HDTenEightyP/NetNews huggingface dataset:
From: WEISE@bscf.uga.edu (MICHAEL WEISE)
Newsgroups: bionet.software
Subject: Re: Internet crackers and security advice
Date: 8 Sep 92 12:15:41 GMT
Organization: University of Georgia, USA
X-News-Reader: VMS NEWS 1.20

In <01GOI3BHJJ048WVYXW@beloit.edu> JONESBB@BELOIT.EDU writes:

>
> text deleted...
> 
> Another point, if you think you are safe on you own Mac or IBM, you
> may not be.  NCSA Telnet for the Mac allows you to open your drive for
> ftp by other users.  If you use telpass to create accounts for your
> friends, then you are probably ok, subject to the discussion about
> passwords above.  However, at least one version of Telnet was
> distributed with the FTP ENABLE menu item defaulting to ON.  This means
> that if you have that version, have never bothered with telpass,
> and you use Telnet to connect to your local mainframe, you are open
> for someone to mess around on your hard disk.  This is the only
> situation I have heard of in which the default settings allow invasion,
> but there may be others.  
> 
> In addition, of course, if you choose the FTP ENABLE menu item, you 
> can manually allow access to your hard drive using ANY version of
> Telnet, and if you have modified your telnet configuration file (named
> "config.tel" as I recall) then you might have opened your system as its
> default behavior.  
>
> more deleted... 
> 
> Ben Jones, BioQUEST

	Interesting point here re a Mac and the NCSA Telnet package.  For
anyone who just discovered that 'config.tel' wasn't set up securely, don't just
edit that file and assume things are fixed.  Note that if you've aready been
using NCSA, the program hase long ago read the original config file and then
created a file named something like 'NCSA Telnet Settings'.  Once this file is
found upon NCSA startup, there is no reread of config.tel.  So... NOTHING
changes after an edit to config.tel unless you also trash the settings file.

		MJW

   _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
 / Michael J. Weise, Ph.D.    \  Univ.of Ga. BioScience Computing Facility \
(   weise@bscf.uga.edu         \   Dept.of Genetics  UGa, Athens  GA  30602 )
 \ _ _ _'Tis_only_me_speak'n._ _\_ _ _ _ _ _ _ (706) 542-1409_ _ _ _ _ _ _ /
From: ajt@rri.sari.ac.uk (Tony Travis)
Newsgroups: bionet.software
Subject: Re: Internet crackers and security advice
Date: 8 Sep 92 14:30:40 GMT
Reply-To: ajt@rri.sari.ac.uk
Distribution: bionet
Organization: Rowett Research Institute
Original-To: bio-software@uk.ac.daresbury

In article <9288133231.MIN-LBPBa20156.bionet-news@uk.ac.daresbury> you write:
: 	Interesting point here re a Mac and the NCSA Telnet package.  For
: anyone who just discovered that 'config.tel' wasn't set up securely, don't just
: edit that file and assume things are fixed.  Note that if you've aready been
: using NCSA, the program hase long ago read the original config file and then
: created a file named something like 'NCSA Telnet Settings'.  Once this file is
: found upon NCSA startup, there is no reread of config.tel.  So... NOTHING
: changes after an edit to config.tel unless you also trash the settings file.

One of the _few_ virtues of Sun's PCNFS is that it is client-only and
the files on your PC hard disk are inaccessible to the rest of the
network.  Sun have done a remarkable job of selling this inherent
limitation in PCNFS as a security 'feature'.

I am also using netatalk to make NFS filesystems available to Macs from
a Sun workstation over ether-talk.  One limitation of this setup that
might now be seen as a security 'feature' by some is that netatalk
cannot co-exist with local-talk ...

The most frequent breaches of security in my experience do not arise
from clever hacking, but from theft of passwords.  I always try to
ensure that people do not let others know their password and I make
sure they don't watch me type mine!

The transmission of plain-text passwords over the network is a
difficult area to protect when logging in remotely though.

However, all failed login attempts, and the network address where they
originate from are noted in the system log.  Not much use if it's a
bogus network address, admittedly, but it is unusual for repeated
failed login attempts to go unnoticed.

It is also traditional at Unix sites to encourage 'good-guy' mentality
where the hackers are allowed to attempt to breach system security
provided they tell the administrator how they got in.  The really good
hackers just want you to know that they _are_ good and they can
actually help to tighten up security where it is needed.

The malicious hackers ('bad-guys' by tradition) are just out to wreck
your system for the hell of it and will use any method they can.  I
really don't know what motivates such people but I believe that the
best defence is to understand what motivates the 'good-guys' so you can
set a thief to catch a thief.

The best system administrators know this and encourage the 'good-guys'.

	Tony.
--
Dr. A.J.Travis,                       |  Tony Travis
Rowett Research Institute,            |  JANET: <ajt@uk.ac.sari.rri>
Greenburn Road, Bucksburn,            |  other: <ajt@rri.sari.ac.uk>
Aberdeen, AB2 9SB. UK.                |  phone: 0224-712751
From: piry@biotec.jouy.inra.fr (Sylvain PIRY)
Newsgroups: bionet.software
Subject: GelReader on Mac IIsi (fwd)
Date: 10 Sep 92 14:26:27 GMT
Distribution: bionet
Original-To: Forum BIONET <bio-soft@uk.ac.daresbury>
Pp-Warning: Illegal Received field on preceding line
Original-Received: by biotec.jouy.inra.fr, Thu, 10 Sep 92
                   16: 26:28 +0200


Hello, netters !

I tried to use GelReader 2.02 on mac IIsi. It works, but it seems to be
impossible to save the file. A #90 error occurs, and the application is
leaved. Of course, I use the LCsi version of GelReader ; the other one
can't even be loaded in memory, but works fine on a IIci.  I sent a
bug-report to NCSA, weeks ago, but... 

Do you know any solution to this problem ? Is there a patch ? A new
release ? Help !

Thanks for all !

                                             Sylvain PIRY

------------------------------------------------------------------------
The light at the end of the tunnel is the headlamp of an oncoming train.
                             (Murphy's law)
------------------------------------------------------------------------
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.software
Subject: Re: Reverse Complement
Date: 11 Sep 92 18:11:07 GMT
Organization: Frederick Cancer Research and Development Center

In article <1992Sep10.165929.3773@magnus.acs.ohio-state.edu>
gchacko@magnus.acs.ohio-state.edu (George W Chacko) writes:
>I need to generate the reverse complement of a DNA sequence on a Unix machine.

A standard Pascal program that will do this is reform.p.Z available by
anonymous ftp from ncifcrf.gov in pub/delila.  (I would put a C translation
there also, but for some reason the translator creates a program that bombs.)

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: afc@gnv.ifas.ufl.edu
Newsgroups: bionet.software
Subject: Re: Analysis of Molecular Variance : A Windows 3.x program
Date: 9 Sep 92 15:40:23 -0500

In article <1992Sep8.151253.1@sc2a.unige.ch>, excoffie@sc2a.unige.ch writes:
> 
>   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 
(description deleted)
>   It can be uploaded by anonymous FTP from    : ACASUN1.UNIGE.CH

Has anyone uploaded this into an archive on this side of the puddle?
Archie told me no, but I don't want to use transatlantic FTP if I don't
have to.

> (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.
> 
>   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 *
> *									      *	
> *******************************************************************************


Andrew Cockburn
USDA
From: WAGNERF@BRUNB.BITNET (Wagner Fontes)
Newsgroups: bionet.software
Subject: RE: Internet Crackers
Date: 12 Sep 92 16:26:44 GMT
Distribution: bionet


Hi !

      I'm not an expert in this issue, but I have some information you
should know, if you don't know it yet.
      There are a few "crackink packages" that include a virus which remains
in the system area and detects password changes, so it will know all the new
passwords. I think the only solution for this is to run a virus detection
software  before changing the password.
      Regarding the other kinds of "crackers", why not use a non-word
combination of letters, or letters, numbers and punctuation ? I don't think
that it would be easy to guess a password like r4t3A.k and it wouldn't
be impossible to memorize it.

Regards

Wagner Fontes
Brazilian Center of Protein Sequencing
Biochemistry and Protein Chemistry Lab.
University of Brasilia
From: jlr%dnet.rxvgen@smithkline.com (jlr (Jean-Louis Ruelle))
Newsgroups: bionet.software
Subject: Re: Hydrophobic Cluster Analysis
Date: 10 Sep 92 15:44:51 GMT
Distribution: bionet
Original-To: "bio-soft@daresbury.ac.uk" <"bio-soft@daresbury.ac.uk"%dnet.INET@com.smithkline>
Original-Cc: JLR@smithkline.com.dl_sun_server

Paula E. Burch writes: 
>Can anyone point me to a program for performing hydrophobic cluster
>analysis of protein sequences? I've read mentions of HCA plot, written
>in Fortran 77, and also HCABAND in BASIC.
>
>The reference is C. Gaboriaud, V. Bissery, T. Benchetrit and J.P. Mornon's
>Hydrophobic cluster analysis: an efficient new way to compare and analyse
>amino acid sequences, FEBS Letters 224(1):149-155 (1987).
(some stuff deleted)

You can find a pretty good implementation of the HCA plot, although b/w only,
as a menu item in the freeware macintosh program called DNAid, available 
at ftp.bio.indiana.edu.

I hope it helps.

Jean-Louis Ruelle                          Dept of Molecular Biology
SmithKline Beecham Biologicals             jlr%rxvgen.dnet@smithkline.com
Rue de l'Institut, 89
1330 Rixensart, Belgium.
From: vivien@ariel.its.unimelb.EDU.AU (Vivien Bonazzi)
Newsgroups: bionet.software
Subject: Mac version of PAUP?
Date: 7 Sep 92 07:01:30 GMT
Organization: University of Melbourne


Netters,

Is there a Mac version of  paup??
If so, where can I get a copy?
Thanks in advance for any help


Vivien

Vivien Bonazzi
vivien@ariel.ucs.unimelb.edu.au
From: kleinschmidt@mcclb0.med.nyu.edu
Newsgroups: bionet.software
Subject: Olson's sequence editor: file format for protein multisequence files
Date: 5 Sep 92 03:45:29 GMT
Organization: NYU Medical Center, New York, NY 10016, USA

Can somebody tell me what the file format for an interleaved or sequential 
protein multi-sequence file would have to be for Gary Olson's SEQUENCE editor 
for VAX/VMS?  I have 30 aligned amino acid sequences with some 350 amino acids 
each and I want to analyze them with Olson's programs, including the program 
Tree.  Nowhere in the program documentation can I find a description of Olson 
file formats.  The public domain program Readseq when asked to convert a 
PIR-format file of these sequences into Olson format will strip the PIR file 
of everything but the amino acid designations.  When such a stripped file 
which supposedly is in Olson format, is presented to SEQUENCE, it won't accept 
it because of improper format.

Jochen Kleinschmidt
NYU Medical Center
kleinschmidt@mcclb0.med.nyu.edu
Newsgroups: bionet.software
From: lee.weller@anat.utas.edu.au (W. L. Weller)
Subject: 3D reconstruction for histology
Organization: University of Tasmania, AUSTRALIA
Date: Tue, 8 Sep 1992 02:31:45 GMT

I'm looking for information on Mac/DOS software for making 3D reconstructions
from serial histological sections.  I'd like to know:
     1.  the name
     2.  its source or contact
     3.  its availability
     4.  the platform it runs on
     5.  any criticisms or backpats (both firsthand and hearsay)
     6.  whether it's free, share or commercial

All pointers and suggestions accepted gratefully!

Lee Weller
Department of Anatomy, University of Tasmania
(lee.weller@anat.utas.edu.au)

                  *Yes, Virginia, there is a Tasmanian devil*
From: CZJ@CU.NIH.GOV
Newsgroups: bionet.software
Subject: Re:  Calculating free Ca2++ with EGTA buffers
Date: 10 Sep 92 13:29:12 GMT
Distribution: bionet

> MAIL VIA INTERNET FROM BIOSCI-REQUEST@genbank.bio.net  THURSDAY  09/10/92  6:15:03 A.M.
>
> Received: from CU.NIH.GOV by NIHCU (Mailer) id 9613;
>               Thu, 10 Sep 92  06:15:03 EDT
> Received: from GENBANK.BIO.NET by CU.NIH.GOV
>     with TCP; Thu, 10 Sep 92 6:15:00 EDT
> Received: by genbank.bio.net (5.65/IG-2.0)
>        id AA05730; Thu, 10 Sep 92 03:15:24 -0700
> Received: by genbank.bio.net (5.65/IG-2.0)
>        id AA05723; Thu, 10 Sep 92 03:15:22 -0700
> Message-Id: <9209101015.AA05723@genbank.bio.net>
> To: bio-soft@genbank.bio.net
> From: Fergus_Doherty@vme.ccc.nottingham.ac.uk
> Subject: Calculating free Ca2++ with EGTA buffers
> Date: 10 Sep 92 10:00:35 GMT
> Sender: list-admin@daresbury.ac.uk
> 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.
>
>

The calculation is straight forward.  You will need the stability
constant for the Ca2+ EGTA complex and the ionization constants
for EGTA.  There used to be a book entitled "Stability Constants"
which contained a complete listing of such.  Check with your
Chemistry Department Librarian regarding current sources.  You
should select constants obtained under the same conditions as
your experiments.  Otherwise you will have to extrapolate them to
the appropriate ionic strength using the Debye-Huckel equation.
Once you have the correct constants it a simple matter of writing
down the laws of mass action nad using a little algebra to obtain
the free Ca2+ concentration.  Since it will be small, several
approximations can be used to simplify the algebra.

Jim Cassatt
From: bdyke@DARWIN.SFBR.ORG (Bennett Dyke)
Newsgroups: bionet.software
Subject: Telebit QBlazer modem
Date: 9 Sep 92 21:20:42 GMT
Distribution: bionet

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


-- 
+----------------------------------------------------------------------------+
|   Bennett Dyke                                                             |
|   Department of Genetics               Internet:  bdyke@darwin.sfbr.org    |
|   Southwest Foundation                    Phone:  (512) 674-1410 Ext 281   |
|   P.O. Box 28147                            Fax:  (512) 670-3317           |
|   San Antonio, TX 78228, USA                                               |
+----------------------------------------------------------------------------+
Newsgroups: bionet.software
From: ALSOBROOK@biomed.med.yale.edu (John Alsobrook)
Subject: PDR software for MAC
Organization: Yale University
Date: Tue, 15 Sep 1992 18:47:30 GMT
X-News-Reader: VMS NEWS 1.20

Greetings netfolk. Is anyone aware of a software version of the PDR (that's
Physician's Desk Reference) for MAC or IBM? Commercial, shareware, or public
domain, makes no difference. Thanks loads.

****************************************************************************
*                                       | "Giving money and power to the   *
* John Alsobrook                        |    government is like giving     *
* Child Study Center                    |     whiskey and car keys to      *
* Yale University School of Medicine    |  teenage boys." - P.J. O'Rourke  *
*--------------------------------------------------------------------------*
*                       blame me, not my parents!                          * 
*                  bitnet: alsobrook@yalemed.bitnet                        *
*               internet:alsobrook@biomed.med.yale.edu                     *
*--------------------------------------------------------------------------*
...and, of course, nothing I ever say is officially sanctioned by Yale...
Newsgroups: bionet.software
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: Thu, 10 Sep 1992 13:23:25 GMT

In <01GOI3BHJJ048WVYXW@beloit.edu> JONESBB@BELOIT.EDU writes:
>This happened to our main users' computer at a university where I used to work,
>but they had already patched all the security holes in their system.  The
>invader entered using "password cracker" software, so I would like to add a
>word about passwords to Don's note.  It seems that there is a list of about
>400 words that are used quite frequently as passwords.  There also exists
>"password cracker" software which tries every entry in this list against a
>given account.  More often than you would think, this list succeeds.  In
>addition, there are known viruses which use the same list to crack accounts 
>and invade new machines.

[Some system-spcific stuff deleted]

>They also put a password filter on the system.  When anyone ever changed
>a password, the new one must have at least one uppercase letter and at
>least one lowercase letter, and I believe they also talked about requiring
>one punctuation  symbol, but finally didn't.  On case-insensitive systems
>like Vaxen, where all passwords are raised to uppercase, my favorite
>scheme is to make my password out of either one word, but misspelled, such
>as zeebraa, or out of two words together, such as dogcat.  The thing is,
>don't make them REAL WORDS, no matter how obscure, even out of literature.

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...

--Cornelius (by no means an expert of computer security).
--
/* 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: WMELCHIOR@NTET.NCTR.FDA.GOV (Bill Melchior, NCTR/FDA)
Newsgroups: bionet.software
Subject: Re: .signature on Big Iron
Date: 11 Sep 92 12:55:39 GMT
Distribution: bionet

Sorry about the hiccup just now.  As I was saying in regard to

>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.

On one of our (VMS) systems we have the MX mailing system, which can 
automatically add a signature to mail messages.  In the LOGIN.COM, make two 
definitions:
    $ DEFINE MX_SIGNATURE <whatever>
    $ DEFINE MX_AUTO_SIGNATURE YES
When I was using it, I defined MX_SIGNATURE as the file containing my 
signature block.

I stopped using this, however, because different nodes on our network use
different mailers, so sometimes the signature would go on and sometimes it
wouldn't.  What I do now is define a key in my EDTINI.EDT file so that
when I'm composing a message with EDT within the mailer, I just hit that key 
and it INCLUDEs the file.

I provide more specific info if needed.
________________________________________________________________________________
The opinions stated are mine, not those of NCTR or its sponsoring organizations.

Bill Melchior                                ||   "You have lawyers the way
National Center for Toxicological Research   ||    other people have mice."
Jefferson, AR  72079                         ||
(501) 543-7206                               ||   -Kenneth Duncan, English
                                             ||    Health & Safety Executive,
WMELCHIOR@NTDOC.NCTR.FDA.GOV                 ||    to US regulators
From: Davison@UH.EDU (Dan Davison)
Newsgroups: bionet.software
Subject: Re: Olson's sequence editor: file format for protein multisequence
Date: 5 Sep 92 17:52:39 GMT
Distribution: bionet

Don Gilbert said:
> 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.

A couple things.  READSEQ should not say "Olsen" then, but say "Olsen
text" or something. This confuses a lot of people who think it
produces the binary file.

The command to read a plain text file into the editor is
        LOAD/NUC FILE.EXT
The command to read a GenBank file into the editor is
        LOAD/GENBANK FILE.EXT
but you will have to hit "return" THREE times for EACH sequence read
in.

In both cases you must be in a olsen file for the LOAD command to
work. If necessary, create a dummy first sequence in the editor.


I have a program which I am willing to share on request called
TRANSFER, written by Jack Chappelear and myself. It reads and writes
Olsen files, and can take data from binary Olsen files and write Paup
NEXUS format, Phylip 3.3 format, a pseudo-GenBank format, and about a
dozen others.  It is a VMS *only* executable and will run only on VMS
version 5 or greater.  

dan
-- 
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77204-5934/davison@uh.edu/DAVISON@UHOU

-----RIP Isaac Asimov 1920-1992     I'll miss him --------------------

Disclaimer: As always, I speak only for myself, and, usually, only to
myself.
Newsgroups: bionet.software