HDTenEightyP/NetNews huggingface dataset:
From: ckeller@mbcr.bcm.tmc.edu (Charles Keller)
Newsgroups: bionet.software
Subject: Developers: try MACAW for Mac
Date: 23 Aug 1992 23:41:13 GMT
Reply-To: ckeller@mbcr.bcm.tmc.edu (Charles Keller)
Originator: ckeller@mbcr.bcm.tmc.edu



Here's an opportunity for a programmer:

Greg Schuler at NCBI has a VERY popular sequence analysis
program... which runs on the PC in windows.  It is called MACAW.

Dr. Schuler had hoped someone in industry would convert
it to the Mac (NCBI lacks the manpower, apparently).  He would
probably provide his code to an interested party gratuitously.

So--- if any programmer out there wants to makes some $,
you could develop MACAW for the Mac.  I'd buy the first copy.

Charles Keller
[ckeller@mbcr.bcm.tmc.edu]
From: HERSH@MACC.WISC.EDU (Richard P. Hershberger)
Newsgroups: bionet.software
Subject: subscribe to Bio-Soft
Date: 30 Aug 92 17:46:00 GMT
Distribution: bionet

subscribe bio-soft Richard P. Hershberger, Ph.D.

R I C H A R D   P.   H E R S H B E R G E R,  P H. D.
hersh@macc.wisc.edu               DNAengneer@aol.com
Inst. for Molec. Virol. UW-Madison, Madison WI 53706
Newsgroups: bionet.software
From: jwa@yog-sothoth.dcrt.nih.gov (James W. Adams)
Subject: Image/MolBio software for GT systems
Organization: National Institutes of Health, Bethesda, MD
Date: Wed, 26 Aug 1992 01:42:03 GMT

I'd be interested in experiences and recommendations concerning software
which specifically takes advantage of the Sun GT graphics accelerator in
the following categories:

Biomedical image processing/visualization/analysis

Molecular modeling and analysis

--
        James W. Adams   --   NIH Scientific Computing Resource Center
        Building 12A, Room 1050              phone: (301) 402-3488
        National Institutes of Health        uucp: uunet!nih-csl!jwa
        Bethesda, MD 20892                   Internet: jwa@alw.nih.gov
From: BAKERK@UK.AC.AFRC.FRIR
Newsgroups: bionet.software
Subject: re:- DNA Strider
Date: 3 Sep 92 16:28:00 GMT
Distribution: bionet
Original-To: BIO-SOFTWARE@UK.AC.DARESBURY

kupiec@edu.ciwemb.mail1 (Bill Kupiec) writes:-
>The latest version of DNA Strider is 1.2. It was released in August '92 and
>includes two more menus and a lot of revisions. Version 1.2 is "32-bit clean"
>and runs under both System 6 and 7. It is also compatible with the Quadras and
>the PowerBooks.
>
>Hope this helps,
>- Bill

Does anybody know of an FTP location for DNA Strider 1.2? I'd very much like 
to check it out, but when I try the string "strider" on ARCHIE all I get are
Sisters of Mercy lyrics. 
Thanks in advance,

Ken.
*************************************************************************
Dr Ken Baker                              JANET : UK.AC.AFRC.FRIR::BAKERK
Department of Protein Engineering      INTERNET :  BAKERK@FRIR.AFRC.AC.UK
AFRC Institute of Food Research             TEL :        (+44) 734 357139
Reading                                     FAX :        (+44) 734 267917
Berks RG6 2EF
UK                          (AFRC = Agricultural & Food Research Council)
*************************************************************************
From: rybicki@uctvax.uct.ac.za
Newsgroups: bionet.software
Subject: Re: Pima users
Date: 31 Aug 92 14:18:38 +0200
Distribution: bionet
Organization: University of Cape Town

In article <RSMITH.92Aug26093605@kite.bcm.tmc.edu>, rsmith@kite.bcm.tmc.edu (Randall Smith) writes:
> 
>>I am now beginning to use the Pattern Induced Multiple Alignement
>>(PIMA 1.22) package .....

[deleted]

I am very interested in any and all VAX software for multiple sequence
alignment / phylogeny generation: please could some kind soul send me the info
on PIMA (and how to get it)?

Thanks in advance,
 _________________________________________________________________________
|                                 |                                       |
|  Ed Rybicki                     |    Now you've got the hang of it      |
|  Dept Microbiology              | There's nothing you can't do with it  |
|  University of Cape Town        |         If you're very into it        |
|  PB Rondebosch 7700             |         You can't go wrong....        |
|  South Africa                   |                                       |
|  fax 27 21 650 4023             |              - Mad John               |
|  ed@micro.uct.ac.za             | (Ogden's Nut-Gone Flake, Small Faces) |
|_________________________________|_______________________________________|
From: PHILROSS@BIOTECHNET.COM
Newsgroups: bionet.software
Subject: polypeptide backbone graphics, cont.
Date: 31 Aug 92 17:37:57 GMT
Distribution: bionet

I am also interested in Mac (or IBM-compatible, I guess) software for 
facile drawing of polypeptide backbones in circles.  Perhaps a 
summary of useful email responses should be posted on this 
newsgroup; I'll be in touch with biogen10@gemini.ldc.lu.se and 
krystek@alcor.bms.com to see if any great suggestions surfaced.  Any 
pragmatic approaches, as well as packages, would be appreciated.

In the past, I've used a command(vector)-driven graphics driver 
(PostScript or HPLG) with "move relative to previous", "draw circle", 
and "text in circle" commands to draw seven-transmembrane 
receptor protein backbones in 2D.  After drawing the first circle, I 
determined (by experiment) the relative coordinates to move, for 
drawing the second circle.  I then used a word processor to select-
and-copy the text for these commands, thus giving a continued 
reiteration of circles.  I then went back and hand edited the text in 
each circle.  It sounds tedious, but it can be much easier than hand-
positioning each circle, particularly if there is repeated structure 
(transmembrane domains and loops) in the polypeptide being drawn.  

Clearly, a mouse-driven interface could compliment and facilitate 
this process, especially if it had auto-alignment features to smooth 
the chain and retain connectedness while line-thickness and circle 
diameter are altered.  The capacity to import a list of characters (the 
peptide sequence) into the circles (a graphical template) would also 
be nice.  Templates for alpha-helices and other conceptualized 
structures could also be nice.

The above assumes 2D (unfolded) representations of the polypeptide 
chain.  2D projections and 3D representations are another question, 
entirely.

Philip C. Ross, Ph.D.

cc: biogen10@gemini.ldc.lu.se
    krystek@alcor.bms.com
From: rsmith@kite.bcm.tmc.edu (Randall Smith)
Newsgroups: bionet.software
Subject: Re: Pima users
Date: 31 Aug 92 14:38:25 GMT
	<1992Aug31.141838.202593@uctvax.uct.ac.za>
Distribution: bionet
Organization: Baylor College of Medicine, Houston, TX
In-reply-to: rybicki@uctvax.uct.ac.za's message of 31 Aug 1992 12:18:38 GMT


In article <1992Aug31.141838.202593@uctvax.uct.ac.za>, rybicki@uctvax.uct.ac.za (Ed Rybicki) writes:
>I am very interested in any and all VAX software for multiple sequence
>alignment / phylogeny generation: please could some kind soul send me
>the info on PIMA (and how to get it)?


PIMA currently runs only under Unix, but here is the distribution info
for others who may be interested:


******************************************************************
                         PIMA 1.22
     Pattern-Induced Multi-sequence Alignment Program
******************************************************************

PIMA is a multiple sequence alignment program that uses a dynamic
programming-based pattern construction method to align a set of
homologous protein sequences (Smith, RF and Smith, TF, 1992, Protein
Engineering 5:35-41; see also Smith and Smith, 1990, PNAS 87:118-122).

The multiple alignment algorithm:

	(1) aligns sequences based on the pattern of conserved sequence
elements/domains common to the sequences being aligned;

	(2) represents gaps within a multiple alignment in a simple and
consistent manner;

	(3) can employ secondary structure-dependent gap penalties for
use in structural modelling of new protein sequences when the
3D-structure of one or more members of the sequence family is known.

	(4) is based on a local (Smith-Waterman) rather than global
(Needleman-Wunch-Sellars) dynamic programing algorithm;

The PIMA package is available free of charge to non-profit organ-
izations; a distribution fee and non-resale agreement is required for
commercial use.

Note: The PIMA package is currently a Unix-only implementation.

Copies can be obtained via INTERNET anonymous ftp to:
mbcrr.harvard.edu = 134.174.70.60; the package is in a single
compressed tar file called pima-1.22.tar.Z in the 'MBCRR-Package'
sub-directory.

-----------------------------------------------------------------------
Randall F. Smith
Human Genome Center and Dept. of Cell Biology
Baylor College of Medicine, Houston TX  77096
rsmith@bcm.tmc.edu

Temple F. Smith
Bio-Molecular Enginnering Research Center
Boston Univ.,  36 Cummington St, Boston, MA 02115
tsmith@darwin.bu.edu
-----------------------------------------------------------------------
Newsgroups: bionet.software.sources
From: bradbury@sftwks.UUCP (Robert Bradbury)
Newsgroups: bionet.software,bionet.molbio.genbank
Subject: Request for information regarding GENBANK updates on UNIX/DOS
Summary: Is anyone handling automatic updates?
Date: 27 Aug 92 11:44:30 GMT
Followup-To: bionet.software
Organization: Softworks Ltd, Seattle, WA

I am currently working on providing access to the sequence databases
and search/comparison software for some Russian scientists.  This
is necessary because there is no FTP access from Russia to the US
[courtesy of our paranoid government :-|] and problems associated
with the reliability/cost of E-mail within Russia.  The only machines
usually available in Russia are PCs making all of the VAXen/Sun/SGI
software irrelevent unless ported to S5 UNIX or DOS.

I am planning to use the updates from GB to produce an up-to-date copy
of the DB under System 5 on a 386 and then send tapes/disks to Russia
every few months.  Eventually if the E-mail/FTP access is resolved
the use of the software to update existing DB could be transfered
directly to Russia.

I have the GBUPDATE package by Brent Hobbs but this seems to create
a single file containing the entire database which is bad for S5 UNIX
(due to ulimits and multiple indirect blocks) and worse for DOS
(file system size limits).  There seem to be messy tradeoffs between
organizing this in flat files (perhaps in directories for each organism)
which would require extra time to open each file verses large files
which would require the creation of some fancy indexing scheme.
Is anyone keeping the database in some kind of flat file system
that they can give me some advice on what works/doesn't work?

If necessary, I could use a database like Oracle to manage this.
Are the descriptions of tables/views/indexes used by the db managers
at the various sites (GB/NCBI/EMBL) available?  What about the
data loading software?  Has anyone tried to replicate/update the
database using the updates with a DBMS or is everyone using GCG on VMS?

And lastly, is there a complete "english" description of the information
in the database entries?

-- 
Robert Bradbury			uunet!sftwks!bradbury

Death is an imposition on the human race, and no longer acceptable
				Alan Harrington, The Immortalist (1969)
From: dbd@THEORY.BCHS.UH.EDU (Dan Davison)
Newsgroups: bionet.software
Subject: UH Gene-Server down temporarily
Date: 28 Aug 92 04:24:12 GMT
Distribution: bionet

Because of an unknown malfunction, UH Gene-Server services will be
down for an unknown amount of time. This includes all e-mail services,
PIR Gopher retrieval, and anonymous FTP.

As soon as the problem is found and repaired an announcement will be
made.

dan davison
gene-server manager
-- 
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77054-5934/davison@uh.edu/DAVISON@UHOU

Working on the human genome project is very different from working on
the human genome; the latter is exciting science, whereas the former
is a banal mixture of metaphysics, politics and, possibly, psychiatry.
-- Sydney Brenner, Nature 358:27 1992

Disclaimer: As always, I speak only for myself, and, usually, only to
myself.
From: joseph@valis.biocad.COM (Joseph Truitt)
Newsgroups: bionet.software
Subject: Re: Pharmacokinetics s/w
Date: 2 Sep 92 00:42:36 GMT

In message <Btouxp.KxF@gate.demon.co.uk>,
James Petts <visigoth.demon.co.uk!pettsj> writes:
>I am looking for software to do pharmacokinetic modelling, preferably for 
>the Mac, but Un*x s/w would be acceptable too. Any suggestions would be 
>most appreciated. E-mail or postings are fine.

----- begin forwarded message from Dale Mehl of BioCAD -----

You might be interested in Catalyst, BioCAD's drug discovery software
system.

Catalyst is used to speed the drug discovery process.  It provides a
means for conceptualizing ligand-receptor relationships in 3D and is an
effective tool for designing new biologically active molecules.  Using
2D molecular structures and biological activity data, you generate a
simple hypothesis that correlates 3D chemical functions with measured
activity.  You can refine and test your hypothesis, generate and search
a 3D database to find novel leads, and design new molecules for
enhanced biological activity.  The quality of the hypothesis improves
as you synthesize and assay new molecules that extend the range of
activities and the diversity of structures.

If this sounds like it addresses your problem, write to Pat Coffey,
BioCAD Corp 1390 Shorebird Way, Mountain View, CA  94043.  (pat@biocad.com)

----- end forwarded message -----

It runs on Silicon Graphics UNIX boxes (RPC Indigo, Iris, etc.)

 ___________________________________________________________________________
|                                                                           |
| joseph@biocad.com 415/903-3923                                            |


Newsgroups: bionet.software
From: t4phage@milton.u.washington.edu (Betty Kutter)
Subject: Sequence Editor wanted
Organization: University of Washington
Date: Fri, 4 Sep 1992 16:11:33 GMT


For the work I have been doing on the bacteriophage T4 genome
I have found that an editor for sequence work would be useful.
I have setup an example at the bottom of this message and
I will explain the various parts.  I would like a work space of unlimited
(something wider than 10K bases) width and 25 to 40 lines in
length.  The work space would be divided into two major areas
separated by some type of ruler.  The top space would allow up to
15 sets of sequences and their names in brackets to be entered and aligned as
shown.  Then a consensus sequence could be entered above the
ruler.  Below the ruler, the consensus sequence would be translated
to the corresponding amino acid sequence.  Preferably this
translation would be "live", changing with any change in the
consensus sequence above the ruler.  As far as output options go,
I am not very optimistic, but some type of sideways printing to an
Epson emulated printer would be adequate.  Chopping up the width
into 50-70 character wide chunks would be tolerable, with a couple
of blank lines between chunks.  Obviously, I have outlined an
optimum editor.  I am willing to look at sub-versions of this
scheme.  And anything that exceeds these specs.  This program will
preferably run under MS-Dos although other applications may yield 
useful source code.


[~ma26b]  GCTCTGTTCCGTAGACAATTAAAGCAAATTTTGTC  [~ma26b]
[~ma13a]  GCTCTGTTCCGTAGACAATTAAAGCAAATTTTGTC  [~ma13a]
                    [~ma33a]  AAAGCAAATTTTGTCTACTGCTAGTCGAT...  [~ma33a]
[mt1a]    GCTCTGTTCCGTAGACAATTAA  [mt1a]   [~p50_0-] GTCGAT...  [~p50_0-]
      [~mt3a]   TTCCGTAGACAATTAAAGCAAATTTTGTCTACTGCTAGTCGA  [~mt3a]
                               
          GCTCTGTTCCGTAGACAATTAAAGCAAATTTTGTCTACTGCTAGTCGAT...
          ---------+---------+---------+---------+---------+
          1       10        20        30        40        50
          AlaLeuPheArgArgGlnLeuLysGlnIleLeuSerThrAlaSerArg
           LeuCysSerValAspAsnTERSerLysPheCysLeuLeuLeuValAsp
            SerValProTERThrIleLysAlaAsnPheValTyrCysTERSer

Shane Peterson - Evergreen State College T4 lab
reply to t4phage@u.washington.edu
From: matt@metis.UUCP (Matt Clark)
Newsgroups: bionet.software
Subject: X windows Software
Date: 3 Sep 92 12:46:17 GMT
Distribution: bionet

Response to 
   Re: Running the Biosym software InsightII/Discover over a network via
Xwindows.

The SYBYL software from Tripos allows you to use generic (non-GL)
X-window terminals to do biopolymer and drug modeling. We allow
you to simultaneously use many X-window terminals as well as the big 
SGI console so you aren't tied to the console as the only source of 
graphics. 

Contact us at 800-323-2960 for more information
From: D54@EARN.TRANAVM1 (suleyman AYDIN)
Newsgroups: bionet.software
Subject: software for titrator ??
Date: 3 Sep 92 18:10:54 GMT
Distribution: bionet
Original-To: BIO-SOFT@UK.AC.DARESBURY


 
Dear BIO-SOFT,
 
Our instrumental analysis lab.  has a good instrument.  But I see
that we are using pens and pencils although it has a RS-232-C port.
 
I wonder if there is a software for it to transmit the values to our
ibm pc /running DOS (or MAC running MOS - of course pc is my favourite!)
using a cable?
 
Secondly, must I (or my lab.) have/purchase a hardware portion
to use the RS-232-C facility.
 
The instrument is:
SCHOTT,  Titronic T200 Automatic Titrator.
It comes with a pH-meter (CG841) as a part of this titrator, and this
pH-meter has a RS-232-C port.
 
I want to use this port for a PC connection?
 
What do I need?
 
Any info is greatly appreciated.
 
 
Suleyman  AYDIN (student of pharmacology)
d31@tranavm1.bitnet
From: bchs1k@menudo.uh.edu (Edward S. Chen)
Newsgroups: bionet.software
Subject: University of Houston Gene-Server
Date: 3 Sep 92 23:44:04 GMT
Organization: University of Houston


The mail server for the University of Houston Gene-Server is alive again.
The technical problem has not been completely diagnosed, so the mail server
may stop working without notice.


Edward S. Chen



-- 
-------------------------------------------------------------------------------
 ... Take us from the dark, out where we can see ...
                                                    --- Paul McCartney
-------------------------------------------------------------------------------
From: pburch@bcm.tmc.edu (Paula Burch)
Newsgroups: bionet.software
Subject: Hydrophobic Cluster Analysis
Date: 4 Sep 92 20:40:05 GMT
Reply-To: pburch@bcm.tmc.edu (Paula Burch)
Organization: Baylor College of Medicine
Originator: pburch@roc.mbcr.bcm.tmc.edu



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).

I have Dr. Mornon's address, but don't really want to wait as long as it 
would take for mail to reach him, and I'm afraid to try directory assistance 
in France to try to get his phone number. Could somebody possibly have an 
e-mail address for him?

All 23 of the papers I found in Medline that mentioned HCA were from 
various European labs--no sign that anyone has ever used it on this 
continent.

Any help would be greatly appreciated.

_________________________________________________________________________
Paula E. Burch, Ph.D.             Molecular Biology Computational Resource
Baylor College of Medicine        internet: pburch@bcm.tmc.edu
Houston, Texas 77030              phone: (713)798-6023
Newsgroups: bionet.software
From: dbd@THEORY.BCHS.UH.EDU (Dan Davison)
Newsgroups: bionet.software
Subject: Gene-Server back up
Date: 28 Aug 92 17:09:06 GMT
Distribution: bionet

The Gene-Server (email, FTP, and Gopher) services are back up.

The problem was a confused disk after an "unscheduled" power outage.

dan davison
gene-server manager
Newsgroups: bionet.software
From: harper@convex.csc.FI (Rob Harper)
Subject: Re: embl/gopher
Organization: Finnish Academic and Research Network Project - FUNET
Distribution: bionet
Date: Fri, 28 Aug 92 19:21:57 GMT

In <9208281632.AA01723@labsun1.med.uottawa.ca> baird@LABSUN1.MED.UOTTAWA.CA (stephen baird) writes:

>to all gopher hunters,	
>    Does anybody know a gopher hole that one can search and retrieve
>sequences from the EMBL database like the great IUBIO gopher hole?	

While in the Indiana GOPHER you can have a look under the option
other Bio-gophers. If you select the BIOFTP site in Switzerland
run by Reinhard Doelz you can do searches on the EMBL database.

RGDS -=ROB=-

--
   Rob Harper                     /   E-mail:          harper@convex.csc.fi    
   Finnish State Computer Centre  /   Molbio/software: harper@nic.funet.fi
   P.O. Box 40, SF-02101 Espoo    /   Telephone:       +358 0 457 2076
   Finland                        /   Fax:             +358 0 457 2302
From: biogen10@gemini.ldc.lu.se (Bo Servenius)
Newsgroups: bionet.software
Subject: Program to draw polypeptide figures
Date: 27 Aug 92 20:43:14 GMT
Organization: Lund University, SWEDEN
X-Useragent: Nuntius v1.1

Dear Netters:

Anyone out there knowing where to find a program that can generate
"polypeptide snakes"  - i.e. modells of polypeptides with a circle
for
each aminoacid? Well I know you can create them with a simple graphic
program like SuperPaint but it is hard to get them really nice and
uniform.

If there is no program available maybe someone have a library with
nice
symbols for a Mac graphical program.


Yours

BOSSE
Newsgroups: bionet.software
From: James Petts <pettsj@visigoth.demon.co.uk>
Subject: Pharmacokinetics s/w
Organization: No Affiliation
Date: Fri, 28 Aug 1992 10:10:35 GMT
X-Useragent: Nuntius v1.1

I am looking for software to do pharmacokinetic modelling, preferably for 
the Mac, but Un*x s/w would be acceptable too. Any suggestions would be 
most appreciated. E-mail or postings are fine.

James Petts
********************************************************************
* "We use the classical theory on Mondays, Wednesdays and Fridays, *   
*  and the quantum theory on Tuesdays, Thursdays and Saturdays."   *
************************************** Wm. Bragg *******************
From: rbm8p@.Virginia.EDU (Rick MacDonald)
Subject: Does bionet.xtallography exist?
Organization: University of Virginia
Date: Sun, 23 Aug 1992 23:26:53 GMT



I've seen a few apparent cross-posts, but our computing center
tells me that we get all of the bionet groups and bionet-dot-
variations-on-crystallography isn't among them.  Are you out
there?

Rick
rbm8p@virginia.edu
From: rc05@GTE.COM (Ramesh Chandak)
Newsgroups: bionet.software
Subject: Please add me to the mailing list.
Date: 31 Aug 92 02:33:36 GMT
Distribution: bionet


- Ramesh M. Chandak
rc05@gte.com

Thank You !
From: wmelchior@NTBTOX.NCTR.FDA.GOV ("Bill Melchior, NCTR/FDA")
Newsgroups: bionet.software
Subject: Mac to PC disk utility?
Date: 27 Aug 92 15:12:41 GMT
Reply-To: wmelchior@NTDOC.NCTR.FDA.GOV
Distribution: bionet

The Mac on our new ABI 373 sequencer is not yet networked, and we have no
other Mac handy.  Does anyone know of a utility that will let us transfer
data from the Mac to a PC via 3 1/2" disk?  Since the Mac can't talk to
anyone but another Mac right now, this would probably have to be something
that would let a PC read a Mac disk.

Thanks, Bill
________________________________________________________________________________
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