HDTenEightyP/NetNews huggingface dataset:
From: PARSONS_A@snd01.pcr.co.uk
Newsgroups: bionet.software
Subject: Synchronisation Problem in GCG with PIR : Solution & description
Date: 7 Jan 93 10:58:17 GMT
Distribution: bionet
Original-To: BIO-SOFT <BIO-SOFT@UK.AC.DARESBURY>

Hi Netfolk,

David Mathog (Caltech) mailed me to post to the net what the solution to my
problem was, as had thanked all those who had helped me.  Reinhard Doelz
(Basel) and Liz Cowe (Oxford) both gave me the answer to fix the problem but Liz
also provided an in depth analysis of the cause - with her agreement I am
posting her analysis and am also alerting MIPS who provided the copy of PIR
in question.

Viva la (le?) Net!

Tony p.


==============================================================================
To: parsons_a@uk.co.pcr.snd01
Subject: GCG syncoronization problem

Tony,

	I have also seen this problem with the PIR files that I get from MIPS
- is this where yours come from too ? The problem seems to be that an extra
character is added to the end of some sequence lines - this can't be seen (or
may appear as an odd control character) and the PIR programs all cope with it
fine. The GCG FASTA program decides the sequence and index don't match and so
stop - if you fetch the sequence that is dying (find this by runing fasta with
/monitor=1) then you will see an extra residue added at random to the end of
the sequence - well I did. But some GCG programs can skip this character so my
solution was to recreate the GCG index files - I first used Chopup so I could 
get short enough lines to check there were no funnies but actually thing this 
step isn't necessary and you can just use dataset and dbindex. 

	I tried getting help from GCG and PIR but both suggested that the 
funny character was being included by MIPS when they make the GCG index so i 
should contact them. By this time I'd done all the reformating so didn't 
bother!

Liz Cowe
Oxford University Molecular Biology Data Centre
liz@vax.path.ox.ac.uk
From: BIONET@FRCGM51.EARN
Newsgroups: bionet.software
Subject: Re: GCG synchronization problem
Date: 8 Jan 93 16:44:00 GMT
              from FRCGM51.BITNET (BIONET) by UKACRL.BITNET (Mailer R2.07) with
               BSMTP id 3776; Fri, 08 Jan 93 15: 44:59 GMT
            from DECNET-MAIL by FRCGM51.BITNET with PMDF#10000; Fri, 8 Jan 1993
Distribution: bionet
X-Envelope-To: bio-software@daresbury.ac.uk
Original-To: bio-software@UK.AC.DARESBURY
X-Vms-To: in%"bio-software@daresbury.ac.uk"


 
> I was trying to search PIR using FASTA and got the following error :-
>
>  *** ERROR in SQNext. Sequence reading is out of synchronization.
>
>
> Any ideas what is going on?
>
>  Log file follows...
 
        I had exactly the same problem, for the first time, with the last
 release I received from MIPS. I could not find out the reason.
        The only way I found to solve the problem was not very clever: run
 PIRtoGCG from the .SEQ and .SEQ files...
 
        Sorry that I can be of no help!
 
   ------------------------------------------------------------
   |  Jean-Loup Risler                |                        |
   | Centre de Genetique Moleculaire  |  risler@frcgm51.bitnet |
   | 91190  Gif sur Yvette  France    |                        |
   -------------------------------------------------------------
From: robison1@husc10.harvard.edu (Keith Robison)
Newsgroups: bionet.software
Subject: Re: Wanted: C++ Libraries for Biological Sequences
Date: 11 Jan 93 15:28:50 GMT

My own set of C++ libraries is undergoing a rewrite to improve
their design and reliability.  I will post a message to this
newsgroup when that rewrite is done identifying an ftp source.

These libraries provide basic functions for manipulating and 
analyzing nucleic acid and DNA sequences, as well as simple
GenBank parsing capabilities and an interface to the
device-independent graphics package contained within
the GCG sequence analysis package.  Also included are
a set of sample programs which demonstrate using the libraries
to:

	translate DNA/RNA into protein
	extract all open reading frames from a DNA/RNA sequence
	perform simple parsing of GenBank flat-files
	perform simple parsing of BLAST output
	look for oligonucleotide repeat regions in DNA
	look for protein regions likely to form coiled-coils
	generate GCG-compatible codon usage tables from sets of sequences
	search for restriction sites in DNA




Keith Robison
Harvard University
Department of Cellular & Developmental Biology
Department of Genetics / HHMI

robison@biosun.harvard.edu
From: BOTSALT@VM.UOGUELPH.CA (david salt)
Newsgroups: bionet.software
Subject: what the hell is a gopher?
Date: 11 Jan 93 17:46:01 GMT
Distribution: bionet

A very simple question from a wanna-be bionaut.
What the hell is a gopher and/or gopher hole?
From: BOTSALT@VM.UOGUELPH.CA (david salt)
Newsgroups: bionet.software
Subject: data input software
Date: 11 Jan 93 17:41:16 GMT
Distribution: bionet

I have a very simple request.
I need a program which can run on an old 8088 (running DOS 5 slowly)
which is able to aquire and store data coming in on an RS232 (from
my gamma counter).
Thanks
David Salt (botsalt@vm.uoguelph.ca)
From: kristoff@NET.BIO.NET (David Kristofferson)
Newsgroups: bionet.software
Subject: BIOSCI/bionet Frequently Asked Questions
Date: 9 Jan 93 10:00:03 GMT
Distribution: bionet


New users of BIOSCI/bionet may want to read the "Frequently Asked
Questions" or "FAQ" sheets for BIOSCI.  There are two FAQ sheets for
the newsgroup system.  FAQ I describes the general purpose and uses of
the BIOSCI/bionet newsgroups.  FAQ II provides details on how to
participate in these forums.  Both of these FAQs are available for
anonymous FTP from net.bio.net [134.172.2.69] in
pub/BIOSCI/biosci1.FAQ and pub/BIOSCI/biosci2.FAQ.  They may also be
requested by sending e-mail to biosci@net.bio.net (use plain English
for your request).  The FAQs are also posted on the first of each
month to the newsgroup BIONEWS/bionet.announce immediately following
the posting of the BIOSCI information sheet.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net
From: PARSONS_A@snd01.pcr.co.uk
Newsgroups: bionet.software
Subject: RE: GCG Synchronisation Problem
Date: 5 Jan 93 14:53:24 GMT
Distribution: bionet
Original-To: BIO-SOFT <BIO-SOFT@UK.AC.DARESBURY>

Many thanks to all those who helped me out of a jam with a GCG
synchronisation problem in particular those at the foot of this
message - makes you wonder what we a re paying GCG maintenance for
sometimes.

Thanks again!

Rick Westerman                System Manager of the AIDS Center Laboratory
westerm@aclcb.purdue.edu      for Computational Biochemistry (ACLCB), BCHM
Phone: (317) 494-0505         bldg., Purdue University, W. Lafayette, IN 47907
  FAX: (317) 494-7897

Cary O'Donnell
*****************************************************************************
AFRC Computing Division    JANET   : ODONNELL@UK.AC.AFRC.ARCB
West Common                INTERNET: ODONNELL@ARCB.AFRC.AC.UK
Harpenden                  Long/Lat: 00d 21m 45s West   51d 48m 30s North
Herts AL5 2JE              Tel: (+44) 582 762271 xt 229 Fax: (+44) 582 761710
U.K.                       (AFRC = Agricultural & Food Research Council)
-----------------------------------------------------------------------------
|    Dr. Reinhard Doelz            | RFC     doelz@urz.unibas.ch         |
|      Biocomputing                | DECNET  20579::48130::doelz         |
|Biozentrum der Universitaet       | X25     022846211142036::doelz      |
From: bdyke@DARWIN.SFBR.ORG (Bennett Dyke)
Newsgroups: bionet.software
Subject: Re: Ethernet card recommendations for MacII
Date: 5 Jan 93 14:12:20 GMT
Distribution: bionet

We have made it a practice to use external SCSI Ethernet boxes,
which are available from several vendors at about $275, with
all Macs without multiple internal slots.  Communications are
said to be a bit slower than with an internal card, but the
single slot of MacIIsi's is saved for other purposes, and we
have maximum flexibility to switch and upgrade processors.

+----------------------------------------------------------------------------+
|   Bennett Dyke                                                             |
|   Department of Genetics               Internet:  bdyke@darwin.sfbr.org    |
|   Southwest Foundation                    Phone:  (210) 674-1410 Ext 281   |
|   P.O. Box 28147                            Fax:  (210) 670-3317           |
|   San Antonio, TX 78228, USA                                               |
+----------------------------------------------------------------------------+


On 5 Jan 1993, Cheung C. Yue wrote:

> 
> I am daydreaming again, hoping to put the Mac IIsi in my laboratory
> on the net.  Not being particularly familiar with Mac's, I would
> like to solicit recommendations for brands of ethernet cards.  Also
> I would welcome suggestions of appropriate software (I suppose NCSA
> Telnet is probably the best).  Finally I wonder if it is possible to
> allow remote control of the Mac over ethernet.  Thanks in advance for
> all your input.
> 
> C Cho Yue
> ccy@po.cwru.edu
> -- 
>
From: pun@cui.unige.ch (PUN Thierry)
Subject: RE: 1D gel analysis (LaboImage)
Organization: University of Geneva, Switzerland
Date: Tue, 5 Jan 1993 08:21:09 GMT
From: bsh@MED.PITT.EDU (Basavaraju Shankarappa)
Newsgroups: bionet.software
Subject: Re: software for silent mutagenesis
Date: 5 Jan 93 22:20:49 GMT
Distribution: bionet

> In article <1992Dec30.185104.9506@alw.nih.gov> usdin@helix.nih.gov (Ted Usdin) writes:
> >Weiner and Scheraga (CABIOS, vol 5 pp191-198, 1989) described a Macintosh
> >program (Gene.Design.?) to assist in introducing restriction sites into DNA without changing the amino
> >acid sequence.  Does anyone know where I can get a copy of this, or a similar
> >program that runs on a Macintosh?
> 
> There is a similar program which runs on a PC called OligoMutantMaker.
> It is available by anonymous ftp from:
> Host fly.bio.indiana.edu
> 
>     Location: /molbio/ibmpc
>            FILE -rw-r--r--       8540  May 14 1991  oligo.doc
>            FILE -rw-r--r--     231882  May 14 1991  oligo.uue
> Dan Jacobson
> danj@welchgate.welch.jhu.edu

	I would like to add that we have also developed a PC compatible
program called SILMUT for identifying regions for the introduction of 
restriction enzyme sites by silent mutagenesis.  Although we have used
the same principle as detailed in the above two programs our approach 
was highly simplified.  This programs just tells you what restriction
enzyme/s can be introduced by silent mutagenesis in a specific sequence
of amino or nucleic acid.  This program is most useful for those who are
contemplating introduction of RE sites to generate casette vectors or
for swapping specific fragments of a gene in a construct.  
	The program is also available on fly.bio.indiana.edu in the 
directory molbio/ibmpc as two files: Silmut.xxx.  
	The work has been published in Biotechinques 12: 882-884 (1992).
The program sets include source codes for the program which has been internally
documented.  The programs work in PC and unix machines but if anyone can 
make it work on a Mac, we would welcome that.

Raj Shankarappa
bsh@med.pitt.edu 
Newsgroups: bionet.software
From: lmh@theory.lcs.mit.edu (Minghsun Liu)
Subject: Computerized lab notebook?
Organization: MIT Laboratory for Computer Science
Date: Sun, 10 Jan 1993 10:47:05 GMT


Hello All!

A few weeks ago I was having a discussion with a friend who
just bought a computer to be used in his research.  (Typical
applications such as keeping track of bacterial strains and making
presentations for the lab meetings only.)  And I mentioned that with
the advent and gaining popularity of notebook-sized portable
computers,  (I am not sure what the situation is in places outside of
Boston but I have seen people WORKING with their Mac PowerBook in
subway trains more than once!)  

I mentioned that I wondered if working biologists were ready to trade in their
trusty lab notebooks for computer software that could replace it.  Yes,
I know I probably haven't even fully appreciated the kind of diverse
needs that different people want in their computerized lab notebook.
I am just wondering if there exist a kind of "philosophical" or
"emotional" attachment to a regular lab notebook.  Better yet, is
anyone out there actually using such a software?

Any comments would be appreciated!

- Minghsun Liu
  lmh@medg.lcs.mit.edu
  lmh@genome.wi.mit.edu
From: hkaplan@UDCVAX.BITNET (Howard Kaplan)
Newsgroups: bionet.software
Subject: RE: Computerized lab notebook?
Date: 10 Jan 93 17:56:28 GMT
Distribution: bionet


As many biologists' lab is in the field, which could be in places with extreme
conditions (you should see my collection of waterproof inks, paper and pouches)
a battery operated, small keyboard, not 100% reliable instrument, often oper-
ated while wearing gloves, would be less than desirable.  On the other hand,
individual preference will be the final determinant, as it always is.
An interesting, related article appears in today's (10 Dec) Washington Post in
the travel section about how to travel with a notebook computer, detailing
many of the problems one encounters and how to overcome or accomodate them.
                                Howard Kaplan
        `                       HKAPLAN@UDCVAX.BITNET
From: mrl775@tigger.jvnc.net
Newsgroups: bionet.software
Subject: Re: Computerized Lab Notebooks
Date: 12 Jan 93 04:57:59 GMT
Organization: TheNews

In article <C0nMB2.IDG@news2.cis.umn.edu> ernest@lenti.med.umn.edu (Ernest
Retzel (1535 49118)) writes:
>A big part of my work life centers around my work computer; I, for one, keep
>trying to get an ISDN experiment running to my home...I want that data, and
>I don't want a copy of it to carry.  And I hate paper!
>
>my 0.02.
>

Just to add to the discussion... not so much about lab notebooks on computer,
but on notebook computers....

I run my internet connection off of my powerbook 170 (with a powerport gold
tied into the JvNC net SLIP server), and do a lot of my work there.  I also tie
into the office, using appletalk remote access, again on powerports.  By
running Timbuktu on the pb170 and my fx in the office, I can get to anything I
need from the home or the road.  I also run the filesharing stuff of system 7,
if I just need to grab a file.  To keep the sync problems down, I confine most
of my work to specific tasks, some on the pb, some on the fx (and a bunch on
the indigo, but thats a different story).  

So, the key is, you don't need ISDN running to the house, unless you need LOTS
of data flowing.  I find ARA and my set up to suit me fine.

In the future, things like the notebook sparc 2, a notebook with 24 spec marks
and 250-500 MB of disk, will make notebook computing almost like desktop
computing, and you won't need that desktop (or deskside) machine to go with it.

any, had to add my $0.02...

Keith
From: ernest@lenti.med.umn.edu (Ernest Retzel (1535 49118))
Newsgroups: bionet.software
Subject: Re: Computerized Lab Notebooks
Date: 10 Jan 93 20:01:49 GMT
Organization: University of Minnesota

I can think of lots of reasons why *not* to do it....

On the other hand, I can also recall, several years ago, a presentation about
the UK-equivalent of extension agents showing the farmers how to use the
computers for increasing their productivity out of the back of their 
pick-up trucks.

There are several Virtual Notebook projects out there; they have varying
degrees of flexibility, and most are expensive.  At least one of them [the
Baylor project] really does feel like a better idea...

A big part of my work life centers around my work computer; I, for one, keep
trying to get an ISDN experiment running to my home...I want that data, and
I don't want a copy of it to carry.  And I hate paper!

my 0.02.

Ernie Retzel
Newsgroups: bionet.software
From: ernest@lenti.med.umn.edu (Ernest Retzel (1535 49118))
Subject: Re: Experiences with Entrez under UNIX?
Organization: University of Minnesota
Date: Fri, 8 Jan 1993 07:44:35 GMT

Equally easy on both Suns and SGI's.
It "just works."

One of the SuperGeeks in the group [read: very hard to impress...]
went so far as to say it, and the Vibrant Toolkit, are one of the 
nicest jobs he has seen.

Ernie Retzel
ernest@lenti.med.umn.edu
Newsgroups: bionet.software
From: danj@welchgate.welch.jhu.edu (Dan Jacobson)
Subject: Re: Gopher hole for DB taxonomies?
Keywords: gopher, NCBI, Swiss-Prot, PIR, GenBank
Organization: Johns Hopkins Univ. Welch Medical Library
Date: Fri, 8 Jan 1993 21:19:16 GMT

In article <robison1.726426590@husc.harvard.edu> robison1@husc10.harvard.edu (Keith Robison) writes:
>Do any of the biogophers out there have the capability
>to search the taxonomy files which NCBI has generated
>for the major databases?
>
>(If not, this is a HINT :-)
>
>
>

Ok, I took your subtle HINT :-)  - you can now search the taxonomy files
for Genbank and Swiss-Prot at the gopher hole: merlot.welch.jhu.edu

Go to the following directory and subdirectory:

 -->  13. Search Databases at Welchlab (....)

        -->  3.  Database Taxonomy (Genbank, Swiss-Prot ...)/

                 -->  1.  Genbank Taxonomy <?>
                      2.  Swiss-Prot Taxonomy <?>




Happy searching,


Dan Jacobson


danj@welchgate.welch.jhu.edu
From: bwilliam@oyster.smcm.edu (Bill Williams)
Newsgroups: bionet.software
Subject: Re: Ethernet card recommendations for MacII
Date: 12 Jan 93 17:46:43 GMT
Organization: St. Mary's College of Maryland
X-UserAgent: Nuntius v1.1.1d17
X-XXMessage-ID: <A7786EC7770101D2@williams.smcm.edu>
X-XXDate: Tue, 12 Jan 93 17:49:11 GMT

In article <1iaoi4INN3vf@usenet.INS.CWRU.Edu> Cheung C. Yue,
ccy@po.CWRU.Edu writes:
>I am daydreaming again, hoping to put the Mac IIsi in my laboratory
>on the net.  Not being particularly familiar with Mac's, I would
>like to solicit recommendations for brands of ethernet cards.  Also
>I would welcome suggestions of appropriate software (I suppose NCSA
>Telnet is probably the best).

I have a NuvoLink SC box on my IIcx, and it has worked perfectly for
about a year, now.  I got the box, instead of a card, because at the
time I had an SE and expected to move up. If there is some chance you
will be changing machines, I think the box is an excellent investment. 

I use the following software: 
 
MacTCP, which I got free with Eudora, as my router.
Eudora, which I got free with MacTCP :-), as my mail program.
Nuntius for news.
Fetch for FTP.
TurboGopher for Gopher.
NCSA Telnet (MacTCP version) for the increasingly rare occasions in
which I need to log on to another machine. 

You will probably note something that all of the above programs have in
common:  they are free!
___________________________________
William E. Williams, bwilliam@oyster.smcm.edu
Divison of Natural Sciences and Mathematics
St. Mary's College of Maryland
St. Mary's City, MD 20686
From: ccy@po.CWRU.Edu (Cheung C. Yue)
Newsgroups: bionet.software
Subject: Ethernet card recommendations for MacII
Date: 5 Jan 1993 01:33:56 GMT
Organization: Case Western Reserve University, Cleveland, OH (USA)
Reply-To: ccy@po.CWRU.Edu (Cheung C. Yue)
NNTP-Posting-Host: hela.ins.cwru.edu


I am daydreaming again, hoping to put the Mac IIsi in my laboratory
on the net.  Not being particularly familiar with Mac's, I would
like to solicit recommendations for brands of ethernet cards.  Also
I would welcome suggestions of appropriate software (I suppose NCSA
Telnet is probably the best).  Finally I wonder if it is possible to
allow remote control of the Mac over ethernet.  Thanks in advance for
all your input.

C Cho Yue
ccy@po.cwru.edu
--
From: seb1005@mbfs.bio.cam.ac.uk (Steven Brenner)
Newsgroups: bionet.software
Subject: Wanted: C++ Libraries for Biological Sequences
Date: 9 Jan 93 14:13:56 GMT
Organization: U. of Cambridge, England


	Has anyone developed or know of inexpensive or free C++ libraries
for reading and manipulating Biolgical Sequences and Structures.  I am 
most interested in working with Brookhaven Protein Database Files, but 
would also be interesting in finding out about code for other types of
information.

	I will post a summary to this group if I receive any interesting
replies.

Steven E. Brenner               |  Internet    seb1005@mbfs.bio.cam.ac.uk
Department of Biochemistry      |  JANET       seb1005@uk.ac.cam.bio.mbfs
University of Cambridge         |  Laboratory  +44 223 333671
Tennis Court Road               |  Home        +44 223 314964
Cambridge CB2 1QW, UK           |  Lab Fax     +44 223 333345
From: Allan H. Levy <a-levy@uiuc.edu>
Subject: Re: Ethernet card recommendations for MacII
X-Xxdate: Fri, 8 Jan 93 17:05:49 GMT
X-Useragent: Nuntius v1.1.1d16
Organization: Univ of Ill. Col. of Med. at Urbana-Champaign
Date: Fri, 8 Jan 1993 23:00:51 GMT
X-Xxmessage-Id: <A77364EDF5015719@levy.med.uiuc.edu>

Date: 5 Jan 1993 01:33:56 GMT

We use Asante cards and find they work well. Yes, you might have guessed
it, I use NCSA Telnet.

Also, try Eudora as a mail interface to your Unix mainframe for your
email.
Newsgroups: bionet.software
From: gonnet@inf.ethz.ch (Gaston Gonnet)
Subject: Re: Program to compare all members of a group of sequences
Organization: Dept. Informatik, Swiss Federal Institute of Technology (ETH), Zurich, CH
Date: Mon, 4 Jan 1993 10:28:45 GMT

In article <1992Dec30.051200.21456@tigger.jvnc.net> mrl775@tigger.jvnc.net writes:
> Hello
>
>Does anyone know of a program that will take a set of sequences, and find
>common local alignments (sort of like what blast and blast3 do, but with each
>member of the set).  I am looking to define cofactor binding sites, and have a
>list of sequences that all bind the cofactor, but have no good method of
>comparing them all together (a multiple alignment doesnt work).  Any hints,
>pointers, source, executables would be appreciated.
======================================================
We compute multiple alignments based on local (all-against-all)
alignments.  This may solve your problem.  You can try this by
submitting a request to our automatic server.

Send a mail message to  cbrg@inf.ethz.ch  with the body

help AllAll

and you will receive a description on how to submit requests.

Gaston H. Gonnet, Informatik, Zurich
From: pacoid@wixer.cactus.org (Paco Xander Nathan)
Subject: Re: LabView hardware
Organization: FringeWare Inc., +1 512 477 1366
Distribution: bionet
Date: Tue, 5 Jan 93 01:45:05 GMT

In article <1993Jan02.165323.24056@foxmail.gfc.edu> dpowers@foxmail.gfc.edu (Donald R. Powers) writes:
>I have LabView II and would like to set it up to monitor several
>instruments on my Mac IIci.  Can anyone suggest a reasonably priced A/D
>device I can use for an interface?  Most of what I have involves a
>simple voltage inpute.  However, it is possible I might need a
>differential input at some point.  Thanks!

Check with Radient in SF - 415 296 8040..  I wrote a review on them
for the last issue of Mondo 2000 - they have a CNX box that'll take
8 inputs into a Mac(A or D) and the whole system sells for around $350
which is a lot less than a LabView II ..  Tell 'em I sent you :-)

Paco Xander Nathan
Newsgroups: bionet.software
From: mimq@hippo.ru.ac.za (Molapo Qhobela)
Subject: Analysis of 1-D Gels
Keywords: PAGE, AGAROSE GEL ANALYSIS
Organization: Rhodes University, Grahamstown, South Africa
Date: Tue, 5 Jan 1993 06:50:24 GMT

Hi,

Can anyone out there help me out. I am looking for a DOS based software
package that can be used to analyse 1-D gels, with the ultimate aim of
perantage determination of samples. I currently use a package called
GelManager by Peter Jackman, but it only calculates similarities between
samples. I saw a similar posting on this subject a few months back, but
I never saw the responses.

Thanks in advance for your help. Please reply to this posting or
directly to me at mimq@hippo.ru.ac.za

Cheers

Molapo
-- 
   Molapo Qhobela PhD.                |  Do not ever get caught with 
   Rhodes University - Microbiology   |       your plants down!!
   Internet: mimq@hippo.ru.ac.za      |  Consult a Plant Pathologist 
   Telefax: +27 (0461) 24377          |            via APS