From owner-software@net.bio.net Fri Nov 01 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!surfnet.nl!news.unisource.nl!xs4all!xs4all!user From: a_team@dds.nl (Anneke Harbers and Ard Jonker) Newsgroups: bionet.software Subject: Re: Macintosh thumbnails of images software Date: Sat, 02 Nov 1996 21:39:49 +0100 Organization: a_team Lines: 8 Message-ID: References: NNTP-Posting-Host: asd07-08.dial.xs4all.nl X-XS4ALL-Date: Sat, 02 Nov 1996 21:39:26 MET I missed the original posting, but I gather it is about saving overviews of what pictures you have. Try PictureAlbumLight. It allowes file and video source import of images, with a specified (maximum) size. Intuitive. ard From owner-software@net.bio.net Fri Nov 01 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!panix!bloom-beacon.mit.edu!boulder!ural.colorado.edu!hertz From: hertz@ural.colorado.edu (Gerald Z. Hertz) Newsgroups: bionet.software Subject: Re: DNA consesus search software Date: 2 Nov 1996 05:24:21 GMT Organization: University of Colorado at Boulder Lines: 62 Message-ID: <55elu5$an0@lace.colorado.edu> References: <327663F3.3433@scripps.edu> NNTP-Posting-Host: ural.colorado.edu X-Newsreader: NN version 6.5.0 #17 (NOV) Wade Walke writes: >I'm looking for a program that can accept input of multiple small (10-20 >bp long) DNA sequences (possibly hundreds of different sequences) then >compare and analyze them for various consensus motifs. These sequences >will not all fall into a single consensus motif so I cannot use a simple >alignment program. I what to know if any such program exists and if not >is there anyone willing to write such a program given the proper >incentive? >Wade Walke >dwwalke@scripps.edu I have a set of programs for doing what you wish. The programs were written for UNIX and are located at ftp://beagle.colorado.edu/pub/Consensus The file "consensus.readme" describes what I have in the directory. Currently, the anonymous ftp directory contains the following major programs: 1) consensus 2) wconsensus 3) patser 4) gmat-inf-gc The "consensus" program is the current version of the program described in Stormo and Hartzell (1989, PNAS, 86:1183-1187) and Hertz et al. (1990, CABIOS, 6:81-92). However, this program has many more options than the published version. The most major change is that each sequence may contribute zero or more words to the pattern being generated, rather than being required to contribute exactly once. Also, the algorithm is no longer dependent on the order in which the sequences are presented to the program. "wconsensus" differs from the "consensus" program in that the user does not supply the width of the pattern being sought, although the user must adjust a bias that determines the final width. This program can allow terminal deletions in case some of your sequences are missing the ends of your motif. The "patser" program allows one to score the words of a sequence against an alignment matrix obtained from the "consensus" or "wconsensus" program. The "gmat-inf-gc" program can do a crude graphing of the information content at each position of an alignment obtained with the "consensus" or "wconsensus" program. I also have alignment programs that can introduce gaps (insertions and deletions) into the alignment. I do not currently have these programs in my anonymous ftp directory, but will supply them upon request. Jerry Hertz Gerald Z. Hertz | telephone: (303) 492-1474 Dept. of MCD Biology | fax: (303) 492-7744 University of Colorado | internet: hertz@boulder.colorado.edu Campus Box 347 | Boulder, CO 80309-0347 | From owner-software@net.bio.net Fri Nov 01 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!surfnet.nl!news.unisource.nl!xs4all!xs4all!usenet From: marker@xs4all.nl (Niels Groot) Newsgroups: bionet.software Subject: Re: Silent mutation software Date: 2 Nov 1996 21:07:09 GMT Organization: XS4ALL, networking for the masses Lines: 20 Distribution: world Message-ID: <55gd5u$30k@news.xs4all.nl> References: NNTP-Posting-Host: 194.109.46.169 Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-XS4ALL-Date: Sat, 02 Nov 1996 22:07:10 MET X-Newsreader: WinVN 0.99.7 In article , yoramg2@LEONARDO.LS.HUJI.AC.IL says... > >I'm looking for a program that can find silent restriction sites. I have >Silmut, but it limited to 100 enzymes that are 6-cutters. > >***************************************************************************** >Yoram Gerchman >Division of Microbial & Molecular Ecology >The Institute of Life Sciences >Hebrew University of Jerusalem >Israel > Take a look at http://www.xs4all.nl/~marker, SeqSearch v1.0 is a Windows based program that besides other tools will do the trick. Niels Groot From owner-software@net.bio.net Fri Nov 01 22:00:00 1996 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!mr.net!www.nntp.primenet.com!nntp.primenet.com!nntp.uio.no!nntp.zit.th-darmstadt.de!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!uni-erlangen.de!winx03!wuff.mayn.de!wuff.franken.de!news.cs.uni-magdeburg.de!news.boerde.de!magicalf!news From: "David R. Waddell" Subject: Re: Macintosh thumbnails of images software Sender: news@magicalf.boerde.de (News Admin) Message-ID: X-Newsgroups-To: nntp://194.94.137.240/bionet.software Date: Thu, 31 Oct 1996 10:54:29 GMT X-News-Servers: 194.94.137.240 X-Nntp-Posting-Host: esw-05.ipk-gatersleben.de Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary="Cyberdog-AltBoundary-003A31CB" References: Mime-Version: 1.0 X-Mailer: Cyberdog/1.1 Organization: Private UNIX site Lines: 31 --Cyberdog-AltBoundary-003A31CB Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable We use Kodak's Shoebox. However, it is a fairly old program (not native PPC) and I have not heard about it being updated or maintained. Adobe delivered a program called Adobe Fetch that is for organizing images on their Illustrator 6.0 CD. I have not yet tried it out though. --Cyberdog-AltBoundary-003A31CB Content-Type: multipart/mixed; boundary="Cyberdog-MixedBoundary-003A31CB" Content-Transfer-Encoding: 7bit --Cyberdog-MixedBoundary-003A31CB Content-Type: text/enriched; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable 12GenevaWe use Kodak's Shoebox. However, it is a fairly old program (not native PPC) and I have not heard about it being updated or maintained. Adobe delivered a program called Adobe Fetch that is for organizing images on their Illustrator 6.0 CD. I have not yet tried it out though. --Cyberdog-MixedBoundary-003A31CB-- --Cyberdog-AltBoundary-003A31CB-- From owner-software@net.bio.net Sat Nov 02 22:00:00 1996 Path: biosci!rutgers!uwm.edu!www.nntp.primenet.com!nntp.primenet.com!news.sprintlink.net!news-peer.sprintlink.net!uunet!in1.uu.net!news.Arizona.EDU!usenet From: Tarak Parekh Newsgroups: bionet.software Subject: Phylip query Date: Sun, 03 Nov 1996 12:39:43 -0700 Organization: The University of Arizona Lines: 9 Message-ID: <327CF4FF.76E6@cs.arizona.edu> NNTP-Posting-Host: pcito.medmicro.arizona.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Hello, I have Phylip 3.5 for windows, and am a novice user of it. I wish to know if you could include the bootstrat frequencies in the consense of a multitreee file. If yes, how do you do it ? Please email me if possible, thanks, tarak Email : tarak@cs.arizona.edu From owner-software@net.bio.net Sat Nov 02 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!uwm.edu!news.he.net!news1.good.net!news.good.net!news-dc.gsl.net!news.gsl.net!news.sprintlink.co.za!osprey.global.co.za!news From: cvzgv123@Global.co.za (cvzgv123) Newsgroups: bionet.software Subject: Turbo Pascal Date: Sun, 03 Nov 1996 21:02:17 GMT Organization: Global Internet Access Lines: 3 Message-ID: <55jfa4$9n5@osprey.global.co.za> Reply-To: cvzgv123@Global.co.za NNTP-Posting-Host: mdm-po165.jhb168-anx3.net.global.co.za X-Newsreader: Forte Free Agent 1.0.82 I'm looking for the software of Turbo Pascal ver.xx Lost mine..... From owner-software@net.bio.net Sun Nov 03 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.erols.net!EU.net!Austria.EU.net!01-newsfeed.univie.ac.at!03-newsfeed.univie.ac.at!mail.boku.ac.at!news From: Andreas Wernitznig Newsgroups: bionet.software Subject: Re: RASMOL: Merging two structures Date: Mon, 04 Nov 1996 11:14:26 +0100 Organization: Univ. for Agriculture Lines: 9 Message-ID: <327DC202.104D@edv1.boku.ac.at> References: <32707A34.BC1@edv1.boku.ac.at> <54r1v1$632@gwdu19.gwdg.de> <327799a7.17760709@news.ruhr-uni-bochum.de> <32789810.31EB@edv1.boku.ac.at> <55ans8$l2c@winx03.informatik.uni-wuerzburg.de> <55av0d$5b0@epx.cis.umn.edu> Reply-To: h8760592@edv1.boku.ac.at NNTP-Posting-Host: 141.244.88.51 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (WinNT; I) Hiroki wrote: > cat file1.pdb file2.pdb > two.pdb > is what I've been using. Usually I'll change the chainid > in one or the other file first to make selection easier. This function just concatenates the two files. It doesn't put them in the right position and angle. If the structures are from the same source (program) it might work. Andreas From owner-software@net.bio.net Sun Nov 03 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.sprintlink.net!news-peer.sprintlink.net!news-peer.gsl.net!news.gsl.net!portc01.blue.aol.com!audrey01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: frankz33@aol.com (Frankz33) Newsgroups: bionet.software Subject: Hello, my name is frank Date: 3 Nov 1996 23:05:02 -0500 Organization: America Online, Inc. (1-800-827-6364) Lines: 1 Sender: root@newsbf02.news.aol.com Message-ID: <55jq1e$mgu@newsbf02.news.aol.com> References: <84531596837017@bbs.giga.com.ar> Reply-To: frankz33@aol.com (Frankz33) NNTP-Posting-Host: newsbf02.news-fddi.aol.com blah blah blah From owner-software@net.bio.net Sun Nov 03 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!feed1.news.erols.com!uunet!in1.uu.net!fu-berlin.de!news.belwue.de!not-for-mail From: Andreas Gutsche Newsgroups: bionet.software Subject: Visual C++ DAO Date: Mon, 04 Nov 1996 13:42:15 +0100 Organization: InterNetNews at News.BelWue.DE (Stuttgart, Germany) Lines: 10 Message-ID: <327DE4A7.177@develop.fh-reutlingen.de> NNTP-Posting-Host: demo1.fh-reutlingen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (WinNT; I) Hello everybody, I always get errors using the Update-Function of the CDaoRecordset class (mfc 4.0) after adding or editing Records. Editing and adding new Records works fine with the previous ODBC CRecordset class. The new CDaoRecordset class is supposed to work the same way but it does not. If anyone has come across the same problem, please help !!!! Andreas From owner-software@net.bio.net Sun Nov 03 22:00:00 1996 Message-ID: <327DFE1F.22EF@uni-konstanz.de> Date: Mon, 04 Nov 1996 15:30:55 +0100 From: Bernd Langkau Reply-To: bernd.langkau@uni-konstanz.de Organization: University of Constance X-Mailer: Mozilla 3.0Gold (Win95; I) MIME-Version: 1.0 Newsgroups: bionet.software CC: Bernd.Langkau, Thomas.Seebacher Subject: Molbio-Software (Macintosh) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: toprope.verwaltung.uni-konstanz.de Lines: 7 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!mr.net!newshub.tc.umn.edu!fu-berlin.de!news.belwue.de!news.uni-konstanz.de!toprope.verwaltung.uni-konstanz.de A new program for the evaluation of gel images is available from http://www.uni-konstanz.de/tt/software/mwmacro.html or from ftp://ftp.uni-konstanz.de/pub/local/Biologie/MW-Macro.sea.bin. The new shareware program (50.-DM) calculates molecular weights, pI-values and band intensities from scanned gel images. The program requires Macintosh computers and NIH-Image software. From owner-software@net.bio.net Sun Nov 03 22:00:00 1996 Path: biosci!agate!usenet.kornet.nm.kr!newsfeed.dacom.co.kr!arclight.uoregon.edu!hammer.uoregon.edu!csulb.edu!newshub.csu.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!news.ycc.yale.edu!morpheus.cis.yale.edu!skoufs From: Emmanuel Skoufos Newsgroups: bionet.software Subject: Re: ORF Predictor Date: Mon, 4 Nov 1996 13:58:24 -0500 Organization: Yale University Lines: 30 Message-ID: References: <327A2981.5062@ugene1.pprd.abbott.com> NNTP-Posting-Host: morpheus.cis.yale.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: skoufs@morpheus.cis.yale.edu To: Tim Bolling 7-2290 4MD In-Reply-To: <327A2981.5062@ugene1.pprd.abbott.com> On 1 Nov 1996, Tim Bolling 7-2290 4MD wrote: > Can anyone suggest a good ORF prediction program that runs on UNIX? > I am interested in one that would predict the MOST likely reading > frame in an EST (not just all orf that start with a MET and end with > a termination codon and are of a particular size). Thanks for any > suggestions. You can try GRAIL; documentation and guide is at: A good Web-based collection of ORF finding engines is at the Baylor College of Medicine Search launcher pages: Emmanuel Skoufos, Ph.D. Yale University School of Medicine Section of Neurobiology 333 Cedar Street, 236 FMB New Haven, CT 06520 e-mail:emmanouil.skoufos@yale.edu Phone: (203) 785-4336 Fax: (203) 785-6990 gene discovery page: http://www.geocities.com/CapeCanaveral/1915/gdp.html From owner-software@net.bio.net Sun Nov 03 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!news-peer.sprintlink.net!uunet!in3.uu.net!netnews.nwnet.net!news.u.washington.edu!evolution.genetics.washington.edu!joe From: joe@evolution.genetics.washington.edu (Joe Felsenstein) Newsgroups: bionet.software Subject: Re: Phylip query Date: 4 Nov 1996 00:40:52 GMT Organization: University of Washington Genetics Lines: 15 Message-ID: <55je2k$ers@nntp3.u.washington.edu> References: <327CF4FF.76E6@cs.arizona.edu> NNTP-Posting-Host: evolution.genetics.washington.edu Summary: Yes you can, sort of Keywords: PHYLIP, bootstrap, phylogeny In article <327CF4FF.76E6@cs.arizona.edu>, Tarak Parekh wrote: >I have Phylip 3.5 for windows, and am a novice user of it. I wish to >know if you could include the bootstrat frequencies in the consense of a >multitreee file. If yes, how do you do it ? I have posted as well as e-mailed, for reasons of ego. If you want to see the bootstrap frequencies (the numbers of replicates that support each group, they are the numbers printed on the tree file in place of branch lengths. They are also at the nodes on the printed tree that appears on the output file. -- Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41) Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA From owner-software@net.bio.net Sun Nov 03 22:00:00 1996 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!bcc.ac.uk!martin From: martin@bsm.bioc.ucl.ac.uk (Andrew Martin) Subject: Re: RASMOL: Merging two structures Message-ID: <1996Nov4.171407.4399@ucl.ac.uk> Date: Mon, 4 Nov 1996 17:14:07 GMT References: <32707A34.BC1@edv1.boku.ac.at> <54r1v1$632@gwdu19.gwdg.de> <327799a7.17760709@news.ruhr-uni-bochum.de> <32789810.31EB@edv1.boku.ac.at> Organization: University College London X-Newsreader: TIN [version 1.2 PL2] Lines: 33 Andreas Wernitznig (h8760592@edv1.boku.ac.at) wrote: : Marc Saric wrote: : : > >: There is another version of RASMOL (RasMol 2.6-ucb) which has some : > >: enhancements and supports the loading of two structures. : > >: Have a look at http://www.cchem.berkeley.edu:8080/Rasmol/v2.6/ : > But is it possible to superimpose these structures??? : Yes it is possible to superimpose two or more structures. If the : structures are not very simmilar it might become very confusing (->use : the backbone-view). : Are there programs or algorythms which put the two structures to the : best fitting position and angle ? (MS-DOS, Windows, Linux (XWindows), : SGI) Try my ProFit program available through my Web page. It is designed to fit 2 protein structure, letting you specify zones and atoms to fit on. You can then write the fitted structure or calculate RMS over different zones and atoms. : Andreas Andrew -- **************************************************************************** Dr. Andrew C.R. Martin, University College London & SciTech Software EMAIL: martin@biochem.ucl.ac.uk Tel:(Work) +44(0)171 419 3890 URL: http://www.biochem.ucl.ac.uk/~martin (Home) +44(0)1372 275775 **************************************************************************** From owner-software@net.bio.net Mon Nov 04 22:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!news.sprintlink.net!news-pull.sprintlink.net!news.sprintlink.net!news-peer.sprintlink.net!www.nntp.primenet.com!nntp.primenet.com!nntp.uio.no!nntp.zit.th-darmstadt.de!news.th-darmstadt.de!c4.hrz.uni-giessen.de!usenet From: schlaude@paul.bio.uni-giessen.de (Gerd Schlauderer) Newsgroups: bionet.software.gcg,bionet.software Subject: Software/Method to determine an antisense RNA Date: 5 Nov 1996 12:33:05 GMT Organization: University of Giessen, Germany Lines: 21 Message-ID: <55nc61$q9e@c4.hrz.uni-giessen.de> NNTP-Posting-Host: paul.bio.uni-giessen.de X-Newsreader: knews 0.9.6 Xref: biosci bionet.software.gcg:2077 bionet.software:17008 We want to construct an anti-sense RNA to suppress the expression of a protein. Is there a program to check, which sequence parts are not involved in stem-loops? RNA-folding programs like mfold are not feasible for this problem, because the RNA is too large (about 5000 bases). Is it practable to run fasta using a sequencewindow of 20 bases as query and the complementary RNA-sequence as database? The lowest scoring sequences should be ideal for anti-sense RNA binding. Regards, Gerd -- Dr. Gerd Schlauderer --------------------------|------------------- Institut f. Mikrobiologie u. Molekularbiologie | Tel.: 0641-7029646 Frankfurterstr. 107 35392 Giessen | FAX.: 0641-7029659 schlaude@paul.bio.uni-giessen.de ______________|____________________ From owner-software@net.bio.net Mon Nov 04 22:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!EU.net!main.Germany.EU.net!Dortmund.Germany.EU.net!magicwrk From: info@magic-works.com (Magic Works GmbH) Newsgroups: bionet.software Subject: NEW: BLUEGENE SEQUENCE ANALYSIS SOFTWARE Date: Tue, 05 Nov 96 20:02:10 GMT Organization: Magic Works GmbH Lines: 24 Distribution: world Message-ID: <55nd8j$23v@news.Dortmund.Germany.EU.net> NNTP-Posting-Host: magicwrk.pm.eunet.de Keywords: Sequence Editor, Similarity Search X-Newsreader: News Xpress Version 1.0 Beta #1 NEW: BLUEGENE SEQUENCE ANALYSIS SOFTWARE Now BlueGene Version 1.03 for Windows is available. This easy to handle DNA and protein sequence analysis software offers: - Fully graphical sequence editor - loads sequences of any length - multiple editors can be opened - sequence can be annotated by colored symbols - symbols can be commented by free text - integrated analysis (ORFs restriction sites) - interactive linear and circular maps - features, symbols, ORFs, restriction sites are automatically updated when sequence is edited - Features in Genbank entries are automatically converted to symbols in the editor and map - multiple alignment, protein plots and more - ultrafast and sensitive similarity searches in Genbank and Swissprot - outstanding search-engine uses artificial neural networks - DNA query to Genbank - Protein query to Swissprot - Protein query to Genbank (6 reading-frames translated) Free download demo: http://www.bluegene.com From owner-software@net.bio.net Mon Nov 04 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!news.cftnet.com!ns2.mainstreet.net!sloth.swcp.com!tesuque.cs.sandia.gov!lynx.unm.edu!bubba.NMSU.Edu!paris!dkim From: "D. KIM" Newsgroups: bionet.software Subject: How do you extract a "gzip" file? Date: Tue, 5 Nov 1996 11:46:54 -0700 Organization: New Mexico State University Lines: 7 Message-ID: NNTP-Posting-Host: paris.nmsu.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: dkim@paris The subject says it all: How so I extract a gzip file (filename.ps.gz) using either UNIX or DOS? Thanks Daniel Kim From owner-software@net.bio.net Mon Nov 04 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!news-stkh.gsl.net!news.gsl.net!news-peer.gsl.net!news.gsl.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!news.us.world.net!ns2.mainstreet.net!sloth.swcp.com!tesuque.cs.sandia.gov!lynx.unm.edu!bubba.NMSU.Edu!dkim From: dkim@nmsu.edu (D. KIM) Newsgroups: bionet.software Subject: GLASS Secondary Structure analysis pgm Date: 5 Nov 1996 14:11:25 GMT Organization: New Mexico State University, Las Cruces, NM Lines: 12 Message-ID: <55nhud$kaf@bubba.NMSU.Edu> NNTP-Posting-Host: verdi.nmsu.edu Hello group: I am looking for a protein II' structure prediction program called GLASS. Has anyone heard of such a thing? Query to WWW search engines gives me some nice review sites for different pgms of similar function, but not GLASS. Does anyone have a location and description of this pgm? Thank you Daniel Kim From owner-software@net.bio.net Mon Nov 04 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!news.sprintlink.net!news-peer.sprintlink.net!newsfeed.internetmci.com!newsfeeder.gi.net!tin.monsanto.com!rcwieg.monsanto.com!user From: rwiegand@i1.net (Roger Wiegand) Newsgroups: bionet.software Subject: Monsanto Bioinformatics positions Date: Tue, 05 Nov 1996 10:53:13 -0600 Organization: Monsanto Lines: 35 Message-ID: NNTP-Posting-Host: rcwieg.monsanto.com Monsanto, a major life sciences company located in suburban St. Louis, MO, has immediate openings in the bioinformatics section of its genomics effort. You will work in concert with a first-rate programming, database, and support staff to discover new small molecule targets, therapeutic proteins, and potential transgenes for engineering of crop plants. You will have the opportunity to work on human pharmaceuticals with our Searle division, agricultural applications with Ceregen scientists, as well as food, nutrition, and animal health products. You will work with a large and talented group on experimental design and interpretation of data from high throughput sequencing, mapping, and expression microarray technology. These positions require a M.D., Ph.D. or equivalent experience (in pharmacology/physiology, molecular biology, plant physiology, biochemistry, agriculture or a related field) as well as a proven record of accomplishment in bioinformatics. Extensive programming experience, while desirable, is not necessary. Please send a letter and CV to: Roger Wiegand Monsanto AA5I 700 Chesterfield Pkwy Chesterfield, MO 63198 mailto:rwiegand@i1.net FAX (314)537-7444 Monsanto is an equal opportunity employer. -- Thanks, Roger mailto:rwiegand@i1.net From owner-software@net.bio.net Mon Nov 04 22:00:00 1996 Path: biosci!CS.Arizona.EDU!noao!ennfs.eas.asu.edu!cs.utexas.edu!howland.erols.net!surfnet.nl!ruu.nl!news From: Jacob Rousseau Newsgroups: sci.bio.ethology,bionet.neuroscience,bionet.software Subject: Abstracts/Proceedings Workshop Measuring Behaviour '96 Date: Tue, 05 Nov 1996 15:08:58 -0800 Organization: Rudolf Magnus Institute for Neurosciences, Utrecht University Lines: 19 Message-ID: <327FC90A.2ACB@med.ruu.nl> NNTP-Posting-Host: 131.211.185.174 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) Xref: biosci sci.bio.ethology:3606 bionet.neuroscience:16555 bionet.software:17011 Measuring Behavior '96 Workshop Proceedings From 16-18 October, Measuring Behavior '96, the international workshop on methods and techniques in behavioral research, was held in Utrecht, The Netherlands. The proceedings of the meeting are now available on the world wide web. These include the abstracts of all oral papers and posters, as well as short descriptions of the instruments and computer programs demonstrated during the meeting. The address is http://www.diva.nl/noldus/mb96.html. ----------------------------------------------------------------------------- Jacob Rousseau, Voice : 31-30-2538831 Rudolf Magnus Institute for Neurosciences, Fax : 31-30-2539033 Dept. of Medical Pharmacology, E-mail: rousseau@med.ruu.nl Utrecht University, Stratenum, Universiteitsweg 100, 3584 CG Utrecht. The Netherlands. ----------------------------------------------------------------------------- From owner-software@net.bio.net Mon Nov 04 22:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!sol.ctr.columbia.edu!spool.mu.edu!newspump.sol.net!howland.erols.net!swrinde!tank.news.pipex.net!pipex!dish.news.pipex.net!pipex!wave.news.pipex.net!pipex!soap.news.pipex.net!pipex!tube.news.pipex.net!pipex!plug.news.pipex.net!pipex!oleane!pasteur.fr!jussieu.fr!univ-angers.fr!ciril.fr!usenet From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software.gcg,bionet.software Subject: Re: Software/Method to determine an antisense RNA Date: 5 Nov 1996 13:17:22 GMT Organization: IGBMC Lines: 24 Message-ID: <55nep2$qqr@arcturus.ciril.fr> References: <55nc61$q9e@c4.hrz.uni-giessen.de> NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.6 Xref: biosci bionet.software.gcg:2079 bionet.software:17010 In article <55nc61$q9e@c4.hrz.uni-giessen.de>, schlaude@paul.bio.uni-giessen.de (Gerd Schlauderer) writes: >We want to construct an anti-sense RNA to suppress the expression of a >protein. Is there a program to check, which sequence parts are not >involved in stem-loops? >RNA-folding programs like mfold are not feasible for this problem, >because the RNA is too large (about 5000 bases). Is it practable to run >fasta using a sequencewindow of 20 bases as query and the complementary >RNA-sequence as database? The lowest scoring sequences should be >ideal for anti-sense RNA binding. Did you try a dotplot? just my 0.02. Francois. -- Francois Jeanmougin Service de bioinformatique / bioinformatics service IGBMC BP 163 67404 Illkirch France tel :(France) 03 88 65 32 71 / (international) (+33) 3 88 65 32 71 e-mail : jeanmougin@igbmc.u-strasbg.fr "les poissons sans fish, les pieds sans foot" (STTELLLA) From owner-software@net.bio.net Mon Nov 04 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.erols.net!news.sprintlink.net!news-stk-200.sprintlink.net!news.up.net!news.mtu.edu!msunews!news From: Paul Sanschagrin Newsgroups: bionet.software Subject: Re: How do you extract a "gzip" file? Date: Tue, 05 Nov 1996 17:28:55 -0500 Organization: Michigan State University Lines: 27 Message-ID: <327FBFA7.518@sol.bch.msu.edu> References: NNTP-Posting-Host: estrella.bch.msu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; SunOS 5.4 sun4m) To: "D. KIM" D. KIM wrote: > > The subject says it all: How so I extract a gzip file (filename.ps.gz) > using either UNIX or DOS? > > Thanks > > Daniel Kim You need to obtain GNU's gzip program. There is both a MSDOS .exe file and a UNIX tar file (I believe you have to compile, so you may need gcc of you don't have.) The UNIX version decompresses with gzip -d filename, but I'm not sure how the DOS version works. Also, Winzip will handle gzip compresses (among other things). Hope this is useful, -- Paul Sanschagrin sanschag@sol.bch.msu.edu http://www.msu.edu/user/sanschag/ ************************************************************ Those people who tell you not to take chances They are all missing on what life is about You only live once so take hold of the chance Don't end up like the others, the same song and dance -Metallica from "Motorbreath", _Kill 'Em All_ ************************************************************ From owner-software@net.bio.net Mon Nov 04 22:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!news.sprintlink.net!news-pull.sprintlink.net!news.sprintlink.net!news-atl-21.sprintlink.net!www.nntp.primenet.com!nntp.primenet.com!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!uunet!in1.uu.net!not-for-mail From: henryl@connectnet.com (Henry Lee) Newsgroups: bionet.software Subject: RE: Nomenclator Automatically Assigns IUPAC Names to Structures Date: Mon, 04 Nov 96 20:07:11 PST Lines: 21 Distribution: world, USA Message-ID: <55me9u$mdh@news1-alterdial.uu.net> NNTP-Posting-Host: henryl.connectnet.com Mime-Version: 1.0 X-Newsreader: WinVN 0.93.6 November 4, 1996 FOR IMMEDIATE RELEASE San Diego, California, USA -- November 4, 1996 -- ChemInnovation Software Inc. announces the release of Chemistry 4-D Nomenclator(TM). Chemistry 4-D Nomenclator is an expert system that understands IUPAC nomenclature rules and intelligently assigns systematic names to structures. The program also provides a full set of tools for creating publication quality graphics. It is fully integrated with the popular drawing program Chemistry 4-D Draw(TM) Pro and NamExpert(TM) which interprets chemical names and automatically create high-quality structures. Systems: Windows 3.1/95/NT, Macintosh. FOR MORE INFORMATION CONTACT: ChemInnovation Software, (619)566-2846, Fax (619)566-4138, E-mail cis@cheminnovation.com, http://www.cheminnovation.com. From owner-software@net.bio.net Mon Nov 04 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.erols.net!news.sprintlink.net!news-stk-200.sprintlink.net!news.up.net!news.mtu.edu!msunews!news From: Paul Sanschagrin Newsgroups: bionet.software Subject: Re: How do you extract a "gzip" file? (one more thing) Date: Tue, 05 Nov 1996 17:29:47 -0500 Organization: Michigan State University Lines: 23 Message-ID: <327FBFDB.3910@sol.bch.msu.edu> References: NNTP-Posting-Host: estrella.bch.msu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; SunOS 5.4 sun4m) To: "D. KIM" D. KIM wrote: > > The subject says it all: How so I extract a gzip file (filename.ps.gz) > using either UNIX or DOS? > > Thanks > > Daniel Kim I meant to mention that you can get them at: ftp://prep.ai.mit.edu/pub/gnu/ -- Paul Sanschagrin sanschag@sol.bch.msu.edu http://www.msu.edu/user/sanschag/ ************************************************************ Those people who tell you not to take chances They are all missing on what life is about You only live once so take hold of the chance Don't end up like the others, the same song and dance -Metallica from "Motorbreath", _Kill 'Em All_ ************************************************************ From owner-software@net.bio.net Tue Nov 05 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!in3.uu.net!rcogate.rco.qc.ca!neon.mlink.net!news From: asenecal@zercom.net (crumpy_old_man) Newsgroups: bionet.software Subject: Programmer are you looking to adv your prg Date: 5 Nov 1996 03:02:22 GMT Organization: Mlink Internet, Montreal, Canada Lines: 28 Message-ID: <55manu$437@neon.Mlink.NET> NNTP-Posting-Host: 204.191.6.191 Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 Hi ! Tired of waiting for your product to find is place on the market or waiting for the right investor to get to you ? Here is a good way to get your product around without spending a penny. I just open a new Web Page just for that . There you can let other computer user know that your product exist and that it's available right now. Just go to http://www.geocities.com/siliconvaley/heights/8443 and let us know you have a new product that you would like to post on our Web Site. Just submit us the Description , The name , the company name how to reach you etc., and we will post it asap . If there is a demo or sample available write it down too . the only cost will be that you let other people know that there is such place for them to post or to look for something. From owner-software@net.bio.net Tue Nov 05 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.sprintlink.net!news-peer.sprintlink.net!uunet!in1.uu.net!van-bc!unixg.ubc.ca!rlauener From: rlauener@unixg.ubc.ca (Ronald William Lauener) Newsgroups: bionet.software Subject: technical dictionary Date: 6 Nov 1996 08:53:07 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 6 Message-ID: <55pjlj$3os@nntp.ucs.ubc.ca> NNTP-Posting-Host: interchg.ubc.ca X-Newsreader: TIN [version 1.2 PL2] Hi: Can someone recommend a scientific/technical dictionary that can be used with Word for Windows 6.0 in place of the default dictionary/spell-checker. Specifically terms related to biochemistry/signal transduction. Thanks in advance. my e-mail is rlauener@unixg.ubc.ca From owner-software@net.bio.net Tue Nov 05 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.nacamar.de!news-kar1.dfn.de!news-koe1.dfn.de!news.rwth-aachen.de!newsserver.rrzn.uni-hannover.de!infosrv.rz.uni-kiel.de!usenet From: Thon Newsgroups: bionet.software Subject: CADD-Program for DOS-PC Date: Wed, 06 Nov 1996 10:45:47 +0100 Organization: Rechenzentrum der Universitaet Kiel, Germany Lines: 4 Message-ID: <32805E4B.1DF0@mail.uni-kiel.d400.de> NNTP-Posting-Host: srv2.mail.uni-kiel.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5 sun4m) Hi, I search a Computer Aided Drug Design - Program for a PC. Shareware is the best. Thanks From owner-software@net.bio.net Tue Nov 05 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!vixen.cso.uiuc.edu!news.uoregon.edu!newsfeed.orst.edu!newshub.tc.umn.edu!newsstand.tc.umn.edu!limerick.cbs.umn.edu!hiroki From: hiroki@limerick.cbs.umn.edu (Hiroki) Newsgroups: bionet.software Subject: Re: RASMOL: Merging two structures Date: 6 Nov 1996 22:16:52 GMT Organization: University of Minnesota Lines: 25 Message-ID: <55r2ok$fad@epx.cis.umn.edu> References: <32707A34.BC1@edv1.boku.ac.at> <54r1v1$632@gwdu19.gwdg.de> <327799a7.17760709@news.ruhr-uni-bochum.de> <32789810.31EB@edv1.boku.ac.at> <55ans8$l2c@winx03.informatik.uni-wuerzburg.de> <55av0d$5b0@epx.cis.umn.edu> <327DC202.104D@edv1.boku.ac.at> Reply-To: hiroki@limerick.cbs.umn.edu NNTP-Posting-Host: limerick.cbs.umn.edu X-Newsreader: TIN [version 1.2 PL2] Andreas Wernitznig (h8760592@edv1.boku.ac.at) wrote: : Hiroki wrote: : > cat file1.pdb file2.pdb > two.pdb : > is what I've been using. Usually I'll change the chainid : > in one or the other file first to make selection easier. : This function just concatenates the two files. It doesn't put them in : the right position and angle. If the structures are from the same source : (program) it might work. : Andreas Yes, I had responded because someone had written something like: align the structures using ProFit and then "join the files somehow" The first step is to align the structures as was clearly stated. I happen to like ProFit by Dr Andrew Martin for this. Concatenation with cat is easier than with an editor, so I just wanted to add that. Sorry about the some..some..some.. vagueness but the newserver expires files really quickly here, and I didn't want to hunt the archives. hiroki From owner-software@net.bio.net Tue Nov 05 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!vixen.cso.uiuc.edu!qualcomm.com!ihnp4.ucsd.edu!scripps.edu!usenet From: S L Forsburg Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Graphing on the Mac? Date: Wed, 06 Nov 1996 14:30:20 -0800 Organization: The Salk Institute Lines: 24 Message-ID: <3281117D.7CB3@salk.edu> Reply-To: forsburg@salk.edu NNTP-Posting-Host: slfcentris.salk.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; 68K) Xref: biosci bionet.software:17022 comp.sys.mac.scitech:9513 Time to purchase software for an additional PPC Mac. Up till now I have used Cricketgraph, although I don't like the newer version as much as I liked the old ones for ease of use and general friendliness and it seems rather crash-prone on the 040 machines it has been running on. I'm seeking your recommendations....nothing fancy required, just standard sorts of plots or histograms on exponential or arithmetic axes. I have no experience with Deltagraph, which looks like the most reasonable alternative. Comments and opinions sought!! Please cc. to my email address as well as the newsgroup so I can keep track. I will tally the response in this forum. thanks! susan -- >->->->->->->-><-<-<-<-<-<-<-<- Susan L Forsburg PhD MBVL, The Salk Institute forsburg@salk.edu http://flosun.salk.edu/~forsburg From owner-software@net.bio.net Tue Nov 05 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!www.nntp.primenet.com!nntp.primenet.com!enews.sgi.com!news.sgi.com!esiee.fr!jussieu.fr!infobiogen.fr!lovelace.infobiogen.fr!becquart From: becquart@lovelace.infobiogen.fr (Paul Becquart) Newsgroups: bionet.software Subject: Re: NEW: BLUEGENE SEQUENCE ANALYSIS SOFTWARE Date: 6 Nov 1996 14:49:13 GMT Organization: GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France Lines: 9 Distribution: world Message-ID: <55q8h9$lvn@lovelace.infobiogen.fr> References: <55nd8j$23v@news.Dortmund.Germany.EU.net> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL2] : NEW: BLUEGENE SEQUENCE ANALYSIS SOFTWARE : Now BlueGene Version 1.03 for Windows is available. Is there a Mac version ? Paul From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!cs.utexas.edu!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!surfnet.nl!news.tue.nl!news.IAEhv.nl!dias!tjerk From: tjerk@dias.iaehv.nl (Tjerk Santegoeds) Subject: Re: How do you extract a "gzip" file? X-Newsreader: TIN [version 1.2 PL2] Organization: -- Message-ID: References: Date: Wed, 6 Nov 1996 22:03:05 GMT Lines: 15 D. KIM (dkim@nmsu.edu) wrote: : The subject says it all: How so I extract a gzip file (filename.ps.gz) : using either UNIX or DOS? Try, "gzip -d filename.ps.gz" or "gunzip filename.ps.gz" (both UNIX) You could have tried "man gzip" of course. Tjerk. -- Tjerk Santegoeds Apeldoorn - The Netherlands From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!vixen.cso.uiuc.edu!f-murphy From: f-murphy@uiuc.edu (Frank Murphy) Newsgroups: bionet.software Subject: EndNote and Microsoft Word 6.0 Date: Wed, 06 Nov 1996 20:38:59 -0600 Organization: University of Illinos at Urbana-Champaign Lines: 6 Message-ID: NNTP-Posting-Host: chaucer.life.uiuc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.1 Hello, Just updates to word 6 (Mac) and am left wondering how to install End Note in this version. I have word 5.1 working great, but they changed it. Thanks in advance From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!agate!howland.erols.net!math.ohio-state.edu!jussieu.fr!univ-angers.fr!ciril.fr!cnusc.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!news.rccn.net!morgana.mat.uc.pt!zoo1.uc.pt!user From: mjmgmatos@gemini.ci.uc.pt (Manuel J. Matos) Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? Date: Thu, 07 Nov 1996 09:36:45 +0000 Organization: Dept Bioquímica - Univ. Coimbra - Portugal Lines: 10 Message-ID: References: <3281117D.7CB3@salk.edu> NNTP-Posting-Host: zoo1.uc.pt Xref: biosci bionet.software:17032 comp.sys.mac.scitech:9519 I also recommend KaleidaGraph as a very good alternative. It is not as fancy as DeltaGraph, but allows you a high degree of control of every element of the graph. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Manuel J. Matos (Manolo) -- mjmgmatos@gemini.ci.uc.pt * * Departamento de Bioquimica * Universidade de Coimbra * * Aptd. 3126 * P - 3000 Coimbra * P O R T U G A L * * tlf. +351-39-22174 *Macintosh user* fax +351-39-33827 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!dispatch.news.demon.net!demon!sirin.demon.co.uk!tmg From: Mikhail Zaitsev Newsgroups: bionet.software,biz.comp.hardware,bln.markt Subject: New CD-ROM from Group 42, the most elusive hacker organization Date: Thu, 7 Nov 1996 00:55:53 +0000 Organization: Sirin Limited Lines: 41 Distribution: world Message-ID: <9p2d$DAZOTgyEwE5@sirin.demon.co.uk> Reply-To: Mikhail Zaitsev NNTP-Posting-Host: sirin.demon.co.uk X-NNTP-Posting-Host: sirin.demon.co.uk MIME-Version: 1.0 X-Newsreader: Turnpike Version 3.01 Xref: biosci bionet.software:17023 biz.comp.hardware:21563 We offer new CD-ROM with exciting information archive: ---------------------------------------------- |"Group 42 Sells Out! International Version".| ---------------------------------------------- This CD-ROM contains detailed information on the subjects of: Anarchy, Drugs, Lockpicking, Phreaking, Viruses, Password Cracking, Cable & Cellular Hacking, Pirate Radio & TV, Electronic Security, Programming, Cryptography, Fake ID, Firearms, Survival, "Warez", Plus many more... After 12 years as the most elusive underground information couriers, this organization (Group 42) surfaces and releases its knowledge to the public... This CD-ROM contains 100's of megs of information and the software necessary to use it. Much of this knowledge has never before been available to the public. This information is presented in a clear and organized manner, fully documented and viewable on any make of computer with any WWW BROWSER. This Is Not Shovelware! For Educational Purposes Only! No sales to minors! You must be 18 to purchase this CD-ROM. Its price is GBP32.68 or USD49.00. Price includes VAT but does not include packing and postage (GBP2.00 for one CD for UK and GBP4.00 or USD6.50 for one CD out of UK by Recorded Royal Mail). Payments: Visa Card, MasterCard, Eurocard, Visa Delta, Switch, JCB, Cash on Delivery (add GBP4.00 for UK or call for other countries), Cheque, Bankers Draft, Telegraphic Transfer, Postal Orders, International Money Order. Please make cheques payable to Sirin Limited. Resellers are invited. Trade discount is available. ------------- Send your mail address for our free software & CD-ROM catalogue. ------------- Mikhail Zaitsev, Sirin Limited tmg@sirin.demon.co.uk http://www.demon.co.uk/sirin/home.html Tel./Fax: 0171-499-8267 (+44-171-499-8267) 98 Park Street, Suite 4, London W1Y 3RJ, UK From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!btnet!dispatch.news.demon.net!demon!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!bhamcs!news.ox.ac.uk!worf.molbiol.ox.ac.uk!rgrant From: rgrant@worf.molbiol.ox.ac.uk (Richard P Grant) Newsgroups: bionet.software Subject: Re: EndNote and Microsoft Word 6.0 Date: 7 Nov 1996 08:57:08 GMT Organization: Oxford University Lines: 19 Message-ID: <55s894$ea3@news.ox.ac.uk> References: NNTP-Posting-Host: worf.molbiol.ox.ac.uk X-Newsreader: TIN [version 1.2 PL2] Frank Murphy (f-murphy@uiuc.edu) gibbered: } Hello, } Just updates to word 6 (Mac) and am left wondering how to install End Note } in this version. I have word 5.1 working great, but they changed it. If you have endnote 2.0, you can get a free upgrade to make it work with word 6. Otherwise, either (1) cut and paste from the standalone Endnote appl into word docs, or (2) (my preferred option) go back to Word 5.1 } Thanks in advance You're welcome. -- Richard P. Grant University of Oxford Nuffield Department Obstetrics and Gynaecology FFPGP http://users.ox.ac.uk/~lady0266 http://www.molbiol.ox.ac.uk/~rgrant ---------------------# hit any user to continue #--------------------- From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.sgi.com!news.mathworks.com!fu-berlin.de!uniol!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? Followup-To: bionet.software,comp.sys.mac.scitech Date: 7 Nov 1996 09:28:10 GMT Organization: University of Wuerzburg, Germany Lines: 27 Message-ID: <55sa3a$2af@winx03.informatik.uni-wuerzburg.de> References: <3281117D.7CB3@salk.edu> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Xref: biosci bionet.software:17031 comp.sys.mac.scitech:9518 James D. Meiss (jdm@boulder.colorado.edu) wrote: > In article <3281117D.7CB3@salk.edu>, forsburg@salk.edu wrote: > >Time to purchase software for an additional PPC Mac. Up till now I > >have used Cricketgraph, although I don't like the newer version as > >much as I liked the old ones for ease of use and general friendliness > >and it seems rather crash-prone on the 040 machines it has been > >running on. I'm seeking your recommendations....nothing fancy > >required, just standard sorts of plots or histograms on exponential or > >arithmetic axes. > > I was very disappointed with Delta graph and would not recommend it. > First--the version I had (3.0 I think) was very buggy. Lots of crashes, and it > wouldn't do things that the manual promised--especially with 3D graphs. > > I use KaleidaGraph and am very happy with it. I second the KaleidaGraph recommendation. It's almost as easy to use as Cricket Graph although far more powerful. It offers user-defined curve fits as long as you don't try to fit more than ten variables at once. There is a special version for PowerMacs. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!panix!feed1.news.erols.com!tezcat!news.bbnplanet.com!cam-news-hub1.bbnplanet.com!bloom-beacon.mit.edu!boulder!jdm From: jdm@boulder.colorado.edu (James D. Meiss) Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? Date: Wed, 06 Nov 1996 22:15:11 -0700 Organization: University of Colorado Lines: 30 Message-ID: References: <3281117D.7CB3@salk.edu> NNTP-Posting-Host: amathmod5.colorado.edu Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.0 Xref: biosci bionet.software:17027 comp.sys.mac.scitech:9515 In article <3281117D.7CB3@salk.edu>, forsburg@salk.edu wrote: >Time to purchase software for an additional PPC Mac. Up till now I >have used Cricketgraph, although I don't like the newer version as >much as I liked the old ones for ease of use and general friendliness >and it seems rather crash-prone on the 040 machines it has been >running on. I'm seeking your recommendations....nothing fancy >required, just standard sorts of plots or histograms on exponential or >arithmetic axes. I have no experience with Deltagraph, which looks >like the most reasonable alternative. >Comments and opinions sought!! I was very disappointed with Delta graph and would not recommend it. First--the version I had (3.0 I think) was very buggy. Lots of crashes, and it wouldn't do things that the manual promised--especially with 3D graphs. Moreover, it seemed to be much more of a "business" oreinted graphing program, and much of the gee-wiz-bang stuff would be of little use for scientific graphs. I use KaleidaGraph and am very happy with it. You'll probably also get many recommendations for Igor, which is, as I understand it, very full featured, but has a steaper learning curve. -- James Meiss Dept of Applied Math University of Colorado jdm@boulder.colorao.edu From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!centauri.hq.nasa.gov!newsfeed.gsfc.nasa.gov!cs.umd.edu!ra.nrl.navy.mil!esp225.nrl.navy.mil!user From: pecora@zoltar.nrl.navy.mil (Lou Pecora) Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? Date: Wed, 06 Nov 1996 21:29:09 -0400 Organization: Naval Research Lab Lines: 35 Message-ID: References: <3281117D.7CB3@salk.edu> NNTP-Posting-Host: esp225.nrl.navy.mil X-Newsreader: Yet Another NewsWatcher 2.0 Xref: biosci bionet.software:17026 comp.sys.mac.scitech:9514 In article <3281117D.7CB3@salk.edu>, forsburg@salk.edu wrote: > Time to purchase software for an additional PPC Mac. Up till now I > have used Cricketgraph, although I don't like the newer version as > much as I liked the old ones for ease of use and general friendliness > and it seems rather crash-prone on the 040 machines it has been > running on. I'm seeking your recommendations....nothing fancy > required, just standard sorts of plots or histograms on exponential or > arithmetic axes. I have no experience with Deltagraph, which looks > like the most reasonable alternative. > Comments and opinions sought!! > > Please cc. to my email address as well as the newsgroup so I can keep > track. I will tally the response in this forum. If you have serious data sets (i.e. much data and/or analysis) I would recommend against Deltagraph (mostly business level) and suggest you try Kaliedagraph (mid-level scientific graphics) or Igor PRO (industrial strength graphics program). The latter is the choice of most serious users. (sure to start a flame war, but no one will deny the high level of robustness of Igor). Lou Pecora code 6343 Naval Research Lab Washington DC 20375 USA == My views are not those of the U.S. Navy. == ------------------------------------------------------------ Check out the 4th Experimental Chaos Conference Home Page: http://natasha.umsl.edu/Exp_Chaos4/ ------------------------------------------------------------ From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: pujadas@quimica.urv.es (Gerard Pujadas) Newsgroups: bionet.software Subject: Wanted gzip for IRIX6.2 Date: 7 Nov 1996 15:10:27 -0000 Lines: 21 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <55su53$hfe@mserv1.dl.ac.uk> Original-To: bio-software@dl.ac.uk Hi to all, My name is Gerard Pujadas and I would like to know where may I ftp a compiled version of gzip for IRIX6.2. Thanks for your attention. Gerard. *************************************************************************** * Gerard Pujadas * * Biotecnologia Computacional * * Dept. Bioquimica i Biotecnologia e-mail: pujadas@quimica.urv.es * * Univ. Rovira i Virgili phone: 34 77 559565 * * Pla=E7a Imperial Tarraco 1 fax: 34 77 559597 = * * 43005 Tarragona (CATALONIA) Europe. * *************************************************************************** From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!fu-berlin.de!news.dfn.de!violet.mpiz-koeln.mpg.de!violet.mpiz-koeln.mpg.de!not-for-mail From: Jan Kim Newsgroups: bionet.software Subject: Re: MAC: PD,SW Chemical formula drawing, where ? Date: 7 Nov 1996 13:07:41 GMT Organization: MPI fuer Zuechtungsforschung Lines: 21 Message-ID: <55smut$345@violet.mpiz-koeln.mpg.de> References: <3275CD36.41C6@geophysik.uni-frankfurt.de> NNTP-Posting-Host: violet.mpiz-koeln.mpg.de Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit X-Newsreader: TIN [UNIX 1.3 unoff BETA release 961022] Thorsten Becker wrote: > I am looking for a shareware/freeware/PD software for the Mac to draw > complicated chemical formula. I know of something like "ChemEdit", but > it does apparently only accept single atom substituents at a C-atom > ring. "ChemDrawNet" is very advanced, but the student's version does > allow one only to VIEW formulae, no word about saving. For TeX / LaTeX, there are packages for typesetting structral formulae in various ways, one of them is called XymTeX. I never needed to typeset formulae myself, though; but I've seen papers done with such packages, they are professional quality (as most stuff done with TeX). And there's no crippleware problem, the packages are available from any CTAN archive, e.g. ftp.dante.de . Greetinx, Jan -- +- Jan Kim -- X.400: S=kim;OU=violet;O=mpiz-koeln;P=mpg;C=de -----+ | Internet: kim@mpiz-koeln.mpg.de | | WWW: http://www.mpiz-koeln.mpg.de/~kim/kim.html | *-----=< hierarchical systems are for files, not for humans >=-----* From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!news-stkh.gsl.net!news.gsl.net!news-peer.gsl.net!news.gsl.net!swrinde!cs.utexas.edu!math.ohio-state.edu!jussieu.fr!centre.univ-orleans.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!elna.ethz.ch!usenet From: "I. Biaggio" Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? Date: Thu, 07 Nov 1996 13:54:58 +0100 Organization: Swiss Federal Institute of Technology, Zurich Lines: 26 Message-ID: <3281DC23.3C0E@iqe.phys.ethz.ch> References: <3281117D.7CB3@salk.edu> NNTP-Posting-Host: nlo14.ethz.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; 68K) To: forsburg@salk.edu Xref: biosci bionet.software:17036 comp.sys.mac.scitech:9521 S L Forsburg wrote: > > Time to purchase software for an additional PPC Mac. Up till now I > have used Cricketgraph, although I don't like the newer version as > much as I liked the old ones for ease of use and general friendliness > and it seems rather crash-prone on the 040 machines it has been > running on. I'm seeking your recommendations....nothing fancy > required, just standard sorts of plots or histograms on exponential or > arithmetic axes. I have no experience with Deltagraph, which looks > like the most reasonable alternative. > Comments and opinions sought!! Deltagraph is not really good for scientific plotting and number crunching. There is Igor, which has a steep learning curve, and there is pro Fit [the Fit stays for curve fitting], which can also do lots of things but is much easier to use than Igor. Many people still use Kaleidagraph, but IMHO pro Fit is, although perhaps less known, a lot better than Kaleidagraph. pro Fit 5.0 is from cherwell scientific (e-mail: csp.usa@cherwell.com, on the web at ). Check it out at -ivan From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!btnet!dispatch.news.demon.net!demon!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!news.ox.ac.uk!sable.ox.ac.uk!bras0036 From: Fin Newsgroups: bionet.software Subject: SOPM Date: Thu, 7 Nov 1996 11:40:32 +0000 Organization: Oxford University Lines: 13 Message-ID: NNTP-Posting-Host: sable.ox.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have been trying, with little success, to download SOPM for an SGI from ibcp.fr by anonymous ftp. When I come to decompress the tar file I get a directory checksum error. Has anyone had any success in setting SOPM up? I've contacted the authors but they have not replied to my emails. Any help anyone can give me will be greatly appreciated. =============================================================================== Matt Finlay bras0036@sable.ox.ac.uk Brasenose College, OXFORD OX1 4AJ http://users.ox.ac.uk/~bras0036 pgp 2.6.2 key avaliable on request "Et in Arcadia Ego......" From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!www.nntp.primenet.com!nntp.primenet.com!nntp.uio.no!sn.no!news-stkh.gsl.net!news.gsl.net!news-penn.gsl.net!news.gsl.net!news.NetVision.net.il!news From: "me" Newsgroups: alt.bbs.adeptsoft,alt.comp.doggysoft,alt.comp.software.financial,alt.destroy.microsoft,alt.fan.dean-stark.software.tester,alt.geo-software,alt.news.microsoft,alt.soft-sys.corel.draw,alt.soft-sys.corel.misc,alt.soft-sys.tooltalk,bionet.software Subject: Click me. Date: 7 Nov 1996 22:36:41 GMT Organization: NetVision LTD. Lines: 7 Message-ID: <01bbccfc$8783b040$b80b5ac2@LivneFam.netvision.net.il> NNTP-Posting-Host: ts010p2.pop9a.netvision.net.il X-Newsreader: Microsoft Internet News 4.70.1155 G o t o : http://www.geocities.com/soho/1111 Thanks... From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!news.ycc.yale.edu!news From: "James T. Platt" Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? Date: 7 Nov 96 17:12:21 -0500 Organization: Yale University Lines: 24 Message-ID: References: NNTP-Posting-Host: plattjt.med.yale.edu Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit X-Mailer: Cyberdog/1.1 X-News-Servers: news.ycc.yale.edu X-Newsgroups-TO: nntp://news.ycc.yale.edu/bionet.software, nntp://news.ycc.yale.edu/comp.sys.mac.scitech Xref: biosci bionet.software:17044 comp.sys.mac.scitech:9523 In article <3281117D.7CB3@salk.edu>, forsburg@salk.edu wrote: >>Time to purchase software for an additional PPC Mac. Up till now I >>have used Cricketgraph, although I don't like the newer version as >>much as I liked the old ones for ease of use and general friendliness >>and it seems rather crash-prone on the 040 machines it has been >>running on. Versions 1.5.3 and higher of CA-Cricket Graph III are PPC native. The older Cricket Graph was easier to use only because it had fewer features. I think that CG III does a good job of making a large number of features as easy as possible to learn and use. Upgrading it is like learning a completely new program. StatView is also that way. James T. Platt platt@biomed.med.yale.edu --------------------------------------------------- This message was created and sent using the Cyberdog Mail System --------------------------------------------------- From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!math.ohio-state.edu!magnus.acs.ohio-state.edu!csn!nntp-xfer-1.csn.net!cbgw1.lucent.com!fnnews.fnal.gov!unixhub!news.Stanford.EDU!goldfish.stanford.edu!user From: ej@white.stanford.edu (EJ Chichilnisky) Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? Date: Thu, 07 Nov 1996 09:49:18 -0800 Organization: Stanford University Lines: 13 Message-ID: References: <3281117D.7CB3@salk.edu> NNTP-Posting-Host: goldfish.stanford.edu Xref: biosci bionet.software:17043 comp.sys.mac.scitech:9522 Another plug for KaliedaGraph. I have used it for years and though it's not 100% perfect, it's a hell of a lot better than DeltaGraph. Igor is a powerful package that's meant for much more than graphing. It's complex and has a fuller data-analysis emphasis, with recording etc. If you just want graphs, stick with KaliedaGraph. If you want to buy into a whole environment, consider Igor. Forget DeltaGraph for science. ej -- EJ Chichilnisky ej@white.stanford.edu From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!www.nntp.primenet.com!nntp.primenet.com!ddsw1!news.mcs.net!van-bc!unixg.ubc.ca!lpss From: lpss@unixg.ubc.ca (Alex Chang) Newsgroups: bionet.software Subject: Looking for a multi-sequence alignment program Date: 7 Nov 1996 18:30:10 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 11 Message-ID: <55t9ri$nhk@nntp.ucs.ubc.ca> NNTP-Posting-Host: netinfo.ubc.ca X-Newsreader: TIN [version 1.2 PL2] This may be a FAQ. My friend is looking for a multi-sequence alignment program, preferably a MS-Window based program. Thanks Alex Chang Pathology University of British Columbia achang@hivnet.ubc.ca From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!btnet!dispatch.news.demon.net!demon!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!bhamcs!news.ox.ac.uk!worf.molbiol.ox.ac.uk!rgrant From: rgrant@worf.molbiol.ox.ac.uk (Richard P Grant) Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? Followup-To: bionet.software,comp.sys.mac.scitech Date: 7 Nov 1996 08:55:11 GMT Organization: Oxford University Lines: 16 Message-ID: <55s85f$ea3@news.ox.ac.uk> References: <3281117D.7CB3@salk.edu> NNTP-Posting-Host: worf.molbiol.ox.ac.uk X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software:17029 comp.sys.mac.scitech:9517 S L Forsburg (forsburg@salk.edu) gibbered: } Time to purchase software for an additional PPC Mac. Up till now I } have used Cricketgraph, although I don't like the newer version as } much as I liked the old ones for ease of use and general friendliness } and it seems rather crash-prone on the 040 machines it has been ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Haha! Thanks! "I am not alone"..... -- Richard P. Grant University of Oxford Nuffield Department Obstetrics and Gynaecology FFPGP http://users.ox.ac.uk/~lady0266 http://www.molbiol.ox.ac.uk/~rgrant ---------------------# hit any user to continue #--------------------- From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software Subject: Re: Wanted gzip for IRIX6.2 Date: 7 Nov 1996 17:16:34 GMT Organization: University of Cambridge Lines: 25 Distribution: bionet Message-ID: <55t5hi$i8f@lyra.csx.cam.ac.uk> References: <55su53$hfe@mserv1.dl.ac.uk> NNTP-Posting-Host: mole.bio.cam.ac.uk In article <55su53$hfe@mserv1.dl.ac.uk>, Gerard Pujadas wrote: > > Hi to all, > > My name is Gerard Pujadas and I would like to know where may I ftp >a compiled version of gzip for IRIX6.2. It is just as easy to compile it yourself. 1) Get the tar file from an ftp site. 2) unpack it with tar xf gzip-1.2.4.tar (or whatever the filename is) 3) cd gzip-1.2.4 4) ./configure 5) make 6) make install You will now have IRIX 6.2 binaries of gzip, gunzip, zcat, zdiff, zgrep, zmore, znew, zforce, gzexe and zcmp A lot better than just one gzip binary, and all in 6 steps! Tim. From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: patricia@quimica.urv.es (Patricia Vaz) Newsgroups: bionet.software Subject: chemx Date: 7 Nov 1996 15:43:19 -0000 Lines: 23 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <55t02n$jm4@mserv1.dl.ac.uk> Original-To: bio-soft@dl.ac.uk could somebody give me some advice about the chemx suite of programmes including the quantum mechanical package? thanks. pat. =========================================== Patricia Vaz Grup de Bioquimica Computacional Departament Bioquimica i Biotecnologia Universitat Rovira i Virgili Pl. Imperial Tarraco, 1 43005 Tarragona SPAIN e-mail: patricia@quimica.urv.es ========================================== From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!agate!howland.erols.net!math.ohio-state.edu!jussieu.fr!univ-angers.fr!ciril.fr!cnusc.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!news.rccn.net!morgana.mat.uc.pt!zoo1.uc.pt!user From: mjmgmatos@gemini.ci.uc.pt (Manuel J. Matos) Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? Date: Thu, 07 Nov 1996 09:37:35 +0000 Organization: Dept Bioquímica - Univ. Coimbra - Portugal Lines: 10 Message-ID: References: <3281117D.7CB3@salk.edu> NNTP-Posting-Host: zoo1.uc.pt Xref: biosci bionet.software:17033 comp.sys.mac.scitech:9520 I also recommend KaleidaGraph as a very good alternative. It is not as fancy as DeltaGraph, but allows you a high degree of control of every element of the graph. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Manuel J. Matos (Manolo) -- mjmgmatos@gemini.ci.uc.pt * * Departamento de Bioquimica * Universidade de Coimbra * * Aptd. 3126 * P - 3000 Coimbra * P O R T U G A L * * tlf. +351-39-22174 *Macintosh user* fax +351-39-33827 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!news.lobo.net!NewsWatcher!user From: peter@sakurasoft.com (Peter Payne) Newsgroups: asu.comp.distributed,fr.usenet.distribution,bionet.software,soc.culture.singapore,alt.politics.italy,soc.culture.spain,soc.culture.brazil,soc.culture.indian,soc.culture.mexican,soc.culture.soviet Subject: Wanted: International distributors for Japanese anime adult games Date: Fri, 08 Nov 1996 02:29:52 +0900 Organization: J-List Lines: 14 Message-ID: NNTP-Posting-Host: 202.230.39.191 X-Newsreader: Yet Another NewsWatcher 2.1.2 Xref: biosci bionet.software:17041 soc.culture.singapore:205500 soc.culture.spain:108920 soc.culture.brazil:59176 soc.culture.indian:257410 soc.culture.mexican:58145 soc.culture.soviet:118465 Hello, I represent Sakura Soft. a company in Texas that is bringing Japanese adult RPG-style games to the North American market. We ar looking for software distributors outside of the U.S. Europe, Asia, anywhere else: if you are a compotent, established producer or distributor of computer software, we would like to talk to you. These are adult games which run on IBM PCs (DOS or Windows), and the quality of the art is excellent. The content is adult, though, and these games are not for anyone under the age of 18. Being "anime" (Japanese animation) games, we expect the market to grow well over the next few years. For a look at the game images, please see www.sakurasoft.com, or email me for more information. Thankyou. From owner-software@net.bio.net Wed Nov 06 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!news-stkh.gsl.net!news.gsl.net!news-peer.gsl.net!news.gsl.net!hunter.premier.net!hammer.uoregon.edu!csulb.edu!news.sgi.com!esiee.fr!jussieu.fr!univ-angers.fr!ciril.fr!cnusc.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!news.rccn.net!morgana.mat.uc.pt!zoo1.uc.pt!user From: mjmgmatos@gemini.ci.uc.pt (Manuel J. Matos) Newsgroups: bionet.software Subject: Re: EndNote and Microsoft Word 6.0 Date: Thu, 07 Nov 1996 09:47:29 +0000 Organization: Dept Bioquímica - Univ. Coimbra - Portugal Lines: 26 Message-ID: References: NNTP-Posting-Host: zoo1.uc.pt In article , f-murphy@uiuc.edu (Frank Murphy) wrote: Hello, Just updates to word 6 (Mac) and am left wondering how to install End Note in this version. I have word 5.1 working great, but they changed it. Thanks in advance There is no mention of the version of EndNote you use, neither if you used the EndNote program or the plug-in module. Anyway there is a module that comes with EndNote 2.1.3 (the current version) that works with Word 6. You probably will get more help if you subscribe to Niles EndNote mailing list and send your questions about EndNote there. To subscribe send a message to with "help" in the body to get instructions. Regards * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Manuel J. Matos (Manolo) -- mjmgmatos@gemini.ci.uc.pt * * Departamento de Bioquimica * Universidade de Coimbra * * Aptd. 3126 * P - 3000 Coimbra * P O R T U G A L * * tlf. +351-39-22174 *Macintosh user* fax +351-39-33827 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!CS.SANDIA.GOV!scistra From: scistra@CS.SANDIA.GOV (Sorin C. Istrail) Newsgroups: bionet.software Subject: RECOMB97: Hotel Reservation and Registration Information Date: 7 Nov 1996 16:46:13 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 114 Sender: daemon@net.bio.net Distribution: world Message-ID: <199611072329.QAA13355@frodo2.cs.sandia.gov> NNTP-Posting-Host: net.bio.net Please call the ElDorado hotel and make your reservation AS SOON AS POSSIBLE. This is a four-star and four-diamond hotel and we have a limited number of rooms avaiblable. ElDorado will direct the overflow to another hotel. FIRST ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY RECOMB 97 http://www.cs.sandia.gov/recomb97 January 20-23, 1997 Eldorado Hotel Santa Fe, New Mexico Sponsored by SIGACT with support from SLOAN Foundation US Department of Energy ELDORADO HOTEL RESERVATIONS INFORMATION **** A four-star, four diamond-hotel **** Phones: 1-800 955-4455 505-988-4455 Fax: 505-995-4544 (reservations only) Webpage: http://www.eldoradohotel.com Email: rez@eldoradohotel.com Room Rates: Single/double $85 Sunday(1/19), Monday(1/20), Tuesday(1/21), Wednesday(1/22), Thursday(1/23), Friday(1/24) Saturday (1/25) Single/Double $135 Saturday(1/18) (For comparison, if reservations are not made at the RECOMB97 group rate, the average single/double rate would be $144 for these types of rooms.) RECOMB97 REGISTRATION INFORMATION A registration form can be obtained from the conference web page http://www.cs.sandia.gov/recomb97 Advanced Registration ACM Member Non-ACM Member $285 $360 Late/On-site Registration (After December 12) ACM Member Non-ACM Member $360 $435 Full time student Advanced Registration $160 Late/On-site Registration (After Decemebr 12) $210 Registration fee includes: one copy of the proceedings, four lunches, eight coffee breaks, and a banquet ticket. Student registration fee includes all of the above except the banquet ticket. For more information check out the conference web page http://www.cs.sandia.gov/recomb97 or contact Sorin Istrail RECOMB97 Conference Chair Sandia National Laboratories Massively Parallel Computing Research Laboratory MS 1110 Albuquerque, NM 87185-1110 Phone: (505) 845-7612 Fax : (505) 845-7442 Secretary: (505) 845-7432 Email: scistra@cs.sandia.gov www : http://www.cs.sandia.gov/~scistra From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!feed1.news.erols.com!howland.erols.net!news.starnet.net!newsreader.wustl.edu!spp!zuker From: zuker@spp.wustl.edu (Michael Zuker) Newsgroups: bionet.software Subject: Biocomputing Postdoc - RNA structure Date: 8 Nov 1996 00:14:36 GMT Organization: Washington University in St. Louis, MO USA Lines: 81 Message-ID: <55tu1c$eqk@newsreader.wustl.edu> NNTP-Posting-Host: spp.ibc.wustl.edu Summary: Biocomputing postdoc for RNA structure analysis Keywords: biocomputing, RNA, secondary structure, thermodynamic parameters, statistical analysis X-Newsreader: TIN [version 1.2 PL2] POSTDOC POSTION - Statistical & Algorithmic Aspects of RNA Structure Institute for Biomedical Computing Washington University St. Louis, MO 63110 USA The Institute for Biomedical Computing is an inter-school faculty unit with a mission to foster the development and application of advanced com- puting technology to problems in medicine and biology. Institute activities include research and training collaborations with both the School of Medicine and the School of Engineering and Applied Science. The Institute consists of research laboratory components which have close ties with several depart- ments in the School of Engineering as well as with most departments in the School of Medicine. The Institute now includes the Biomedical Computer Laboratory (BCL). the Center for Molecular Design (CMD),and the Center for Computational Biology (CCB). Research in the CCB focuses on computational aspects of molecular biol- ogy including molecular sequence interpretation, RNA structure prediction, design and analysis of databases of biological information, and analysis of metabolic systems. Research involves algorithm development, database de- sign, and database analysis. We are searching for a postdoctoral fellow to work in the CCB under the direction of Dr. Michael Zuker. For over 15 years, Dr. Zuker has developed well known algorithms and computer programs for RNA secondary structure prediction in conjunction with the RNA Biophysical Chemistry Group at the University of Rochester headed by Professor D. Turner. During this time, databases of aligned, homologous RNA sequences have been assembled, and conserved secondary structures have been deduced by comparative methods that search for covarying positions. In particular, a collaboration between Mike Gray (Dalhousie University, Halifax, NS) and Robin Gutell (University of Colorado, Boulder) has produced a very large database of small-subunit and large-subunit rRNA secondary structures. There is a wealth of information still hidden within these databases of RNA secondary structures. In particular, 2 questions can be asked. 1. Are the frequencies of base pairs and base pair stacking interactions random? If not, are they consistent with the thermodynamic rules for RNA folding? What is the distribution of loop sizes and the base con- tent of single stranded regions? Are these distributions also consistent with the thermodynamics? Such studies should shed light on the weak- est parts of the thermodynamic parameter set. In particular, valuable knowledge should be gained about multi-branched loops. 2. By computing log-odds ratios for observed frequencies divided by ex- pected random frequencies, one can derive "pseudo-energies" or simply an empirical set of scoring rules for RNA secondary structure predic- tion. This is similar to the derivation of PAM or BLOSSUM matrices for protein sequence alignment. Can these empirical rules, used alone or together with known thermodynamic parameters, improve existing RNA folding algorithms? This position would be for 2 (possibly 3) years on the Medical School campus adjacent to the Department of Biochemistry & Biophysics and the Department of Genetics. We offer an open-minded interdisciplinary envi- ronment. We are a mostly "Unix shop" with SGIs, Suns, and Dec alphas. Applicants should have a doctorate in computer science, molecular biology, or a similar field, with a specialization in computational molecular biology. Previous experience with problems involving the analysis of biomolecular sequences and structures would certainly be beneficial. Please send application material (including vita, publication list, state- ment of research interests, and addresses for references) to Prof. Michael Zuker Institute for Biomedical Computing Washington University, Campus Box 8036 700 S. Euclid Avenue St. Louis, MO 63110 USA Tel: (314) 362-2932 Fax: (314) 362-0234 E-mail: zuker@ibc.wustl.edu ________________________________ From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!cdc2.cdc.net!newsfeed.concentric.net!news-master!news From: Ketchup@cris.com (ketchup) Newsgroups: bionet.software Subject: Re: Looking for a multi-sequence alignment program Date: Fri, 08 Nov 1996 00:51:31 GMT Organization: Concentric Internet Services Lines: 20 Message-ID: <55u0ej$6kv@herald.concentric.net> References: <55t9ri$nhk@nntp.ucs.ubc.ca> NNTP-Posting-Host: cnc501243.concentric.net X-Newsreader: Forte Free Agent 1.0.82 Have a look at GeneDoc: http://www.cris.com/~ketchup/genedoc.shtml Thank you. Karl. >My friend is looking for a multi-sequence alignment program, preferably a >MS-Window based program. >Thanks >Alex Chang >Pathology >University of British Columbia >achang@hivnet.ubc.ca From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!news-stkh.gsl.net!news.gsl.net!news-peer.gsl.net!news.gsl.net!newspump.sol.net!howland.erols.net!newsfeed.internetmci.com!news.webspan.net!ix.netcom.com!netcom.net.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news.ox.ac.uk!is.bbsrc.ac.uk!news From: Andy Phillips Newsgroups: bionet.software Subject: Re: Looking for a multi-sequence alignment program Date: Fri, 08 Nov 1996 11:14:36 +0000 Organization: BBSRC, Institute of Arable Crops Research, LARS Lines: 34 Message-ID: <3283161C.30D9@bbsrc.ac.uk> References: <55t9ri$nhk@nntp.ucs.ubc.ca> NNTP-Posting-Host: pc0628.lars.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02Gold (Win95; I) CC: andy.phillips@bbsrc.ac.uk Alex Chang wrote: > > This may be a FAQ. > > My friend is looking for a multi-sequence alignment program, preferably a > MS-Window based program. > > Thanks > > Alex Chang > Pathology > University of British Columbia > achang@hivnet.ubc.ca I use ClustalW (a DOS program) to generate the inital lineup, and then Genedoc to edit and print it. There are links to both of these (and other alignment programs) in the Software section of my Really Quite Useful MolBio Page: http://www.lars.bbsrc.ac.uk/plantsci/molbiol/molbiol.html The only hassle is getting the files into the right format for Clustal. I use the GCG program TOPIR to convert a file of sequence names in GCG format into a single PIR file. I feel there must be an alternative to this that doesn't require access to GCG, and doesn't involve assembling the PIR file with a text editor. Any suggestions? Andy ------------------------------------------------------------------------ Email : andy.phillips@bbsrc.ac.uk : University of Bristol Home : andy@cycad.demon.co.uk : IACR Long Ashton Research Station Phone : +44-1275-549257 : Long Ashton Fax : +44-1275-394281 : Bristol, BS18 9AF, UK WWW : http://www.lars.bbsrc.ac.uk/plantsci/molbiol/andy.html ------------------------------------------------------------------------ From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!news.sgi.com!esiee.fr!jussieu.fr!univ-angers.fr!ciril.fr!usenet From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: Looking for a multi-sequence alignment program Date: 8 Nov 1996 10:16:32 GMT Organization: IGBMC Lines: 32 Message-ID: <55v1a0$qsi@arcturus.ciril.fr> References: <55t9ri$nhk@nntp.ucs.ubc.ca> <3282FA20.1774@bbsrc.ac.uk> NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.6 In article <3282FA20.1774@bbsrc.ac.uk>, Andy Phillips writes: [...] >The only hassle is getting the files into the right format for Clustal. >I use the GCG program TOPIR to convert a file of sequence names in GCG >format into a single PIR file. I feel there must be an alternative to >this that doesn't require access to GCG, and doesn't involve assembling >the PIR file with a text editor. Any suggestions? First, ClustalW runs on UNIXs, VMS, DOS, MAC (enough?), so I don't think you are using a DOS version of GCG ;-), you will increase clustalw perfs by installing a new version on the same system. Second, Clustalw could read several formats (like fasta format...), so it depends of what is your sequences format first. Installing Readseq from Don Gilbert is a good solution: ftp://ftp.bio.indiana.edu/molbio/readseq Plans on clustalw are (as far as I know): X interface, including readseq...Just waiting for a grant for Julie (anyone has one???). Francois. Remember ClustalW 1.6 on-line help: http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/clustalwOLH.html http://www.u.arizona.edu/~schluter/ClustalW/index.html -- Francois Jeanmougin Service de bioinformatique / bioinformatics service IGBMC BP 163 67404 Illkirch France tel :(France) 03 88 65 32 71 / (international) (+33) 3 88 65 32 71 e-mail : jeanmougin@igbmc.u-strasbg.fr "les poissons sans fish, les pieds sans foot" (STTELLLA) From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!rutgers!gatech!csulb.edu!newshub.csu.net!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!vixen.cso.uiuc.edu!qualcomm.com!ihnp4.ucsd.edu!munnari.OZ.AU!bunyip.cc.uq.oz.au!newshost.gu.edu.au!usenet From: Conor McCarthy Newsgroups: bionet.software Subject: ANN:Chromatogram viewer/basecall editor for Windows Date: Fri, 08 Nov 1996 09:45:22 +1000 Organization: Griffith University Lines: 12 Message-ID: <32827492.75D9@sct.gu.edu.au> NNTP-Posting-Host: ibeacham.sci.gu.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; 68K) Hi, Chromas is a free Windows application which displays and prints chromatograms from Applied Biosystems automated sequencers. It allows editing, searching, reverse complementing and exporting of the sequence. You can download it from: http://trishul.sci.gu.edu.au/~conor/chromas.html Cheers, Conor From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!daresbury!not-for-mail From: jpleiss@tebio1.biologie.uni-stuttgart.de (Juergen Pleiss) Newsgroups: bionet.software Subject: Hydrophobic surface calculation Date: 8 Nov 1996 09:31:41 -0000 Lines: 227 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <55uult$oo3@mserv1.dl.ac.uk> Original-To: jpleiss@tebio1.biologie.uni-stuttgart.de (self copy), bio-soft@dl.ac.uk, bio-www@dl.ac.uk, comp-bio@dl.ac.uk, molmodel@dl.ac.uk > Dear colleagues, > we are searching for a program which calculates the total hydrophobic, > solvent accessible surface of a protein or a small molecule. > It should read in a PDB file and output the surface area in Angstrom**2, > which is hydrophobic _and_ solvent accessible (hydrophobicity defined by > any of the hydrophobicity scales, solvent defined by a probe radius). > Ideally, the program uses a user editable parameter file, which > equivalences atom names (as given in the PDB file), VdW radius and > hydrophobicity index, so that the user can add atoms to it. > I would be glad if you could point me to such a program. > Thank you for your help, > Juergen Pleiss Many thanks to all who have responded. Here is the summary : ---------------------------------------------------------- From: merckel@max.mpibp.uni-frankfurt.de Hi Juergen, NACCESS will give you waht you want. http://www.biochem.ucl.ac.uk/bsm/biocomp/index.html It reads PDB files and generates per atom and per residue surface areas. With grep and awk you can easily get the areas relative to any desired atom type. The code is freely available. HTH Mike ---------------------------------------------------------- From: Stefan Grzybek Hallo Juergen Pleiss, Hast Du schon mal was von Grasp gehoert? Mit diesem Programm kann man sehr schoen Molekueloberflaechen berechnen und darstellen. Allerdings ist es nur fuer Silicon Graphics verfuegbar. Es verwendet Parameterdateien fuer Atomradien und Partialladungen (da es auch fuer elektrostatische Rechnungen geeignet ist) und man kann auch beliebige andere Daten, wie z.B deine Hydrophobizitaets-Daten als Werte aus den B-Faktor und Besetzungs-Werten einer PDB-Datei einlesen. Mit allen moegliche Daten kann man innerhalb des Programmes auch Rechnungen durchfuehren. Es kann auch die Flaeche beliebiger Oberflaechenelemente berechnen - genau das was Du brauchst. Leider ist Grasp nicht kostenlos (auch nicht fuer Hochschulen). Fuer weitere Informationen siehe: http://tincan.bioc.columbia.edu/Lab/grasp Stefan ---------------------------------------------------------- From: Zhan-yang Zhu Try to contact Andrej Sali at Rockefeller University by Name: Sali, Andrej E-mail: sali@rockvax.rockefeller.edu He has the program to do what you want, I think. Good luck! ---------------------------------------------------------- From: Alessandro Giolitti You could probably work a bit through GRID, by Peter Goodford, using the hydrophobic probe. Alessandro Giolitti ---------------------------------------------------------- From: Simon Brocklehurst If you have an SGI, you can do most of what you want with NAOMI. Here is an extract from the user guide showing how to get overall figures for a whole molecule (you can of do more detailed calculations too using different commands). You can't put in your own atom types though. The command: table total_access outputs information on the total solvent accessible surface of the protein. Example output is: NAOMI>OUTPUT Total Solvent Accessible Surface of Protein NAOMI>OUTPUT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAOMI>OUTPUT Total 6242 A^2 NAOMI>OUTPUT Main-chain 1393 A^2 22 % NAOMI>OUTPUT Side-chain 4849 A^2 78 % NAOMI>OUTPUT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAOMI>OUTPUT Total hydrophobic 3318 A^2 53 % NAOMI>OUTPUT Main-chain 677 A^2 20 % NAOMI>OUTPUT Side-chain 2640 A^2 80 % NAOMI>OUTPUT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAOMI>OUTPUT Total hydrophilic 2924 A^2 47 % NAOMI>OUTPUT Main-chain 715 A^2 24 % NAOMI>OUTPUT Side-chain 2209 A^2 76 % NAOMI>OUTPUT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ More info in the on-line User Guide at the web site... http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html -- Simon ---------------------------------------------------------- From: Richard Macdonald The Insight II program from our company, MSI, does most (or all) of what you want. There is a command within Homology and NMR_Refine modules that will calculate the accessible surface area, and will separate the areas into polar/nonpolar (which is another measure of hydrophobicity). The command is called ProStat/Access_Surf (for protein statistics/accessible surface). InsightII can be run in graphics mode, or as a command line program. The results can be presented in a table (graphics mode), or simply printed to the shell (command line mode). The Access_Surf command works on default atom names, radii, and polarity, but all these can all be overridden by specifying an input file. The file contains the atom names and their values, with wild-carding allowed. The mechanism was designed to allow any atomic model (full atom model, or united atom model) to be accomodated. Example input files for several united atom models are given in the User Guide. Now all you need to do is find someone who has InsightII!! -- richard ---------------------------------------------------------- From: mike@dino.fold.fccc.edu (J. Mike Sauder) I assume you're looking for a freeware program? You might want to take a look at NAOMI: http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html or http://molbio.info.nih.gov/modeling/software_list/naomi/doc.html -- Mike S. (m_sauder@fccc.edu) http://www.fccc.edu/research/labs/roder/ ---------------------------------------------------------- From: friedman@cgl.ucsf.EDU Hello, I've done this using the program MS, which calculates molecular surfaces from pdb files. I then use an 'awk' script to run through the MS generated surface file and add all the surface elements for each atom type. The total carbon surface is a reasonable estimate of hydrophobic surface. Hope this helps, Simon ---------------------------------------------------------- From: Finn Drablos It is possible to do this with Grasp. You may need a bit work to get started, but as you are able to control Grasp via scripts, much of the hard work can be made automatic. We have used this to look at the amount of surface area of hydrophobic nature, or with electrostatic potential within a certain range, or involved in hydrogen bonding etc, for various molecules and complexes. --- Finn Drablos ---------------------------------------------------------- From: jose@lpoly.bioc.cwru.edu (jose nazario) while you didn't specify a platform, the first one that comes to mind is hyperchem for the pc. we use it here to do just that, to calculate water accessable surface areas with varying probe sizes. hyperchem can read in a pdb file and you can use it to select hydrophobic resiues and from there calculate the ASA. as for other platforms, there exist a plethora of such programs on UNIX boxes. as far as macintosh and powermacs go, i am at a loss to provide you with information as to what programs will fill your needs. jose nazario ---------------------------------------------------------- ================================================================================ Dr.Juergen Pleiss Institute of Technical Biochemistry University of Stuttgart Email:jpleiss@tebio1.biologie.uni-stuttgart.de Allmandring 31 Phone:(+49)-711-685-3191 D-70569 Stuttgart, Germany Fax: (+49)-711-685-3196 W3 home page: http://www.itb.uni-stuttgart.de:8080/ From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!btnet!netcom.net.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news.ox.ac.uk!is.bbsrc.ac.uk!news From: Andy Phillips Newsgroups: bionet.software Subject: Re: Looking for a multi-sequence alignment program Date: Fri, 08 Nov 1996 09:15:12 +0000 Organization: BBSRC, Institute of Arable Crops Research, LARS Lines: 34 Message-ID: <3282FA20.1774@bbsrc.ac.uk> References: <55t9ri$nhk@nntp.ucs.ubc.ca> NNTP-Posting-Host: pc0628.lars.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02Gold (Win95; I) CC: andy.phillips@bbsrc.ac.uk Alex Chang wrote: > > This may be a FAQ. > > My friend is looking for a multi-sequence alignment program, preferably a > MS-Window based program. > > Thanks > > Alex Chang > Pathology > University of British Columbia > achang@hivnet.ubc.ca I use ClustalW (a DOS program) to generate the inital lineup, and then Genedoc to edit and print it. There are links to both of these (and other alignment programs) in the Software section of my Really Quite Useful MolBio Page: http://www.lars.bbsrc.ac.uk/plantsci/molbiol/molbiol.html The only hassle is getting the files into the right format for Clustal. I use the GCG program TOPIR to convert a file of sequence names in GCG format into a single PIR file. I feel there must be an alternative to this that doesn't require access to GCG, and doesn't involve assembling the PIR file with a text editor. Any suggestions? Andy ------------------------------------------------------------------------ Email : andy.phillips@bbsrc.ac.uk : University of Bristol Home : andy@cycad.demon.co.uk : IACR Long Ashton Research Station Phone : +44-1275-549257 : Long Ashton Fax : +44-1275-394281 : Bristol, BS18 9AF, UK WWW : http://www.lars.bbsrc.ac.uk/plantsci/molbiol/andy.html ------------------------------------------------------------------------ From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!math.ohio-state.edu!jussieu.fr!univ-angers.fr!ciril.fr!cnusc.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!pss100.psi.ch!usenet From: "Roger C. Leemann" Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? with Statview? Date: Fri, 08 Nov 1996 08:53:50 -0800 Organization: Institute for Medical Radiobiology Lines: 13 Message-ID: <3283659E.342F@imr.psi.ch> References: <3281117D.7CB3@salk.edu> Reply-To: leemann@imr.psi.ch NNTP-Posting-Host: pc1364.psi.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win16; I) Xref: biosci bionet.software:17050 comp.sys.mac.scitech:9525 S L Forsburg wrote: > > Time to purchase software for an additional PPC Mac. Up till now I > have used Cricketgraph, although I don't like the newer version as ... I guess my Cricket v1.5 is the older version then. Anybody using Statview out there? I don't use it very often but I think it has some potential. How would it compare to Kaleidagraph or Igor ? -- Roger C. Leemann Inst. for Medical Radiobiology CH-5232 Villigen PSI Switzerland From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!uky.edu!usenet From: "Michael W. Thompson" Newsgroups: bionet.software Subject: Re: Ann: SeqSearch v1.0 for Windows, sequence analysis/storage software Date: Fri, 08 Nov 1996 17:33:21 -0400 Organization: University of Kentucky Lines: 1 Message-ID: <3283A721.C06@pop.uky.edu> References: <55v0a1$dd9@news.xs4all.nl> NNTP-Posting-Host: 128.163.70.124 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Are you sure? The URL doesn't seem to be valid. From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!www.nntp.primenet.com!nntp.primenet.com!news.mathworks.com!newsgate.duke.edu!solaris.cc.vt.edu!hp.fciencias.unam.mx!ihnp4.ucsd.edu!scripps.edu!usenet From: S L Forsburg Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? The answer! Date: Fri, 08 Nov 1996 13:29:24 -0800 Organization: The Salk Institute Lines: 24 Message-ID: <3283A634.26E7@salk.edu> References: <3281117D.7CB3@salk.edu> Reply-To: forsburg@salk.edu NNTP-Posting-Host: slfcentris.salk.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; 68K) Xref: biosci bionet.software:17062 comp.sys.mac.scitech:9527 I originally asked readers for their recommendations for graphing software for the Mac, to replace a not-completely successful experience with Criket Graph. Kaleidagraph is a clear favorite, with only a few power users recommending other packages, most of which are more advanced than I need. I found my way to http://www.synergy.com/ and downloaded a demo package of Kaleidagraph. Incidentally, that's a great way to sell software; I'm much more inclined to buy a package if I can try it out first. After some time fiddling, I pretty much figured out how to make Kaleidagraph do what I wanted to be able to do (although I'm looking forward to a manual for syntax details). Looks like a friendly and capable program. Sold! Thanks to everyone for your comments. Happy plotting. ;-) -- susan >->->->->->->-><-<-<-<-<-<-<-<- Susan L Forsburg PhD MBVL, The Salk Institute forsburg@salk.edu http://flosun.salk.edu/~forsburg From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!feed1.news.erols.com!insync!news.hal-pc.org!usenet From: "F. Dail Singleton, Jr." Newsgroups: bionet.software Subject: New Graphics Shareware Announcement Date: Fri, 08 Nov 1996 12:39:07 -0800 Organization: Houston Area League of PC Users Lines: 23 Message-ID: <32839A6B.707E@hal-pc.org> NNTP-Posting-Host: pm2-101.hal-pc.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win95; I; 16bit) Content-Disposition: inline; filename="NEWSNOTE.TXT" Try EDTECH for Windows 1.01, a new Windows version (with improved user interface) of my long-established (since 1989) DOS SCIENTIFIC PLOTTING & DRAWING PROGRAM (EDitor for TECHnical graphics). It works with both Windows 3.1 and Win 95. You can browse http://www.coast.net/SimTel/win3/graphics.html for file name EDTW3101.ZIP. Browse the README.TXT file. Download: ftp://ftp.coast.net/pub/coast/disk2/win3/graphics/edtw3101.zip (Try early morning, this site is very busy.) E-mail me for additional info. Dail Singleton, Jr., PhD Digital Analytics Scientific Software, Houston, Texas fdails@hal-pc.org Disclaimer: my internet provider, HAL-PC, is non-profit and is not connected with or endorsing my software in any way. From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!vixen.cso.uiuc.edu!qualcomm.com!ihnp4.ucsd.edu!munnari.OZ.AU!news.mel.connect.com.au!harbinger.cc.monash.edu.au!newshost.carno.net.au!student.anu.edu.au!news From: Makoto Kamei Newsgroups: bionet.software Subject: Help required on NCBI Sequin for Linux on Slackware96 Date: Sat, 09 Nov 1996 04:21:09 +1100 Organization: MES Group, RSBS, ANU Lines: 21 Message-ID: <32836C05.26F404C@anu.edu.au> NNTP-Posting-Host: rsbspc302.anu.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; Linux 2.0.24 i586) Hi all, I have just installed Slackware 3.1 (with re-compiled kernel 2.0.24), then re-installed Nentrez and Sequin from NCBI. However, it says; seqsequin: can't resolve symbol 'snprintf' and just will not run. When I had Slackware 3.0 with kernel 1.2.13, there was no such problem. What is going on? I'm just a newbie in this direction so any help will be appreciated. Thanks in advance. Makoto ------------------------------------------------------------ Makoto Kamei _ "The Tap Dancing, Sensitive New Age Geneticist" @/ <8 /! Makoto.Kamei@anu.edu.au ~ ~ m-kamei@waite.adelaide.edu.au WWW page at http://www.waite.adelaide.edu.au/~m-kamei From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!www.nntp.primenet.com!nntp.primenet.com!nntp.uio.no!nntp.zit.th-darmstadt.de!fu-berlin.de!news.dfn.de!news.embl-heidelberg.de!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!univ-angers.fr!ciril.fr!cnusc.fr!univ-lyon1.fr!news.univ-aix.fr!newsup.univ-mrs.fr!u372-dutp.univ-mrs.fr!user From: gquerat@inserm-u372.univ-mrs.fr (Gilles Querat) Newsgroups: bionet.software Subject: Re: Looking for a multi-sequence alignment program Date: 8 Nov 1996 16:29:22 GMT Organization: INSERM U372 Lines: 23 Message-ID: References: <55t9ri$nhk@nntp.ucs.ubc.ca> <3282FA20.1774@bbsrc.ac.uk> <55v1a0$qsi@arcturus.ciril.fr> NNTP-Posting-Host: u372-dutp.univ-mrs.fr In article <55v1a0$qsi@arcturus.ciril.fr>, pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) wrote: > In article <3282FA20.1774@bbsrc.ac.uk>, > Andy Phillips writes: > [...] > >The only hassle is getting the files into the right format for Clustal. > > > Second, Clustalw could read several formats (like fasta format...), > so it depends of what is your sequences format first. Installing Readseq > from Don Gilbert is a good solution: > ftp://ftp.bio.indiana.edu/molbio/readseq > > I have fetch the Mac version of readseq from the indiana.edu site but, so far, I have been unable to run it on either 68K or PPC. Does anyone have a suggestion? Gilles -- Gilles Querat INSERM U372 Marseille France From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!angis.su.OZ.AU!tim From: tim@angis.su.OZ.AU (Tim Littlejohn) Newsgroups: bionet.software Subject: Re: Ann: SeqSearch v1.0 for Windows, sequence analysis/storage , software Date: 8 Nov 1996 14:56:52 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3283A721.C06@pop.uky.edu> NNTP-Posting-Host: net.bio.net On Fri, 8 Nov 1996, Michael W. Thompson wrote: > Are you sure? The URL doesn't seem to be valid. Try: http://www.xs4all.nl/~marker/ not http:\\www.xs4all.nl\~marker as originally posted. Cheers, Tim -------------------------------------------------------------------------- | ANGIS- The Australian National Genomic Information Service | | http://www.angis.su.oz.au email: tim@angis.su.oz.au | | Phone Toll Free: 1 800 728 028 FAX: 61-2-9351 2948 | -------------------------------------------------------------------------- From owner-software@net.bio.net Thu Nov 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.erols.net!surfnet.nl!news.unisource.nl!xs4all!xs4all!usenet From: marker@xs4all.nl (Niels Groot) Newsgroups: bionet.software Subject: Ann: SeqSearch v1.0 for Windows, sequence analysis/storage software Date: 8 Nov 1996 09:59:29 GMT Organization: XS4ALL, networking for the masses Lines: 18 Message-ID: <55v0a1$dd9@news.xs4all.nl> NNTP-Posting-Host: asd12-27.dial.xs4all.nl Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-XS4ALL-Date: Fri, 08 Nov 1996 10:59:29 MET X-Newsreader: WinVN 0.99.7 The final beta of SeqSearch v1.0 for Windows can be found at http:\\www.xs4all.nl\~marker Features: - Multi-user storage of data - Seperate storage of sequences, plasmids, constructs, oligo's and motifs - Extended Restriction Site analysis - Clone Bench - Mismatch primer design - Codon mutagenesis primer design - Silent Mutagenesis - Hydrophobic plot - Fragment analysis - Motif Search - Reading Frame analysis - Oligo Info From owner-software@net.bio.net Fri Nov 08 22:00:00 1996 Path: biosci!biosci!not-for-mail From: Biologische Anstalt Helgoland <100634.1171@CompuServe.COM> Newsgroups: bionet.general,bionet.population-bio,bionet.software,misc.jobs.offered Subject: Stellenanzeige 1/2 Date: 8 Nov 1996 20:00:27 -0800 Organization: BAH Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <55v3dk$cft$2@mhafn.production.compuserve.com> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.general:23940 bionet.population-bio:2099 bionet.software:17067 misc.jobs.offered:1511885 Verwaltung der BAH, Tel: 040/89 69 3 - 106/104; 11.1996/b -------------------- STELLENAUSSCHREIBUNG -------------------- An der Biologischen Anstalt Helgoland, einer Forschungseinrichtung im Geschaeftsbereich des Bundesministeriums fuer Bildung, Wissenschaft, Forschung und Technologie, ist in der Abteilung Experimentelle Oekologie im Rahmen eines DFG-Projektes zur Klimawirkungsforschung (Privatarbeitsververhaeltnis mit Herrn Dr. Greve) voraussichtlich zum 1. Januar 1997 die Stelle eines/r --------------------------------------- Mathematisch-technischen Assistenten/in --------------------------------------- zu besetzen. Die Anstellung erfolgt bis zum 31.03.1998. Die Verguetung erfolgt je nach Qualifikation nach dem Bundesangestelltentarifvertrag (BAT). From owner-software@net.bio.net Fri Nov 08 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!sn.no!www.nntp.primenet.com!nntp.primenet.com!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!feed1.news.erols.com!uunet!in3.uu.net!excelsior.flash.net!usenet From: "Tom Noble" Newsgroups: austin.forsale,bionet.software,biz.comp.software,comp.forsale,comp.forsale.computers,comp.forsale.hardware,comp.misc.forsale,misc.comp.forsale,misc.computer.forsale,misc.computers.forsale,misc.for.sale,misc.foresale,misc.foresale.computers,mi Subject: Item For Sale Date: 8 Nov 1996 21:17:43 GMT Organization: Flashnet Communications Lines: 14 Message-ID: <01bbcdba$3c484140$88ccc2d0@tnoble.flash.net> NNTP-Posting-Host: otc1-136.flash.net X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.software:17065 biz.comp.software:10072 I have the following items for sale: 1. Windows 95 (Full Version) w/book & reg card (3 1/2" disk) Asking $100 2. MS Office Standard w/ book & reg card (3 1/2" disk) Asking $100 Windows 95 & MSOffice as a package deal $190 + shipping 3. Windows 3.1 w/book (3 1/2" disk) Asking $15 4. Irwin EZ Tape backup drive (Internal) for DOS/Windows w/book (31/2" & 5 1/4" disk) + 1 tape (120 - 250 MB) Asking $95 A total of $310 + shipping, but I'll take $280 + shipping. From owner-software@net.bio.net Fri Nov 08 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!sn.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!usenet.eel.ufl.edu!news.ultranet.com!homer.alpha.net!news From: "Bob wheaton" Newsgroups: bionet.software Subject: LOOKING FOR SOFTWARE. Date: 9 Nov 1996 01:13:52 GMT Organization: Alpha.net -- Milwaukee, WI Lines: 10 Message-ID: <01bbcddb$cbd9c880$64cd2e9c@default> NNTP-Posting-Host: ppp100.genevaonline.com X-Newsreader: Microsoft Internet News 4.70.1155 Neeed two items: 1. proper driver for mustek scanner for win95. 2. Looking for software to setup computer businesses; bulletinboards, voicemail, etc. CAN ANYONE HELP ME? Please e-mail to: bjkwhe@genevaonline.com -- R.C.W. From owner-software@net.bio.net Fri Nov 08 22:00:00 1996 Path: biosci!rutgers!uwm.edu!news-peer.gsl.net!news.gsl.net!hunter.premier.net!hammer.uoregon.edu!arclight.uoregon.edu!news.sprintlink.net!news-peer.sprintlink.net!newsfeed.internetmci.com!news.ycc.yale.edu!morpheus.cis.yale.edu!skoufs From: Emmanuel Skoufos Newsgroups: bionet.software Subject: Re: Wanted gzip for IRIX6.2 Date: Fri, 8 Nov 1996 16:35:36 -0500 Organization: Yale University Lines: 33 Message-ID: References: <55su53$hfe@mserv1.dl.ac.uk> NNTP-Posting-Host: morpheus.cis.yale.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: skoufs@morpheus.cis.yale.edu To: Gerard Pujadas In-Reply-To: <55su53$hfe@mserv1.dl.ac.uk> On 7 Nov 1996, Gerard Pujadas wrote: > > Hi to all, > > My name is Gerard Pujadas and I would like to know where may I ftp > a compiled version of gzip for IRIX6.2. > You can go to: or Emmanuel -------- Emmanuel Skoufos, Ph.D. Yale University School of Medicine Section of Neurobiology 333 Cedar Street, 236 FMB New Haven, CT 06520 e-mail:emmanouil.skoufos@yale.edu Phone: (203) 785-4336 Fax: (203) 785-6990 gene discovery page: http://www.geocities.com/CapeCanaveral/1915/gdp.html From owner-software@net.bio.net Fri Nov 08 22:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!data.ramona.vix.com!sonysjc!decwrl!lll-winken.llnl.gov!fnnews.fnal.gov!unixhub!news.Stanford.EDU!rjh From: rjh@leland.stanford.edu (Robert Hohlfelder) Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? Date: 9 Nov 1996 22:08:26 GMT Organization: Stanford University Lines: 25 Message-ID: References: NNTP-Posting-Host: nixdonhomer.stanford.edu X-Newsreader: Yet Another NewsWatcher 2.2.0b7 Xref: biosci bionet.software:17070 comp.sys.mac.scitech:9532 This certainly is an active thread! I have used Kaleidagraph for years. It produces nice looking plots and offers good control over the appearance of plots. I like the curve-fitting; it's fast and powerful. Additionally, I have found it to be extremely stable. I never worry about KG crashing even with lots of data and graph windows open. I don't like KG's macro/programming language; it's absolutely painful to use for any serious data analysis. I use Mathematica for that and export text data files into KG. I'm too scared of Igor's learning curve. However, the people I know who use Igor _really_ like it, and it seems to have extremely powerful fitting and data manipulation capabilities. A previous poster mentioned proFit, which I'd never heard of. I checked out the web page ( http://www.cherwell.com/cherwell/ProdHome/proFit.html ), and it looks very interesting! - Robert -- Robert Hohlfelder rjh@leland.stanford.edu http://www-leland.stanford.edu/~rjh/ (415) 723-1284 From owner-software@net.bio.net Fri Nov 08 22:00:00 1996 Path: biosci!bloom-beacon.mit.edu!panix!feed1.news.erols.com!howland.erols.net!news-peer.gsl.net!news.gsl.net!portc01.blue.aol.com!newsstand.cit.cornell.edu!galadriel.chem.cornell.edu!user From: Melissa.Hines@Cornell.edu (Melissa A. Hines) Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? Date: Sat, 09 Nov 1996 18:48:19 -0500 Organization: Cornell University Lines: 32 Sender: mah11@cornell.edu (Verified) Message-ID: References: NNTP-Posting-Host: galadriel.chem.cornell.edu Xref: biosci bionet.software:17071 comp.sys.mac.scitech:9534 In article , rjh@leland.stanford.edu (Robert Hohlfelder) wrote: > I'm too scared of Igor's learning curve. However, the people I know who > use Igor _really_ like it, and it seems to have extremely powerful fitting > and data manipulation capabilities. Igor's learning curve really isn't THAT steep. At Cornell, we use it in the undergraduate chemistry labs without any problems. A fair percentage of our students have NO programming experience coming in. By the end of the term, the students are comfortable writing fairly detailed programs in Igor's macro language. Igor is one of those programs that you learn one step at a time, as your needs grow. First you learn the basic graphing functions (which have a very straightforward GUI). Then you learn simple analysis (curve fitting, etc.). And then you start writing macros. . . Igor is truly addictive. For 2D data display and analysis, there is little that Igor can't do. In 3D, I can't make such a sweeping generalization, but things are coming along by leaps and bounds. Right now, the 3D capabilities of Igor are comparable to other programs that I have used. Give the guys at WaveMetrics another 6 mos or so, and Igor will reign supreme in this area as well. You can pick up the demo by ftp'ing to d31rz0.stanford.edu. Melissa -- Melissa A. Hines Voice/FAX: (607) 255-3040 Dept. of Chemistry E-mail: Melissa.Hines@Cornell.edu Cornell University From owner-software@net.bio.net Fri Nov 08 22:00:00 1996 Path: biosci!VISHNU.JUSSIEU.FR!michel From: michel@VISHNU.JUSSIEU.FR (Michel SEIGNEURET) Newsgroups: bionet.software Subject: drawing of transmembrane helices Date: 8 Nov 1996 19:54:13 -0800 Organization: Universites Paris VI/Paris VII - France Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <55uta6$g4l@vishnu.jussieu.fr> NNTP-Posting-Host: net.bio.net Dear collegues, Could someone indicate me whether the following types of programs are available somewhere: 1)one that draws an helical wheel model starting from the aminoacid sequence of an helix. 2)one that uses a transmembrane protein aminoacid sequence and limits of putative transmembrane helices as input and generates a drawing of the transmembrane folding. Thanks in advance. Michel M. Seigneuret Lab. de Biophysique Cellulaire et RMN Universite Paris 7 France From owner-software@net.bio.net Sat Nov 09 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!feed1.news.erols.com!howland.erols.net!newsfeed.internetmci.com!uunet!in3.uu.net!01-newsfeed.univie.ac.at!news.iif.hu!news From: h12492gor@ella.hu (gyorgy gorog) Newsgroups: bionet.software Subject: [Q] Hardy-Weinberg, HLA, linkage diseq. software Date: 10 Nov 1996 10:16:40 GMT Organization: IIF Lines: 16 Message-ID: <09961009202536.OUI26.h12492gor@ella.hu> Reply-To: h12492gor@ella.hu NNTP-Posting-Host: gygorog.dial.iif.hu X-Newsreader: OUI PRO 1.5.0.2 Dear Colleagues, I am looking for a comprehensive statistics package for a HLA typing lab involved in kidney transplantation, paternity testing, diseases/HLA research. Any info appreciated. Thanks! -- gyorgy gorog h12492gor@ella.hu 11/10/96 11:18 [ Standard Disclaimer ] From owner-software@net.bio.net Sat Nov 09 22:00:00 1996 Path: biosci!IRIS.LSC.PKU.EDU.CN!liuxz From: liuxz@IRIS.LSC.PKU.EDU.CN ("Xiaozhou Liu") Newsgroups: bionet.software Subject: Sequence Analysis software Date: 10 Nov 1996 06:46:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <9611102152.ZM19033@IRIS.lsc.pku.edu.cn> NNTP-Posting-Host: net.bio.net Hi, Does anybody know a protein sequence analysis software which can predict the antigenic index and glycosyl sites and secondary structure? I heard of a program named UWGCG or WVGCG which was produced by Wisconsin Univ. But I can't find it.Could you please provide me some information? Thank you very much. Xiaozhou From owner-software@net.bio.net Sat Nov 09 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!www.nntp.primenet.com!nntp.primenet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!arclight.uoregon.edu!usenet.eel.ufl.edu!news.alt.net!newspost1.alt.net!usenet From: Rick Bright Newsgroups: bionet.software Subject: Solution Calculator Date: Sun, 10 Nov 1996 12:35:55 -0600 Organization: Auburn University at Montgomery Lines: 6 Message-ID: <3286208B.2ECE@mnw.net> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) I am looking for a program that will automatically calculate molarity, volume, or mass to make solutions and will calculate dilutions from stock solutions. Rick Bright rbright@mnw.net From owner-software@net.bio.net Sat Nov 09 22:00:00 1996 Path: biosci!bloom-beacon.mit.edu!panix!feed1.news.erols.com!howland.erols.net!www.nntp.primenet.com!nntp.primenet.com!news.mindspring.com!usenet From: expomed@mindspring.com (Marty Thomas) Newsgroups: bionet.software Subject: Re: E-mail newsgroup software Date: 10 Nov 1996 02:43:26 GMT Organization: Expomed Inc. Lines: 25 Message-ID: <563fge$dhm@camel2.mindspring.com> References: <54tm9c$ar1@halley.pi.net> NNTP-Posting-Host: ip117.akron2.oh.interramp.com Mime-Version: 1.0 X-Newsreader: WinVN 0.93.14 In article <54tm9c$ar1@halley.pi.net>, ruben@pi.net says... > >Hi all, > >I'm freelance a journalist and I was wondering if anybody knows about >a program which can " suck" e-mail adressess out of newsgroups. > >TIA > >Ruben Brave > I know a person working on a email program that will do what you are asking. I am not sure when it will be ready for use. Send me an email in a couple of weeks and I will check with him to see how it is coming. -- =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+ Marty Thomas expomed@mindspring.com http://www.winc.com/commerce/expomed/ Featured Software: Visual Man CD, Visible Human CD,Smartclaim practice management software,Corel Epilepsy CD and more... For a free DOS catalog send email with a mailing address. <><><><><><><>E<>X<>P<>O<>M<>E<>D<><>I<>N<>C<><><><><><><><> From owner-software@net.bio.net Sat Nov 09 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!sn.no!www.nntp.primenet.com!nntp.primenet.com!enews.sgi.com!news.sgi.com!news.msfc.nasa.gov!bcm.tmc.edu!news From: Harley Gorrell Newsgroups: bionet.software Subject: Re: Mulitple alignment editor Date: 10 Nov 1996 13:50:04 -0600 Organization: Baylor College of Medicine, Houston, Tx Lines: 14 Message-ID: References: <554cgv$rap@arcturus.ciril.fr> <3275fb18.0@cisun2000.unil.ch> <32760F46.41C6@sanger.ac.uk> NNTP-Posting-Host: ginger.imgen.bcm.tmc.edu X-Newsreader: Gnus v5.2.40/Emacs 19.34 Ewan Birney writes: > I would still be really interested in an emacs 'multiple alignment' > editor. I think this would be ideal. Anybody out here doing it... Ask Jim Blandy where you can get a copy of 'Ale'. It is an alignment editor written in emacs. The version I have is 0.1.183 from several months ago. harley. -- 'I need the kiss of Kathleen Turner right now' - The kiss of Kathleen Turner, Falco From owner-software@net.bio.net Sat Nov 09 22:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!www.nntp.primenet.com!nntp.primenet.com!usenet.eel.ufl.edu!news.bright.net!news From: "Randy Robinett" Newsgroups: bionet.software,biz.comp.software Subject: Long Distance Phone Call Limiter Date: 10 Nov 1996 21:44:31 GMT Organization: BrightNet Ohio Lines: 13 Message-ID: <01bbcf53$3fc486e0$8677d4cd@randyrob> NNTP-Posting-Host: defi2-cs-14.dial.bright.net X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.software:17079 biz.comp.software:10103 I am looking for a program that will not let you dial a long distance phone number without entering a password before dialing. I am sure I am not the only one with a teenage child that makes too many calls and has no job to pay for the calls. I am willing to hook all my phone through my computer if there is a program available. Thanks, Randy Robinett robinett@bright.net From owner-software@net.bio.net Sun Nov 10 22:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!worf.molbiol.ox.ac.uk!rgrant From: rgrant@worf.molbiol.ox.ac.uk (Richard P Grant) Newsgroups: bionet.software Subject: Re: Graphing on the Mac? The answer! Followup-To: bionet.software Date: 11 Nov 1996 09:10:33 GMT Organization: Oxford University Lines: 26 Message-ID: <566qi9$4gi@news.ox.ac.uk> References: <3281117D.7CB3@salk.edu> <3283A634.26E7@salk.edu> NNTP-Posting-Host: worf.molbiol.ox.ac.uk X-Newsreader: TIN [version 1.2 PL2] Glad you're happy! Can you tell us how well K-graph writes/reads other formats? Can it write PICTs, will it read C-graph / Excel data files / charts?? I think we should be told. S L Forsburg (forsburg@salk.edu) gibbered: } I found my way to http://www.synergy.com/ and downloaded a demo package } of Kaleidagraph. Incidentally, that's a great way to sell software; } I'm much more inclined to buy a package if I can try it out first. } After some time fiddling, I pretty much figured out how to make } Kaleidagraph do what I wanted to be able to do (although I'm looking } forward to a manual for syntax details). Looks like a friendly and } capable program. Sold! } Thanks to everyone for your comments. Happy plotting. ;-) -- Richard P. Grant University of Oxford Nuffield Department Obstetrics and Gynaecology FFPGP http://users.ox.ac.uk/~lady0266 http://www.molbiol.ox.ac.uk/~rgrant ---------------------# hit any user to continue #--------------------- From owner-software@net.bio.net Sun Nov 10 22:00:00 1996 Path: biosci!agate!howland.erols.net!math.ohio-state.edu!jussieu.fr!univ-angers.fr!ciril.fr!cnusc.fr!univ-lyon1.fr!in2p3.fr!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!elna.ethz.ch!usenet From: "I. Biaggio" Newsgroups: bionet.software,comp.sys.mac.scitech Subject: Re: Graphing on the Mac? Date: Mon, 11 Nov 1996 10:11:10 +0100 Organization: Swiss Federal Institute of Technology, Zurich Lines: 20 Message-ID: <3286EDAD.1D88@iqe.phys.ethz.ch> References: NNTP-Posting-Host: nlo14.ethz.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; 68K) To: Robert Hohlfelder Xref: biosci bionet.software:17081 comp.sys.mac.scitech:9539 > and graph windows open. I don't like KG's macro/programming language; it's > absolutely painful to use for any serious data analysis. I use Mathematica [...] > A previous poster mentioned proFit, which I'd never heard of. I checked > out the web page ( http://www.cherwell.com/cherwell/ProdHome/proFit.html > ), and it looks very interesting! > > - Robert Robert, you bring up an interesting point about macro language. After all, one needs to write the functions if one wants to plot them... The macro language of pro Fit is very similar to the standard programming language PASCAL, which means that you can do pretty much everything with it. (and also that you don't have to "learn" it if you know programming) ivan From owner-software@net.bio.net Sun Nov 10 22:00:00 1996 Path: biosci!rutgers!gatech!csulb.edu!newshub.csu.net!www.nntp.primenet.com!nntp.primenet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!in2.uu.net!excelsior.flash.net!usenet From: "Tom Noble" Newsgroups: bionet.software,biz.comp.software,comp.forsale,comp.forsale.computers,comp.forsale.hardware,comp.misc.forsale,misc.comp.forsale,misc.computer.forsale,misc.computers.forsale,misc.for.sale,misc.foresale,misc.foresale.computers,misc.forsale,misc Subject: FS: MS Office 95 Date: 11 Nov 1996 15:41:55 GMT Organization: Flashnet Communications Lines: 4 Message-ID: <01bbcfe6$b0459b00$0fccc2d0@tnoble.flash.net> NNTP-Posting-Host: opm1-15.flash.net X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.software:17088 biz.comp.software:10123 I have a copy of MS Office95 (standard version 3 1/2" disk) $100 + shipping. If interested send email to tnoble@flash.net. From owner-software@net.bio.net Sun Nov 10 22:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!is.bbsrc.ac.uk!news From: Andy Phillips Newsgroups: bionet.software Subject: Re: Sequence Analysis software Date: Mon, 11 Nov 1996 09:18:55 +0000 Organization: BBSRC, Institute of Arable Crops Research, LARS Lines: 23 Message-ID: <3286EF7F.B27@bbsrc.ac.uk> References: <9611102152.ZM19033@IRIS.lsc.pku.edu.cn> NNTP-Posting-Host: pc0628.lars.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02Gold (Win95; I) CC: andy.phillips@bbsrc.ac.uk Xiaozhou Liu wrote: > > Hi, > > Does anybody know a protein sequence analysis software which can predict > the antigenic index and glycosyl sites and secondary structure? I heard > of a program named UWGCG or WVGCG which was produced by Wisconsin Univ. > But I can't find it.Could you please provide me some information? Thank > you very much. > > Xiaozhou Try www.gcg.com Andy ------------------------------------------------------------------------ Email : andy.phillips@bbsrc.ac.uk : University of Bristol Home : andy@cycad.demon.co.uk : IACR Long Ashton Research Station Phone : +44-1275-549257 : Long Ashton Fax : +44-1275-394281 : Bristol, BS18 9AF, UK WWW : http://www.lars.bbsrc.ac.uk/plantsci/molbiol/andy.html ------------------------------------------------------------------------ From owner-software@net.bio.net Sun Nov 10 22:00:00 1996 Path: biosci!rutgers!news.sgi.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!news.pbi.net!samba.rahul.net!rahul.net!a2i!viper.inow.com!news.he.net!night.primate.wisc.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!news From: Michael Hogan Newsgroups: bionet.software Subject: GCG Web site Date: Mon, 11 Nov 1996 10:11:26 -0600 Organization: University of Wisconsin, Madison Lines: 10 Message-ID: <3287502E.41C6@gcg.com> NNTP-Posting-Host: 128.104.224.10 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V3.2 alpha) The GCG WWW site was unavailable due to a problem with the file system on that machine. The problem is fixed now and the url http://www.gcg.com should work again. We apologize for any inconvenience. ----- Michael Hogan, PhD phone: (608) 231-5200 Genetics Computer Group, Inc. fax: (608) 231-5202 575 Science Dr., Suite B e-mail: hogan@gcg.com Madison, WI 53711 From owner-software@net.bio.net Sun Nov 10 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!feed1.news.erols.com!uunet!in2.uu.net!excelsior.flash.net!usenet From: "Tom Noble" Newsgroups: bionet.software,biz.comp.software,comp.forsale,comp.forsale.computers,comp.forsale.hardware,comp.misc.forsale,misc.comp.forsale,misc.computer.forsale,misc.computers.fo