HDTenEightyP/NetNews huggingface dataset:
From: cvl@athena.mit.edu (Craig V Lewis)
Newsgroups: bionet.biology.computational
Subject: Re: Computerized lab notebook?
Date: 10 Jan 93 19:39:26 GMT
Distribution: bionet
Organization: Massachusetts Institute of Technology
Originator: biocomp@lerkim.umiacs.umd.edu

I strongly recommend against the use of a computer as your sole data record!!

They are far too sensitive to several hazards; magnetic fields, physical
shock, liquid spills, and software viruses may all eliminate data
irretrievably.  There exist commercial programs capable of wiping data
from hard disks so completely that they meet government security standards.
Just imagine spilling a critical sample into your computer immediately
after analysis.  The sample is gone and the data are gone;  you will have to 
repeat the experiment, wasting valuable time.  Now try the same trick on
your paper lab notebook; any reasonably well chosen ink will not run 
significantly and you spend 5 minutes with a hairdryer to resurrect your
data.

In addition, most commercial computers do not provide a secure time stamp
for the data.  A skilled computer operator can very quickly modify creation
dates and data without leaving any trace of doing so.  Paper notebooks are
much harder to modify without leaving at least some suspicious traces, and 
the art of analyzing handwritten and typed documents has been very highly
developed.  Interested parties should read the David Baltimore case for 
examples of the analysis techniques applied to lab notebooks.

I hope I've made the case strongly enough, because I feel it is of critical
importance.  I work on computers 8-12 hours per day, but I never trust them
with anything utterly essential without having a printed back-up or stored
copies in a wide variety of locations.

Which reminds me, I have to print some things out now. : )
--
 Craig Lewis                            cvl@athena.mit.edu                   
 Woods Hole Oceanographic Institution   (508)457-2000x4814                   
 Nobody but me has any idea what I'm doing; and I don't know either.
From: wcalvin@stein.u.washington.edu (William Calvin)
Newsgroups: bionet.biology.computational
Subject: Re: Computerized lab notebook?
Date: 11 Jan 93 14:39:08 GMT
Distribution: bionet
Organization: University of Washington
Originator: biocomp@lerkim.umiacs.umd.edu

lmh@theory.lcs.mit.edu (Minghsun Liu) writes:
>I mentioned that I wondered if working biologists were ready to trade in their
>trusty lab notebooks for computer software that could replace it.  Yes,
>I know I probably haven't even fully appreciated the kind of diverse
>needs that different people want in their computerized lab notebook.
>I am just wondering if there exist a kind of "philosophical" or
>"emotional" attachment to a regular lab notebook.  Better yet, is
>anyone out there actually using such a software?

Convenience surely depends on how well you can sketch things adjacent to
text.  One major advantage of computerizing it all is backup:  easy to
lose a bound notebook (or a laptop computer) but it is so easy to keep
safe copies that it has become much harder to truly lose something.

There will be a period of transition, regarding the quasi-legal status of
written notes for patent and other such purposes; handwriting and bound
notebooks provide some assurrance against alterations afterwards.  But the
same transition is being made re using laptops for travel expenses and
keeping those records for tax audits.  I think that original paper records
are slowly on the way out.  One of these days, someone will invent a way
of sealing computer records against alteration (probably commercial
services that will receive them by file transfer on Internet, and keep
them under seal) that will gain enough popularity to become an acceptable
standard.
    William H. Calvin   WCalvin@U.Washington.edu
From: lmh@theory.lcs.mit.edu (Minghsun Liu)
Newsgroups: bionet.biology.computational
Subject: Computerized lab notebook?
Date: 10 Jan 93 17:54:21 GMT
Distribution: bionet
Organization: MIT Laboratory for Computer Science
Originator: biocomp@lerkim.umiacs.umd.edu



(I have posted this article also to bionet.software.  I thought I
would try to get comments from (what I perceive to be) a different
but still relevant group of netters.)

Hello All!

A few weeks ago I was having a discussion with a friend who
just bought a computer to be used in his research.  (Typical
applications such as keeping track of bacterial strains and making
presentations for the lab meetings only.)  And I mentioned that with
the advent and gaining popularity of notebook-sized portable
computers,  (I am not sure what the situation is in places outside of
Boston but I have seen people WORKING with their Mac PowerBook in
subway trains more than once!)  

I mentioned that I wondered if working biologists were ready to trade in their
trusty lab notebooks for computer software that could replace it.  Yes,
I know I probably haven't even fully appreciated the kind of diverse
needs that different people want in their computerized lab notebook.
I am just wondering if there exist a kind of "philosophical" or
"emotional" attachment to a regular lab notebook.  Better yet, is
anyone out there actually using such a software?

Any comments would be appreciated!

- Minghsun Liu
  lmh@medg.lcs.mit.edu
  lmh@genome.wi.mit.edu
From: jr_1@mbuk.bio.cam.ac.uk (Jem Rashbass)
Newsgroups: bionet.biology.computational
Subject: Computer models of Neoplasia
Date: 5 Jan 93 13:31:46 GMT
Distribution: bionet
Organization: Dept of Histopathology, Cambridge UK
Originator: biocomp@lerkim.umiacs.umd.edu

Does anyone know where I might a computer model of neoplastic cells?

Many Thanks,

Jem Rashbass,                       jr_1@mbuk.bio.cam.ac.uk,
Dept of Histopathology
Addenbrookes Hospital
Cambridge UK.
From: rob@fosters.med.utah.edu (Rob Sargent)
Newsgroups: bionet.biology.computational
Subject: Re: Computerized lab notebook?
Date: 11 Jan 93 14:42:35 GMT
Distribution: bionet
Organization: University of Utah
Originator: biocomp@lerkim.umiacs.umd.edu


The technology is available to supply the bench worker with a
comprehensive, multimedia record-keeping tool. As an impediment to the
implimentation of such a tool, emotional/historical attachment to the
written form is probably not any stronger than was the attachment to
typewriters/hardcopy in the office setting.

One the tool is robust and easy and affordable it will be ubiquitous.

(I just hope I write it.)

rjs
--
Rob Sargent                      s-mail: Dept. of Human Genetics    
e-mail: rob@fosters.med.utah.edu         U. of Utah Medical School     
				         Eccles Genetics Bldg
				         Salt Lake City, Utah  84112
From: kristoff@net.bio.net (David Kristofferson)
Newsgroups: bionet.biology.computational
Subject: BIOSCI/bionet Frequently Asked Questions
Date: 11 Jan 93 10:00:02 GMT
Distribution: bionet
Originator: biocomp@lerkim.umiacs.umd.edu


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: goldman@ala.btk.utu.fi (Adrian Goldman, BTK x8029)
Newsgroups: bionet.biology.computational
Subject: Re: superimpose
Date: 5 Jan 93 09:56:18 GMT
Distribution: bionet
Organization: Turku Centre for Biotechnology, Finland
Originator: biocomp@lerkim.umiacs.umd.edu

In <1992Dec31.051642.25575@mailer.cc.fsu.edu> rrk@iris3.chem.fsu.edu writes:

> 
> I am looking for a reference that describes the method of superimposing one
> molecular structure onto another.
> 
> I am trying to superimpose a peptide with one set of torsion angles onto the
> same peptide with another set of torsion angles.
> 
> Randy

Well, one reference to start from is Rossmann & Argos, JBC, vol 250,
p7525 (1975).  It should refer you back to an earlier reference by
Bob Diamond.

You should also seriously consider whether what you want to do makes
sense.  The parts of your peptide that are the same will be skewed away
from each other to help fit the parts that aren't.  (The algorithms
typically minimise the least square separation of (eg) alpha-carbons.)

          Adrian Goldman

Goldman@ala.btk.utu.fi
From: kristoff@NET.BIO.NET (David Kristofferson)
Newsgroups: bionet.journals.contents
Subject: BIOSCI/bionet Frequently Asked Questions
Date: 7 Jan 93 10:00:03 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: zyu@CGILS.APS.UOGUELPH.CA
Newsgroups: bionet.journals.contents
Subject: subscription
Date: 7 Jan 93 18:01:11 GMT
Distribution: bionet

Hi, there:
	I am trying to subscribe to this newsgroup. Your consideration will
be appreciated.
From: zyu@CGILS.APS.UOGUELPH.CA
Newsgroups: bionet.journals.contents
Subject: subscription
Date: 7 Jan 93 17:58:20 GMT
Distribution: bionet

Hi, there:
	I am trying to subscribe to this newsgroup. Your consideration will
be appreciated.
Organization: Queen's University at Kingston
Date: Mon, 4 Jan 1993 09:41:33 EST
From: <FORSDYKE@QUCDN.QueensU.CA>
Newsgroups: bionet.journals.note
Subject: Re: In defense of PNAS

Regarding John Lazzaro's defence of the Proceedings of the National Academy of
Sciences:

    This follows from the "Charter of Authors' Rights." proposed article 1.

"1.Judgements concerning the acceptance, reviewing and publication of a
paper should be concerned with the characteristics of the paper itself
and not with the race, sex, creed or colour of the author."(Ref.2)

    David Kristofferson (ref.3) expanded on this, implying that the character-
istics of the author might include his/her status in the heirarchy.

    If this were so, I then pointed out that the authorship discrimination
practiced by the Proceedings of the National Academy of Sciences would aptly
reflect the principle David was espousing.

John Lazzaro then wrote arguing that PNAS is a special case (ref.1):

   In response to this I would point out that there are MANY very distinguished
people in US science who are NOT members of the Academy. How is it that some
distinguished scientists are in the club, but not others?      Privileged
access to publication in a prestigious journal based on membership of some
heirarchy seems to conflict with the proposed first article.

   Lazzaro has since attempted to buttress his case with further arguments.
While I accept the principle that making rules which cover every case is often
not possible, I personally do not find Lazzaro's arguments that PNAS is a
special case very convincing. The following note I received from someone whose
anonymity I will respect, does not detract from my assessment of Lazzaro's case

"The US. NAS is frequently in a state of embarassment when Nobel
prizes are awarded to non-members. There have also been several cases
where individuals declined membership since they "did science not
politics."

  As a Canadian I am not in a position to check the validity of this assertion,
but it does not sound too way out. Does anyone else have a view on this matter?

       Sincerely, Don Forsdyke. Discussion Leader.

(1) Lazzaro, J. (1992) Bnt.jrnl.note 1228, 2324
(2) Forsdyke, D.R. (1992) Bnt.jrnl.note 1221, 1105
(3) Kristofferson, D. (1992) Bnt.jrnl.note 1222, 1631
(4) Forsdyke, D.R. (1992) Bnt.jrnl.note 1228, 1500







                                        Sincerely,
                                                  Don Forsdyke
                                                  Discussion Leader

(1) Forsdyke, D. R. (1992) Bionet.Journals.Note 1221, 1105
(2) Christoffersen, D. (1992) Bionet.Journals.Note 1222, 1631
(3) Baxter, A. (1992) Bionet.Journals.Note 1224, 750/
From: robison1@husc10.harvard.edu (Keith Robison)
Newsgroups: bionet.journals.note
Subject: Re: In defense of PNAS
Date: 5 Jan 93 16:07:51 GMT
  <1ia36jINNg17@agate.berkeley.edu> <93005.085026FORSDYKE@QUCDN.QueensU.CA>

Just a reminder of what PNAS stands for:

	Proceedings of the National Academy of Sciences

     It is rather silly to tell any organization how to run their (bi-)monthly
newsletter.  Originally, these "Proceedings" journals really were 
compilations of what was said at each society's meetings, but of
course these papers aren't really "read" out loud anymore.  
     Would PNAS be a better journal if it quit being the P of the NAS?  
Undoubtedly, since a great amount of junk and crockery gets published there.
But it's their right to operate in such an idiosyncratic manner if
they so choose. 


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

robison@biosun.harvard.edu
From: anderson@CSHL.ORG (John Anderson)
Newsgroups: bionet.journals.note
Subject: UNsubscribe me from jrnlnote
Date: 5 Jan 93 18:44:11 GMT
Distribution: bionet

Please unsubscribe me from bionet.journals.note.

Thanks
-------
John E. Anderson
W. M. Keck Structural Biology Laboratory
Cold Spring Harbor Laboratory
Organization: Queen's University at Kingston
Date: Tue, 5 Jan 1993 08:50:26 EST
From: <FORSDYKE@QUCDN.QueensU.CA>
Newsgroups: bionet.journals.note
Subject: Re: In defense of PNAS
 <93004.094133FORSDYKE@QUCDN.QueensU.CA> <1ia36jINNg17@agate.berkeley.edu>

Lassaro says:
>You are changing the focus of the discussion from the details of a policy, to
>rumour and innuendo. There is only one issue to resolve:
>
>Is PNAS any different from an edited book?

Forsdyke replies: Yes it is different, because journals are not edited books
and we are discussing journals. But considering books, if I were asked to edit
a book I would approach potential contributors based solely on their expertise
not on whether they happened to be members of a certain club, access to which
is rumoured to be rather politicised.
Organization: Penn State University
Date: Mon, 11 Jan 1993 16:28:50 EST
From: <MEK104@psuvm.psu.edu>
Newsgroups: bionet.journals.note
Subject: subscription info wanted


A colleague of mine would like the address to subcribe to
Bionet.journals.note.  If anyone has it, I would appreciate you sending it
along to me.  Penn State provides this network for all account holders so
I've never had to subscribe.

thanks again,

Mark Kubiske                < MEK104@PSUVM.PSU.EDU >
School of Forest Resources
Penn State University

Newsgroups: bionet.journals.note
From: mroussel@alchemy.chem.utoronto.ca (Marc Roussel)
Subject: Re: In defense of PNAS
Organization: Department of Chemistry, University of Toronto
Date: Tue, 5 Jan 1993 14:41:22 GMT

In article <93005.085026FORSDYKE@QUCDN.QueensU.CA> <FORSDYKE@QUCDN.QueensU.CA>
writes:
>Lassaro says:
>>Is PNAS any different from an edited book?
>
>Yes it is different, because journals are not edited books
>and we are discussing journals.

     The "edited book" argument strikes me as being a little weak (PNAS is
clearly not a book, as Forsdyke points out), but isn't the title of this
particular periodical (PROCEEDINGS of the NAS) a warning that this is not
a regular journal?  When a scholarly society operates a real journal, it
usually labels it clearly as such (for instance, Journal of the American
Chemical Society) but when the publication in question is labeled
"Proceedings" or "Transactions", I usually assume the sort of clubbish
publication rules which apply to PNAS.  (I realize that there are
exceptions.)  Doesn't everyone?

				Marc R. Roussel
                                mroussel@alchemy.chem.utoronto.ca
From: lazzaro@boom.CS.Berkeley.EDU (John Lazzaro)
Newsgroups: bionet.journals.note
Subject: Re: In defense of PNAS
Date: 5 Jan 1993 18:46:48 GMT
Organization: University of California, Berkeley
NNTP-Posting-Host: boom.cs.berkeley.edu

> (Marc R. Roussel) writes:

>[..] but isn't the title of this particular periodical (PROCEEDINGS of
>the NAS) a warning that this is not a regular journal?  [ ..]

> (Keith Robison) writes:
>Just a reminder of what PNAS stands for:
>	Proceedings of the National Academy of Sciences
>     It is rather silly to tell any organization how to run their (bi-)monthly
>newsletter. [..]  It's their right to operate in such an idiosyncratic manner if
>they so choose. 



Exactly, there is freedom of the press in this country, and it extends
to scientific journals. My points have nothing to do with the
proported political nature of PNAS. I am simply protesting an attempt
to place restrictions on the freedom to publish. If people don't like
PNAS or any other publication, don't read it, petition your library to
unsuscribe, petition you colleagues to submit elsewhere, but don't try
to enforce rules and regulations on publishers and editors.
From: lazzaro@boom.CS.Berkeley.EDU (John Lazzaro)
Newsgroups: bionet.journals.note
Subject: Re: In defense of PNAS
Date: 5 Jan 1993 18:32:14 GMT
Organization: University of California, Berkeley
NNTP-Posting-Host: boom.cs.berkeley.edu

In article <93005.085026FORSDYKE@QUCDN.QueensU.CA> <FORSDYKE@QUCDN.QueensU.CA> writes:
>But considering books, if I were asked to edit
>a book I would approach potential contributors based solely on their expertise
>not on whether they happened to be members of a certain club [../

Once again, you have the analogy wrong. The only member of the club in
this case is you, the chosen editor, who can choose any person you
want.
Organization: Queen's University at Kingston
Date: Thu, 7 Jan 1993 16:33:39 EST
From: <FORSDYKE@QUCDN.QueensU.CA>
Newsgroups: bionet.journals.note
Subject: Is PNAS a special case?

======================================================================== 32

In article <robison1.726250071@husc.harvard.edu>, robison1@husc10.harvard.edu
(Keith Robison) says:
>
>     It is rather silly to tell any organization how to run their (bi-)monthly
>newsletter.

Forsdyke: No one is trying to do that. The issue is whether PNAS is a special
          case to be regarded as an exception even though it appears to
          violate Article 1 of a proposed Charter of Authors' Rights.

>     Would PNAS be a better journal if it quit being the P of the NAS?
>Undoubtedly, since a great amount of junk and crockery gets published there.
>But it's their right to operate in such an idiosyncratic manner if
>they so choose.
>
      A charter of Editors' Rights might postulate the right to operate
      idiosyncratically. Here there would be a conflict between Author's
      Rights and Editor's rights! Note that the FIRST "proceedings", the
      Proceedings of the Royal Society, which began in the 17th century, does
      not, I believe, demonstrate this idiosyncrasy.
                                                    Don Forsdyke
From: vioque@cica.es (Agustin Vioque)
Newsgroups: bionet.journals.note
Subject: subscribe
Date: 5 Jan 93 09:11:41 GMT
Distribution: bionet
Content-Identifier: 90
Original-To: jrnlnote@uk.ac.daresbury (Receipt Notification Requested) (Non Receipt Notification Requested)
Conversion: Prohibited

subscribe
From: lazzaro@boom.CS.Berkeley.EDU (John Lazzaro)
Newsgroups: bionet.journals.note
Subject: Re: In defense of PNAS
Date: 4 Jan 1993 19:29:23 GMT
Organization: University of California, Berkeley
NNTP-Posting-Host: boom.cs.berkeley.edu

In article <93004.094133FORSDYKE@QUCDN.QueensU.CA> <FORSDYKE@QUCDN.QueensU.CA> writes:
>
>   Lazzaro has since attempted to buttress his case with further arguments.
>While I accept the principle that making rules which cover every case is often
>not possible, I personally do not find Lazzaro's arguments that PNAS is a
>special case very convincing. The following note I received from someone whose
>anonymity I will respect, does not detract from my assessment of Lazzaro's case
>
>"The US. NAS is frequently in a state of embarassment when Nobel
>prizes are awarded to non-members. There have also been several cases
>where individuals declined membership since they "did science not
>politics."
>

You are changing the focus of the discussion from the details of a policy, to
rumour and innuendo. There is only one issue to resolve:

Is PNAS any different from an edited book?

I have made a convincing case that there is no difference, and you
have chosen to ignore my arguments and turn to political issues.  I
have no interest in a discussion on that level. The specific case of
PNAS is not the salient issue, the issue is the validity of the
"edited book" journal format as an important form of scientific
expression that should not be excluded by any policies.
From: PARSONS_A@snd01.pcr.co.uk
Newsgroups: bionet.molbio.bio-matrix
Subject: RE: GCG Synchronisation Problem
Date: 5 Jan 93 14:53:22 GMT
Distribution: bionet
Original-To: BIOMATRX <BIOMATRX@UK.AC.DARESBURY>

Many thanks to all those who helped me out of a jam with a GCG
synchronisation problem in particular those at the foot of this
message - makes you wonder what we a re paying GCG maintenance for
sometimes.

Thanks again!

Rick Westerman                System Manager of the AIDS Center Laboratory
westerm@aclcb.purdue.edu      for Computational Biochemistry (ACLCB), BCHM
Phone: (317) 494-0505         bldg., Purdue University, W. Lafayette, IN 47907
  FAX: (317) 494-7897

Cary O'Donnell
*****************************************************************************
AFRC Computing Division    JANET   : ODONNELL@UK.AC.AFRC.ARCB
West Common                INTERNET: ODONNELL@ARCB.AFRC.AC.UK
Harpenden                  Long/Lat: 00d 21m 45s West   51d 48m 30s North
Herts AL5 2JE              Tel: (+44) 582 762271 xt 229 Fax: (+44) 582 761710
U.K.                       (AFRC = Agricultural & Food Research Council)
-----------------------------------------------------------------------------
|    Dr. Reinhard Doelz            | RFC     doelz@urz.unibas.ch         |
|      Biocomputing                | DECNET  20579::48130::doelz         |
|Biozentrum der Universitaet       | X25     022846211142036::doelz      |
From: kristoff@NET.BIO.NET (David Kristofferson)
Newsgroups: bionet.molbio.bio-matrix
Subject: BIOSCI/bionet Frequently Asked Questions
Date: 8 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