HDTenEightyP/NetNews huggingface dataset:
From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert)
Subject: Re: GCG unix     -   up-arrow in history function????
Organization: Biology, Indiana University - Bloomington
Date: Mon, 14 Dec 1992 13:24:24 GMT

You seem to be aware of tcsh, which is a non-standard Unix shell
("user interface") that supports arrow keys for recycling command
lines.  You can find tcsh to install on most Unix systems thru
various ftp archives that support unix.  Several people here
use it with gcg software.  When the gcg package says you "must"
use csh, I don't think they mean that the close cousin tcsh
won't work, just that they haven't tested it.  They mainly mean
that their shell scripts use c-shell syntax, as opposed to
bourne shell (sh) syntax.  The tcsh shell also uses c-shell syntax
for script processing.
-- Don
-- 
Don Gilbert                                     gilbert@bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
From: BIONET@FRCGM51.EARN
Newsgroups: bionet.software
Subject: Re: Mac_to_PC
Date: 14 Dec 92 17:23:00 GMT
              from FRCGM51.BITNET (BIONET) by UKACRL.BITNET (Mailer R2.07) with
               BSMTP id 2582; Mon, 14 Dec 92 16: 25:31 GMT
           from DECNET-MAIL by FRCGM51.BITNET with PMDF#10000; Mon, 14 Dec 1992
Distribution: bionet
X-Envelope-To: bio-software@daresbury.ac.uk
Original-To: bio-software@UK.AC.DARESBURY
X-Vms-To: in%"bio-software@daresbury.ac.uk"


 
        Dear fellow netters,
 
        Following my initial posting about reading a Mac diskette on my PC,
 there has been a number of answers on this B-Board, and I have also received
 some "private" answers. Here they are for the benefit of the community:
 
 1) I have received a copy of CLINK which, in my hands, worked correctly. But
 I understand that it is a hacker version of a commercial program (MAC-IN-DOS)
 so I stop here.
 
 2) David Nordell kindly sent me a copy of MAC-ETTE which, this time, is a
 freeware program. It works quite fine.
 
 3) I have also received the following message from JONKER@AMV.UVA.NL, which
 tells how to retrieve MAC-ETTE:
 
>
> Yes, yesterday I tried a utility from sumex-aim/mac-info/misc/mac-ette
> (anonymous ftp); a public domain program (shareware type I think)
> that reads and writes mac 1.4 MB flopps. Worked rather well just the
> first time we tried it.... on a dos machine rather remarkable ;)
>
> ard
>
>
        Hence, there is at least one shareware program, MAC-ETTE, that
 everybody can fetch and that works fine.
 
        Thanks to all those who cared to answer!
 
 Jean-Loup Risler
 Centre de Genetique Moleculaire        RISLER@FRCGM51.BITNET
 91190  Gif sur Yvette  France
Newsgroups: bionet.info-theory
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Subject: Re: entropy estimates from a finite sample
Organization: Frederick Cancer Research and Development Center
Date: Wed, 16 Dec 1992 02:04:00 GMT

In article <1992Dec7.234446.180@rp.CSIRO.AU> awoolf@rp.CSIRO.AU (Andrew Woolf) writes:

>What is the `H function' you're referring to? The H he uses in his seminal paper
>is only of use if the distribution (either continuous or discrete) is known.

Yes, Shannon's H will estimate the entropy of a source.  What did you think
it did?  We can know the distributions in the case of binding sites
in molecular biology so there is no problem there.  The maximum entropy
methods allow one to estimate the distribution.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
Newsgroups: bionet.info-theory
From: awoolf@rp.CSIRO.AU (Andrew Woolf)
Subject: Re: entropy estimates from a finite sample
Organization: CSIRO Division of Radiophysics/Australia Telescope National Facility 
Date: Mon, 7 Dec 1992 23:44:46 GMT

> > Given a finite number of independant samples from an
> >unknown (assumed stationary) distribution, are there well-known methods for
> >estimating the entropy of the source ? 
> 
> Hunh?  Won't Shannon's H function do that?

What is the `H function' you're referring to? The H he uses in his seminal paper
is only of use if the distribution (either continuous or discrete) is known.
 
> >i.e. Given a finite set of samples {x(i)} from a stationary source with
> >probability distribution p(x), are there methods for forming an estimate
> >of the entropy  \int p(x) log(p(x)) dx 
> >(where the integral is taken over the entire space of x, which may be
> >multidimensional in general).
> 
> For continuous functions there is a problem about how to put the data into
> bins.  One size of bin will give different results from another, and it is not
> clear to me which how to deal with this.  Should one just try various bin sizes
> and maximize the uncertainty?  (It is easy to minimize - just have 1 bin!)
> Maybe there is a way to avoid the bins altogether.  Anybody know methods?
 
I think here you have seen the essence of the problem. Your response in fact
begs the question I was originally asking. However, you have implicitly assumed
the only way to do it is to assume a distribution in the form of a histogram.
That is one way to go, and is included in the methods I refer to directly below.

> > One way would be to estimate the distribution p(x)
> >and then calculate the entropy on that basis.
> >(There are known methods for estimating unknown distributions from
> >finite samples). 
> 
> Such as...

The histogram method you referred to! More generally, you can form an estimate
         __
p(x) =   \  K(x - x[j]),
         /  
         --
          j

where the K(x) is a so-called `kernel' function with essentially limited support,
and the {x[j]} are the finite collection of samples you have. Useful K's are
gaussians, triangle functions, rectangle functions etc. There are also maximum-
likelihood methods. A good book that discusses both of these is Tapia and
Thompson, "Nonparametric Probability Density Estimation", John Hopkins Uni Press.
As I said, this would be one approach (ie estimate p(x) from the samples, then
calculate entropy), but I was wondering if there were other more direct methods.

> > It would also be good to have some idea of the confidence
> >limits of the entropy estimate. 
> 
> Some references on these :

Thanks for the references. I shall look them up. And thanks to the other people
who posted references, too.

> 
>   Tom Schneider
>   National Cancer Institute
>   Laboratory of Mathematical Biology
>   Frederick, Maryland  21702-1201
>   toms@ncifcrf.gov

Andrew Woolf

-- 
  Andrew Woolf                        | PO Box 76, Epping, NSW 2121, AUSTRALIA
  Signal & Imaging Technology Program | Email : awoolf@rp.csiro.au 
  CSIRO Division of Radiophysics      | Phone : +61 2 868 0497
From: kristoff@NET.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.general
Subject: Re: Gateway for PHOTOSYN under discussion
Date: 12 Dec 92 00:06:52 GMT
Distribution: bionet

> I agree about the bionet-grouping. It would be much easier
> for a biologist to follow biological newsgroups if they 
> lie close to each other.
> 
> About your discussion on not joining bionet-groups and
> mailing lists because of administrational problems: 
> I thought that the mailing list would persist, the only 
> difference would be an address change and the fact that 
> Intelligenetics would run the list physically in their computer. 

The mailing lists would persist if they decided to join BIOSCI, but
would not run under LISTSERV at a third site (i.e., external to the
two existing BIOSCI nodes).  The list would be run jointly by IG and
SERC Daresbury for their respective service areas.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net
Newsgroups: bionet.general
From: jorgensonke@cc.uvcc.edu
Subject: Newsgroup for Diabetes
Organization: Utah Valley Community College
Date: 12 Dec 92 12:13:12 -0700

Is there a newsgroup out there that will discuss the disease of diabetes?  If
you know of one, please email me the name of it.  If you know of any BBS that
deals with it, please send me that information also.

Thanks in advance.

Keith Jorgenson
From: kristoff@NET.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.general
Subject: Re: PHOTOSYN as a Newsgroup
Date: 14 Dec 92 18:30:57 GMT
Distribution: bionet

> 
> So, where does that leave PHOTOSYN as a news group?
> 

Tony,

	You raise some valid points.  To date I have not received any
formal proposal from Johnathan.  If he submits one then we are
required to pursue the usual discussion and voting process, and you
can attempt to raise NO votes to turn the proposal down.

	Regarding expiration of news, expiration dates can be set
differently for different newsgroups.  As long as your site does not
go down for an extended period of time you should be O.K.  Mail does
not stay queued to a site forever either.

Dave
From: suter@VAX.MPIZ-KOELN.MPG.dbp.de
Newsgroups: bionet.general
Subject: processes taking place in the cytosol ?
Date: 14 Dec 92 16:26:27 GMT
Distribution: bionet

Subj:	transcription/recombination/rna processing in the cytoplasm ?
=============================================================================
we have here in the lab an on-going discussion, which goes like this: if
one transfects an eukaryotic cell with a plasmid, can this piece of DNA be
transcribed in the cytosol, can the formed rna be spliced in the cytosol, 
and could pieces of the DNA recombine there also ?
true, after translation most of the proteins needed for these processes
are available in the cytosol, but is this sufficient ?
and will a DNA molecule, after entering the cell, not be immediately transported
to the nucleus ?

some people have use e-nucleation to study this, but i suspect that the nucleus
might leak before leaving the cell.
do any of you have ideas or even a reference on this ? 

so hip it hurts,

clemens
===============================================================================
Clemens Suter-Crazzolara, PhD
Max-Planck-Institut fuer Zuechtungsforschung
Abteilung Genetische Grundlagen der Zuechtungsforschung
Carl-von-Linne Weg 10
5000 Koeln 30
Tel. xx49-221-5062.221           fax. xx49-221-5062.21
suter@vax.mpiz-koeln.mpg.dbp.de
===============================================================================
From: tdo@stam.nl (Thijs Doorenbosch)
Newsgroups: bionet.general
Subject: info required on trehalose
Date: 21 Dec 92 00:18:51 GMT
Organization: Stam Tijdschriften bv, Rijswijk, The Netherlands

Dear fellow-scientists,

As a science writer, I am interested in the function of the disaccharide

trehalose as a protein-degradation-preventing molecule in vitro (as 
conservative

agent) and in vivo, in plants of arid environments or genetically 
modified

plants. I really would appreciate if anyone of you could supply me with 
data,

names, phonenumbers, references or (review)articles. 

Thanks in advance!!
Newsgroups: bionet.general
From: Y3111DAA@vm.univie.ac.at
Subject: Request from the Department of Botany, University of Zagreb
Organization: University of Vienna
Date: Thu, 17 Dec 1992 16:04:53 GMT

We received a request for information from a faculty member
at the University of Zagreb.  He is trying to develop
animal and plant data bases in connection with
geographic information systems.  We have identified the
majority of groups or programs he lists.  However, we
are having difficulty identifying contacts and
addresses for the following:

International Specimen Information System (ISIS)
Databank for Italian Flora and Vegetation
European Taxonomic, Floristic and Biosystematic
  Documentation System

Any information you can provide would be greatly
appreciated.  Please respond directly via e-mail
to the above address, or to Kahn@pan.cedar.univie.ac.at

Sincerely,
Douglas J. Kahn
Manager
CEDAR Project
From: MARIANA@BRUNB.BITNET ("Mariana de S. Castro")
Newsgroups: bionet.general
Subject: Seeds gene cloning ?
Date: 15 Dec 92 16:36:10 GMT
Distribution: bionet


    Hi, netters!

.    I am interested in any kind of information about  the cloning

of genes  which  encode proteins found in seeds of the Leguminosae

family.

.    Thanks!

.Mariana de S. Castro
.University of Brasilia - Brazil

.
From: malige@labri.greco-prog.fr (Vincent MALIGE [91-92])
Newsgroups: bionet.general
Subject: Program to align secondary structures of nucleic acids.
Date: 17 Dec 92 11:25:05 GMT
Organization: Laboratoire Bordelais de Recherche en Informatique


	I'm a french student in computer science, preparing a PhD on the "Genome"
project. I'm actually working on a program which allows to align secondary
structures of nucleic acids. Does anyone know if such a program already exists?
If so, can you give me a ftp site or a bibliography.

	Thanks in advance,

		Vincent MALIGE
From: malige@labri.greco-prog.fr (Vincent MALIGE [91-92])
Newsgroups: bionet.general
Subject: Program to align secondary structures of nucleic acids.
Date: 17 Dec 92 11:32:51 GMT
Organization: Laboratoire Bordelais de Recherche en Informatique

Dear netters,

	I'm a french student in computer science, preparing a PhD on the "Genome"
project. I'm actually working on a program which allows to align secondary
structures of nucleic acids. Does anyone know if such a program already exists?
If so, can you give me a ftp site or a bibliography.

	Thanks in advance,

		Vincent MALIGE




-- 
-------------------------------------------------------------------------------
Adress  : Vincent Malige                        
          LaBRI                                 
          Universite Bordeaux I
          351 Cours de la Liberation
          33405 TALENCE Cedex

Tel : 56-84-84-27
Fax : 56-84-66-69

e-mail : malige@labri.greco-prog.fr
-------------------------------------------------------------------------------
From: AC6380@SHIP.BITNET
Newsgroups: bionet.general
Subject: PEMF Study Search
Date: 13 Dec 92 19:40:12 GMT
Distribution: bionet



Ladies and Gentlemen,
        I am totally unfamiliar with the world of biomedical research, so bear
with me please.  An organization for which I do some work is trying to
obtain copies of two studies recently published in Sweden.  Both are
studies on the health effects of electromagnetic fields.  The first was
published by Ander Ahlbom and Maria Feychting of the Institute of Environmental
Medicine at the Karolinska Institute in Stockholm.  The second is
by Birgitta Floderus of the Dept. of Neuromedicine at the National
Institute of Occupational Health in Solna, a suburb of Stockholm.
        We have been unable to obtain copies of either of these studies.
We would be most appreciative if you could perhaps give me some idea of
how and where I might be able to obtain english translations of these two
studies.  Thanks very much for your help.  If you wish to reply, please do
so in English or German.  These are the only two languages I can understand.

Arthur E. Clark



e-mail:  ac6380@ark.ship.edu
         ac6380@ship.bitnet
Newsgroups: bionet.general
Subject: Re: PHOTOSYN as a Newsgroup
From: marder@agri.huji.ac.il
Date: 15 Dec 92 15:42:09 IST
Distribution: bionet,world
Organization: The Hebrew University of Jerusalem - Faculty of Agriculture

In article <1992Dec12.225210.3570@gserv1.dl.ac.uk>, ajt@rri.sari.ac.uk (Tony Travis) writes:
>
> I accept that bionet.plants is fairly active compared to some of the
> other bionet groups, but I don't regard less than ten messages per day
> to be a lot of mail.

Neither do I consider 10/day a lot, but most of PHOTOSYN would!

> At the risk of boring everyone to death, let me repeat that I have a
> full subscription to BIOSCI coming in here as mail and "procmail" puts
> it into folders for me that are periodically split into separate
> articles and posted locally as bionet.* news.

Unfortunately most subscribers wouldn't be able (or willing) to do this.
Also, many wouldn't have the local support to have someone work it out for
them.

> I don't see the logic of justifying the creation of bionet.photosyn on
> the basis of the low volume of traffic on the PHOTOSYN list?  If you
> expect the majority of existing PHOTOSYN subscribers to subscribe to a
> BIOSCI version of their list (ie. not reading it as news) the only
> advantage I can see is that it brings PHOTOSYN to a wider (bionet)
> audience.
>
Tony, the problem is not just volume, but also relevence.
Widening PHOTOSYN may indeed lead to >10 messages per day, but I hope that
these would be 10 messages of interest to the readership.  On the other
hand, simply combining PHOTOSYN with another list would simply dilute the
traffic - in this latter case, even 3/day might be too much if most are
irrelevent.

> I suggested that Jonathan posted articles from PHOTOSYN to
> bionet.plants for precisely that reason, and he _has_ encouraged
> PHOTOSYN subscribers to use bionet.plants but I've not seen the epic
> debates about photosynthesis that I had hoped would evolve from this.
>
> So, where does that leave PHOTOSYN as a news group?
PHOTOSYN surely provides a service, even without the epic debates!  There
is a steady subscription which has now reached 280 (increasing some 20 per
cent yearly). There are several postings per week - nearly all are useful
to a large subgroup of readers.  Most of my customers are perfectly happy
with the status quo, but that may be because they don't know better.  I
would like to give them something better i.e. BIONET, but I need to do this
very gently (to avoid alienating people).
   Also, at the present growth rate, we are headed for problems.  I am well
aware of the defficiencies of LISTSERV and unwilling to spend an
ever-increasing amount of time maintaining PHOTOSYN in its present form
while there are better alternatives.

--
                                 '      Jonathan B. Marder
Internet: MARDER@AGRI.HUJI.AC.IL |      Department of Agricultural Botany
Bitnet:   MARDER@HUJIAGRI        | /\/  The Hebrew University of Jerusalem
Phone:    (08 or +9728) 481918   |/  \  Faculty of Agriculture
Fax:      (08 or +9728) 467763   /      P.O.Box 12, Rehovot 76100, ISRAEL
From: kristoff@net.bio.net (David Kristofferson)
Newsgroups: bionet.general
Subject: Re: PHOTOSYN as a Newsgroup
Date: 16 Dec 92 20:05:25 GMT
Distribution: bionet,world
Organization: BIOSCI International Newsgroups for Biology

harper@convex.csc.FI (Rob Harper) writes:

>I have been reading the PHOTOSYN debate for some time. Here are my thoughts
>for what they are worth.

Always glad to hear from you, Rob.


>	1)LISTSERV list-owners know more about the drawbacks of
>	  LISTSERV than the regular user... Though they keep the horror
>	  stories to themselves. (The politics of service)
>	2)With luck a user might be able to subscribe to a LISTSERV
>          but 90% of them do not know how to unsubscribe.
>	3)Getting logs of notebooks or doing LDBASE searches of LISTSERV
>	  are completely UFO ideas to most biologists.

>CONCLUSIONS: Joe Biologist wants mail and he does not care where it comes
>             from as long as it arrives and he can make a reply to it. 
>	     And if there is no bouncing mail so much the better.

>OPTIONS: If you want to give your users a soft landing into the world
>	 of BIONET, then why not proceed as follows:

>	1) Let Dave handle the administration of your list, but you
>	   remain as chief-whip to keep things in order.

This was the plan.  We do not have time to get involved in running
discussions on all of the lists.  Johnathan or someone else in the
group would have to serve as discussion leader.

>	2) Begin with only the mail distribution, so that the transistion
>	   will be gradual. REVIEW your list and send the stat file to
>	   Dave with the E-mail addresses of your members
>	3) Do not impliment the bidirectional link to Usenet just yet...
>           which would circumvent the need to have a call for votes,
>	   where you might run the risk of failure.
>	4) If the mailing list funtions well for a 6 month period,
>           and it passes the criteria which have been laid down for
>	   the "continuation" of BIONET newsgroups, then it should 
>	   automatically become linked to Usenet.

This is the "prototype newsgroup" arrangment which we have recently
implemented for two mailing lists.  After six months the group would
be put out to vote; if it doesn't pass then Johnathan might have to
take it back, but given the number of subscribers this is an unlikely
scenario.  I note that the ARABIDOPSIS group went directly from an
active mailing list to a full-fledged newsgroup and they appear to be
content with the result.  I need a formal proposal from Johnathan
before we can proceed though.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net
Newsgroups: bionet.general
From: harper@convex.csc.FI (Rob Harper)
Subject: Re: PHOTOSYN as a Newsgroup
Organization: Finnish Academic and Research Network Project - FUNET
Distribution: bionet,world
Date: Wed, 16 Dec 92 06:45:12 GMT

In <1992Dec15.154209.1@agri.huji.ac.il> marder@agri.huji.ac.il writes:

>   Also, at the present growth rate, we are headed for problems.  I am well
>aware of the defficiencies of LISTSERV and unwilling to spend an
>ever-increasing amount of time maintaining PHOTOSYN in its present form
>while there are better alternatives.

I have been reading the PHOTOSYN debate for some time. Here are my thoughts
for what they are worth.

	1)LISTSERV list-owners know more about the drawbacks of
	  LISTSERV than the regular user... Though they keep the horror
	  stories to themselves. (The politics of service)
	2)With luck a user might be able to subscribe to a LISTSERV
          but 90% of them do not know how to unsubscribe.
	3)Getting logs of notebooks or doing LDBASE searches of LISTSERV
	  are completely UFO ideas to most biologists.

CONCLUSIONS: Joe Biologist wants mail and he does not care where it comes
             from as long as it arrives and he can make a reply to it. 
	     And if there is no bouncing mail so much the better.

OPTIONS: If you want to give your users a soft landing into the world
	 of BIONET, then why not proceed as follows:

	1) Let Dave handle the administration of your list, but you
	   remain as chief-whip to keep things in order.
	2) Begin with only the mail distribution, so that the transistion
	   will be gradual. REVIEW your list and send the stat file to
	   Dave with the E-mail addresses of your members
	3) Do not impliment the bidirectional link to Usenet just yet...
           which would circumvent the need to have a call for votes,
	   where you might run the risk of failure.
	4) If the mailing list funtions well for a 6 month period,
           and it passes the criteria which have been laid down for
	   the "continuation" of BIONET newsgroups, then it should 
	   automatically become linked to Usenet.

That fourth option has never been discussed on Bionet, but I think that
if you establish a mailing list that is providing a steady turn over of 
messages that have CONTENT, then it is a very simple matter to link the
mailing list to USENET.

Rob "draft beer... not resolutions" Harper











--
 ~ 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: peitsch@ulbio1 ()
Subject: TNF & CD40L
Organization: University of Lausanne CH (Switzerland)
X-Newsreader: TIN [version 1.1 PL8]
Date: Wed, 16 Dec 1992 13:38:37 GMT
From: q00023@TIGGER.STCLOUD.MSUS.EDU
Newsgroups: bionet.immunology
Subject: How to start insect cell line for research
Date: 14 Dec 92 18:57:01 GMT
Distribution: bionet

Dear helper,

	I am looking for ways to start insect cell culture for class research
. I have looked at some articles and cataloges but they were not that useful
.Therefore I am asking for anyone who has the experience and information of the 
related topic will help me out with that.I appreciate your great help.

Thanks in advance,

Gabriel Cheung
From: HXIE@MACC.WISC.EDU (HUIWEN XIE)
Newsgroups: bionet.immunology
Subject: off
Date: 12 Dec 92 04:51:00 GMT
Distribution: bionet

Please sign me off. Thanks.
From: q00023@TIGGER.STCLOUD.MSUS.EDU
Newsgroups: bionet.immunology
Subject: How to start insect cell culture"
Date: 15 Dec 92 17:42:07 GMT
Distribution: bionet