From owner-software@net.bio.net Sat Feb 01 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!news.voicenet.com!news From: "George A. Heavner" Newsgroups: bionet.software Subject: Re: Short seq search? Date: Sat, 01 Feb 1997 20:41:39 -0500 Organization: Voicenet - Internet Access - (215)674-9290 Lines: 10 Message-ID: <32F3F0D3.2F14@voicenet.com> References: <32F371F8.71B1@usfca.edu> NNTP-Posting-Host: paoli26-pri.voicenet.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (WinNT; U) Chihara wrote: > > Is there a program that will search genbank or prosite etc. for short > amino acid sequnces? i.e. 5-7 residues? > Thanks Try a BLAST search at http://www.ncbi.nlm.nih.gov/BLAST/ George A. Heavner From owner-software@net.bio.net Sat Feb 01 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!www.nntp.primenet.com!nntp.primenet.com!news.maxwell.syr.edu!insync!Gamma.RU!srcc!news.rcom.ru!infopro!not-for-mail From: "Ekaterina E. Mikhailova" Newsgroups: bionet.software,bionet.molec-model Subject: Re: Program for molecular modeling. Date: 2 Feb 1997 05:17:02 GMT Organization: WinWare Lines: 36 Message-ID: <01bc10c8$6cf79600$7601f2c3@any.rcom.spb.su> References: <32ECCC08.7352@rockvax.rockefeller.edu> NNTP-Posting-Host: dialup-118.infopro.spb.su X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.software:17763 bionet.molec-model:1350 Roberto Sanchez wrote in article <32ECCC08.7352@rockvax.rockefeller.edu>... > Panapat Uawithya wrote: > > > > Dear all, > > I wold like to know the name of the software other than from MSI and > > Waht_if. Are there any that can do molecular modeling for protein? > > Have a look at our page for MODELLER at : > > http://guitar.rockefeller.edu/modeller/modeller.html > > Modeller is a protein modeling program mainly used in comparative > modeling. It is free to academics. > > best wishes, > > Roberto Hi! Dear Panapat! Probably, the program that you are looking for is on the http://www.scivision.com It is called SciProtein for Alchemy 2000 Alexei Leznikov alex@isc.nw.ru Winware Unlimited St. Petersburg RUSSIA From owner-software@net.bio.net Sat Feb 01 22:00:00 1997 Path: biosci!agate!spool.mu.edu!howland.erols.net!usenet.kornet.nm.kr!ames!purdue!oitnews.harvard.edu!news From: Robin Colgrove Newsgroups: bionet.software Subject: Re: Short seq search? Date: Sat, 01 Feb 1997 23:02:29 -0500 Organization: Beth Israel Hospital, Harvard Medical School Lines: 7 Message-ID: <32F411CC.543E@louis.bidmc.harvard.edu> References: <32F371F8.71B1@usfca.edu> Reply-To: robin@louis.bidmc.harvard.edu NNTP-Posting-Host: louis.bidmc.harvard.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) I wrote such a program back in the mid 80's before the "blast" era. It's in C. I haven't thought mouch about it since there are so many net tools around these days but if it would be useful, I can dig it our and post it. robin colgrove From owner-software@net.bio.net Sat Feb 01 22:00:00 1997 Path: biosci!agate!howland.erols.net!vixen.cso.uiuc.edu!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.software Subject: Software/code to search for palindromes? Date: 2 Feb 1997 01:53:34 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 21 Message-ID: Reply-To: aiyar@ebv.oncology.wisc.edu NNTP-Posting-Host: ebv.oncology.wisc.edu X-Newsreader: slrn (0.9.2.1 BETA UNIX) I am looking for C/C++ source, or a compiled binary that will let me search through sequences for perfect or imperfect palindromes. If only a binary is available, it must run under one of the following OSes: IRIX DOS Windows MacOS Linux Digital Unix Thank you, Ashok -- Ashok Aiyar, Ph.D. McArdle Laboratory for Cancer Research aiyar@ebv.oncology.wisc.edu From owner-software@net.bio.net Sat Feb 01 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!newsfeeds.sol.net!hunter.premier.net!www.nntp.primenet.com!nntp.primenet.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!su-news-feed4.bbnplanet.com!jeeves.usfca.edu!news From: Chihara Newsgroups: bionet.software Subject: Short seq search? Date: Sat, 01 Feb 1997 16:40:24 +0000 Organization: University of San Francisco Lines: 3 Message-ID: <32F371F8.71B1@usfca.edu> Reply-To: chihara@usfca.edu NNTP-Posting-Host: annex41.usfca.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Macintosh; I; 68K) Is there a program that will search genbank or prosite etc. for short amino acid sequnces? i.e. 5-7 residues? Thanks From owner-software@net.bio.net Sun Feb 02 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!howland.erols.net!news.nacamar.de!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: Short seq search? Date: 3 Feb 1997 00:47:07 GMT Organization: University of Wuerzburg, Germany Lines: 17 Message-ID: <5d3cib$7ep@winx03.informatik.uni-wuerzburg.de> References: <32F371F8.71B1@usfca.edu> <32F3F0D3.2F14@voicenet.com> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] George A. Heavner (gheavner@voicenet.com) wrote: > Chihara wrote: > > Is there a program that will search genbank or prosite etc. for short > > amino acid sequnces? i.e. 5-7 residues? > > Try a BLAST search at http://www.ncbi.nlm.nih.gov/BLAST/ BLAST usually doesn't work with short query sequences because the alignment produced is not significant. However, FASTA searches work fine. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Sun Feb 02 22:00:00 1997 Path: biosci!daresbury!yama.mcc.ac.uk!hydraulix.bangor.ac.uk!thunder!bss194 From: bss194@thunder (K.James) Newsgroups: bionet.software Subject: Re: Oligonucleotide databases Date: 3 Feb 1997 11:03:30 GMT Organization: University of Wales, Bangor. Lines: 29 Message-ID: <5d4gm2$l8n@hydraulix.bangor.ac.uk> References: <32F21D41.66AB@anl.gov> NNTP-Posting-Host: thunder.bangor.ac.uk X-Newsreader: TIN [version 1.2 PL2] James Akowski (akowski@anl.gov) wrote: : Hello, : Does anyone know of software for cataloging/organizing : oligonucleotides? I want to start a database before the number of : oligos in our lab gets too large. We have Excel and QuatroPro but I do : not wish to spend time learning these - I would appreciate any pointers : to existing templates/front-ends for these programs or any other PC or : Unix database software for oligonucleotides. Being in the same position a year ago I wrote some VBA code in Excel to do this. You are welcome to a copy if you want it. Its main limitations are that it stores the details as a flat file within the spreadsheet, no relational database this one! Also it has no special printout option to dump a search result to the printer. It stores name, sequence, owner, design method, date etc. and maintains the list's integrity by indexing on the oligo name i.e. when you enter a new oligo it won't let you give it the same name as an existing one. It will also ensure certain information is entered. Data is entered using a dialog with dropdowns for designer, supplier, date and so on. Searching uses Excel's own search dialogs. -- Keith James Ph.D. - k.james@bangor.ac.uk PGP 2.6.2i Key ID 469A9FA1 Biodegradation Group *Encrypt and Survive* School of Biological Sciences Nightmare: Quake me up now! University of Wales, Bangor, UK -------http://oracle.bangor.ac.uk/sbs/research/biodegradation/------- From owner-software@net.bio.net Sun Feb 02 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!hermod.uio.no!nntp.uio.no!newsfeeds.sol.net!newspump.sol.net!howland.erols.net!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in3.uu.net!137.208.127.3!newsfeed.wu-wien.ac.at!usenet From: bunka@i112pc09.vu-wien.ac.at (Sebastian Bunka) Newsgroups: bionet.software Subject: Re: Looking for BOB Date: 3 Feb 1997 09:52:12 GMT Organization: Vet. University Vienna Lines: 23 Message-ID: <5d4cgc$id@cantine.wu-wien.ac.at> References: NNTP-Posting-Host: i112pc09.vu-wien.ac.at Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 0.9.8 In article , m.mitchell@icrf.icnet.uk (Mike Mitchell) writes: > I am trying to find a source for BOB, the Blast Output Browser. Can any one > help? > You can check for the source of tbob, a blast output parser: Host bioinformatics.weizmann.ac.il Location: /pub/software/unix FILE -r--r--r-- 25842 May 30 1994 tbob.tar.gz SWB -- ;-) ------------------------------------------------------------------------ Sebastian Bunka ph. (+43-1) 250 77 4208 Institute of FAX (+43-1) 250 77 4290 Medical Chemistry email: Sebastian.Bunka@vu-wien.ac.at University of Veterinary Medicine - Vienna - Austria ------------------------------------------------------------------------ From owner-software@net.bio.net Sun Feb 02 22:00:00 1997 Newsgroups: bionet.software Path: biosci!agate!spool.mu.edu!howland.erols.net!news.sprintlink.net!news-peer.sprintlink.net!rill.news.pipex.net!pipex!uknet!usenet1.news.uk.psi.net!uknet!uknet!newsfeed.ed.ac.uk!leeds.ac.uk!news From: bmb5meb@bmb.leeds.ac.uk (M E Beck) Subject: Re: MS Word to HTML converter Message-ID: <32F5EB0E.41C6@bmb.leeds.ac.uk> NNTP-Posting-Host: bmbsgi11.leeds.ac.uk X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP22) Content-Type: text/plain; charset=us-ascii Organization: University of Leeds MIME-Version: 1.0 Date: Mon, 3 Feb 1997 13:41:42 +0000 (GMT) References: <32F0B4DD.41C6@bmb.leeds.ac.uk> <32f3edce.6348911@news.uhura.minet.net> Lines: 32 Content-Transfer-Encoding: 7bit Thanks for everyone's help on this. I've tried Internet Assistant and it does exactly what I want, saving me from a lot of HTML coding! :) Mike. Russell Holliman wrote: > > Have you tried Microsoft's Internet Assistant for Word? Have not tried > it myself, but it is supposed to be a (free) add-in for word that lets > you save the document directly to an HTML file from within word. > > You can download it from their web site at: > http://www.microsoft.com/word/internet/ia/ > > Hope this helps. > > Russell Holliman > > On Thu, 30 Jan 1997 14:50:18 +0000 (GMT), bmb5meb@bmb.leeds.ac.uk (M E > Beck) wrote: > > >Hi there, > > > >I'm trying to create some online documentation which is currently in > >MS Word format. Does anyone know of any freely available conversion > >program which will convert from this format to HTML, keeping as much of > >the formatting (bold type, italics, etc.) as possible? > > > >All help appreciated, > > > >Mike. > > From owner-software@net.bio.net Sun Feb 02 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Richard Cooke Newsgroups: bionet.software Subject: Re: Looking for BOB Date: 3 Feb 1997 14:51:24 -0000 Lines: 30 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5d4u1c$4m2@mserv1.dl.ac.uk> X-Sender: cooke@gala.univ-perp.fr Original-To: bio-software@dl.ac.uk In article , m.mitchell@icrf.icnet.uk (Mike Mitchell) wrote: > I am trying to find a source for BOB, the Blast Output Browser. Can any one > help? > There used to be a graphical interface called BOB at ftp://milo.dcrt.nih.gov/pub. The source is available as well as executables for a fair number of platforms but I don't know if it has been updated to read more recent BLAST output. Andy (big nose) Law replied: >I've written a Macintosh version. Is that a graphical Mac version, Andy? Is it available? Richard Cooke (medium-sized nose in Edinburgh some time ago) Richard Cooke LPBMP UMR5545 CNRS UNIVERSITE DE PERPIGNAN FRANCE Tel: +33 (0)468662131 Fax: +33 (0)468668499 cooke@univ-perp.fr From owner-software@net.bio.net Sun Feb 02 22:00:00 1997 Path: biosci!angis.su.OZ.AU!tim From: tim@angis.su.OZ.AU (Tim Littlejohn) Newsgroups: bionet.software Subject: Re: Looking for BOB Date: 3 Feb 1997 02:30:32 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <5d4cgc$id@cantine.wu-wien.ac.at> NNTP-Posting-Host: net.bio.net The original distribution site for tbob is from the Canadian Organelle Genome Program's site at: http://megasun.bch.umontreal.ca/abouttb.html Cheers, Tim Littlejohn -------------------------------------------------------------------------- | ANGIS- The Australian National Genomic Information Service | | http://www.angis.su.oz.au email: tim@angis.su.oz.au | | Phone Toll Free: 1 800 728 028 FAX: 61-2-9351 2948 | -------------------------------------------------------------------------- From owner-software@net.bio.net Sun Feb 02 22:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!Andy.Law From: Andy.Law@bbsrc.ac.uk (Andy Law) Newsgroups: bionet.software Subject: Re: Looking for BOB Date: Mon, 03 Feb 1997 09:47:11 +0000 Organization: Roslin Institute Lines: 18 Message-ID: References: NNTP-Posting-Host: pc0734.ri.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.4 In article , m.mitchell@icrf.icnet.uk (Mike Mitchell) wrote: > I am trying to find a source for BOB, the Blast Output Browser. Can any one > help? > I've written a Macintosh version. I think you can get tbob at ftp.ebi.ac.uk (/pub/software/unix ??). I'm not sure if BOB was there though. Later, Andy Law ------------------ ( Andy.Law@bbsrc.ac.uk ) ( Big Nose in Edinburgh ) From owner-software@net.bio.net Sun Feb 02 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!sn.no!www.nntp.primenet.com!nntp.primenet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in3.uu.net!198.168.54.138!rcogate.rco.qc.ca!altitude!usenet From: Xuefeng Yu Newsgroups: bionet.software Subject: experimental design software Date: Mon, 03 Feb 1997 10:41:05 -0500 Organization: Communications Accessibles Montreal, Quebec Canada Lines: 3 Message-ID: <32F60710.74C1@ibex.ca> NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; 68K) I'm looking for statistical experimental design software for Mac or Windows. If anybody know where I can find a good one please let me know. My email address is yuxu@ibex.ca From owner-software@net.bio.net Sun Feb 02 22:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!ermine.ox.ac.uk!enriquez From: Pita Enriquez Harris Newsgroups: bionet.software Subject: Plasmid drawing software for PC?? Date: Mon, 3 Feb 1997 14:07:01 +0000 Organization: Oxford University Lines: 18 Message-ID: NNTP-Posting-Host: ermine.ox.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone know of a good program for drawing/managing DNA constructs on a PC? If you know of where I can get a free download of a demo, that would be especially helpful! Thanks, Pita ****************************************************************************** Dr. Pita Enriquez Harris "Waste no more time arguing what a Nuffield Department of Medicine good man should be. Be one." Oxford Radcliffe Hospital Marcus Aurelius http://users.ox.ac.uk/~enriquez ****************************************************************************** From owner-software@net.bio.net Mon Feb 03 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!www.nntp.primenet.com!nntp.primenet.com!cs.utexas.edu!news.unt.edu!news From: "C. J. Fields" Newsgroups: bionet.software Subject: Re: Plasmid drawing software for PC?? Date: Tue, 04 Feb 1997 00:12:05 -0600 Organization: University of North Texas Lines: 36 Message-ID: <32F6D335.69D3@gab.unt.edu> References: Reply-To: cfields@gab.unt.edu NNTP-Posting-Host: den1-2-24.dialup.unt.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Pita Enriquez Harris wrote: > > Does anyone know of a good program for drawing/managing DNA constructs on > a PC? > > If you know of where I can get a free download of a demo, that would be > especially helpful! > > Thanks, > Pita Try Don Gilbert's excellent IUBIO archive at: gopher://fly.bio.indiana.edu:70/11/IUBio-Software%2bData It should be under molecular biology in ibmpc. VNTI has a great demo, and I think a few others may be floating around (Plasmid Toolkit is a more affordable one). I believe there are ftp and html links as well, if you don't like gophers. -- C. J. Fields Graduate Student, Dept. of Biological Sciences The University of North Texas Denton, TX email : cfields@gab.unt.edu \\\\\\\\\\\\\\\\\\\\oooooooooooooooo//////////////////// "Giving money and power to government is like giving whiskey and car keys to teenage boys" -P. J. O'Rourke "Join the military. Travel to exotic places, meet exciting people, then kill them" -Anonymous ////////////////////oooooooooooooooo\\\\\\\\\\\\\\\\\\\\ From owner-software@net.bio.net Mon Feb 03 22:00:00 1997 Path: biosci!agate!howland.erols.net!surfnet.nl!news.unisource.nl!xs4all!not-for-mail From: marker@xs4all.nl (Niels Groot) Newsgroups: bionet.software Subject: Re: Plasmid drawing software for PC?? Date: 4 Feb 1997 06:35:10 GMT Organization: XS4ALL, networking for the masses Lines: 30 Message-ID: <5d6lau$cuo$1@news1.xs4all.nl> References: NNTP-Posting-Host: news.xs4all.nl Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-XS4ALL-Date: Tue, 04 Feb 1997 07:35:10 CET X-Newsreader: WinVN 0.99.7 In article , enriquez@ermine.ox.ac.uk says... > > > >Does anyone know of a good program for drawing/managing DNA constructs on >a PC? > >If you know of where I can get a free download of a demo, that would be >especially helpful! > >Thanks, >Pita you could take a look at SeqSearch v1.1 at http://www.xs4all.nl/~marker -multi user -multi sequence database including contructs -restriction site analyis -mismatch primer design -clone bench -silent mutagenesis analysis -mutagenic primer design -hydrophobicity plots -DNA consensus search regards Niels marker@xs4all.nl From owner-software@net.bio.net Mon Feb 03 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!Oslo2.Norway.EU.net!Norway.EU.net!nntp.uio.no!news.maxwell.syr.edu!news.bc.net!unixg.ubc.ca!info.ucla.edu!ihnp4.ucsd.edu!news.service.uci.edu!mangalam From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software,bionet.molbio.methds-reagnts Subject: Re: Restriction Enzymes in DNA Strider? Date: Tue, 04 Feb 1997 14:52:21 -0800 Organization: Dev+Cell Biology, UC Irvine Lines: 53 Message-ID: References: NNTP-Posting-Host: skink.bio.uci.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 Xref: biosci bionet.software:17786 bionet.molbio.methds-reagnts:54367 In article , nc1@acpub.duke.edu (Namjin Chung) wrote: > I use the above software for some sequence processing, and I think it's > simple but very good software. The only one thing I'm not satisfied with > it is that it would not allow custom restriction by a selected set of > REs. While MacVector allows you to cut DNA with the enzyme set you > currently have, it is big and key-locked. > > Does anybody know how to solve this problem? TIA. You can solve this with DNA Strider by making subfiles of the enzymes that you want and renaming them "RELibrary" as you need them, although you'll have to restart Strider evey time you want to use another subset. Not a very elegant way of doing it, but it allows you to keep using the program you're used to. Most commercial sequence analysis apps allow you to specify subsets of enzymes by explicit groupings, or other characteristics, such as all 5' cutters, those that cut more or less than X times, those that recognize only sequences more than Y bases, etc. I've put a web interface on my *FREE* restriction enzyme analysis app 'tacg', and you can specify enzymes via overhang, magnitude of recognition sequence, number of cuts, explicit picks, subsets via different files (ie enzymes from different vendors, or sorted via price), etc, etc, etc. Also works with the transcription factor database, as a quick and dirty version of Dan Prestridge's 'signalscan'. Output is via linear map, 1/3/6 frames of translation in 1 or 3 letter code, pseudo-graphical ladder map and/or gel simulation, fragments (sorted or not), cut site, etc. It handles sequence into the millions of bases, if you have the RAM; it was designed for scanning genome sized chunks of DNA. The idea was to get Strider-like output for unix systems via a command-line program. It just happened that it's relatively easy to port it to the web, so I did. YOu can get a better idea about it by peeking at the web page: http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg.main.html the Web form is at: http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg.main.html If you use Netscape, you can upload files to it as well as using paste-in; I'm not sure about other browsers. Cheers Harry -- Harry J Mangalam, MolBio+Biochem / Dev+Cell Bio, Rm 4201, BioSciII UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 From owner-software@net.bio.net Mon Feb 03 22:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!Andy.Law From: Andy.Law@bbsrc.ac.uk (Andy Law) Newsgroups: bionet.software Subject: Re: Looking for BOB Date: Tue, 04 Feb 1997 09:39:12 +0000 Organization: Roslin Institute Lines: 40 Distribution: bionet Message-ID: References: <5d4u1c$4m2@mserv1.dl.ac.uk> NNTP-Posting-Host: pc0734.ri.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.4 > > Andy (big nose) Law replied: > > >I've written a Macintosh version. > > Is that a graphical Mac version, Andy? Is it available? > Yes, it is a graphical version. It puts the list of high scores in the top pane of a window and as you select different hits in that list, it displays the corresponding alignment in the lower pane. Its not quite finished (I'm working on an extra bit to allow you to pull the hit sequence via a Web browser link to an SRS server) and I have to go through a complex "permission to publish" procedure, but hopefully in the next couple of months. When you tie this together with Internet Config and another program that I wrote to filter the results automatically, you get quite an elegant system for those who prefer to use a Mac as their main machine i.e. Run Blasts on Unix Machine | Download to Mac by FTP | Internet Config hands off files ending '.blast' to Blast Filter | Blast Filter checks for significant hits | +--------------+--------------+ | | Significant Hits No Significant hits | MacBOB Andy Law ------------------ ( Andy.Law@bbsrc.ac.uk ) ( Big Nose in Edinburgh ) From owner-software@net.bio.net Mon Feb 03 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!howland.erols.net!ix.netcom.com!netcom.net.uk!amd-5x86-166mhz From: berrall@netcomuk.co.uk (Nick Berrall) Newsgroups: bionet.software Subject: Visit The Windows Goodies Website Date: Tue, 04 Feb 97 19:06:30 GMT Organization: NETCOM Internet Ltd. Lines: 9 Message-ID: <5d81b6$mfb$3@taliesin.netcom.net.uk> NNTP-Posting-Host: dialup-07-33.netcomuk.co.uk X-Newsreader: News Xpress 2.0 The Windows Goodies Website Please Visit The Windows Goodies Website for software, wallpaper images and wave files at http://www.geocities.com/SiliconValley/Pines/7030/index.html You can also pick up free Java scripts for your Homepages. From owner-software@net.bio.net Mon Feb 03 22:00:00 1997 Newsgroups: bionet.software Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!arclight.uoregon.edu!feed1.news.erols.com!howland.erols.net!vixen.cso.uiuc.edu!uchinews!ellis.uchicago.edu!cjenkins From: Cheryl Jenkins Subject: Need Help Learning Access X-Sender: cjenkins@ellis.uchicago.edu X-Nntp-Posting-Host: ellis.uchicago.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Message-ID: Sender: news@midway.uchicago.edu (News Administrator) Reply-To: Cheryl Jenkins Organization: University of Chicago -- Academic Computing Services Mime-Version: 1.0 Date: Tue, 4 Feb 1997 18:51:40 GMT Lines: 7 I just took an Access Class and I'm having problems. Is there a self-help book out there like "Access for Dummies" or something I can use as a learning tool at my own pace? Thanx. From owner-software@net.bio.net Mon Feb 03 22:00:00 1997 Path: biosci!BTBSOFTWARE.COM!bactbob From: bactbob@BTBSOFTWARE.COM (Bob Freeman) Newsgroups: bionet.software Subject: Free Chlamydia Software, expires 1-98 Date: 3 Feb 1997 22:01:50 -0800 Organization: BtB Software Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <32F6D0BB.1327@btbsoftware.com> NNTP-Posting-Host: net.bio.net Chlamydia software for the Abbott LCx and related systems: Includes Billing, searching, worksheets, rapid entry, lab slips, statistics. For more information,please see our web site and click on "free Chlamydia Software". The software will expire 1-1-98 -- Bob Freeman BtB Software PO Box 2215 El Centro, CA 92244-2215 Phone/Fax: 619-353-6623 http://www.btbsoftware.com/bactbob From owner-software@net.bio.net Mon Feb 03 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!howland.erols.net!quagga.ru.ac.za!ru.uni.net.za!uct.uni.net.za!uct.ac.za!news From: Ed Rybicki Newsgroups: bionet.software Subject: Re: Windows: sequence analysis Date: Tue, 04 Feb 1997 15:57:00 -0400 Organization: Microbiology Dept, Univ Cape Town Lines: 26 Message-ID: <32F7948C.79E@molbiol.uct.ac.za> References: <5cpibd$jnl$1@mark.ucdavis.edu> Reply-To: ed@molbiol.uct.ac.za NNTP-Posting-Host: 137.158.64.94 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win16; I) To: Zhaomin Yang Zhaomin Yang wrote: > > Hi, all, > > Wondering if someone can recommend a good sequence analysis program(s) for > Windows. I used to use Strider, but the lab I'm in now doesn't have Macs. > It would be great if the program can draw plasmid maps and can be used for > designing primers. > > Zhaomin Hi - we have recently started to use DNAMAN from Lynnon Biosoft up in Canada; it is remarkably full-featured (if a bit idiosyncratic), and will do multiple sequence alignment, translation, dna frag assembly, PCR primer and oligo design...it is also CHEAP ($260 or so). Works well under Win 3.1 and is LIGHTNING fast on even long sequence multiple alignments. Also does shading of alignments (another perennial q). -- Ed Rybicki, PhD Dept Microbiology | ed@molbiol.uct.ac.za University of Cape Town | rybicki@uctvms.uct.ac.za Private Bag, Rondebosch | phone: x27-21-650-3265 7700, South Africa | fax: x27-21-689 7573 WWW URL: http://www.uct.ac.za/microbiology/ed.html "Out here on the perimeter, there are no stars..." From owner-software@net.bio.net Mon Feb 03 22:00:00 1997 Newsgroups: bionet.software Path: biosci!agate!howland.erols.net!rill.news.pipex.net!pipex!warwick!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!news From: Heikki Lehvaslaiho Subject: Re: Looking for BOB Sender: news@ebi.ac.uk (usenet news) Message-ID: <32F5BEEB.41C6@ebi.ac.uk> Date: Mon, 3 Feb 1997 10:33:15 GMT Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii References: Mime-Version: 1.0 X-Mailer: Mozilla 3.0 (X11; I; IRIX64 6.2 IP19) Organization: EBI Lines: 22 Mike Mitchell wrote: > > I am trying to find a source for BOB, the Blast Output Browser. Can any one > help? TBOB is one of the products of OGMP - Organelle Genome Megasequencing Program (http://megasun.bch.umontreal.ca/ogmpproj.html) in Canada. You'll find the TBOB source and documentation from: gopher://megasun.bch.umontreal.ca/11/CMB/Databases/Blast/tbob/ -Heikki ______ _/ _/____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From owner-software@net.bio.net Mon Feb 03 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!status.gen.nz!news.express.co.nz!actrix.gen.nz!usenet From: lrollo@actrix.gen.nz (Lindsay Rollo) Newsgroups: bionet.software Subject: OCR for Scientific/Engineering Material Date: Tue, 04 Feb 1997 20:24:48 GMT Organization: Actrix Networks Limited Lines: 19 Message-ID: <33019af7.9747175@news.actrix.gen.nz> NNTP-Posting-Host: lrollo.actrix.gen.nz Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent .99g/32.339 I am trying to identify OCR software that specifically caters for scientific, engineering and other technical special requirements. In particular I'm interested in software that: [1] allows bulk additions to the program's dictionary to allow the rapid inclusion of specialist vocabularies; [2} provides drop down boxes of user-selected special characters to permit immediate entry of both special symbols and characters commonly used in scientific and technical disciplines, eg, the superscript symbol to denote degrees of temperature. If anyone has experience of this type of data or information capture I'd be very pleased to receive e-mails. Lindsay J Rollo lrollo@actrix.gen.nz Wellington, New Zealand From owner-software@net.bio.net Mon Feb 03 22:00:00 1997 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!arclight.uoregon.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!howland.erols.net!cs.utexas.edu!newshost.convex.com!newsgate.duke.edu!phanes94.mc.duke.edu!user From: nc1@acpub.duke.edu (Namjin Chung) Newsgroups: bionet.software,bionet.molbio.methds-reagnts Subject: Restriction Enzymes in DNA Strider? Date: 4 Feb 1997 16:28:10 GMT Organization: Duke University Medical Center Lines: 15 Message-ID: NNTP-Posting-Host: phanes94.mc.duke.edu Xref: biosci bionet.software:17782 bionet.molbio.methds-reagnts:54352 Dear DNA Strider Users: I use the above software for some sequence processing, and I think it's simple but very good software. The only one thing I'm not satisfied with it is that it would not allow custom restriction by a selected set of REs. While MacVector allows you to cut DNA with the enzyme set you currently have, it is big and key-locked. Does anybody know how to solve this problem? TIA. Namjin Chung, who knows little and asks a lot! Program in Molecular Cancer Biology Duke University Medical Center Durham, North Carolina From owner-software@net.bio.net Mon Feb 03 22:00:00 1997 Newsgroups: bionet.software Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!Norway.EU.net!EU.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!strath-cs!dcl-cs!bath.ac.uk!bspwrb From: bspwrb@bath.ac.uk (W R Bennett) Subject: Male and female symbols in Microsoft Word Organization: School of Biological Sciences, University of Bath, UK Message-ID: Date: Mon, 3 Feb 1997 23:46:04 GMT Lines: 16 Hi, Does anyone know if there exist male and female symbols lurking in some obscure corner of Word 7.0 for Win95? This would be rather useful for writing papers on mouse genetics, but four of us have now wasted hours rummaging through the fonts to no avail. Can anyone help? Many thanks, Bill Bennett Developmental Biology Unit, School of Biology and Biochemistry University of Bath bspwrb@bath.ac.uk From owner-software@net.bio.net Tue Feb 04 22:00:00 1997 Path: biosci!BGUMAIL.BGU.AC.IL!aflaloc From: aflaloc@BGUMAIL.BGU.AC.IL (Claude Aflalo) Newsgroups: bionet.software Subject: Re: Restriction Enzymes in DNA Strider? Date: 4 Feb 1997 23:34:34 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 78 Sender: daemon@net.bio.net Distribution: world Message-ID: References: NNTP-Posting-Host: net.bio.net On 4 Feb 1997, Namjin Chung wrote: > Dear DNA Strider Users: > > I use the above software for some sequence processing, and I think it's > simple but very good software. The only one thing I'm not satisfied with > it is that it would not allow custom restriction by a selected set of > REs. While MacVector allows you to cut DNA with the enzyme set you > currently have, it is big and key-locked. > > Does anybody know how to solve this problem? TIA. > > > Namjin Chung, who knows little and asks a lot! > Program in Molecular Cancer Biology > Duke University Medical Center > Durham, North Carolina > Here is a tips collection which will answer that To select one or a few enzymes on strider: Hold down the option key when selecting digest, or graphic map. This will bring up another menu. At the bottom of the menu there is a choice between triple, double, unique, or none. Select none. To select a specific enzyme, click on individual enzymes in the enzyme list. To select more than one, hold down the aplle (command?) key while selecting the enzyme. _____________________________________ : In article , : jpcd0@mole.bio.cam.ac.uk (John Dixon) writes: : > P.S. BTW, does anyone know if it is possible to deselect enzymes : > when generating a full restriction map, to avoid the huge stacks of : > four cutters above the sequence and the enormous list of tiddly : > fragments in the site analysis below? : : The only way I know of doing this is to delete enzymes manually from your : RE : data file. In the same way, you can add new enzymes. : : - I tried modifying this file when I had the original problem, using : the word processor that it was originally created in, and had problems : with Strider crashing. Do you have any hints about how to modify it? : e.g. What word processor/editor do you use, and what format do you : choose to save it in? I have problems editing the RE library file. I just load it into SimpleText or Teachtext (its predecessor) and edit away. The format goes like:- Spe I, a/ctagt, Sph I, gcatg/c, Taq I, t/cga, (etc) %%%%%% ; comment comment comment This could also be done in a word processor such as Word as long as you save it in plain text (ASCII). Niggle/Problem The only problem arises with the fact that I want 2 RE libraries, one for all the enzymes in the freezer and one for all those we could buy if needed (ie the NEB one supplied. I keep these as two files "RE library NEB" and "RE library -20". To use one of these erase "RE library", I duplicate the desired file, rename that duplicate "RE library" and run Strider. ----------------------------- Claude Aflalo ######################## Phones: Office 972-7-6472118 #### Dept. of Life Sciences Lab 972-7-6472119 Ben Gurion University of the Negev Fax 972-7-6472890 P.O.Box 653 email: aflaloc@bgumail.bgu.ac.il Beer Sheva 84105 Israel URL: http://www.bgu.ac.il/life/aflalo.html From owner-software@net.bio.net Tue Feb 04 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!cpk-news-feed2.bbnplanet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!howland.erols.net!usc!comserv-g-01.usc.edu!user From: t@hsc.edu Newsgroups: bionet.software Subject: Re: Restriction Enzymes in DNA Strider? Date: Tue, 04 Feb 1997 21:01:03 +0100 Organization: University of Southern California, Los Angeles, CA Lines: 28 Sender: tianjian@comserv-g-01.usc.edu Message-ID: References: NNTP-Posting-Host: comserv-g-01.usc.edu Dear Chung: DNA Strider has the function for you to select a set of enzymes. Just hold the "Option" and select the "graphic Map" within the "Enz". Then, select the enzyme names (by hold "shift" to do multiple selection). Try it. Tian-Jian Chen Fellow in Clinic Molecular Genetics CHLA In article , nc1@acpub.duke.edu (Namjin Chung) wrote: > Dear DNA Strider Users: > > I use the above software for some sequence processing, and I think it's > simple but very good software. The only one thing I'm not satisfied with > it is that it would not allow custom restriction by a selected set of > REs. While MacVector allows you to cut DNA with the enzyme set you > currently have, it is big and key-locked. > > Does anybody know how to solve this problem? TIA. > > > Namjin Chung, who knows little and asks a lot! > Program in Molecular Cancer Biology > Duke University Medical Center > Durham, North Carolina From owner-software@net.bio.net Tue Feb 04 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeeds.sol.net!europa.clark.net!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!cpk-news-feed1.bbnplanet.com!uky.edu!usenet From: yliu0@pop.uky.edu Newsgroups: bionet.software Subject: Re: Male and female symbols in Microsoft Word Date: Wed, 05 Feb 1997 09:20:51 GMT Organization: University of Kentucky Computing Services Lines: 38 Message-ID: <5d98ut$i6e@service3.uky.edu> References: NNTP-Posting-Host: node-01-10.dialin.uky.edu X-Newsreader: Forte Free Agent 1.0.82 It is inside word 7.0. Go to menu "insert" -> "symbol". From font list choose "CommonBullets", male and female symbols are inside. ---------------------------------------------------------------------------- Department of Chemistry Phone :(606) 254-9375 University of Kentucky LIU YUE Email : yliu0@pop.uky.edu --------------------------------------------------------------------------- HOMEPAGE Personal:sac.uky.edu/~yliu0 Software:www.engr.uky.edu/~yliu0 --------------------------------------------------------------------------- bspwrb@bath.ac.uk (W R Bennett) wrote: >Hi, >Does anyone know if there exist male and female symbols lurking in some >obscure corner of Word 7.0 for Win95? This would be rather useful for >writing papers on mouse genetics, but four of us have now wasted hours >rummaging through the fonts to no avail. Can anyone help? >Many thanks, >Bill Bennett >Developmental Biology Unit, School of Biology and Biochemistry >University of Bath >bspwrb@bath.ac.uk From owner-software@net.bio.net Tue Feb 04 22:00:00 1997 Path: biosci!rutgers!news.columbia.edu!panix!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in2.uu.net!204.238.120.21!jump.net!grunt.dejanews.com!not-for-mail Date: Wed, 05 Feb 1997 12:11:06 -0600 From: sxr3008@megahertz.njit.edu Subject: ms word to html Newsgroups: alt.hypertext,alt.windows95,alt.html,bionet.software Message-ID: <855165652.25149@dejanews.com> Organization: New Jersey Institute of Technology To: sxr3008@megahertz.njit.edu http: //megahertz.njit.edu/~sxr3008 X-Article-Creation-Date: Wed Feb 05 18:00:52 1997 GMT X-Originating-IP-Addr: 128.235.228.144 (ppp-228-144.njit.edu) X-Http-User-Agent: Mozilla/3.01Gold (Win95; I) X-Authenticated-Sender: sxr3008@megahertz.njit.edu Lines: 13 Hi, there: I am trying to write my own word-to-html converter. But I don't know how the MS word's .doc file is formated. There must be some format specification like html's tags or DTD. But I have no idea where to find it out. Can anybody give some hints? TIA. Shaomei -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-software@net.bio.net Tue Feb 04 22:00:00 1997 Path: biosci!UCONNVM.UCONN.EDU!knecht From: knecht@UCONNVM.UCONN.EDU (David Knecht) Newsgroups: bionet.software Subject: Seqvu Date: 5 Feb 1997 09:16:55 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net We have found Seqvu to be an excellent companion to Clustal in terms of viewing and manipulating sequence alignments on the Macintosh. When I tried to register the program, the Garvan INstitute (Sydney, AU, which claims responsibility on the splash screen) either no longer exists or no longer supports the program. Does anyone know if someone is supporting it? Is there a good alternative anyone knows of for viewing and tweeking alignments? Thanks- Dave Dr. David Knecht Department of Molecular and Cell Biology University of Connecticut U-125 Storrs, CT 06269 Knecht@uconnvm.uconn.edu From owner-software@net.bio.net Tue Feb 04 22:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!worldnet.att.net!news.maxwell.syr.edu!news.bc.net!uvaix3e1.comp.UVic.CA!hera.bioc.uvic.ca!cupton From: cupton@uvic.ca (Chris Upton) Newsgroups: bionet.molbio.proteins,bionet.software Subject: pI calculation Followup-To: bionet.molbio.proteins Date: Wed, 5 Feb 97 00:49:28 GMT Organization: University of Victoria Lines: 22 Message-ID: NNTP-Posting-Host: hera.bioc.uvic.ca X-Newsreader: VersaTerm Link v1.1.6 Xref: biosci bionet.molbio.proteins:9910 bionet.software:17787 Hi, I'm looking for a way to query a protein database (eg Swiss-Prot) by pI. ie get all proteins with pI > 8. I'm not sure if there's programs to allow calc of pI for all proteins in the database. I guess output file could be large :-) Then I might want to sort them.... Hmm, alternatively it would be nice to at least be able to get the pI for 1-200 proteins. Is there anything that will allow batch processing? I seem to think I did this in the very distant past with 200 proteins, either with GCG or IG. Any advice appreciated.... Cheers, Chris Upton Chris Upton Biochemistry & Microbiology University of Victoria phone 250-721-6507 BC Canada fax 250-721-8855 From owner-software@net.bio.net Tue Feb 04 22:00:00 1997 Path: biosci!rutgers!uwm.edu!news-peer.gsl.net!news.gsl.net!mr.net!newshub.tc.umn.edu!lynx.unm.edu!bubba.NMSU.Edu!usenet From: "Donald D. Bustamante" Newsgroups: bionet.software Subject: Re: Male and female symbols in Microsoft Word Date: Tue, 04 Feb 1997 10:10:13 -0800 Organization: National Biotechnology Information Facility Lines: 28 Message-ID: <32F77B85.FFC@psl.nmsu.edu> References: NNTP-Posting-Host: 128.123.33.156 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (WinNT; I) W R Bennett wrote: > > Hi, > > Does anyone know if there exist male and female symbols lurking in some > obscure corner of Word 7.0 for Win95? This would be rather useful for > writing papers on mouse genetics, but four of us have now wasted hours > rummaging through the fonts to no avail. Can anyone help? > > Many thanks, > > Bill Bennett > Developmental Biology Unit, School of Biology and Biochemistry > University of Bath > > bspwrb@bath.ac.uk Select "Insert" from the pull down menu, then symbol. Change the font to "Bookshelf Symbol 3" -- Donald D. Bustamante, Project Manager National Biotechnology Information Facility Physical Science Laboratory Box 30002, Dept. 3548 Las Cruces, New Mexico USA 88003 (505)-522-9209 FAX: (505)-522-9434 URL: http://www.nbif.org From owner-software@net.bio.net Tue Feb 04 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!sn.no!nntp.uio.no!newsfeeds.sol.net!feed1.news.erols.com!howland.erols.net!surfnet.nl!newsfeed.sunet.se!news01.sunet.se!sunic!02-newsfeed.univie.ac.at!03-newsfeed.univie.ac.at!news.univie.ac.at!news-admin@univie.ac.at From: "Gunther Rezniczek" Newsgroups: bionet.software Subject: Re: Plasmid drawing software for PC?? Date: 5 Feb 1997 10:58:56 GMT Organization: University of Vienna Lines: 26 Message-ID: <01bc1353$94c9d5c0$48518283@Vectra-5122-CBL.abc.univie.ac.at> References: NNTP-Posting-Host: vectra-5122-cbl.abc.univie.ac.at X-Newsreader: Microsoft Internet News 4.70.1155 Pita Enriquez Harris wrote in article ... > > > Does anyone know of a good program for drawing/managing DNA constructs on > a PC? > > If you know of where I can get a free download of a demo, that would be > especially helpful! > > Thanks, > Pita There is a program called WinPlas 2.5 from Rich Goldstein. It is easy to use and produces good output. A demo can be downloaded from the web ... I can't remember the URL, but just search the net for WinPlas and/or Goldstein and you should have no trouble. Hope this helps, Gunther. From owner-software@net.bio.net Tue Feb 04 22:00:00 1997 Path: biosci!BGUMAIL.BGU.AC.IL!raveh From: raveh@BGUMAIL.BGU.AC.IL (Dina Raveh BGU) Newsgroups: bionet.software Subject: (none) Date: 5 Feb 1997 01:38:18 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net subscribe bio-soft@net.bio.net ********************************** Dina Raveh Department of Life Sciences Ben Gurion University of the Negev Beersheva, 84105 Israel Tel. 972-7-6461371 Fax. 972-7-6472992 From owner-software@net.bio.net Tue Feb 04 22:00:00 1997 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!news-xfer.netaxs.com!news.maxwell.syr.edu!news.bc.net!torn!butler.ac.BrockU.CA!mcuggy From: mcuggy@PROBLEM_WITH_INEWS_GATEWAY_FILE (Michael Cuggy) Newsgroups: bionet.software Subject: rarefraction Date: 5 Feb 1997 20:49:18 GMT Organization: Brock University Lines: 4 Message-ID: <5darof$6ve@butler.ac.BrockU.CA> NNTP-Posting-Host: craton.geol.brocku.ca X-Newsreader: TIN [version 1.2 PL2] Hi I need to find a program to do rarefraction on the Mac. Can anyone point me where to look. Please reply by e-mail if possible. Thank you. Michael Cuggy From owner-software@net.bio.net Tue Feb 04 22:00:00 1997 Path: biosci!rutgers!news-relay.ncren.net!newsgate.duke.edu!mmorales From: mmorales@acpub.duke.edu (Michael Morales) Newsgroups: bionet.software Subject: Short Similarity Search Date: 5 Feb 1997 22:22:43 GMT Organization: Duke University, Durham, NC, USA Lines: 9 Message-ID: <5db17j$jl8@newsgate.duke.edu> NNTP-Posting-Host: bio6.acpub.duke.edu X-Newsreader: TIN [version 1.2 PL2] I am performing in situ hybridization using short (35-50 nucleotides) oligonucleotide probes. I want to check the databases by FASTA and BLAST for other sequences that may have similarity to these. Are there any special settings or programs that are optimal for use with short sequences? Any favorite sites? Any help would be greatly appreciated. Mike Morales From owner-software@net.bio.net Tue Feb 04 22:00:00 1997 Path: biosci!rutgers!gatech!EU.net!Norway.EU.net!nntp.uio.no!in1.nntp.cais.net!news.us.net!usenet From: Jeff Marshall Newsgroups: alt.hypertext,alt.windows95,alt.html,bionet.software Subject: Re: ms word to html Date: Wed, 05 Feb 1997 13:51:03 -0500 Organization: US Net - MD,DC,VA ISP - info@us.net Lines: 35 Message-ID: <32F8D697.432B@infocomm.net> References: <855165652.25149@dejanews.com> Reply-To: jeff@infocomm.net NNTP-Posting-Host: 206.225.29.5 Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----------55913A393D027" X-Sender: Jeff Marshall (Unverified) X-Mailer: Mozilla 4.0b1 (WinNT; I) X-Priority: Normal ------------55913A393D027 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Hi, Word has an okay HTML assistant that already converts Word text to HTML. If you haven't looked at that yet, you may want to go over to http://microsoft.com and get the assistant. Jeff Marshall ------------55913A393D027 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii
Hi,
 
Word has an okay HTML assistant that already converts Word text to HTML.  If you haven't looked at that yet, you may want to go over to http://microsoft.com and get the assistant.
 
Jeff Marshall
------------55913A393D027-- From owner-software@net.bio.net Tue Feb 04 22:00:00 1997 Path: biosci!IAFRICA.COM!ccantina From: ccantina@IAFRICA.COM ("C. Cantina") Newsgroups: bionet.software Subject: Chemical structures Date: 5 Feb 1997 12:34:46 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: <32F977DA.3344@iafrica.com> Reply-To: ccantina@iafrica.com NNTP-Posting-Host: net.bio.net Hi there, does anyone know of a program which allows one to draw chemical structures, including DNA/RNA sequences? I would like to find one if posible which works with Word Perfect. Please, inform me if someone knows where to find this software. Thanks C Cantina From owner-software@net.bio.net Tue Feb 04 22:00:00 1997 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!news1.mpcs.com!news.radio.cz!voskovec.radio.cz!news.radio.cz!CESspool!news.apfel.de!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!newsserver.rrzn.uni-hannover.de!tubsibr!rzlimes.gbf-braunschweig.de!news From: reichelt@gbf-braunschweig.de (Joachim Reichelt) Newsgroups: bionet.software,bionet.molec-model Subject: Re: Program for molecular modeling. Date: 5 Feb 1997 13:50:59 GMT Organization: GBF Braunschweig Lines: 16 Message-ID: <5da383$a0s@rzlimes.gbf-braunschweig.de> References: NNTP-Posting-Host: msfjre.gbf-braunschweig.de Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.6 Xref: biosci bionet.software:17796 bionet.molec-model:1357 In article , u3601087@mahidol.ac.th says... > >Dear all, > I wold like to know the name of the software other than from MSI and >Waht_if. Are there any that can do molecular modeling for protein? > Thank you in advance, > Have a look at our page for BRAGI at : http://www.gbf-braunschweig.de/zwe/MSF/bragi_group/Bragie.html BRAGI is free to academics. best wishes, From owner-software@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!news.maxwell.syr.edu!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!howland.erols.net!panix!cmcl2.nyu.edu!news.nyu.edu!not-for-mail From: coetzeew@is2.nyu.edu Newsgroups: bionet.software Subject: Re: (none) Date: Thu, 06 Feb 1997 13:22:43 -0500 Organization: New York University Lines: 5 Message-ID: <32FA2173.6FC7@is2.nyu.edu> References: <199702060315.OAA10453@anugpo.anu.edu.au> NNTP-Posting-Host: mcpd44.med.nyu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Shoba.Ranganathan wrote: > > help With what? From owner-software@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!news.belnet.be!swsbe6.switch.ch!scsing.switch.ch!elna.ethz.ch!retrograde.ethz.ch!user From: mantei@neuro.biol.ethz.ch (Ned Mantei) Newsgroups: bionet.software,bionet.molbio.methds-reagnts Subject: Re: Restriction Enzymes in DNA Strider? Date: Thu, 06 Feb 1997 09:37:53 +0100 Organization: Dept. of Neurobiology, ETH-Zurich Lines: 20 Message-ID: References: NNTP-Posting-Host: retrograde.ethz.ch Xref: biosci bionet.software:17808 bionet.molbio.methds-reagnts:54446 In article , nc1@acpub.duke.edu (Namjin Chung) wrote: > Dear DNA Strider Users: > > I use the above software for some sequence processing, and I think it's > simple but very good software. The only one thing I'm not satisfied with > it is that it would not allow custom restriction by a selected set of > REs. If you hold down the option key while choosing "Graphic map..." from the menu "Enz", you can choose from the restriction enzymes in the file RELibrary.RELibrary can be edited by a word processor (save as "Text only"). Or is this not what you meant? -- Ned Mantei Dept. of Neurobiology, Swiss Federal Institute of Technology CH-8093 Zurich, Switzerland mantei@neuro.biol.ethz.ch Fax: +41-1-633-1046 From owner-software@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!agate!spool.mu.edu!howland.erols.net!rill.news.pipex.net!pipex!oleane!pasteur.fr!jussieu.fr!univ-lyon1.fr!news From: bioch@lnsd-res.univ-lyon1.fr (biochimie) Newsgroups: bionet.software Subject: Re: Rapd analysis Date: 6 Feb 1997 10:09:05 GMT Organization: INSERM U189 Lines: 31 Message-ID: <5dcak1$2sb@tempo.univ-lyon1.fr> References: <5ctb87$m3r@news.csus.edu> NNTP-Posting-Host: pc-bioch2.univ-lyon1.fr Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 X-Newsreader: WinVN 0.99.5 In article <5ctb87$m3r@news.csus.edu>, sac30867@saclink2.csus.edu says... > >Panapat Uawithya (u3601087@mahidol.ac.th) wrote: >: Are there any software that can >: 1 analyze for rapd >: 3 If possible freeware or shareware. >: 4 PC or UNIX > >the RAPD analysis package runs in DOS and is free and (surprise) analyzes >RAPDs. I forgot the name of the file, but it is available from the >SimTel archives in the biology directory. The latest version (i think) >is 1.04. > >NIH-Image PC is available in beta test from somewhere. I'm still trying >to get it to analyze a gel for me, so I can't comment on how well it >works (yet!). It, also, is free & runs under Win95. You can get ImagePC on the Web site Of Scion Corporation at the following address : http://www.scioncorp.com/Image P.GEORGE -- INSERM U189 Laboratoire de BIOCHIMIE Faculte de Medecine LYON-SUD BP 12 69921 OULLINS CEDEX Tel : 78-86-31-58 Fax : 78-50-71-52 Directeur : Pr Pierre LOUISOT From owner-software@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!news1.best.com!nntp2.ba.best.com!jdulaney From: jdulaney@nntp.best.com (John Dulaney) Newsgroups: bionet.software Subject: NEED: UNLIMITED INSTALLER or NEVERLOCK or similar Date: 6 Feb 1997 06:13:10 GMT Lines: 1 Message-ID: <5dbspm$imf$3@nntp2.ba.best.com> NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] E-mail please. john From owner-software@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!ANU.EDU.AU!sxr224 From: sxr224@ANU.EDU.AU ("Shoba.Ranganathan") Newsgroups: bionet.software Subject: (none) Date: 5 Feb 1997 19:15:23 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <199702060315.OAA10453@anugpo.anu.edu.au> Reply-To: Shoba.Ranganathan@anu.edu.au NNTP-Posting-Host: net.bio.net help From owner-software@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!worldnet.att.net!news.u.washington.edu!root From: "R. Henne" Newsgroups: bionet.software Subject: Re: Chemical structures Date: Wed, 05 Feb 1997 17:59:05 -0800 Organization: University of Washington Lines: 23 Message-ID: <32F93AE9.2781@u.washington.edu> References: <32F977DA.3344@iafrica.com> NNTP-Posting-Host: beatrice01.u.washington.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-User: henne X-Mailer: Mozilla 2.02 (X11; I; AIX 2) C. Cantina wrote: > > Hi there, > > does anyone know of a program which allows one to draw chemical > structures, including DNA/RNA sequences? I would like to find one if > posible which works with Word Perfect. > > Please, inform me if someone knows where to find this software. > Thanks > > C Cantina I like Isis Draw. It comes with nucleotide and amino acid structures. It is free for academic and personal use. It also plays well with other Windows apps. There is also a Mac version at the same site. It worked with MS Word but I haven't tried it with Word Perfect. Here is the URL: http://www.mdli.com/prod/ioffer.html Randy From owner-software@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!CSU.edu.au!jwilkinson From: jwilkinson@CSU.edu.au ("Jenny Wilkinson") Newsgroups: bionet.software Subject: Re: Male and female symbols in Microsoft Word Date: 5 Feb 1997 16:30:01 -0800 Organization: Charles Sturt University - Riverina Lines: 11 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net It is inside word 7.0. Go to menu "insert" -> "symbol". From font list choose "CommonBullets", male and female symbols are inside. How about in Word 6? or are these symbols only in Word 7. jenny From owner-software@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!portc02.blue.aol.com!audrey01.news.aol.com!not-for-mail From: zevsolltec@aol.com (ZevSolltec) Newsgroups: bionet.software Subject: Senior Programmer Analyst Needed Date: 6 Feb 1997 19:42:59 GMT Organization: AOL http://www.aol.com Lines: 14 Message-ID: <19970206194200.OAA14800@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Senior Programmer Analyst Plan and execute major, complex programming projects related to medical and scientific imaging on Macintosh, Windows 95 and NT platforms. Requires a BS in computer science, three years experience programming in C or C++; knowledge of basic hardware architecture and add-on devices, specifically those used in image acquisition such as frame-grabber boards; or equivalent. Desirable: Master degree, and knowledge of biological sciences. Salary Commensurate. Send resume to Zev Sunleaf, Department of Biological Sciences, 138 Biology Building, University of Iowa, Iowa City, IA 52242-1324. The University of Iowa is an Affirmative Action/Equal Opportunity Employer. Women and minority candidates are encouraged to apply. From owner-software@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!agate!howland.erols.net!ix.netcom.com!news.enteract.com!news.inetnebr.com!netserv.unmc.edu!netserv!gspahwa From: gspahwa@netserv.unmc.edu (Gurcharan Pahwa) Newsgroups: bionet.software Subject: GCG Date: 6 Feb 1997 17:36:40 GMT Organization: University of Nebraska Medical Center Lines: 10 Message-ID: <5dd4r8$7v3@netserv.unmc.edu> NNTP-Posting-Host: 137.197.98.10 X-Newsreader: TIN [version 1.2 PL2] Wisconsin Sequence Analysis Package from GCG is a Unix based sequence analysis software and has most of the features of Macvector and other PC compatible sequence analysis softwares. E-mail doc@gcg.com http://www.gcg.com They have graphical user,s interface. Surf their Web site. Disclaimer: THis is in response to your query and not the promotion of the product. From owner-software@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!bloom-beacon.mit.edu!news.starnet.net!news.starnet.net!news.utdallas.edu!news.swmed.edu!news From: Mark Walberg Newsgroups: bionet.software,bionet.molbio.methds-reagnts Subject: Re: Restriction Enzymes in DNA Strider? Date: Thu, 06 Feb 1997 11:03:05 +0000 Organization: UT Southwestern Medical Center Lines: 15 Message-ID: <32F9BA6A.4764@simmons.swmed.edu> References: Reply-To: walberg@simmons.swmed.edu NNTP-Posting-Host: scc17.swmed.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; 68K) Xref: biosci bionet.software:17812 bionet.molbio.methds-reagnts:54474 Namjin Chung wrote: > > Dear DNA Strider Users: > The only one thing I'm not satisfied with > it is that it would not allow custom restriction by a selected set of > REs. > Does anybody know how to solve this problem? TIA. > Namjin Chung, who knows little and asks a lot! > Program in Molecular Cancer Biology > Duke University Medical Center > Durham, North Carolina Hold the option key down when you select the Graphic Map. This will give you a window allowing you to select any enzyme that you have in your RE library. -MW From owner-software@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!warwick!leicester!pc5 From: ray@le.ac.uk (Raymond Dalgleish) Newsgroups: bionet.software Subject: Re: Male and female symbols in Microsoft Word Date: Thu, 06 Feb 97 11:40:34 GMT Organization: Department of Genetics, University of Leicester, UK Lines: 22 Message-ID: <5dcfvi$d58_001@gene.le.ac.uk> References: NNTP-Posting-Host: pc5.gene.le.ac.uk X-Newsreader: News Xpress Version 1.0 Beta #4 In article , jwilkinson@CSU.edu.au ("Jenny Wilkinson") wrote: > >It is inside word 7.0. > >Go to menu "insert" -> "symbol". From font list choose >"CommonBullets", male and female symbols are inside. > >How about in Word 6? or are these symbols only in Word 7. > >jenny > Microsoft produced a set of true type fonts containing mostly symbols that aided in the conversion of Word Perfect documents to Word. The fonts (five of them I think) can be downloaded from Microsoft's web site. The file might be available elsewhere as wpcnv.exe . The female and male symbols are in the font called Iconic Symbols Ext. Enjoy! Raymond Dalgleish From owner-software@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!demos!news.florin.ru!usenet From: Konstantin Savov Newsgroups: bionet.software Subject: improved Web access to botanical databases Date: Thu, 06 Feb 1997 21:59:57 -0500 Organization: DataX/FLORIN, Inc. Lines: 32 Message-ID: <32FA9AAD.15FB@florin.ru> NNTP-Posting-Host: alpha.florin.ru Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; OSF1 V4.0 alpha) DataX/FLORIN ANNOUNCES IMPROVED WEB ACCESS TO BOTANICAL DATABASES Web access to the databases published on our site has been adjusted with a new revision of FLORIN Taxonomy Web Application. The latter is customizable for needs of a particular database now. The following databases are currently available on http://www.florin.ru/florin/db/: - Catalogue of Authentic Specimens of Moscow State University Herbarium (MW); - Mosses of the former USSR, by Dr. Michael Ignatov; - A Taxonomic Revision of Pseudodracontium (Araceae - Aroideae - Thomsonieae), by Dr. Michael Serebryanyi; - Lotus database, by Dr. Tatyana Kramina. Now, you may - search for data using customized query forms, - get lists of taxa and browse through them without filling in a query form, - get reports (synopsis, taxonomic tree) generated from a database by clicking one button. Any feedback is appreciated. Thank you in advance. ------------------------------------------------------- Konstantin Savov E-mail: kps@florin.ru FLORIN Project Leader Voice: +7(095)158-9520 Fax: +7(095)158-5700 DataX/FLORIN, Inc. Moscow, Russia ------------------------------------------------------- FLORIN Home Page: From owner-software@net.bio.net Wed Feb 05 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeeds.sol.net!feed1.news.erols.com!howland.erols.net!news.nacamar.de!fu-berlin.de!news.belwue.de!News.Uni-Marburg.DE!not-for-mail From: klieber@mailer.uni-marburg.de (Hans-Georg Klieber) Newsgroups: bionet.software Subject: What is your favorite patch-clamp hardware/software? Date: Thu, 06 Feb 1997 08:16:16 GMT Organization: University of Marburg, Germany Lines: 25 Message-ID: <32f99325.3279390@news.uni-marburg.de> NNTP-Posting-Host: mppp029.ppp.uni-marburg.de X-Newsreader: Forte Free Agent 1.1/32.230 Dear colleagues, I would like to collect your opinions on the advanteges and disadvanteges of the electrophysiology equipment that you use for patch-clamping. I am particularly interested in your experience regarding - amplifiers - computer controlled measurement (whole cell, single channel), hardware & software - choice of mass storage - software to further evaluate the measurments Your responses are greatly appreciated. I will provide a summary of all contributions. Thank you for your help, Hans-Georg Klieber -- Dr. Hans-Georg Klieber, klieber@mailer.uni-marburg.de Physiological Institute, University of Marburg, Germany Office: +49-6421-286521, Home: -25680 http://staff-www.uni-marburg.de/~klieber/ From owner-software@net.bio.net Thu Feb 06 22:00:00 1997 Path: biosci!rutgers!gatech!news.sprintlink.net!news-peer.sprintlink.net!howland.erols.net!math.ohio-state.edu!jussieu.fr!univ-lyon1.fr!news.univ-aix.fr!usenet From: Daniel GAUTHERET Newsgroups: bionet.molbio.evolution,bionet.general,bionet.software Subject: Ph.D./Postdoc Position: Computational/wet Biology Date: Fri, 07 Feb 1997 12:14:17 +0100 Organization: Universites d' Aix en Provence Lines: 43 Message-ID: <32FB0E89.41C6@gauss.cnrs-mrs.fr> NNTP-Posting-Host: gauss.cnrs-mrs.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) Xref: biosci bionet.molbio.evolution:5634 bionet.general:25525 bionet.software:17820 =========== Computational/wet Biology on the French Riviera =========== Feb 1997 The Laboratory of Structural & Genetic Information, (EP 91-CNRS) of the Institute of Structural Biology & Microbiology (IBSM) offers immediate doctoral and post-doctoral opportunities in the following areas of computational biology: - 1. Analysis of ESTs and Genomic sequence data in Plants - 2. Analysis of microbial genomes - 3. Human genomics and human paleogenetics (study on "ancient DNA") A solid background in Plant and/or Microbial biology is needed for positions 1 & 2, as well as a working knowledge of the usual sequence analysis tools (GenBank, Blast, etc). Ideal candidates would have been previously involved in a sequencing project. Candidates for position 3 should be prepared to equally divide their work into wet and "in silico" biology. Again a working knowledge of sequence analysis techniques is needed. The laboratory is already well equipped in term of hardware, software and basic bioinformatics skills. We are now looking to reinforce our biological/ genomics potential to take advantage of the computer systems now in place. More information on the activity of the laboratory can be found on our internet server: http://igs-server.cnrs-mrs.fr Please address your CV and two references to: ================================================================ Jean-Michel Claverie, Dr. Sc. jmc@igs.cnrs-mrs.fr Tel: +33 4 91 16 45 48 Fax: +33 4 91 16 45 49 Director, Laboratory of Structural & Genetic Information, EP 91 - CNRS Institute of Structural Biology & Microbiology (IBSM) 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, FRANCE ================================================================ E-mail is preferred. Candidates from all countries of the EEC are encouraged to apply. From owner-software@net.bio.net Thu Feb 06 22:00:00 1997 Path: biosci!rutgers!gatech!EU.net!Norway.EU.net!nntp.uio.no!news.apfel.de!news-fra1.dfn.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!newsserver.rrzn.uni-hannover.de!tubsibr!rzlimes.gbf-braunschweig.de!news From: reichelt@gbf-braunschweig.de (Joachim Reichelt) Newsgroups: bionet.software,bionet.molec-model Subject: Re: Program for molecular modeling. Date: 7 Feb 1997 09:29:24 GMT Organization: GBF Braunschweig Lines: 41 Message-ID: <5deslk$hi6@rzlimes.gbf-braunschweig.de> References: <5da383$a0s@rzlimes.gbf-braunschweig.de> NNTP-Posting-Host: msfjre.gbf-braunschweig.de Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.6 Xref: biosci bionet.software:17821 bionet.molec-model:1359 In article <5da383$a0s@rzlimes.gbf-braunschweig.de>, reichelt@gbf-braunschweig.de says... > ... >Have a look at our page for BRAGI at : > >http://www.gbf-braunschweig.de/zwe/MSF/bragi_group/Bragie.html Sorry, I had a Typo, please read it http://www.gbf-braunschweig.de/zwe/MSF/bragi_group/BragiE.html > >BRAGI is free to academics. > >best wishes, > -- Mit freundlichen Gruessen Best Regards Joachim Reichelt ------------------------------------------------------------------------- Joachim Reichelt MSF - Zentrale Wiss. Einrichtung "Strukturforschung" GBF - Gesellschaft fuer Biotechnologische Forschung Mascheroder Weg 1 D-38124 Braunscheig _/_/_/ _/_/_/ _/_/_/_/ _/ _/ _/ _/ _/ Tel: +(49) 531 6181 352 _/ _/ _/ _/ +(49) 531 6181 224 _/ _/ _/_/_/ _/_/_/ FAX: +(49) 531 6181 355 _/ _/ _/ _/ _/ EMAIL: _/ _/ _/ _/ _/ REICHELT@gbf-braunschweig.de _/_/_/ _/_/_/ _/ WWW: http://www.gbf-braunschweig.de/zwe/MSF/index.html http://www.gbf-braunschweig.de/zwe/MSF/bragi_group/Bragi.html -- Disclaimer -- Standard > Keyword : Opinions, my own, nobody else's, whatsoever ... From owner-software@net.bio.net Thu Feb 06 22:00:00 1997 Path: biosci!agate!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!news.pbi.net!nntp.mainstreet.net!ns2.mainstreet.net!sloth.swcp.com!tesuque!lynx.unm.edu!bubba.NMSU.Edu!usenet From: "Donald D. Bustamante" Newsgroups: alt.hypertext,alt.windows95,alt.html,bionet.software Subject: Re: ms word to html Date: Thu, 06 Feb 1997 07:43:25 -0800 Organization: National Biotechnology Information Facility Lines: 27 Message-ID: <32F9FC1D.86@psl.nmsu.edu> References: <855165652.25149@dejanews.com> NNTP-Posting-Host: 128.123.33.156 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (WinNT; I) sxr3008@megahertz.njit.edu wrote: > > Hi, there: > > I am trying to write my own word-to-html converter. But I don't know > how the MS word's .doc file is formated. There must be some format > specification like html's tags or DTD. But I have no idea where to find > it out. Can anybody give some hints? > > TIA. > > Shaomei > > -------------------==== Posted via Deja News ====----------------------- > http://www.dejanews.com/ Search, Read, Post to Usenet Word has the capability to do this. It may be necessary to upgrade your copy of Word; if so, it is available from http://www.microsoft.com -- Donald D. Bustamante, Project Manager National Biotechnology Information Facility Physical Science Laboratory Box 30002, Dept. 3548 Las Cruces, New Mexico USA 88003 (505)-522-9209 FAX: (505)-522-9434 URL: http://www.nbif.org From owner-software@net.bio.net Thu Feb 06 22:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news-xfer.netaxs.com!feed1.news.erols.com!howland.erols.net!rill.news.pipex.net!pipex!warwick!lyra.csx.cam.ac.uk!news.ox.ac.uk!andrew.rambaut From: andrew.rambaut@zoology.ox.ac.uk (Andrew Rambaut) Newsgroups: bionet.software Subject: Another Mac Multiple Alignment Program Date: Fri, 07 Feb 1997 16:38:43 +0000 Organization: Zoology Department, University of Oxford Lines: 23 Message-ID: NNTP-Posting-Host: andyrmac.zoo.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.3 I have written a multiple alignment editor for my own use due to frustration about what was available so far. I use the current version all the time and find it very useful. I think its best feature is the ability to translate in real time from DNA to amino acids whilst editing the alignment. Thus any changes you make whilst looking at the AAs are actually made to the underlying DNA sequences. There are loads of bugs and loads of features still to be implemented. The manual is only half written. At present I have no time to complete the project but if anyone would like to take a look and try it out: ftp://evolve.zoo.ox.ac.uk/packages/Se-Al/Se-Al10a1.hqx http://evolve.zoo.ox.ac.uk/Se-Al/Se-Al/html This is a FAT binary. Please, see what you think and get back to me. I will try and help with any problems. ===================================================================== Andrew Rambaut, Zoology Department, EMAIL - Andrew.Rambaut@zoology.ox.ac.uk University of Oxford, South Parks Road, Oxford, England. ===================================================================== From owner-software@net.bio.net Thu Feb 06 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!EU.net!Germany.EU.net!main.Germany.EU.net!fu-berlin.de!unlisys!blackbush.xlink.net!scsing.switch.ch!rzunews.unizh.ch!newsadm From: Rolf Kocherhans Newsgroups: bionet.software Subject: Beta testers wanted for molbio prg. Date: Fri, 07 Feb 1997 10:27:04 +0100 Organization: University of Zurich, Switzerland Lines: 28 Message-ID: <32FAF568.3EEA@vetvir.unizh.ch> Reply-To: rolfk@vetvir.unizh.ch NNTP-Posting-Host: 130.60.22.38 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) I need some beta testers to test some SuperCard projects which I made on the Mac for the WWW. They are accessible over the WWW with the Roadster plug in from Allegiant ! If you do not know what I talk about just connect to the URL, download the plug in and you will be very surprised. I have no access to IBM computers so I actually need some people testing with the roadster plug in for windows. You can find the plugin here: http://www.allegiant.com/roadster/ You can find the page at: http://www.unizh.ch/vetvir/programs.html You can find two different programs there at the moment, one designs Adaptors or Linkers and the other calculates Ligation dilutions. The programs are very primitive and have no manual but they should be easy to use. Please let me know how they work in any case ! Cheers Rolf mailto:rolfk@vetvir.unizh.ch From owner-software@net.bio.net Thu Feb 06 22:00:00 1997 Newsgroups: bionet.software Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!news-peer.gsl.net!news.gsl.net!howland.erols.net!rill.news.pipex.net!pipex!uknet!usenet1.news.uk.psi.net!uknet!uknet!bcc.ac.uk!mol28.ioo.ucl.ac.uk!user From: j.keen@ucl.ac.uk (Jeffrey Keen) Subject: Re: Seqvu Sender: news@ucl.ac.uk (Usenet News System) Message-ID: Date: Fri, 7 Feb 1997 09:42:41 GMT References: Organization: Institute of Ophthalmology, London Lines: 15 In article , knecht@UCONNVM.UCONN.EDU (David Knecht) wrote: > We have found Seqvu to be an excellent companion to Clustal in terms of > viewing and manipulating sequence alignments on the Macintosh. When I > tried to register the program, the Garvan INstitute (Sydney, AU, which > claims responsibility on the splash screen) either no longer exists or no > longer supports the program. Does anyone know if someone is supporting it? > Is there a good alternative anyone knows of for viewing and tweeking > alignments? Thanks- Dave Try http://www.cris.com/~ketchup/genedoc.shtml for the multiple alignment editor "GenDoc" - though its only for MSWindows so far. Jeffrey Keen From owner-software@net.bio.net Thu Feb 06 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!worldnet.att.net!cbgw2.lucent.com!news.bu.edu!usenet From: James Freeman Newsgroups: bionet.software Subject: Online Genomic Analysis Tool From The BMERC Date: Fri, 07 Feb 1997 14:25:17 -0500 Organization: BioMolecular Engineering Resource Center Lines: 53 Message-ID: <32FB819D.4487EB71@darwin.bu.edu> NNTP-Posting-Host: hinshelwood.bu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 4.1.4 sun4m) CC: jfreeman@darwin.bu.edu BMERC/MBCRR Bulletin: February 1997 WWW interface for searching several Genomes at once: (NEW--Includes E. Coli!) The E. Coli genome has just been sequenced as of the last week of January. At BMERC, we have added the E. Coli genome to our genome blast page. The E. Coli genome is of particular interests to Molecular Biologists because the vast majority of functions assigned to E. Coli have been done by experimentation. Most other genomes have their functions assigned by homology. The complete and nearly complete genomes of Saccharomyces Cerevisiae , Methanococcus Jannaschii, E. Coli, and Bacillus Subtilis are now available. Our WWW Blast interface allows you to search, using your sequence, against two subsets of the available putative open reading frames of these genomes using blastp. A Search Against Annotated ORF's and a Search Against Unannotated ORF's of these genomes are the search options available from this page. Your output will consist of detailed references for the significant blast matches and the raw blast output. The detailed references consist of a reference key, the annotation where available, the protein sequence, and the dna for the ORF's. We are also providing a tool for function keyword searching.We have built a table that relates E. Coli to the other three main genomes using blast with a Karlan Altschul score of < 10E-17. This keyword searching tool will print a list of every sequence identifier that is close to the E. Coli gene of the cluster where the keyword is found. The WWW address for our Blast Genome Analysis blast page is: http://bmerc-www.bu.edu/genome/genomeblastp.html The WWW address for the E Coli functional search is: http://bmerc-www.bu.edu/genome/ecoli-keyword.html If you have any questions/comments on this WWW page, please send them to Jim Freeman at jfreeman@darwin.bu.edu -- Jim Freeman P: mammon@tiac.net W: jfreeman@darwin.bu.edu Programmer/Analyst at Bio-Molecular Engineering Center at BU Etiam unum capillum umbram suam habet. http://www.tiac.net/users/mammon/index.html From owner-software@net.bio.net Fri Feb 07 22:00:00 1997 Path: biosci!agate!howland.erols.net!news-peer.gsl.net!news.gsl.net!news-hk.gsl.net!news.gsl.net!newsgate.cuhk.edu.hk!news.polyu.edu.hk!usenet From: bcyeung@polyu.edu.hk (bcyeung) Newsgroups: alt.hypertext,alt.windows95,alt.html,bionet.software Subject: Re: ms word to html Date: Sat, 08 Feb 1997 08:34:01 GMT Organization: polyu.edu.hk Lines: 19 Message-ID: <32fc3a07.10451493@hkpu01.polyu.edu.hk> References: <855165652.25149@dejanews.com> NNTP-Posting-Host: 158.132.16.169 X-Newsreader: Forte Free Agent 1.1/32.230 On Wed, 05 Feb 1997 12:11:06 -0600, sxr3008@megahertz.njit.edu wrote: >Hi, there: > >I am trying to write my own word-to-html converter. But I don't know >how the MS word's .doc file is formated. There must be some format >specification like html's tags or DTD. But I have no idea where to find >it out. Can anybody give some hints? > >TIA. > >Shaomei > >-------------------==== Posted via Deja News ====----------------------- > http://www.dejanews.com/ Search, Read, Post to Usenet Windows 95 have the internet assistant for change word doccument file to html file automatically , try to download the freeware from http://www.microsof.com From owner-software@net.bio.net Fri Feb 07 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeeds.sol.net!nntp.uio.no!Norway.EU.net!sn.no!newsfeed.tip.net!puff.lmv.lm.se!newsfeed3.telia.com!masternews.telia.net!newssrv.ita.tip.net!mikasa.iol.it!news From: edoardo.shockwav@iol.it (Edo) Newsgroups: bionet.software Subject: male and female symbol Date: Fri, 07 Feb 1997 20:56:18 GMT Organization: Italia Online Lines: 34 Message-ID: <32fc8e3a.2129086@news.iol.it> NNTP-Posting-Host: 194.20.26.68 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent .99g/32.339 I am looking for a TTF (True Type Font, for windows) that includes the male and female symbols. Is there anyone that could help me? Edo o o o o o o o o o o oooo o o o o o o o o o o o oooo ooo o o o o o o o o o o ooo o o ooooo o o From owner-software@net.bio.net Fri Feb 07 22:00:00 1997 Path: biosci!agate!howland.erols.net!torn!kwon!hone!informer1.cis.McMaster.CA!roger.interlynx.net!usenet From: Lars Thomsen Newsgroups: bionet.software Subject: Re: What is your favorite patch-clamp hardware/software? Date: Sat, 08 Feb 1997 05:34:13 -0800 Organization: Interlynx Lines: 278 Message-ID: <32FC80D3.3EC1@interlynx.net> References: <32f99325.3279390@news.uni-marburg.de> NNTP-Posting-Host: ppp05-max1.interlynx.net Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="----------9B1215B2B560" X-Sender: Lars Thomsen (Unverified) X-Mailer: Mozilla 4.0b1 (Win95; I) To: Hans-Georg Klieber X-Priority: Normal This is a multi-part message in MIME format. ------------9B1215B2B560 Content-Type: multipart/alternative; boundary="----------4BBA602038701" ------------4BBA602038701 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Dear Hans Georg Klieber I have used several software packages for my patch clamp data acquisition and analysis. Here are my comments which also covers customer support from the companies providing the software. Axon Instruments is providing a software package for DOS called PClamp6 and it is well supported with a thick and comprehensive manual and they have a good tech support that answers the phone or your email. The program is getting outdated. It suffers from the limitations in DOS and a menu structure that is diffuse so that you will find e.g. hardware settings in many different submenus instead of just one. I know that they are coming out with a new version for Win95 (maybe also Win31) and that could help a lot. The problem with data acquisition programs under Win95 or Win31 is that the screen update is normally slow and "jumpy". However, if they have used the new technology embedded in DirectX from Microsoft then they might have aschieved something useful, but I want to see it before I buy it. Pclamp6 is divided into two applications for data acquisition (FetchEx and ClampEx). FetcEx which is used for recording gapfree data (contineous recording) does not support gapfree data and I sometimes use the program called Axotape instead. I could say more bad things but infact PClamp6 is doing the job and if you enable the telegraphed output then the program automatically reads the gain from your amplifier so that you dont have to scripple it down in your logbook. That is a neat feature that I should be normal but few hardware companies support it. I use Axon Instruments Axopatch 200A and they have now made a 200b version with a cooled headstage that gives you extremely lownoise recording if you wants to do single channel work. The Axon 200A is without doubt the best I have tried. I wish they were as good programmers as they are hardware designers. I use the dataacquisition that was sitting on my setup when I arrived in the lab it is called TL-1 or something and I have no good feelings about that. The new Digidata looks much better. Cambrigde Electronic Design UK has a package called Patch and Voltage Clamp 6 and it is very similar to the Pclamp6. The manual is horrible but the support is really good from CED and if you find a bug then you can get a fix in no time. I dont like the Patch and Voltage Clamp software from CED it is a clumsy program but they have another package that is really good. It is called Spike2 and it is their major software and Axon doesn't really match it with any of their current products. I had to do some pharmacological experiments and Spike2 gave me everything that I needed. The best thing is that you can record several channels at different speed. That is not possible with anything from Axon. The power of this is that if you e.g. have a temperature probe sitting in your setup then you can record from that at e.g. 100Hz while you record you patch data at 10KHz...see that is smart. Another feature that simply is brilliant for the working electrophysiologist ist the ability to disable recording for periods of times - just by a click on a button. Imagine that you have to do a dose-response curve, beween each application of the agonist you have to wait e.g. 5 minutes, instead of recording the space between the "active periods" then you simply disable writing to disc. The program still keeps track of time. That is possible via the 1401plus which is the data acquisition unit from CED. It is quite expensive but it is worth the money. A look at Axons newest Digidata convinced me that they had copied the look of the 1401plus, but I doubt they also have copied the inside of the machine. All my regards to the CED team. The new spike2 for windows (including NT and Win95) gives you the options for customizing your program. You can build scripts into it. I made an article about the DOS version (Thomsen et al Journal of Neuroscience Methods 65, 19-26 1996). Other analysis programs. If you have a Mac then you are lucky because then you can get Axograph which is a brilliant program that has all that Pclamp6 is missing. Armed with Pclamp6 and Axograph you can do a lot. I know that another software company called Bruxton Corporation (formerly known as SKALAR Instruments) they have also made a quite impressive application and that is for the PC. Other data acquisition programs If I was going to buy something new just to increase my experience then I would take a good look a the new cards from National Instruments and some of the many dataacquisiton packages they make. The problem is that whatever dedicated package you buy you will always meet the limitations faster than you thought you would. Therefore it is a must to have access to a programming language that is easy and bugfree. National Instruments supports Visual basic and I dont think that you can find anything easier than that. VB5 is coming out in marts 97 and it will give you impressive performance compared to VB4 (upto 2000 % increase in e.g. form loading) Finally I will mention my own program which is freeware. It reads my datafiles created with Pclamp6 and somebody in the lab uses PClamp52 so I made it read that format too. What I would do : Pharmacological experiments - buy the Axon 200 A, the 1401plus and Spike2 for Windows from Cambrigde Electronic Design Whole cell recording - buy the Axon 200A, Digidata and Pclamp6 and use ClampEx. Single channel recording - good luck Best Regards -- Lars Thomsen, MSc. PhD 115 South Oval, Hamilton, L8S1R2 Ontario Canada email lthomsen@interlynx.net homepage http://home.interlynx.net/~lthomsen/index.htm tlp 1 905 777 0720 fax 1 905 777 0738 ------------4BBA602038701 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii
Dear Hans Georg Klieber
I have used several software packages for my patch clamp data acquisition and analysis. Here are my comments which also covers customer support from the companies providing the software. 
 
Axon Instruments is providing a software package for DOS called PClamp6 and it is well supported with a thick and comprehensive manual and they have a good tech support that answers the phone or your email. The program is getting outdated. It suffers from the limitations in DOS and a menu structure that is diffuse so that you will find e.g. hardware settings in many different submenus instead of just one. I know that they are coming out with a new version for Win95 (maybe also Win31) and that could help a lot. The problem with data acquisition programs under Win95 or Win31 is that the screen update is normally slow and "jumpy". However, if they have used the new technology embedded in DirectX from Microsoft then they might have aschieved something useful, but I want to see it before I buy it. Pclamp6 is divided into two applications for data acquisition (FetchEx and ClampEx). FetcEx which is used for recording gapfree data (contineous recording) does not support gapfree data and I sometimes use the program called Axotape instead. I could say more bad things but infact PClamp6 is doing the job and if you enable the telegraphed output then the program automatically reads the gain from your amplifier so that you dont have to scripple it down in your logbook. 
 
That is a neat feature that I should be normal but few hardware companies support it.  I use Axon Instruments Axopatch 200A and they have now made a 200b version with a cooled headstage that gives you extremely lownoise recording if you wants to do single channel work. The Axon 200A is without doubt the best I have tried. I wish they were as good programmers as they are hardware designers. I use the dataacquisition that was sitting on my setup when I arrived in the lab it is called TL-1 or something and I have no good feelings about that. The new Digidata looks much better. 
 
 
Cambrigde Electronic Design UK has a package called Patch and Voltage Clamp 6 and it is very similar to the Pclamp6. The manual is horrible but the support is really good from CED and if you find a bug then you can get a fix in no time. I dont like the Patch and Voltage Clamp software from CED it is a clumsy program but they have another package that is really good. It is called Spike2 and it is their major software and Axon doesn't really match it with any of their current products. I had to do some pharmacological experiments and Spike2 gave me everything that I needed. The best thing is that you can record several channels at different speed. That is not possible with anything from Axon. The power of this is that if you e.g. have a temperature probe sitting in your setup then you can record from that at e.g. 100Hz while you record you patch data at 10KHz...see that is smart. Another feature that simply is brilliant for the working electrophysiologist ist the ability to disable recording for periods of times - just by a click on a button. Imagine that you have to do a dose-response curve, beween each application of the agonist you have to wait e.g. 5 minutes, instead of recording the space between the "active periods" then you simply disable writing to disc. The program still keeps track of time. That is possible via the 1401plus which is the data acquisition unit from CED. It is quite expensive but it is worth the money. A look at Axons newest Digidata convinced me that they had copied the look of the 1401plus, but I doubt they also have copied the inside of the machine. All my regards to the CED team. The new spike2 for windows (including NT and Win95) gives you the options for customizing your program. You can build scripts into it. I made an article about the DOS version (Thomsen et al Journal of Neuroscience Methods 65, 19-26 1996).
 
Other analysis programs.
If you have a Mac then you are lucky because then you can get Axograph which is a brilliant program that has all that Pclamp6 is missing. Armed with Pclamp6 and Axograph you can do a lot.
 
I know that another software company called Bruxton Corporation (formerly known as SKALAR Instruments)  they have also made a quite impressive application and that is for the PC.
 
Other data acquisition programs
If I was going to buy something new just to increase my experience then I would take a good look a the new cards from National Instruments and some of the many dataacquisiton packages they make. The problem is that whatever dedicated package you buy you will always meet the limitations faster than you thought you would. Therefore it is a must to have access to a programming language that is easy and bugfree. National Instruments supports Visual basic and I dont think that you can find anything easier than that. VB5 is coming out in marts 97 and it will give you impressive performance compared to VB4 (upto 2000 % increase in e.g. form loading)
 
Finally I will mention my own program which is freeware. It reads my datafiles created with Pclamp6 and somebody in the lab uses PClamp52 so I made it read that format too. 
 
What I would do :
Pharmacological experiments - buy the Axon 200 A, the 1401plus and Spike2 for Windows from Cambrigde Electronic Design
 
Whole cell recording - buy the Axon 200A, Digidata and Pclamp6 and use ClampEx.
 
Single channel recording - good luck 
 
Best Regards
-- 
Lars Thomsen, MSc. PhD
115 South Oval, Hamilton, L8S1R2 Ontario Canada
email lthomsen@interlynx.net
homepage http://home.interlynx.net/~lthomsen/index.htm
tlp 1 905 777 0720  fax 1 905 777 0738
 
------------4BBA602038701-- ------------9B1215B2B560 Content-Transfer-Encoding: 7bit Content-Description: Address Book Card for Lars Thomsen Content-Disposition: inline; filename="nsmailBQ.TMP" Content-Type: text/x-vCard; charset=us-ascii; name="nsmailBQ.TMP" BEGIN:VCARD FN:Lars Thomsen N:Thomsen;Lars ORG:McMaster University ADR:;;115 South Oval;Hamilton;Ontario;L8S1R2 EMAIL;INTERNET:lthomsen@interlynx.net TITLE:MSc PhD TEL;WORK:1 905 5259140 x22584 TEL;FAX:1 905 7770720 TEL;HOME:1 905 7770738 X-NAV-HTML:T END:VCARD ------------9B1215B2B560-- From owner-software@net.bio.net Fri Feb 07 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!news-peer.gsl.net!news.gsl.net!news.sprintlink.net!news-peer.sprintlink.net!howland.erols.net!news.nacamar.de!fu-berlin.de!news.th-darmstadt.de!news.uni-mainz.de!usenet From: "Dr. K. Eimert" Newsgroups: bionet.software Subject: Re: Windows: sequence analysis Date: Wed, 05 Feb 1997 12:17:00 +0100 Organization: Forschungsanstalt Geisenheim Lines: 18 Message-ID: <32F86C2C.8AE@geisenheim.fa.fh-wiesbaden.de> References: <5cpibd$jnl$1@mark.ucdavis.edu> <32F7948C.79E@molbiol.uct.ac.za> Reply-To: eimert@geisenheim.fa.fh-wiesbaden.de NNTP-Posting-Host: 194.94.6.60 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Hi Ed, that sounds really good. Unfortunately, I couldn' find any info on this company (or program). Could you post their address, please? Do they have a WEB site or a demo or sw version available on some ftp sites (my searches didn't turn out anything, though)? Thanx in advance, Klaus ------------------------------------------------------------------------ Dr. Klaus Eimert Dept. of Botany State Research Institute Geisenheim Von-Lade-Str. 1 Tel.: + 49 6722 502 469 D-65366 Geisenheim FAX: + 49 6722 502 460 Germany e-mail: eimert@geisenheim.fa.fh-wiesbaden.de ------------------------------------------------------------------------ From owner-software@net.bio.net Fri Feb 07 22:00:00 1997 Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!nntp.uio.no!news.apfel.de!fu-berlin.de!news.th-darmstadt.de!news.uni-mainz.de!usenet From: "Dr. K. Eimert" Newsgroups: bionet.software Subject: Q: inducible promoters for transgenics? Date: Thu, 06 Feb 1997 08:18:31 +0100 Organization: Forschungsanstalt Geisenheim Lines: 23 Message-ID: <32F985C7.3B28@geisenheim.fa.fh-wiesbaden.de> Reply-To: eimert@geisenheim.fa.fh-wiesbaden.de NNTP-Posting-Host: 194.94.6.60 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Dear Netters, I am in need of an inducible promoter for plant transformation. It is important that this promoter would not "leak" if not induced, e.g., the hs-promoter would not work for us. Does anybody have experience with the glucocorticoid-inducible promoter? I seem to remember a paper some three (or more) years ago dealing with a Cu-inducible promoter. Did anybody try this one? Are the inducing concentrations of Cu toxic for the plants? Is there any review dealing with this topic, by chance? I'd appreciate any help or comments! Thanx in advance, Klaus ------------------------------------------------------------------------ Dr. Klaus Eimert Dept. of Botany State Research Institute Geisenheim Von-Lade-Str. 1 Tel.: + 49 6722 502 469 D-65366 Geisenheim FAX: + 49 6722 502 460 Germany e-mail: eimert@geisenheim.fa.fh-wiesbaden.de ------------------------------------------------------------------------ From owner-software@net.bio.net Fri Feb 07 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.inet.co.th!nectec!news.mahidol.ac.th!mucc.mahidol.ac.th!u3601087 From: Panapat Uawithya Newsgroups: bionet.software Subject: need help in PDB size measure Date: Sat, 8 Feb 1997 20:32:04 +0700 Organization: Mahidol University, Thailand Lines: 16 Message-ID: NNTP-Posting-Host: 202.28.162.1 Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I want to size an dangle of each secondary structure in PDB . I try measure using kinemage but it's very difficult and borsum .Are there any program that can measure it more accurate and easy. """"""" ********************************************************* | - - | Name Panapat Uawithya (|[O O]|) Nickname Nuk | \ | Address 13 soi 13 Saeree vlg1 Huamark Bangkapi ( `' ) Bangkok Thailand 10250 \ ~ / Tel 662-319-4925 \ / E-mail address u3601087@mucc.mahidol.ac.th /*\ Homepage www.mahidol.ac.th/~u3601087 ****************************************************************************** From owner-software@net.bio.net Fri Feb 07 22:00:00 1997 Newsgroups: bionet.software,bionet.molbio.methds-reagnts Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!torn!utnut!oci!kinase.oci.utoronto.ca From: jwoodget@oci.utoronto.ca (Jim Woodgett) Subject: Re: Restriction Enzymes in DNA Strider? Content-Type: text/plain; charset=US-ASCII Message-ID: <9702070934.AA22100@kinase.oci.utoronto.ca> Sender: news@oci.utoronto.ca Reply-To: jwoodget@oci.utoronto.ca (Jim Woodgett) Organization: Ontario Cancer Institute X-Newsreader: InterCon tcpCONNECT4 4.0.3d03 References: Mime-Version: 1.0 Date: Fri, 7 Feb 1997 14:34:22 GMT Lines: 41 Xref: biosci bionet.software:17830 bionet.molbio.methds-reagnts:54564 In article , mantei@neuro.biol.ethz.ch (Ned Mantei) writes: > This is a reply message which refers to the following message: News: > > In article , nc1@ > acpub.duke.edu (Namjin Chung) wrote: > > Dear DNA Strider Users: > > I use the above software for some sequence processing, and I think it's > > simple but very good software. The only one thing I'm not satisfied > > with it is that it would not allow custom restriction by a selected set > > of REs. > If you hold down the option key while choosing "Graphic map..." from the > menu "Enz", you can choose from the restriction enzymes in the file > RELibrary.RELibrary can be edited by a word processor (save as "Text > only"). Or is this not what you meant? The Option key also works with the "Digestion..." menu choice. When the list of enzymes comes up (its a separate window) you can select as many enzymes as you want to cut with by holding the shift key down. To deselect all, click on the space at the upper left of the listing. You can also combine particular cutters with double, triple cutters etc with a button selection in the dialog box. Once you've chosen a selection of REs and displayed the map or digest, any subsequent maps/digests of other sequences will also use the same selection unless you reselect the REs or quit/restart the application. All this is in the manual. Jim Woodgett Associate Professor: University of Toronto Senior Scientist: Ontario Cancer Institute mailto:jwoodget@oci.utoronto.ca 610 University Avenue http://kinase.oci.utoronto.ca/woodgettlab.html Toronto, Ontario M5G 2M9 phone (416) 946-2962 fax: (416) 946-2963 From owner-software@net.bio.net Fri Feb 07 22:00:00 1997 Path: biosci!genesys-tech.com!jgolden From: jgolden@genesys-tech.com (jim golden) Newsgroups: bionet.software Subject: job opportunity in Madison, WI - update Date: 8 Feb 1997 08:43:42 -0800 Organization: genesys technologies Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <32FCABB4.7FDF@genesys-tech.com> NNTP-Posting-Host: net.bio.net Thanks to all that have sent me resumes regarding the software/bioinformatics position at GeneSys Technologies, Inc. Unfortunately, because of the large volume of responses I received, I don't have time to answer everyone individually. The position was filled this week, but I will keep all the resumes I received on file since we are expecting rapid expansion this year in the areas of robotics and image processing. The quality of the applicants has been very high, and I encourage those looking for a position in bioinformatics to check out the 17 January 1997 issue of the journal Science for several want ads in this area. There a many research-oriented firms recruiting for projects in sequencing, gene finding, and analysis. Thanks again to all who responded. Jim Golden Director of Bioinformatics GeneSys Technologies, Inc. 9757 Wilkinson Rd. Mazomanie, WI 53560 From owner-software@net.bio.net Sat Feb 08 22:00:00 1997 Path: biosci!biosci!not-for-mail From: Rong-i Hong Newsgroups: bionet.molbio.proteins,bionet.xtallography,bionet.software,bionet.molec-model,bionet.biophysics,sci.chem Subject: Protein 2nd structure assignment Date: 9 Feb 1997 14:00:30 -0800 Organization: Oxford University Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: <32FB0643.41C6@bioch.ox.ac.uk> References: <32E977EB.5290@plaza.snu.ac.kr> <32F0B455.43D4@chem.gla.ac.uk> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molbio.proteins:9946 bionet.xtallography:3183 bionet.software:17841 bionet.molec-model:1364 bionet.biophysics:2621 sci.chem:75051 Dear All, We are doing some work about assignments of protein secondary sturcture elements. Are there any programs, other than DSSP, DEFINE and STRIDE, to define secondary structure based on the atomic coordinates? If so, could you let me know where I might acquire such programs? Thanks in advance. ------------------------------------------------------------ Rong-I Hong Lab. of Molecular Biophysics EMail: rong@bioch.ox.ac.uk University of Oxford Tel: 01865-275 369 Rex Richards Building Fax: 01865-275 182 Oxford, OX1 3QU United Kingdom ------------------------------------------------------------ From owner-software@net.bio.net Sat Feb 08 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!cs.utexas.edu!howland.erols.net!torn!hone!informer1.cis.McMaster.CA!roger.interlynx.net!usenet From: Lars Thomsen Newsgroups: bionet.software Subject: Re: What is your favorite patch-clamp hardware/software? Date: Sat, 08 Feb 1997 20:04:33 -0800 Organization: Interlynx Lines: 118 Message-ID: <32FD4CD1.4D86@interlynx.net> References: <32f99325.3279390@news.uni-marburg.de> <32FC80D3.3EC1@interlynx.net> NNTP-Posting-Host: ppp43-cas1.interlynx.net Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="----------790956C2599B4" X-Sender: Lars Thomsen (Unverified) X-Mailer: Mozilla 4.0b1 (Win95; I) To: Lars Thomsen X-Priority: Normal This is a multi-part message in MIME format. ------------790956C2599B4 Content-Type: multipart/alternative; boundary="----------63615737B2F5" ------------63615737B2F5 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii In my previous answer I wrote : "FetctEx which is used for recording gapfree data (contineous recording) does not support gapfree data and I sometimes use the program called Axotape instead" This should have been : FetcEx which is used for recording gapfree data (contineous recording) does not support "tags" and I sometimes use the program called Axotape instead. Tags are small time events stored in the end of the file. They are nice when you are doing something to your cell e.g. adding a agonist and then you make a time tag so you can keep track of what is happening. more about tags: I have only seen a advanced tagging system from Biologic and their computer controlled solution changer. The software was made so that you could call up solutions from a database and use them as tags. More or less what I remember. However, it should be standard in all electrophysiological acquisition programs that you can call up a database for the tagging. For highspeed recording you could set the tags that you use before. New data acquisition systems are build in a modular way so that you use two computers instead of one. The acquistion computer is dedicated to the timing and sampling and has a lot of memory, the PC is used as the control interface and allows you to do a lot of things that not was possible in the old days where you could ruin the timing of the sampling. The dual computer system gives you a buffer effect that allows you to do some sort of multitasking. A good example is the 1401plus from Cambridge Electronic Design. -- Lars Thomsen, MSc. PhD 115 South Oval, Hamilton, L8S1R2 Ontario Canada email lthomsen@interlynx.net homepage http://home.interlynx.net/~lthomsen/index.htm tlp 1 905 777 0720 fax 1 905 777 0738 ------------63615737B2F5 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii
In my previous answer I wrote :
"FetctEx which is used for recording gapfree data (contineous recording) does not support gapfree data and I sometimes use the program called Axotape instead"
This should have been :
FetcEx which is used for recording gapfree data (contineous recording) does not support "tags" and I sometimes use the program called Axotape instead. Tags are small time events stored in the end of the file. They are nice when you are doing something to your cell e.g. adding a agonist and then you make a time tag so you can keep track of what is happening.
 
more about tags:
I have only seen a advanced tagging system from Biologic and their computer controlled solution changer. The software was made so that you could call up solutions from a database and use them as tags. More or less what I remember. However, it should be standard in all electrophysiological acquisition programs that you can call up a database for the tagging. For highspeed recording you could set the tags that you use before. New data acquisition systems are build in a modular way so that you use two computers instead of one. The acquistion computer is dedicated to the timing and sampling and has a lot of memory, the PC is used as the control interface and allows you to do a lot of things that not was possible in the old days where you could ruin the timing of the sampling. The dual computer system gives you a buffer effect that allows you to do some sort of multitasking. A good example is the 1401plus from Cambridge Electronic Design.
 
-- 
Lars Thomsen, MSc. PhD
115 South Oval, Hamilton, L8S1R2 Ontario Canada
email lthomsen@interlynx.net
homepage http://home.interlynx.net/~lthomsen/index.htm
tlp 1 905 777 0720  fax 1 905 777 0738
 
------------63615737B2F5-- ------------790956C2599B4 Content-Transfer-Encoding: 7bit Content-Description: Address Book Card for Lars Thomsen Content-Disposition: inline; filename="nsmailJC.TMP" Content-Type: text/x-vCard; charset=us-ascii; name="nsmailJC.TMP" BEGIN:VCARD FN:Lars Thomsen N:Thomsen;Lars ORG:McMaster University ADR:;;115 South Oval;Hamilton;Ontario;L8S1R2 EMAIL;INTERNET:lthomsen@interlynx.net TITLE:MSc PhD TEL;WORK:1 905 5259140 x22584 TEL;FAX:1 905 7770720 TEL;HOME:1 905 7770738 X-NAV-HTML:T END:VCARD ------------790956C2599B4-- From owner-software@net.bio.net Sat Feb 08 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!nntp.uio.no!news.apfel.de!news-fra1.dfn.de!news-koe1.dfn.de!main.Germany.EU.net!Dortmund.Germany.EU.net!gsf.de!news From: Burkhard Morgenstern Newsgroups: bionet.software Subject: New alignment program DIALIGN Date: Fri, 07 Feb 1997 12:53:14 +0100 Organization: GSF Forschungszentrum fuer Umwelt und Gesundheit mbH Lines: 48 Message-ID: <32FB17AA.41C6@gsf.de> NNTP-Posting-Host: ariane.gsf.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; OSF1 V3.2 alpha) We would like to announce the availability of an alignment program called DIALIGN ******* DIALIGN is a completely novel program for pairwise as well as multiple alignment of nucleic acid and protein sequences. It is especially suited to detect local similarities in otherwise completely unrelated sequences and it does not employ any kind of gap penalty. The method is described in B. Morgenstern, A. Dress, T. Werner: Multiple DNA and protein sequence alignment based on segment-to-segment comparison Proc. Natl. Acad. Sci. 93 pp. 12098 - 12103 (1996) DIALIGN executables for various UNIX platforms (DEC, SGI, CONVEX, HP, SUN) together with a detailed user guide, online help and a test example are available at http://www.gsf.de/biodv/dialign.html or via ftp: ftp://ariane.gsf.de/pub/unix/dialign More detailed information on DIALIGN is available at our web page. If you have any questions, please feel free to contact us by e-mail. Burkhard Morgenstern ---------------------------------------------------------- Dr. Burkhard Morgenstern GSF - National Research Center for Environment and Health, Institute of Biomathematics and Biometry Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany morgenstern@gsf.de From owner-software@net.bio.net Sat Feb 08 22:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!rill.news.pipex.net!pipex!tank.news.pipex.net!pipex!duke.telepac.pt!news.telepac.pt!usenet From: nop53686@mail.telepac.pt (Miguel Garcia) Newsgroups: bionet.software Subject: I/O PROGRAM Date: Sun, 09 Feb 1997 19:30:22 GMT Lines: 9 Message-ID: <32fe2113.453525@news.telepac.pt> NNTP-Posting-Host: lc1_p6.telepac.pt X-Newsreader: Forte Free Agent 1.1/32.230 Does anyone knows if there is at anywhere an oriented objects software (or simply windows based) for free to manipulate I/O PC cards? If yes, please contact me. Thanks Miguel Garcia Técnico Electrónica (Desenvolvimento Projectos Automação) e-mail:nop53686@mail.telepac.pt From owner-software@net.bio.net Sat Feb 08 22:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!swrinde!ihnp4.ucsd.edu!munnari.OZ.AU!news.mel.connect.com.au!news.mel.aone.net.au!news.nlc.net.au!news From: "Cameron Johnson" Newsgroups: bionet.software Subject: Great Software deals Date: 9 Feb 1997 04:39:33 GMT Organization: NHJ NORTHLINK COMMUNICATIONS Lines: 7 Distribution: inet Message-ID: <01bc1643$5fc1fd60$618518cb@default> NNTP-Posting-Host: dialine24.nlc.net.au Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Internet News 4.70.1155 To Everyone If anyone is looking for Software at low Prices then Go to http://www.nlc.net.au/~cameron/software.html After finding the software you want email me and in the subject box type I want Whatever software title you want. Cameron Johnson From owner-software@net.bio.net Sat Feb 08 22:00:00 1997 Path: biosci!agate!howland.erols.net!torn!hone!informer1.cis.McMaster.CA!roger.interlynx.net!usenet From: Lars Thomsen Newsgroups: bionet.software Subject: Re: What is your favorite patch-clamp hardware/software? Date: Sat, 08 Feb 1997 20:52:09 -0800 Organization: Interlynx Lines: 140 Message-ID: <32FD57F9.470F@interlynx.net> References: <32f99325.3279390@news.uni-marburg.de> NNTP-Posting-Host: ppp43-cas1.interlynx.net Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="----------4D3F2E2B38B46" X-Sender: Lars Thomsen (Unverified) X-Mailer: Mozilla 4.0b1 (Win95; I) To: Hans-Georg Klieber X-Priority: Normal This is a multi-part message in MIME format. ------------4D3F2E2B38B46 Content-Type: multipart/alternative; boundary="----------18B62044158A7" ------------18B62044158A7 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii More about controlling an experiment : The TTL ports of the dataacquisition system can be used to control your setup. If you system can record that a TTL output has be fired then it is smart, because then you have a way to store an event marker in your data trace. If your system allows you to record TTL in but not TTL out commands then you can hook your TTL output to a TTL input and then record that - its a little bit primitive but it works and you get your eventmarker. The events are normally stored in separate event channels which only contain a very limited information even when sampled at high frequencies, the reason is that only the time location is stored, maybe with a comment attached to it. The event markers are unvaluable when making the analysis of continuous data. A simple searchroutine finding the next event in an event channel can take you to the next interesting point in the datafile. If you have a good event marker system then you can record all your data in one file rather than splitting it up in fractions. Right now I am using PClamp6 and there is no way to store events so I suffer under the load of many many datafiles, which is needed to keep track of the flow of the experiment. When you have your events then it is a piece of cake of doing analysis even with huge datafiles. I recorded 6.5 GB of data from enteric neurones during my PhD and without the eventmarkes my analysis would have been a nighmare. At present momement I am trying to find a way to change my solutions with a little robot controlled by TTL pulses from my computer. I have tried several systems but right now I think I am on the track of something good. The beauty is that if you can store these events together with all other kinds of events e.g. focal stimulation or whatever.. I cant help it but I have never seen anything as smart as the system from Cambrigde Electronic Design. I would wish they would make some scripts for Spike2 so that it would run whole cell experiments, I made some but it is always hard because it takes time to develop software and the experiments are after all the most important. The smart thing about Spike2 is that it is one program that can be customized to do anything. A feature that I would like is that if you e.g. do a lot of different files during one recording then you can save it all as a "project" simililar to Microcal Origin 4. Best Regards Lars Thomsen -- Lars Thomsen, MSc. PhD 115 South Oval, Hamilton, L8S1R2 Ontario Canada email lthomsen@interlynx.net homepage http://home.interlynx.net/~lthomsen/index.htm tlp 1 905 777 0720 fax 1 905 777 0738 ------------18B62044158A7 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii
More about controlling an experiment :
 
The TTL ports of the dataacquisition system can be used to control your setup. If you system can record that a TTL output has be fired then it is smart, because then you have a way to store an event marker in your data trace. If your system allows you to record TTL in but not TTL out commands then you can hook your TTL output to a TTL input and then record that - its a little bit primitive but it works and you get your eventmarker. The events are normally stored in separate event channels which only contain a very limited information even when sampled at high frequencies, the reason is that only the time location is stored, maybe with a comment attached to it. The event markers are unvaluable when making the analysis of continuous data. A simple searchroutine finding the next event in an event channel can take you to the next interesting point in the datafile. If you have a good event marker system then you can record all your data in one file rather than splitting it up in fractions. Right now I am using PClamp6 and there is no way to store events so I suffer under the load of many many datafiles, which is needed to keep track of the flow of the experiment. When you have your events then it is a piece of cake of doing analysis even with huge datafiles. I recorded 6.5 GB of data from enteric neurones during my PhD and without the eventmarkes my analysis would have been a nighmare.  At present momement I am trying to find a way to change my solutions with a little robot controlled by TTL pulses from my computer. I have tried several systems but right now I think I am on the track of something good. The beauty is that if you can store these events together with all other kinds of events e.g. focal stimulation or whatever..
I cant help it but I have never seen anything as smart as the system from Cambrigde Electronic Design. I would wish they would make some scripts for Spike2 so that it would run whole cell experiments, I made some but it is always hard because it takes time to develop software and the experiments are after all the most important. The smart thing about Spike2 is that it is one program that can be customized to do anything. A feature that I would like is that if you e.g. do a lot of different files during one recording then you can save it all as a "project" simililar to Microcal Origin 4.
 
Best Regards 
Lars Thomsen
-- 
Lars Thomsen, MSc. PhD
115 South Oval, Hamilton, L8S1R2 Ontario Canada
email lthomsen@interlynx.net
homepage http://home.interlynx.net/~lthomsen/index.htm
tlp 1 905 777 0720  fax 1 905 777 0738
 
------------18B62044158A7-- ------------4D3F2E2B38B46 Content-Transfer-Encoding: 7bit Content-Description: Address Book Card for Lars Thomsen Content-Disposition: inline; filename="nsmail7F.TMP" Content-Type: text/x-vCard; charset=us-ascii; name="nsmail7F.TMP" BEGIN:VCARD FN:Lars Thomsen N:Thomsen;Lars ORG:McMaster University ADR:;;115 South Oval;Hamilton;Ontario;L8S1R2 EMAIL;INTERNET:lthomsen@interlynx.net TITLE:MSc PhD TEL;WORK:1 905 5259140 x22584 TEL;FAX:1 905 7770720 TEL;HOME:1 905 7770738 X-NAV-HTML:T END:VCARD ------------4D3F2E2B38B46-- From owner-software@net.bio.net Sat Feb 08 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!nntp.uio.no!news.apfel.de!news-fra1.dfn.de!news-koe1.dfn.de!main.Germany.EU.net!Dortmund.Germany.EU.net!gsf.de!news From: Burkhard Morgenstern Newsgroups: bionet.software Subject: New alignment program DIALIGN Date: Fri, 07 Feb 1997 12:35:16 +0100 Organization: GSF Forschungszentrum fuer Umwelt und Gesundheit mbH Lines: 48 Message-ID: <32FB1374.41C6@gsf.de> NNTP-Posting-Host: ariane.gsf.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; OSF1 V3.2 alpha) We would like to announce the availability of an alignment program called DIALIGN ******* DIALIGN is a completely novel program for pairwise as well as multiple alignment of nucleic acid and protein sequences. It is especially suited to detect local similarities in otherwise completely unrelated sequences and it does not employ any kind of gap penalty. The method is described in B. Morgenstern, A. Dress, T. Werner: Multiple DNA and protein sequence alignment based on segment-to-segment comparison Proc. Natl. Acad. Sci. 93 pp. 12098 - 12103 (1996) DIALIGN executables for various UNIX platforms (DEC, SGI, CONVEX, HP, SUN) together with a detailed user guide, online help and a test example are available at http://www.gsf.de/biodv/dialign.html or via ftp: ftp://ariane.gsf.de/pub/unix/dialign More detailed information on DIALIGN is available at our web page. If you have any questions, please feel free to contact us by e-mail. Burkhard Morgenstern ---------------------------------------------------------- Dr. Burkhard Morgenstern GSF - National Research Center for Environment and Health, Institute of Biomathematics and Biometry Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany morgenstern@gsf.de From owner-software@net.bio.net Sun Feb 09 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Ivo Wiesner Newsgroups: bionet.software Subject: [Q]:your experience with DNAsis, PC-Gene, Omiga Date: 10 Feb 1997 13:41:11 -0000 Lines: 11 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5dn8hn$25m@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: bio-software@dl.ac.uk Dear Netter, considering to buy some local sequence analysis software for IBM-PC I would much appreciate your recommendations and experience, esp. about the differences (for practical user) between DNAsis, PC-Gene, OMIGA or other pckages? What would be currently the point of choice? (considering Pentium CPU) Thank you for your replies directly to my address nfix@jcu.cz Ivo Wiesner From owner-software@net.bio.net Sun Feb 09 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!hunter.premier.net!uunet!in2.uu.net!198.168.54.138!rcogate.rco.qc.ca!altitude!usenet From: Christine Dumas Newsgroups: bionet.software Subject: Re: Windows: sequence analysis Date: Mon, 10 Feb 1997 09:06:47 -0500 Organization: Lynnon BioSoft Lines: 21 Message-ID: <32FF2B77.6AC2@lynnon.qc.ca> References: <5cpibd$jnl$1@mark.ucdavis.edu> <32F7948C.79E@molbiol.uct.ac.za> Reply-To: cdumas@lynnon.qc.ca NNTP-Posting-Host: dynppp-28.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) CC: eimert@geisenheim.fa.fh-wiesbaden.de Ed Rybicki wrote: > Hi - we have recently started to use DNAMAN from Lynnon Biosoft up in > Canada; it is remarkably full-featured (if a bit idiosyncratic), and > will do multiple sequence alignment, translation, dna frag assembly, PCR > primer and oligo design...it is also CHEAP ($260 or so). Works well > under Win 3.1 and is LIGHTNING fast on even long sequence multiple > alignments. Also does shading of alignments (another perennial q). > -- Here is the address of Lynnon BioSoft: Lynnon BioSoft 88, rue Adam Vaudreuil, Quebec Canada J7V 8P5 Tel: (514) 455-4894 Fax: (514) 455-4269 email: mail@lynnon.qc.ca support: support@lynnon.qc.ca From owner-software@net.bio.net Sun Feb 09 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!news-peer.gsl.net!news.gsl.net!howland.erols.net!rill.news.pipex.net!pipex!uknet!usenet1.news.uk.psi.net!uknet!uknet!newsfeed.ed.ac.uk!singer.cent.gla.ac.uk!lenzie!gpaa29 From: gpaa29@lenzie (Francis L.Burton) Newsgroups: bionet.software Subject: Re: What is your favorite patch-clamp hardware/software? Date: 10 Feb 1997 10:06:01 GMT Lines: 16 Message-ID: <5dmru9$2u9@singer.cent.gla.ac.uk> References: <32f99325.3279390@news.uni-marburg.de> <32FC80D3.3EC1@interlynx.net> NNTP-Posting-Host: lenzie.cent.gla.ac.uk X-Newsreader: NN version 6.5.0 #18 (NOV) I don't know what my favourite hardware/software would be if I was still working in the patch-clamping field. I used EPC-7 with analysis software I wrote myself -- it got the job done. The most impressive system I ever saw was ISO2 which was demoed by its creator M. Friedrich at the 1993 IUPS meeting in Glasgow. It was (is?) a fast multitasked system allowing simultaneous voltage pulse generation, digitization and display. It had a pretty comprehensive set of analysis functions. The main flaw in the design was its dependence on particular a A/D and high resolution display card, though that allowed it to leave the competition in the dust in terms of performance. Francis From owner-software@net.bio.net Sun Feb 09 22:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!news-peer.gsl.net!news.gsl.net!howland.erols.net!rill.news.pipex.net!pipex!oleane!in2p3.fr!swidir.switch.ch!serra.unipi.it!mikasa.iol.it!news From: edoardo.shockwav@iol.it (Edo) Newsgroups: bionet.software Subject: Re: male and female symbol Date: Mon, 10 Feb 1997 09:53:22 GMT Organization: Italia Online Lines: 12 Message-ID: <32fe0861.4006105@news.iol.it> References: <32fc8e3a.2129086@news.iol.it> NNTP-Posting-Host: 194.20.26.70 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent .99g/32.339 I finally found it! Thank you to all the kind people that wrote me. Edo On Fri, 07 Feb 1997 20:56:18 GMT, edoardo.shockwav@iol.it (Edo) wrote: >I am looking for a TTF (True Type Font, for