HDTenEightyP/NetNews huggingface dataset:
From: nmodena@ncsu.edu (Stephen Modena)
Subject: .signature on Big Iron
Originator: nmodena@post.cc.ncsu.edu
Organization: North Carolina State University Computing Center
Distribution: usa
Date: Fri, 11 Sep 1992 04:57:52 GMT


>Steve: Thank you for the information.  And re: email addresses in signature
>blocks, how *does* one generate that block? UNIX has the sig command, but
>I'm on a VMS system.  Help, tips, pointers gratefully accepted.
>
>-Richard O'Grady
> 410/516-6919
> ogrady@jhuvms.hcf.jhu.edu

The name escapes me, but there's a very knowledgable support person on
WELCH.jhu.edu, I believe, who could give Richard a ring and help
him out.

Not that any of you other Big Iron VMS-ophiles ought to hesitate to
get specific in Richard's emailbox.  :^)  Believe me, this 486 DOS
clone is about all I can handle most days.

Steve
---
+------------------------------------------------------------------+
|     In person:  Steve Modena     AB4EL                           |
|     On phone:   (919) 515-5328                                   |
|     At e-mail:  nmodena@unity.ncsu.edu                           | 
|                 samodena@csemail.cropsci.ncsu.edu                |
|                 [either email address is read every day]         |
|     By snail:   Crop Sci Dept, Box 7620, NCSU, Raleigh, NC 27695 |
+------------------------------------------------------------------+
         Lighten UP!  It's just a computer doing that to you.
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
         


Newsgroups: bionet.software
From: gerkos@reis56.alleg.edu (Stacey Gerko)
Subject: request: cystic fibrosis and computers
Keywords: genome, Linda, cystic fibrosis, pattern matching
Reply-To: gerkos@alleg.edu
Organization: Allegheny College
Date: Wed, 9 Sep 1992 17:28:27 GMT

I am doing a project on computers and the Human Genome Project.  I will be  
looking specifically at the cystic fibrosis genes.  By taking out the  
"garbage" DNA in a person's genome, I will be able to compare what is left  
with the known cystic fibrosis sequence.  This project will be done using  
Linda.
If anyone knows of any good articles on cystic fibrosis, Linda, the Human  
Genome Project, or pattern matching algorithms, I would greatly appreciate  
hearing from you.

Thanks,

Stacy Gerko
Allegheny College
gerkos@alleg.edu
From: s9205@gte.com (Rohit Gupta)
Newsgroups: bionet.software
Subject: Object-oriented DBMS
Date: 15 Sep 92 20:45:42 GMT
Organization: GTE Laboratories, Waltham MA


Does anyone know of any Object-oriented Database software written for storing biotechnology-related information ? Does anyone know of any research being done using OODBs for biotechnology ?


Thanks

Rohit Gupta
Newsgroups: bionet.software,bionet.general,embnet.general
From: JWALKER@SBBIOVM.EARN (Jeff Walker)
Newsgroups: bionet.software
Subject: FTP
Date: 10 Sep 92 17:31:13 GMT
Distribution: bionet
Original-To: bio-software@UK.AC.DARESBURY

could anyone give me step-by-step instructions for uploading macintosh
software into ftp'able format so that others could download it?  Thanks.
 
                                           Jeff Walker
                                           SUNY at Stony Brook
From: duong@chestnut.chem.upenn.edu (Duc Duong)
Newsgroups: bionet.software,bionet.molbio.proteins
Subject: Software computation for structural protein..
Date: 16 Sep 92 01:19:53 GMT
Followup-To: bionet.software
Organization: University of Pennsylvania

Hi..

I am looking for the software that read in the NOE Distances (Nuclear
Overhouses Effect) then it calculates the structure of the protein
(linear, helix, double hexlix,..etc). The distance is less than
5Angstroms. The data is collected by using solution NMR method. I am
sure that I read about the software before but I don't recall right now.
Any help or suggestion will greatly appreciated. E-mail please. Thank
you. 

						duc
From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Subject: Re: Telebit QBlazer modem
Organization: Crop Science Dept., NCSU, Raleigh, NC 27695-7620
Distribution: bionet
Date: Thu, 10 Sep 1992 09:19:14 GMT

In article <9209092120.AA08211@darwin.sfbr.org> bdyke@DARWIN.SFBR.ORG (Bennett Dyke) writes:
>Has anyone had experience with hooking up a Telebit QBlazer modem
>to a SparcStation?  These are nifty little boxes (V.42bis, etc.)
>that work very well between PCs, but we are having an awful time
>connecting them to workstations.  Does anybody know the termcap
>or getty secret?
>
>Thanx in advance.
>
>Bennett

That's a real good question I'd like the answer to also, for furture reference.

Since you offered no description of the problem involved, I'll make the
wild suggestion that you should play SuperUser and set the driver on the
TeleBit port to piority level 001......'cuz when that Telebit starts to
move data, I'd imagine that the Sparc will go into suspended animation
anyway!  :^)

Anyhow, TeleBit's toll-free number is 1-800-835-3248 and I have it in
a letter right here that they know how to handle "UNIX".  

Steve
---
+------------------------------------------------------------------+
|     In person:  Steve Modena     AB4EL                           |
|     On phone:   (919) 515-5328                                   |
|     At e-mail:  nmodena@unity.ncsu.edu                           | 
|                 samodena@csemail.cropsci.ncsu.edu                |
|                 [ either email address is read each day ]        |
|     By snail:   Crop Sci Dept, Box 7620, NCSU, Raleigh, NC 27695 |
+------------------------------------------------------------------+
         Lighten UP!  It's just a computer doing that to you.
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
         
Newsgroups: bionet.software
From: excoffie@sc2a.unige.ch
Subject: Analysis of Molecular Variance : A Windows 3.x program
Organization: University of Geneva, Switzerland
Date: Tue, 8 Sep 1992 13:12:53 GMT


  This is an annoucement for the public release of a WINDOWS 3.x based program

to analyze the GENETIC STRUCTURE OF POPULATIONS using MOLECULAR INFORMATION.


  This program (WINAMOVA ver 1.04) is based on a paper by Excoffier, Smouse and 

Quattro (1992), and computes variance components for 2 levels of population 

structure as well as their associated modified F-statistics (called here Phi-

statistics).


  This version can handle a maximum of 255 molecular haplotypes, 100 populations

and 100 groups of populations. It requires haplotype frequency information for

each population, as well as a matrix of inter-haplotypic squared (euclidian) 

distances. 


  Conventional multi-allelic F-statistics may also be computed.


  The program includes a non-parametrical (permutational) test for the 

significance of both variance components and Phi-statistics.


  It can be uploaded by anonymous FTP from    : ACASUN1.UNIGE.CH

(username : anonymous) in the directory       :  pub/amova

under the form of an archived file called WINAMOVA.ZIP, including 

executable versions for Windows 3.0 and Windows 3.1, plus example files.


           The program is FREEWARE and can be distributed freely in its 
           original form, but I would appreciate receiving an E-mail from
           interested users, as well as comments, suggestions, and bug
           reports.

(Windows 3.x is a product from Microsoft Corporation)


  Reference cited :
  =================

Excoffier, L, Smouse, PE, and Quattro, JM (1992) Analysis of molecular variance
      inferred from metric distances among DNA haplotypes: Application to human
      mitochondrial DNA restriction data. Genetics 131:479-491.


*******************************************************************************
*                                                                             *
*  Laurent Excoffier                					      *	
*  Genetics and Biometry Laboratory           Tel    : 41-22-343.69.30        *
*  Dept. of Anthropology and Ecology 					      *	
*  University of Geneva                       Fax    : 41-22-300.03.51        *
*  12, rue Gustave Revilliod                  				      *	
*  1227 Carouge-Geneva, Switzerland           E-mail : excoffie@sc2a.unige.ch *
*									      *	
*******************************************************************************
Newsgroups: bionet.software
From: stodola@orion (Robert K. Stodola)
Subject: Re: Internet crackers and security advice
Organization: Fox Chase Cancer Center
Date: Mon, 7 Sep 1992 15:07:03 GMT

In article <Bu6tvF.881@usenet.ucs.indiana.edu> gilbertd@sunflower.bio.indiana.edu (Don Gilbert) writes:

>For those of you who manage Unix or VMS systems, I strongly
>recommend that you read thru the CERT advisories that apply to
>your systems, including their general advisories on Internet
>intruders, if you haven't done so recently.   If you have an 
>Internet-connected computer, the only way to insure it isn't
>broken into by bad people is to be vigilant on security.

All excellent advice.  To some extent, being vigilant is not
sufficient.  Some training (formal or otherwise) and keeping
up with the state of the art in computer security is required.
Some people actually make a full time job of it.  What you suggest
is a step in the right direction [and more than most do], but if
you have an internet system which you mean to keep reasonably
secure, you will either have to invest a lot of time, or some
money to pay someone who will.  My brother-in-law used to spend
hours trying to keep squirrels out of the bird-feeders, and always
failed.  He contends that while he is smarter than the squirrels,
they had more motivation and time.  In this case there are a lot
of squirrels, some are smarter than you, and they also have
a lot of time and some bizarre form of motivation.

For those unwilling to dedicate their lives or grant funds
to computer security, I'd also suggest they read the guides
to system security that come with the VMS and better Unix systems.
These document features which will help secure your system, if
used properly.  Many security holes are simply not setting up
your system properly, and will rarely be found in CERT advisories.

There are some excellent books on the topic in general (though these
obviously cannot address the latest specific SunOS hole), and
some newsgroups (comp.security.announce, comp.security.misc, alt.security,
and alt.security.index) which tend to have a very low signal to noise ratio.
There are also some FAQ sheets for at least one of these groups which
may serve to concentrate some of the information, and eliminate a lot
of the noise.

Also be aware that some vendors (obviously not SwisscheeseOS) are
rather circumspect about exposing holes via CERT on the theory that
they are telling everyone how to break into all the systems of people
who don't get the CERT advisory.  Particularly if you don't have
a software update contract with the vendor, you should make sure you
are hooked into their security advisory system.
-- 

stodola@fccc.edu -- Robert K. Stodola (occasionally) speaks for himself.
From: WMELCHIOR@NTET.NCTR.FDA.GOV (Bill Melchior, NCTR/FDA)
Newsgroups: bionet.software
Subject: Re: .signature on Big Iron
Date: 11 Sep 92 12:45:03 GMT
Distribution: bionet

>>Steve: Thank you for the information.  And re: email addresses in signature
>>blocks, how *does* one generate that block? UNIX has the sig command, but
>>I'm on a VMS system.  Help, tips, pointers gratefully accepted.

One technique available at my site is to use the autosignature feature of 
the MX mailing program.
From: ABOLA@PB1.PDB.BNL.GOV
Newsgroups: bionet.software
Subject: re: REQUEST: INFO ON MEDLARS & TOXNET
Date: 6 Sep 92 12:33:28 GMT
Distribution: bionet

> 
>Hello,
> 
>Back in July, I read a posting reagarding MEDLARS (Medical Literature and
>Retrieval System. That posting also said that MEDLARS includes a system of
>toxicological databanks: TOXNET. I would like to ask the readers on the net for
>more information about this service.
> 
>In particular, I am interested in knowing:
> 
>- Can MEDLARS and TOXNET be accessed through the Internet?
>- How can I get an index of the databanks available in TOXNET?
>- Does anyone know whether TOXNET includes extensive data from liver studies?
> 
>I will appreciate any in info e-mailed to :
> 
>armando@synapse.ee.ufl.edu
> 
>Thanks in advance!
> 
>Armando Barreto.
>

Armando:

Get in touch with 

	MEDLARS Management Section
	National Library of Medicine
	Bldg. 38A, Rm 4N421
	8600 Rockville Pike
	Bethesda, Maryland 20894

	(800) 638-8480

They will send you an information packet describing their databases
and how to access them.  I have not seen anything about internet access 
in their literature.   
 
 
enrique
From: zxmkr08@mailserv.zdv.uni-tuebingen.de (Cornelius Krasel)
Subject: Re: Internet crackers and security advice
Organization: Comp. Center (ZDV) U of Tuebingen, FRG
Distribution: bionet
Date: Fri, 11 Sep 1992 13:07:37 GMT

In <1992Sep10.174623.5573@ccu.umanitoba.ca> frist@ccu.umanitoba.ca () writes:

>In article <zxmkr08.716131405@mailserv> zxmkr08@mailserv.zdv.uni-tuebingen.de (Cornelius Krasel) writes:
>>I have seen a password cracking program in action. Unfortunately it
>>does not help to simply include digits or punctuation into "real words",
>>since at least this program was prepared for it and cracked things like
>>z1ebra without any problems. As far as I remember, the program used
>>several approaches: first, it tried all usernames available on this 
>>particular computer; second, it tested an internal (editable) word
>>list; third, it checked changes in spelling, such as mixed upper-
>>or lowercase, or interspersed digits. It was fairly successful...

>Perhaps I'm displaying my ignorance of operating systems here, but 
>shouldn't it be fairly easy for the system to detect a cracking program?
>By definition, the process of trying to login thousands of times with
>a long series of possible passwords, as described above, should be
>easily distinguishable from the user who fumbles his password and finally
>logs in on the 5th try. I would think such a tally of unsuccessful 
>login attempts could automatically trigger a message to be sent to
>the system operator at, say, the 20th failure. Shouldn't such an easy
>fix be built in to any operating system?  Maybe I'm oversimplifying
>the situation.

In UNIX there exists a file /etc/passwd which contains (among other
things) the crypted password. Cracking is performed on this file,
not by repeated attempts to log in. If you have an account on a
UNIX machine, you should be able to read (and therefore to copy)
this file.

On this computer the crypted passwords have been moved away from
/etc/passwd somehow (if you want to know how they did this, you
probably should concact the system manager :-) since I don't know).

Cornelius.
--
/* Cornelius Krasel, Department of Physiological Chemistry, U Tuebingen    */ 
/* email: krasel@mailserv.zdv.uni-tuebingen.de (Internet)                  */
/*        krasel@chemie.uni-tuebingen.dbp.de (WIN/X400)                    */
/* "People are DNA's way of making more DNA." (anonymous)                  */
From: jun@hcx.rockefeller.edu (Susie Jun)
Newsgroups: bionet.software
Subject: DNA helical wheel drawing programs
Keywords: pc, drawing programs, DNA, helical wheel 
Reply-To: jun@hcx (Susie Jun)
Organization: Rockefeller Univ.,N.Y.C 10021
Date: Thu, 10 Sep 92 18:14:40 EDT

Are there any programs which will draw helical wheels
for  short DNA sequences, either for Mac or IBM?
Please email to:
    jun@rockvax.rockefeller.edu
Thanks in advance,
--Susie
From: kleinschmidt@mcclb0.med.nyu.edu
Newsgroups: bionet.software
Subject: Re: Calculating free Ca2++ with EGTA buffers
Date: 11 Sep 92 03:49:38 GMT
Organization: NYU Medical Center, New York, NY 10016, USA

Three years ago, I wrote a program named CABUFFER that allows you to 
calculate the free concentrations of all ionic species in a mixture of
up 
to four divalent ions (e.g. Mg, Ca, Sr, Ba) and up to four different 
divalent ion buffers (e.g. EGTA, EDTA, NTA, HEDTA, citrate etc.). 
Free 
parameters are temperature, pH and ionic strength.  The program was
written 
in structured Basic and compiled with Borland's Turbo Basic v. 1.0 or
with 
Microsoft's Quickbasic v 4.0 under MS-DOS.  It runs very fast on PC's 
outfitted with a math coprocessor.  A slightly less capable program,
CABUF, 
that runs reasonably fast even on machines without math coprocessor is
also 
available.  At that time, and perhaps still now, CABUFFER probably was
one 
of the best and most flexible programs of that sort available in the
public 
domain.
 
This program has been passed around and is presently being used by a
number 
of labs, apparently with good results.  I can make it available to
anyone 
who cares for it.  Way back, I actually meant to write a paper on the
use 
of Ca-buffers in physiology and on the traps one can fall into doing
that.  
Alas, the manuscript was never completed but early drafts of various 
sections are on the diskette.  They may make tedious but instructive 
reading for those who care to understand what they are doing when they
make 
up and use Ca-buffers.  Unfortunately, all the equations are missing
from 
the electronic version; I couldn't get them into ASCII format.
 
All the files take up about 280 Kb of space, including an introductory 
readme file.  The CABUFFER exe file is about 80 Kb long.  The Basic
source 
code is also provided, so that you can modify it and recompile it with 
Turbo Basic or Quickbasic.  I can send all of this out on diskette, or 
better still, see if I can put the files into a public directory on
our VAX 
from which you can download them via anonymous ftp.  I will have to
talk to 
our system administrator about this.
 
I have little time to support this program.  Also, if you use it, you
do so 
at your own risk.  But I believe that its use is easy and
self-explanatory, 
and I also think that it is largely bug-free.  In absolutely critical 
applications you should always rely on using carefully calibrated 
Ca-sensitive electrodes (this is a major undertaking!).  Short of
that, 
this program may get you somewhere, certainly in simple EGTA buffers.
 
Jochen Kleinschmidt
NYU Medical Center
kleinschmidt@mcclb0.med.nyu.edu
 
Newsgroups: bionet.software
From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert)
Subject: Re: Olson's sequence editor: file format for protein multisequence files
Organization: Biology, Indiana University - Bloomington
Date: Sat, 5 Sep 1992 13:13:07 GMT

It has always been a trial to get sequence data from other sources
into the Olsen editor, which was designed mainly for entering
data from keyboard.   At one point, it would only accept raw sequence
(as you found readseq making) in single files/sequence using a special
command (I don't recall what).  The version you have may also read in
multi-sequence files that are in Genbank format, but I don't recall
what the commands for that might be.  The default input format it is
looking for is it's own special binary format, which readseq is not
able to reproduce.

-- don

-- 
Don Gilbert                                     gilbert@bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
Newsgroups: bionet.software
Subject: MacPattern v2.0 available
From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs)
Date: 14 Sep 92 14:04:51 +0100
Followup-To: bionet.software
Distribution: world
Organization: EMBL Data Library

The new version v2.0 of MacPattern is now available.

MacPattern is a Macintosh application which was originally designed for
protein pattern searches using the PROSITE pattern database.

Version 2.0 added the following new features:

- Support for Steven Henikoff's BLOCKS databases (Henikoff and Henikoff,
  Nucleic Acids Res. 19 (1991), 6565-6572).

  BLOCKS is a database of aligned protein fragments characteristic for
certain 
  protein families. These blocks are used by MacPattern for searches with 
  site-specific scoring matrices, thus complementing the standard PROSITE 
  consensus pattern searches approach.

  As for PROSITE, MacPattern displays a list of all entries in BLOCKS, and
a
  user can select the one (s)he wants to use. A simple click at an entry
  name in this list causes the complete database entry to be displayed, so 
  MacPattern can also be used as a convenient database browser.

  A full search of a 300+ protein sequence against all 2106 blocks in
BLOCKS 
  Release 5 takes about 8 minutes on a Macintosh IIcx.

- Statistical evaluation of protein sequences using general scoring schemes
  (Karlin and Brendel, Science 257 (1992), 39-49).

  This method was introduced by Karlin and Altschul (PNAS 87 (1990),
2264-2268) 
  to identify statistically significant segments in protein sequences. 
  MacPattern includes a set of scoring schemes described in recent
publications 
  by Karlin and colleagues, such as charge clusters, DNA-binding domains,
etc.,
  and allows the addition of new ones by the user.

Both new features require a great amount of floating-point operations.
Although MacPattern can be used on any Macintosh system, a Macintosh with a
mathematical co-processor is highly recommended!

Other changes in v2.0 include:

- Maximum number of entries allowed in Prosite or Blocks databases
increased 
  from 1,000 to 10,000.

- Entry names or accession numbers can be displayed in database browser
window.

- A couple of minor changes plus the inevitable bug fixes.


MacPattern can be obtained 

1) by electronic mail from netserv@embl-heidelberg.de:
   Get Mac_Software:macpattern.hqx

2) by anonymous ftp from ftp.embl-heidelberg.de:
   /pub/software/mac/macpattern.hqx

3) by electronic mail from the author (fuchs@embl-heidelberg.de)

4) on floppy disk from the author:
   Rainer Fuchs, EMBL Data Library, Postfach 10.2209, W-6900 Heidelberg,
Germany


Rainer Fuchs
EMBL Data Library
Fuchs@EMBL-Heidelberg.DE
From: Fergus_Doherty@vme.ccc.nottingham.ac.uk
Newsgroups: bionet.software
Subject: Calculating free Ca2++ with EGTA buffers
Date: 10 Sep 92 10:00:35 GMT
Distribution: bionet
Original-To: BIO-SOFT@uk.ac.daresbury

Can anyone help me to calculate free Ca2++ in EGTA/CA buffers?  Basically 
I want to determine the effect of Ca on enzyme activity, and relatedly 
translocation of an enzyme to membranes-which is Ca -dependent.  I need 
to include EGTA to completely inhibit the enzyme, and then add back Ca.
This must have been done thousands of times but I am completely 
bamboozeld by the books I've looked at.  What I need is a simple 
explanation and perhaps a program, spreadsheet or Hypercard stack 
for the calculations (so Mac, or PC Excel).  Thanks.
FErgus Doherty, Biochemistry, Nottingham University, UK.
Newsgroups: bionet.software
From: armando@synapse.ee.ufl.edu (Armando Barreto)
Subject: REQUEST: INFO ON MEDLARS & TOXNET
Keywords: MEDLARS, TOXNET, TOXICOLOGICAL DATABANKS
Reply-To: armando@synapse.ee.ufl.edu
Date: Sun, 6 Sep 92 02:33:05 GMT


Hello,

Back in July, I read a posting reagarding MEDLARS (Medical Literature and  
Retrieval System. That posting also said that MEDLARS includes a system of  
toxicological databanks: TOXNET. I would like to ask the readers on the net for  
more information about this service. 

In particular, I am interested in knowing:

- Can MEDLARS and TOXNET be accessed through the Internet?
- How can I get an index of the databanks available in TOXNET?
- Does anyone know whether TOXNET includes extensive data from liver studies?

I will appreciate any in info e-mailed to :

armando@synapse.ee.ufl.edu

Thanks in advance!

Armando Barreto.

 
Newsgroups: bionet.software