From owner-software@net.bio.net Mon Jun 01 23:00:00 1998
Path: biosci!INFOSEL.NET.MX!laborato
From: laborato@INFOSEL.NET.MX ("Eduardo Perez Campos")
Newsgroups: bionet.software
Subject: RV: Anti-Freezing Software
Date: 2 Jun 1998 06:51:42 -0700
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How do you  catch  KERNEL32.DLL, VxDs  crashes?

Edward

-----Original Message-----
De: Kim Bruning <K.F.Bruning@NOSPAM.stud.biol.ruu.nl>
Para: bio-soft@net.bio.net <bio-soft@net.bio.net>
Fecha: Martes 2 de Junio de 1998 12:32 AM
Asunto: Re: Anti-Freezing Software


>
>Robert Vosweide heeft geschreven in bericht
><01bd8d43$7e30e220$27234891@hongli>...
><snip>
>
>>A big freeze is a freeze in Kernel32.dll or VxDs.
>>CrashGuard detects every type of crash.
>>However, it does not catch all crashes that occur in KERNEL32.DLL, VxDs,
>>and certain device drivers.
>
>
>Then why not simply remove the offenders from your HD? ;-)
>
>
>
>





From owner-software@net.bio.net Mon Jun 01 23:00:00 1998
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From: Daniel Wetzler <Daniel.Wetzler@uni-koeln.de>
Newsgroups: bionet.software,biz.comp.software,comp.lang.java.softwaretools,comp.mail.list-admin.software,comp.os.ms-windows.nt.software.backoffice
Subject: Re: Anti-Freezing Software
Date: Tue, 02 Jun 1998 14:52:17 +0200
Organization: Regional Computing Center, University of Cologne
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online schrieb:

>         I would like to know which software is the best to prevent my
> PC from
> freezing and I would also like to know if there is a demo for this
> program,
> by the way I'm using Windows 95.

Buy a Mac...  ;-)


From owner-software@net.bio.net Mon Jun 01 23:00:00 1998
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From: i.j.h.roberts@reading.ac.uk (I. Roberts)
Newsgroups: bionet.software
Subject: Sequence Analysis Windows 95?
Date: 2 Jun 1998 13:22:21 GMT
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Does anybody know if there is a good, cheap/free program (like DNA strider for 
the Mac) for sequence analysis ie restriction maps, translations etc for 
Windows 95.
I know there are a few things on the WWW but they are not as convenient or as 
good.

Thanks,


From owner-software@net.bio.net Mon Jun 01 23:00:00 1998
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Date: 02 Jun 1998 13:39:00 +0100
From: logies@ml.han.de (Michael Logies)
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	<01bd8705$c2bb8f60$09234891@hongli> <356AE450.F8B60166@doc.ic.ac.uk>
	<01bd8d43$7e30e220$27234891@hongli>
Subject: Re: Anti-Freezing Software
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> CrashGuard detects every type of crash.

Crashguard is the worst program I had on my PC ever. Didn't help  
against crashes. But after deinstalling I had an instable system  
crashing a few times/hour. I had to go back to a tape backup of the  
windows-directory and the registry.

Regards

M.

--
   logies@ml.han.de (Michael Logies, D-49134 Wallenhorst, germany)
   http://www.logies.de/

From owner-software@net.bio.net Mon Jun 01 23:00:00 1998
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From: "Kim Bruning" <K.F.Bruning@NOSPAM.stud.biol.ruu.nl>
Subject: Re: Anti-Freezing Software
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Robert Vosweide heeft geschreven in bericht
<01bd8d43$7e30e220$27234891@hongli>...
<snip>

>A big freeze is a freeze in Kernel32.dll or VxDs.
>CrashGuard detects every type of crash.
>However, it does not catch all crashes that occur in KERNEL32.DLL, VxDs,
>and certain device drivers.


Then why not simply remove the offenders from your HD? ;-)




From owner-software@net.bio.net Mon Jun 01 23:00:00 1998
Path: biosci!rutgers!news-relay.ncren.net!news.wfu.edu!news
From: jmihic@wfubcm.edu (John Mihic)
Newsgroups: bionet.software
Subject: Re: Questions about Amino acid seq alignments
Date: 2 Jun 1998 15:16:00 GMT
Organization: Wake Forest University
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In article <6krndk$cih@ustsu10.ust.hk>, netson@hotmail.com says...
>
>Dear all,
>
>    Which software can be use to align multiple sequences of amino acid of
>proteins?  The software that can work in Window95, Dos or WWW platform is
>preferred.  I have used ClustalW for win95 in the alignment but I found that
>there are some bugs in ClustalW.   Also, I would like to know how to creat
>the alignment in the multiple sequence .msf  format or FASTA format?  Since
>the file in these format will be edited by GeneDoc.

There is a freeware program available from NCBI called Macaw 
(ftp://ncbi.nlm.nih.gov/pub/macaw/) that runs under Windows (3.1, 95 and NT) 
as well as Mac.  This program allows you to do multiple amino acid or 
nucleotide sequence alignments. It can read in FASTA format files from Entrez 
(http://www3.ncbi.nlm.nih.gov/Entrez/).  I've used the program for a while now 
and like it. It does what I need to do and the price can't be beat.

John Mihic


From owner-software@net.bio.net Mon Jun 01 23:00:00 1998
Path: biosci!INFOSEL.NET.MX!laborato
From: laborato@INFOSEL.NET.MX ("Eduardo Perez Campos")
Newsgroups: bionet.software
Subject: RV: Anti-Freezing Software
Date: 2 Jun 1998 06:51:38 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
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NNTP-Posting-Host: net.bio.net


How do you  catch  KERNEL32.DLL, VxDs  crashes?

Edward

-----Original Message-----
De: Kim Bruning <K.F.Bruning@NOSPAM.stud.biol.ruu.nl>
Para: bio-soft@net.bio.net <bio-soft@net.bio.net>
Fecha: Martes 2 de Junio de 1998 12:32 AM
Asunto: Re: Anti-Freezing Software


>
>Robert Vosweide heeft geschreven in bericht
><01bd8d43$7e30e220$27234891@hongli>...
><snip>
>
>>A big freeze is a freeze in Kernel32.dll or VxDs.
>>CrashGuard detects every type of crash.
>>However, it does not catch all crashes that occur in KERNEL32.DLL, VxDs,
>>and certain device drivers.
>
>
>Then why not simply remove the offenders from your HD? ;-)
>
>
>
>




From owner-software@net.bio.net Tue Jun 02 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail
From: wgschech@med.uni-tuebingen.de
Newsgroups: bionet.software
Subject: EXCEL - 2nd order fit question
Date: Wed, 03 Jun 1998 11:49:38 GMT
Organization: Deja News - The Leader in Internet Discussion
Lines: 21
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hi all,

when calculating regressions with excel, I sometimes use a polynomic
fit. It's easy to display the corresponding function in the graph
window using the TrendLine option. But then I have to read the
coefficients and type them in manually.

Is there a function for directly making a second order fit or getting
access to the coefficients? RGP doesn't work since it makes only
linear regressions.

I want to avoid programming my own viasual basic routines for that
purpose.

Any ideas?

All input is welcome.
Wolfgang

-----== Posted via Deja News, The Leader in Internet Discussion ==-----
http://www.dejanews.com/   Now offering spam-free web-based newsreading

From owner-software@net.bio.net Tue Jun 02 23:00:00 1998
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From: "Rodrigo Lopez" <rls@ebi.ac.uk>
Newsgroups: bionet.software
Subject: Re: Sequence Analysis Windows 95?
Date: Wed, 3 Jun 1998 12:16:38 +0100
Organization: EMBL-EBI
Lines: 26
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Why not check the biocatalog at the EBI.

http://www.ebi.ac.uk/biocat/biocat.html

R:)

I. Roberts wrote in message <6l0uad$bkt$1@susscsc1.rdg.ac.uk>...
>Does anybody know if there is a good, cheap/free program (like DNA strider
for
>the Mac) for sequence analysis ie restriction maps, translations etc for
>Windows 95.
>I know there are a few things on the WWW but they are not as convenient or
as
>good.
>
>Thanks,
>


begin 666 Rodrigo Lopez.vcf
M0D5'24XZ5D-!4D0-"E9%4E-)3TXZ,BXQ#0I..DQO<&5Z.U)O9')I9V\-"D9.
M.E)O9')I9V\@3&]P97H-"D5-04E,.U!2148[24Y415).150Z<FQS0&5B:2YA
G8RYU:PT*4D56.C$Y.3@P-C S5#$Q,38S.%H-"D5.1#I60T%21 T*
`
end


From owner-software@net.bio.net Tue Jun 02 23:00:00 1998
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From: Jennifer Hallinan <jsh@forbio.com.au>
Newsgroups: bionet.software
Subject: Mapping Software
Date: Wed, 03 Jun 1998 14:31:25 +1000
Organization: ForBio Research
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I am looking for URLs for any public domain QTL analysis/ RAPD
analysis/mapping programs that may exist. Any suggestions welcome!

Thanks,

Jennifer

From owner-software@net.bio.net Tue Jun 02 23:00:00 1998
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From: Peter Kulmburg <kulmburg@aug.ukl.uni-freiburg.de>
Newsgroups: bionet.software
Subject: cricket graph III 1.5.3   - a summary
Date: 3 Jun 1998 14:43:35 +0100
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Original-To: bio-software@dl.ac.uk

Dear collegues,

thank you for the many mails I got, however, the outcome is quite
disappointing from my point of view:

1) Apparently, there is an update from 1.5.2 to 1.5.3 which adds PowerPC
compatibility and more stability under system 8.

2) It is only available in the USA. I found a web side with descriptions:

	http://www.provantage.com/fp_03507.htm

3) The 800 telephone number seems to work only in the USA, so I can not
contact the company.

4) There is an email address:

	Sales@provantage.com

however, nobody answers my mail, probably because it comes from outside the
USA.

Conclusion: what about all the internet if then a product is only available
in the USA? That is even more stupid since 1.5.2 was readily available in
Europe.

If somebody falls over the update discettes for 1.5.3 on any server, please
tell me.

Thank you so far, sincerely yours		Peter
Peter KULMBURG        at home  Tel./Fax:+33 3 89.68.28.83
at work:    Tel.: +49 761 270/7208 or 7207        Fax: /7217

From owner-software@net.bio.net Tue Jun 02 23:00:00 1998
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From: "Carlos Alberto Di Noro" <dinorocarlos@ciudad.com.ar>
Newsgroups: ar.ciencias.fisica,bionet.immunology,bionet.microbiology,bionet.software,bionet.software.gcg,bionet.toxicology,chile.mercado.software
Subject: suscripcion
Date: Tue, 2 Jun 1998 23:32:26 -0300
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Xref: biosci bionet.immunology:14137 bionet.microbiology:13607 bionet.software:21186 bionet.software.gcg:3138 bionet.toxicology:2253

Deseo suscribirme a su grupo de noticias. mi direcciones
dinorocarlos@ciudad.com.ar



From owner-software@net.bio.net Tue Jun 02 23:00:00 1998
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From: richard_steinman@cmagroup.com
Newsgroups: bionet.software
Subject: Florida; Sr. Software Engineer; NT, C++, DICOM, Imaging
Date: 3 Jun 1998 23:26:01 GMT
Organization: Career Marketing Associates
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SE Florida; Sr. Software Engineer; NT, C++, DICOM, Imaging

-Senior Software Engineer
-Southeast Florida Coastal
-Salaried, Full-Time, Excellent Benefits 
(Relocation Assistance Available)

Medical DICOM knowledge would be a major plus. Experience with C/C++ and 
NT required. Image manipulation, compression, edge detection, analysis, 
all good things to have. 

Please refer to JO# 5253RJS in your response.

richard_steinman@cmagroup.com 

Richard Steinman
Team Leader
rjs@cmagroup.com
IT & Software Solutions Team
Career Marketing Associates
http://www.cmagroup.com/IT.html

From owner-software@net.bio.net Tue Jun 02 23:00:00 1998
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From: Robert Negm <rnegm@med-med1.bu.edu>
Newsgroups: bionet.software
Subject: Strain Database
Date: Wed, 03 Jun 1998 12:09:48 -0400
Organization: Boston University
Lines: 42
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To whom it may concern,

This is in response to the several emails last week I received last week
asking, "I have downloaded StrainMan 1.0 from your web site at
www.caesarsoftware.com, now what do I do?"

Here are my answers.

First, StrainMan is a powerful database that manages detailed
information related to microbial strains for the individual laboratory.
Users may enter their strain information including PICT files into
strain records and assign a precise description of the frozen culture's
location in your laboratory. Therefore, once you have download the
installer and installed wither the Mac or Windows version of the program
on your computer, then start creating strain records by pressing the new
button to the right of the list and enter in the appropriate information
into each field. Users can also describe the media requirement for the
growth of each strain in their collection, thereby facilitating the time
required to design an experiment.

Second, the program allows users to customize their database by adding
their own constructed plasmids, phage, transposons, antibiotics, and
nutrients. This allows fast development of strain records. For example,
tab to "Plasmids" on the main list and create a new plasmid, then save
it. Then edit an old strain record and attach the new plasmid to a
strain record."

Third, in addition to printing detailed reports about your strain
collection, users may publish their strain collection so that by
knowing  the TCP address of a computer running StrainMan, you may browse
or query the strain collection using an internet browser. StrainMan
features a secure administrator so that only privileged users and guests
can access of view your database

If you have additional questions I will be happy to answer them, but as
always all of this information is in the users manual.

Sincerely,

Robert Negm



From owner-software@net.bio.net Tue Jun 02 23:00:00 1998
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From: "Valentin Marchant" <kinestrn@netcene.com>
Newsgroups: ar.ciencias.fisica,bionet.immunology,bionet.microbiology,bionet.software,bionet.software.gcg,bionet.toxicology,chile.mercado.software
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Date: Wed, 3 Jun 1998 11:24:46 -0000
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Xref: biosci bionet.immunology:14142 bionet.microbiology:13611 bionet.software:21191 bionet.software.gcg:3139 bionet.toxicology:2254


Carlos Alberto Di Noro wrote in message
<6l28tq$liq40@origin.prima.com.ar>...
>Deseo suscribirme a su grupo de noticias. mi direcciones
>dinorocarlos@ciudad.com.ar




From owner-software@net.bio.net Wed Jun 03 23:00:00 1998
Path: biosci!eva!alex
From: alex@eva (Alexander Kanapin)
Newsgroups: bionet.software
Subject: CDS parse software for UNIX - is something available?
Date: 4 Jun 1998 01:11:31 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
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	Hello!

I am looking for softwrare (source code) for simple parsing of GenBank 
CDS field. Does anybody know about such tools? I need some kind of 
automatic splicing - to read CDS data and produse new sequence string 
according to CDS coordinates of coding regions from entry sequence.

Many thanks in advance for any informytion about the problem.

	Alex



-- 
Alexander Kanapin, PhD                         alex@hki-jena.de
Hans-Knoell-Institut fuer Naturstoff-Forschung
Beutenbergstrasse 11, Jena                Tel.: +49-3641-65-6689
Postfach 100 813, D-07708 Jena, Germany   Fax: +49-3641-609818

From owner-software@net.bio.net Wed Jun 03 23:00:00 1998
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From: Brian Fristensky <frist@cc.umanitoba.ca>
Newsgroups: bionet.software
Subject: Re: CDS parse software for UNIX - is something available?
Date: Thu, 04 Jun 1998 18:08:53 -0500
Organization: University of Manitoba
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Alexander Kanapin wrote:

> I am looking for softwrare (source code) for simple parsing of GenBank
> CDS field. Does anybody know about such tools? I need some kind of
> automatic splicing - to read CDS data and produse new sequence string
> according to CDS coordinates of coding regions from entry sequence.
> 


The XYLEM package is specifically designed for creating and
managing sequence database subsets. It includes a program
called FEATURES that, given a set of GenBank Accession
numbers or LOCUS names, extracts all features corresponding
to one or more feature keys (eg. CDS, mRNA, exon, etc.).
ANY legal feature can be parsed to yeild a sequence. Even
when features are scattered across SEGMENTED GenBank
entries (eg. exons of a large gene were sequenced, but
not introns) FEATURES will properly reassemble them, 
according to join() statements in the Features Table
of the entry. For example, given the feature

CDS            
join(M38619:160..256,M38620:11..307,                                       
M38621:11..179,M38622:11..176, 
                M38623:11..250,11..103) 
                /product="green visual pigment" 
                /gene="G101"
                /codon_start=1 

sequences from six different entries would be joined to
recreate the CDS.

FEATURES also allows extraction of sequence fragments
using Feature Table expressions . For example, give the
following feature:

         CDS             305..640
                         /gene="flaL"
                         /label=ORF2
                         /note="flaD (sin) homologue; putative"
                         /codon_start=1

Any of the following expressions would return the same sequence:

M60287:305..640
M60287:ORF2
M60287:/label=ORF2
M60287:/gene="flaL"
M60287:/note="flaD (sin) homologue; putative" 

Expressions allow you to extract sequence fragments even
when they are not explicitly annotated, or to work around
errors in annotation.

To learn more about XYLEM, or download Solaris binaries or
source code, see:

http://home.cc.umanitoba.ca/~psgendb/XYLEM.html

===============================================================================
Brian Fristensky                | Let me get this straight:
Department of Plant Science     |  
University of Manitoba          | A company that dominates the desktop,
Winnipeg, MB R3T 2N2  CANADA    | and can afford to hire an army of the 
frist@cc.umanitoba.ca           | world's best programmers, markets 
Office phone:   204-474-6085    | what is arguably the world's LEAST
FAX:            204-474-7528    | reliable operating system?            
http://home.cc.umanitoba.ca/~frist/    What's wrong with this picture?
===============================================================================

From owner-software@net.bio.net Wed Jun 03 23:00:00 1998
Path: biosci!USA.NET!sanchez54
From: sanchez54@USA.NET
Newsgroups: bionet.software
Subject: Finally..My Psoriasis is Symptom-Free
Date: 4 Jun 1998 02:33:49 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
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From owner-software@net.bio.net Wed Jun 03 23:00:00 1998
Path: biosci!lhc.nlm.nih.gov!not-for-mail
From: Roland Walker <walker@ncbi.nlm.nih.gov>
Newsgroups: bionet.software
Subject: Re: CDS parse software for UNIX - is something available?
Date: Thu, 04 Jun 1998 16:12:05 -0400
Organization: National Center for Biotechnology Information
Lines: 14
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To: Alexander Kanapin <alex@eva>
X-Priority: 3 (Normal)

Alexander Kanapin wrote:
> I am looking for softwrare (source code) for simple parsing of GenBank
> CDS field. Does anybody know about such tools? I need some kind of
> automatic splicing - to read CDS data and produse new sequence string
> according to CDS coordinates of coding regions from entry sequence.

Such a program (called feature2fasta) is included in the SEALS package

  http://www.ncbi.nlm.nih.gov/Walker/SEALS/index.html

Just write me if you have any questions about how to make the script
do exactly what you want.

R

From owner-software@net.bio.net Wed Jun 03 23:00:00 1998
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From: alwang@blue.seas.upenn.edu (Al Wang)
Newsgroups: bionet.software
Subject: PDB -> SwissPROT conversion?
Date: 4 Jun 1998 21:57:28 GMT
Organization: University of Pennsylvania
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Hi,

Does anyone know what's a good way to take a Brookhaven PDB file, extract 
the sequence information, and save it in SwissPROT format?  If it can 
also extract the secondary structure features, even better.  

Thanks,
Al



--
__________________________________________
al wang
alwang@doubt.com
http://www.seas.upenn.edu/~alwang/

"What's My Solution?" 
"Noise Pollution!"

From owner-software@net.bio.net Wed Jun 03 23:00:00 1998
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From: Robert Negm <rnegm@med-med1.bu.edu>
Newsgroups: bionet.software
Subject: StrainMan 1.0 Question
Date: Thu, 04 Jun 1998 15:02:15 -0400
Organization: Boston University Medical Center
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From owner-software@net.bio.net Wed Jun 03 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!204.71.76.137!news.campus.mci.net!uky.edu!ukcc.uky.edu!NRMOLL00
From: NRMOLL00@ukcc.uky.edu (Nancy R.Mollette)
Newsgroups: bionet.software
Subject: any programs to chart/record/identify spore patterns?
Date: Thu, 04 Jun 98 12:40:28 EDT
Organization: The University of Kentucky
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Keywords: mycology, mushrooms

can anyone direct me to a PC program that can help identify spoor patterns
in mushrooms?
thanks
 
 
 
 

From owner-software@net.bio.net Wed Jun 03 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newshub.northeast.verio.net!news.pn.com!nntp.pn.com!mozo.cc.purdue.edu!purdue!news.bu.edu!not-for-mail
From: Robert Negm <rnegm@med-med1.bu.edu>
Newsgroups: bionet.software
Subject: StrainMan 1.0 Question
Date: Thu, 04 Jun 1998 15:04:23 -0400
Organization: Boston University Medical Center
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To whom it may concern,

I am writing to answer a common question regarding StrainMan 1.0 from
Caesar Software at http://www.caesarsoftware.com.

The highly asked question I have been receiving is, "How can I use
StrainMan to find the strains in my collection that harbor plasmids,
which also contain a unique restriction site?"


The answer is the following. Create a new plasmid or edit one currently
in the plasmid list by first, selecting the "Plasmid" tab in the main
list and then pressing the "New" or "Edit" button. Once you have opened
the plasmid record click on the "Genetics" tab. Click on the "Sequence"
button. Here you may paste the sequence of DNA into the large field.
After you paste the DNA sequence of the plasmid into a text field, press

the "OK" button. Then press the digest button, and StrainMan will scan
this strand and its complement  for restriction site motifs.  Save the
new or modified plasmid record. Select a strain from your collection by
clicking on the "Strain" tab in the main list and clicking on a strain
in the collection. Once the strain record is open, then select the
"Plasmid & Phage" and press the "Attach" button to the right of the
plasmid list. Now click on the plasmid that you recently entered into
the StrainMan database that contains its  restriction map and press the
"Select" button. Press the "Save" button on the strain record.

Now you may search for this strain by using the search engine from
"Search" pull-down menu and select "Search". Select the "Plasmid: enzyme

name", and enter in the restriction enzyme name into the right field.
Press the "More Choices" button then select the "Plasmid: # cut sites",
then enter "1" into the field on the right. Press the "Find" button and
StrainMan will retrieve all strains in your collection meeting the this
criteria.

Remember, if there are rare enzymes not already present in StrainMan,
then users must enter the enzyme name and motif into the enzyme list. To

do this select "Enzymes" from the "Utilities" pull-down menu, enter the
enzyme abbreviated name and motif. Look at other enzymes by clicking on
them to see how to annotate the exact restriction site by placing a
quotation mark and a comma between the one-letter nucleotide
abbreviations for top and bottom strands, respectively.

As always, all of this information is present in the users manual and
the on-line help. If you have any more questions, then please feel free
to contact me directly.


Sincerely,

Robert Negm, PhD
Scientific Advisor
Caesar Software LLC
http://www.caesarsoftware.com






From owner-software@net.bio.net Thu Jun 04 23:00:00 1998
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From: letondal@pasteur.fr (Catherine  Letondal)
Newsgroups: bionet.software
Subject: Re: PDB -> SwissPROT conversion?
Date: 5 Jun 1998 09:34:42 GMT
Organization: Institut Pasteur, Paris
Message-ID: <6l8e3i$chv$1@montespan.pasteur.fr>
References: <6l7588$j4n$1@netnews.upenn.edu>
Reply-To: letondal@pasteur.fr (Catherine  Letondal)
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In article <6l7588$j4n$1@netnews.upenn.edu>, alwang@blue.seas.upenn.edu (Al Wang) writes:
>Hi,
>
>Does anyone know what's a good way to take a Brookhaven PDB file, extract 
>the sequence information, and save it in SwissPROT format?  If it can 
>also extract the secondary structure features, even better.  
>
>Thanks,
>Al

I am looking for the same kind information. There is a description of a program called
PDB2PIR on the PIR Web (see http://nbrfa.georgetown.edu/pir/software.html)
but it has not been put on their ftp server.
I am waiting for an answer from the author of the program (Dr. John S. Garavelli, 
Associate Director of PIR).

Regards,

>__________________________________________
>al wang
>alwang@doubt.com
>http://www.seas.upenn.edu/~alwang/
>
>"What's My Solution?" 
>"Noise Pollution!"
>


From owner-software@net.bio.net Thu Jun 04 23:00:00 1998
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From: Michele Clamp <michele@speed.ebi.ac.uk>
Newsgroups: bionet.software
Subject: Re: CDS parse software for UNIX - is something available?
Date: 05 Jun 1998 10:43:38 +0100
Organization: MRC Human Genome Mapping Project Resource Centre
Lines: 427
Message-ID: <n1n2bsdvzp.fsf@speed.ebi.ac.uk>
References: <199806040809.KAA09942@eva.hki-jena.de> <35772905.5014D7A@cc.umanitoba.ca>
NNTP-Posting-Host: speed.ebi.ac.uk
X-Newsreader: Gnus v5.5/Emacs 20.2

> Alexander Kanapin wrote:
> 
> > I am looking for softwrare (source code) for simple parsing of GenBank
> > CDS field. Does anybody know about such tools? I need some kind of
> > automatic splicing - to read CDS data and produse new sequence string
> > according to CDS coordinates of coding regions from entry sequence.
> > 
> 

The following perl script I think may do what you want.  It produces its 
protein coding sequences by translating the DNA and I've come across 
a few discrepancies between the DNA translations and the quoted 
translation in the feature table (e.g. you get stop codons turning up 
unexpectedly).  It's also human specific because of the DNA translation
so you'll have to add more coding tables if you want to use it
for other organisms.

#!/usr/local/bin/perl

# Michele Clamp 25/7/97
#
# Reads a Genbank format database file and outputs various features/
# sequences.  Originally written for outputting coding and non-coding
# sequence of complete genes.

if (! @ARGV) {
  usage();
  exit(0);
}

use Getopt::Std;
getopts('lLdaNksocniftEIeCAhS');


if ($opt_h) {
    usage();
}

# -h = help
# -l = length .
# -d = DEFINITION .
# -a = ACCESSION .
# -N = NID 
# -o = ORGANISM .
# -c = Coding sequence - dna
# -C = Coding sequence - aa
# -f = 5' sequence
# -t = 3' sequence
# -e = exon list
# -E = exon sequences
# -I = intron sequences
# -A = all sequence - dna
# -S = SRS format sequences - numbers at the right

$| = 1;

while (<>) {
    #LOCUS marks the beginning of a new entry
    if (/^LOCUS +(\S+) + (\S+)/) {
        $id = $1;
        $length = $2;

        if ($opt_l) {
            print("$length\n");
        }

        #Read the entry until //
        while (($line = <>) && ($line !~ /^\/\//)) {
            #Do the easy stuff first
            if ($line =~ /^ACCESSION +(\S+)/) {
                $acc = $1;
                if ($opt_a) {
                    print("$acc\n");
                }
            }

            if ($line =~ /^DEFINITION +(.*)\n/) {
                $def = $1;
                if ($opt_d) {
                    print("$def\n");
                }
            }
            
            if ($line =~ /ORGANISM +(.*)\n/) {
                $org = $1;
                if ($opt_o) {
                    print("$org\n");
                }
            }
            
            if ($line =~ /^NID +(.*)\n/) {
                $nid = $1;
                if ($opt_N) {
                    print("$nid\n");
                }
            }
            #We only want to process sequence stuff if we have to
            if ($opt_c || $opt_C || $opt_n || $opt_i || $opt_f || 
                $opt_t || $opt_e || $opt_b || $opt_E || $opt_I || opt_A)  {

                #Found the CDS line which defines where the exons are
                if ($line =~ /^ +CDS +/)    {
                    $cds = "";
                    #Read in the cds lines
                    while ($line !~ /\)/) {
                        chop($line);
                        $cds .= $line;
                        $line = <>;
                    }

                    chop($line);
                    $cds .= $line;
                    
                    $cds =~ s/ //g;
                    $cds =~ s/.*join\((.*)\).*/$1/;

                    #Exons are in an array
                    @exons = split(/\,/,$cds);

                    undef(@exstart);
                    undef(@exend);

                    #loop over the exons and push the
                    #start and end points into arrays
                    foreach $exon (@exons) {
                        if ($exon =~ /\.\./) {
                            ($start,$end) = split(/\.\./,$exon);
                            push(@exstart,$start);
                            push(@exend,$end);
                        } else {
                            print(STDERR "Can't split exon $exon of $id\n");
                        }
                    }

                    #Exon list - print if option
                    if ($opt_e) {
                        for ($i = 0; $i <= $#exstart; $i++) {
                            print("$exstart[$i] - $exend[$i]\n");
                        }
                        print("\n");
                    }

                } # end if ($line = CDS
                
                if ($line =~ /\/translation=\"(.*)\n/) {
                    $trans = $1;
                    while ($trans !~ /\"/) {
                        $line = <>;
                        $line =~ s/\n//g;
                        $line =~ s/ //g;
                        $trans .= $line;
                    }

                    $trans =~ s/\"//g;

                    #Take off Start codon
                    $trans = substr($trans,1);
                    $trans =~ s/(.{72})/$1\n/g;
                }
                
                #Get the sequence out - read the dna sequence
                #paste the exons together and translate
                if ($line =~ /ORIGIN/ && !$opt_S) {
                    $sum = 0;
                    $seq = "";

                    while ($sum < $length) {
                        $tmp = <>;
                        $tmp =~ s/ +\S+ +(.*)\n/$1/;
                        $tmp =~ s/ //g;
                        $seq .= $tmp;
                        $sum = length($seq);
                    }
                    if ($length != length($seq)) {
                        print(STDERR "ERROR: Sequence lengths don't match\n");
                        $len = length($seq);
                        print(STDERR "Sequence length in feature table = $length\n");
                        print(STDERR "Sequence length from entry = $len\n");
                    }
                }
                #This is for genbank entries retrieved using SRS
                #The sequence is not preceded by ORIGIN and the
                #numbers are at the end of the line as opposed to before
                if ($opt_S && ($line =~ /BASE/)) {
                    $sum = 0;
                    $seq = "";
                    
                    while (($sum < $length) && (($tmp = <>) !~ /^\/\//)) {
                        if ($tmp !~ /Length/) {
                            $tmp =~ s/ +(.*) +.*\n/$1/;
                            $tmp =~ s/ //g;
                            $seq .= $tmp;
                            $sum = length($seq);
                        }
                    }
                    if ($length != length($seq)) {
                        print(STDERR "ERROR: Sequence lengths don't match\n");
                        $len = length($seq);
                            print(STDERR "Sequence length in feature table = $length\n");
                        print(STDERR "Sequence length from entry = $len\n");
                    }
                }

            }
        } # end while (($line = <>

        if ($opt_c || $opt_C || $opt_n || $opt_i || $opt_f || 
            $opt_t || $opt_e || $opt_b || $opt_E || $opt_I || opt_A)  {
            
            #print all the dna out
            if ($opt_A) {
                ($chopseq = $seq) =~ s/(.{72})/$1\n/g;
                print(">$id\n$chopseq\n");
            }
            #Now process the CDS list for the coding dna only
            $exstr = "";
            $protein = "";
            
            for ($i = 0; $i <= $#exstart; $i++) {
                $tmpstr = substr($seq,$exstart[$i]+1,$exend[$i] - $exstart[$i]+1);
                $exstr .= $tmpstr;
                if ($opt_E) {
                    $tmpstr =~ s/(.{72})/$1\n/g;
                    $start = $exstart[$i]; $end = $exend[$i];
                    print(">${id}_exon$i $start - $end\n$tmpstr\n");
                }

            }
            
            #We also want to extract the non-coding sequence
            #We'll annotate the 5', 3' and intronic

            if ($opt_f) {
                #5' and 3' first
                $seq5 = substr($seq,0,$exstart[0]-1);
                $seq5 =~ s/(.{72})/$1\n/g;
                $end = $exstart[0] - 1;
                print(">${id}_5UTR 1 - $end\n$seq5\n");
            }
            
            if ($opt_I) {
                #Now the introns
                for ($i = 0; $i < $#exstart; $i++) {
                    $seqi = substr($seq,$exend[$i],$exstart[$i+1] - $exend[$i] - 1);
                    $start = $exend[$i]+1; $end = $exstart[$i+1] - 1;
                    $seqi =~ s/(.{72})/$1\n/g;
                        print(">${id}_intron$i $start-$end\n$seqi\n");
                }
            }

            if ($opt_t) {
                #And the 3'
                $seq3 = substr($seq,$exend[$#exend] ,$length - $exend[$#exend]);
                $seq3 =~ s/(.{72})/$1\n/g;
                $start = $exend[$#exend]+1; $end = $length;
                   print(">${id}_3UTR $start-$end\n$seq3\n\n");
            }

            if ($opt_C) {
                $protein = translate($exstr,2);
                $protein =~ s/(.{72})/$1\n/g;
                
                #Take off stop codon
                $protein =~ s/\*$//;
                print(">$id\n$protein\n");
            
                if ($protein =~ /\*../) {
                    print(STDERR "WARNING: Coding sequence $id contains stop codons\n");
                }
            }
            if ($opt_c) {
                $exstr =~ s/(.{72})/$1\n/g;
                print(">$id\n$exstr\n");
            }
        }
    } # end if (/^LOCUS...
}


sub translate  {
    my($seq,$frame) = @_;
    my($i);
    if ($frame == "") {
        $frame = 1;
    }
    
    $aa{"TTT"} = "F";
    $aa{"TTC"} = "F";
    $aa{"TTA"} = "L";
    $aa{"TTG"} = "L";

    $aa{"TCT"} = "S";
    $aa{"TCC"} = "S";
    $aa{"TCA"} = "S";
    $aa{"TCG"} = "S";

    $aa{"TAT"} = "Y";
    $aa{"TAC"} = "Y";
    $aa{"TAA"} = "*";
    $aa{"TAG"} = "*";

    $aa{"TGT"} = "C";
    $aa{"TGC"} = "C";
    $aa{"TGA"} = "*";
    $aa{"TGG"} = "W";

    $aa{"CTT"} = "L";
    $aa{"CTC"} = "L";
    $aa{"CTA"} = "L";
    $aa{"CTG"} = "L";

    $aa{"CCT"} = "P";
    $aa{"CCC"} = "P";
    $aa{"CCA"} = "P";
    $aa{"CCG"} = "P";

    $aa{"CAT"} = "H";
    $aa{"CAC"} = "H";
    $aa{"CAA"} = "Q";
    $aa{"CAG"} = "Q";

    $aa{"CGT"} = "R";
    $aa{"CGC"} = "R";
    $aa{"CGA"} = "R";
    $aa{"CGG"} = "R";

    $aa{"ATT"} = "I";
    $aa{"ATC"} = "I";
    $aa{"ATA"} = "I";
    $aa{"ATG"} = "M";

    $aa{"ACT"} = "T";
    $aa{"ACC"} = "T";
    $aa{"ACA"} = "T";
    $aa{"ACG"} = "T";

    $aa{"AAT"} = "N";
    $aa{"AAC"} = "N";
    $aa{"AAA"} = "K";
    $aa{"AAG"} = "K";

    $aa{"AGT"} = "S";
    $aa{"AGC"} = "S";
    $aa{"AGA"} = "R";
    $aa{"AGG"} = "R";

    $aa{"GTT"} = "V";
    $aa{"GTC"} = "V";
    $aa{"GTA"} = "V";
    $aa{"GTG"} = "V";

    $aa{"GCT"} = "A";
    $aa{"GCC"} = "A";
    $aa{"GCA"} = "A";
    $aa{"GCG"} = "A";

    $aa{"GAT"} = "D";
    $aa{"GAC"} = "D";
    $aa{"GAA"} = "E";
    $aa{"GAG"} = "E";

    $aa{"GGT"} = "G";
    $aa{"GGC"} = "G";
    $aa{"GGA"} = "G";
    $aa{"GGG"} = "G";

    $seq =~ tr/a-z/A-Z/;

    $start = $frame-1;

    for ($i = $start; $i < length($seq); $i = $i + 3) {
        $codon = substr($seq,$i,3);
        $acid = $aa{$codon};
#       print("$codon = $acid\n");
        $protein .= $acid;
    }

    return($protein);
}
    
sub usage {

# -h = help
# -l = length .
# -d = DEFINITION .
# -a = ACCESSION .
# -N = NID 
# -o = ORGANISM .
# -c = Coding sequence - dna
# -C = Coding sequence - aa
# -i = intronic sequece
# -f = 5' sequence
# -t = 3' sequence
# -e = exon list
# -E = exon sequences
# -I = intron sequences
# -A = all sequence - dna

    print("Usage codnocod -hldaNocCfteEIA < genbankfile\n");
    print("
Reads genbank format sequence entries and outputs various features

          -h = help
          -l = length 
          -d = DEFINITION 
          -a = ACCESSION 
          -N = NID 
          -o = ORGANISM 
          -c = Coding sequence - dna
          -C = Coding sequence - aa
          -f = 5' sequence
          -t = 3' sequence
          -e = exon list
          -E = exon sequences
          -I = intron sequences
          -A = all sequence - dna
          -S = entries retrieved using SRS - no ORIGIN line and sequence is
               numbered on the right

");
    exit(0);
}

-- 
Dr Michele Clamp ,        EMBL-European Bioinformatics Institute 
Hinxton, Cambs CB10 1SD,  email : michele@ebi.ac.uk
UK                        Tel:  01223 494682    Fax: 01223 494468

From owner-software@net.bio.net Thu Jun 04 23:00:00 1998
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From: agapow@latcs1.cs.latrobe.edu.au (p-m agapow)
Newsgroups: bionet.software
Subject: Conserve 3.2.1 - Biodiversity software updated
Date: 5 Jun 1998 04:40:28 GMT
Organization: Calvin Coolidge Home for Dead Biologists
Lines: 41
Distribution: world
Message-ID: <6l7srs$5v3$1@lion.cs.latrobe.edu.au>
NNTP-Posting-Host: latcs1.cs.latrobe.edu.au

Conserve v3.2.1 for the Macintosh
---------------------------------

At http://www.gen.latrobe.edu.au/Computing/software.html people can
download the latest version of Conserve, a Macintosh program that uses
phylogenetic information to calculate biodiversity and test the
feasability of conservation schemes.

What does it do?
----------------

While it would be best to preserve all species, in the management
of biodiversity it is often necessary to set priorities.  Other
things being equal, these should be set on the basis of evolutionary
distinctiveness (a la Wilson), and Conserve enables you to do this
using genetic distances and also to test whether particular assemblages
of populations preserve statistically significantly more biodiversity
than other assemblages.  Biodiversity is determined using GD (probability
of more than one allele) or PD (length of evolutionary history) methods,
from data in the form of unrooted trees produced in TREEFILE format, as
produced by various programs in the PHYLIP package.  Taxa may be grouped
into sets using various options and the effects of removing species singly
or in sets determined.  Multiple trees produced from the same data using
the bootstrap method in PHYLIP (using SEQBOOT) enables calculation of the
confidence limits for the biodiversity preserved by any assemblage.
The number of taxa is limited only by the size of your computer.

Why upgrade?
------------

Conserve 3 contains many GUI improvements over version 2 as well
significant speedups and better calculations. Users of earlier 3.x
versions are encouraged to upgrade to correct a few bugs.

http://www.gen.latrobe.edu.au/Computing/software.html


--
Paul-Michael Agapow (agapow@latcs1.oz.au), LaTrobe University, Melbourne



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From: Kentucky Trailer Trash <invalid.address@any.domain.com>
Newsgroups: bionet.software
Subject: Re: Sequence Analysis Windows 95?
Date: Thu, 04 Jun 1998 21:34:06 -0400
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I. Roberts wrote:

> Does anybody know if there is a good, cheap/free program (like DNA strider for
> the Mac) for sequence analysis ie restriction maps, translations etc for
> Windows 95.

Yes, there's Prophet, a project of the NIH.  You can download it from
http://www-prophet.bbn.com/


From owner-software@net.bio.net Thu Jun 04 23:00:00 1998
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From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts)
Newsgroups: bionet.software
Subject: Re: PDB -> SwissPROT conversion?
Date: 5 Jun 1998 13:28:38 GMT
Organization: University of Cambridge
Lines: 125
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NNTP-Posting-Host: mole.bio.cam.ac.uk

In article <6l7588$j4n$1@netnews.upenn.edu>,
Al Wang <alwang@blue.seas.upenn.edu> wrote:
>Hi,
>
>Does anyone know what's a good way to take a Brookhaven PDB file, extract 
>the sequence information, and save it in SwissPROT format?  If it can 
>also extract the secondary structure features, even better.  

I can't help exactly, but if it gets you half way there, here is my
perl script that extracts the sequence information from a PDB file and
creates a FASTA format sequence file from it:

#!/usr/local/bin/perl

# pdb2fasta (C) T J R Cutts 1998

# This script extracts the SEQRES records from a PDB file, and writes out
# separate FASTA format sequence files, one for each strand in the PDB
# file.  The title line of the FASTA file is constructed from the COMPND
# records of the PDB file, and the strand letter.

    %lookup=(
	     'A' => 'A',
	     'C' => 'C',
	     'G' => 'G',
	     'T' => 'T',
	     'U' => 'U',
	     
	     'ALA' => 'A',
	     'ASX' => 'B',
	     'CYS' => 'C',
	     'ASP' => 'D',
	     'GLU' => 'E',
	     'PHE' => 'F',
	     'GLY' => 'G',
	     'HIS' => 'H',
	     'ILE' => 'I',
	     'LYS' => 'K',
	     'LEU' => 'L',
	     'MET' => 'M',
	     'ASN' => 'N',
	     'PRO' => 'P',
	     'GLN' => 'Q',
	     'ARG' => 'R',
	     'SER' => 'S',
	     'THR' => 'T',
	     'VAL' => 'V',
	     'TRP' => 'W',
	     'XXX' => 'X',
	     'TYR' => 'Y',
	     'GLX' => 'Z',
	     '...' => '.',
	     'END' => '*' 
	     );

die "Usage: pdb2fasta <pdbfile> <outfile>\nA separate output file will be created for each strand in the PDB file.\n"
    unless ($#ARGV==1);

@pdb=();

open(P, "<$ARGV[0]") || die "Could not open $ARGV[0]";

# Put the file, stripped of its carriage returns, in an array.
foreach (<P>)
{
    chomp;
    push(@pdb, $_);
}

close(P);

%strand = ();

# Extract the SEQRES and COMPND records
@seqres=grep(/^SEQRES/, @pdb);
@cmpnd=grep(/^COMPND/, @pdb);

# Create a suitable FASTA title line from the COMPND records
$cmpnd='>'.join(' ', @cmpnd);
$cmpnd =~ s/COMPND//g;
$cmpnd =~ s/\s+/ /g;

foreach $line (@seqres)
{
    # Split the SEQRES line from positions 19-70 into an array of residues
    @residues = split(/\s+/, substr($line, 19, 51));
    
    # For each of these, uppercase the residue, look up its single letter
    # equivalent in the hash at the top of this script, and then append
    # that single letter to this strand's variable for output.
    foreach $res (@residues)
    {
	$res = uc($res);
	$strand{substr($line, 11, 1)} .= $lookup{$res};
    }
    
}

# For each strand discovered, create a FASTA format file printed nicely
# with 60 residues per line.

foreach $key (keys %strand)
{
    $filename = ($key eq " ") ? "${ARGV[1]}.tfa" : "${ARGV[1]}_$key.tfa";
    open (O, ">$filename") ||
	die "Could not open $filename for writing";

    print O "$cmpnd - strand $key\n";
    for ($n = 0 ; $n < length($strand{$key}); $n+=60)
    {
	print O substr($strand{$key}, $n, 60)."\n";
    }

    close O;
}

# That's it!



-- 
--------------------------------------------------------------------------
Dr T J R Cutts                                        Tel: +44 1223 333596
Dept. of Biochemistry, 80 Tennis Court Rd.
Cambridge, CB2 1GA, UK

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From: Paul@pdchem.demon.co.uk (Paul Davis)
Newsgroups: bionet.software
Subject: Re: PDB -> SwissPROT conversion?
Date: Fri, 05 Jun 98 15:58:16 GMT
Organization: Myorganisation
Message-ID: <897062296snz@pdchem.demon.co.uk>
References: <6l7588$j4n$1@netnews.upenn.edu>
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In article <6l7588$j4n$1@netnews.upenn.edu>
           alwang@blue.seas.upenn.edu "Al Wang" writes:

> Does anyone know what's a good way to take a Brookhaven PDB file, extract 
> the sequence information, and save it in SwissPROT format?  If it can 
> also extract the secondary structure features, even better.  
> 

The program STRIDE by Frishman and Argos, which I obtained
from

http://www.embl-heidelberg.de/argos/stride/stride_info.html

will generate secondary structure assignments from the
atomic coordinates in a PDB file.  While the assignments
will not always correspond exactly to the HELIX, SHEET and
TURN records of a PDB file (where these are present), they
are made in a consistent manner and are possibly more useful
in comparative studies.

STRIDE can also output the sequence in fasta format.

See Proteins 23: 566-579 (1995)

-Paul
-- 

--------------------------------------------------------------------
Paul Davis                                   paul@pdchem.demon.co.uk


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From: francis.durst@bota-ulp.u-strasbg.fr (Francis Durst)
Newsgroups: bionet.software
Subject: Re: PDB -> SwissPROT conversion?
Date: Fri, 5 Jun 1998 18:23:35
Organization: CNRS
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In article <6l7588$j4n$1@netnews.upenn.edu> alwang@blue.seas.upenn.edu (Al Wang) writes:
>From: alwang@blue.seas.upenn.edu (Al Wang)
>Subject: PDB -> SwissPROT conversion?
>Date: 4 Jun 1998 21:57:28 GMT

>Hi,

>Does anyone know what's a good way to take a Brookhaven PDB file, extract 
>the sequence information, and save it in SwissPROT format?  If it can 
>also extract the secondary structure features, even better.  

>Thanks,
>Al

The Swiss-pdb viewer (at http://expasy.hcuge.ch/) which works fine on MacOS 
and Win95/NT, will import any .pdb file and save the seq in Fasta format. 

En plus, the last version, 3.0 is an excellent viewer and has provision for 
'mutation' of residues, changing bond angles and other niceties.

Francis
===============================================================
Francis Durst, IBMP
Strasbourg, France

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From: Peter Rice <pmr@sanger.ac.uk>
Newsgroups: bionet.software
Subject: Re: PDB -> SwissPROT conversion?
Date: 05 Jun 1998 15:54:58 +0100
Organization: The Sanger Centre
Lines: 31
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In article <6l7588$j4n$1@netnews.upenn.edu>, alwang@blue.seas.upenn.edu (Al Wang) writes:
> >Does anyone know what's a good way to take a Brookhaven PDB file, extract 
> >the sequence information, and save it in SwissPROT format?  If it can 
> >also extract the secondary structure features, even better.  

The simplest is to look in SWISSPROT. You will find the sequence (complete
even if the PDB entry is a fragment) and the secondary structure assignments.

Of course, there are cases where this does not apply:

o more than one structure for a protein, where SWISSPROT may have only one
  example

o Immunoglobulin and other entries that SWISSPROT excludes to avoid
  redundancy

o new PDB entries that have not yet made it into SWISSPROT or SWISSNEW


From a quick check with SRS it looks like 2332 PDB entries are not in
SWISSPROT 35 (Jan 98), and 1236 PDB entries are not in SWISSPROT 35 plus
the latest SWISSNEW updates (Jun 98)

... but many of these are DNA entries so it is not too bad

-- 
----------------------------------------------------------------------
Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr@sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/

From owner-software@net.bio.net Thu Jun 04 23:00:00 1998
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From: micaelj@my-dejanews.com
Newsgroups: bionet.software
Subject: Vector detection and masking
Date: Fri, 05 Jun 1998 08:57:16 GMT
Organization: Deja News - The Leader in Internet Discussion
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Does anyone know of a good non-commercial UNIX tool that can scan the ends of
your sequnces for parts of vectors and possibly mask them? Something like
vector_clip in Staden, but not being part of a commercial package.
I am doing a small survey of available tools on the net for this task and I
would be very grateful for every hint.

/Micael Jacobsson, M.Sc. student

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From: bpmurray*STUFFER*@socrates.ucsf.edu (Bernard Murray)
Newsgroups: bionet.software
Subject: Re: PDB -> SwissPROT conversion?
Date: Fri, 05 Jun 1998 20:20:48 -0700
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In article <897062296snz@pdchem.demon.co.uk>, Paul@pdchem.demon.co.uk wrote:

> In article <6l7588$j4n$1@netnews.upenn.edu>
>            alwang@blue.seas.upenn.edu "Al Wang" writes:
> 
> > Does anyone know what's a good way to take a Brookhaven PDB file, extract 
> > the sequence information, and save it in SwissPROT format?  If it can 
> > also extract the secondary structure features, even better.  
> > 
> 
> The program STRIDE by Frishman and Argos, which I obtained
> from
> 
> http://www.embl-heidelberg.de/argos/stride/stride_info.html
> 
> will generate secondary structure assignments from the
> atomic coordinates in a PDB file
[snip]

Similarly, you can load the structure into RasMol and then type
"show sequence" on the command line to have the sequence displayed
(three letter format, not SwissProt) and you can then cut'n'paste
to your heart's content.  Alas, I don't think there's an easy
way to grap the secondary structrure assignments - you'll need a
standalone version of the embedded DSSP algorithm.
     Personally I echo a previous post to the effect that it is
much easier to use links to the appropriate protein database.
I believe the Brookhaven WWW site has hot links from their PDB
entries to GenBank/SwissProt or whatever and NCBI's ENTREZ browser
links the 3D structures to sequence files.  Many protein sequence
files now seem to incorporate PDB-derived secondary structural
information in their remarks.  Of course, you don't have this
luxury if this is a novel PDB file.
     When playing with PDB files generated by CHARMM I have used
AWK scripts to extract the residue names from the PDB file lines
containing the C-alpha (CA) atoms and then to convert three letters
to one letter.  However, as pointed out in previous posts, most
automatic methods are fooled by multiple chains or gaps so manual
intervention is almost always needed.
     Good luck,
          Bernard
-- 
Bernard Murray, PhD
Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA

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From: francis.durst@bota-ulp.u-strasbg.fr (Francis Durst)
Newsgroups: bionet.software
Subject: Re: PDB -> SwissPROT conversion?
Date: Sat, 6 Jun 1998 10:31:07
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In article <6l7588$j4n$1@netnews.upenn.edu> alwang@blue.seas.upenn.edu (Al Wang) writes:
>From: alwang@blue.seas.upenn.edu (Al Wang)
>Subject: PDB -> SwissPROT conversion?
>Date: 4 Jun 1998 21:57:28 GMT

>Hi,

>Does anyone know what's a good way to take a Brookhaven PDB file, extract 
>the sequence information, and save it in SwissPROT format?  If it can 
>also extract the secondary structure features, even better.  

>Thanks,
>Al

Hi there,

Yesterday I pointed that the Swiss pdb viewer could extract the seq, you can 
also use Antheprot which has its own viewer and can also use Rasmol, and 
extract the aa seq, save in fasta format, make all sorts of predictions 
(interesting to compare with the actual stracture) etc..
The Antheprot version I have is 3_5b, works fine on a PC

Francis

>--
>__________________________________________
>al wang
>alwang@doubt.com
>http://www.seas.upenn.edu/~alwang/

>"What's My Solution?" 
>"Noise Pollution!"

===============================================================
Francis Durst, IBMP
Strasbourg, France

From owner-software@net.bio.net Fri Jun 05 23:00:00 1998
Path: biosci!NCBI.NLM.NIH.GOV!francis
From: francis@NCBI.NLM.NIH.GOV
Newsgroups: bionet.software
Subject: Re: Archive?
Date: 6 Jun 1998 05:59:36 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
Lines: 25
Sender: daemon@net.bio.net
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NNTP-Posting-Host: net.bio.net

> From: Arne Mueller <amuelle3@gwdg.de>
> Subject: Archive?

> Hi All,
> 
> is there an archive of bionet.spftware on the net? I'd like to have the
> opportunity to search in old news of this group.

Hello Arnie,

all bionet news are archived at:  http://www.bio.net/archives.html

bionet.software is archived at:   http://www.bio.net/hypermail/BIO-SOFTWARE/



cheers,

f.

--
| B.F. Francis Ouellette  
| GenBank Coordinator
|
| francis@ncbi.nlm.nih.gov   

From owner-software@net.bio.net Fri Jun 05 23:00:00 1998
Path: biosci!agate!howland.erols.net!ais.net!news.indiana.edu!not-for-mail
From: gilbertd@bio.indiana.edu (Don Gilbert)
Newsgroups: bionet.software
Subject: Re: Archive?
Date: 6 Jun 1998 16:22:01 GMT
Organization: Biology, Indiana University - Bloomington
Lines: 7
Message-ID: <6lbqb9$vtt$1@jetsam.uits.indiana.edu>
References: <35792445.55172CE0@gwdg.de>
NNTP-Posting-Host: chipmunk.bio.indiana.edu

another archive of bionet news can be found at
  http://iubio.bio.indiana.edu/Network-News/

- don
--
-- d.gilbert--biocomputing--indiana-u--bloomington-in-47405
-- gilbertd@bio.indiana.edu

From owner-software@net.bio.net Fri Jun 05 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.gwdg.de!not-for-mail
From: Arne Mueller <amuelle3@gwdg.de>
Newsgroups: bionet.software
Subject: Archive?
Date: Sat, 06 Jun 1998 11:13:09 +0000
Organization: GWDG, Goettingen
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Hi All,

is there an archive of bionet.spftware on the net? I'd like to have the
opportunity to search in old news of this group.

	Thanks, 

	Arne

-- 
Arne Mueller            
Institut fuer Mikrobiologie und Genetik
Abt. Molekulare Genetik und 
Praeparative Molekularbiologie
Universitaet Goettingen
Grisebachstr. 8
37077 Goettingen        
Germany
phone: +49-551-399654   | fax  : +49-551-393805   
email: amuelle3@gwdg.de | http://www.img.bio.uni-goettingen.de

From owner-software@net.bio.net Fri Jun 05 23:00:00 1998
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From: lander100 <lander100@hotmail.com>
Newsgroups: bionet.software
Subject: AutoName v1.0 32bit
Date: Sat, 06 Jun 1998 11:58:19 +0200
Lines: 30
Message-ID: <357912BB.4D9C4460@hotmail.com>
NNTP-Posting-Host: goa-e.franken.de
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--------------8B4041BC36616D30910E0DA6
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

AutoName v1.0 32bit This little tool enables you to
rename all or only selected files in any directory at a glance.
New names are build by specifying a constant part and a dynamic
(numeric) part. Dynamic parts are incremented starting at a free
number. This is helpful to classify a lot of files like
downloaded pictures, which are originally named accidentally.

HTTP://www.franken.de/users/goa-e/index.html

--------------8B4041BC36616D30910E0DA6
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<HTML>
AutoName v1.0 32bit This little tool enables you to
<BR>rename all or only selected files in any directory at a glance.
<BR>New names are build by specifying a constant part and a dynamic
<BR>(numeric) part. Dynamic parts are incremented starting at a free
<BR>number. This is helpful to classify a lot of files like
<BR>downloaded pictures, which are originally named accidentally.

<P><A HREF="http://www.franken.de/users/goa-e/index.html">HTTP://www.franken.de/users/goa-e/index.html</A></HTML>

--------------8B4041BC36616D30910E0DA6--


From owner-software@net.bio.net Fri Jun 05 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!feed2.news.erols.com!erols!woodstock.news.demon.net!demon!dispose.news.demon.net!demon!news.demon.co.uk!demon!mail2news.demon.co.uk!not-for-mail
From: Paul@pdchem.demon.co.uk (Paul Davis)
Newsgroups: bionet.software
Subject: Re: PDB -> SwissPROT conversion?
Date: Sat, 06 Jun 98 09:16:29 GMT
Organization: Myorganisation
Message-ID: <897124589snz@pdchem.demon.co.uk>
References: <6l7588$j4n$1@netnews.upenn.edu> <897062296snz@pdchem.demon.co.uk> <bpmurray*STUFFER*-0506982020480001@macmac-2.ucsf.edu>
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In article <bpmurray*STUFFER*-0506982020480001@macmac-2.ucsf.edu>
           bpmurray*STUFFER*@socrates.ucsf.edu "Bernard Murray" writes:

> 
> Similarly, you can load the structure into RasMol and then type
> "show sequence" on the command line to have the sequence displayed
> (three letter format, not SwissProt) and you can then cut'n'paste
> to your heart's content.  Alas, I don't think there's an easy
> way to grap the secondary structrure assignments - you'll need a
> standalone version of the embedded DSSP algorithm.
> 

Try this on the RasMol command line:-

          structure
          save molscript <filename>
          
The first command uses RasMol's embedded DSSP algorithm to assign
secondary structure, overriding any HELIX and SHEET records in the
original PDB file.

The second command writes an input file for the MolScript program,
containing the secondary structure assignments.

>    Personally I echo a previous post to the effect that it is
> much easier to use links to the appropriate protein database.
> I believe the Brookhaven WWW site has hot links from their PDB
> entries to GenBank/SwissProt or whatever and NCBI's ENTREZ browser
> links the 3D structures to sequence files.  Many protein sequence
> files now seem to incorporate PDB-derived secondary structural
> information in their remarks.  

This is true; however I have been caught out once or twice in the
past when using the HELIX and STRAND Feature Tables in SWISS-PROT.
Just occasionally I have found them to contain inaccuracies, and
so I would recommend checking them yourself.


> Of course, you don't have this
> luxury if this is a novel PDB file.
>      When playing with PDB files generated by CHARMM I have used
> AWK scripts to extract the residue names from the PDB file lines
> containing the C-alpha (CA) atoms and then to convert three letters
> to one letter.  However, as pointed out in previous posts, most
> automatic methods are fooled by multiple chains or gaps so manual
> intervention is almost always needed.
>      Good luck,
>           Bernard

-Paul
-- 

--------------------------------------------------------------------
Paul Davis                                   paul@pdchem.demon.co.uk


From owner-software@net.bio.net Fri Jun 05 23:00:00 1998
Path: biosci!agate!logbridge.uoregon.edu!ais.net!darla.visi.com!news-out.mcia.org!news-out.visi.com!iaxs.net!news2.norlight.net!news.itis.com!not-for-mail
From: Petr Kuzmic <pkuzmic@biokin.com>
Newsgroups: bionet.software
Subject: Re: Archive?
Date: Sat, 06 Jun 1998 07:41:57 -0500
Organization: BioKin Consulting
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Arne Mueller wrote:

> is there an archive of bionet.spftware on the net? 

http://www.bio.net/hypermail/BIO-SOFTWARE/

	-- Petr

_____________________________________________________________
Petr Kuzmic Ph.D. * BioKin Ltd. * Madison, WI 53708-8336, USA
pkuzmic@biokin.com * http://www.biokin.com * 608.256.1269 fax

From owner-software@net.bio.net Fri Jun 05 23:00:00 1998
Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-dc-2.sprintlink.net!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!fu-berlin.de!elch.in-berlin.DE!news
From: "Corran Horn" <lamer@aol.com>
Newsgroups: alt.binaries.dominion.shareware,alt.binaries.shareware,alt.binaries.shareware.ibm.pc,alt.binaries.sounds.midi.originals,alt.binaries.sounds.midi.pop,alt.binaries.sounds.midi.rock,alt.music.midi,alt.romance.chat,at.tuwien.software,bionet.software
Subject: SHAREWARE SITE UPDATED!
Date: Fri, 5 Jun 1998 23:58:42 +0200
Organization: Individual Network Berlin e.V.
Lines: 20
Message-ID: <897170276.927257@elch.in-berlin.de>
NNTP-Posting-Host: elch.in-berlin.de (192.109.42.5)
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X-Cache: nntpcache 2.3.2.1 (see http://www.nntpcache.org/)

CORRAN HORN'S DOWNLOAD PAGE!
FREE SHAREWARE,MIDIS AND NEW: CHAT!!!!
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From owner-software@net.bio.net Fri Jun 05 23:00:00 1998
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From: a.blumsohn@aol.com (Aubrey Blumsohn)
Newsgroups: bionet.software
Subject: New medical software site
Date: Sat, 06 Jun 1998 19:13:55 GMT
Organization: BT Internet
Lines: 10
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NNTP-Posting-Host: host5-99-53-166.btinternet.com
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A New medical software Web Site
==============================
This site contains a collection of software written by myself and
others with particular emphasis on scientific plotting, medical
biochemistry, chemical pathology and laboratory utilities. Preference
is shown for free rather than commercial software.

http://www.btinternet.com/~ablumsohn/beesoft.htm

Aubrey Blumsohn

From owner-software@net.bio.net Sat Jun 06 23:00:00 1998
Path: biosci!pravda.ucr.edu!awabi.library.ucla.edu!208.134.241.18!newsfeed.internetmci.com!208.140.2.17!reggie.win.bright.net!not-for-mail
From: "malvitz" <malvitz@win.birght.net>
Newsgroups: bionet.software,biz.comp.software,comp.lang.java.softwaretools,comp.mail.list-admin.software,comp.os.ms-windows.nt.software.backoffice
Subject: Re: Anti-Freezing Software P.S. Macs Suck }:-)]>
Date: Sat, 6 Jun 1998 22:56:38 -0500
Organization: BrightNet Wisconsin
Lines: 13
Message-ID: <6ld1v0$sar$1@reggie.win.bright.net>
References: <01bd85d5$d70502c0$102852d1@www.sa00bum.hellafax.com> <3573F581.115DF7E0@uni-koeln.de>
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Daniel Wetzler wrote in message <3573F581.115DF7E0@uni-koeln.de>...
>online schrieb:
>
>>         I would like to know which software is the best to prevent my
>> PC from
>> freezing and I would also like to know if there is a demo for this
>> program,
>> by the way I'm using Windows 95.
>
>Buy a Mac...  ;-) d/f   }:-)]>
>



From owner-software@net.bio.net Sat Jun 06 23:00:00 1998
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From: Iddo Friedberg <idoerg@cc.huji.ac.il>
Newsgroups: bionet.software
Subject: Re: PDB -> SwissPROT conversion?
Date: Sun, 07 Jun 1998 10:02:04 +0300
Organization: The Hebrew University, Jerusalem
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To: Al Wang <alwang@blue.seas.upenn.edu>

Al Wang wrote:
> 
> Hi,
> 
> Does anyone know what's a good way to take a Brookhaven PDB file, extract
> the sequence information, and save it in SwissPROT format?  If it can
> also extract the secondary structure features, even better.
> 


I'd just like to add a comment which might be relevant in this case: PDB
residue numbering is, at times, non-consecutive, or may contain
non-numeric characters (e.g. 31A). This may cause problems if somehow
you wish to later correlate your sequence file with the PDB file.

I recommend using DSSP, and then running a script on the resulting DSSP
file. That way you preserve PDB residue numbering, consecutive
numbering, and 2ndary structure.

About DSSP:
http://www.sander.embl-heidelberg.de/dssp/


Iddo


-- 
Iddo Friedberg
Phone: (972)-2-6758647
email: idoerg@cc.huji.ac.il
web: http://www.ls.huji.ac.il/~idoerg
More info: finger idoerg@cc.huji.ac.il

From owner-software@net.bio.net Sat Jun 06 23:00:00 1998
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From: "malvitz" <malvitz@win.birght.net>
Newsgroups: bionet.software
Subject: Know where Ican get a file format converter for Windows??
Date: Sat, 6 Jun 1998 22:50:09 -0500
Organization: BrightNet Wisconsin
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This is a multi-part message in MIME format.

------=_NextPart_000_017F_01BD919D.75114140
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subject says it all.
e-mail me nickmalvitz@geocities.com

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</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT size=3D2>subject says it all.</FONT></DIV>
<DIV><FONT size=3D2>e-mail me <A=20
href=3D"mailto:nickmalvitz@geocities.com">nickmalvitz@geocities.com</A></=
FONT></DIV></BODY></HTML>

------=_NextPart_000_017F_01BD919D.75114140--


From owner-software@net.bio.net Sun Jun 07 23:00:00 1998
Path: biosci!news.Stanford.EDU!newsfeed.concentric.net!netnews.com!howland.erols.net!newsxfer.itd.umich.edu!news2.acs.oakland.edu!cwis-20.wayne.edu!usenet
From: nsps@Lande-Sparc2.alt.image.medical (NSPS Application Account)
Newsgroups: bionet.software
Subject: job opening in detroit
Date: 08 Jun 1998 15:04:53 GMT
Organization: Wayne State University
Lines: 41
Distribution: world
Message-ID: <NSPS.98Jun8110453@Lande-Sparc2.alt.image.medical>
NNTP-Posting-Host: 146.9.11.236

 Job Opening, Software Engineer/Sterotactics Computer Scientist

Detroit Medical Center, Department of Neurological Surgery, invites applications for a Sterotactics
Computer Scientist (Full Time Position). 

ESSENTIAL FUNCTIONS
*Software development for Computer Assisted Surgery,
*Clinical support of CAS in operating room,
*Design program logic, analysis problems, and develop program layout. Select, determine and    develop algorithm for simulation and treatment planning,
*Compile and prepare test data and test routines
*Prepare, present, and assist in publication of scientific results,
*Participate in development of grant proposals through research and preparation of specifications   to gain hospital or grant funding.
*To perform related divisional and departmental duties as assigned,
*local network administration.

QUALIFICATIONS
*Ph.D. Degree in Computer Science,
*Medical image processing knowledge desirable,
*Strong skills on  C, C++, Motif, Java, UNIX, and Solaris OS,
*Experience with Sun Sparc, HP, Digital workstations,
*Ability to work independently and act as project leader,
* Well suited for laboratory research and development,
*Rank commensurate with credentials,

Applicants should submit an up-to-date curriculum vitae and the names of three references by July
15, 1998.

Contact:
Lucia Zamorano, MD., Dr. Med.
Professor of Neurological Surgery and
Radiation Oncology
Chief Divisions of Neuro-Oncology
Stereotaxis, Radiosurgery and Epilepsy        
4160 John R., Suite 930                 
Detroit, MI 48201
USA

Phone:    313-966-0382
Fax:      313-966- 0368
E-mail:   zamorano@neurosurg.wayne.edu
WWW:      http://www.neurosurg.wayne.edu/

From owner-software@net.bio.net Sun Jun 07 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!news-was.dfn.de!newsjunkie.ans.net!newsfeeds.ans.net!news1.rmi.net!not-for-mail
From: richard_steinman@cmagroup.com
Newsgroups: bionet.software
Subject: Florida; Sr. Software Engineer; NT, C++, DICOM, Imaging
Date: 8 Jun 1998 14:45:08 GMT
Organization: Career Marketing Associates
Lines: 22
Message-ID: <6lgtdk$ikp$1@news1.rmi.net>
NNTP-Posting-Host: 206.247.5.4


West Palm, Florida; Sr. Software Engineer; NT, C++, DICOM, Imaging

-Senior Software Engineer
-Southeast Florida Coastal
-Salaried, Full-Time, Excellent Benefits 
(Relocation Assistance Available)

Medical DICOM knowledge would be a major plus. Experience with C/C++ and 
NT required. Image manipulation, compression, edge detection, analysis, 
all good things to have. 

Please refer to JO# 5253RJS in your response.

richard_steinman@cmagroup.com 

Richard Steinman
Team Leader
rjs@cmagroup.com
IT & Software Solutions Team
Career Marketing Associates
http://www.cmagroup.com/IT.html

From owner-software@net.bio.net Sun Jun 07 23:00:00 1998
Path: biosci!CLUB.MED.UNIV-ANGERS.FR!laurec
From: laurec@CLUB.MED.UNIV-ANGERS.FR (olivier)
Newsgroups: bionet.software
Subject: Simulation / endocrinology
Date: 8 Jun 1998 02:11:57 -0700
Organization: Université d'Angers
Lines: 15
Sender: daemon@net.bio.net
Distribution: world
Message-ID: <357BA9B1.4CD07918@club.med.univ-angers.fr>
Reply-To: olivier.laurec@univ-angers.fr
NNTP-Posting-Host: net.bio.net

Hello,

I search for a teach software about simulation of hormon in
endocrinology.


__________________________________________________________________
Olivier LAUREC
Technicien (Informatique - Electronique)   UNIVERSITE D'ANGERS
E_mail: olivier.laurec@univ-angers.fr      Lab. de Neurophysiologie
Phone : 02 41 73 58 85                     Rue Haute de Recul=E9e
Fax   : 02 41 73 58 87                     49045 ANGERS   -  FRANCE
___________________________________________________________________



From owner-software@net.bio.net Sun Jun 07 23:00:00 1998
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From: "Kim Bruning" <K.F.Bruning@NOSPAM.stud.biol.ruu.nl>
Subject: Re: Anti-Freezing Software P.S. Macs Suck }:-)]>
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malvitz heeft geschreven in bericht <6ld1v0$sar$1@reggie.win.bright.net>...
>Daniel Wetzler wrote in message <3573F581.115DF7E0@uni-koeln.de>...
>>online schrieb:
>>
>>>         I would like to know which software is the best to prevent my
>>> PC from
>>> freezing and I would also like to know if there is a demo for this
>>> program,
>>> by the way I'm using Windows 95.
>>
>>Buy a Mac...  ;-) d/f   }:-)]>
>>
Buy a RISC PC :->






From owner-software@net.bio.net Sun Jun 07 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!woodstock.news.demon.net!demon!news.demon.co.uk!demon!mail2news.demon.co.uk!not-for-mail
From: amartin@stagleys.demon.co.uk (Andrew Martin)
Newsgroups: bionet.software
Subject: Re: PDB -> SwissPROT conversion?
Date: Sun, 7 Jun 1998 22:20:52 GMT
Organization: Private Address
Message-ID: <Eu7Cqt.1vM@stagleys.demon.co.uk>
References: <6l7588$j4n$1@netnews.upenn.edu> <6l8e3i$chv$1@montespan.pasteur.fr>
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Catherine  Letondal (letondal@pasteur.fr) wrote:


: In article <6l7588$j4n$1@netnews.upenn.edu>, alwang@blue.seas.upenn.edu (Al Wang) writes:
: >Hi,
: >
: >Does anyone know what's a good way to take a Brookhaven PDB file, extract 
: >the sequence information, and save it in SwissPROT format?  If it can 
: >also extract the secondary structure features, even better.  
: >
: >Thanks,
: >Al

: I am looking for the same kind information. There is a description of a program called
: PDB2PIR on the PIR Web (see http://nbrfa.georgetown.edu/pir/software.html)
: but it has not been put on their ftp server.
: I am waiting for an answer from the author of the program (Dr. John S. Garavelli, 
: Associate Director of PIR).

I have a pdb2pir program which anyone is welcome to a copy of. It
is moderately intelligent and can read from just the ATOM records
or optionally include information from the SEQRES records as well.
Note this is PIR output and not SwissProt as originally requested
so there's certainly no feature information!

Please EMail me if you are interested - either by replying to this
posting (my home address) or at martin@biochem.ucl.ac.uk

Best wishes,

Andrew



From owner-software@net.bio.net Sun Jun 07 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!152.163.199.19!portc03!audrey03.news.aol.com!not-for-mail
From: btjohn5656@aol.com (BTJohn5656)
Newsgroups: bionet.software
Subject: long file names
Date: 8 Jun 1998 22:40:12 GMT
Lines: 8
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can I prevent windows nt from generating long file name aliases on an ntfs
partition? how can I do that?

Bell John
http://www.totalmarketing.com/125430
Special Interest Videos & CD Roms
Over 10,000 titles in stock.


From owner-software@net.bio.net Sun Jun 07 23:00:00 1998
Path: biosci!news.Stanford.EDU!newsfeed.concentric.net!netnews.com!news.maxwell.syr.edu!news-peer.gip.net!news.gsl.net!gip.net!portc01.blue.aol.com!audrey03.news.aol.com!not-for-mail
From: btjohn5656@aol.com (BTJohn5656)
Newsgroups: bionet.software
Subject: internet connection
Date: 8 Jun 1998 21:16:39 GMT
Lines: 17
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how can I connect my computer running windows nt dirctly to the internet ? I
mean what kind of equipment do I need? what kind of phone lines?

please help me answer the questions above in relation to the following
scenarios:

# when I have only one computer
# when I have a group of netowrked computers


Bell John
--------------------------------------------------------------------------
----------------------------------------------
http://www.totalmarketing.com/125430

Special Interest Videos & CD Roms
Over 10,000 titles in stock.

From owner-software@net.bio.net Sun Jun 07 23:00:00 1998
From: "Richard Seymour" <anarchy@DeleteThis_anarchysoftware.com>
Subject: Re: Anti-Freezing Software P.S. Macs Suck }:-)]>
Newsgroups: bionet.software,biz.comp.software,comp.lang.java.softwaretools,comp.mail.list-admin.software,comp.os.ms-windows.nt.software.backoffice
References: <01bd85d5$d70502c0$102852d1@www.sa00bum.hellafax.com> <3573F581.115DF7E0@uni-koeln.de> <6ld1v0$sar$1@reggie.win.bright.net> <6lhfec$lot$1@news.bayarea.net>
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The only software I have that has *never* bugged out on me are those CD's I
get from AOL.

And of course, it's because I never actually install them.


-- 
Richard Seymour, Anarchy Software, Inc.
anarchy@DeleteThis_anarchysoftware.com

From owner-software@net.bio.net Sun Jun 07 23:00:00 1998
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From: "Barry Allard" <ba@levy.com>
Newsgroups: bionet.software,biz.comp.software,comp.lang.java.softwaretools,comp.mail.list-admin.software,comp.os.ms-windows.nt.software.backoffice
Subject: Re: Anti-Freezing Software P.S. Macs Suck }:-)]>
Date: Mon, 8 Jun 1998 12:51:49 -0700
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PCs freeze, Macs freeze, Reel-time mission-critical servers freeze.
Anti-freeze software is useless; it can't fix buggy software, OSes, nor
hardware.
One possible solution is to demand manufactures provide better quality
products instead of using the general public as beta testers.

Barry Allard
ba@levy.com

malvitz wrote in message <6ld1v0$sar$1@reggie.win.bright.net>...
>Daniel Wetzler wrote in message <3573F581.115DF7E0@uni-koeln.de>...
>>online schrieb:
>>
>>>         I would like to know which software is the best to prevent my
>>> PC from
>>> freezing and I would also like to know if there is a demo for this
>>> program,
>>> by the way I'm using Windows 95.
>>
>>Buy a Mac...  ;-) d/f   }:-)]>
>>
>
>



From owner-software@net.bio.net Sun Jun 07 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!psinntp!newsjunkie.ans.net!newsfeeds.ans.net!news1.rmi.net!not-for-mail
From: richard_steinman@cmagroup.com
Newsgroups: bionet.software
Subject: Florida; Sr. Software Engineer; NT, C++, DICOM, Imaging
Date: 8 Jun 1998 14:45:13 GMT
Organization: Career Marketing Associates
Lines: 27
Message-ID: <6lgtdp$ikq$1@news1.rmi.net>
NNTP-Posting-Host: 206.247.5.4


West Palm, Florida; Sr. Software Engineer; NT, C++, DICOM, Imaging

-Senior Software Engineer
-Southeast Florida Coastal
-Salaried, Full-Time, Excellent Benefits 

(Relocation Assistance Available)

Medical DICOM knowledge would be a major plus. Experience with C/C++ and 

NT required. Image manipulation, compression, edge detection, analysis, 

all good things to have. 


Please refer to JO# 5253RJS in your response.

richard_steinman@cmagroup.com 

Richard Steinman
Team Leader

rjs@cmagroup.com
IT & Software Solutions Team
Career Marketing Associates
http://www.cmagroup.com/IT.html

From owner-software@net.bio.net Sun Jun 07 23:00:00 1998
Path: biosci!agate!howland.erols.net!woodstock.news.demon.net!demon!dispose.news.demon.net!demon!delos!server1.netnews.ja.net!server2.netnews.ja.net!pegasus.csx.cam.ac.uk!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!antares!alan
From: Alan Robinson <alan@ebi.ac.uk>
Newsgroups: bionet.software
Subject: [ANNOUNCE] Conference on Bioinformatics
Date: Mon, 8 Jun 1998 11:39:24 +0100
Organization: MRC Human Genome Mapping Project Resource Centre
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                                --ooOOoo--

                       Objects in Bioinformatics '98

            Object-Oriented Technology, Software Components and 
           Distributed Computing for Bioinformatics and Genomics. 

                       *****************************
                        http://www.ebi.ac.uk/oib98/
                       *****************************

                         3rd and 4th August, 1998. 
                       Wellcome Trust Genome Campus, 
                        Hinxton, near Cambridge, UK. 


Following last years successful OiB-97 conference, OiB-98 has been set for
August 3rd-4th, 1998. The conference is organised by the European
Bioinformatics Institute and will be held in the conference facilities at
the Wellcome Trust Genome Campus in the grounds of Hinxton Hall,
Cambridge, UK.

'Objects in Bioinformatics' focuses upon the role of object-oriented
technology, software components, design patterns and distributed
computing in bioinformatics and genomics. The conference is aimed at 
those who are interested in, are developing, or have developed
object-oriented software that will be of use to the bioinformatics and
genomics community in both academia and industry.  The conference aims
to address the problems now facing our scientific community of: 

    o  Heterogeneous computing environments
    o  Effective standards for the representation of data
    o  The distributed nature of applications, resources and data across
       computer networks (i.e. intranets, extranets and the Internet)
    o  The ever-present data deluge that is hitting biology
    o  The development of tools and resources to aid the biologist and
       bioinformatician

A theme of this year's conference will be the implication and application
of distributed object technology (such as CORBA) to biology and
bioinformatics, and the work of the Life Sciences Research Task Force of
the Object Management Group in promoting standards. 

The conference will include lectures and poster sessions on the rapidly
expanding and developing fields of object-oriented software and
distributed computing from both an academic and industrial perspective. 

Invited talks will cover the application of reusable components, tools,
software libraries, distributed object technology and the role of Life
Sciences Research Task Force. Speakers will also include specialists from
outside the domain of biology that have already experienced our current
data problems. 

Poster stands (including a limited number with a dedicated networked
computer), are available upon which delegates may showcase their work and
projects. Participants are encouraged to submit a brief abstract for a
poster relevant to the conference themes to promote and display their work
in the field, and fuel dialogue. 

In the same spirit as OiB-97, the cost of registration for the conference
has been kept as low as possible with a nominal fee of 50 GBP for early
registration. The closing date for early registration and submission of
abstracts is July 1st, 1998. Late registration will be possible from July
2nd onwards, however the registration fee will increase to 100 GBP. 

N.B. Following OiB-98, the Life Sciences Research (LSR) group will be
holding a technical meeting with work groups where efforts will continue
in encouraging the formation of domain standards. Interested OiB
participants are encouraged to attend these (and other) meetings of the
LSR group, although numbers will be limited for logistic reasons. 
Registration for this meeting is separate from OiB - details can be found
in the group's web pages. 

OiB-98 is supported by BioInform, Millennium Pharmaceuticals, NetGenics,
Object Design, Silicon Graphics and Synomics.


Details of registration and accommodation may be found at the conference
Web site -

		http://www.ebi.ac.uk/oib98/


Yours sincerely,
Alan Robinson.


--
============================================================
Alan J. Robinson                      Tel:+44-(0)1223 494625
EMBL Outstation                       Fax:+44-(0)1223 494468
European Bioinformatics Institute     Email:  alan@ebi.ac.uk
Wellcome Trust Genome Campus
Hinxton, Cambridge,
CB10 1SD, UK                http://industry.ebi.ac.uk/~alan/
============================================================


From owner-software@net.bio.net Mon Jun 08 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!psinntp!newsjunkie.ans.net!newsfeeds.ans.net!news1.rmi.net!not-for-mail
From: richard_steinman@cmagroup.com
Newsgroups: bionet.software
Subject: Job: Florida; Sr. Software Engineer; NT, C++, DICOM, Imaging
Date: 9 Jun 1998 14:02:39 GMT
Organization: Career Marketing Associates
Lines: 22
Message-ID: <6ljf9v$3s2$1@news1.rmi.net>
NNTP-Posting-Host: 206.247.5.4


West Palm, Florida; Sr. Software Engineer; NT, C++, DICOM, Imaging

-Senior Software Engineer
-Southeast Florida Coastal
-Salaried, Full-Time, Excellent Benefits 
(Relocation Assistance Available)

Medical DICOM knowledge would be a major plus. Experience with C/C++ and 
NT required. Image manipulation, compression, edge detection, analysis, 
all good things to have. 

Please refer to JO# 5253RJS in your response.

richard_steinman@cmagroup.com 

Richard Steinman
Team Leader
rjs@cmagroup.com
IT & Software Solutions Team
Career Marketing Associates
http://www.cmagroup.com/IT.html

From owner-software@net.bio.net Mon Jun 08 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!newspeer.monmouth.com!rain.fr!jussieu.fr!univ-lille1.fr!u-strasbg.fr!news
From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin)
Newsgroups: biz.comp.software,bionet.software
Subject: Re: Anti-Freezing Software
Followup-To: junk
Date: 9 Jun 1998 07:53:36 GMT
Organization: CRC - Universite Louis Pasteur - Strasbourg France
Lines: 44
Message-ID: <6lipm0$fg5@news.u-strasbg.fr>
References: <01bd85d5$d70502c0$102852d1@www.sa00bum.hellafax.com>
    <EtGHxB.nyI@fys.ruu.nl>
    <7opiGDf98QgB-pn2-0voJdQvkvQnQ@rnaworld.bio.ukans.edu>
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In article <7opiGDf98QgB-pn2-0voJdQvkvQnQ@rnaworld.bio.ukans.edu>,
	PGegen@UKans.nolospamare.edu (Dr. Peter Gegenheimer) writes:

> First, keep  your computer out of the cold room ...
> Second, reformat & install OS/2 Warp... (or buy an SGI O2).

	Fantastic!!! A new flamewar!!! Can I play with you???

	According to : Gert Vriend. 
	http://www.sander.embl-heidelberg.de/whatif/
------------
	WARNING

WHAT IF does not run equally well on all SGI O2 machines. WHAT IF does 
not run properly on high impact graphics machines. WHAT IF does not run 
properly on SGI's with operating system 6.4 or higher. 

SGI is puting bugs in their new releases faster than that I can make 
work-arounds. If you want WHAT IF to work properly on any of the above 
mentioned machines, please put some pressure on you local SGI representative 
to let them support me better. Otherwise, just buy a Linux-based PC; That 
saves you half the money, WHAT IF runs better on those, and the graphics 
is also faster. 

Sorry, but it is just me alone doing all the programming, and we have a 
scietific review coming up.... Gert. 
-----------

	Sorry. Please respect the Followup-To

						François (Linux addict).

P.S.: Modeller also run very well on Linux machines, even on my little P200.
-- 
François Jeanmougin     | groupe de bioinformatique / bioinformatics groupe
tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France









From owner-software@net.bio.net Mon Jun 08 23:00:00 1998
Path: biosci!news.Stanford.EDU!agate!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!newsfeed.kornet.nm.kr!usenet.kornet.nm.kr!not-for-mail
From: "Jae Wook Shin" <cyborg@soback.kornet.nm.kr>
Newsgroups: bionet.software
Subject: www.softplaza.com
Date: Tue, 9 Jun 1998 16:50:22 +0900
Organization: Korea Telecom
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From owner-software@net.bio.net Mon Jun 08 23:00:00 1998
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From: shj908@ms18.hinet.net (xxx)
Newsgroups: bionet.software
Subject: ´ú¸Õ
Date: Tue, 9 Jun 1998 10:45:52 +0800
Organization: DCI HiNet
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°Ý­Ô¤@­Ó¦nªB¤Í¡I

From owner-software@net.bio.net Mon Jun 08 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gip.net!news-dc.gip.net!news.gsl.net!gip.net!duke.telepac.pt!news.telepac.pt!not-for-mail
From: PEDRO VAZ <zasvaz@mail.telepac.pt>
Newsgroups: bionet.software
Subject: Programa Idrisi for Windows
Date: Tue, 09 Jun 1998 01:29:35 +0200
Lines: 11
Message-ID: <357C73DF.6319B7D2@mail.telepac.pt>
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Content-Transfer-Encoding: 8bit
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Será que alguém tem facilidade em arranjar-me uma versão qualquer deste
software (Idrisi for windows)?

Sou finalista de biologia na FCUL e estou a realizar um estudo no âmbito
da ecologia de paisagem que envolve questões de distribuição espacial de
carnívoros em uma paisagem agricola muito fragmentada num Parque Natural
do Sudoeste de Portugal.

Se alguém tiver bibliografia de um ou mais destes assuntos, agradeço que
me contacte.


From owner-software@net.bio.net Mon Jun 08 23:00:00 1998
Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!feeder.qis.net!news-xfer.netaxs.com!xfer.kren.ne.kr!xfer.kren.nm.kr!newsfeed.kornet.nm.kr!usenet.kornet.nm.kr!not-for-mail
From: "Jae Wook Shin" <cyborg@soback.kornet.nm.kr>
Newsgroups: bionet.software
Subject: www.softplaza.com
Date: Tue, 9 Jun 1998 17:29:34 +0900
Organization: Korea Telecom
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NNTP-Posting-Host: 203.251.174.140
X-Newsreader: Microsoft Outlook Express 4.72.2106.4
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4

The software specialized cyber shopping mall ,
www.softplaza.com opened finally !!!

Please visit there where every information on software is .
You can purchase any software in the world .

We  also looking for a business partners who like to
import or export softwares .

Any body interested , please reply to this e-mail.

Thank you,

Softplaza.com
Tel: 822-517-3707
Fax;822-517-3706
Korea, Seoul




From owner-software@net.bio.net Mon Jun 08 23:00:00 1998
Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-nysernet-5.sprintlink.net!news-dc-2.sprintlink.net!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!news-peer.gip.net!news.gsl.net!gip.net!xfer.kren.ne.kr!xfer.kren.nm.kr!newsfeed.kornet.nm.kr!usenet.kornet.nm.kr!not-for-mail
From: "Jae Wook Shin" <cyborg@soback.kornet.nm.kr>
Newsgroups: bionet.software
Subject: www.softplaza.com
Date: Tue, 9 Jun 1998 17:58:44 +0900
Organization: Korea Telecom
Lines: 20
Message-ID: <6lkhfp$5f6$7@news.kornet.nm.kr>
NNTP-Posting-Host: 203.251.174.140
X-Newsreader: Microsoft Outlook Express 4.72.2106.4
X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4

The software specialized cyber shopping mall ,
www.softplaza.com opened finally !!!

Please visit there where every information on software is .
You can purchase any software in the world .

We  also looking for a business partners who like to
import or export softwares .

Any body interested , please reply to this e-mail.

Thank you,

Softplaza.com
Tel: 822-517-3707
Fax;822-517-3706
Korea, Seoul




From owner-software@net.bio.net Mon Jun 08 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!feed2.news.erols.com!erols!news.magicnet.net!not-for-mail
From: "Mark G. Woodruff" <mwoodruff@valenciasystems.com.spamNotAndLetSlipTheDogsOfWar>
Newsgroups: bionet.software,biz.comp.software,comp.lang.java.softwaretools,comp.mail.list-admin.software,comp.os.ms-windows.nt.software.backoffice
Subject: Re: Anti-Freezing Software P.S. Macs Suck }:-)]>
Date: 9 Jun 1998 15:16:06 GMT
Organization: MagicNet, Inc.
Lines: 7
Message-ID: <6ljjjn$mlt$1@comet3.magicnet.net>
References: <01bd85d5$d70502c0$102852d1@www.sa00bum.hellafax.com> <3573F581.115DF7E0@uni-koeln.de> <6ld1v0$sar$1@reggie.win.bright.net> <6lhfec$lot$1@news.bayarea.net> <01bd931d$431312a0$e700000a@zeppo>
NNTP-Posting-Host: pm59-35.magicnet.net
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Actually both VM and MVS are both extremely reliable operating systems. And
you can get one of those little PC/390 boxes for well under $20K. You could
probably pick up a used 4381 for under $5K, although your power bill per
month might be the same as the purchase price.




From owner-software@net.bio.net Mon Jun 08 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!204.186.110.126!ptdnetP!newsgate.ptd.net!news.cc.ukans.edu!not-for-mail
From: PGegen@UKans.nolospamare.edu (Dr. Peter Gegenheimer)
Newsgroups: biz.comp.software,bionet.software
Subject: Re: Anti-Freezing Software
Date: 9 Jun 1998 05:47:06 GMT
Organization: Univ. Kansas (Biochemistry)
Lines: 17
Message-ID: <7opiGDf98QgB-pn2-0voJdQvkvQnQ@rnaworld.bio.ukans.edu>
References: <01bd85d5$d70502c0$102852d1@www.sa00bum.hellafax.com> <EtGHxB.nyI@fys.ruu.nl>
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On Sat, 23 May 1998 13:22:23, "Kim Bruning" 
> > I would like to know which software is the best to prevent my PC from
> >freezing and I would also like to know if there is a demo for this program,
> >by the way I'm using Windows 95.

First, keep  your computer out of the cold room ...
Second, reformat & install OS/2 Warp... (or buy an SGI O2). 

o------------------------------------------------------------------o
| Dr. Peter Gegenheimer       | Vox:785-864-3939  FAX:785-864-5321 |
| Department of Biochemistry, |   PGegen@UKans.removethis.edu          |
|   Cell & Molecular Biology  |   http://RNAworld.Bio.UKans.edu/   |
| Department of Botany        |                                    |
| University of Kansas        |                                    |
| 2045 Haworth Hall           | "The sleep of reason produces      |
| Lawrence  KS  66045-2106    |  monsters."                  Goya  |
o_____________________________|____________________________________o 

From owner-software@net.bio.net Tue Jun 09 23:00:00 1998
Newsgroups: bionet.software
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!la-news-feed1.bbnplanet.com!news.bbnplanet.com!newsfeed1.earthlink.net!ais.net!usenet.INS.CWRU.Edu!neoucom.edu!usenet
From: Tim Teyler <tjt@neoucom.edu>
Subject: New TEACHING SOFTWARE
X-Nntp-Posting-Host: e120b.neuro.neoucom.edu
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Date: Wed, 10 Jun 1998 17:01:41 GMT
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New CARDIAC PHYSIOLOGY TEACHING SOFTWARE.....

	Didactic Systems is please to announce the release of PRACTICAL CARDIAC
PHYSIOLOGY, by Jorge Bach.  PRACTICAL CARDIAC PHYSIOLOGY is an
interactive program that teaches the theoretical and practical aspects
of cardiac physiology.  It is designed for biomedical/medical students
at the undergraduate/graduate level, as well as for professionals
wishing to review cardiac physiology.

Topics include.......
	- structure of the cardiac fiber 
       - myocardial molecular mechanics 
       - ionic basis of cardiac activity 
       - superficial electrical activity 
       - electrocardiography 
       - cardiac cycle & pump function 
       - echocardiography 
       - blood circulation 
       - practical examples 

PRACTICAL CARDIAL PHYSIOLOGY is available for Windows computers.  An
interactive DEMO may be downloaded from the Didactic Systems WebSite:

		http://140.220.22.22/didactic/

Comments and questions should be directed to tjt@neoucom.edu

From owner-software@net.bio.net Tue Jun 09 23:00:00 1998
From: "H W Shoop III" <hws@email.msn.com>
Subject: banner software
Date: Wed, 10 Jun 1998 13:42:35 -0400
Lines: 6
X-Newsreader: Microsoft Outlook Express 4.71.1712.3
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Newsgroups: alive.internet.providers.nl.xs4all,alt.childcare,alt.os.windows95.crash.crash.crash,alt.windows95,bionet.software,comp.software.testing,comp.software-eng,ifci.support.windows95,microsoft.public.es.windows95,microsoft.public.fr.windows95,microsof
NNTP-Posting-Host: 1Cust26.max4.washington.dc.ms.uu.net [153.34.50.154]
Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-nysernet-5.sprintlink.net!news-dc-2.sprintlink.net!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!207.68.143.79!upnetnews03!upnetnews02

Where can I find  freesoftware to make banners for a website. Please reply
to hws@msn.com

Thanks in advance



From owner-software@net.bio.net Tue Jun 09 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gip.net!news.gsl.net!gip.net!portc01.blue.aol.com!audrey03.news.aol.com!not-for-mail
From: btjohn5656@aol.com (BTJohn5656)
Newsgroups: bionet.software
Subject: subnet or segment?
Date: 10 Jun 1998 01:04:38 GMT
Lines: 18
Message-ID: <1998061001043800.VAA11358@ladder03.news.aol.com>
NNTP-Posting-Host: ladder03.news.aol.com
X-Admin: news@aol.com
Organization: AOL http://www.aol.com
X-Newsreader: AOL Offline Reader

Can a router be used to subdivide an IP network that   has all computers
configured with the same network id?

And If that is possible what each segment is called? subnet? 

If the answer is yes, what is a TCP/IP network that have the same network id
called? subnet? 

Please help solve the confusion.


Thanks

Bell John
http://www.totalmarketing.com/125430
Special Interest Videos & CD Roms
Over 10,000 titles in stock.


From owner-software@net.bio.net Tue Jun 09 23:00:00 1998
Path: biosci!GASOU.EDU!qfang
From: qfang@GASOU.EDU ("Q. Quentin Fang")
Newsgroups: bionet.software
Subject: Need your help:  Where can I find free MacPPP
Date: 10 Jun 1998 11:15:36 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
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Distribution: world
Message-ID: <3.0.5.32.19980610141153.007b2670@gsaix2.cc.gasou.edu>
NNTP-Posting-Host: net.bio.net

Hi there:

I would like to connect my home Mac (Power PC) to our university ppp
server.  Where can I download a free Mac PPP program for Mac OS 8.0?
Thanks in advance.
   -- Q.  Quentin Fang
       (qfang@gasou.edu)

From owner-software@net.bio.net Wed Jun 10 23:00:00 1998
From: "Pilar" <la_oficina@camerdata.es>
References: <usbFZbJl9GA.257@upnetnews02.moswest.msn.net>
Subject: Re: banner software
Date: Thu, 11 Jun 1998 09:13:32 +0200
Lines: 13
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Newsgroups: alive.internet.providers.nl.xs4all,alt.childcare,alt.os.windows95.crash.crash.crash,alt.windows95,bionet.software,comp.software.testing,comp.software-eng,ifci.support.windows95,microsoft.public.es.windows95,microsoft.public.fr.windows95,microsof
NNTP-Posting-Host: [195.76.104.143]
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http://www.ulead.com/webutilities.index.htm



H W Shoop III escribió en mensaje ...
>Where can I find  freesoftware to make banners for a website. Please reply
>to hws@msn.com
>
>Thanks in advance
>
>



From owner-software@net.bio.net Wed Jun 10 23:00:00 1998
Path: biosci!news.Stanford.EDU!newsfeed.concentric.net!news.he.net!news.tacom.army.mil!news.webspan.net!news.millennianet.com!newsmaster
From: Jason Arcand <jarcand@burnham-inst.org>
Newsgroups: bionet.software.x-plor,bionet.software
Subject: Help with simulated peptide annealing in X-Plor
Date: Wed, 10 Jun 1998 22:33:33 -0700
Organization: Millennia Communications, LLC
Lines: 9
Message-ID: <357F6C2D.41C6@burnham-inst.org>
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Xref: biosci bionet.software.x-plor:1925 bionet.software:21251

Hello,

I am a new user of X-Plor...  I wish to "anneal" several peptide models
that I have built in InsightII.  Could anyone help me out with this
process?  I have encountered numerous errors along the way so far and
hope someone has already worked through all these bugs.  Thanks,

Jason Arcand
jarcand@burnham-inst.org

From owner-software@net.bio.net Wed Jun 10 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news.sprintlink.net!newsfeed.nacamar.de!nntp.news.xara.net!xara.net!rill.news.pipex.net!pipex!sun4nl!surfnet.nl!barba.uci.kun.nl!not-for-mail
From: kappe@caos.kun.nl (kappe)
Newsgroups: bionet.software
Subject: large DNA sequences --> smaller overlapping sequences
Date: Thu, 11 Jun 1998 10:44:06 GMT
Organization: Universitair Centrum Informatievoorziening, The Netherlands
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Message-ID: <357fb343.155862388@news.uci.kun.nl>
NNTP-Posting-Host: caospc17.caos.kun.nl
X-Newsreader: Forte Free Agent 1.11/32.235

Hi,

Does anybody know of a program to split up a large DNA-sequence file
(4 Mb) into smaller files/sequences of 200 kb with 10 kb overlap?

Thank you,
Guido Kappe

kappe@caos.kun.nl

From owner-software@net.bio.net Wed Jun 10 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!lhc.nlm.nih.gov!not-for-mail
From: Roland Walker <walker@ncbi.nlm.nih.gov>
Newsgroups: bionet.software
Subject: Re: large DNA sequences --> smaller overlapping sequences
Date: Thu, 11 Jun 1998 10:48:56 -0400
Organization: National Center for Biotechnology Information
Lines: 22
Message-ID: <357FEE58.C916A4B9@ncbi.nlm.nih.gov>
References: <357fb343.155862388@news.uci.kun.nl>
Reply-To: walker@ncbi.nlm.nih.gov
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To: kappe <kappe@caos.kun.nl>
X-Priority: 3 (Normal)

kappe wrote:
> Does anybody know of a program to split up a large DNA-sequence file
> (4 Mb) into smaller files/sequences of 200 kb with 10 kb overlap?

The SEALS package

  http://www.ncbi.nlm.nih.gov/Walker/SEALS/index.html

contains a number of little widgets for common manipulations of
sequence such as this.

If your sequence was in FASTA format in a file called 'chromosome.fa'
you could split it with this command

  fenestrate chromosome.fa -window= 200_000 -overlap=10_000 

To save each subsquence in different files you might try

  fenestrate chromosome.fa -window= 200_000 -overlap=10_000 | \
  shatter -word= -5

Roland

From owner-software@net.bio.net Wed Jun 10 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newshub.northeast.verio.net!news.pn.com!nntp.pn.com!mozo.cc.purdue.edu!purdue!news.bu.edu!not-for-mail
From: Jene Jockey <jenejockey@pobox.com>
Newsgroups: bionet.software
Subject: Importing Excel file into StrainMan database
Date: Thu, 11 Jun 1998 16:16:24 -0400
Organization: Advanced Systems, Inc.
Lines: 29
Message-ID: <35803B12.8F78F2AE@pobox.com>
Reply-To: jenejockey@pobox.com
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Custom Importing into StrainMan from http://www.caesarsoftware.com.


Choose Import from the File menu.
Click on the Get File button.
Select the file to be imported.
The list on the right shows a preview of the data
in the file you selected. If the data does not look
the way you expect it to, try changing the
delimiter characters until the fields are displayed
properly.

Indicate the destination table for the data by
choosing a table from the popup at the top left of
the screen.

Using the arrow buttons, or, by dragging and
dropping, indicate the fields in the table (the
leftmost list) into which the data on the right is to
be imported.
Click the Import button to begin importing. A
large file may take up to several minutes
depending on the amount of data imported and the speed of your computer.

Sincerely,

Gene Jockey,
Advanced Systems, Inc.


From owner-software@net.bio.net Wed Jun 10 23:00:00 1998
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From: learn@u.washington.edu (Jerry Learn)
Newsgroups: bionet.software
Subject: Re: Need your help:  Where can I find free MacPPP
Date: Thu, 11 Jun 1998 08:53:45 -0700
Organization: University of Washington
Lines: 21
Distribution: world
Message-ID: <learn-1106980853450001@tench.microbiol.washington.edu>
References: <3.0.5.32.19980610141153.007b2670@gsaix2.cc.gasou.edu>
NNTP-Posting-Host: tench.microbiol.washington.edu
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X-face: 4sx$YUe#v'|&_+SwB7*{hy1Rb,03L5DM_U)nbQ{gz$$G2WbyOuofM<?{]u5|2
        UVsx&b~@,Bcu

In article <3.0.5.32.19980610141153.007b2670@gsaix2.cc.gasou.edu>,
qfang@GASOU.EDU ("Q. Quentin Fang") wrote:

> Hi there:
> 
> I would like to connect my home Mac (Power PC) to our university ppp
> server.  Where can I download a free Mac PPP program for Mac OS 8.0?
> Thanks in advance.
>    -- Q.  Quentin Fang
>        (qfang@gasou.edu)


FreePPP version 2.6.2 is available through www.download.com:
<ftp://ftp.download.com/pub/mac/internet/freeppp262.sit.hqx>

Best of Luck

-- 
Jerry Learn <Learn@u.washington.edu>
U. of Washington 
Seattle, WA  98195-7740  USA      

From owner-software@net.bio.net Wed Jun 10 23:00:00 1998
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!newsfeed.nacamar.de!dispose.news.demon.net!demon!news.demon.co.uk!demon!cammol1.demon.co.uk!NewsWatcher!user
From: see_sig@cmtech.co.delete.uk (Richard P. Grant)
Newsgroups: bionet.software
Subject: Re: Need your help:  Where can I find free MacPPP
Date: Thu, 11 Jun 1998 08:50:19 +0100
Organization: Cambridge Molecular
Distribution: world
Message-ID: <see_sig-1106980850340001@192.168.0.84>
References: <3.0.5.32.19980610141153.007b2670@gsaix2.cc.gasou.edu>
NNTP-Posting-Host: cammol1.demon.co.uk
X-NNTP-Posting-Host: cammol1.demon.co.uk:212.228.79.177
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X-Complaints-To: abuse@demon.net
Lines: 26

Hi,

There is a perfectly good PPP on the OS 8.0 CD.  It's better than anything
that was written for sys 7.x.  You might have to use the installer to get
it, but it's worth doing that to make sure you have OT installed.  

HTH,

Richard

In article <3.0.5.32.19980610141153.007b2670@gsaix2.cc.gasou.edu>,
qfang@GASOU.EDU ("Q. Quentin Fang") wrote:

: Hi there:
: 
: I would like to connect my home Mac (Power PC) to our university ppp
: server.  Where can I download a free Mac PPP program for Mac OS 8.0?
: Thanks in advance.
:    -- Q.  Quentin Fang
:        (qfang@gasou.edu)

-- 
Richard P. Grant MA DPhil  | rgrant at  cmtech.co.uk
Senior R&D Scientist       | work: http://www.cmtech.co.uk/
Cambridge Molecular        | home: http://www.avnet.co.uk/adastra
      -- Standard corporate disclaimers apply --

From owner-software@net.bio.net Thu Jun 11 23:00:00 1998
From: s95007285@usp.ac.fj
Newsgroups: bionet.software
Subject: Doctors System
Message-ID: <kQak$kJC7hfC@usp>
Date: 12 Jun 98 10:04:01 +1200
Summary: Doctors System
Keywords: Doctors
Distribution: world
Organization: The University of the South Pacific
Lines: 23
Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!202.84.255.3!news.hkt.net!news.is.com.fj!usp.ac.fj!s95007285

DOCTORS SYSTEM

Doctors system available at very reasonable price
	- Year 2000 compatiable
	- Windows Based
	- Password Protected
	- Pulldown/sub menus
	- Microsoft Utility integrated
	  Eg. Spell check, cut/paste, record sortor etc
	- background picture setup
	- patient history at a touch of a button
	- Patient disease/Allergic nomination
	- pleanty reports (for analysis)
	- data presented in graphs (pie chart, bar graph etc)
	- Evaluation package available(Conditions apply)
	

	FOR MORE INFORMATION CONTACT:
	Shailendra Prakash
	Phone  : (679) 370-207
	Fax    : (679) 370-207
	Postal : P O Box 16798, Suva, Fiji Islands


From owner-software@net.bio.net Thu Jun 11 23:00:00 1998
Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!news.idt.net!newsfeed.internetmci.com!204.59.152.222!news-peer.gip.net!news.gsl.net!news-santiago.gip.net!gip.net!news.rdc.cl!news.puc.cl!pelicano.dpi.udec.CL!not-for-mail
From: "Leonardo" <lmerino@condor.dpi.udec.cl>
Newsgroups: ar.ciencias.fisica,bionet.immunology,bionet.microbiology,bionet.software,bionet.software.gcg,bionet.toxicology,chile.mercado.software
Subject: Re: suscripcion<--Asi no se hace, locooo...!
Date: 12 Jun 1998 20:52:48 GMT
Organization: Universidad de Concepción
Lines: 14
Message-ID: <01bd963b$1cf07740$725d4a98@Clementepc.udec.cl>
References: <6l28tq$liq40@origin.prima.com.ar> <6l3plf$pjt$1@aconcagua.ctcreuna.cl>
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Xref: biosci bionet.immunology:14198 bionet.microbiology:13690 bionet.software:21261 bionet.software.gcg:3153 bionet.toxicology:2268

No te debes suscribir, solo lees y mandas mensajes a los grupos de tu
interes

Valentin Marchant <kinestrn@netcene.com> wrote in article
<6l3plf$pjt$1@aconcagua.ctcreuna.cl>...
> 
> Carlos Alberto Di Noro wrote in message
>