From owner-software@net.bio.net Sun Jan 02 22:00:00 1994 Newsgroups: bionet.software Path: biosci!news.cs.umb.edu!hsdndev!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Subject: preview don's c++ class app library Message-ID: Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: sunflower.bio.indiana.edu Organization: Biology, Indiana University - Bloomington Date: Sat, 1 Jan 1994 00:10:03 GMT Lines: 30 My holiday gift to the world is a bit delayed, but here is a peak at it: a C++ application library, built on NCBI's Vibrant and core toolkit, for software developers. Don's Class Application library (DCLAP) will let me, and others if they want, write applications in a relatively easy way, using this oop application library. The applications will compile and run on any platforms that NCBI's Vibrant toolkit supports, that currently being Macintosh, MS-Windows and Motif-XWindows. MyApp-sparc-motif was compiled on my Sun Sparcstation, using a Motif library. It requires, I believe, the shared motif run-time libraries on your Sparc system to work. MyApp.hqx was compiled for Macintoshes. I don't have an MS-Windows system (yet), so can't provide that version. Other-Bio-Gophers is a gopher doc that one of the demos can read. The source for this C++ library will be made available free to the public -- but it still needs much work. This tidbit is at ftp.bio.indiana.edu:/util/dclap/preview -- Don Gilbert -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Sun Jan 02 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: risler@cgmvax.cgm.cnrs-gif.fr Newsgroups: bionet.software Subject: Re: Transmembrane region prediction Date: 3 Jan 1994 10:08:07 -0000 Lines: 26 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2g8qq7$8dk@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk > >Does anyone know if there is a program out there that predicts transmembrane >regions using the algorithm of Eisenberg, Schwarz, Komaromy and Wall (J. >Mol. Biol. 179:125-142. (1984))? I have a user who is interested in that >specific algorithm. > A FORTRAN version of Eisenberg's algorithm (Eisenberg et al., PNAS 81 (1984) 140-144) has been written by G.D. Fasman and W.A. Gilbert (see TIBS 15 (1990) 89-92). I've dowloaded the MOMENT program from W. Gilbert's server. Works fine. I can mail you the source if you wish. Cheers, Jean-Loup --------------------------------------------------------------------- Jean-Loup Risler Tel: (33 1) 69 82 31 34 CNRS Fax: (33 1) 69 07 49 73 Centre de Genetique Moleculaire Email: risler@cgmvax.cgm.cnrs-gif.fr 91198 Gif sur Yvette Cedex France --------------------------------------------------------------------- From owner-software@net.bio.net Sun Jan 02 22:00:00 1994 Path: biosci!hubcap!darwin.sura.net!spool.mu.edu!uwm.edu!msuinfo!thomashaw-at.css.msu.edu From: bloksber@pilot.msu.edu (Leonard N. Bloksberg) Newsgroups: bionet.software,bionet.software.gcg Subject: Re: Printing GCG graphics with PC Date: Sun, 02 Jan 1994 14:41 EDT Organization: Michigan State U., Crop & Soils Dept. Lines: 64 Distribution: world Message-ID: <19940102144109.bloksber@thomashaw-at.css.msu.edu> References: <2g2pmv$hmo@TAMUTS.TAMU.EDU> <2f51mn$o0n@TAMUTS.TAMU.EDU> <19931228130241.bloksber@thomashaw-at.css.msu.edu> NNTP-Posting-Host: thomashaw-at.css.msu.edu X-Newsreader: FTPNuz (DOS) v1.0 Xref: biosci bionet.software:6832 bionet.software.gcg:249 In Article <2g2pmv$hmo@TAMUTS.TAMU.EDU> "dln4300@TAMUTS.TAMU.EDU (David L. Northcliffe)" says: > In article <19931228130241.bloksber@thomashaw-at.css.msu.edu>, > Leonard N. Bloksberg wrote: > >I have done this on both my old vax account, and my new unix account. It > >is very simple, and I usually set it up in my login.com or .login as the > >default for my account. The commands are the same on both accounts, but the > >syntax my change a little. Try a couple permutations to see what works on > >your system, then write it into your login file as your default. First, you > >must set up your HP Laserprinter on LPTI (look up the commands for another > >printer). It will not read LPTII, and I cannot get it to re-set. I have > >gotten it to go to a network printer that was networked through LPTI. The > >command is: > >. > >hpgl laserjetiii term > >. > > About two years ago I did a lot of experimenting with different GCG > graphics configurations. Here are the resulting modifications in our > login.com file (of course this is Vax syntax): > > $! ********* Graphics/Plotting Mode Command Abbreviations ******** > $! > $ tk :=='Tektronix' Tek4014 Term: > $! > $ tv :=='Tektronix' VersaTerm-Tek4105 Term: > $! > $ ps :=='PostScript' LaserWriter Term: > $! > $ lj :=='HPGL' LaserJetIII Term: a4 > $! > $ hp :=='HPGL' HP7550 hpout.hpgl a4 > $! > $ eps :== 'PostScript' EPSF psout.epsf > $! > $! > > The command "lj", pass-through printing to LaserJet, has never worked for > me before, but it just worked 5 minutes ago. Hmmmmmmm. It did goof up > the margin, however, so I might have to set the page to something else > besides A4. > > .............................................................................. > David Northcliffe > dln4300@rigel.tamu.edu > dln4300@tamuts.tamu.edu > > I had some problem with this too. Turns out that most programs re-set margins on the HP Laserjet to program settings. Some programs (especially true pass-through type jobs) just take the default settings on the printer. Most programs that I have ever seen use 66 lines per page as default, but every HP Laserjet I have used comes with 60 lines per page as default. You can re-set your laserjet by pressing "On-Line" to take it off line, and using "Menu" and "+", "-", and "Enter" to re-set the printer defaults. This should work for this problem. . As for the rest of your comments, thanks for a very informative post. :-) . Good Luck. . . Leonard N. Bloksberg . bloksber@pilot.msu.edu . . From owner-software@net.bio.net Sun Jan 02 22:00:00 1994 Newsgroups: bionet.software Path: biosci!hubcap!darwin.sura.net!europa.eng.gtefsd.com!library.ucla.edu!news.mic.ucla.edu!unixg.ubc.ca!nntp.cs.ubc.ca!newsserver.sfu.ca!sfu.ca!chapmaa From: chapmaa@fraser.sfu.ca (John G Chapman) Subject: *WhitePages Project* Message-ID: Sender: news@sfu.ca Organization: Simon Fraser University, Burnaby, B.C., Canada Date: Sun, 2 Jan 1994 04:12:51 GMT Lines: 36 **************************************************************************** NetMinder WhitePages Project CPProgma Software Inc. is in the process of putting together a public domain "White Pages/Yellow Pages" type E-Mail directory. The data collected will be put into DBASE IV format for use in the NetMinder for MS Windows Internet address database program. This data could also be viewed by any other program supporting this format and will be available to the public via FTP free of charge. Already hundreds of entries have been voluntarily provided and placed in a searchable database. If you want to be listed please send the following information to cpprogma.software@deepcove.com Email Address Full Name Company Name Physical Address Telephone Number One Line Description of self or business/organization (optional) If there are any questions regarding the project please feel free to send them to the same address. A demonstration version of the NetMinder Internet Address Book for MS Windows is available for FTP from ftp.uu.net in the /tmp/NETMINDER/ directory as ntmdr11.zip, and also from many other FTP sites. Unzip it to a floppy and follow the directions provided by the installation program. John Chapman Systems Manager CPProgma Software Inc. chapmaa@sfu.ca cpprogma.software@deepcove.com From owner-software@net.bio.net Sun Jan 02 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!vixen.cso.uiuc.edu!sdd.hp.com!col.hp.com!csn!tali.hsc.colorado.edu!mwmt17.hsc.colorado.edu!user From: weil_j@defiance.hsc.colorado.edu (John V. Weil) Newsgroups: bionet.software Subject: PHS 398 grant forms(?) Followup-To: bionet.software Date: 3 Jan 1994 23:13:53 GMT Organization: CVP Research Lab Lines: 6 Message-ID: NNTP-Posting-Host: mwmt17.hsc.colorado.edu Does anyone know where I can find NIH grant forms (PHS 398) in either DOS or Windows format?? Many Thanks, -- John V. Weil From owner-software@net.bio.net Sun Jan 02 22:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!sunic!EU.net!julienas!dmi.ens.fr!dmi!claros From: claros@biologie.ens.fr (Manuel G. CLAROS) Subject: Re: Transmembrane region prediction Message-ID: Sender: news@ens.fr (USENET News System) Nntp-Posting-Host: lgmmac0.ens.fr Organization: Ecole Normale Supˇrieure, Gˇnˇtique Molˇculaire X-Newsreader: VersaTerm Link v1.1.1 References: <2g8qq7$8dk@mserv1.dl.ac.uk> Distribution: bionet Date: Mon, 3 Jan 94 10:48:45 GMT Lines: 19 > >Does anyone know if there is a program out there that predicts transmembrane >regions using the algorithm of Eisenberg, Schwarz, Komaromy and Wall (J. >Mol. Biol. 179:125-142. (1984))? I have a user who is interested in that >specific algorithm. > I have developed this algorithm, for other that predict transmembrane domains, in Pascal. To predict transmembrane domains there is another algorithm developed by G. von Heijne. He and I have constructed the program TopPred (available in the EMBO server). TopPred has been developed also in Pascal for Macintosh. Manuel _____________________________Manuel_G._CLAROS__________________________________ | Ecole Normale Superieure - CNRS | E-mail: claros@biologie.ens.fr | | Lab. Genetique Moleculaire | Fax: 331-44 32 39 41 | | 46 rue d'Ulm | Phone: 331-44 32 39 39 | | 75005 Paris (France) | | _______________________________________________________________________________ From owner-software@net.bio.net Sun Jan 02 22:00:00 1994 Newsgroups: bionet.software Path: biosci!hubcap!darwin.sura.net!howland.reston.ans.net!xlink.net!zib-berlin.de!netmbx.de!Germany.EU.net!EU.net!ub4b!reks.uia.ac.be!news From: przemko@reks.uia.ac.be (Przemko) Subject: workstation Message-ID: <1994Jan3.131757.21289@reks.uia.ac.be> Sender: news@reks.uia.ac.be (USENET News System) Organization: University of Antwerp X-Newsreader: Date: Mon, 3 Jan 1994 13:17:57 GMT Lines: 15 Hi and Happy New Year! I hope it is the right newsgroup for this question. We are currently looking into buying a workstation. This machine would be used to run various programs related to molecular biology. So it would be something like IG Suite, some DNA and protein analysis (secondary, maybe tertiary structures), multiple alignements, the works. I am looking for some input relating to the workstation itself. From the net experience (I know many things are program dependent...) what kind of workstation could you recommend. Silicon Graphics, Sun, Alpha? I will summarize the responses and post it back. Thanks a lot! Przemko From owner-software@net.bio.net Sun Jan 02 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!news.univie.ac.at!fstgds15.tu-graz.ac.at!balu.kfunigraz.ac.at!bimk03.kfunigraz.ac.at!koraimann From: koraimann@bkfug.kfunigraz.ac.at (Dr. G. Koraimann) Newsgroups: bionet.software Subject: Re: gcg newsgroup??? Date: Mon, 3 Jan 1994 18:04:31 Organization: University of Graz Lines: 41 Distribution: world Message-ID: References: <1993Dec29.172553.28549@nomina.lu.se> <1993Dec29.212548.67@immunbio.mpg.de> NNTP-Posting-Host: bimk03.kfunigraz.ac.at X-Newsreader: Trumpet for Windows [Version 1.0 Rev Final Beta #8] In article <1993Dec29.212548.67@immunbio.mpg.de> GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) writes: >Subject: Re: gcg newsgroup??? >From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) >Date: 29 Dec 93 21:25:48 +0100 >In <1993Dec29.172553.28549@nomina.lu.se> Bo writes: >> There used to be a newsgroup called >> >> bit.listserv.info-gcg >> >> isn't it alive anylonger or has it been renamed?? >This group (which was in fact a Bitnet mailing list named INFO-GCG) has been >moved to a real newsgroup within the bionet hierarchy: bionet.software.gcg >Regards & and a happy New Year > Christoph Gartmann >+----------------------------------------------------------------------------+ >| Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 | >| Immunbiologie PSI : PSI%(0262)45050160374::GARTMANN | >| Postfach 1169 Internet: gartmann@immunbio.mpg.de | >| D-79011 Freiburg, FRG | >+------------- Do you know MENUE, the user environment for VMS? -------------+ Hi! Why don´t I see this newsgroup in the listing of all the newsgroups? (I mean the bionet.software.gcg group !) Any ideas?? DR.G.KORAIMANN Institut für Mikrobiologie Universitätsplatz 2 A- 8010 Graz AUSTRIA - EUROPE Tel: (316) 380 5620 Fax: (316) 381548 e-mail: koraimann@bkfug.kfunigraz.ac.at From owner-software@net.bio.net Mon Jan 03 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!cs.utexas.edu!swrinde!sgiblab!munnari.oz.au!newshost.anu.edu.au!rscmacl10.anu.edu.au!user From: crowther@rsc3.anu.edu.au (Jeff) Newsgroups: bionet.software Subject: Re: Commercial Mac Primer Design Software ? Followup-To: bionet.software Date: Tue, 04 Jan 1994 18:22:33 +1000 Organization: Usually Quite Poor Lines: 49 Distribution: bionet Message-ID: References: <2f739e$bpq@mserv1.dl.ac.uk> NNTP-Posting-Host: 150.203.36.10 In article <2f739e$bpq@mserv1.dl.ac.uk>, plewniak@titus.u-strasbg.fr (BIOSCI) wrote: > > Jeff Martino asked : > > >In your opinion what's the best _commercial_ Macintosh program for > >PCR/sequencing primer design. > > .... > > >Quote: "I want to enter a template sequence, show the acceptable region of > >the template I want the primer(s) to bind, and let the program choose the best > >primer or pair -- minimized secondary structure, minimized self-dimer, > >minimized dimer with other amplimer, etc." > > > >--Jeff Martino > > > > We use here Oligo which was written by Wojciech Rychlik (Rychlic et al. 1990, > Nucleic Acids Res. 18, 6409-6412)....................... > >................. > I don't know if this is actually the best one since it's the only one I've > ever used on a Macintosh (has anyone heard of another one?... ) but it > certainly looks like one that might fit your requirements. You could also look into GENE JOCKEY Biosoft 22 Hills Road Cambridge CB2 1JP UK Might not be as good as Oligo above but has been recently overhauled for the new edition. Have not seen the improvments as no upgrade from version we use to new one was forthcoming and don't want to by the program twice. There is a distributor in USA now, I think Biosoft but not sure of address, that you have to get from UK.......Sorry. -- My Best Regards Jeff From owner-software@net.bio.net Mon Jan 03 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!xlink.net!zib-berlin.de!netmbx.de!Germany.EU.net!EU.net!ub4b!reks.uia.ac.be!news From: przemko@reks.uia.ac.be (Przemko) Subject: Re: Transmembrane region prediction Message-ID: <1994Jan4.085154.27763@reks.uia.ac.be> Sender: news@reks.uia.ac.be (USENET News System) Organization: University of Antwerp X-Newsreader: Date: Tue, 4 Jan 1994 08:51:54 GMT Lines: 28 In article claros@biologie.ens.fr (Manuel G. CLAROS) writes: >> >>Does anyone know if there is a program out there that predicts transmembrane >>regions using the algorithm of Eisenberg, Schwarz, Komaromy and Wall (J. >>Mol. Biol. 179:125-142. (1984))? I have a user who is interested in that >>specific algorithm. >> >I have developed this algorithm, for other that predict transmembrane >domains, in Pascal. To predict transmembrane domains there is another >algorithm developed >by G. von Heijne. He and I have constructed the program TopPred (available in >the EMBO server). TopPred has been developed also in Pascal for Macintosh. > >Manuel >_____________________________Manuel_G._CLAROS__________________________________ >| Ecole Normale Superieure - CNRS | E-mail: claros@biologie.ens.fr | >| Lab. Genetique Moleculaire | Fax: 331-44 32 39 41 | >| 46 rue d'Ulm | Phone: 331-44 32 39 39 | >| 75005 Paris (France) | | >_______________________________________________________________________________ Hello, I have looked in the EMBL server as well as in couple others but could find only the Mac version. Could you tell me where the DOS version would be? ThanX Przemko From owner-software@net.bio.net Mon Jan 03 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!paladin.american.edu!darwin.sura.net!jhunix.hcf.jhu.edu!welchlink.welch.jhu.edu!jcarroll From: jcarroll@welchlink.welch.jhu.edu (JOHN L. CARROLL) Newsgroups: bionet.software Subject: Re: PHS 398 grant forms(?) Date: 4 Jan 1994 02:25:48 GMT Organization: Johns Hopkins Univ. Welch Medical Library Lines: 15 Distribution: world Message-ID: <2gak3cINNa9p@jhunix.hcf.jhu.edu> References: NNTP-Posting-Host: welchlink.welch.jhu.edu In article weil_j@defiance.hsc.colorado.edu (John V. Weil) writes: >Does anyone know where I can find NIH grant forms (PHS 398) in either DOS >or Windows format?? PHS 398 templates for MS-WORD used to be available on the NIH gopher. If you don't have this gopher available on a local menu I can supply you with the address. John C. -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ John L. Carroll JHU-JHMS-CMSC Baltimore, Maryland Voice: 410 955-2035 Internet: jcarroll@welchlink.welch.jhu.edu Fax: 410 955-1030 From owner-software@net.bio.net Mon Jan 03 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!warwick!pipex!howland.reston.ans.net!usenet.ins.cwru.edu!ukma!seqanal.mi.uky.edu!fasm From: fasm@seqanal.mi.uky.edu (Primer Fac. BCH) Newsgroups: bionet.software Subject: Re: PHS 398 grant forms(?) Date: 4 Jan 1994 01:45:11 GMT Organization: University of Kentucky, Dept. of Math Sciences Lines: 15 Message-ID: <2gahn7$dft@s.ms.uky.edu> References: NNTP-Posting-Host: seqanal.mi.uky.edu X-Newsreader: TIN [version 1.1 PL9] John V. Weil (weil_j@defiance.hsc.colorado.edu) wrote: : Does anyone know where I can find NIH grant forms (PHS 398) in either DOS : or Windows format?? : Many Thanks, : -- : John V. Weil If anyone has them I'd appreciate a copy also. Thanks, Paul Brandt tcv@seqanal.mi.uky.edu From owner-software@net.bio.net Mon Jan 03 22:00:00 1994 Path: biosci!biosci!not-for-mail From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software Subject: Re: gcg newsgroup??? Followup-To: poster Date: 3 Jan 1994 16:22:20 -0800 Organization: BIOSCI International Newsgroups for Biology Lines: 542 Distribution: bionet Message-ID: <2gacrs$igl@net.bio.net> References: <1993Dec29.172553.28549@nomina.lu.se> <1993Dec29.212548.67@immunbio.mpg.de> Reply-To: biosci-help@net.bio.net NNTP-Posting-Host: net.bio.net >>This group (which was in fact a Bitnet mailing list named INFO-GCG) has been >>moved to a real newsgroup within the bionet hierarchy: bionet.software.gcg > >Hi! > >Why don´t I see this newsgroup in the listing of all the newsgroups? >(I mean the bionet.software.gcg group !) >Any ideas?? > >DR.G.KORAIMANN Which "listing of all the newsgroups" are you referring to? If you are referring to your local news configuration, your news administrator may not have acted on our message to create the newsgroup when it was set up *many* months ago. Many sites require manual intervention instead of acting on newsgroup creation messages automatically. I include the latest BIOSCI info sheet for Europe below. If you find other groups in our list that you don't have locally, you should contact your systems administrator and make sure that they act on bionet hierarchy creation notices. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net ---------------------------------------------------------------------- THE BIOSCI ELECTRONIC NEWSGROUP NETWORK INFORMATION SHEET (last revised 8-DEC-93) ---------------------------------------------------------------------- This is the BIOSCI information sheet for Europe, Africa, and Central Asia. If you are located in the Americas or the Pacific Rim countries, please request that version of the BIOSCI information sheet by sending e-mail to the Internet address: biosci-help@net.bio.net. New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/doc/biosci.FAQ. It may also be requested by sending e-mail to biosci-help@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. ---------------------------------------------------------------------- Introduction ------------ The BIOSCI newsgroup network was developed to allow easy worldwide communications between biological scientists who work on a variety of computer networks. BIOSCI is supported by the National Science Foundation, Department of Energy, and National Institutes of Health in the U.S.A. and by the Science and Engineering Research Council Daresbury Laboratory in the United Kingdom. BIOSCI services are available to users free of charge. BIOSCI messages are distributed by two means: USENET news software and electronic mail. WE STRONGLY ENCOURAGE ALL INTERESTED USERS TO EXPLORE GETTING "USENET NEWS" SOFTWARE AT YOUR SITE. The software is in the public domain, and you will find it much more convenient than subscribing to newsgroups by e-mail. Please consult your systems manager (the software may already be available on a machine at your institution) or contact biosci-help@net.bio.net for a list of software available free of charge on the Internet. NOTE, however, that the installation and maintenance of news software requires the assistance of a trained systems operator in most cases and is not a task to be undertaken by a computer novice. Why is news software preferable to e-mail? News software recovers messages automatically after network interruptions, whereas your e-mail address may have to be removed from the subscription list at times if your computer/network malfunctions and undelivered mail starts bouncing back to the BIOSCI administrative sites. You will have to manually retrieve lost messages from the archives if your e-mail subscription is suspended. News software organizes messages by topic and subtopic for easy browsing. In contrast if you subscribe by e-mail to more than one discussion list, messages from multiple lists arrive into your personal mail file in chronological order of posting only and are mixed in with your personal messages. You have to connect the discussion threads yourself if you use e-mail. In summary, e-mail participation should be seen as a LAST RESORT to be used only if news software can not be installed locally. Fortunately, BIOSCI offers advantages for e-mail users too. By having distribution sites or "nodes" on each major network, BIOSCI allows its e-mail users to contact people around the world without having to learn a variety of computer addressing tricks. Any user can simply post a message to his/her regional BIOSCI node and copies of that message will be distributed automatically to all other subscribers on all of the participating networks, including the Internet, USENET, BITNET, EARN, NETNORTH, HEANET, and JANET. List of BIOSCI newsgroups ------------------------- BIOSCI messages are distributed on the newsgroups in the "bionet" hierarchy of USENET and on the corresponding mailing lists indicated below. Contents of the USENET newsgroups and the e-mail distributions are *identical*, i.e., messages sent in by e-mail are also forwarded to USENET and messages posted to USENET newsgroups are also distributed to e-mail subscribers. An expanded description of the purpose of each newsgroup follows this list. MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY + bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS ** bionet.announce BIO-JOURNALS ** bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY ** bionet.biology.computational DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography RAPD bionet.molbio.rapd SCIENCE-RESOURCES ** bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast + full name is BIOLOGICAL-INFORMATION-THEORY-AND-CHOWDER-SOCIETY ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. List of BIOSCI Newsgroup Topics ------------------------------- MAILING LIST NAME TOPIC ----------------- ----- ACEDB-SOFT Discussions by users and developers of genome databases using the ACEDB software. AGEING Discussions about ageing research AGROFORESTRY Discussions about agroforestry research ARABIDOPSIS Newsgroup for the Arabidopsis Genome Project BIOFORUM Discussions about biological topics for which there is not yet a dedicated newsgroup BIOLOGICAL-INFORMATION- THEORY-AND-CHOWDER-SOCIETY Applications of information theory to biology BIONAUTS Question/answer forum for help using electronic networks, locating e-mail addresses, etc. BIONEWS ** General announcements of widespread interest to biologists BIO-JOURNALS ** Tables of Contents of biological journals BIO-MATRIX Applications of computers to biological databases BIO-SOFTWARE Information on software for the biological sciences BIOTHERMOKINETICS Discussions about the kinetics, thermodynamics and control of biological processes at the cellular level CELL-BIOLOGY Discussions about cell biology including cancer research at the cellular level CHLAMYDOMONAS Discussions about the biology of the green alga Chlamydomonas and related genera CHROMOSOMES Discussions about mapping and sequencing of eucaryote chromosomes COMPUTATIONAL-BIOLOGY ** Mathematical and computer applications in biology DROSOPHILA Discussions about biological research on Drosophila EMBL-DATABANK Messages to and from the EMBL database staff EMPLOYMENT Job opportunities in biology (see BIOSCI FAQ *before* posting commercial job openings) GDB Messages to and from the Genome Data Bank staff GENBANK-BB Messages to and from the GenBank database staff GENETIC-LINKAGE Newsgroup for genetic linkage analysis HIV-MOLECULAR-BIOLOGY Discussions about the molecular biology of HIV HUMAN-GENOME-PROGRAM NIH-sponsored newsgroup on human genome issues IMMUNOLOGY Discussions about research in immunology INFO-GCG Discussions about the GCG sequence analysis software JOURNAL-NOTES Practical advice on dealing with professional journals METHODS-AND-REAGENTS Requests for information and lab reagents MOLECULAR-EVOLUTION Discussions about research in molecular evolution MYCOLOGY Discussions about research on filamentous fungi NEUROSCIENCE Discussions about research in the neurosciences N2-FIXATION Discussion about biological nitrogen fixation PHOTOSYNTHESIS Discussions about photosynthesis research PLANT-BIOLOGY Discussions about research in plant biology POPULATION-BIOLOGY Discussions about research in population biology PROTEIN-ANALYSIS Discussions about research on proteins and messages for the PIR and SWISS-PROT databank staffs. PROTEIN-CRYSTALLOGRAPHY Discussion about crystallography of macromolecules and messages for the PDB staff RAPD Discussions about Randomly Amplified Polymorphic DNA SCIENCE-RESOURCES ** Information from/about scientific funding agencies TROPICAL-BIOLOGY Discussions about research in tropical biology VIROLOGY Discussions about research in virology WOMEN-IN-BIOLOGY Discussions about issues concerning women biologists YEAST Discussions about the molecular biology and genetics of yeast ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. BIOSCI Newsgroup Discussion Leaders ----------------------------------- Most scientific specialty newsgroups (except for a few created several years ago) have individuals who are responsible for stimulating discussion on the newsgroup. General purpose forums such as METHODS-AND-REAGENTS do not have discussion leaders. If a group that you are interested in does not seem to have much activity recently, please contact the discussion leader and ask why. NEWSGROUP NAME Discussion Leader and their e-mail address -------------- ------------------------------------------ ACEDB-SOFT Mike Cherry (cherry@genome.stanford.edu) AGEING Sydney Shall (bafa1@central.sussex.ac.uk) AGROFORESTRY Gerry Lawson (F_GJL@vaxa.nerc-bush.ac.uk) ARABIDOPSIS Chris Somerville (21847CRS@msu.edu) BIOFORUM None BIOLOGICAL-INFORMATION- THEORY-AND-CHOWDER-SOCIETY Tom Schneider (toms@ncifcrf.gov) BIONAUTS Rob Harper (harper@convex.csc.fi) BIONEWS ** David Kristofferson (kristoff@net.bio.net) BIO-JOURNALS ** David Kristofferson (kristoff@net.bio.net) BIO-MATRIX Dan Davison (davison@uh.edu) BIO-SOFTWARE None BIOTHERMOKINETICS John Woods (eanv20@castle.edinburgh.ac.uk) CELL-BIOLOGY Ola Myklebost (ola.myklebost@dnr.uio.no) CHLAMYDOMONAS Elizabeth H. Harris (chlamy@acpub.duke.edu) and Antonio R. Franco (bf1rodri@cc.uco.es) CHROMOSOMES Bruce Roe (broe@aardvark.ucs.uoknor.edu) and Greg Lennon (greg@mendel.llnl.gov) COMPUTATIONAL-BIOLOGY ** Phil J. Curtiss (curtiss@umiacs.umd.edu) DROSOPHILA Michael Ashburner (m.ashburner@gen.cam.ac.uk) EMBL-DATABANK None (datalib@embl-heidelberg.de) EMPLOYMENT None GDB Kerryn Brandt (kab@welchgate.welch.jhu.edu) GENBANK-BB Dennis Benson (benson@ncbi.nlm.nih.gov) GENETIC-LINKAGE Steve Bryant (s_bryant@icrf.ac.uk) HIV-MOLECULAR-BIOLOGY Mika Salminen (msalminen@nphi.fi) HUMAN-GENOME-PROGRAM Jane Peterson (jp2@cu.nih.gov) IMMUNOLOGY Donald Forsdyke (forsdyke@qucdn.queensu.ca) INFO-GCG John Cargill (cargill@ocicl.oci.utoronto.ca) JOURNAL-NOTES Donald Forsdyke (forsdyke@qucdn.queensu.ca) METHODS-AND-REAGENTS None MOLECULAR-EVOLUTION Dan Davison (davison@uh.edu) MYCOLOGY Tom Adams (tom@bio.tamu.edu) Leland Ellis (leland@straylight.tamu.edu) Greg May (gsmay@bcm.tmc.edu) NEUROSCIENCE Vincent A Mazzarella (vamg6792@uxa.cso.uiuc.edu) N2-FIXATION Eng-Leong Foo (eng-leong_foo_mircen-ki%micforum@mica.mic.ki.se) PHOTOSYNTHESIS Johnathan Marder (marder@agri.huji.ac.il) PLANT-BIOLOGY Tony Travis (ajt@rri.sari.ac.uk) POPULATION-BIOLOGY None PROTEIN-ANALYSIS Amos Bairoch (bairoch@cmu.unige.ch) and John Garavelli (garavelli@nbrf.georgetown.edu) PROTEIN-CRYSTALLOGRAPHY Morten Kjeldgaard (morten@oase.kemi.aau.dk) RAPD James Farmer (farmerj@yvax.byu.edu) SCIENCE-RESOURCES ** David Kristofferson (kristoff@net.bio.net) TROPICAL-BIOLOGY Matti Nummelin (saarikko@cc.helsinki.fi) VIROLOGY Robert Coelen (robert@arbo.microbiol.uwa.oz.au) WOMEN-IN-BIOLOGY Cassandra Smith (cls@buenga.bu.edu) YEAST Francis Ouellette (francis@ncbi.nlm.nih.gov) ** Note that newsgroups flagged with ** are moderated. Participating in BIOSCI Using USENET News Software -------------------------------------------------- Users who have access to USENET news software and the bionet USENET groups can participate immediately, i.e., they do not need to "subscribe" to anything. They can read and reply to messages using their local news software (e.g., "nn" or "rn") and post new messages of their own. Users will have to consult their local systems managers for help in using news software. There are many different programs available and the BIOSCI staff can not provide training in news software use. Fortunately, most news software is fairly simple to use and can be learned quickly. When posting new messages, USENET users should be sure to set the message "distribution" to "world" or "bionet" or else your message may not be distributed beyond your local computer. In most cases, messages are posted directly to the newsgroups without editorial intervention. Some groups (indicated in the lists above) are "moderated," however. This means that postings to these newsgroups will be sent to the newsgroup moderator who will decide whether or not the message is suitable for posting to the newsgroup in question. Participating in BIOSCI by E-mail --------------------------------- PLEASE NOTE THAT IF YOU HAVE ACCESS TO USENET NEWS YOU DO NOT NEED AN E-MAIL SUBSCRIPTION!! Simply read and post to the newsgroups in the "bionet" newsgroup hierarchy using your USENET news software. E-mail Subscription Requests and other Information -------------------------------------------------- For users in Europe, Africa, and Central Asian countries, e-mail subscription and cancellation requests are handled automatically by an e-mail server, although personal assistance is also available via the biosci@daresbury.ac.uk address. Once your e-mail address is added to a subscription list, mail will be sent to your address automatically each time someone posts a message. This will continue until you remove your address from the subscription list. To obtain instructions automatically on BIOSCI e-mail server use, please send a message to the address MXT@dl.ac.uk NOTE!! WE WILL ASSUME THAT YOU HAVE FOLLOWED THESE INSTRUCTIONS and will DELETE any message to the administrative address biosci@daresbury.ac.uk that simply requests us to carry out manually "subscribe" or "unsubscribe" commands without further explanation. IF YOU NEED HUMAN ASSISTANCE, PLEASE SAY SO PROMINENTLY AND EXPLICITLY AT THE BEGINNING OF YOUR MAIL. For example, please put the line ASSISTANCE NEEDED at the beginning of the body of your message or in the Subject: line of your message to biosci@daresbury.ac.uk. E-mail Address Changes ---------------------- If you have subscribed to a newsgroup and are now leaving an institution or changing your e-mail address, it is IMPERATIVE that you send a note to biosci@daresbury.ac.uk and cancel your subscription! Non-existent addresses or overflowing mailboxes cause computer mail programs to send back "daemon" messages which might bother everybody on the newsgroup. We will immediately remove any address causing such a problem, but would prefer it if you would notify us in advance as a courtesy to the rest of the user community. Interruption of E-mail Service ------------------------------ It is our policy to remove any address from our mailing lists which becomes inaccessible and causes mail to bounce back to the sender. This might happen to you if your local computer or network fails for a significant period of time. If you notice that you are no longer receiving BIOSCI postings, it may be because your address was removed for the above reason. It will be necessary for you to contact biosci@daresbury.ac.uk and resubscribe. Please see the BIOSCI FAQ, mentioned at the beginning of this document, for more details on how BIOSCI handles addresses which reject mail. Posting Messages to Newsgroups by E-mail ---------------------------------------- Those who use e-mail to post messages should send their mail to the following addresses in the U.K.: ********************************************************************** DO NOT, REPEAT, DO NOT POST SUBSCRIPTION OR CANCELLATION REQUESTS DIRECTLY TO ANY OF THE NEWSGROUP E-MAIL POSTING ADDRESSES. PLEASE USE ONLY THE ADDRESS biosci@daresbury.ac.uk for subscription or cancellation requests as explained above. Your posting could go to several thousand people. Supposing that each person spends a couple of seconds to figure out that you did this, before they go on to the next message. You will have wasted the equivalent of several hours of one person's time, not to mention wasted computer time and disk storage. ********************************************************************** MAILING LIST NAME Mailing Address ----------------- ---------------- ACEDB-SOFT acedb@daresbury.ac.uk AGEING ageing@daresbury.ac.uk AGROFORESTRY ag-forst@daresbury.ac.uk ARABIDOPSIS arab-gen@daresbury.ac.uk BIOFORUM bioforum@daresbury.ac.uk BIO-INFORMATION-THEORY + bio-info@daresbury.ac.uk BIONAUTS bio-naut@daresbury.ac.uk BIONEWS ** bionews@daresbury.ac.uk BIO-JOURNALS ** bio-jrnl@daresbury.ac.uk BIO-MATRIX biomatrx@daresbury.ac.uk BIO-SOFTWARE bio-soft@daresbury.ac.uk BIOTHERMOKINETICS btk-mca@daresbury.ac.uk CELL-BIOLOGY cellbiol@daresbury.ac.uk CHLAMYDOMONAS chlamy@daresbury.ac.uk CHROMOSOMES biochrom@daresbury.ac.uk COMPUTATIONAL-BIOLOGY ** comp-bio@daresbury.ac.uk DROSOPHILA dros@daresbury.ac.uk EMBL-DATABANK embl-db@daresbury.ac.uk EMPLOYMENT biojobs@daresbury.ac.uk GDB gdb@daresbury.ac.uk GENBANK-BB genbankb@daresbury.ac.uk GENETIC-LINKAGE gen-link@daresbury.ac.uk HIV-MOLECULAR-BIOLOGY hiv-biol@daresbury.ac.uk HUMAN-GENOME-PROGRAM gnome-pr@daresbury.ac.uk IMMUNOLOGY immuno@daresbury.ac.uk INFO-GCG info-gcg@daresbury.ac.uk JOURNAL-NOTES jrnlnote@daresbury.ac.uk METHODS-AND-REAGENTS methods@daresbury.ac.uk MOLECULAR-EVOLUTION mol-evol@daresbury.ac.uk MYCOLOGY mycology@daresbury.ac.uk NEUROSCIENCE neur-sci@daresbury.ac.uk N2-FIXATION n2fix@daresbury.ac.uk PHOTOSYNTHESIS photosyn@daresbury.ac.uk PLANT-BIOLOGY plantbio@daresbury.ac.uk POPULATION-BIOLOGY pop-bio@daresbury.ac.uk PROTEIN-ANALYSIS proteins@daresbury.ac.uk PROTEIN-CRYSTALLOGRAPHY xtal-log@daresbury.ac.uk RAPD rapd@daresbury.ac.uk SCIENCE-RESOURCES ** sci-res@daresbury.ac.uk TROPICAL-BIOLOGY trop-bio@daresbury.ac.uk VIROLOGY virology@daresbury.ac.uk WOMEN-IN-BIOLOGY womenbio@daresbury.ac.uk YEAST yeast@daresbury.ac.uk + full name is BIOLOGICAL-INFORMATION-THEORY-AND-CHOWDER-SOCIETY ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. Retrieval of old postings from the BIOSCI archives -------------------------------------------------- Users with Internet access can use either the WAIS or gopher software to search the BIOSCI archives located at net.bio.net as described in the BIOSCI FAQ. E-mail users can retrieve messages from our waismail e-mail server. For waismail instructions, send the word help in a message to waismail@net.bio.net. Please leave the Subject: line of your message blank. BIOSCI "prototype" newsgroups ----------------------------- To assist areas of research in developing their own electronic communication forums, BIOSCI at net.bio.net will set up on request a mailing list *without* an associated USENET newsgroup. The mailing list is created only at net.bio.net, the U.S. BIOSCI node, and all subscription requests must be sent to biosci@net.bio.net regardless of one's geographical location. There is no charge for this or any other BIOSCI service, as usual. This procedure waives the rule that requires each new newsgroup proposal to be put to a vote of the readership first (see the BIOSCI FAQ, mentioned at the beginning of this document, for details on creating new full-fledged newsgroups and prototype newsgroups). Each mailing list ("prototype newsgroup") must have a scientist volunteer to serve as its discussion leader and an initial list of e-mail subscribers. The prototype newsgroup has six months to build up its readership after which time it is put out for a vote for full newsgroup status (i.e., to have both a mailing list *and* parallel USENET newsgroup created at both BIOSCI nodes in the U.S. and U.K.). If you are interested in establishing such a forum for your research specialty, please contact biosci-help@net.bio.net. The current prototype newsgroups are listed below. Please send subscription requests to biosci@net.bio.net and NOT to the newsgroup posting addresses. Prototype newsgroups may *not* be fully archived, so please be sure to save any messages that you may want to refer to again. Posting Address Purpose --------------- ------- emf-bio@net.bio.net Discussions on the electromagnetic field interactions with biological systems. pep-libs@net.bio.net Discussion on generation and use of peptide molecular repertoires displayed on phage or prepared as synthetic peptide combinatorial libraries. rna@net.bio.net Discussions about RNA editing, RNA splicing, and ribozyme activities of RNA. urodeles@net.bio.net Discussions among research scientists using urodele amphibians (axolotls, salamanders, and newts) in any biological field. yac@net.bio.net Dicussions about yeast artificial chromosomes FURTHER QUESTIONS??? Please address them to biosci@daresbury.ac.uk. PLEASE DO NOT DIRECT BIOSCI QUESTIONS TO THE PERSONAL E-MAIL ADDRESSES OF PEOPLE ON THE BIOSCI STAFF!! DUE TO OUR VOLUME OF MAIL, ANSWERS MAY BE DELAYED OR NOT SENT AT ALL!! From owner-software@net.bio.net Mon Jan 03 22:00:00 1994 Path: biosci!daresbury!news!ajb From: ajb@s-crim1.dl.ac.uk (Alan Bleasby) Newsgroups: bionet.software Subject: Re: gcg newsgroup??? Date: 04 Jan 1994 00:12:16 GMT Organization: SERC Daresbury Lab, Warrington, U.K. Lines: 23 Distribution: world Message-ID: References: <1993Dec29.172553.28549@nomina.lu.se> <1993Dec29.212548.67@immunbio.mpg.de> NNTP-Posting-Host: s-crim1.dl.ac.uk In-reply-to: koraimann@bkfug.kfunigraz.ac.at's message of Mon, 3 Jan 1994 18:04:31 Dr G. Koraimann writes: > Why don't I see this newsgroup in the listing of all the newsgroups? I'm not sure what listing is referred to. This group is advertised, as are all BIONET/BIOSCI groups in the monthly FAQ and information postings. If you don't have access to USENET NEWS then the relevant addresses are info-gcg@daresbury.ac.uk info-gcg@net.bio.net You can subscribe via email (if no USENET access) by sending a request to (e.g.) biosci@daresbury.ac.uk Rgds Alan Bleasby SEQNET/BIOSCI SERC Daresbury Laboratory Warrington WA4 4AD UK SEQNET is a UK EMBnet node From owner-software@net.bio.net Mon Jan 03 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!darwin.sura.net!blaze.cs.jhu.edu!jhunix.hcf.jhu.edu!welchlink.welch.jhu.edu!jcarroll From: jcarroll@welchlink.welch.jhu.edu (JOHN L. CARROLL) Newsgroups: bionet.software Subject: Re: PHS 398 grant forms(?) Date: 4 Jan 1994 03:16:30 GMT Organization: Johns Hopkins Univ. Welch Medical Library Lines: 20 Distribution: world Message-ID: <2gan2eINNebg@jhunix.hcf.jhu.edu> References: <2gahn7$dft@s.ms.uky.edu> NNTP-Posting-Host: welchlink.welch.jhu.edu In article <2gahn7$dft@s.ms.uky.edu> fasm@seqanal.mi.uky.edu (Primer Fac. BCH) writes: >John V. Weil (weil_j@defiance.hsc.colorado.edu) wrote: >: Does anyone know where I can find NIH grant forms (PHS 398) in either DOS >: or Windows format?? Template files can be FTP'd from: ftp.u.washington.edu in directory: pub/user-supported/templates I posted earlier that this used to be available on an NIH gopher but seems not be be there any longer. I checked out the above FTP site, MAC and MSDOS/WIN files are there. John C. -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ John L. Carroll JHU-JHMS-CMSC Baltimore, Maryland Voice: 410 955-2035 Internet: jcarroll@welchlink.welch.jhu.edu Fax: 410 955-1030 From owner-software@net.bio.net Mon Jan 03 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Bob Harrison Newsgroups: bionet.software Subject: IBI Digitizer Date: 4 Jan 1994 18:57:43 -0000 Lines: 6 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gce77$s8b@mserv1.dl.ac.uk> X-Vms-To: IN%"bio-soft@net.bio.net" X-Vms-Cc: RBHR Original-To: bio-soft@net.bio.net I have an IBI Digitizer w/o any IBI software. Can anyone tell me how to hook it to my Gateway 2000 (IBMPC compatible) and which software to use to run it?? Thanks Bob Harrison From owner-software@net.bio.net Mon Jan 03 22:00:00 1994 Path: biosci!rutgers!sgigate.sgi.com!sgiblab!darwin.sura.net!europa.eng.gtefsd.com!uunet!ddsw1!not-for-mail From: abirnbau@MCS.COM (Adam Birnbaum) Newsgroups: bionet.software Subject: Phsysiology education software Summary: Simulation of human physiology for medical education Keywords: physiology, simulation, medicine Message-ID: <2gc5cl$crb@genesis.Mcs.Com> Date: 4 Jan 94 16:27:01 GMT Organization: MCSNet Subscriber, Chicago, IL Lines: 24 NNTP-Posting-Host: genesis.mcs.com Last month a posted a message about our physiology simulation program for medical education, and so many people seemed interested that I think it's appropriate for me to repost the message. Our company has developed a computer simulation of human physiology for education in first year or more advanced physiology. The simulation runs in real time in Windows 3.1, and requires a 486DX33 to run, since it is solving a host of differential and algebraic equations to produce data on the coupled cardiovascular, pulmonary and renal systems. The interface allows you to look at numerous pressure waveforms, gas exchange data, electrolyte levels and countless other pieces of information. Several clinical interventions are available, including fluid infusions, vasoactive drugs, and ventilator controls. Please send me email if you would like more information, or if you are interested in a demo program. Adam Birnbaum Critical Concepts Suite 502 1525 E. 53rd Street Chicago, Illinois 60615 From owner-software@net.bio.net Mon Jan 03 22:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!zib-berlin.de!netmbx.de!Germany.EU.net!EU.net!julienas!dmi.ens.fr!dmi!claros From: claros@biologie.ens.fr (Manuel G. CLAROS) Subject: Re: Transmembrane region prediction Message-ID: Sender: news@ens.fr (USENET News System) Nntp-Posting-Host: lgmmac0.ens.fr Organization: Ecole Normale Supˇrieure, Gˇnˇtique Molˇculaire X-Newsreader: VersaTerm Link v1.1.1 References: <1994Jan4.085154.27763@reks.uia.ac.be> Date: Tue, 4 Jan 94 07:43:36 GMT Lines: 17 In Article <1994Jan4.085154.27763@reks.uia.ac.be>, przemko@reks.uia.ac.be >Hello, >I have looked in the EMBL server as well as in couple others but could >find only the Mac version. >Could you tell me where the DOS version would be? >ThanX >Przemko > There is not any DOS version. Sorry. Manuel _____________________________Manuel_G._CLAROS__________________________________ | Ecole Normale Superieure - CNRS | E-mail: claros@biologie.ens.fr | | Lab. Genetique Moleculaire | Fax: 331-44 32 39 41 | | 46 rue d'Ulm | Phone: 331-44 32 39 39 | | 75005 Paris (France) | | _______________________________________________________________________________ From owner-software@net.bio.net Mon Jan 03 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: "Michael D. Baron" <"/G=michael/S=baron/OU=morbillivirus/OU=pirbright/OU=i a h/"@AFRC.ac.uk> Newsgroups: bionet.software Subject: displaying alignments (thanks) Date: 4 Jan 1994 12:14:55 -0000 Lines: 45 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gbmjv$7mi@mserv1.dl.ac.uk> Sensitivity: Company-Confidential Original-To: bio-software@dl.ac.uk (Non Receipt Notification Requested) (IPM Return Requested) Dear netters, with reference to my posting to the net just before Christmas, I would like to thank all those of you who took the time and trouble to reply. I must especially thank (and apologise to) Rick Westerman: now that he has explained what PRETTYBOX is doing, it is clear that it does what he intended it to do, and I am properly corrected. I would like to emphasise that I did not really mean to say that all the programs were "wrong" (that they didn't do what I want is in no way the same as saying that "they all have faults" - maybe what I want to do is something stupid ;-) ). Since different scientists are going to want to emphasise different things with their data, naturally programs will differ in what they are designed to do. I was merely making a general enquiry in the hope that someone had had the same aim as me. As it happens, a number of people communicated that they *had* wanted to do what I described, but none of the programs available did it (because, of course, they were designed to do something else). As Mark Reboul suggested, it might be worth a little discussion about what kind of rules we want an alignment *display* program to follow when it makes a decision as to what residues to highlight. For example, I think of such a highlighting tool as something to automate the questions that I would ask about each position in the alignment if I was doing the whole thing manually, or if I was inspecting a new alignment, and I start the process by asking not "What is the consensus residue?" but "Is there a consensus?". The second level is then something like "Is this a fully conserved (all/mostly identical) or partially conserved (all/mostly similar) residue?" (Note that I am avoiding specifiying how such questions are answered by a program, or how concepts like 'similar' are defined.) If we could reach a consensus (;-)) on what us users wanted, perhaps this would be of use to someone who is (going to be) writing software. What do other sequence-gazers think? Yours, Michael Baron (BARON@AVRI.AFRC.AC.UK) From owner-software@net.bio.net Mon Jan 03 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!warwick!pipex!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!csd4.csd.uwm.edu!glenne From: glenne@csd4.csd.uwm.edu (Neuromancer ) Newsgroups: bionet.software Subject: What o/s should a programmer specializing in biotech use? Date: 4 Jan 1994 21:06:22 GMT Organization: Computing Services Division, University of Wisconsin - Milwaukee Lines: 12 Distribution: world Message-ID: <2gcloeINNbre@uwm.edu> NNTP-Posting-Host: 129.89.7.4 Originator: glenne@csd4.csd.uwm.edu I have decided that I would like to be a programmer that specializes in biotechnology. At this point I am deciding on which programming language and operating system to focus on. Would it be best for me to specialize in C++ under unix and perhaps get some x-windows (maybe motif) programming experience? Or should I be focusing on MSDOS/Windows, System 7, or something else? As always, many thanks, Glenn glenne@csd4.csd.uwm.edu From owner-software@net.bio.net Mon Jan 03 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!athena.mit.edu!fuellen From: fuellen@athena.mit.edu (Georg Fuellen) Newsgroups: sci.bio.technology,sci.comp-aided,comp.lang.misc,bionet.software,comp.software-eng Subject: C++/C is a mess, but there is nothing better around for programming in biotech. (was: what o/s is best for a programmer specializing in biotech? Followup-To: sci.bio.technology Date: 4 Jan 1994 20:09:13 GMT Organization: Massachusetts Institute of Technology Lines: 34 Distribution: world Message-ID: <2gcida$ldc@senator-bedfellow.MIT.EDU> References: <2gcbc8INNa8g@uwm.edu> NNTP-Posting-Host: m1-142-20.mit.edu Xref: biosci sci.bio.technology:679 sci.comp-aided:273 comp.lang.misc:3060 bionet.software:6849 comp.software-eng:7679 In article <2gcbc8INNa8g@uwm.edu>, glenne@csd4.csd.uwm.edu (Neuromancer ) writes: [to sci.bio.technology, to which followups are directed] |> The responses I got in this newsgroup helped me decide that I want to |> be a programmer that specializes in biotechnology. At this point I am |> deciding on which programming language and operating system to focus on. |> |> My guess is that it would be best for me to specialize in C++ under unix [...] Right now, C++/C may be good for getting a job, but the language can be a real mess. I used C++ as a computer scientist at a molecular biology group, but if you want to start a project from scratch using C++ and you want to avoid all the possible design errors C++ allows you to do, maybe use some tools or class libraries as well, obey some coding standard, etc, then you'll spend quite a bit of time without being productive. Good C++ programming costs a lot of time in the beginning; if you prepare for future reuse in a serious way, most benefits are down the road. You'll miss them almost certainly if you rush into coding. Anyway, my boss ran out of patience, and I more or less had to stop using C++. Luckily, the next project made much more short-term progress, so I could keep my job until he left academia. ** I am still looking for a better programming language, without success, and my conclusion is: C++/C is really bad, but there is nothing better around. CAN ANYBODY PROVE ME WRONG ? ** On a final note, you should be flexible regarding the platform/operating system: at least UNIX, Mac, PC. This is no big deal compared to the intrinsic problems of C++. gcc/g++ for example runs under lots of operating systems. georg fuellen@mit.edu The convex hull of all disclaimers made on usenet last year applies to this mess From owner-software@net.bio.net Tue Jan 04 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!sunic!trane.uninett.no!nac.no!nntp-oslo.uninett.no!usenet From: istmjeld@nvh.veths.no (Ole Mjelde) Newsgroups: bionet.software Subject: TEACHING PROGRAMS Date: 5 Jan 1994 15:53:10 GMT Organization: NVH Lines: 28 Message-ID: <2genp6$p6n@ratatosk.uninett.no> NNTP-Posting-Host: 5196.veths.no X-Newsreader: WinVN 0.83.2 Hi, Can somebody please help me!!! I am looking for computer programs which can be used in teaching students how the body works. I have seen a program where the user can see spesific parts of the body on the computer screen. Some of the pictures can also be turned, so that you can see the body for different angles. In addition there is a text describing the picture. Does anybody know of any more programs? I am interested in both human and animal teaching programs. Please E-mail to me, or put your answer on the nett. My address is istmjeld@nvh.veths.no Ole Mjelde Oslo, Norway From owner-software@net.bio.net Tue Jan 04 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!phibred.com!news From: Glenn Brooke, Ph.D. Subject: kinetics software for Mac Message-ID: X-Xxdate: Wed, 5 Jan 94 16:54:20 GMT Sender: news@phibred.com (USENET News System) Organization: Pioneer Hi-bred International, Inc. X-Useragent: Version 1.1.3 Date: Wed, 5 Jan 1994 22:58:30 GMT Lines: 4 We have a couple of scientists who need Mac software for kinetics work, along the lines of Enzfitter [does anyone have the address for group that markets Enzfitter, by the way?] What software is recommended? From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!uunet!world!art From: art@world.std.com (Al Thompson) Subject: Scientific Software Message-ID: Sender: art@world.std.com (Al Thompson) Organization: The World Public Access UNIX, Brookline, MA Date: Thu, 6 Jan 1994 18:24:23 GMT Lines: 71 I am sending this to nearly every news group that even hints in its title that it might have some remote connection to my subject. So, if I send it to an inappropriate group please accept my apologies in advance. Late last week a posting from J. Jowett appeared in bionet.software. In it he laments the lack of available software for the biomedical, and probably other scientific communities. In particular he includes the two following paragraphs: >For a while now I have been aghast at how difficult it has been to get a >hold of and find out about good programs for the PC that carry out >cloning type operations and keep track of DNA sequences- so that when you >want to look up a restriction map of a vector that maybe in it's 4th >generation, you have to sift through a pile of notes about which fragment >came from where! > >[...] Lots deleted. > >It seems that software for science is seriously lacking, maybe we should >quit and learn how to program computers! it would appear there is a >vacuum where there could be many extremely useful programs - and I can't >believe they would be beyond technical faesibility to write. I have Ph.D. in biophysics and did indeed "quit" and start programming computers. In fact, I drifted into computers nearly twenty five years ago while doing a post-doc in biophysics when it became clear we needed some fairly heavy programs. I would have much rather bought them, but nobody had anything like that for sale, so I was elected to write them. Little did I know how long it would take and how intellectually consuming it would become. This got me to thinking that this problem might be more widespread than I had thought. To address this, and possibly propose a solution, I have a couple of pertinent questions on the subject and would very much appreciate it if you would take a few minutes to answer them and respond to me via email. I will summarize the responses. 1. Just what kind of software do want and/or need? 2. How many of your colleagues want the same things? 3. Has your work been slowed, or inhibited by the lack of software? 4. If appropriate software was available would this have a positive effect on your work? That is, do you think you would you find yourself planning more effective experiments? 5. Do you want or need real time data gathering or instrument control programs? 6. How many of your colleagues want or need real time data gathering or instrument control programs? 7. Would you or your colleagues make more use of computers if you were not burdened with the need to produce your own software? 8. How much do you expect to pay for substantial pieces of software? When answering this question, please remember how much time is involved in producing large programs. 9. About how many people at your organization make use of the internet? Thank you for your trouble. Allan Thompson 10 Flora St. Haverhill, MA 01830 (508) 374-7782 art@world.std.com From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!doc.ic.ac.uk!warwick!pipex!uunet!emba-news.uvm.edu!brianf From: brianf@med.uvm.edu (Brian Foley) Subject: NCBI BLAST output format: Question. Message-ID: <1994Jan6.200957.10541@emba.uvm.edu> Sender: news@emba.uvm.edu Organization: University of Vermont -- Division of EMBA Computer Facility X-Newsreader: TIN [version 1.2 PL1] Date: Thu, 6 Jan 1994 20:09:57 GMT Lines: 17 Can someone tell me what is the best software for viewing the output from an NCBI BLAST search? Whether I read the output in my UNIX e-mail, my Mac e-mail, or convert it to a text editor (MS-Word) document, the alignments do not line up without messing with them. It seems that the output uses TABs rather than spaces to format the output, and these TABs do not correspond to the ones I have. Perhaps if I just knew what the TAB settings were... Does the BLAST output look great when it is imported into WordPerfect or some other text editor? -- ******************************************************************** * Brian Foley * If we knew what we were doing * * Molecular Genetics Dept. * it wouldn't be called research * * University of Vermont * * From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!destroyer!news1.oakland.edu!vela.acs.oakland.edu!sglanger From: sglanger@vela.acs.oakland.edu (LANGER STEVEN C) Newsgroups: bionet.software Subject: nema III Date: 6 Jan 1994 19:14:52 GMT Organization: Oakland University, Rochester, Michigan, U.S.A. Lines: 12 Distribution: na Message-ID: <2ghnvc$moj@oak.oakland.edu> NNTP-Posting-Host: vela.acs.oakland.edu I'm trying to find out about the NEMA III standard for portable networking of medical records across TCP/IP networks. Does anyone know where I could find out more about this? thanks in advance, steve -- "You need only reflect that one of the best ways to get yourself a reputation as a dangerous citizen these days is to go about repeating the very phrases which our founding fathers used in the struggle for independence." - C.A. Beard From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Path: biosci!presto.ig.com!summers From: summers@presto.ig.com (Murray Summers) Newsgroups: bionet.software Subject: Re: Intelligenetics Date: 6 Jan 1994 12:57:23 GMT Organization: IntelliGenetics, Inc., Mountain View, California USA Lines: 25 Distribution: bionet Message-ID: <2gh1rj$3st@net.bio.net> References: NNTP-Posting-Host: presto.ig.com X-Newsreader: TIN [version 1.2 PL2] a (a) wrote: : Could someone tell me the e-mail adress of Intelligenetics. : Thanks. : Philippe-Alexandre Gilbert Philippe-Alexandre: It depends on what you need, but you can always come to me and I will redirect based on your inquiry. As you can see from the header, I can be reached at summers@presto.ig.com; technical help can be gotten from consult@presto.ig.com. Best, Murray R. Summers Senior Sales Representative IntelliGenetics, Inc. 700 E. El Camino Real, Suite 300 Mountain View, CA 94040 415-962-7300 415-962-7302 (FAX) b From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!digex.net!access3!bobwall From: bobwall@access3.digex.net (Bob Wall) Newsgroups: bionet.software Subject: Re: From Procite to Reference Manager Date: 6 Jan 1994 07:30:28 -0500 Organization: Express Access Online Communications, Greenbelt, MD USA Lines: 26 Message-ID: References: NNTP-Posting-Host: access3.digex.net Keywords: Datafile conversion Arild.Tangeras@PKI.UiB.no (Arild.Tangeras@pki.UiB.no) writes: >How do I transfer records from Procite to Referene Manager? >Any help, or suggestions for another discussion group that can help? >Arild Tanger†s. Research Information Systems provides such a service. They charge for that service, but I don't know how much. Give them a call (619-438-5562). You can also do it "by hand." The strategy would be to export your procite references to an ascii file and then import them into ref man. RefMan is not very flexible about importing so the format of the file has to be just right. Fortunately with Procite you can customize the export to ascii to match RefMan's requirements. It is not such a big job if your citations are all or mostly in one format in Procite (ie, Journal-long) but if you have a lot of different types (Journal-shor, book-long, etc) it would take a LOT of work to get it right. It would be nice if some Information Professional would write a freeware format style sheet for doing this (hint, hint ). Bob From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!pavo.csi.cam.ac.uk!mbfs.bio.cam.ac.uk!sgb12 From: sgb12@mbfs.bio.cam.ac.uk (Sean Buchanan (Bioc)) Subject: Promoter analysis Message-ID: <1994Jan6.104602.12519@infodev.cam.ac.uk> Sender: news@infodev.cam.ac.uk (USENET news) Nntp-Posting-Host: mbfs.bio.cam.ac.uk Organization: U. of Cambridge, England Date: Thu, 6 Jan 1994 10:46:02 GMT Lines: 6 I have some Drosophila promoter sequence which I would like to analyse for transcription factor sites etc. Can anyone advise me of available software. I have tried looking in the GCG "help" file, but cannot find what I am looking for. Any pointers or suggestions would be greatly appreciated. Sean. From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!sunic!trane.uninett.no!alf.uib.no!hjerte.ai.uib.no!Arild.Tangeras From: Arild.Tangeras@PKI.UiB.no (Arild.Tangeras@pki.UiB.no) Newsgroups: bionet.software Subject: From Procite to Reference Manager Date: 6 Jan 1994 09:49:24 GMT Organization: University of Bergen, Norway Lines: 6 Message-ID: NNTP-Posting-Host: hjerte.ai.uib.no Keywords: Datafile conversion How do I transfer records from Procite to Referene Manager? Any help, or suggestions for another discussion group that can help? Arild Tanger†s. From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!usc!usc!not-for-mail From: marziasz@zygote.hsc.usc.edu (Carolyn Marziasz) Newsgroups: bionet.software Subject: Software for identifying promoter elements? Date: 6 Jan 1994 01:54:02 -0800 Organization: University of Southern California, Los Angeles, CA Lines: 16 Sender: marziasz@zygote.hsc.usc.edu Message-ID: <2ggn3q$1pp@zygote.hsc.usc.edu> NNTP-Posting-Host: zygote.hsc.usc.edu Keywords: TFD,promoter,transcription factor binding sites Hello all. Does anyone out there know of any software for searching the TFD database with a promoter sequence? In other words, I have the sequence for a putative promoter and would like to easily identify possible transcription factor binding sites in the sequence. Is there a simple way to do this without having to search the sequence with each binding site seperately? For example, could I compare my sequence with the sequences in the TFD database all at once? Any help or advice would be very welcome. I have access to Unix, Mac and IBM computers. Thanks again, William M. Rideout III From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!news.intercon.com!psinntp!phinet!smithkline.com!eshlemanew From: eshlemanew@smithkline.com Subject: MassSpec data file conversion Message-ID: <5JAN199415310025@smithkline.com> News-Software: VAX/VMS VNEWS 1.41 Sender: news@netnews.smithkline.com (USENET News System) Organization: SmithKline Beecham Date: Wed, 5 Jan 1994 20:31:00 GMT Lines: 10 Hi, We are looking to convert MassSpec data files from Nermag format to the newer HP file format. Does anyone out there have a cheap (free) program that performs this conversion? Any help would be appreciated. Thanks, Eric Eshleman eshlemanew@sb.com From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!uunet!utcsri!newsflash.concordia.ca!sifon!athena.ulaval.ca!NewsWatcher!user From: a (a) Subject: Intelligenetics Message-ID: Followup-To: bionet.software Sender: news@athena.ulaval.ca Nntp-Posting-Host: 132.203.140.7 Organization: a Date: Wed, 5 Jan 1994 22:53:13 GMT Lines: 6 Could someone tell me the e-mail adress of Intelligenetics. Thanks. Philippe-Alexandre Gilbert From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!newsserver.jvnc.net!yale.edu!news.yale.edu!rudnick.med.yale.edu!rudnick From: rudnick@biomed.med.yale.edu (Gary Rudnick) Subject: Cross-platform (Mac and Windows) MolBiol Software Message-ID: Lines: 20 Sender: news@news.yale.edu (USENET News System) Nntp-Posting-Host: rudnick.med.yale.edu Organization: Yale University X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Date: Thu, 6 Jan 1994 12:45:18 Are any of the good commercial programs for analyzing DNA and protein sequences available for both Mac and MS-Windows platforms? We have various machines here and we would prefer to have a single application with the same file format for both kinds of machine. We would like to do primer design, alignments, transmembrane topology prediction, sequence editing, plasmid map drawing, restriction digest analysis, etc. Searching a local database for sequence matches is not required, as we generally do that over the network. If there's a big response to this, I will post a summary. Thanks for any and all help. ================================================================ Gary Rudnick |voice (203) 785-4548 Department of Pharmacology |fax (203) 785-7670 Yale University School of Medicine |bitnet RUDNICK@YALEMED 333 Cedar Street, P.O. Box 208066 |internet: New Haven, CT 06520-8066 |RUDNICK@BIOMED.MED.YALE.EDU ---------------------------------------------------------------- What separates the men from the boys is the price of their toys. From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!uunet!newsflash.concordia.ca!sifon!athena.ulaval.ca!NewsWatcher!user From: pagilbert@cti.ulaval.ca (Philippe-Alexandre Gilbert) Subject: Intelligenetics Message-ID: Followup-To: bionet.software Sender: news@athena.ulaval.ca Nntp-Posting-Host: 132.203.140.7 Organization: Universite Laval Date: Thu, 6 Jan 1994 14:14:00 GMT Lines: 12 Could someone tell me the e-mail adress of Intelligenetics ? Thanks. Philippe-Alexandre Gilbert -- Philippe-Alexandre Gilbert tel: (418)656-2964 Centre de Traitement de l'Information e-mail: pagilbert@cti.ulaval.ca Universite Laval Quebec, Canada From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!ee.und.ac.za!csir.co.za!hippo.ru.ac.za!itu1.sun.ac.za!ernstjdt From: ernstjdt@itu.sun.ac.za (Ernst J du Toit) Newsgroups: bionet.software Subject: Looking for Medical Clip Art Date: 6 Jan 1994 14:19:00 GMT Organization: University of Stellenbosch Lines: 14 Message-ID: <2gh6kk$581@itu1.sun.ac.za> NNTP-Posting-Host: itu1.sun.ac.za X-Newsreader: TIN [version 1.1 PL8] Hi Are there any ftp archives on the Internet that has medical Clip Art? I'm looking for line drawings of human organs to include in paper documentation. Any pointers will be appreciated. Thank you Ernst ernstjdt@maxwell.ctech.ac.za From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Bill Kupiec Newsgroups: bionet.software Subject: Re: NCBI BLAST output format Date: 6 Jan 1994 21:06:45 -0000 Lines: 20 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2ghuh5$hep@mserv1.dl.ac.uk> Original-To: Bio Software RE>NCBI BLAST output format: Q Brian, > Can someone tell me what is the best software for viewing the > output from an NCBI BLAST search? Whether I read the output in > my UNIX e-mail, my Mac e-mail, or convert it to a text editor > (MS-Word) document, the alignments do not line up without > messing with them. In your text editor (MS-Word, WordPerfect), change the font to a mono-spaced typeface such as Courier or Monaco and the alignments should line up perfectly. -Bill *------------------------------------------------------------* Bill Kupiec kupiec@mail1.ciwemb.edu, AppleLink: KUPIEC Operations Manager, Carnegie Institution of Washington *------------------------------------------------------------* From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!cs.utexas.edu!sdd.hp.com!col.hp.com!csn!tali.hsc.colorado.edu!mwmt18.hsc.colorado.edu!user From: weil_j@defiance.hsc.colorado.edu (John V. Weil) Newsgroups: bionet.software Subject: Re: Scientific Software Followup-To: bionet.software Date: 6 Jan 1994 21:27:33 GMT Organization: CVP Research Lab Lines: 21 Message-ID: References: NNTP-Posting-Host: mwmt18.hsc.colorado.edu In article , art@world.std.com (Al Thompson) wrote: > > 5. Do you want or need real time data gathering or instrument control > programs? > > 6. How many of your colleagues want or need real time data gathering or > instrument control programs? A powerful and highly versatile system is available for this pupose from National Instruments which includes chart recorder emulation and object oriented software system which can produce "virtual instrements" (amplifiers, filters, integrators etc). Although some savy is required to get things up and running, this is an attractive user-implementable approach to data aquistion and analysis on-line or 0ff-line. I have no connection with National Instruments. -- John V. Weil From owner-software@net.bio.net Wed Jan 05 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: plewniak@titus.u-strasbg.fr (BIOSCI) Newsgroups: bionet.software Subject: RE:Program for identifying promoters Date: 6 Jan 1994 13:40:11 -0000 Lines: 57 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gh4br$rg5@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk >Hello all. > >Does anyone out there know of any software for searching the TFD database >with a promoter sequence? In other words, I have the sequence for a >putative promoter and would like to easily identify possible transcription >factor binding sites in the sequence. Is there a simple way to do this without >having to search the sequence with each binding site seperately? For example, >could I compare my sequence with the sequences in the TFD database all at once? > >Any help or advice would be very welcome. I have access to Unix, Mac and >IBM computers. > >Thanks again, > >William M. Rideout III > Hello, I) If you have access to GCG package you may use TFD with findpatterns, map, mapplot and mapsort. (I mean the GCG version of TFD sites!) II) The program tfd2prosite.c is available on the EMBL server. It converts sites (or DOMAINS) table SITE.DAT (or DOMAINS.DAT) to a Prosite-like format. The new file (SITES.PAT or DOMAINS.PAT) can be used with Prosite-based programs such as Macpattern (available on EMBL server.)... To get these send the following message to NETSERV@EMBL-Heidelberg.DE : GET MAC_SOFTWARE:TFD2PROSITE.C GET MAC_SOFTWARE:MACPATTERN.HQX You'll need a C compiler for tfd2prosite.c though... Note : tfd2prosite.c and macpattern were developped at EMBL by Rainer Fuchs. I hope this helps a little... Frederic PLEWNIAK LGME 11 rue Humann 67085 STRASBOURG Cedex FRANCE plewniak@titus.u-strasbg.fr From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!hubcap!darwin.sura.net!howland.reston.ans.net!vixen.cso.uiuc.edu!ninja!studier From: studier@ninja.life.uiuc.edu (Jim Studier) Newsgroups: bionet.software Subject: want alignment program Date: 7 Jan 94 01:09:00 GMT Organization: University of Illinois at Urbana Lines: 11 Message-ID: NNTP-Posting-Host: ninja.life.uiuc.edu Can anybody tell me where I can ftp a copy of the alignment program described in: Lawrence, Charles E. Science vol262,p208,1993 (October 8) "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment" Jim Studier (studier@ninja.life.uiuc.edu) From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!news.cs.umb.edu!hsdndev!husc-news.harvard.edu!husc.harvard.edu!husc10!robison1 Newsgroups: bionet.software Subject: Re: NCBI BLAST output format: Question. Message-ID: From: robison1@husc10.harvard.edu (Keith Robison) Date: 6 Jan 94 22:08:17 GMT References: <1994Jan6.200957.10541@emba.uvm.edu> Organization: Harvard University, Cambridge, Massachusetts NNTP-Posting-Host: husc10.harvard.edu Lines: 92 I've developed a filter which converts netBLAST output to HTML, the hypertext format used with the World Wide Web (Mosaic, Lynx, Cello, etc). It's a simple perl script which can be easily re-configured. The filter adds hyperlinks to the matched database items to links to the relevant database entries, as well as some links for moving around the output. It definitely works best with a GUI browser such as Mosaic` -- it's a bit link-rich for screen-based browsers. The main drawback is that you have to keep around separate HTML and non-HTML files, because there isn't (yet?) a way to get an HTML browser to run data through a filter prior to viewing. Enjoy! Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI krobison@nucleus.harvard.edu -------------Cut here with virtual scissors---------------------- #!/usr/local/bin/perl # blast2html -- converts output from NCBI Network BLAST server # to HTML hypertext # Keith Robison November 1993 # krobison@nucleus.harvard.edu # # HTML Markups # # 1) Database accession numbers are links to retrieve database entries # 2) Poisson score in top summary is a link to alignment # 3) Angle bracket at start of alignment description is link back to summary # # Citation: # Robison, K. A simple hypertext BLAST output browsing scheme. # Unpublished. # # Freedom to use and modify this program is granted so long as the # citation above remains intact and modifications are documented. # # Current Version $Acc = '[A-Z]\d{5}'; # Regexp for GB/EMBL/DDJB/SP accession number $PIRAcc = '[A-Z][A-Z0-9]\d{4}'; # Regexp for PIR accession number $Word = '\w*'; # Regexp for a word # WWW link stems for databases $Embl = 'http://golgi.harvard.edu/htbin/expasygate?get-embl-entry?'; $Genbank = 'http://golgi.harvard.edu/htbin/getseq-gb-a?'; # EMBL has richer hyperlinks, but ExPasy currently has only subset $Pir = 'http://golgi.harvard.edu/htbin/getseq-pir-a?'; # Choose the desired SwissProt server $SwissProt = 'http://golgi.harvard.edu/htbin/expasygate?get-sprot-entry?'; # $SwissProt = 'http://expasy. while ($_ = ) { #Beginning of report body stuff -- title, 'pre-formatted' instruction s#Query= *($Word)(.*)#$1
Query=  
$1
$2
#o;

  #generate section markers at alignment
  s#^>($Word)\|($Acc)\|($Word) #>$1|$2|$3 #o;

  # make Poisson score link to alignment
  #  note: $6 is in regexp to prevent premature matches
  #    1       2        3       4    5          6
  #    db     acc      loc     des  poi        cnt
  s#^($Word)\|($Acc)\|($Word) (.* )(\d[0-9e\-\.]{2,})( *\d*$)#$1|$2|$3 $4$5$6#o;
 
  # make database links
  s# ($Acc) # $1 #go;             # "Naked" acc->GB
  s#(g[pb]u?)\|($Acc)#$1\|$2#go;  # GenBank/GenPept
  s#(embu?)\|($Acc)#$1\|$2#go;       # Embl
  s#(spu?)\|($Acc)#$1\|$2#go; # SwissProt
  s#pir\|($PIRAcc)#pir\|$1#go;           # PIR
  #
  # PDB --> ?
  # dbest --> ?

  print $_;
}
print "
"; From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Newsgroups: bionet.software Path: biosci!news.cs.umb.edu!hsdndev!newsfeed.rice.edu!cs.utexas.edu!uunet!emba-news.uvm.edu!brianf From: brianf@med.uvm.edu (Brian Foley) Subject: Re: NCBI BLAST output format Message-ID: <1994Jan7.011551.18695@emba.uvm.edu> Sender: news@emba.uvm.edu Organization: University of Vermont -- Division of EMBA Computer Facility X-Newsreader: TIN [version 1.2 PL1] References: <2ghuh5$hep@mserv1.dl.ac.uk> Distribution: bionet Date: Fri, 7 Jan 1994 01:15:51 GMT Lines: 45 Bill Kupiec (kupiec@mail1.ciwemb.edu) wrote: : RE>NCBI BLAST output format: Q : Brian, : > Can someone tell me what is the best software for viewing the : > output from an NCBI BLAST search? Whether I read the output in : > my UNIX e-mail, my Mac e-mail, or convert it to a text editor : > (MS-Word) document, the alignments do not line up without : > messing with them. : In your text editor (MS-Word, WordPerfect), change the font to a mono-spaced : typeface such as Courier or Monaco and the alignments should line up : perfectly. It's not just the alignments but also the histogram and other output. And it still looks bad even in courier font. : -Bill : *------------------------------------------------------------* : Bill Kupiec : kupiec@mail1.ciwemb.edu, AppleLink: KUPIEC : Operations Manager, Carnegie Institution of Washington : *------------------------------------------------------------* I should have mentioned that I was using courier font. It still does not line up. And when I start pushing a line over by adding spaces at the left edge, not all characters on the line move together. A few just to the right of the cursor shift, then the rest of the line might jump over by five spaces as the next space is added, while those characters just to the right of the cursor only move by the expected one space. To me it looks like some of the spacing is done with TABs. This would cause such behavior. Apparently, I am the only one having such difficulties, so it must be specific to the Mac and MS-Word text editor I am using. I will try something different now, and see if that fixes everything. Several people wrote to me personally and assured me that the BLAST output does look nicely formatted on their systems. Thanks for all the responses. -- ******************************************************************** * Brian Foley * If we knew what we were doing * * Molecular Genetics Dept. * it wouldn't be called research * * University of Vermont * * From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Newsgroups: bionet.software Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!uchdcc!uconce!quintrala!dcampos From: dcampos@quintrala.dis.udec.cl (Daniel Campos) Subject: Multimedia and Biology Sender: usenet@halcon.dpi.udec.cl Message-ID: <1994Jan07.165127.15576@halcon.dpi.udec.cl> Date: Fri, 07 Jan 1994 16:51:27 GMT Organization: Universidad de Concepcion, Concepcion - Chile X-Newsreader: TIN [version 1.2 PL2] Lines: 20 [ Article crossposted from comp.multimedia ] [ Author was Daniel Campos ] [ Posted on Fri, 07 Jan 1994 16:43:30 GMT ] Does anyone knows about multimedia software oriented to developmental biology and / or human reproduction ? We are trying to build a database of multimedia software products for the Biological Sciences Faculty of our University. Cheers!!! Daniel dcampos@quintrala.dis.udec.cl Daniel Campos Multimedia Unit University of Concepcion Concepcion - CHILE From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Newsgroups: bionet.software From: Duncan@genesys.demon.co.uk (Duncan Clark) Path: biosci!bcm!cs.utexas.edu!uunet!news.sprintlink.net!demon!genesys.demon.co.uk!Duncan Subject: Re: Program for identifying promoters Distribution: world References: <2gh4br$rg5@mserv1.dl.ac.uk> Organization: GeneSys Ltd. Reply-To: Duncan@genesys.demon.co.uk X-Newsreader: Simple NEWS 1.90 (ka9q DIS 1.21) Lines: 13 Date: Fri, 7 Jan 1994 16:11:37 +0000 Message-ID: <757959097snz@genesys.demon.co.uk> Sender: usenet@demon.co.uk Hi Netters, Rather than having a program that compares a putative promoter sequence with others is there a program (DOS) that will take say 300bp upstream of a gene and output any possible promoter consensus sequence? Duncan -- ----------------------------------------------------------------------------- Duncan Clark | Internet: duncan@genesys.demon.co.uk GeneSys Ltd. | Compuserve: 100015.1406@compuserve.com ----------------------------------------------------------------------------- From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: MARK@CUCCFA.CCC.COLUMBIA.EDU (T. Mark Reboul) Newsgroups: bionet.software Subject: Re: want alignment program Date: 7 Jan 1994 16:03:44 -0000 Lines: 18 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gk150$7os@mserv1.dl.ac.uk> Original-To: bio-soft@net.bio.net Jim Studier wrote: > Can anybody tell me where I can ftp a copy of the > alignment program described in: > > Lawrence, Charles E. > Science vol262,p208,1993 (October 8) > > "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy > for Multiple Alignment" > > Jim Studier (studier@ninja.life.uiuc.edu) Anonymous FTP to ncbi.nlm.nih.gov, then cd to pub/gibbs. Mark Reboul Columbia-Presbyterian Cancer Center Computing Facility mark@cuccfa.ccc.columbia.edu From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Newsgroups: bionet.software Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!darwin.sura.net!gatekeeper.es.dupont.com!esds01.es.dupont.com!MOLDOVBJ@esvx12.es.dupont.com From: moldovbj@esvx12.es.dupont.com Subject: opportunities in biocomputing Message-ID: <1994Jan7.141832.4126@es.dupont.com> Sender: news@es.dupont.com (USENET News System) Nntp-Posting-Host: esvx12.es.dupont.com Reply-To: moldovbj@esvx12.es.dupont.com Organization: DuPont (Opinions are those of the writer only) Date: Fri, 7 Jan 1994 14:18:32 GMT Lines: 12 Although I know this is the wrong newsgroup for this posting, I can't find any place better to ask this question. I have a Ph.D. in Biology, with my training being in molecular biology and some protein biochemistry. Primarily I have worked on gene regulation and DNA-protein interactions. I'm currently doing a postdoc in an industrial setting, and have come to the following realization. I would be much happier if I were doing a project that involved computers rather than being a bench scientist. So, now that I am committed to entering the world of computational biology, how do I find the opportunitites in the field? I've got lots of computer experience, although none of that can be shown on my CV. Since this is the wrong area to discuss this, please email me or direct me to the best newsgroup. Thanks! From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: MARK@CUCCFA.CCC.COLUMBIA.EDU (T. Mark Reboul) Newsgroups: bionet.software Subject: Re: displaying alignments (thanks) Date: 7 Jan 1994 15:03:44 -0000 Lines: 170 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gjtkg$57u@mserv1.dl.ac.uk> Original-To: bio-soft@net.bio.net Happy New Year to all Bio-Soft/Bionet.Software participants! Regarding present and future programs for automated illustrative shading of multiple sequence alignments, Michael Baron wrote: > As it happens, a number of people communicated that they *had* wanted > to do what I described, but none of the programs available did it > (because, of course, they were designed to do something else). As Mark > Reboul suggested, it might be worth a little discussion about what > kind of rules we want an alignment *display* program to follow when it > makes a decision as to what residues to highlight. Based on recent involvements with this issue, I have identified the shading scheme desired by some of my users. They want a shading program which merely automates the highlighting of majority column occupations. That the numbers in some mutation score matrix analytically justify the choice of a particular amino acid as one column's consensus element is of no concern to them. They don't want the shading program doing analysis. Their need for analysis vanished as soon as the alignment was generated. (Of course, users at other sites may have different needs!) Here are the simple shading rules which my users would like to have applied to mutual alignments of multiple amino acid sequences. The following would apply to each column of an alignment: o If more than half of the elements are one amino acid, then shade those all in black. Call that amino acid the "majority occupier" in the column. o In cases where the above has occurred, if any of the other elements fall in the same amino acid family as that majority occupier, then shade those other family members in gray. o In cases where there is no majority occupier, if more than half of the column elements all fall into the same a.a. family, then shade all of those family members in gray. That's it. In this very straightforward scheme, two shading colors are required: black and gray. Now, where I said "more than half" above, there's a question of whether that should mean precisely greater than half, or greater than OR EQUAL to half. If the latter, troubling problems can arise. For example, what do you do if you have an alignment of 8 sequences, and in one column there are 4 I's and 4 L's -- which do you shade black and which do you shade gray? Do we need to specify one more rule, causing all 8 to be shaded gray in such a case? Keeping the interpretation of "more than half" as precisely greater than half avoids such questions, but also means that a column with C,D,E,G,I,I,I,I will have nothing shaded, which is not necessarily what a user wants. The "perfect" shading program ought to have an option allowing the user to switch from the default .gt. half rule to the .ge. rule. My users care very much about the a.a. family groupings implicit in shading decisions. In fact, they want that relation to be explicit, and independent of the numbers in the mutation matrix (which were used in constructing the m.s.a.). They would like the user to have control over the family groupings used in shading decisions (according to my proposed rules above). It would be useful if the program had built into it a default a.a. family grouping, 2 or 3 alternate "standard" groupings (selectable at the user-prompt level), and an option allowing the user to specify his/her own custom a.a. family assignments (presumably via a text file confirming to some simple format). I note that Kay Hofmann's Box- Shade program, along with its *.SIM file, can support asymmetric family membership assignments, which is a useful capability to preserve in the shading program next to be developed or perfected. The default family grouping might be the one already used in GCG's GenRunData:Simplify.Txt [text below from GenHelp Simplify Description output] -- A = P,A,G,S,T (neutral, weakly hydrophobic) D = Q,N,E,D,B,Z (hydrophilic, acid amine) H = H,K,R (hydrophilic, basic) I = L,I,V,M (hydrophobic) F = F,Y,W (hydrophobic, aromatic) C = C (cross-link forming) (grouping due to Jimenez & Martinez at UCSF). An alternate standard grouping might be the following one from Branden & Tooze, _Introduction to Protein Structure_, 1991, pages 6-7, which seems very different -- A,V,F,P,M,I,L (hydrophobic) D,E,K,R (charged) S,T,Y,H,C,N,Q,W (polar) G (glycine) (I don't know where the ambiguous codes B and Z fit into this one.) My comments above are specific to amino acid sequence alignments. A shading program may need to obey a different rationale in handling nucleotide sequence alignments. Black would still highlight majority occupations. Gray might be used in connection with ambiguous nucleotides: highlighting ambiguous matches to a majority (unambiguous) element, or highlighting a column's majority of matching/consistent ambiguous nucleotides, etc. (It sounds potentially more complicated than handling amino acids -- may not be possible to work out a fully consistent scheme.) Positive reactions, negative t(h)rashing, or other comments? Mark Reboul Columbia-Presbyterian Cancer Center Computing Facility mark@cuccfa.ccc.columbia.edu P.S. -- Kay Hofmann, creator of BoxShade, raised his own interesting questions about all this back in '91 in the Info-GCG forum. For those who may not have seen that, I excerpt the relevant part of his posting below. =============================================================================== Date: Sat, 9 Nov 1991 19:40:20 GMT From: Kay Hofmann Subject: Re: PRETTYBOX v1.1 . . [initial text omitted by Mark Reboul] . Problem 1: Think of an alignment having at a certain position two sequences with a Glu (E) and, say, five sequences having a hydrophobic residue (I,L,F,V,M). Now any program has to decide if the two identical E's should be marked, leaving the rest unlabeled or if the 5 similar residues should override the identity. This problem has to be extended to more complex cases involving a weighting of similar vs. identical residues Problem 2: (related to 1) How should similarity should be treated in general? One obvious method would be using Dayhoff-type scores which would in turn solve the 'identity vs. similarity' problem. The problem with those score is that identity of frequently occuring residues have lower scores than exchanges between less frequent amino acids. Strict use of these tables would lead to diagrams where His-Gln would be marked while any number of Ala at the same position are not recognized. Problem 3: (unsolvable) If you have at a seqeunce position 5x Gly and 5x His only one of these identities can be marked, the other one has to remain blank. Depending on the purpose of your multiple alignment, this can lead to very annoying effects if the 'wrong' group is labeled by the program. Example: seq1 GRTEILV seq2 GRTEILV seq3 AAAIWWW seq4 QQQILLL seq5 LLLIQQQ you see how the consensus of seq1 and seq2 would be interrupted because the (unrelated) seq3,seq4 and seq5 all have an Ile at position 4. . . [more text omitted here by Reboul] . ------------------------------------------------------------------------ Kay Oliver Hofmann Tel. ++49 201 478 6980 Institut fuer Biochemie (med. Fak.) FAX ++49 201 478 6979 Universitaet Koeln Joseph Stelzmann Str. 52 INTERNET: D-5000 Koeln 41 KHOFMANN@cipvax.biolan.uni-koeln.de ------------------------------------------------------------------------ From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!uunet!olivea!news.bu.edu!wyc From: wyc@bu.edu (Yecheng Wu) Newsgroups: bionet.software Subject: Re:Sequence analysis packages, which? Date: 7 Jan 1994 14:56:41 GMT Organization: Boston University Lines: 14 Message-ID: <2gjt79$oqv@news.bu.edu> NNTP-Posting-Host: crsa.bu.edu X-Newsreader: TIN [version 1.2 PL0] Scanalytics/CSPI has a package called DNAscan, which reads DNA sequences automatically from gels or autoradiograms. It runs on PC in Microsoft Windows environment. If you need more information or want to have a demo, you can contact our west coast people: Ramon Galoo at 619-483-0161 Good luck. Yecheng Wu, PhD Scanalytics/CSPI 508 663 7598 From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!vixen.cso.uiuc.edu!robertson4.life.uiuc.edu!user From: d-lampe@uiuc.edu (David Lampe) Newsgroups: bionet.software Subject: Re: Promoter analysis Followup-To: bionet.software Date: 7 Jan 1994 14:53:03 GMT Organization: Univ. Illinois Lines: 23 Distribution: world Message-ID: References: <1994Jan6.104602.12519@infodev.cam.ac.uk> NNTP-Posting-Host: robertson4.life.uiuc.edu In article <1994Jan6.104602.12519@infodev.cam.ac.uk>, sgb12@mbfs.bio.cam.ac.uk (Sean Buchanan (Bioc)) wrote: > > I have some Drosophila promoter sequence which I would like to analyse for > transcription factor sites etc. Can anyone advise me of available software. > I have tried looking in the GCG "help" file, but cannot find what I am > looking for. Any pointers or suggestions would be greatly appreciated. > > Sean. Sean, Use the program FINDPATTERNS in GCG and ask it to search the database tfsites.dat with your sequence. Use FETCH to bring tfsites.dat into your directory and the use the command FINDPATTERNS /DATA=TFSITES.DAT to run the program. Good luck David Lampe Dept. Entomology University of Illinois d-lampe@uiuc.edu From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: "Keith D. Wilkinson" Newsgroups: bionet.software Subject: Re: NCBI BLAST output format: Question. Date: 7 Jan 1994 14:18:02 -0000 Lines: 26 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gjquq$2qe@mserv1.dl.ac.uk> Reply-To: "Keith D. Wilkinson" Original-To: bio-soft@net.bio.net > To: bio-soft@net.bio.net > From: brianf@med.uvm.edu (Brian Foley) > Subject: NCBI BLAST output format: Question. > Sender: news@emba.uvm.edu > X-Newsreader: TIN [version 1.2 PL1] > Date: Thu, 6 Jan 1994 20:09:57 GMT > > > Can someone tell me what is the best software for viewing the > output from an NCBI BLAST search? Whether I read the output in my > UNIX e-mail, my Mac e-mail, or convert it to a text editor (MS-Word) > document, the alignments do not line up without messing with them. > It seems that the output uses TABs rather than spaces to > format the output, and these TABs do not correspond to the ones > I have. Perhaps if I just knew what the TAB settings were... > > Does the BLAST output look great when it is imported into > WordPerfect or some other text editor? > The problem is the default use of proportional fonts with you Mac (or unix box). Try saving the search in Word and then using a 10 pt Courier font. This should result in correct spacing and alignment. From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: Jeroen Coppieters Newsgroups: bionet.software Subject: Fasta on Mac Date: 7 Jan 1994 15:37:36 -0000 Lines: 21 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gjvk0$6hi@mserv1.dl.ac.uk> Original-To: bio-soft@gargamel.rug.ac.be I downloaded fasta16c24b.shar.Z. the documentation (fasta16.doc) mentions that this program should run on Macintosh, but does not indicate which C-compiler it is compatible with. There is no installation chapter for Mac (there is for PC and Unix) Is there a version available with Mac specific instructions for installation? I would like to use the program together with the EMBL CD-ROM Has anybody done this? Jeroen ===================================================================== jecop@gengenp.rug.ac.be / Jeroen Coppieters \ \ /\/\ /\/ Lab of Genetics \ \ / /\ \/ /\ University of Gent. \ /\/ \/\/ \ /\ AG GC C Ledeganckstraat 35 \ / \ T A G A A B-9000 Gent (Belgium) \/ A AA GA 32-9-2645189 ===================================================================== From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: preuss Newsgroups: bionet.software Subject: nseqtool?? Date: 7 Jan 1994 13:51:26 -0000 Lines: 12 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gjpcu$1dv@mserv1.dl.ac.uk> Reply-To: tm12kpkp@rz.uni-sb.de X-Nupop-Charset: English Return-Receipt-To: tm12kpkp@rz.uni-sb.de Original-To: bio-soft@net.bio.net Hi netters, I am looking for a programm called nseqtools for IBM-PC. I saw it somewhere but I don't remember where. Please help. K.D.Preuss Phone:+6841-166123 Physiologie II FAX: +6841-166655 Universitaet des Saarlandes E-mail:tm12kpkp@rz.uni-sb.de 66421 Homburg/Saar Germany From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: "RYBICKI, ED" Newsgroups: bionet.software Subject: Re: NCBI BLAST output format: Question. Date: 7 Jan 1994 08:01:12 -0000 Lines: 28 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gj4s8$dcn@mserv1.dl.ac.uk> Reply-To: ed@micro.uct.ac.za Original-To: brianf@med.uvm.edu, bio-soft@net.bio.net > To: bio-soft@net.bio.net > From: brianf@med.uvm.edu (Brian Foley) > Subject: NCBI BLAST output format: Question. > Date: Thu, 6 Jan 1994 20:09:57 GMT > > Can someone tell me what is the best software for viewing the > output from an NCBI BLAST search? Try WinBlast from NCBI: runs under Windows 3.1, has a window for hits, and another for the alignment of a specific hit. Also allows saving of sequences, and a host of other functions (as well as formatting of BLAST server requests). It has a friend called IRX which allows search and retrieval and viewing/saving of sequences as well. Solid gold...! ____________________________________________________________________ | Ed Rybicki, PhD | | | (ed@micro.uct.ac.za) | "Lord, won't you buy me | | Dept Microbiology | A Mer-ce-des Benz | | University of Cape Town | My friends all have Porsches | | | I must make amends..." | | | Private Bag, Rondebosch | | | 7700, South Africa | - Janis Joplin | | fax: xx27-21-650 4023 | (Pearl, 1971) | -------------------------------------------------------------------- First Albert, now Frank...go well, axemen! From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!uknet!daresbury!not-for-mail From: Miloslav Juricek - SCBI Newsgroups: bionet.software Subject: Re: NCBI BLAST output format: Question. Date: 7 Jan 1994 07:17:09 -0000 Lines: 41 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2gj29l$bni@mserv1.dl.ac.uk> Reply-To: Miloslav Juricek - SCBI Original-To: Brian Foley On Thu, 6 Jan 1994, Brian Foley wrote: > Can someone tell me what is the best software for viewing the > output from an NCBI BLAST search? Whether I read the output in my > UNIX e-mail, my Mac e-mail, or convert it to a text editor (MS-Word) > document, the alignments do not line up without messing with them. > It seems that the output uses TABs rather than spaces to > format the output, and these TABs do not correspond to the ones > I have. Perhaps if I just knew what the TAB settings were... > > Does the BLAST output look great when it is imported into > WordPerfect or some other text editor? > > -- > ******************************************************************** > * Brian Foley * If we knew what we were doing * > * Molecular Genetics Dept. * it wouldn't be called research * > * University of Vermont * * > > There is a shareware Windows program called WINBLAST, which is designed to: 1. Format a blast search query through window's dialog box. 2. View the search results and save selected alignments to file. 3. Autamatically format a retrieval request for database entries corresponding to selected alignments. I don't remember any more from which FTP site I got it originally, for sure it shall be available from the author - A. V. Sivaprasad, avs@biochem.adelaide.edu.au. Mila Juricek Dept. of Biochemistry Mahidol University Bangkok From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!haven.umd.edu!darwin.sura.net!newsserver.jvnc.net!raffles.technet.sg!iss.nus.sg!gsingh From: gsingh@iss.nus.sg (Gurminder Singh) Newsgroups: bionet.software Subject: 2nd CFP: VRST - Virtual Reality Software & Technology Date: 7 Jan 1994 09:02:14 GMT Organization: Institute Of Systems Science, NUS. Lines: 295 Message-ID: <2gj8em$sk4@holodeck.iss.nus.sg> NNTP-Posting-Host: raccoon.iss.nus.sg X-Newsreader: TIN [version 1.2 PL2] ************************************************** * * * V R S T ' 9 4 * * * * Conference on * * Virtual Reality Software and Technology * * * * August 23-26, 1994 * * Singapore * * * * Sponsored by ACM SIGCHI and ISS, Singapore * * In Cooperation with ACM SIGGRAPH & CGS * * * * * * C A L L F O R P A R T I C I P A T I O N * * * * * * Papers, Panels and Tutorials due: * * February 7, 1994 * * Demos due: February 28, 1994 * * * ************************************************** VRST'94, the Conference on Virtual Reality Software and Technology, presents a high-quality forum for innovative virtual reality research and development. The conference will bring together virtual reality researchers and developers for a four day program. Papers, panels, tutorials and demos are sought on a wide range of topics in virtual reality. A special issue of the ACM Transactions on Computer-Human Interaction (TOCHI) will be published, containing rigorously reviewed, extended versions of selected papers from the conference. PAPERS Authors are encouraged to submit high-quality papers about research and development in virtual reality. The field of virtual reality is evolving, hence the scope of the conference is broad. We encourage submissions which describe work -- finished or in progress, theory or practice -- on the following or related subjects: o Software Architectures for VR o VR Interaction and Navigation Techniques o Tools and Techniques for Modeling VR Systems o Distributed VR Systems o Tactile and Force Feedback o Motion Tracking o Telepresence and Telerobotics o Spatial Audio o VR Input and Output Devices o Innovative Applications of VR o Human Factors of VR o Evaluation of VR Techniques and Systems. Papers should be at most 6000 words or 10 pages. Submissions should consist of 6 copies of the paper and a cover letter indicating the primary author's name, affiliation, address, phone and fax numbers and email address. The title page should include an abstract (less than 200 words) and 5 keywords. Papers in hardcopy form must be received no later than February 7, 1994 by: Gurminder Singh Institute of Systems Science National University of Singapore Heng Mui Keng Terrace Kent Ridge Singapore 0511 REPUBLIC OF SINGAPORE gsingh@iss.nus.sg +65 772-3651 +65 774-4998 (fax) PANELS Panels provide an opportunity for lively discussion of topical or controversial issues. Contrasting opinions, perspectives, or approaches are initially presented by knowledgeable panelists. Discussion of the issues is extended by audience participation. Proposals for panels will be evaluated on the basis of the significance of the issues and the prospects for productive discussion. A panel proposal should be no more than two pages in length. It should include: o A description of the panel topic, including why this topic is important to the conference attendees. o A brief position statement for each panelist. o A cover sheet that includes the panel title, length of time desired for the panel, panelists' names and affiliations, and the panel organizer's name, affiliation, address, email- address, and phone and fax numbers. Submissions must be received no later than February 7, 1994 by: Mark Green Department of Computing Science University of Alberta Edmonton, Alberta T6G 2H1 CANADA mark@cs.ualberta.ca +1 403-492-4584 +1 403-492-1071 (fax) TUTORIALS Proposals for tutorial offerings by developers, researchers and educators are invited. Tutorials will be evaluated on the basis of their relevance to the VRST attendees and on the technical quality of the tutorial. Past experience and qualifications of the instructors, along with overall balance of the tutorial program, are significant factors. Instructors must request tutorial proposal requirements from the Tutorials Chair. Submissions in hardcopy must be received no later than February 7, 1994. Send questions and requests for submission form to: Hiroo Iwata Institute of Engineering Mechanics University of Tsukuba Tsukuba, 305 JAPAN iwata@kz.tsukuba.ac.jp +81 298-53-5362 +81 298-53-5207 (fax) DEMONSTRATIONS Demonstrations enable the developers of systems to present their systems to conference attendees. Proposals will be evaluated on the basis of their potential as interesting demonstrations and for bringing new and exciting ideas to the conference. Submit six copies of a five page proposal describing why a demonstration is the best way to present the work, its relevance to the VRST attendees, a demonstration story board with a few screen pictures, and a detailed description of the equipment support needed. Submission in hardcopy form must be received by February 28, 1994. You are encouraged to discuss your requirements over email with the Demonstrations Chair. Send questions and requests for information to: Luis Serra Institute of Systems Science National University of Singapore Heng Mui Keng Terrace Kent Ridge Singapore 0511 REPUBLIC OF SINGAPORE luis@iss.nus.sg +65 772-2014 +65 774-4998 (fax) _________________________________________________________________ General Chair: Juzar Motiwalla, ISS, Singapore Program Co-Chairs: Gurminder Singh, ISS, Singapore Steven Feiner, Columbia University, USA Daniel Thalmann, SFIT, Switzerland Program Committee: William Bricken, U Washington, USA Pere Brunet, U Politecnica de Catalunya, Spain Steve Bryson, NASA Ames, USA Michael Deering, Sun, USA Kim Fairchild, ISS, Singapore Lennart Fahlen, SICS, Sweden Michael Gigante, RMIT, Australia Martin Goebel, Fraunhofer Institute, Germany Mark Green, U Alberta, Canada Michitaka Hirose, U Tokyo, Japan Hiroo Iwata, U Tsukuba, Japan Rob Jacob, Naval Research Lab, USA Tosiyasu L. Kunii, U Tokyo, Japan Beth Marcus, Exos, USA Margaret Minsky, Interval Research, USA Randy Pausch, U Virginia, USA Timothy Poston, ISS, Singapore Alfred Schmitt, U Karlsruhe, Germany Luis Serra, ISS, Singapore Mel Slater, U London, UK Susumu Tachi, U Tokyo, Japan Nadia M Thalmann, U Geneva, Switzerland Colin Ware, U New Brunswick, Canada Beth Wenzel, NASA Ames, USA David Zeltzer, MIT, USA Michael Zyda, Naval Postgrad School, USA International Coordination Committee: Michitaka Hirose, U Tokyo, Japan Rob Jacob, Naval Research Lab, USA Daniel Thalmann, SFIT, Switzerland _________________________________________________________________ About the Sponsors ACM/SIGCHI Founded in 1947, the Association for Computing Machinery (ACM) is the largest and oldest educational and scientific computer organization in the industry today. ACM's name reflects the concerns of its founders (i.e., machinery), but ACM's vitality stems from its members - their ideas and experience. ACM is a society of individuals, a living vehicle for the continuity of professional standards and traditions. From a dedicated group of 78, ACM is now 85,000 strong, with 34 special interest groups (SIGs), including SIGCHI (Special Interest Group for Computer Human Interaction), and more than 600 chapters and student chapters. The scope of SIGCHI consists of the study of the human-computer interaction process and includes research, design, development and evaluation efforts for interactive systems. The focus of SIGCHI is on how people communicate and interact with a broadly defined range of computer systems. SIGCHI servers as a forum for the exchange of ideas among computer scientists, human factors specialists, psychologists, social scientists, systems designers, graphic designers and end users. Over 6,200 professionals work together toward common goals and objectives. For further information, email to ACMHELP@ACM.ORG or call +1 212-626-0500 Institute of Systems Science, Singapore The Institute of Systems Science (ISS) is a leading computer research laboratory in the Pacific region with close to 100 research staff. ISS aims to provide international and regional leadership in next generation technologies and spin-offs. The research focus of the Institute broadly covers seven strategic areas: Multimedia Systems, Natural Language Processing, Broadband Networking, Archival and Retrieval of Multimedia Information, Neural Networks and Fuzzy Logic, Medical Imaging: Rendering and Analysis, and Accelerated Computing. ISS also offers M.Sc. and Ph.D. degrees by research. For further information on ISS, contact K.T. Goh at gohkt@iss.nus.sg or +65 772-2469. _________________________________________________________________ GENERAL INFORMATION Location: Singapore Situated at one of the most important crossroads of the world, Singapore is truly a place where East and West come together. Here you will find Chinese, Indian and Malay communities living harmoniously together, their long established cultures forming a unique backdrop to a clean and modern garden city. English is spoken everywhere and is the common business language of all. Few places on earth promise such delight for the palate, with gourmet cuisines from over 30 countries. Singapore's climate is warm and welcoming all year round, with temperatures ranging from 28 degrees Celsius in the day, to 23 degrees Celsius by night. Further information on ISS and Singapore is available on the World Wide Web (WWW) server at ISS. To access it through Mosaic, type mosaic http://www.iss.nus.sg/ISS_HomePage.html Airfares Here is a list of discounted-economy return airfares from various cities around the world to Singapore. You maybe able to get even cheaper fares from your travel agent. This information is provided to help you with your planning and the fares listed below are not guaranteed. LA/SF US$1100 Washington DC US$1200 New York US$1200 London 399 Pounds Stockholm 6000SEK Frankfurt DM 1450,00 Tokyo 88,000 yen -- Gurminder Singh Email: gsingh@iss.nus.sg Institute of Systems Science GSingh.CHI@Xerox.com National University of Singapore FAX: (65)778-2571 Kent Ridge, Singapore 0511 Phone: (65)772-3651 From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!hubcap!darwin.sura.net!tulane!ames!agate!dog.ee.lbl.gov!network.ucsd.edu!sdcc12!me28tl From: me28tl@sdcc12.ucsd.edu (tzu-ping lin) Newsgroups: bionet.software Subject: Sequence analysis packages, which? Summary: Need advice on software purchase Keywords: DNA sequence digitizer Message-ID: <59074@sdcc12.ucsd.edu> Date: 7 Jan 94 07:56:50 GMT Sender: news@sdcc12.ucsd.edu Distribution: usa Lines: 14 Nntp-Posting-Host: sdcc12.ucsd.edu Hi, everyone. We are considering purchasing a software/hardware package for aquiring DNA sequences from gels and analyzing those sequences. We have both Mac (LC III) and PC (386, 486 running Windows) in the lab. We are looking for a system with easy data input (from autorad films) and reliable contig management. We have brochures from Intelligenetics (GeneWorks and PC Gene) and Hitachi (Mac DNAsis). Does anyone have experience with either or both systems? Do you think either computer platform has any particular advantage over the other (I personally favor the Mac)? Any information welcome. Tzu-Ping Lin, UCSD AOL:tpl@aol.com CI$:72647.345@compuserve.com From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!hubcap!darwin.sura.net!howland.reston.ans.net!vixen.cso.uiuc.edu!sdd.hp.com!caen!msuinfo!harbinger.cc.monash.edu.au!vaxc.cc.monash.edu.au!mic123d From: mic123d@vaxc.cc.monash.edu.au Newsgroups: bionet.software Subject: Problems with SeqED Message-ID: <1994Jan7.170556.93142@vaxc.cc.monash.edu.au> Date: 7 Jan 94 17:05:56 +1100 Organization: Computer Centre, Monash University, Australia Lines: 15 To who ever is out there having SeqED problems!!! We would like to know if any one is having problems using SeqED v1.0.3. We are running the program on a Macintosh IIvi 5Meg RAM / 80Meg on the hard disk and we are running System 7.1. Basically the .problems that we are experiencing occur when trying to save data using both the SAVE and the SAVE AS command. We are also having on screen errors such as MY-1, MNF-1, ED-1 and SeqED error #9112. If anyone is having similar problems -how are you dealing with them (apart from not using SeqED)? We have been told by ABI that SeqED may not be compatible with System 7.1 ???? Is there an alternative program to SeqED (ie that is better than SeqED) and how is it possible to obtain this program. Also if the is an EMail address for ABI in America could please forward that as well. Carmel Ruffolo Microbiology Dept. Monash Uni. VIC AUSTRALIA. From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!hubcap!darwin.sura.net!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!msuinfo!harbinger.cc.monash.edu.au!bruce.cs.monash.edu.au!darrenp From: darrenp@bruce.cs.monash.edu.au (Daz) Newsgroups: bionet.software Subject: Re: Vector Cloning Software Date: 7 Jan 1994 03:22:41 GMT Organization: Computer Science, Monash University, Australia Lines: 27 Distribution: world Message-ID: <2giki1$jfg@harbinger.cc.monash.edu.au> References: <1993Dec27.210418.1@molbiol.ox.ac.uk> NNTP-Posting-Host: dibbler.cs.monash.edu.au X-Newsreader: TIN [version 1.2 251093BETA PL3] jjowett@molbiol.ox.ac.uk wrote: : To Whom it may concern : For a while now I have been aghast at how difficult it has been to get a hold : of and find out about good programs for the PC that carry out cloning type : operations and keep track of DNA sequences- so that when you want to look : up a restriction map of a vector that maybe in it's 4th generation, you have : to sift through a pile of notes about which fragment came from where! : I am posting this message for those of you who have been similarly frustrated : to let you know about what a friend let me know of, and that is Vector PC. It : is the answer to the above problems! We have someone here working on a program for unix/X windows that will cope with complex restriction mapping problems - eg where there are large numbers of sub experiments etc. It is designed more for the mapping side of things rather than the construction of DNA. If you would be interested in trying this out for us, you might like to send me some email. We are in a bit of a catch 22 situation where we need to have it all working to get people to use it, but to finsish it, we need to see what people want ! - so if you even have some data you'd like us to run past it, feel free to mail it to us. Yours sincerely, Darren Platt. From owner-software@net.bio.net Thu Jan 06 22:00:00 1994 Path: biosci!hubcap!darwin.sura.net!europa.eng.gtefsd.com!uunet!munnari.oz.au!newshost.anu.edu.au!rsbspc59.anu.edu.au!John.Hancock From: John Hancock Newsgroups: bionet.software Subject: SIMPLE34 - Detection of simple sequences Date: 7 Jan 1994 02:49:15 GMT Organization: RSBS, ANU Lines: 103 Distribution: world Message-ID: <2giijb$sm0@manuel.anu.edu.au> NNTP-Posting-Host: 150.203.38.79 X-UserAgent: Nuntius v1.1.1d12 X-XXMessage-ID: X-XXDate: Fri, 7 Jan 94 21:53:11 GMT ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATA C C A SIMPLE34 A C C GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCG Version 1.0 of SIMPLE34 is available free of charge to academic users. -> WHAT DOES IT DO? SIMPLE34 extends and makes more widely available the SIMPLE program originally described by Tautz, Trick & Dover (Nature 322, 652-656, 1986). Details of this implementation will be published in 1994 in CABIOS. The aim of the program is to estimate the level of local sequence repetition in nucleotide sequences. It does this by analysing the degree of clustering of short sequence motifs (3- and 4-mers). A significant level of clustering of short motifs has been suggested to reflect the action of replication slippage in the recent evolutionary history of sequences and is associated with length polymorphism in a variety of sequences including ribosomal RNAs, the mitochondrial control region and the transcription factor TBP. The program provides the following information: -- A measure, the RELATIVE SIMPLICITY FACTOR (RSF), which represents the degree of motif clustering within the sequence relative to random sequences of the same base composition, doublet composition and length as the input sequence. The program calculates confidence limits for the level of motif clustering within the sequence being statistically significant. -- A graphical representation (in POSTSCRIPT format) of the distribution of motif clustering along the sequence. -- The locations of sites showing significantly more motif clustering than is seen in the random sequences. -- The sequence motifs associated with significantly high levels of clustering. A detailed description of the operation of SIMPLE34 can be found in the file simple34.doc included with the program. -> PLATFORMS SIMPLE34 is written in FORTRAN77 and is available for Vax and Sun platforms. -> AVAILABILITY SIMPLE34 can be obtained over the network from the Australian National University by anonymous FTP or Gopher. Anonymous FTP: Host Name: life.anu.edu.au Directory: /pub/molecular_biology/software/simple Subdirectories software/vax and software/sun contain the directories simple34. FTP the complete directory for best results. File types: Text Gopher: Name = simple34 Host = life.anu.edu.au Path = /molecular_biology/software/simple Subdirectories software/vax and software/sun contain the directories simple34. FTP the complete directory for best results. -> HOW DO I USE SIMPLE34? SIMPLE34 accepts plain (Staden) format RNA or DNA sequences up to 50,000 bases in length. Instructions for setting up the programs are included in the readme files accompanying the two versions. Running the script/command procedure "setup" will compile the program. For Vax users, instructions for adding aliases for the command procedures that come with the program are included in the readme file. This is done automatically on Sun systems. -> WHO CAN I CONTACT ABOUT SIMPLE34? Comments, suggestions for improvements and gripes can be sent to John Hancock at the following addresses: E-mail: John.Hancock@anu.edu.au Phone: +61-6-249-5916 Fax: +61-6-249-4437 Post: Research School of Biological Sciences, Austr