with someone in the publication
of articles in the area of Policy Analysis/GA's/
Catastrophy Theory.   THANKS.
Reply by mail or to:
L. D. Chambers
140 Treasure Road
Queens Park
Western Australia 6107.
From: pj@linz.ensmp.fr (Pierre JOUVELOT <jouvelot@cri.ensmp.fr>)
Subject: Automatioc 2D electrophoresis gel analysis?
Organization: Ecole des Mines de Paris, France
Date: 11 Jan 93 14:12:53


I would like to know about existing systems for automatic 2D
electrophoresis gel analysis for protein identification.  What are they?
What are their performances (accuracy) ?  What are their deficiencies
and problems?  What kind of automatic image analysis algorithms are
used?  What are the standard references?  Any comment is welcome.

Please reply by e-mail since I don't read this newsgroup very often.

Thanks,

Pierre (jouvelot@cri.ensmp.fr)
--
Centre de Recherche en Informatique 			(cri)
Ecole Nationale Supe'rieure des Mines de Paris		(ensmp)
France							(fr)
From: kristoff@NET.BIO.NET (David Kristofferson)
Newsgroups: bionet.general
Subject: BIOSCI/bionet Frequently Asked Questions
Date: 4 Jan 93 10:00:02 GMT
Distribution: bionet


New users of BIOSCI/bionet may want to read the "Frequently Asked
Questions" or "FAQ" sheets for BIOSCI.  There are two FAQ sheets for
the newsgroup system.  FAQ I describes the general purpose and uses of
the BIOSCI/bionet newsgroups.  FAQ II provides details on how to
participate in these forums.  Both of these FAQs are available for
anonymous FTP from net.bio.net [134.172.2.69] in
pub/BIOSCI/biosci1.FAQ and pub/BIOSCI/biosci2.FAQ.  They may also be
requested by sending e-mail to biosci@net.bio.net (use plain English
for your request).  The FAQs are also posted on the first of each
month to the newsgroup BIONEWS/bionet.announce immediately following
the posting of the BIOSCI information sheet.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net
Newsgroups: bionet.general
From: T80SMS1@NIU.bitnet
Newsgroups: bionet.general
Subject: A question of publication ethics
Date: 4 Jan 93 17:14:00 GMT
Distribution: bionet

A situation as arisen involving a conflict between authors of
a paper.  What I wish to do is see if others agree with my
advice.  The situation is as follows.  A woman did a MS thesis
and is now in conflict with her former advisor over the
publication.  The advisor provided some of the initial idea
and the basic experimental design.  The student did all of the
work involving implementing the basic design, analysing the
data, and writing it up.  She is the senior author on the
manuscript in question.  The problem is that the advisor (who
is an @#%@) wants to include data that the student does not
feel is relevant, keeps asking for new analyses and new
rewrites, etc.  This has been going on for almost 2 years.
   My advice to the student was that as senior author she has
the final say on the paper.  Once she is satisfied on the
content of the manuscript, she has the right to tell the
junior author that he can either go along with her
decisions or take his name off of the paper.  (The other
option is for her to simply give up and let him write it as
he wants, if it ever gets published.)
   So, my basic question is, what are the ethics of a situation
when authors of a manuscript are in conflict over its content.
Who has the final say?  What if they cannot agree?  Obviously
this issue has wider implications than this particular case
(for example, post-docs or junior scientists in a big lab).
Does anyone have any anecdotes that they wish to share?  Note
that in this case the student can tell her former advisor to
"Buzz off" with no consequences.  Clearly, any answer might
differ in other circumstances.

*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*
* Samuel M. Scheiner                 +                            *
* Department of Biological Sciences  +    Education is a          *
* Northern Illinois University       +                            *
* DeKalb, Illinois 60115             +    subversive activity!    *
* Phone:  (815) 753-7847             +                            *
* Fax:    (815) 753-0461             +                            *
* Bitnet: t80sms1@niu                +                            *
*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*
From: cliff@WATSON.IBM.COM ("Cliff Pickover ", 914 945-3630)
Newsgroups: bionet.general
Subject: Muscle Contraction
Date: 6 Jan 93 21:08:00 GMT
Distribution: bionet

Hi, I'm aware of the actin/myosin and phosphocreatine/creatine
mechanisms of muscle contraction in vertebrate muscles.  Is this same
mechanism used in crustaceans?

If you respond, please send a note to cliff@watson.ibm.com as
I sometimes have difficulty reading the forum.

Thanks, Cliff
From: cliff@WATSON.IBM.COM ("Cliff Pickover ", 914 945-3630)
Newsgroups: bionet.general
Subject: Arthropod Size
Date: 6 Jan 93 18:41:44 GMT
Distribution: bionet

Could anyone review with me why an crustacean such as a lobster
could not survive if it were the size of an elephant.
Is it a physiological problem (surface area to volume ratio for
gills)?  Could such an organism walk on land or would it
collapse under its own weight?

If you respond, please send a note to cliff@watson.ibm.com as
I sometimes have difficulty reading the forum.

Thanks, Cliff
From: wastec@unpsun1.cc.unp.ac.za (Centre For Waste Technology)
Newsgroups: bionet.general
Subject: RE: INFO. ON MSc - RIVER MODEL
Date: 7 Jan 93 13:49:26 GMT
Distribution: bionet
Original-To: bioforum@uk.ac.daresbury
Original-Cc: wastec@ZA.AC.UND.CC.Bertha
X-Mailer: ELM [version 2.3 PL11]

Hello all readers,
 
RE: INFORMATION ON MULTI-STAGE RIVER MODEL.

We are building a multi-stage physical river model to determine the
specific impact of point and diffuse source of pollution discharge.  The
response of one microbial population - responsible for catabolism of
organic molecules in river waters - to selected molecules in river
waters - to selected molecules associated with water pollution will be
determined.  This information will be used to assist in the subsequent
development of a predictive computer based model.

INFORMATION REQUESTED:

- Specifacations, parameters for experimental streams/rivers
(multistage).
- Methodology for qualitative and quantitative characterization of
microbial populations associated with catobolic processes in fresh water
systems.

If you have any questions or advice please contact me via Barry Dudley.
 
Yours sincerely
Charles Hunter
MSc Student
 
#############################################################

Barry Dudley
International Centre for Waste Technology
Department of Microbiology and Plant Pathology
University of Natal
PO Box 375
Pietermaritzburg
3200
South Africa
Email wastec@unpsun1.cc.unp.ac.za

############################################################
From: cliff@WATSON.IBM.COM ("Cliff Pickover ", 914 945-3630)
Newsgroups: bionet.general
Subject: Growth hormone
Date: 6 Jan 93 16:36:32 GMT
Distribution: bionet

I'm familiar with the application of externally applied growth hormones
in humans to increase their size.
Would anyone know if similar substances exist to increase the size
of organisms such as lobsters and other crustaceans?

If you respond, please send a note to cliff@watson.ibm.com as
I sometimes have difficulty reading the forum.

Thanks, Cliff
From: toby@stein.u.washington.edu (Toby Bradshaw)
Newsgroups: bionet.general
Subject: Re: A question of publication ethics
Date: 4 Jan 1993 21:36:49 GMT
Organization: University of Washington, Seattle
Distribution: bionet
NNTP-Posting-Host: stein.u.washington.edu

In article <Jan.4.10.45.39.1993.29884@net.bio.net> kristoff@net.bio.net (David Kristofferson) writes:
>>    My advice to the student was that as senior author she has
>> the final say on the paper.
>
>Traditionally the head of the laboratory has always had the final say
>on the contents of papers, regardless of the order of the authors,
>unless they specifically give this privilege up to another author.

Said "heads" often have not provided even the germ of an idea, nor the
experimental design, in contrast to the case presented by S. Scheiner.  My
view is that "heads", if they have provided nothing but space, money, and
moral support, deserve a nice acknowledgement and not authorship.  Science
needs a place to work, money to work with, and sometimes a pat on the
back.  It doesn't need coauthors who have provided _only_ the above, or
we might as well put the university president's name on the paper, too. 
Any person contributing significant (subjective) intellectual resources
deserves the option of authorship, and anyone who has provided key, novel
(both subjective) ideas or _any_ data has veto power over its/their
publication.  The physical data are easier to protect from unwanted
publication than the ideas, as a rule. 

Data gathered by technician(s) working under the specific direction of the
PI belong to the PI, and the technician's contribution need not
necessitate coauthor status.  Should the technician pursue an original
idea (luckily, all the good ones do), the data, its use, and coauthorship
(including veto power over publication) belong to the technician. 

All the above IMHO, of course.  My (admittedly narrow) world view
is that "heads" receive too much credit, and technicians not
enough.  Your mileage no doubt varies substantially.  And, no,
I have never been a lab tech.  I _have_ spent grant money on
work that never had my name on it, returning the ethical
favor shown (not just told) to me when I was a student.

Toby Bradshaw                       |
Department of Biochemistry          |  Will make genetic linkage maps
and College of Forest Resources     |            for food.
University of Washington, Seattle   |
toby@u.washington.edu               |
From: kristoff@net.bio.net (David Kristofferson)
Newsgroups: bionet.general
Subject: Re: A question of publication ethics
Date: 4 Jan 93 18:45:39 GMT
Distribution: bionet
Organization: BIOSCI International Newsgroups for Biology

>    My advice to the student was that as senior author she has
> the final say on the paper.

Traditionally the head of the laboratory has always had the final say
on the contents of papers, regardless of the order of the authors,
unless they specifically give this privilege up to another author.
Are there any other channels for resolving grievances on your campus,
e.g., through arbitration of some kind?

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net

Newsgroups: bionet.general
From: wnelson@cmgm.stanford.edu (Will Nelson)
Subject: Re: A question of publication ethics
Organization: Stanford University, California, USA
Distribution: bionet
Date: Thu, 7 Jan 1993 04:59:25 GMT

T80SMS1@NIU.bitnet writes:

>A situation as arisen involving a conflict between authors of
>a paper.  What I wish to do is see if others agree with my
>advice.  The situation is as follows.  A woman did a MS thesis
>and is now in conflict with her former advisor over the
>publication.  ...

I ran into a similar situation as I was finishing up the
collection of my doctoral dissertation data. My mentor kept
suggesting small add-on experiments that were not part
of the initial design and frankly had no possibility of
valid statistical analysis. Unfortunately, I was not in
a position in tell him to kiss off, since I wouldn't have
received my degree.

What I did was to speak with a lawyer, and found out that
these types of things have no place in a court of law. Ie,
I couldn't sue him.

I then spoke with another professor who was on my commitee,
and he more or less intervened and found a compromise that
was acceptable to the both of us. 

The bottom line is that the mentor/mentee relationship is
not that different from master/slave.

I received my degree, the paper got published after
a couple of revisions, and now I'm out of the field.

I suspect that many graduate students have even more horrible
experiences that they could relate. These things are not at all
uncommon.
--
Will Nelson
Computer Resource Administrator
The Beckman Center at Stanford
will@cmgm.stanford.edu
Newsgroups: bionet.general,bionet.software
From: gonnet@inf.ethz.ch (Gaston Gonnet)
Subject: Phylogenetic tree of various globins
Organization: Dept. Informatik, Swiss Federal Institute of Technology (ETH), Zurich, CH
Date: Tue, 12 Jan 1993 15:27:32 GMT

During last December, someone requested to our automatic
server the multiple alignment, phylogenetic tree, etc.
of a large set of sequences (hemoglobins, myoglobins,
leghemoglobins, 630 sequences in total).

The job could not be run at the time due to lack of resources,
and I promised the requester to send the answer back once we
could allocate it to a machine with enough memory.  Well,
the job has been done, but I cannot find the original message,
(we must have deleted some files incorrectly) and hence cannot
send the answer back as promised.  Please contact me if you
are still interested in the results.  (Sorry to use the net for
this purpose).

At that time, the question of how large a phylogenetic tree
can be constructed, was also raised.  Our algorithm has the
following characteristics:

For the construction of a phylogenetic tree between n sequences

Storage: It uses two input matrices, both n x n, one with the
	distance between sequences and one with the variance
	of these distances.  Since these are double words, and
	this is the dominant use of storage, you will need
	16*n^2 bytes.

Time: (On a DEC5000 workstation, just the phylogenetic tree
	construction)
	n= 50	 5.3 secs		(random distances)
	n=100	22.0 secs		(random distances)
	n=200	96.9 secs		(random distances)
	n=630   31.3 mins		(tree mentioned above)

	(In the long run, ie. for much higher n, an O(n^3) term
	should dominate the time).

The algorithm approximates the unrooted tree, with variable
length branches, which minimizes the weighted sum of squares
of distance differences (between the given distance and the
"tree" distace).

For more information on these trees and multiple alignments,
send by e-mail the line "help AllAll" to cbrg@inf.ethz.ch


Gaston H. Gonnet, Informatik, ETH, Zurich
Newsgroups: bionet.general