HDTenEightyP/NetNews huggingface dataset:
From: Heikki.Lehvaslaiho@Helsinki.FI (Heikki Lehv{slaiho)
Newsgroups: bionet.software
Subject: Re: nohup_Primer_& ??
Date: 14 Apr 92 07:41:48 GMT
Organization: Meilahti Medical Depts, University of Helsinki

In article <1992Apr14.001432.24351@magnus.acs.ohio-state.edu>, gchacko@magnus.acs.ohio-state.edu (George W Chacko) writes:
> 
> Has anyone ever run background jobs with Primer (the Eric Lander version) 
> in the Unix environment? If so tell me how please. When the program
> compares 700 forward and backward primers it can take a while.

When you have entered all the input and the program starts crunching, 
press CTRL-Z to suspend it:

[1]  + 18441 Suspended              primer

The number in square brackets shows you the number of the job. Next at 
your normal UNIX prompt, type bg to start running the process at the 
background. If you want it back to the foreground type fg. If you have 
several processes running simultaneously, add the number to the command. 
Command jobs shows all your jobs.

I have done this several times, but there really are so many potential 
primer pairs always available that I find it best to restrict severely 
the criteria by which primers are selected. Start by lowering the allowed 
number of complementary nucleotides (both to themselves and to each other) 
and using at least two nucleotides long 3' GC clamp. Also, determining 
strictly the target, subsequence and/or product length greatly speeds up the 
calculation. You probably get better primers, too. Remember, it's always 
possible to loosen the criteria if your first run didn't find any primers.

Hope this helps,

        	-Heikki

Heikki Lehv{slaiho  <Heikki.Lehvaslaiho@Helsinki.FI>
Meilahti Medical Departments, University of Helsinki
Haartmaninkatu 3, SF-00290 Helsinki, FINLAND
Phone: +358-0-434 6408         FAX: +358-0-434 6491
From: dje@matt.ksu.ksu.edu (Daniel Jay Enebo)
Newsgroups: bionet.software
Subject: Molecular Biology Software for Windows
Date: 14 Apr 1992 20:21:27 -0500
Organization: Kansas State University
NNTP-Posting-Host: matt.ksu.ksu.edu

 
We are looking for info and opinions on molecular biology software packages fo
r PC clones.  We have a 33/386 and use Windows 3.1.  What is available out the
re?  Anything like MacVector??  What about GeneWorks?? We need all the standar
d features: plasmid construction, RNA folding, protein analysis (ie. hydrophob
icity etc.), PCR primers, seq. alignment, sequence project management, etc.
Any help will be greatly appreciated.
 
P.S.  We only have a few days to select a package.          
 
Thanks,
Dan
 
-- 
|  Daniel Enebo             |  dje@matt.ksu.edu       |
|  Division of Biology      | ----------------------- |
|  Kansas State University  |  Cell Cycle Regulation  |
Newsgroups: bionet.software
From: sasha@cco.caltech.edu (Alexander Zeyliger)
Subject: 3D image reconstruction from 2D projections?
Summary: Are there algorithms available?
Keywords: tomography, image reconstruction
Organization: California Institute of Technology, Pasadena
Date: Wed, 15 Apr 1992 22:01:42 GMT

Hi

I was just given a project on 3D image reconstruction from 2D projections.
However, I am having problems locating an efficient algorithm that does that.
If you know anything about it and don't mind, please send me email or post
a note to this newsgroup.

Thanks a lot
Alexander Zeyliger

sasha@cco.caltech.edu
:)
Newsgroups: bionet.software
From: gchacko@magnus.acs.ohio-state.edu (George W Chacko)
Subject: nohup_Primer_& ??
Organization: The Ohio State University
Date: Tue, 14 Apr 1992 00:14:32 GMT

Has anyone ever run background jobs with Primer (the Eric Lander version) 
in the Unix environment? If so tell me how please. When the program
compares 700 forward and backward primers it can take a while.

Thanks


George
From: francis@cs.mcgill.ca (Francis OUELLETTE)
Newsgroups: bionet.software
Subject: Re: Molecular Biology Software for Windows
Date: 15 Apr 92 12:24:45 GMT
Article-I.D.: cs.1992Apr15.122445.14255
Organization: SOCS, McGill University, Montreal, Canada

In article dje@matt.ksu.ksu.edu (Daniel Jay Enebo) writes:

>We are looking for info and opinions on molecular biology software packages fo
>r PC clones.  We have a 33/386 and use Windows 3.1.  What is available out the
>re?  Anything like MacVector??  What about GeneWorks?? We need all the standar
>d features: plasmid construction, RNA folding, protein analysis (ie. hydrophob
>icity etc.), PCR primers, seq. alignment, sequence project management, etc.
>Any help will be greatly appreciated.

The only "molecular_biology_related_software" that I know that run
under MS-Windows are MACAW (available from your favorite FTP site) and
Entrez (only available as a beta version at this time fom NCBI).

MACAW is a multiple sequence editor/alignment tool, and Entrez is a 
relational medline/genbank retrieval tool (which also require a CD-ROM
drive).  Both of these products are from NCBI actually, and I found
that MACAW lacks a good user manual.  If there is one out there,
_please_ let me know.  My users (and myself ;-) need all the manuals
we can get!

best of luck,

francis

--
| B.F. Francis Ouellette
| Manager, Yeast Chromosome I Project
| Dept of Biology, McGill University, Montreal, Qc, Canada
| francis@binkley.cs.mcgill.ca
From: kristoff@genbank.bio.net (David Kristofferson)
Newsgroups: bionet.software
Subject: Re: Are vector sequences available through genbank.bio.net?
Date: 7 Apr 92 17:44:53 GMT
Organization: GenBank Online Service

djt2@po.CWRU.Edu (Dennis J. Templeton) writes:

>Are vector sequences available through genbank.bio.net?   I have seen
>references to such a "synthetic DNA" database, but I don't see it on the DB
>list in the on-line genbank access.  Am I looking in the wrong place? or
>just SOL?

>Specifically, I'm looking for seq's of the Hieter yeast vectors pRS303-306
>and pRS 313-316 (Genetics 122:19-27).

All synthetic sequences in GenBank are in the file gbsyn.seq but I
could not find the above in release 71.

				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff@genbank.bio.net
From: danj@WELCHGATE.WELCH.JHU.EDU (Dan Jacobson x-8453)
Newsgroups: bionet.software
Subject: *Question on Restriction Mapping Software
Date: 17 Apr 92 01:06:52 GMT
Distribution: bionet


Qing Wang writes:

>Does anyone know any public software for assembly restriction mapping
>of a gene segment digested by different endonucleases? 

I'm not exactly sure what you want but it sounds like you may want
to take a look at COMAP (kudos to Kay Hoffman).

You can obtain Comap from the following ftp sites (as well as the EMBL
and Houston fileservers):

Host evolution.bchs.uh.edu

    Location: /pub/gene-server/incoming
           FILE -rw-r--r--     445952  Jan 13 00:52  comap.zip

Host fly.bio.indiana.edu

    Location: /molbio/ibmpc
           FILE -rw-r--r--     445952  Dec 13 14:43  comap.zip

Host nic.funet.fi

    Location: /pub/sci/molbio/msdos
           FILE -rw-rw-r--     445952  Dec 16 12:19  comap.zip

Kudos to Rob Harper, Don Gilbert and Dan Davison for the ftp sites.


Best of luck,

Dan Jacobson

danj@welchgate.welch.jhu.edu
From: bss2aj@surrey.ac.uk (Alan Jennings)
Newsgroups: bionet.software
Subject: Canon BJ10ex printer drivers
Date: 16 Apr 92 16:34:15 GMT
Article-I.D.: surr.5965.9204161635
Distribution: bionet


 Dear netters,

	Does anyone know where I could get hold of a driver for the
above printer for GEM and Wordperfect? Any help appreciated...


	Alan

_____________________________________________________________
Alan Jennings                  |  "Time is an illusion.......
University of Surrey, UK.      |   lunchtime doubly so."
e-mail bss2aj@surrey.ac.uk     |   - Ford Prefect
From: info@aiims.ernet.in
Newsgroups: bionet.software
Subject: T-cell epitope mapping PC program
Date: 9 Apr 92 20:41:06 GMT
Distribution: bionet


Dear Netters,

	My collegues are looking for an IBM PC program to identify
T and B-cell epitopes on protein sequences. [T-cell and B-cell epitope
mapping on protein sequences].
 
Can anyone help me to know the availablity of such programs preferrably in
public domain?

Thanks in advance.

R. Dhanasekaran
e-mail: info@aiims.ernet.in
From: ANSC6@UMDC.UMD.EDU
Newsgroups: bionet.software
Subject: Hypercell
Date: 6 Apr 92 20:41:33 GMT
Distribution: bionet

Anyone have any experience with Hypercell for teaching?  Is it worth
$1,000/copy?

Mark Varner
ansc6@umdc.umd.edu
From: MANGALAM@SALK-SC2.SDSC.EDU
Newsgroups: bionet.software
Subject: HyperChem Demo FTPable
Date: 17 Apr 92 01:55:44 GMT
Distribution: bionet

Re: the >386 PC Molecular Modelling Program HyerChem...

The (barely interactive) HyperChem demo is FTPable from Don Gilbert's most
excellent bioarchive at ftp.bio.indiana.edu, put in the /Incoming directory
with a short readme (hyprchem.rm), describing its (considerable) hardware 
requirements.  It may have jiggled its way into the /molbio/pc directory by 
now, though.
  It's freely distributable, so spread it around - Autodesk certainly won't 
mind.
  The demo, even zipped, is a monster (~1.2MB), so download considerately.

Harry Mangalam                                       Vox:(619) 453-4100, x250
Dept of Biocomputing                                       Fax:(619) 552-1546
The Salk Institute                                 mangalam@salk-sc2.sdsc.edu
10010 N Torrey Pines Rd                            mangalam@salk-sgi.sdsc.edu
La Jolla CA 92037 				         mangalam@salk.bitnet
From: bwilliam@oyster.smcm.edu
Newsgroups: bionet.software
Subject: Re: Hypercell
Date: 7 Apr 92 16:41:09 GMT
Distribution: usa
Organization: St. Mary's College of Maryland

In article <9204062043.AA15925@genbank.bio.net> ANSC6@UMDC.UMD.EDU writes:
>Anyone have any experience with Hypercell for teaching?  Is it worth
>$1,000/copy?

How could it POSSIBLY be? I called the publisher to complain about this
ridiculous pricing policy more than a year ago and got the usual polite
nothings.  

					-W2
From: rahbe@jouy.inra.fr (Yvan Rahbe)
Newsgroups: bionet.software
Subject: Chromatography integrator
Keywords: HPLC Integration Peak
Date: 17 Apr 92 11:22:43 GMT
Organization: INRA - Agron. Res. - Zoology Dept.

Dear netters,

We are looking for a MacIntosh software dedicated to Chromatogram management
(peak recognition & integration -automatic and manual corrections-, zooming
facilities...). We do not need the acquisition module of a full HPLC package,
but if there is one that is cheap enough and reasonably powerfull, it is
welcome. We therefore need to have information on the format of data that feed
this integration package.

Does anyone know of a freeware or shareware product doing this on Mac?
Any information on commercial package for the Mac would interest us.
(Of course, there are plenty of commercial Chromato-softs for the PCs)

Any hint on a way of finding this kind of information on the net would also be
apreciated (I have ftp access, gopher and wais on the Mac. But what server
would respond positively to such a request?)

Please answer by mail, and I'll forward an abstract of relevant answers   to
this group.

Thanks

Yvan Rahbe
INRA-INSA Biologie 406
20, ave A. Einstein F69621 Villeurbanne cedex
                    France
fax:    +33 - 72 43 85 11
e-mail: rahbe@lyon.inra.fr
From: MANGALAM@SALK-SC2.SDSC.EDU
Newsgroups: bionet.software
Subject: HyperChem Mol. Modelling SW
Date: 16 Apr 92 19:33:14 GMT
Article-I.D.: genbank.9204161831.AA20397
Distribution: bionet

Hi Netters,
   Because of the traffic lately about Molecular Modelling Software for the PC 
and in general, I'll pass this on:  Perhaps some of you have seen the very 
splashy, colorful, and somewhat bizarre ads for an Autodesk product 
called HyperChem.  I bit and ordered the demo and despite some infantile intro 
screens, it is an intriguing bit of work.  In a word, it's sort of an 
Insight/Discover (very) Lite. But!

   1) It's Windows based and therefore linkable to spreadsheets, and other 
Windows programs (and in fact you can [supposedly] write macros in Excel to 
execute HyperChem functions). It also looks very easy to use.
   2) It required a _BIG_ PC. While the brochure says you can runit on a 386 
with 4 MB, I couldn't see running it on anything less than a fast 486 with
8MB and a Windows Accelerator for any useful work. 
   3) Besides the display stuff, it [thinks it] can do minimizations and 
energy calculations, displaying the interim structures as it does so. It was 
a canned demo, so I don't think that the calculations that it displayed were 
actually being done - if they were, it would be acceptable speed (on a 25MHz 
386/387).
   4) And this is the the good news - I just got off the phone to Autodesk 
for the pricing and for 90 days the intro price for academics is $600, not 
cheap, but not bad considering the real price will be $3500.

   All in all, for those who want to play with or need to display molecules, 
have a big PC and don't want to pay for an Indigo and Insight/Discover 
(academic combos would probably start at about $12,000), it's worth a look at
the demo and certainly try to play with a working version.   The number is 1
800 424 9737 for info. 

   I called Autodesk and the demo is uploadable if people are interested.

   Std disclaimers apply.


Harry Mangalam                                       Vox:(619) 453-4100, x250
Dept of Biocomputing                                       Fax:(619) 552-1546
The Salk Institute                                 mangalam@salk-sc2.sdsc.edu
10010 N Torrey Pines Rd                            mangalam@salk-sgi.sdsc.edu
La Jolla CA 92037 				         mangalam@salk.bitnet
From: Rob.Harper@CONVEX.CSC.FI (Rob Harper)
Newsgroups: bionet.software
Subject: Services at NIC (finland)
Date: 15 Apr 92 10:27:25 GMT
Article-I.D.: genbank.9204150954.AA04395
Distribution: bionet


Over the Easter period nic.funet.fi will undergo an upgrade in operating
system, and addition disks will be added. Therefore there will be some
disruptions in the normal services available from nic.funet.fi

Be patient.

   Rob Harper                     /   E-mail:          harper@convex.csc.fi
   Finnish State Computer Centre  /   Molbio/software: harper@nic.funet.fi
   P.O. Box 40, SF-02101 Espoo    /   Telephone:       +358 0 457 2076
   Finland                        /   Fax:             +358 0 457 2302
From: dok418@CVX12.INET.DKFZ-HEIDELBERG.DE (Barbara Maier)
Newsgroups: bionet.software
Subject: f.y.i
Date: 10 Apr 92 07:54:38 GMT
Distribution: bionet


International Symposium on

COMPUTATIONAL METHODS IN GENOME RESEARCH

1 - 4 July 1992, Deutsches Krebsforschungszentrum

Heidelberg, Germany

Sponsored by the Commission of the European Communities

Organizing Committee:
M. Bishop (Cambridge), H. Lehrach (London),
B. Loder (Brussels), J. Reich (Berlin), Otto Ritter (Heidelberg),
Ch. Sander (Heidelberg), S. Suhai (Heidelberg)

Topics will include:
DNA and protein sequence and structure analysis
Genetic and physical mapping
Genomic data models and databases
Genome projects: status and perspectives

Lecturers will include:
S. Altschul (Bethesda), H. Bilofsky (Heidelberg),
M. Bishop (Cambridge), G. Cameron (Heidelberg),
Ch. Cantor (Berkeley), Ph. Dessen (Paris),
R. Durbin (Cambridge), G. Gonnet (Zuerich),
H. Lehrach (London), V. Markowitz (Berkeley),
T. Marr (New York), J. Thierry-Mieg (Montpellier)
E. Myers (Tucson), W.R. Pearson (Charlottesville)
O. Ritter (Heidelberg), Ch. Sander (Heidelberg),
T. Slezak (Livermore), W.T. Taylor (London)

A poster session will be held and limited oral presentations will be selected.
Funds are available to partially subsidize transportation and/or living costs
mainly for postdoctorals and graduate students.

Registration:
The registration fees for the symposium will be DM 200 (DM 100 for students).
It is advisable to register as early as possible due to space limitations. For
further information and registration form please contact:

Dr. Sandor Suhai
Deutsches Krebsforschungszentrum
Im Neuenheimer Feld 280
D - 6900 Heidelberg
Phone: +49/62 21/42 23 69
Fax:       +49/62 21/42 23 33
E-mail: dok252@cvx12.dkfz-heidelberg.de
From: CFARMER1@UA1VM.BITNET ("Chet Farmer, Asst. Dir., Project IDEALS")
Newsgroups: bionet.software
Subject: ANNOUNCEMENT OF SAGSET CONF
Date: 9 Apr 92 22:23:58 GMT
Distribution: bionet


  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* *                                                                 * *
*     ----------------------                                          *
*     Call for participation:  ---------------------                  *
*     ----------------------   Joint 1992 conference:  ///////////    *
*                              ---------------------   S A G S E T    *
*                                                       I S A G A     *
*   Society for the Advancement of Games and           \\\\\\\\\\\    *
*   Simulations in Education and Training                             *
*                   International Simulation and Gaming Association   *
*                                                                     *
*   Conference theme:        Developing transferable skills through   *
*   ----------------                          simulation and gaming   *
*                                                                     *
*   18-21 August, 1992       Napier University, Edinburgh, Scotland   *
*                                                                     *
*   For further information:                          Fred Percival   *
*   =======================       SAGSET/ISAGA Conference Secretary   *
*                                                 Napier University   *
*                                                 219 Colinton Road   *
*   Telephone:  44 / 31-455-4394                 Edinburgh EH14 1DJ   *
*   Facsimile:  44 / 31-455-7989                           Scotland   *
*                                                                     *
* *                                                                 * *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

+-----------------------------------------------------------------------+
|  Chet Farmer, Assistant Director   |   English / 103 Morgan           |
|  Project IDEALS -- FIPSE, DoE      |   Tuscaloosa, AL  35487-0244     |
|  University of Alabama             |   tel 205-348-9494               |
+-----------------------------------------------------------------------+
From: Qing.Wang@dartmouth.edu (Qing Wang)
Newsgroups: bionet.software
Subject: Question on Restriction Mapping Software
Date: 16 Apr 92 21:49:16 GMT
Article-I.D.: dartvax.1992Apr16.214916.25886
Organization: Dartmouth College, Hanover, NH

Does anyone know any public software for assembly restriction mapping
of a gene segment digested by different endonucleases? Thank you for
your help.

Qing Wang 
qing.wang@dartmouth.edu
From: danj@WELCHGATE.WELCH.JHU.EDU (Dan Jacobson)
Newsgroups: bionet.software
Subject: *MapMaker
Date: 6 Apr 92 20:00:53 GMT
Article-I.D.: welchgat.9204062000.AA11713
Distribution: bionet


Matthew Wiener writes:

>Somebody here is looking for MAPMAKER [1], a program to construct primary
>genetic linkage maps.  The reference says it is available for the asking.
>FTP, e-mail, whatever--the VMS version is preferred to the Unix version.
>
>[1] Eric Lander, Philip Green, Jeff Abrahmason, Aaron Barlow, Mark J Daly,
>Stephen E Lincoln, Lee Newburg, "MAPMAKER: An Interactive Computer Package
>for Constructing Primary Genetic Linkage Maps of Experimental and Natual
>Populations", GENOMICS 1, pp174-181 (1987).
>-- 
>-Matthew P Wiener (weemba@libra.wistar.upenn.edu)


I found the following information on MapMaker - this was culled from a summary
on linkage software first posted by Steve Thompson and later reposted by myself.


Best of luck,

Dan Jacobson

danj@welchgate.welch.jhu.edu


********************************************************************************

         ********************MapMaker Information********************

From: csb@jax.org (Carolyn Blake)
Organization: The Jackson Laboratory, Bar Harbor, ME 04609

Mapmaker is available for other 'not fancy' systems as well. We have it running
under UNIX with no fancy graphics capabilities.

You may also wish to contact Dr. Alan Hillyard (alh@morgan.jax.org). He
maintains GBase, a linkage map database of the mouse, and is currently working
on databases of linkage maps for other species.
********************************************************************************

From: "Gunnell, Mark" <gunnell@fcrfv1.ncifcrf.gov>

We are currently running MapMaker version 1.9 under VMS version 5.4-2, and it
does not require anything beyond standard ascii terminals.  We obtained the
package from:

	MAPMAKER
	Dr. Eric Lander
	Whitehead Institute
	9 Cambridge Center
	Cambridge, MA 02142
	mapm%mitwibr@mitvma.mit.edu
From: dmerberg@GENETICS.COM
Newsgroups: bionet.software
Subject: Re: Gribskov's profile method: ?'s (also posted w/ INFO-GCG)
Date: 16 Apr 92 15:33:26 GMT
Article-I.D.: genetics.9204161533.AA00298
Distribution: bionet

Hello out there,

Steve Thompson writes:


>for Washington State University.  I am very impressed with its power and
>elegance and have assembled and analyzed many profiles for the various
>researchers that I work with.  However, I perceive a sorely lacking aspect of
>the method in the absence of an algorithm for performing local dynamic
>programming methods between two different profiles.

I have also found profile analysis very powerful in revealing novel
relationships between proteins.  And I have also thought it would be
useful to compare profiles in a quantitative way.  There was a program,
PRALI, by Martin Vingron (CABIOS 1989, 5:115-121) which aligned groups
of aligned sequences quite nicely.  However, it is not in GCG style and
might require too much massaging of sequences between formats for many
people.  Also I'm not sure whether Martin is still distributing it.  A
GCG style program that aligned profiles (or perhaps more conveniently,
aligned MSF files) would be a valuable contribution.  I think I could
write such a beast although there are probably others out there who
could devote more time to it and produce one faster.  If I don't hear
that someone is actively working on one I'll have a try at it.


> is anyone
>or is any archive interested in these profiles as I develop them?  It seems a
>shame to only have them available to the WSU academic community.  Naturally, if
>any of them were to be utilized in anybody's research I would expect
>acknowledgements.  I presently have more than a dozen "high-quality" profiles
>prepared apart from the library already utilized by ProfileScan and am creating
>new ones all of the time.

The more good profiles available the more powerful the technology is. 
I would certainly be interested in having additional profiles in the
library.  Perhaps an archive curator would like to start a collection
from various sources.

Dave Merberg
Genetics Institute
dmerberg@genetics.com
Xref: sparky bionet.software:768 bionet.molbio.methds-reagnts:739
From: djt2@po.CWRU.Edu (Dennis J. Templeton)
Newsgroups: bionet.software,bionet.molbio.methds-reagnts
Subject: NIH grant templates (PHS398) for Mac Word and Excel available
Date: 15 Apr 92 16:00:48 GMT
Reply-To: djt2@po.CWRU.Edu (Dennis J. Templeton)
Organization: Case Western Reserve University, Cleveland, OH (USA)


After asking around if anyone had updated templates for the revised NIH 
grant form PHS398, and getting no responses (but many requests to pass 
them along when I found them), I finally made the revisions myself.

I have posted a file containing these Word 4/5 and Excel 2.2 files to the
newsgroup bionet.resources.  Download this file, un Binhex (4.0) and
UnStuff to use.  

Good Luck,

Dennis Templeton

P.S.  I don't have the DOS equivalent to these files, but the Word template
could be saved in Word for Win format and may retain the proper formatting.