From owner-software@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!news.idt.net!dispose.news.demon.net!demon!news.demon.co.uk!demon!irchouse.demon.co.uk!Richard From: Richard Seaby Newsgroups: bionet.software Subject: Re: software for biodiversity Date: Tue, 2 Dec 1997 09:06:31 +0000 Organization: PISCES Conservation Ltd Distribution: world Message-ID: References: <34831B7D.293F@tc.umn.edu> NNTP-Posting-Host: irchouse.demon.co.uk X-NNTP-Posting-Host: irchouse.demon.co.uk [194.222.28.248] MIME-Version: 1.0 X-Newsreader: Turnpike Version 3.03a <0m8AKmNUbsiAkpxCmBEjIFZCRF> Lines: 40 Species Diversity and Richness is a program to aid ecologists and environmentalists in the calculation and application of diversity indices and estimating total species richness for a habitat. The program is available for both Windows 95 and 3.1 operating systems. It is designed for ease of use and includes an informative help system. Species Diversity and Richness is also a good educational program for both undergraduate and postgraduate students. Instruction book available in English, Spanish and Portuguese. Price 50 UK pounds Sterling (+ VAT in UK Only) Postage and packing - within UK 2 UK pounds Sterling, rest of world 5 UK pounds Sterling. For more information visit our web site at http://www.irchouse.demon.co.uk In article <34831B7D.293F@tc.umn.edu>, praveen gupta writes >I am looking for a software that can calculate bidiversity factor and >other important things. If you have any information please let me know >the name of the software, company that makes it (if possible) and any >other information regarding that software. > >I would be glad to get URL if it is freely available. > >Thanks. >Praveen Dr Richard Seaby PISCES Conservation Ltd IRC House The Square Pennington Tel - 44 (0)1590 676622 Lymington Fax - 44 (0)1590 675599 Hants Email - pisces@irchouse.demon.co.uk SO41 8GN Website - Http://www.irchouse.demon.co.uk From owner-software@net.bio.net Mon Dec 01 22:00:00 1997 Newsgroups: bionet.software Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!torn!utnut!oci!news From: "Rizwan Haq" Subject: Re: sequence software Message-ID: X-Mimeole: Produced By Microsoft MimeOLE V4.71.1712.3 Lines: 33 Sender: news@oci.utoronto.ca Organization: Ontario Cancer Institute - U of Toronto X-Newsreader: Microsoft Outlook Express 4.71.1712.3 References: <3475E241.58E3@mail.utexas.edu> <3476FA92.135E856D@gwdg.de> Date: Tue, 2 Dec 1997 01:08:31 GMT I had this problem and contacted the people at the web site. Apparently if you are not from a US site, you have to sign a waiver and they will give you a guest account to their ftp site. Rizwan Brian Rous wrote in message ... >On Sat, 22 Nov 1997, Arne Mueller wrote: > >> >> I've heard about a windows based program "Prophet" which is easy to use >> (but not as powerfull as gcg is!). A friend of mine as used it and he >> says it's ok. I think you can download a free demoversion. Habve look >> at http://www-prophet.bbn.com/seq-analysis.htm >> >> thanx, >> >> Arne >> > >Does anyone know how I can get hold of this software? It looks very good >and the site says that it is free, but the link to try and download it >from the site doesn't seem to work. I've tried e-mailing the "report >problems" mail address, but haven't had a reply. > >Anyone got any ideas? Or got it on another FTP site? > >Many thanks, > > Brian Rous > From owner-software@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!rutgers!uwm.edu!www.nntp.primenet.com!globalcenter0!news.primenet.com!nntp.primenet.com!dispose.news.demon.net!demon!news.demon.co.uk!demon!genesys.demon.co.uk!demon.co.uk!duncan From: "Dr. Duncan Clark" Newsgroups: bionet.software Subject: Re: sequence software Date: Mon, 1 Dec 1997 17:29:14 +0000 Organization: GeneSys Ltd Distribution: world Message-ID: References: <3475E241.58E3@mail.utexas.edu> <3476FA92.135E856D@gwdg.de> NNTP-Posting-Host: genesys.demon.co.uk X-NNTP-Posting-Host: genesys.demon.co.uk [158.152.17.110] MIME-Version: 1.0 X-Newsreader: Turnpike Version 3.04 Lines: 25 In article , Brian Rous writes >It looks very good >and the site says that it is free, but the link to try and download it >from the site doesn't seem to work. I've tried e-mailing the "report >problems" mail address, but haven't had a reply. The NIH-Prophet FTP server is not allowing anonymous logins. It will accept an email login name but requires a password (email address is no good). I assume it is currently setup for private downloads/uploads by the developers. The program specifications look very good. Duncan -- The problem with being on the cutting edge is that you occasionally get sliced from time to time.... Duncan Clark DNAmp Ltd. TEl/FAX 01252376288 http://www.dnamp.com http://www.genesys.demon.co.uk From owner-software@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!news-was.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!news-zh.switch.ch!news.belnet.be!news.vub.ac.be!imol.vub.ac.be!imolpc1 From: willy.verheulpen@(nospam)imol.vub.ac.be (Willy A Verheulpen) Newsgroups: bionet.software Subject: Re: De-Archiving Win95 CAB files??? Date: Tue, 02 Dec 1997 09:39:28 GMT Organization: Brussels Free University (VUB) Lines: 19 Message-ID: <660ksq$fju@imol2.vub.ac.be> References: <65kb08$i0e$2@madrid.visi.net> <881012494.8703@dejanews.com> NNTP-Posting-Host: imolpc1.vub.ac.be X-Newsreader: News Xpress 2.01 In article <881012494.8703@dejanews.com>, Elocutus of Borg wrote: >In article <65kb08$i0e$2@madrid.visi.net>, > mab@visi.net wrote: >> Does anyone know of a program to manually de-archive Windows95 >> CAB archived files? > >Mike-- > >I _think_ Dr. Dobbs provided a utility for this. You may want to surf >over to http://www.ddj.com and check it out. FWIW ... Powertoys on the Microsoft site contains a .cab reader + extract utility .. -------------------------------------------------------------- Willy Verheulpen Institute for Mol. Biology & Biotechnology Brussels Free University Scientia Vincere Tenebras Paardenstr 65 B-1640 Sint Genesius Rode Belgium remove (nospam) in the address to reply .... From owner-software@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!rutgers!gatech!134.222.90.2.MISMATCH!EU.net!news0.Belgium.EU.net!newsr.Belgium.EU.net!not-for-mail From: "Z.Huang" Newsgroups: bionet.software Subject: Re: sequence software Date: Mon, 01 Dec 1997 15:14:44 -0800 Organization: Gut Hormone Lab, K.U.Leuven Lines: 33 Message-ID: <348344E4.7C88@med.kuleuven.ac.be> References: <3475E241.58E3@mail.utexas.edu> <3476FA92.135E856D@gwdg.de> NNTP-Posting-Host: marvin.kulnet.kuleuven.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) Cache-Post-Path: marvin.kulnet.kuleuven.ac.be!unknown@gihvtr1.med.kuleuven.ac.be I also tried several times but it obviously refused my visit. As you have done already, I e-mail them for login name and password but get no response so far. So I have to treat this site as bad link. Huang Z K.U.Leuven Belgium Brian Rous wrote: > > On Sat, 22 Nov 1997, Arne Mueller wrote: > > > > > I've heard about a windows based program "Prophet" which is easy to use > > (but not as powerfull as gcg is!). A friend of mine as used it and he > > says it's ok. I think you can download a free demoversion. Habve look > > at http://www-prophet.bbn.com/seq-analysis.htm > > > > thanx, > > > > Arne > > > > Does anyone know how I can get hold of this software? It looks very good > and the site says that it is free, but the link to try and download it > from the site doesn't seem to work. I've tried e-mailing the "report > problems" mail address, but haven't had a reply. > > Anyone got any ideas? Or got it on another FTP site? > > Many thanks, > > Brian Rous From owner-software@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!204.71.76.137!news.campus.mci.net!n-f-m From: "Michael W. Thompson" Newsgroups: bionet.software Subject: Re: Multiple DNA seq alignment Date: Mon, 01 Dec 1997 21:53:39 -0500 Organization: CampusMCI Lines: 19 Message-ID: <34837833.46D23B39@hotmail.com> References: <9711258804.AA880495225@smtpgate.bcsew.edu> Reply-To: nospam@nospam.noway.nohow NNTP-Posting-Host: s26-pm03.uky.campus.mci.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.02 [en] (Win95; I) dmdinauer@SMTPGATE.BCSEW.EDU wrote: > I'm looking for DNA sequence software which will align multiple seq's > files and show all the differences. DNASIS performs this task readily > but I do not currently have this software. Try MACAW, which is available from NCBI for free from their anonymous FTP server at ncbi.nlm.nih.gov Michael W. Thompson Dept. of Biochemistry University of Kentucky From owner-software@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!134.222.90.2!EU.net!news0.Belgium.EU.net!newsr.Belgium.EU.net!not-for-mail From: "Z.Huang" Newsgroups: bionet.software Subject: Re: Multiple DNA seq alignment Date: Tue, 02 Dec 1997 14:24:36 -0800 Organization: Gut Hormone Lab, K.U.Leuven Lines: 21 Message-ID: <34848AA4.2601@med.kuleuven.ac.be> References: <9711258804.AA880495225@smtpgate.bcsew.edu> <34837833.46D23B39@hotmail.com> NNTP-Posting-Host: marvin.kulnet.kuleuven.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) Cache-Post-Path: marvin.kulnet.kuleuven.ac.be!unknown@gihvtr1.med.kuleuven.ac.be Michael W. Thompson wrote: > > dmdinauer@SMTPGATE.BCSEW.EDU wrote: > > > I'm looking for DNA sequence software which will align multiple seq's > > files and show all the differences. DNASIS performs this task readily > > but I do not currently have this software. > > > > Try MACAW, which is available from NCBI for free from their anonymous FTP > server at ncbi.nlm.nih.gov > > Michael W. Thompson > Dept. of Biochemistry > University of Kentucky GeneDoc is much more better. Using Yahoo search engine to locate the download site and then enjoy it. Huang Z From owner-software@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.internetmci.com!134.222.90.2!EU.net!news0.Belgium.EU.net!newsr.Belgium.EU.net!not-for-mail From: "Z.Huang" Newsgroups: bionet.software Subject: Re: sequence software Date: Tue, 02 Dec 1997 13:45:36 -0800 Organization: Gut Hormone Lab, K.U.Leuven Lines: 48 Message-ID: <34848180.31EA@med.kuleuven.ac.be> References: <3475E241.58E3@mail.utexas.edu> <3476FA92.135E856D@gwdg.de> <348344E4.7C88@med.kuleuven.ac.be> NNTP-Posting-Host: marvin.kulnet.kuleuven.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) Cache-Post-Path: marvin.kulnet.kuleuven.ac.be!unknown@gihvtr1.med.kuleuven.ac.be Z.Huang wrote: > > I also tried several times but it obviously refused my visit. As you have > done already, I e-mail them for login name and password but get no > response so far. So I have to treat this site as bad link. > > Huang Z > K.U.Leuven > Belgium > > Brian Rous wrote: > > > > On Sat, 22 Nov 1997, Arne Mueller wrote: > > > > > > > > I've heard about a windows based program "Prophet" which is easy to use > > > (but not as powerfull as gcg is!). A friend of mine as used it and he > > > says it's ok. I think you can download a free demoversion. Habve look > > > at http://www-prophet.bbn.com/seq-analysis.htm > > > > > > thanx, > > > > > > Arne > > > > > > > Does anyone know how I can get hold of this software? It looks very good > > and the site says that it is free, but the link to try and download it > > from the site doesn't seem to work. I've tried e-mailing the "report > > problems" mail address, but haven't had a reply. > > > > Anyone got any ideas? Or got it on another FTP site? > > > > Many thanks, > > > > Brian Rous Finally I received guest account from the company and downloaded the software successfully. In general this software works well in considering it's rare character of freeware in similar products. I just tried primer and probe analysis function in prophet5.0 but didn't fell so satisfied. I can choose much of primers from GCG package but I can only get one set of primer from prophet in term of the same cDNA sequence. Anyway I think this software is still a good stuff I have ever seen(for win95). Huang Zhong Gut Hormone Lab K.U.Leuven Belgium From owner-software@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!194.22.194.4!masternews.telia.net!newsfeed.sunet.se!news99.sunet.se!news01.sunet.se!193.166.5.150.MISMATCH!news.funet.fi!news.utu.fi!not-for-mail From: Janos Korponai Newsgroups: bionet.software Subject: software for biodiversity Date: Tue, 02 Dec 1997 10:48:49 +0200 Organization: University of Turku Lines: 6 Message-ID: <3483CB71.302@utu.fi> NNTP-Posting-Host: silakka.eko.utu.fi Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win16; I) Here is one: http://www.ecol.klte.hu/nucosa.html Janos Korponai Univ. Turku From owner-software@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.erols.net!newsfeed.internetmci.com!193.174.75.126!news-was.dfn.de!news-fra1.dfn.de!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Frank Visser Newsgroups: bionet.molbio.gene-linkage,bionet.software Subject: Radiation hybrid mapping programs Date: 02 Dec 1997 16:10:59 +0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 35 Sender: fvisser@francium Message-ID: NNTP-Posting-Host: francium.hgmp.mrc.ac.uk X-Newsreader: Gnus v5.4.37/XEmacs 19.15 Xref: biosci bionet.molbio.gene-linkage:1658 bionet.software:20058 Hello, We (the UK based HGMP-RC) are thinking of providing for our users a nice web-based interface to a radiation hybrid mapping program. The problem with the radiation hybrid mapping programs is that there are a number of them available, and it is not entirely clear to us which one to provide to our users. The requirements are: - Trusted, i.e. the algorithm/implementation is trusted by the Linkage community to generate 'correct' results - Batch: must be able to run without direct intervention from the user. Most Unix based programs can do this, so that is not a big problem - Must gave exact lod scores, not just "greater than 3" or something. A quick perusal of the software list at rockefeller showed the following entries: MAP+H Shields et al. PNAS 88, 6501-6505) RHMAP (Boehnke et al, AJHG 49, 1174-1188) RHMAPPER (Stein et al. Whitehead Institute) I have also heard of a program called RH, and there are possibly even more candidates. Does anyone have any suggestions which one to choose for our interface backend? Frank Visser --- F. Visser e-mail: fvisser@hgmp.mrc.ac.uk From owner-software@net.bio.net Mon Dec 01 22:00:00 1997 Path: biosci!agate!howland.erols.net!EU.net!news0.Belgium.EU.net!newsr.Belgium.EU.net!not-for-mail From: "Z.Huang" Newsgroups: bionet.software Subject: Re: HELP!!!!! (Got a problem with Direct X Drivers) Date: Tue, 02 Dec 1997 15:02:41 -0800 Organization: Gut Hormone Lab, K.U.Leuven Lines: 24 Message-ID: <34849391.7187@med.kuleuven.ac.be> References: <65v4kb$47n$1@epos.runnet.ru> NNTP-Posting-Host: marvin.kulnet.kuleuven.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) To: Cyril Borisov Cache-Post-Path: marvin.kulnet.kuleuven.ac.be!unknown@gihvtr1.med.kuleuven.ac.be Hi, First of all you must make certain what's language version of win95 you are using now. Second of all check the DirectX 5.0 language version and make sure that it's language version is correspond with win95 language version. There are several language version of DirectX availale in net including english, chinese, japan, spain, ... Just choose the right one. Enjoy. Huang Z Cyril Borisov wrote: > > Sorry to bother you, but I've got a problem installing the DirectX Drivers > 5.0. > > During the install process, it (my Win '95) writes that "This language > version of DX 5.0 is not supported by this version of Windows". > What does it mean & what should I do on this situation? > All advices accepted. > > Thanks beforehand, Cyril Borisov From owner-software@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.direct.ca!news.uoregon.edu!news.u.washington.edu!evolution.genetics.washington.edu!joe From: joe@evolution.genetics.washington.edu (Joe Felsenstein) Newsgroups: bionet.software Subject: Re: Making gif's of dendrograms, UNIX ? Date: 3 Dec 1997 01:34:13 GMT Organization: University of Washington Genetics Lines: 26 Message-ID: <662cul$31h$1@nntp3.u.washington.edu> References: NNTP-Posting-Host: evolution.genetics.washington.edu X-Trace: nntp3.u.washington.edu 881112853 3121 (None) 140.142.64.7 X-Complaints-To: help@cac.washington.edu Summary: getting to GIF Keywords: dendrogram, GIF In article , Brian Osborne wrote: >I am generating alignments and the associated >dendrograms (*.dnd) using clustalw (command line). >I would like to take the *.dnd file and make it into >a GIF, again, from the command line. I've used >Phylip, but this cannot make GIFs, as far as I >can tell. One possibility would be to use Phylip >to make a .ps file, then do a ps -> gif I suppose. >Is there any utility that can do this directly, >for UNIX? There are utilities (I think in the PBMPlus package) called ps2ppm and ppmtogif that could do it. I did not put GIF into PHYLIP's Drawgram and Drawtree programs mostly because, aside from programming difficulty, there were at one point possible legal problems from CompuServe. I gather these have now receded and I should have done it. You could alternatively use an output like PICT or PCX that can be read by a drawing program, and then ask the drawing program to import that and then export a GIF 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 Tue Dec 02 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!news.misty.com!news-feed.inet.tele.dk!bofh.vszbr.cz!news.maxwell.syr.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!192.87.106.104!surfnet.nl!gate.news.unisource.nl!news.unisource.nl!news.bart.net!not-for-mail From: gdekker@noord.bart.nl (Gerard Dekker) Newsgroups: bionet.software Subject: Drivers and other utils Date: Wed, 03 Dec 1997 00:56:50 GMT Organization: bART Internet Services Lines: 6 Message-ID: <348cae4a.84238913@news.bart.nl> NNTP-Posting-Host: s41.rotterdam.bart.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent 1.5/32.452 If you need any drivers and don't know the way to get it.... go to my page and there is way to get it. You can even mail me if you still can't find it... Look at: http://noord.bart.nl/~gdekker From owner-software@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!newsserver.rrzn.uni-hannover.de!news.rz.uni-kiel.de!not-for-mail From: "Hansjoerg Plendl" Newsgroups: bionet.software Subject: PED 4 - pedigree drawing software Date: Wed, 3 Dec 1997 12:14:49 +0100 Organization: Rechenzentrum der Universitaet Kiel, Germany Lines: 10 Message-ID: <663eol$bmt$1@www-proxy.rz.uni-kiel.de> NNTP-Posting-Host: 194.94.172.201 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 PED 4 - pedigree drawing software for Win95, NT, and Win3.1 (with Win32s). For more information, please visit http://ourworld.compuserve.com/homepages/plendl/ped.htm Follow the link to the download area for a free evaluation copy. Hansjoerg Plendl plendl@medgen.uni-kiel.de From owner-software@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!newsfeed.eerie.fr!jussieu.fr!univ-lille1.fr!u-strasbg.fr!news From: pingouin@chouchen.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: Making gif's of dendrograms, UNIX ? Date: 3 Dec 1997 08:05:33 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 47 Message-ID: <6633sd$o2j@news.u-strasbg.fr> References: <662cul$31h$1@nntp3.u.washington.edu> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: chouchen.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.8 In article <662cul$31h$1@nntp3.u.washington.edu>, joe@evolution.genetics.washington.edu (Joe Felsenstein) writes: > In article , > Brian Osborne wrote: >>I am generating alignments and the associated >>dendrograms (*.dnd) using clustalw (command line). >>I would like to take the *.dnd file and make it into >>a GIF, again, from the command line. I've used >>Phylip, but this cannot make GIFs, as far as I >>can tell. One possibility would be to use Phylip >>to make a .ps file, then do a ps -> gif I suppose. >>Is there any utility that can do this directly, >>for UNIX? > > There are utilities (I think in the PBMPlus package) called > ps2ppm and ppmtogif that could do it. Well, I don't know what you really want to do with the .dnd file from Clustal, but I saw so much errors with the pileup.figure tree that I think I have to put a warning here : The .dnd file generated by Clustal is NOT a phylogenetic tree. This tree is only made using % identity derived from the pairwise alignment and is used as a guide tree for the clustering alignement (generating clusters by using the nearest neighbours in the tree). We also found recently that we perhaps could use this tree to overweight a sequence in the alignement (making a sequence drive the alignment). We have to test it before documenting it, it's quite a hack ;-). As said in the Clustal documentation, please use the Phylip package if you are interested in tree. Clustal ftp update site: ftp://ftp-igbmc.u-strasbg.fr/pub/ HTML documentation (there are several mirrors, check altavista) http://www-igbmc/BioInfo/ClustalW/Top.html for the command line version http://www-igbmc/BioInfo/ClustalX/Top.html for the windowed version (courtesy from EMBnet/CMB Spain). Also, lot of details will appear in Nucleic Acid Research next week (last issue of 1997). François. -- François Jeanmougin | groupe de bioinformatique / bioinformatics groupe tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France From owner-software@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!GENOME.BIOTECH.WASHINGTON.EDU!eugene From: eugene@GENOME.BIOTECH.WASHINGTON.EDU (Eugene Kolker) Newsgroups: bionet.software Subject: RECOMB98: Call for Posters Date: 2 Dec 1997 17:39:05 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712030138.RAA01129@genome.biotech.washington.edu> NNTP-Posting-Host: net.bio.net CALL FOR RECOMB 98 POSTERS Please send a one-page abstract (about 200 words, plain justified text, formatted to fit European Standard A-4: 8.5X11 inch or 21.5X28 cm) of your Poster including title, author(s), affiliation and abstract-text to Martin Vingron DKFZ, Theoretische Bioinformatik (0815) INF 280 69120 Heidelberg Germany The actual poster space will be about 15 pages. A booklet with the accepted poster abstracts will be produced and available at the conference. Deadline for poster abstract submission: January 1, 1998 Notification of acceptance/rejection: January 16, 1998 From owner-software@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.fast.net!news-xfer.netaxs.com!netnews.com!netnews.com!news2.euro.net!newsfeed.adam.ixe.net!newsfeed.xs4all.nl!xs4all!nestorix2.xs4all.nl!not-for-mail From: "Flappie" Newsgroups: bionet.software Subject: Not just another software site! Date: Wed, 3 Dec 1997 22:25:31 +0100 Organization: XS4ALL, networking for the masses Lines: 12 Message-ID: <664ipa$omu$1@news2.xs4all.nl> NNTP-Posting-Host: flappie.xs4all.nl X-XS4ALL-Date: Wed, 03 Dec 1997 22:26:02 CET X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 We try to make your life easier on the web....it all started out as a joke...but now we're addicted to our site! We want to make it so good that it can compete with the best. You can help us do so! Please visit our site (http://sector5.mypage.org) and let us know what you think about it. Give us tips about making it a better site! The best tips will recieve a free T-shirt! Thx for your help! Sector 5 Computer Company Ps:You can stop by for the great downloads to! From owner-software@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!news-peer.gip.net!news.gsl.net!gip.net!news.new-york.net!news.columbia.edu!news-not-for-mail From: Justin Lee Newsgroups: bionet.software Subject: Mini Analysis Program Date: Wed, 03 Dec 1997 13:25:46 -0500 Organization: Columbia University Lines: 26 Message-ID: <3485A42A.AC178BAB@columbia.edu> Reply-To: cjl2@columbia.edu NNTP-Posting-Host: bb110101.cpmc.columbia.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.02 [en] (Win95; U) Hi, I have written a mini analysis program to analyse spontaneous miniature EPSCs or IPSCs under Windows environment. It can detect 3pA peaks with 5pA noise. It can also be used for any spontaneous activities, such as spontaneous action potential firing, current recordings for electochemical measurements, etc.. Please visit at http://128.59.170.42 to download the program and try it out. I also have several other programs useful for electophysiology and immunocytochemistry. Justin Lee -- Columbia University Department of Physiology 630 W. 168th Street BB1106 New York, NY 10032 Phone (212) 305-3817 Fax (212) 305-5775 e-mail cjl2@columbia.edu http://128.59.170.42 ftp://128.59.170.42 From owner-software@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!europa.clark.net!192.174.65.44!newscore.univie.ac.at!03-newsfeed.univie.ac.at!fstgal00.tu-graz.ac.at!spaniel From: smith@umes07.avl.co.at (Search Spaniel) Newsgroups: bionet.software Subject: Software-search the web quickly with Search Spaniel Date: Wed, 03 Dec 97 17:35:21 GMT Organization: Search Spaniel Lines: 4 Message-ID: <250108696@searchspaniel.com> NNTP-Posting-Host: isdn024.tu-graz.ac.at To Software-search the most search engines in the shortest time, use the internet's newest search engine - Search Spaniel at: http://www.searchspaniel.com/ From owner-software@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!NATURE.BERKELEY.EDU!bosborne From: bosborne@NATURE.BERKELEY.EDU (Brian Osborne) Newsgroups: bionet.software Subject: Making gif's of dendrograms, UNIX ? Date: 2 Dec 1997 16:26:46 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net To the group, I am generating alignments and the associated dendrograms (*.dnd) using clustalw (command line). I would like to take the *.dnd file and make it into a GIF, again, from the command line. I've used Phylip, but this cannot make GIFs, as far as I can tell. One possibility would be to use Phylip to make a .ps file, then do a ps -> gif I suppose. Is there any utility that can do this directly, for UNIX? Thanks once again, Brian O. bosborne@nature.berkeley.edu From owner-software@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!204.59.152.222!news-peer.gip.net!news.gsl.net!gip.net!news.idt.net!dispose.news.demon.net!demon!bullseye.news.demon.net!demon!newsfeed.xs4all.nl!xs4all!nestorix2.xs4all.nl!not-for-mail From: "Flappie" Newsgroups: bionet.software Subject: Not just another software site! Date: Wed, 3 Dec 1997 17:01:08 +0100 Organization: XS4ALL, networking for the masses Message-ID: <663vp1$4ab$1@news2.xs4all.nl> NNTP-Posting-Host: flappie.xs4all.nl X-XS4ALL-Date: Wed, 03 Dec 1997 17:01:37 CET X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Lines: 10 We try to make your life easier on the web....it all started out as a joke...but now we're addicted to our site! We want to make it so good that it can compete with the best. You can help us do so! Please visit our site and let us know what you think about it. Give us tips about making it a better site! The best tips will recieve a free T-shirt! Thx for your help! Sector 5 Computer Company Ps:You can stop by for the great downloads to! From owner-software@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.internetmci.com!193.174.75.126!news-was.dfn.de!news-fra1.dfn.de!news-ber1.dfn.de!news-lei1.dfn.de!news-nue1.dfn.de!uni-erlangen.de!lrz-muenchen.de!wap18.zi.biologie.uni-muenchen.de!strimmer From: Korbinian Strimmer Newsgroups: bionet.software Subject: PUZZLE 4.0 Date: Wed, 3 Dec 1997 14:20:51 +0100 Organization: [posted via] Leibniz-Rechenzentrum, Muenchen (Germany) Lines: 60 Distribution: world Message-ID: NNTP-Posting-Host: wap18.zi.biologie.uni-muenchen.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Announcing PUZZLE version 4.0: Maximum Likelihood Analysis for Nucleotide, Amino Acid, and Two-State Data December 1997 Copyright 1995-97 by Korbinian Strimmer and Arndt von Haeseler Zoologisches Institut, Universitaet Muenchen, Muenchen, Germany What's new in PUZZLE 4.0 compared to version 3.1: - computation of clock-like branch lengths (also for amino acids and for non-binary trees) - automatic likelihood ratio clock test - two-state ML model for presence-absence data - display of most probable assignment of rates to sites - identification of groups of identical sequences - possibility to read multiple input trees - Kishino-Hasegawa test to check whether trees are significantly different - BLOSUM 62 model of amino acid substitution (Henikoff-Henikoff 1992) - improvements to user interface - SH model can be applied to 1st and 2nd codon positions - automatic check for compatible compiler settings - fix of gcc compatibility problem. PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated under the clock-assumption. In addition, PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio clock test, Kishino-Hasegawa test). The models of substitution provided by PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity is modelled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set. PUZZLE is available free of charge from http://www.zi.biologie.uni-muenchen.de/~strimmer/puzzle.html (PUZZLE home page) ftp://ftp.ebi.ac.uk/pub/software (European Bioinformatics Institute) ftp://ftp.pasteur.fr/pub/GenSoft (Institut Pasteur) http://iubio.bio.indiana.edu/soft/molbio/evolve (IUBio archive www) ftp://iubio.bio.indiana.edu/molbio/evolve (IUBio archive ftp) PUZZLE is written in ANSI C. It will run on most personal computers and workstations if compiled by an appropriate C compiler. Executables are available for MacOS, Windows 95/NT, and OS/2. UNIX and VMS makefiles are also provided. From owner-software@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!fu-berlin.de!news-ber1.dfn.de!news-fra1.dfn.de!news-kar1.dfn.de!news-stu1.dfn.de!news.belwue.de!news.uni-mannheim.de!usenet From: Eckart Bindewald Newsgroups: bionet.software Subject: Computing atom coordinates of a protein Date: Wed, 03 Dec 1997 22:56:28 +0100 Organization: Informatik 5, Universitaet Mannheim Lines: 11 Message-ID: <3485D58C.366A98E@mp-sun1.informatik.uni-amnnheim.de> NNTP-Posting-Host: mp-pc25.informatik.uni-mannheim.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; Linux 1.99.4 i586) Hello! Does anyone know of available C/C++ source code for computing the cartesian coordinates of the atoms of a protein given its torsion angles? Thank you for your help. Eckart email: eckart@mp-sun1.informatik.uni-mannheim.de From owner-software@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!sdu.edu.cn!lilab From: lilab@sdu.edu.cn (lab of MYXO) Newsgroups: bionet.software Subject: Circular Genetic Map Drawing Software Needed! Date: 3 Dec 1997 03:36:33 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <3485438D.3E52@sdu.edu.cn> Reply-To: lilab@sdu.edu.cn NNTP-Posting-Host: net.bio.net Can anyone tell me if there are free software for circular genetic map drawing on the net? Thanks in advance! Sincerely yours, LI Jian _______________________________________________ Li Jian State Key Laboratory of Microbial Technology Department of Microbiology, Life Science College Shandong University Jinan 250100, P.R.China Tel:(86)(0531)8906961(ext.2431) Fax:(86)(0531)8915234 Email: lilab@sdu.edu.cn _______________________________________________ From owner-software@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!208.134.241.18!newsfeed.internetmci.com!206.229.87.25!news-peer.sprintlink.net!news.sprintlink.net!Sprint!worldnet.att.net!news.u.washington.edu!learn From: learn@u.washington.edu (Jerry Learn) Newsgroups: bionet.software Subject: Re: Making gif's of dendrograms, UNIX ? Date: Wed, 03 Dec 1997 08:51:00 -0800 Organization: University of Washington Lines: 73 Message-ID: References: <662cul$31h$1@nntp3.u.washington.edu> <6633sd$o2j@news.u-strasbg.fr> NNTP-Posting-Host: tench.microbiol.washington.edu X-Trace: nntp3.u.washington.edu 881167873 14724 (None) 140.142.64.2 X-Complaints-To: help@cac.washington.edu X-Newsreader: MT-NewsWatcher 2.3.3 In article <6633sd$o2j@news.u-strasbg.fr>, jeanmougin@igbmc.u-strasbg.fr wrote: > > In article , > > Brian Osborne wrote: > >>I am generating alignments and the associated > >>dendrograms (*.dnd) using clustalw (command line). > >>I would like to take the *.dnd file and make it into > >>a GIF, again, from the command line. I've used > >>Phylip, but this cannot make GIFs, as far as I > >>can tell. One possibility would be to use Phylip > >>to make a .ps file, then do a ps -> gif I suppose. > >>Is there any utility that can do this directly, > >>for UNIX? > > Well, I don't know what you really want to do with the .dnd file > from Clustal, but I saw so much errors with the pileup.figure tree that > I think I have to put a warning here : > The .dnd file generated by Clustal is NOT a phylogenetic tree. > This tree is only made using % identity derived from the pairwise > alignment and is used as a guide tree for the clustering alignement > (generating clusters by using the nearest neighbours in the tree). > We also found recently that we perhaps could use this tree to overweight > a sequence in the alignement (making a sequence drive the alignment). > We have to test it before documenting it, it's quite a hack ;-). > > As said in the Clustal documentation, please use the Phylip > package if you are interested in tree. > > Clustal ftp update site: > ftp://ftp-igbmc.u-strasbg.fr/pub/ > > HTML documentation (there are several mirrors, check altavista) > http://www-igbmc/BioInfo/ClustalW/Top.html for the command line version > http://www-igbmc/BioInfo/ClustalX/Top.html for the windowed version > (courtesy from EMBnet/CMB Spain). > > Also, lot of details will appear in Nucleic Acid Research next week > (last issue of 1997). > I concur with François' caveats about using the guide tree from clustal as a phylogenetic tree. However, the current versions of clustal can be used to produce neighbor-joining trees, once you have examined the alignment to correct possible errors (this, of course, should be done before any further analysis). The clustal package has the added feature of producing a NJ phylogram with bootstrap values at the nodes. But as far as I know treetool is the only UNIX program (SunOS/Solaris only) that can be used to visualize these trees. And as François suggests, if you are serious about constructing phylogenetic trees get programs (PAUP) or packages (PHYLIP) that specialize in phylogenetic reconstruction. PHYLIP is available for free from . Also note that the URLs given for the HTML documentation will not work in most places -- try these instead: for the command line version for the windowed version Best of Luck, Jerry Learn Research Associate Health Sci. Ctr., Rm. K443-C | Dept. of Microbiology | Learn@u.washington.edu University of Washington | Phone: (206) 616-4286 Box 357740 | FAX: (206) 616-1575 Seattle, WA 98195-7740 USA | From owner-software@net.bio.net Tue Dec 02 22:00:00 1997 Path: biosci!GENOME.BIOTECH.WASHINGTON.EDU!eugene From: eugene@GENOME.BIOTECH.WASHINGTON.EDU (Eugene Kolker) Newsgroups: bionet.software Subject: RECOMB98: Call for Posters Date: 2 Dec 1997 17:39:03 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712030138.RAA01127@genome.biotech.washington.edu> NNTP-Posting-Host: net.bio.net CALL FOR RECOMB 98 POSTERS Please send a one-page abstract (about 200 words, plain justified text, formatted to fit European Standard A-4: 8.5X11 inch or 21.5X28 cm) of your Poster including title, author(s), affiliation and abstract-text to Martin Vingron DKFZ, Theoretische Bioinformatik (0815) INF 280 69120 Heidelberg Germany The actual poster space will be about 15 pages. A booklet with the accepted poster abstracts will be produced and available at the conference. Deadline for poster abstract submission: January 1, 1998 Notification of acceptance/rejection: January 16, 1998 From owner-software@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!newsfeed.eerie.fr!jussieu.fr!univ-angers.fr!ciril.fr!univ-lille1.fr!u-strasbg.fr!news From: pingouin@chouchen.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software Subject: Re: Making gif's of dendrograms, UNIX ? Date: 4 Dec 1997 07:56:55 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 53 Message-ID: <665no7$pp4@news.u-strasbg.fr> References: <662cul$31h$1@nntp3.u.washington.edu> <6633sd$o2j@news.u-strasbg.fr> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: chouchen.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.8 In article , learn@u.washington.edu (Jerry Learn) writes: > I concur with François' caveats about using the guide tree from clustal as > a phylogenetic tree. Oh! Thanks ;-). Also, I don't want Clustal users to be flamed by reviewers... [...] > The clustal package has the added feature of producing a NJ phylogram with > bootstrap values at the nodes. But as far as I know treetool is the only > UNIX program > (SunOS/Solaris only) > that can be used to visualize these trees. hmmm. I didn't check so much, but the Macintosh TreeView also works well here. In fact, the trees are in standard Phylip format (we feel that the phylip format is standard, it is easy to use, read and manipulate, we choose it for the guide tree also), so all the Phylip compatible programs should be able to read the NJ trees. > And as François suggests, if you are serious about constructing > phylogenetic trees get programs (PAUP) or packages (PHYLIP) that > specialize in phylogenetic reconstruction. PHYLIP is available for free > from . And PAUP was recently included in GCG9.1 (Just hard to manage here between GCG8.1 with EGCG and GCG9 with PAUP. Quite confusing for users...). > Also note that the URLs given for the HTML documentation will not work in > most places -- try these instead: Ooooouuups. I didn't check. #?%µ££%% Netscape! > for the command > line version > for the windowed > version Yep, those are the good URLs, but there is probably a fast mirror around your location. Also the ClustalX one is just a page (no image, just tables), you can save as source and use it locally. > Best of Luck, > Jerry Learn Thanks for correcting the mistakes. François. -- François Jeanmougin | groupe de bioinformatique / bioinformatics groupe tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France From owner-software@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.internetmci.com!199.44.2.10!nntp.cntfl.com!news.gnt.net!not-for-mail From: "Jack M. King" Newsgroups: bionet.software Subject: FS: COREL WEB GRAPHICS SOFTWARE Date: Wed, 03 Dec 1997 22:36:36 -0600 Organization: Confederate National Enterprises Lines: 22 Message-ID: <34863354.CE9E56EE@gnt.net> NNTP-Posting-Host: x2p40.gnt.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (Win95; U) I have the following for sale: Corel Web Graphics Suite consisting of: 1) WEB.DESIGNER -> powerful web page publisher 2) WEB.MOVE -> create exciting animations and bring your web pages to life. 3) WEB.DRAW -> utilize the power of CorelDRAW 5 technology. 4) WEB.WORLD -> transform your web site into a virtual reality visitors can explore. 5) WEB.GALLERY -> over 7,500 internet-ready clipart images And More.... If interested, make me an offer. Jack M. King jhnyreb@gnt.net From owner-software@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!not-for-mail From: islam Newsgroups: bionet.software Subject: Re: Computing atom coordinates of a protein Date: Thu, 04 Dec 1997 02:20:15 -0800 Organization: Imperial Cancer Research Fund Lines: 29 Message-ID: <348683DF.41C6@icrf.icnet.uk> References: <3485D58C.366A98E@mp-sun1.informatik.uni-amnnheim.de> NNTP-Posting-Host: palm.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX 6.3 IP32) Eckart, I have a program, called Joiner, which will read a set of torsion angles and generate the appropriate structure in PDB format. HHOWEVER, at present, it is only available as a Silicon Graphics Irix binary. If this is of use please email me. ____________________________________________ Suhail A Islam Biomolecular Modelling Laboratory Imperial Cancer Research Fund, P.O. Box 123 44 Lincoln's Inn Fields, London WC2A 3PX Tel: (0171) 269 3380, Fax: (0171) 269 3479 email: islam@icrf.icnet.uk http://www.icnet.uk/bmm/ ____________________________________________ Eckart Bindewald wrote: > > Hello! > > Does anyone know of available C/C++ source code for computing the > cartesian coordinates of the atoms of a protein given its torsion > angles? > > Thank you for your help. > > Eckart > > email: eckart@mp-sun1.informatik.uni-mannheim.de From owner-software@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!server1.netnews.ja.net!rill.news.pipex.net!pipex!uunetukout!newsfeed.ecrc.net!newsfeed.nacamar.de!chico.franken.de!news-nue1.dfn.de!news-lei1.dfn.de!news.uni-jena.de!news.fh-jena.de!news From: Rene Schueler Newsgroups: bionet.software Subject: NEU : 21 Kanal EEG-Simulator Date: Thu, 04 Dec 1997 10:08:41 +0100 Organization: FH Jena Lines: 15 Message-ID: <34867319.21CF@mt.fh-jena.de> Reply-To: rene.schueler@mt.fh-jena.de NNTP-Posting-Host: mt26.mt.fh-jena.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.01Gold [de] (Win95; I) Kurzinformation : Test von EEG-Geräten nun auf 21 Kanälen möglich. 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Weitere Informationen unter : http://www.angelfire.com/biz/biomedjena Stop. oder : BioMed Jena GmbH Marktstrasse 24 07747 Jena Tel.: (03641) 64 29 95 BioMed Jena GmbH From owner-software@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!207.103.147.20!news.voicenet.com!dsinc!nntp.upenn.edu!taurus.fccc.edu!not-for-mail From: Ying Hu Newsgroups: bionet.software Subject: Re: POP2: an ASN.1 to SYBASE converter/population tool Date: Thu, 04 Dec 1997 16:56:30 -0500 Organization: Fox Chase Cancer Center Lines: 11 Message-ID: <3487270E.41C6@fccc.edu> References: <34830D6C.167EB0E7@bch.umontreal.ca> NNTP-Posting-Host: rudkin.rm.fccc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V3.0 alpha) Nicolas Brossard wrote: > AVAILABILITY: ? > ------------- > pop2 can be obtained at the following FTP site: > > ftp://megasun.bch.umontreal.ca/pub/pop2 Are you sure that address is right ? From owner-software@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!webtv.net!uunet!in5.uu.net!news-peer-east.sprintlink.net!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!206.63.63.70!nwnews.wa.com!nwfocus.wa.com!nntp.alaska.net!not-for-mail From: "Joe " Newsgroups: ak.forsale,bionet.software,bit.software,biz.comp.software,comp.software,cs.software Subject: FS: Microspft Office 95, games and more!!! Date: 4 Dec 1997 01:41:33 GMT Organization: Internet Alaska Inc. Lines: 28 Message-ID: <01bd0055$44e1a2a0$a58b70d1@huguelet> NNTP-Posting-Host: anc-p40-165.alaska.net X-Newsreader: Microsoft Internet News 4.70.1155 I have the following software forsale. The prices aren't firm, there only suggestions. Nuclear Strike- Brand new, still have all the manuels etc... My computer can't handle it though (not all requirments met) $35 Comanche- Love this game but am ready to sell it and get something else $15 Battleground Gettysburg- Got it as a gift, good looking game but I am not really into the Civil War $20 Cyberia- Another good game... Beat it though $15 Aces over Europe $15 Microsoft Office 95 (Includes full Ver. of: Word, Excel, Powerpoint, Schedule and Access) $40 7th Guest (2 Cd's) $25 Prices are negociable. Buyer pays for shipping charges! From owner-software@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!uthct.edu!wu From: wu@uthct.edu (Cathy Wu) Newsgroups: bionet.software Subject: New Release 2.0 - ProClass Protein Family Database Date: 4 Dec 1997 06:56:49 -0800 Organization: The University of Texas Health Center at Tyler Lines: 65 Sender: daemon@net.bio.net Distribution: world Message-ID: <3486C53F.CDBD7178@uthct.edu> Reply-To: wu@uthct.edu NNTP-Posting-Host: net.bio.net The Bioinformatics Research Group of the University of Texas Health Center at Tyler is pleased to announce the Release 2.0 of its ProClass Protein Family Database. The database is available for on-line search at: http://diana.uthct.edu/proclass.html Free copies of the ProClass Database and its query program can be obtained via anonymous FTP to: ftp://diana.uthct.edu/pub/ProClass/ The ProClass Protein Family Database, cited in a recent Science Genome issue (Vol. 278, No. 5338, p. 615, Genome Maps), is a non-redundant database organized according to family relationships as defined collectively by PIR superfamilies and ProSite patterns. The objectives are to facilitate protein family information retrieval, unveil domain and family relationships, and classify multi-domained proteins. This is achieved by combining global and motif sequence similarities into a single classification scheme. The current ProClass release consists of 103,312 sequence entries retrieved from PIR-international (Release 54.0, September 1997) and SwissProt (Release 34.0, November 1996) databases. It has three sub-databases, ProClass_Family (PCFam), ProClass_Sequence (PCSeq) and ProClass_Motif (PCMotif) for the collections of family, sequence and motif entries. Major features of ProClass Release 2.0 are: - Compilation of ProClass_Motif. The data set provides an up-to-date and comprehensive source of motif sequences and alignments for all ProSite patterns. Included are several thousands of new family members which are not catalogued in ProSite (Release 13.0), but identified by our GeneFIND family identification system (version 2.0, December 1997, http://diana.uthct.edu/genefind.html). - Hypertext links to all major family databases. Included are links to the underlying raw databases (PIR, SwissProt and ProSite), family/superfamily alignments (PIR_ALN, MIPS), other family/domain databases (BLOCKS, PRINTS, ProDom, Pfam), and structural class databases (SCOP, CATH, HSSP). References: - Wu, C. H., Zhao, S. and Chen, H. L. (1996). A protein class database organized with ProSite protein groups and PIR superfamilies. Journal of Computational Biology, 3(4), 547-561. - Wu, C. H. and Shivakumar, S. (1998). ProClass protein family database: New version with motif alignments. Proceedings of the Pacific Symposium on Biocomputing '98, (In Press). If you have any questions or comments, please contact me at wu@uthct.edu. -- Cathy H. Wu, Ph.D. Associate Professor of Biomathematics University of Texas Health Center at Tyler P. O. Box 2003, Tyler, TX 75710 E-Mail : wu@uthct.edu Phone : (903) 877-7962 Fax : (903) 877-5914 WWW URL: http://diana.uthct.edu/~wu GeneFIND Web Server: http://diana.uthct.edu From owner-software@net.bio.net Wed Dec 03 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!206.229.87.25!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!207.208.45.33!newsfeeds.interaccess.com!d182.dialnet2.interaccess.com!user From: jas@option-wizard.com (jas@option-wizard.com) Newsgroups: bionet.software Subject: GeoQuery Date: 4 Dec 1997 15:05:48 GMT Organization: Sarkett & Associates, Inc. Lines: 7 Message-ID: NNTP-Posting-Host: d182.dialnet2.interaccess.com Looking for a copy of GeoQuery for Mac to use with Symantec Act! GeoQuery is out of business. jas@interaccess.com -- Option Wizard Software for Excel http://option-wizard.com From owner-software@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!NCGR.ORG!gbs From: gbs@NCGR.ORG ("Gautam B. Singh, PhD") Newsgroups: bionet.software Subject: ABI Images Date: 4 Dec 1997 16:12:01 -0800 Organization: National Center for Genome Resources Lines: 17 Sender: daemon@net.bio.net Distribution: world Message-ID: <348746AA.3A76@ncgr.org> NNTP-Posting-Host: net.bio.net Hi: Is there a utility to translate the binary sequence reads from an ABI machines to a JPG/GIF file? We need to make some raw sequences available on our Web site. Thanks. -- Gautam B. Singh, Ph.D. Senior Scientist, Algorithms Research National Center for Genome Resources 1800 Old Pecos Trail Santa Fe, NM 87505 Ph: (505) 995 4418 Fax: (505) 995 4461 E-Mail: gbs@ncgr.org From owner-software@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!agate!newsgate.duke.edu!nntprelay.mathworks.com!news.mathworks.com!gatech!news.cis.uab.edu!maze.dpo.uab.edu!NewsWatcher!user From: tan@neptune.cmc.uab.edu (Robert Tan) Newsgroups: bionet.molec-model,bionet.software,comp.sys.sgi.hardware Subject: Origin 200/2000 benchmarks required for molecular simulation Date: Thu, 04 Dec 1997 14:37:13 -0600 Organization: University of Alabama at Birmingham Lines: 12 Message-ID: NNTP-Posting-Host: 138.26.45.218 Xref: biosci bionet.molec-model:1951 bionet.software:20086 If you have timings for molecular dynamics on the Origin 200 and the 2000 I would appreciate hearing from you. Ideally I would like to compare the machines using Amber (the Web site has Origin 200 benchmarks but not the 2000) or another standard molecular mechanics/dynamics program, for a medium to large simulation (20-50 thousand atoms), on a 175 MHz Origin 200 on the one hand and a 195 MHz Origin 2000 on the other, single processor times and four processor times if possible. But if you have any comparisons between the two machines in molecular modeling I would appreciate hearing from you. Thank you. -- Robert K.-Z. Tan -- E-mail: tan@neptune.cmc.uab.edu -- Phone: (205)934-0580 From owner-software@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!sanbi.ac.za!andrey From: andrey@sanbi.ac.za (Andrey A Ptitsyn) Newsgroups: bionet.software Subject: BLAST output to HTML Date: 5 Dec 1997 07:34:19 -0800 Organization: SANBI Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <34880EBA.644BC57C@sanbi.ac.za> NNTP-Posting-Host: net.bio.net Hi Netters, I have lost my bookmarks in a hardware accident. There was a Perl script, converting BLAST output to HTML, avalable for anonymous FTP. Could somebody, please, remind me the URL? Thank you in advance, Andrey A. Ptitsyn From owner-software@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!NET.BIO.NET!biosci-help From: biosci-help@NET.BIO.NET (BIOSCI Administrator) Newsgroups: bionet.software Subject: ATTN: BIO-SOFT/bionet.software to be automoderated for spam Date: 5 Dec 1997 11:36:59 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 123 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: biosci-help@net.bio.net NNTP-Posting-Host: net.bio.net As announced earlier in bionet.forum, we will soon implement a new policy to control spam in unmoderated bionet groups. The original message is copied directly below. Appended after it is a copy of my proposed new group charter for BIO-SOFT/bionet.software. It is not intended to change the status quo for serious scientific discussion, but only to eliminate commercial and pornographic spam messages. If you have any suggestions for change in the text or in the policy, please let me know within the next few days. Thanks, Serge Taylor Biosci Administrator Stanford University ============== original message ============================== As part of our effort to eliminate "spam" messages which are offensive and distracting to the scientific discussions which the Biosci newsgroups are designed to facilitate, we are creating a new type of moderated newsgroup -- "Moderated (only to filter out spam)". Our rationale is that only what usenet recognizes as "moderated" newsgroups can filter mail postings, yet it has proven difficult to find volunteer moderators from each newsgroup. Our intention is to use a combination of human and software filters to eliminate the most egregious examples of spam. Since we value diversity of opinion in scientific communications, and recognize that our efforts are unavoidably subject to both Type I and Type II errors, we aim to err on the side of allowing arguably scientifically relevant communications to be posted. We intend to convert all the unmoderated bionet newsgroups to the new status as soon as possible, and forsee two situations: (1) Where a charter exists for an established but unmoderated group, we will take the current charter and add the following language (taken From the policy statement which we send to anyone who wishes to start a new newsgroup or convert an unmoderated to moderated newsgroup, and suitably customized to the newsgroup where necessary) on "Moderation Policy": "Moderation Policy: Mass-posted commercial messages, chain letters, and similar postings not germane to the stated purpose of the charter will be deleted without comment. Inappropriate messages posted in good faith will be returned to the sender where feasible. Messages not strictly within the charter but likely to be of interest to many subscribers will be accepted. Use of the newsgroup for commercial purposes is prohibited." The proposed new charter will be posted to the newsgroup for a short comment period. (2) Where a charter does not exist for an established unmoderated group, we will solicit the newsgroup's discussion leader(s), where listed, to draft a non-controversial charter and submit it to the newsgroup for a short comment period. If at any time a moderated-for-spam newsgroup wishes to convert to a regular "moderated" group, with its own moderator, we shall be happy to treat such a request just as we do the request to change from unmoderated to moderated status. Finally, if a currently moderated group wishes to take advantage of the spam filtering software to ease the administrative burden on the moderator, we will discuss the logistics and policy guidelines with the group's moderator. (We will notify moderators when we are ready to offer this facility; we are not currently ready.) We hope that these new arrangements will protect the integrity of our newsgroups and allow us to focus on other ways of improving Biosci. Thank you for your patience and understanding as we deal with the spam problem. Serge Taylor Biosci Administrator Stanford University Libraries ========== proposed modified charter ==================== Proposal for BIO-SOFT/bionet.software (moderated-for-spam) USENET newsgroup name: bionet.software Status: Moderated-for-spam One line Description: Information about software for biology Moderation address: bio-soft@net.bio.net Moderator: Biosci Administration Mailing list name: BIO-SOFT E-mail addresses: bio-soft@net.bio.net bio-soft@daresbury.ac.uk Charter for BIO-SOFT/bionet.software Purpose: Discussions of software for biology Moderation Policy: This newsgroup is moderated by automatic spam filtering software and by Biosci personnel, implementing the following policy: Mass-posted commercial messages, chain letters, and similar postings not germane to the stated purpose of the charter will be deleted without comment. Inappropriate messages posted in good faith will be returned to the sender where feasible. Messages not strictly within the charter but likely to be of interest to many subscribers will be accepted. Use of the newsgroup for commercial purposes is prohibited. From owner-software@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!dispose.news.demon.net!demon!bullseye.news.demon.net!demon!newsfeed.xs4all.nl!xs4all!nestorix2.xs4all.nl!not-for-mail From: "Flappie" Newsgroups: bionet.software Subject: Not just another software site! Date: Fri, 5 Dec 1997 14:54:28 +0100 Organization: XS4ALL, networking for the masses Message-ID: <66913i$p9k$1@news2.xs4all.nl> NNTP-Posting-Host: flappie.xs4all.nl X-XS4ALL-Date: Fri, 05 Dec 1997 14:54:58 CET X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Lines: 12 We try to make your life easier on the web....it all started out as a joke...but now we're addicted to our site! We want to make it so good that it can compete with the best. You can help us do so! Please visit our site (http://sector5.mypage.org) and let us know what you think about it. Give us tips about making it a better site! The best tips will recieve a free T-shirt! Thx for your help! Sector 5 Computer Company Ps:You can stop by for the great downloads to! From owner-software@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!207.178.62.6!news.wolfe.net!not-for-mail From: jjones@wolfenet.com (Jerry) Newsgroups: alt.comp.software.financial,bionet.software,bionet.software.gcg,bionet.software.pc,comp.software,biz.comp.software.demos,comp.sys.ibm.pc.software Subject: Software Needed Date: 5 Dec 1997 08:59:37 GMT Organization: Your Organization Lines: 9 Message-ID: <668fpp$p8p$1@sparky.wolfe.net> NNTP-Posting-Host: yak-ts1-p07.wolfenet.com Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.8 (x86 32bit) Xref: biosci bionet.software:20090 bionet.software.gcg:2911 Does anybody know where I can find shareware that will print out invoices and/or receipts? Thanks. Jerry -- It ain't easy being me; but somebody's got to do it... From owner-software@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!agate!awabi.library.ucla.edu!208.134.241.18!newsfeed.internetmci.com!205.252.116.205!howland.erols.net!recycled.news.erols.com!enews.sgi.com!chronicle.mti.sgi.com!news.corp.sgi.com!not-for-mail From: Ghislain de Jacquelot Newsgroups: bionet.molec-model,bionet.software,comp.sys.sgi.hardware Subject: Re: Origin 200/2000 benchmarks required for molecular simulation Date: Fri, 05 Dec 1997 11:45:12 +0100 Organization: Silicon Graphics, Inc. Lines: 25 Message-ID: <3487DB38.167E@lyon.sgi.com> References: NNTP-Posting-Host: alpha.lyon.sgi.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX64 6.2 IP26) To: Robert Tan Xref: biosci bionet.molec-model:1953 bionet.software:20089 Robert Tan wrote: > > If you have timings for molecular dynamics on the Origin 200 and the 2000 > I would appreciate hearing from you. Ideally I would like to compare the > machines using Amber (the Web site has Origin 200 benchmarks but not the > 2000) or another standard molecular mechanics/dynamics program, for a > medium to large simulation (20-50 thousand atoms), on a 175 MHz Origin 200 > on the one hand and a 195 MHz Origin 2000 on the other, single processor > times and four processor times if possible. But if you have any > comparisons between the two machines in molecular modeling I would > appreciate hearing from you. Thank you. > Hi, Take a look at the following address. You'll find single CPU results for both O200 and O2000. Note that the results on these machines are 1 year-old and would probably be better with the latest compilers (MipsPro 7.2). http://www.sissa.it/furio/Mdbnch/results.txt Hope this helps, Ghislain. > -- > Robert K.-Z. Tan -- E-mail: tan@neptune.cmc.uab.edu -- Phone: (205)934-0580 From owner-software@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!agate!newsgate.duke.edu!nntprelay.mathworks.com!enews.sgi.com!news.sgi.com!news.nsg.sgi.com!news.corp.sgi.com!not-for-mail From: Ghislain de Jacquelot Newsgroups: bionet.molec-model,bionet.software,comp.sys.sgi.hardware Subject: Re: Origin 200/2000 benchmarks required for molecular simulation Date: Fri, 05 Dec 1997 11:41:53 +0100 Organization: Silicon Graphics, Inc. Lines: 24 Message-ID: <3487DA71.41C6@lyon.sgi.com> References: NNTP-Posting-Host: alpha.lyon.sgi.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX64 6.2 IP26) To: Robert Tan Xref: biosci bionet.molec-model:1952 bionet.software:20088 Robert Tan wrote: > > If you have timings for molecular dynamics on the Origin 200 and the 2000 > I would appreciate hearing from you. Ideally I would like to compare the > machines using Amber (the Web site has Origin 200 benchmarks but not the > 2000) or another standard molecular mechanics/dynamics program, for a > medium to large simulation (20-50 thousand atoms), on a 175 MHz Origin 200 > on the one hand and a 195 MHz Origin 2000 on the other, single processor > times and four processor times if possible. But if you have any > comparisons between the two machines in molecular modeling I would > appreciate hearing from you. Thank you. Hi, Take a look at the following address, you'll find single CPU results for our boxes. Note that O200/O2000 results are 1 year old, and may probably be better with the latest compilers (MipsPro7.2). Hope this helps, Ghislain. > > -- > Robert K.-Z. Tan -- E-mail: tan@neptune.cmc.uab.edu -- Phone: (205)934-0580 From owner-software@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!agate!howland.erols.net!news-peer.gip.net!news.gsl.net!gip.net!news.voicenet.com!dsinc!nntp.upenn.edu!taurus.fccc.edu!not-for-mail From: Ying Hu Newsgroups: bionet.software Subject: Re: POP2: an ASN.1 to SYBASE converter/population tool Date: Fri, 05 Dec 1997 09:04:59 -0500 Organization: Fox Chase Cancer Center Lines: 17 Message-ID: <34880A0B.41C6@fccc.edu> References: <34830D6C.167EB0E7@bch.umontreal.ca> <3487270E.41C6@fccc.edu> NNTP-Posting-Host: rudkin.rm.fccc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V3.0 alpha) Ying Hu wrote: > > Nicolas Brossard wrote: > > AVAILABILITY: > > ? > > > ------------- > > pop2 can be obtained at the following FTP site: > > > > ftp://megasun.bch.umontreal.ca/pub/pop2 > > Are you sure that address is right ? I am sorry, the address is correct ! Ying From owner-software@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!news2.chicago.iagnet.net!iagnet.net!news.maxwell.syr.edu!newsfeed.eerie.fr!jussieu.fr!univ-lyon1.fr!news.univ-aix.fr!newsup.univ-mrs.fr!news From: Bernard.Bellon@abil.univ-mrs.fr Newsgroups: bionet.software Subject: Re: BLAST output to HTML Date: Fri, 05 Dec 1997 22:58:37 +0100 Organization: UNIVERSITE MARSEILLE Lines: 7 Message-ID: <34887909.1C9A@abil.univ-mrs.fr> References: <34880EBA.644BC57C@sanbi.ac.za> NNTP-Posting-Host: criup5.univ-mrs.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Macintosh; I; PPC) To: Andrey A Ptitsyn >I have lost my bookmarks in a hardware accident. There was a Perl >script, converting BLAST output to HTML, avalable for anonymous FTP http://golgi.harvard.edu/gilbert-bi.html http://www-alt.pasteur.fr/~tekaia/blastfasta.html Bernard Bellon Universite Aix-Marseille From owner-software@net.bio.net Thu Dec 04 22:00:00 1997 Path: biosci!dnastar.com!timb From: timb@dnastar.com (Tim Burland) Newsgroups: bionet.software Subject: Commercial activity on bionet Date: 5 Dec 1997 14:52:18 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 56 Sender: daemon@net.bio.net Distribution: world Message-ID: <3.0.3.32.19971205165259.0092f600@198.150.22.9> NNTP-Posting-Host: net.bio.net I am seeking clarification of the policy on commerical activity for BIOSCI/bionet newsgroups, in particular for bionet.software. My enquiry is prompted by this commerical message posted by one of our competitors in the sequence analysis software business: Subject: Sequencher moving to Windows NT/95 (ANNOUNCE) From: howardc@GENECODES.COM (Howard Cash) Date: 1997/11/20 Message-ID: Newsgroups: bionet.software The message is a new product announcement. My company might also like to post new product announcements to this forum, but some BIOSCI policy statements would seem to prohibit this action. For example, a message at http://www.bio.net/BIOSCI/biosci.FAQ.html#q4 states that "Commercial activities on BIOSCI are in general prohibited", and goes on to say that "BIOSCI will takes steps to terminate network access to any reader who willfully violates our commercial use policies." On this basis, one might expect access to be terminated for our competitor above. In contrast, a usenet policy statement at ftp://rtfm.mit.edu/pub/usenet/news.announce.newusers/Rules_for_posting_to_Us enet states that "Announcement of professional products or services on Usenet is allowed, provided suitable restraint is exercised." In this case, it appears that product announcements may be acceptable. If so, we would naturally want to announce our own new products in bionet.software. However, a message from biosci-help: Subject: ATTN: BIO-SOFT/bionet.software to be automoderated for spam From: biosci-help@NET.BIO.NET (BIOSCI Administrator) Date: 1997/12/05 Message-ID: Newsgroups: bionet.software, includes the bionet.software charter. This charter concludes with the statement "Use of the newsgroup for commercial purposes is prohibited." It is hard to see how the above product announcement could be acceptable under this charter. I am anxious that a level playing field be established at bionet.software for competing commercial interests, and would appreciate clarification of this issue. I am sending this message to bio-soft@net.bio.net as this is the email address listed for moderation and there is no individual moderator or discussion leader listed for bionet.software. Thank you for your attention. Sincerely, Tim Burland VP & General Manager DNASTAR Inc 1228 South Park St Madison WI 53715 608 258 7420 From owner-software@net.bio.net Fri Dec 05 22:00:00 1997 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!208.134.241.18!newsfeed.internetmci.com!4.1.16.34!cpk-news-hub1.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!news.alt.net!ix.netcom.com!news From: James C. Hoffman Newsgroups: bionet.software Subject: Tech writer produces medical catalogs Date: Sat, 06 Dec 1997 10:30:51 GMT Organization: Netcom Lines: 8 Message-ID: <66b9h2$dqd@sjx-ixn10.ix.netcom.com> NNTP-Posting-Host: rvl-md1-18.ix.netcom.com X-NETCOM-Date: Sat Dec 06 2:30:58 AM PST 1997 X-Newsreader: NETCOMplete/3.2 Hi-I'm a technical writer that can help you with your medical catalog and documentation needs and I can also put them online. E-mail me back at tdsjms@ix.netcom.com if interested. You can see a sample of my work on my home page at http://www2.netcom.com/~tdsjms/hofftek.html It is under construction, but the programming and documentation pages are available. I have experience in just about any system. Thanks. Joan From owner-software@net.bio.net Fri Dec 05 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!ais.net!vixen.cso.uiuc.edu!ux4.cso.uiuc.edu!h-yao From: hung-chang yao Newsgroups: bionet.software Subject: looking for software for DNA/RNA probe/primer selection Date: Sat, 6 Dec 1997 15:08:41 -0600 Organization: University of Illinois at Urbana-Champaign Lines: 7 Message-ID: NNTP-Posting-Host: ux4.cso.uiuc.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: h-yao@ux4.cso.uiuc.edu I am looking for a software for selecting proper primer or probe for PCR or other molecular biology purposes. Softwares for Win95 is preferred. Your help is highly appreciated. Humphrey h-yao@uiuc.edu From owner-software@net.bio.net Sat Dec 06 22:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!ais.net!news1.chicago.iagnet.net!iagnet.net!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Commercial activity on bionet Date: 7 Dec 1997 02:53:07 GMT Organization: Biology, Indiana University - Bloomington Lines: 25 Message-ID: <66d32j$4gb$1@dismay.ucs.indiana.edu> References: <3.0.3.32.19971205165259.0092f600@198.150.22.9> NNTP-Posting-Host: chipmunk.bio.indiana.edu My recollection is that Howard Cash (GeneCodes) may well have done this kind of thing before: strained or broken the biosci/bionet rules prohibiting commercial annoucements. I and probably other readers would welcome a move toward the usenet style, to allow restrained commercial announcements of products that are closely relevant to a newsgroup topic (biology software here). We all know now how bad unrestrained commercial posting can get, and the move to automoderate the bionet groups is great. But those of us who read here also are generally interested in learning of new commercial products in relevant to biocomputing. If the readership consensus is not to allow commercial postings though, Tim's point that GeneCodes should be restricted from further such posts is well made. -- Don (personnally I also think Howard C. should be censored for sounding like he is jumping from a floundering MacOS ship, though I suppose he just meant to say his company is adding another OS choice.) -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Sun Dec 07 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!rill.news.pipex.net!pipex!uunetukout!join.news.pipex.net!pipex!uunetukin!server1.netnews.ja.net!news.nott.ac.uk!Fergus.Doherty From: Fergus.Doherty@nottingham.ac.uk (Fergus Doherty) Newsgroups: bionet.software Subject: PEST finding software? Date: Mon, 08 Dec 1997 15:45:10 +0000 Organization: Nottingham University Lines: 9 Message-ID: NNTP-Posting-Host: wmbpm8.nottingham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 Anyone know of a site that provides a service searching for PEST sequences? -- Fergus Doherty, School of Biomedical Sciences, Nottingham University, Fergus.Doherty@nottingham.ac.uk 0115 970 9366 (74-41366 internal) From owner-software@net.bio.net Sun Dec 07 22:00:00 1997 Message-ID: <348BF35C.A8C9CD80@decode.is> Date: Mon, 08 Dec 1997 13:17:16 +0000 From: "Daníel Óskarsson" Organization: deCode genetics X-Mailer: Mozilla 4.03 [en] (WinNT; I) MIME-Version: 1.0 Newsgroups: bionet.software Subject: Looking for a sequence editor that runs under windows. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: 193.4.145.222 Lines: 17 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!193.10.88.112!newsfeed.sunet.se!news99.sunet.se!news01.sunet.se!193.4.58.52.MISMATCH!news.isnet.is!news.vortex.is!193.4.145.222 I am looking for a sequence editing software that runs under windows, It would be a plus if it could also run on macs. I have tried prophet and heard about DNASIS. I would like to have the sequence to sequence plot abilities from DNASIS. --------------------------------------------------------------------------- Daniel Oskarsson Tel: (354) 5701963 daniel@decode.is Fax: (354) 5701903 URL: http://www.decode.is --------------------------------------------------------------------------- From owner-software@net.bio.net Sun Dec 07 22:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software Subject: Re: Commercial activity on bionet Date: 08 Dec 1997 09:21:46 +0000 Organization: The Sanger Centre Lines: 29 Sender: pmr@unst.sanger.ac.uk Message-ID: References: <3.0.3.32.19971205165259.0092f600@198.150.22.9> <66d32j$4gb$1@dismay.ucs.indiana.edu> NNTP-Posting-Host: unst.sanger.ac.uk X-Newsreader: Gnus v5.5/Emacs 20.2 gilbertd@bio.indiana.edu (Don Gilbert) writes: > I and probably other readers would welcome a move toward the usenet style, > to allow restrained commercial announcements of products that are > closely relevant to a newsgroup topic (biology software here). > We all know now how bad unrestrained commercial posting can > get, and the move to automoderate the bionet groups is great. > But those of us who read here also are generally interested > in learning of new commercial products in relevant to biocomputing. In addition to bionet.software.* I also read the soc.genealogy.* newsgroups, where brief announcements of new software releases are accepted without complaint. These are usually brief release notes and a URL. There may be flames from dissatisfied customers, but not from competitors. I find announcements useful. They should be "legal, decent, honest and truthful" to quote UK advertising codes. Of course, if they are not then the resulting flame war should be enough to put any company off posting again :-) -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-software@net.bio.net Sun Dec 07 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!newsfeed.internetmci.com!164.67.42.145!awabi.library.ucla.edu!132.239.254.208!ihnp4.ucsd.edu!munnari.OZ.AU!harbinger.cc.monash.edu.au!newshost.carno.net.au!not-for-mail From: JohnA@rsbs-central.anu.edu.au (John Armstrong) Newsgroups: bionet.software Subject: Re: looking for software for DNA/RNA probe/primer selection Date: Mon, 08 Dec 1997 02:58:58 GMT Lines: 12 Message-ID: <66fk4f$pgg$1@clarion.carno.net.au> References: NNTP-Posting-Host: 150.203.38.97 X-Newsreader: Forte Free Agent 1.0.82 hung-chang yao wrote: >I am looking for a software for selecting proper primer or probe for PCR >or other molecular biology purposes. Softwares for Win95 is preferred. >Your help is highly appreciated. >Humphrey >h-yao@uiuc.edu You might like to try our package GPRIME, details can be found at http://life.anu.edu.au/molecular/software/gprime.html From owner-software@net.bio.net Sun Dec 07 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!enews.sgi.com!news.idt.net!wuff.mayn.de!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!jkb From: jkb@mrc-lmb.cam.ac.uk (James Bonfield) Newsgroups: bionet.software,bionet.software.staden Subject: Staden Package: new 1997.1 release Date: 8 Dec 1997 15:45:21 GMT Organization: MRC Laboratory of Molecular Biology, Cambridge UK Lines: 54 Distribution: world Message-ID: <66h4mh$orc$1@lyra.csx.cam.ac.uk> NNTP-Posting-Host: alf2.mrc-lmb.cam.ac.uk Xref: biosci bionet.software:20105 bionet.software.staden:581 The latest release of the Staden Package (1997.1) has just been released. The most important features of this release are listed below, although the complete changes (of which there are many more than listed below) are on our web pages at: http://www.mrc-lmb.cam.ac.uk/pubseq/1997.1.html For a quick pictorial overview of the most recent components, see http://www.mrc-lmb.cam.ac.uk/pubseq/screendumps.html James Bonfield 1997.1 Release Notes Summary ---------------------------- An entirely new program named Nip4 is now available. This is the first release of our replacement for nip (the Nucleotide Investigation Program). The key features are a good graphical user interface, methods to import external data and algorithms, and direct communication with Gap4. Nip4 is designed to allow tight integration of third parties algorithms. The organisation of the code makes it straightforward for other groups to add their own algorithms to the programs. Coupled with our use of dynamic loading this means that these additional functions can be made available as compiled code by their authors, hence allowing them to retain complete control of their distribution. We believe this will be an attractive option for many people developing new algorithms: they can concentrate on the algorithms without worrying about the user interface, and they can make them available as an additional option to a (we wish!) widely used program. Further documentation on the processes involved will be made available in the new year, however we are interested in feedback on this topic now. Gap4: * Many bug fixes * Automatic contig ordering function * Find internal join (and other) result auto-navigation * Improved editor search methods (by quality, discrepancies, and from file). * Communication mechanism to allow direct manipulation linking of cursors in Gap4 and external programs. (This is currently possible between Gap4 and Nip4). -- James Bonfield (jkb@mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 213556 Medical Research Council - Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, England. Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/ From owner-software@net.bio.net Sun Dec 07 22:00:00 1997 Message-ID: <348BF3F9.D2520E5@decode.is> Date: Mon, 08 Dec 1997 13:19:53 +0000 From: "Daníel Óskarsson" Organization: deCode genetics X-Mailer: Mozilla 4.03 [en] (WinNT; I) MIME-Version: 1.0 Newsgroups: bionet.software Subject: GapBlast->HTML ? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: 193.4.145.222 Lines: 17 Path: biosci!agate!howland.erols.net!EU.net!news.isnet.is!news.vortex.is!193.4.145.222 Hello Does anyone know of a script that formats gap-blast output into a "nice" HTML format similar to the one that gap-blast querys at NCBI return? -- --------------------------------------------------------------------------- Daniel Oskarsson Tel: (354) 5701963 daniel@decode.is Fax: (354) 5701903 URL: http://www.decode.is --------------------------------------------------------------------------- From owner-software@net.bio.net Sun Dec 07 22:00:00 1997 Path: biosci!rutgers!uwm.edu!news-penn.gip.net!news-peer.gip.net!news.gsl.net!gip.net!ais.net!newsfeed.concentric.net!global-news-master From: Ketchup*REMOVE*@concentric.net (ketchup) Newsgroups: bionet.software Subject: Re: Looking for a sequence editor that runs under windows. Date: Mon, 08 Dec 1997 18:39:05 GMT Organization: Concentric Internet Services Lines: 27 Message-ID: <66hefk$4dg@examiner.concentric.net> References: <348BF35C.A8C9CD80@decode.is> NNTP-Posting-Host: ts001d42.cup-ca.concentric.net X-Newsreader: Forte Free Agent 1.0.82 Have a look at GeneDoc, though there is no direct MAC version. http://www.cris.com/~ketchup/genedoc.shtml Karl. >I am looking for a sequence editing software that runs under windows, It >would be a plus >if it could also run on macs. >I have tried prophet and heard about DNASIS. I would like to have the >sequence to sequence >plot abilities from DNASIS. >--------------------------------------------------------------------------- >Daniel Oskarsson Tel: (354) 5701963 >daniel@decode.is Fax: (354) 5701903 URL: http://www.decode.is >--------------------------------------------------------------------------- From owner-software@net.bio.net Sun Dec 07 22:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!newsfeed.dacom.co.kr!newsfeed.direct.ca!ais.net!newsfeed.concentric.net!global-news-master From: Ketchup*REMOVE*@concentric.net (ketchup) Newsgroups: bionet.software Subject: Re: looking for software for DNA/RNA probe/primer selection Date: Mon, 08 Dec 1997 18:38:03 GMT Organization: Concentric Internet Services Lines: 26 Message-ID: <66hedm$4dg@examiner.concentric.net> References: <66fk4f$pgg$1@clarion.carno.net.au> NNTP-Posting-Host: ts001d42.cup-ca.concentric.net X-Newsreader: Forte Free Agent 1.0.82 GeneDoc has some simple pattern search abilities for alignments that may be useful to you. http://www.cris.com/~ketchup/genedoc.shtml Karl. JohnA@rsbs-central.anu.edu.au (John Armstrong) wrote: >hung-chang yao wrote: >>I am looking for a software for selecting proper primer or probe for PCR >>or other molecular biology purposes. Softwares for Win95 is preferred. >>Your help is highly appreciated. >>Humphrey >>h-yao@uiuc.edu >You might like to try our package GPRIME, details can be found at >http://life.anu.edu.au/molecular/software/gprime.html From owner-software@net.bio.net Mon Dec 08 22:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!newsfeed.ecrc.net!news.space.net!news.klaus-datentechnik.de!news From: Ben Newsgroups: bionet.software Subject: Harddisk recording Date: Tue, 09 Dec 1997 02:34:10 +0100 Organization: Klaus Datentechnik GmbH Lines: 3 Message-ID: <348CA012.3789B331@wtal.de> NNTP-Posting-Host: modem12.kdt.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (Win95; I) I need to record 12 hours / 8000 Hz / 8 Bit / Mono with SB16. Where I can get software for that ? Who can help ? From owner-software@net.bio.net Mon Dec 08 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!199.60.229.5!newsfeed.direct.ca!fu-berlin.de!uniol!news.uni-stuttgart.de!news From: Martin Ligr Newsgroups: bionet.software Subject: Re: PEST finding software? Date: Tue, 09 Dec 1997 02:05:10 +0100 Organization: Universitaet Stuttgart Lines: 18 Message-ID: <348C9946.41C6@po.uni-stuttgart.de> References: NNTP-Posting-Host: biochem13.chemie.uni-stuttgart.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX 5.3 IP22) Fergus Doherty wrote: > > Anyone know of a site that provides a service searching for PEST sequences? > Try http://www.at.embnet.org/embnet/tools/bio/PESTfind/ ----- Martin Ligr Institut fuer Biochemie Universitaet Stuttgart Pfaffenwaldring 55 D-70569 Stuttgart Germany phone: +49-(0711)-685-4383 fax: +49-(0711)-685-4392 From owner-software@net.bio.net Mon Dec 08 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!is.bbsrc.ac.uk!news From: Martin Trick Newsgroups: bionet.software.acedb,bionet.software Subject: Position: Brassica genome bioinformatics Date: Tue, 09 Dec 1997 16:57:02 -0800 Organization: BBSRC Biotechnology and Biological Sciences Research Council Lines: 72 Message-ID: <348DE8DE.AED326C4@bbsrc.ac.uk> NNTP-Posting-Host: pc0419.jic.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------E2C9E5A0449FBD9592236D6D" X-Mailer: Mozilla 4.03 [en] (Win16; I) Xref: biosci bionet.software.acedb:1543 bionet.software:20112 --------------E2C9E5A0449FBD9592236D6D Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Position: Brassica genome bioinformatics As advertised in New Scientist (6/12/97, p78), applications are invited for a position immediately available at the John Innes Centre, Norwich UK in Brassica Bioinformatics. The successful candidate will curate and further develop a Brassica genome database funded by the UK BBSRC UKCropNet initiative (http://synteny.nott.ac.uk). A key aim is to integrate genetic data from Brassica which can be integrated with that from the closely related Arabidopsis genome. A degree in a biological subject with a strong background in genetics is required, together with an interest and aptitude in applying database methods to facilitate genome research. Experience of any of UNIX, Perl or Java would be an advantage. The post is available for approximately two years and will be appointed between £13860 and £16500 (Band 7), at a level depending on qualifications and experience. For further information please contact Martin Trick (tel: +44 1603 452571 or martin.trick@bbsrc.ac.uk) or see www.uea.ac.uk/nrp/jic/b90trick.htm. For written particulars and an application form, please contact the Personnel Officer (jicpers@bbsrc.ac.uk), John Innes Centre, Norwich Research Park, Colney, Norwich, Norfolk, NR4 7UH, quoting reference number BR/330. The closing date for application forms will be 5th January 1998. Interviews are expected to be held February 4-5 1998. The John Innes Centre is a registered charity (No. 511709) grant-aided by the Biotechnology and Biological Sciences Research Council and is an Equal Opportunities Employer. --------------E2C9E5A0449FBD9592236D6D Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit             Position: Brassica genome bioinformatics

As advertised in New Scientist (6/12/97, p78), applications are invited for a position  immediately available at the John Innes Centre, Norwich UK in Brassica Bioinformatics.
The successful candidate will curate and further develop a Brassica genome database funded by the UK BBSRC UKCropNet initiative (http://synteny.nott.ac.uk). A key aim is to integrate genetic data from Brassica which can be integrated with that from the closely related Arabidopsis genome. A degree in a biological subject with a strong background in genetics is required, together with an interest and aptitude in applying database methods to facilitate genome research. Experience of any of UNIX, Perl or Java would be an advantage.

The post is available for approximately two years and will be appointed between £13860 and £16500 (Band 7), at a level depending on qualifications and experience. For further information please contact Martin Trick (tel: +44 1603 452571 or martin.trick@bbsrc.ac.uk) or see www.uea.ac.uk/nrp/jic/b90trick.htm. For written particulars and an application form, please contact the Personnel Officer (jicpers@bbsrc.ac.uk), John Innes Centre, Norwich Research Park, Colney, Norwich, Norfolk, NR4 7UH, quoting reference number BR/330. The closing date for application forms will be 5th January 1998. Interviews are expected to be held February 4-5 1998.

The John Innes Centre is a registered charity (No. 511709) grant-aided  by the Biotechnology and Biological Sciences Research Council and is an Equal Opportunities Employer. --------------E2C9E5A0449FBD9592236D6D-- From owner-software@net.bio.net Mon Dec 08 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!199.60.229.5!newsfeed.direct.ca!feed2.news.erols.com!winter.news.erols.com!not-for-mail From: "Jeff Reidler" Newsgroups: bionet.software Subject: Commercial Image Software FREE Date: Mon, 8 Dec 1997 21:25:23 -0200 Organization: Erol's Internet Services Lines: 10 Message-ID: <66iaao$gfj$1@winter.news.erols.com> References: <3.0.3.32.19971205165259.0092f600@198.150.22.9> <66d32j$4gb$1@dismay.ucs.indiana.edu> NNTP-Posting-Host: fdk-as6s40.erols.com X-Trace: winter.news.erols.com 881634456 16883 207.172.145.167 (9 Dec 1997 02:27:36 GMT) X-Complaints-To: abuse@erols.com X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Scion Corporation has just released FREE software for image analysis and processing for Mac and Windows 95 and NT on their website http://www.scioncorp.com for immediate download. These programs are derived from NIH Image and extended to 24 bit color acquisition. From owner-software@net.bio.net Tue Dec 09 22:00:00 1997 Path: biosci!rutgers!gatech!205.252.116.205.MISMATCH!howland.erols.net!newsfeed.internetmci.com!164.67.42.145!awabi.library.ucla.edu!132.239.254.208!ihnp4.ucsd.edu!munnari.OZ.AU!harbinger.cc.monash.edu.au!pellew.ntu.edu.au!usenet From: Garry Myers Newsgroups: bionet.software Subject: dotplot software Date: Wed, 10 Dec 1997 15:17:22 +0930 Organization: Menzies School of Health Research Lines: 19 Message-ID: <348E2CE9.13350B0C@menzies.su.edu.au> NNTP-Posting-Host: krypton.menzies.su.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; U) X-Priority: 3 (Normal) Hi, I'm looking for software to perform dotplots either on a Windows platform or SunOS4.1.3. I'm aware of (and would like to use) Dotter (Unix) but can't get it compiled under 4.1.3 (does anyone has a 4.1.3 binary?). I use compare + dotplot under GCG v8.1 currently but wish to run something locally. Cheers, Garry. --- Garry Myers Molecular Genetics Unit Menzies School of Health Research Australia From owner-software@net.bio.net Tue Dec 09 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!131.103.1.116!news2.chicago.iagnet.net!iagnet.net!newsfeed.direct.ca!Supernews60!supernews.com!ixa.net!news.aa.net!not-for-mail From: psewell@aa.net (Paul Sewell) Newsgroups: bionet.software Subject: shareware Date: Wed, 10 Dec 1997 05:34:01 GMT Organization: Alternate Access Inc. Lines: 30 Message-ID: <348e29c0.5399323@news.aa.net> NNTP-Posting-Host: 204.157.220.10 X-Newsreader: Forte Free Agent 1.11/32.235 Cache-Post-Path: moon.aa.net!unknown@cust171.pm6.everett.aa.net happy holidays where ever you are......:-) Why not take the time to come and visit The Jumpgate. http://www.aa.net/~psewell A vast file area for you to browse and download many useful and interesting programs. The screen savers area has over 200 files including some great Christmas ones for the upcoming festive season. The desktop themes area has a large amout of themes and utilities to suit all tastes. Come and chat in The Jumpgates chat room where there is allways a good social gathering.. Other areas include Quake , babylon 5 , Music and Formula 1 Grand Prix 2. A forum and message board will be added within the next week. The Jumpgate is updated on a daily bases so when you arrive enter your e-mail address and subscribe to The Jumpgates update newsletter. Dont forget to sign the guest book and let me know what you think of my site and if you have any comments or ideas to improve The Jumpgate. Hope to see you there soon... Thanks for your time. Paul Sewell Http://www.aa.net/~psewell From owner-software@net.bio.net Tue Dec 09 22:00:00 1997 Path: biosci!agate!ihnp4.ucsd.edu!munnari.OZ.AU!news.mel.connect.com.au!news.syd.connect.com.au!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!news-peer.gip.net!news.gsl.net!gip.net!portc01.blue.aol.com!newstf02.news.aol.com!audrey02.news.aol.com!not-for-mail From: yoroya@aol.com (Yoroya) Newsgroups: bionet.software Subject: PC-based Image Analysis Software Date: 10 Dec 1997 04:29:24 GMT Lines: 20 Message-ID: <19971210042901.XAA25619@ladder02.news.aol.com> NNTP-Posting-Host: ladder02.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com Dear biomedical researcher/clinical diagnostician: "Inquiry" is a PC-based image analysis package that can analyze whole-body, receptor, and metabolic autoradiographic images, chromosome spreads for morphometric karyotyping, 1-D and 2-D electrophoretic gels for densitometric analysis, images for quantitative in situ hybridization studies, images for 3-D tumor and lesion volume studies, grain counting, and more. This $4,995 image analysis system is the most powerful and versatile one on the market today and only intended for the serious biomedical researcher and clinical diagnostician willing to make an investment in the best that money can buy. Don't be fooled by cheap imitations. Nothing out there can match the quality and versatility of "Inquiry". Visit our website and ask for more information, or contact me directly. Sincerely, Robert L. Hummel Tel: 410-876-8055 Website: http://www.loats.com Sales & Marketing Fax: 410-876-5843 E-mail: loats@loats.com Loats Associates, Inc. 201 East Main Street Westminster, MD 21157 From owner-software@net.bio.net Tue Dec 09 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!Cabal.CESspool!bofh.vszbr.cz!eerie.fr!jussieu.fr!univ-lyon1.fr!newsserver.cilea.it!sirio.cineca.it!menelao.polito.it!pcgen07.molinette.unito.it!graziani From: graziani@molinette.unito.it (Andrea Graziani) Newsgroups: bionet.software Subject: Looking for an image analysis software Date: Wed, 10 Dec 1997 18:07:57 Organization: Politecnico di Torino - Italia Lines: 10 Message-ID: NNTP-Posting-Host: pcgen07.molinette.unito.it X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] Hi, I am looking for a software to do densitometry on gel images already taken by a camera and saved as TIFF files. I capture images from a agarose gel by a Kodak camera, my problem is to quantify the bands, and I do not know how to do it. Thanks If you like you can answer me by e-mail Andrea Graziani From owner-software@net.bio.net Tue Dec 09 22:00:00 1997 Newsgroups: bionet.software Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.131!news-pen-1.sprintlink.net!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsxfer3.itd.umich.edu!rill.news.pipex.net!pipex!uunetukout!server1.netnews.ja.net!server5.netnews.ja.net!leeds.ac.uk!news From: t.j.keen@leeds.ac.uk (T. Jeffrey Keen) Subject: Re: PEST finding software? Message-ID: NNTP-Posting-Host: sjuh-pc146.leeds.ac.uk Organization: Leeds University Date: Wed, 10 Dec 1997 15:35:27 +0000 (GMT) References: X-Newsreader: MT-NewsWatcher 2.3.5 Lines: 9 The most recent version of MacPattern has a PEST sequence search routine. ftp://ftp.ebi.ac.uk/pub/software/mac/macpattern/MacPattern.3.6.sea.hqx In article , Fergus.Doherty@nottingham.ac.uk (Fergus Doherty) wrote: > Anyone know of a site that provides a service searching for PEST sequences? From owner-software@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!daresbury!uninett.no!news-feed.ifi.uio.no!recycled.news.erols.com!howland.erols.net!newsfeed.internetmci.com!152.163.199.19!portc03.blue.aol.com!audrey01.news.aol.com!not-for-mail From: yoroya@aol.com (Yoroya) Newsgroups: bionet.software Subject: Macintosh-based Image Analysis Software Date: 11 Dec 1997 04:45:08 GMT Lines: 19 Message-ID: <19971211044500.XAA00879@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com Dear biomedical researcher/clinical diagnostician: "3-D BrainStation" is a Macintosh-based image analysis package that can analyze anatomical images from CT or MRI scans or metabolic images from PET or SPECT scans. It can also fuse these anatomical and metabolic images thereby acting as a powerful research or diagnostic tool for the neuroscientist or clinician. This $7,500 image analysis system is the most powerful and versatile one on the market today and only intended for the serious biomedical researcher and clinical diagnostician willing to make an investment in the best that money can buy. Don't be fooled by cheap imitations. Nothing out there can match the quality and versatility of "3-D BrainStation". Visit our website and ask for more information, or contact me directly. Sincerely, Robert L. Hummel Tel: 410-876-8055 Sales & Marketing E-mail: loats@loats.com Loats Associates, Inc. URL: http://www.loats.com From owner-software@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!newsfeed.internetmci.com!152.163.199.19!portc03.blue.aol.com!audrey01.news.aol.com!not-for-mail From: yoroya@aol.com (Yoroya) Newsgroups: bionet.software Subject: PC-based Image Analysis System Date: 11 Dec 1997 04:43:08 GMT Lines: 20 Message-ID: <19971211044300.XAA00629@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com Dear biomedical researcher/clinical diagnostician: "Inquiry" is a PC-based image analysis package that can analyze whole-body, receptor, and metabolic autoradiographic images, chromosome spreads for morphometric karyotyping, 1-D and 2-D electrophoretic gels for densitometric analysis, images for quantitative in situ hybridization studies, images for 3-D tumor and lesion volume studies, grain counting, and more. This $4,995 image analysis system is the most powerful and versatile one on the market today and only intended for the serious biomedical researcher and clinical diagnostician willing to make an investment in the best that money can buy. Don't be fooled by cheap imitations. Nothing out there can match the quality and versatility of "Inquiry". Visit our website and ask for more information, or contact me directly. Sincerely, Robert L. Hummel Tel: 410-876-8055 Sales & Marketing E-mail: loats@loats.com Loats Associates, Inc. URL: http://www.loats.com From owner-software@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!howland.erols.net!newsfeed.internetmci.com!152.163.199.19!portc03.blue.aol.com!audrey01.news.aol.com!not-for-mail From: yoroya@aol.com (Yoroya) Newsgroups: bionet.software Subject: Re: Looking for an image analysis software Date: 11 Dec 1997 04:26:30 GMT Lines: 2 Message-ID: <19971211042600.XAA28409@ladder01.news.aol.com> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Organization: AOL http://www.aol.com References: Visit our website at http://www.loats.com and take a look at our PC-based image analysis system entitled, "Inquiry". From owner-software@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!howland.erols.net!winter.news.erols.com!not-for-mail From: "Jeff Reidler" Newsgroups: bionet.software Subject: Re: Looking for an image analysis software Date: Wed, 10 Dec 1997 23:02:31 -0200 Organization: Erol's Internet Services Lines: 12 Message-ID: <66nop6$mts$1@winter.news.erols.com> References: NNTP-Posting-Host: fdk-as2s03.erols.com X-Trace: winter.news.erols.com 881813094 23484 207.172.144.130 (11 Dec 1997 04:04:54 GMT) X-Complaints-To: abuse@erols.com X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Andrea Graziani wrote in message ... >I am looking for a software to do densitometry on gel images already taken by >a camera and saved as TIFF files. You might use the freeware at http://www.scioncorp.com and combine it with the gel doc macros at http://rsb.info/nih.gov/nih-image. You might also subscribe to the nih-image newsgroup and pose the question to the group or leave a message at support@scioncorp.com. Jeff From owner-software@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!agate!newsgate.duke.edu!nntprelay.mathworks.com!newsfeed.internetmci.com!158.43.192.17!rill.news.pipex.net!pipex!uunetukout!server1.netnews.ja.net!news.nott.ac.uk!news.derby.ac.uk!news From: S.Kay1@student.derby.ac.uk (susan Kay) Newsgroups: bionet.software,bionet.users.addresses,alt.comp.dragon,alt.drugs.caffeine Subject: Caffeine......why is this nesgroup empty ?? Date: 11 Dec 1997 04:24:09 GMT Organization: University of Derby Lines: 14 Message-ID: <66npt9$kb3@unix3.derby.ac.uk> NNTP-Posting-Host: ae61.derby.ac.uk Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.8 (16bit) Xref: biosci bionet.software:20125 bionet.users.addresses:3495 Where has everyone gone ? Have you found a new caffeine high ? When should you get worried as to how much caffeine you've had? Is pro plus better than coffee ?? someone respond.... from susan s.kay1@student.derby.ac.uk From owner-software@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!agate!logbridge.uoregon.edu!scanner.worldgate.com!rover.ucs.ualberta.ca!tribune.usask.ca!canopus.cc.umanitoba.ca!not-for-mail From: Brian Fristensky Newsgroups: bionet.software Subject: Re: dotplot software Date: Thu, 11 Dec 1997 12:21:31 -0600 Organization: University of Manitoba Lines: 38 Message-ID: <34902F2B.1496@cc.umanitoba.ca> References: <348E2CE9.13350B0C@menzies.su.edu.au> NNTP-Posting-Host: brassica.cc.umanitoba.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5.1 sun4u) Garry Myers wrote: > I'm looking for software to perform dotplots either on a Windows > platform or SunOS4.1.3. I'm aware of (and would like to use) Dotter > (Unix) but can't get it compiled under 4.1.3 (does anyone has a 4.1.3 > binary?). I use compare + dotplot under GCG v8.1 currently but wish to > run something locally. > > Garry Myers > Molecular Genetics Unit > Menzies School of Health Research Australia The matrix similarity search programs from the FSAP package will do what you want. The matrix is printed with characters, rather than high-resolution graphics. This has two advantages: 1) output can be printed on any printer 2) a character scoring scheme, originated by Jim Ostell, gives you more information than dots do. Most FSAP programs can be run from GDE. SUN Solaris executables, as well as C source code, are available. You find out more about the FSAP package at http://home.cc.umanitoba.ca/~psgendb/FSAP.html =============================================================================== Brian Fristensky | Department of Plant Science | "Computers are useless: University of Manitoba | All they give you are answers." Winnipeg, MB R3T 2N2 CANADA | frist@cc.umanitoba.ca | Pablo Picasso Office phone: 204-474-6085 | FAX: 204-474-7528 | http://home.cc.umanitoba.ca/~frist/ =============================================================================== From owner-software@net.bio.net Wed Dec 10 22:00:00 1997 From: jeanne.sparrow@channing.harvard.edu Subject: Looking for biologic specimen tracking software Date: Thu, 11 Dec 1997 13:12:35 -0600 Message-ID: <881867011.1607991301@dejanews.com> Newsgroups: bionet.software,bionet.general,sci.bio.technology,sci.med.laboratory Organization: Deja News Posting Service Path: biosci!agate!newsgate.duke.edu!nntprelay.mathworks.com!news.maxwell.syr.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Thu Dec 11 19:03:31 1997 GMT X-Authenticated-Sender: jeanne.sparrow@channing.harvard.edu X-Http-User-Agent: Mozilla/3.01 (X11; I; SunOS 5.5 sun4m) X-Originating-IP-Addr: 134.174.249.40 (wirth.bwh.harvard.edu) Lines: 13 Xref: biosci bionet.software:20128 bionet.general:28893 I am looking for data management software to track storage of biologic specimens. Desired functions include receiving, recording, storing, retreiving and tracking of samples in a multiuser setting. Especially interested in systems using newer technologies - client/server, SQL. PC or UNIX. Positive and/or negative comments about your system also appreciated. Jeanne Sparrow Channing Lab/Brigham and Women's Hospital Boston -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-software@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!Cabal.CESspool!bofh.vszbr.cz!eerie.fr!jussieu.fr!univ-lyon1.fr!newsserver.cilea.it!sirio.cineca.it!menelao.polito.it!not-for-mail From: antonio Newsgroups: bionet.software Subject: cerco ICQ Date: Thu, 11 Dec 1997 13:53:32 +0100 Organization: inrete Lines: 2 Message-ID: <348FE24C.6D93B259@inrete.it> NNTP-Posting-Host: dial102.inrete.it Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (Win95; I) dove posso trovare ICQ!! grazie grazie From owner-software@net.bio.net Wed Dec 10 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.algonet.se!fci-se!fci!nntprelay.mathworks.com!newsgate.duke.edu!news-relay.ncren.net!ussun2n!news@ussun2n.glaxo.com From: "Gary H. Merrill" Newsgroups: bionet.info-theory,bionet.software,sci.cognitive,comp.ai,comp.ai.nat-lang,comp.ai.neural-nets,comp.cog-eng,sci.med.informatics Subject: CFP: AAAI Workshop on Knowledge Sharing Across Biological and Medical KBS Date: Thu, 11 Dec 1997 13:12:47 -0500 Organization: GlaxoWellcome Inc Lines: 80 Message-ID: <34902D1F.6E2A@glaxowellcome.com> Reply-To: ghm48805@glaxowellcome.com NNTP-Posting-Host: 152.51.45.146 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (WinNT; I) Xref: biosci bionet.info-theory:5811 bionet.software:20126 TITLE AAAI-98 Workshop on KNOWLEDGE SHARING ACROSS BIOLOGICAL AND MEDICAL KNOWLEDGE BASED SYSTEMS DATE AND LOCATION National Conference on Artificial Intelligence (AAAI-98) in Madison, Wisconsin, July 26 - July 27, 1998. See the AAAI web site at http://www.aaai.org for additional details. DESCRIPTION The amount of biological and medical information is growing at an exponential rate and overwhelming researchers and clinicians. Various groups have applied the technology of knowledge base systems to help in the effective utilization of available information. These systems have been used for applications in information retrieval, natural language processing, database integration, machine learning, data mining, and decision-making. While there is a substantial overlap of knowledge represented in these knowledge based systems there has been very limited dialog among the various groups creating these systems. This one-day workshop explores ways in which the knowledge contained in the various systems can be shared. Specifically, the workshop goals include: 1. Understanding the scope of knowledge contained in various knowledge based systems in biology and medicine. 2. Understanding strengths and limitations of different knowledge representation formalisms, inference engines, and knowledge acquisition methods for biological and medical systems. 3. Identifying strategies for knowledge sharing across different development groups as we move toward more comprehensive knowledge bases for researchers and clinicians in biology and medicine. SUBMISSIONS Potential presenters should submit a short paper (up to 5-8 pages) addressing any of the issues relevant to the workshop goals. Others interested in participating should submit a 1-2 page statement of background and interest. E-mail in PostScript or MS Word format to Dhiraj K. Pathak at dp33010@glaxowellcome.com. Submission Deadline: March 11, 1998 Notification Date: April 1, 1998 ORGANIZING COMMITTEE Dhiraj K. Pathak, Glaxo Wellcome (Co-chair) (dp33010@glaxowellcome.com) Gary H. Merrill, Glaxo Wellcome (Co-chair) (ghm48805@glaxowellcome.com) Carol Bean, National Library of Medicine (bean@nlm.nih.gov) Andy Brass, University of Manchester (abrass@manchester.ac.uk) Ed Hammond, Duke University (hammo001@mc.duke.edu) Rober Jenders, Columbia University (jenders@cucis.cis.columbia.edu) -- Gary H. Merrill Principal Consultant Information Access Technology (919) 483-0973 ghm48805@glaxowellcome.com From owner-software@net.bio.net Thu Dec 11 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!128.174.5.49!vixen.cso.uiuc.edu!news.indiana.edu!news.iupui.edu!not-for-mail From: "Charlie Mantel" Newsgroups: bionet.software Subject: Re: dotplot software (**FREE**) Date: Thu, 11 Dec 1997 20:47:23 -0500 Organization: Indiana University - Purdue Univeristy At Indianapols,IN Lines: 20 Message-ID: <66q59v$14a$1@hercules.iupui.edu> References: <348E2CE9.13350B0C@menzies.su.edu.au> NNTP-Posting-Host: c1p35.dialin.iupui.edu X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Try going to the homepage of Scripps Inst. There is a whole bunche of software available **FREE** at their site of flow cytometry software links. The one I use is WinMDI (the mdi stands for "multiple document interface"....and it works GREAT!!! I use it every day. It does 2d or 3d dotplots and also histograms.....just try it,,,you'll see. :) Garry Myers wrote in message <348E2CE9.13350B0C@menzies.su.edu.au>... >Hi, > >I'm looking for software to perform dotplots either on a Windows >platform or SunOS4.1.3. I'm aware of (and would like to use) Dotter >(Unix) but can't get it compiled under 4.1.3 (does anyone has a 4.1.3 >binary?). I use compare + dotplot under GCG v8.1 currently but wish to >run something locally. > > From owner-software@net.bio.net Thu Dec 11 22:00:00 1997 Path: biosci!GENOME.BIOTECH.WASHINGTON.EDU!eugene From: eugene@GENOME.BIOTECH.WASHINGTON.EDU (Eugene Kolker) Newsgroups: bionet.software Subject: Recomb98: list of accepted papers Date: 12 Dec 1997 10:09:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 168 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712121808.KAA29610@genome.biotech.washington.edu> NNTP-Posting-Host: net.bio.net The following 38 papers were selected by the RECOMB98 Program Committee for presentations among 123 submissions. For more details please visit our web site: http://www.mssm.edu/biomath/recomb98.html PAPER 001 P. Agarwal, V. Bafna Detecting non-adjoining correlations within signals in DNA. PAPER 002 A. Ben-Dor, B. Chor, D. Graur, R. Ophir, D. Pelleg From four-taxon trees to phylogenies: The case of mammalian evolution. PAPER 003 G. Benson An Algorithm for Finding Tandem Repeats of Unspecified Pattern. PAPER 004 B. Berger, T. Leighton Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete. PAPER 005 M. Bonet, M. Steel, T. Warnow, S. Yooseph Better Methods for Solving Parsimony and Compatiblity. PAPER 006 C. C. Chen, J. P. Singh, R. B. Altman The Hierarchical Organization of Molecular Structure Computations. PAPER 007 P. Crescenzi, D. Goldman, C. Papadimitriou, A. Piccolboni, M. Yannakakis On the Complexity of Protein Folding. PAPER 008 D. Fasulo, T. Jiang, R. M. Karp, N. Sharma Constructing Maps Using the Span and Inclusion Relations. PAPER 009 A. V. Finkelstein, A. Ya. Badretdinov How Fast a Protein Chain Can Fold to Its Most Stable Structure? PAPER 010 R. M. Fye, C. J. Benham A Formally Exact Method to Numerically Analyze Local Denaturation in Superhelical DNA PAPER 011 I. Gelfand, A. Kister, C. Kulikowski, O. Stoyanov Algorithmic Determination of Core Positions in the VL and VH Domains of Immunoglobulin Molecules PAPER 012 R. A. Goldstein, J. M. Koshi, D. P. Mindell Beyond mutation matrices: Physical-Chemistry based evolutionary models. PAPER 013 W. N. Grundy Family-based Homology Detection via Pairwise Sequence Comparison. PAPER 014 I. Holmes, R. Durbin Dynamic Programmimg Alignment Accuracy. PAPER 015 T. Hwa, M. Lassig Optimal Detection of Sequence Similarity by Local Alignment. PAPER 016 R. M. Karp, R.Shamir Algorithms for Optical Mapping. PAPER 017 P. E. Kearney Ordinal Beats Additive. PAPER 018 E. Koonin, R. Tatusov, M.Y. Galperin, M.N. Rozanov Genome analysis using clusters of orthologous groups (COGs). PAPER 019 J. K. Lee, V. Dancik, M. S. Waterman Estimation for restriction sites observed by optical mapping using reversible-jump markov chain monte carlo. PAPER 020 H. Lenhof, K. Reinert, M. Vingron A Polyhedral Approach to RNA Sequence Structure Alignment. PAPER 021 A. M. Lesk Assessment of Ab Initio Protein Structure Prediction. PAPER 022 R. Liu, T. W. Blackwell, D. J. States A structure based similarity measure for nucleic acid sequence comparison. PAPER 023 B. Ma, M. Li, L. Zhang On Reconstructing Species Trees From Gene Trees In Term of Duplications PAPER 024 L. Parida, B. Mishra Partitioning K Clones: Hardness Results and a Practical Solution to the K-Popultaions Problem. PAPER 025 D. G. Politte, D. R. Maffitt, D. J. States Estimaiton of Allele Frequencies From Color-Multiplexed Electropherograms. PAPER 026 M. Regnier A Unified Approach to Word Statistics PAPER 027 B. A. Reva, A. V. Finkelstein, J. Skolnick A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins. PAPER 028 I. Rigoutsos, A. Floratos Motif Discovery in Biological Sequences Without Alignment or Enumeration. PAPER 029 E. Rocke, M. Tompa An Algorithm for Finding Novel Gapped Motifs in DNA sequences. PAPER 030 M. Sagot, E. W. Myers Identifying satellites in nucleic acid sequences. PAPER 031 D. Sankoff, M. Blanchette Multiple genome rearrangement. PAPER 032 F. Sun Modeling DNA shuffling. PAPER 033 S. R. Sunyaev, I. V. Rodchenkov Analysis of the Position Dependent Amino Acid Probabilities and its Application to the Search for Remote Homologues. PAPER 034 A. Vologodskii Maxwell demon and topology simplification by type II topoisomerases. PAPER 035 W. L.Walker, D. S. Goodsell, E. M.Landaw The Theoretical Limits of DNA sequence discrimination of Polyamides. PAPER 036 T. D. Wu, S. C. Schmidler, T. Hastie, D. L. Brutlag Regression Analysis of Multiple Protein Structures PAPER 037 Y. Xu, D. Xu, E. C. Uberbacher A New Method for modeling and solving the protein fold recognition problem. PAPER 038 Z. Zhang, P. Berman, W. Miller Alignments Without Low-Scoring Regions. If you do NOT want to be in our mailing list, please reply with Subject line "Recomb98: remove". Sorry, if you get this mail twice. From owner-software@net.bio.net Thu Dec 11 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!141.211.144.13!newsxfer3.itd.umich.edu!news2.chicago.iagnet.net!iagnet.net!129.79.5.185!news.indiana.edu!news.iupui.edu!not-for-mail From: "Charlie Mantel" Newsgroups: bionet.software Subject: Re: Looking for an image analysis software Date: Thu, 11 Dec 1997 20:50:39 -0500 Organization: Indiana University - Purdue Univeristy At Indianapols,IN Lines: 19 Message-ID: <66q5a0$14a$2@hercules.iupui.edu> References: NNTP-Posting-Host: c1p35.dialin.iupui.edu X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Try doing a web search for a program called "Image Tool". I found it somewhere,,,i cant rememeber,,,,and d/l for free trial,,,,it works great for gels. Andrea Graziani wrote in message ... >Hi, >I am looking for a software to do densitometry on gel images already taken by >a camera and saved as TIFF files. I capture images from a agarose gel by a >Kodak camera, my problem is to quantify the bands, and I do not know how to do >it. >Thanks > If you like you can answer me by e-mail > > Andrea Graziani > From owner-software@net.bio.net Thu Dec 11 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!ais.net!news-out.internetmci.com!newsfeed.internetmci.com!198.82.160.249!solaris.cc.vt.edu!newsgate.duke.edu!news-relay.ncren.net!nntp-xfer.ncsu.edu!not-for-mail From: Burkhard Morgenstern Newsgroups: bionet.software Subject: alignment program DIALIGN 2 online Date: Fri, 12 Dec 1997 11:29:16 -0500 Organization: North Carolina State University Lines: 21 Message-ID: <3491665C.5DD3@gsf.de> NNTP-Posting-Host: poole.statgen.ncsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5.1 sun4u) We would like to announce the release of DIALIGN 2, an improved version of our novel alignment program DIALIGN. The method was originally described in B. Morgenstern, T. Werner, A.W.M. Dress (1996), "Multiple DNA and protein sequence alignment based on segment-to-segment comparison." Proc. Natl. Acad. Sci. USA, 93, 12098 - 12103. Unlike global alignment methods, DIALIGN is capable of finding local similarities among distantly related sequences. An online version of DIALIGN 2 is available at http://bibiserv.TechFak.Uni-Bielefeld.DE/dialign/ If you have any comments, suggestions or criticism on DIALIGN, please feel free to contact us! Burkhard Morgenstern From owner-software@net.bio.net Thu Dec 11 22:00:00 1997 Path: biosci!GENOME.BIOTECH.WASHINGTON.EDU!eugene From: eugene@GENOME.BIOTECH.WASHINGTON.EDU (Eugene Kolker) Newsgroups: bionet.software Subject: Recomb98: list of accepted papers Date: 12 Dec 1997 10:09:12 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 168 Sender: daemon@net.bio.net Distribution: world Message-ID: <199712121808.KAA29612@genome.biotech.washington.edu> NNTP-Posting-Host: net.bio.net The following 38 papers were selected by the RECOMB98 Program Committee for presentations among 123 submissions. For more details please visit our web site: http://www.mssm.edu/biomath/recomb98.html PAPER 001 P. Agarwal, V. Bafna Detecting non-adjoining correlations within signals in DNA. PAPER 002 A. Ben-Dor, B. Chor, D. Graur, R. Ophir, D. Pelleg From four-taxon trees to phylogenies: The case of mammalian evolution. PAPER 003 G. Benson An Algorithm for Finding Tandem Repeats of Unspecified Pattern. PAPER 004 B. Berger, T. Leighton Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete. PAPER 005 M. Bonet, M. Steel, T. Warnow, S. Yooseph Better Methods for Solving Parsimony and Compatiblity. PAPER 006 C. C. Chen, J. P. Singh, R. B. Altman The Hierarchical Organization of Molecular Structure Computations. PAPER 007 P. Crescenzi, D. Goldman, C. Papadimitriou, A. Piccolboni, M. Yannakakis On the Complexity of Protein Folding. PAPER 008 D. Fasulo, T. Jiang, R. M. Karp, N. Sharma Constructing Maps Using the Span and Inclusion Relations. PAPER 009 A. V. Finkelstein, A. Ya. Badretdinov How Fast a Protein Chain Can Fold to Its Most Stable Structure? PAPER 010 R. M. Fye, C. J. Benham A Formally Exact Method to Numerically Analyze Local Denaturation in Superhelical DNA PAPER 011 I. Gelfand, A. Kister, C. Kulikowski, O. Stoyanov Algorithmic Determination of Core Positions in the VL and VH Domains of Immunoglobulin Molecules PAPER 012 R. A. Goldstein, J. M. Koshi, D. P. Mindell Beyond mutation matrices: Physical-Chemistry based evolutionary models. PAPER 013 W. N. Grundy Family-based Homology Detection via Pairwise Sequence Comparison. PAPER 014 I. Holmes, R. Durbin Dynamic Programmimg Alignment Accuracy. PAPER 015 T. Hwa, M. Lassig Optimal Detection of Sequence Similarity by Local Alignment. PAPER 016 R. M. Karp, R.Shamir Algorithms for Optical Mapping. PAPER 017 P. E. Kearney Ordinal Beats Additive. PAPER 018 E. Koonin, R. Tatusov, M.Y. Galperin, M.N. Rozanov Genome analysis using clusters of orthologous groups (COGs). PAPER 019 J. K. Lee, V. Dancik, M. S. Waterman Estimation for restriction sites observed by optical mapping using reversible-jump markov chain monte carlo. PAPER 020 H. Lenhof, K. Reinert, M. Vingron A Polyhedral Approach to RNA Sequence Structure Alignment. PAPER 021 A. M. Lesk Assessment of Ab Initio Protein Structure Prediction. PAPER 022 R. Liu, T. W. Blackwell, D. J. States A structure based similarity measure for nucleic acid sequence comparison. PAPER 023 B. Ma, M. Li, L. Zhang On Reconstructing Species Trees From Gene Trees In Term of Duplications PAPER 024 L. Parida, B. Mishra Partitioning K Clones: Hardness Results and a Practical Solution to the K-Popultaions Problem. PAPER 025 D. G. Politte, D. R. Maffitt, D. J. States Estimaiton of Allele Frequencies From Color-Multiplexed Electropherograms. PAPER 026 M. Regnier A Unified Approach to Word Statistics PAPER 027 B. A. Reva, A. V. Finkelstein, J. Skolnick A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins. PAPER 028 I. Rigoutsos, A. Floratos Motif Discovery in Biological Sequences Without Alignment or Enumeration. PAPER 029 E. Rocke, M. Tompa An Algorithm for Finding Novel Gapped Motifs in DNA sequences. PAPER 030 M. Sagot, E. W. Myers Identifying satellites in nucleic acid sequences. PAPER 031 D. Sankoff, M. Blanchette Multiple genome rearrangement. PAPER 032 F. Sun Modeling DNA shuffling. PAPER 033 S. R. Sunyaev, I. V. Rodchenkov Analysis of the Position Dependent Amino Acid Probabilities and its Application to the Search for Remote Homologues. PAPER 034 A. Vologodskii Maxwell demon and topology simplification by type II topoisomerases. PAPER 035 W. L.Walker, D. S. Goodsell, E. M.Landaw The Theoretical Limits of DNA sequence discrimination of Polyamides. PAPER 036 T. D. Wu, S. C. Schmidler, T. Hastie, D. L. Brutlag Regression Analysis of Multiple Protein Structures PAPER 037 Y. Xu, D. Xu, E. C. Uberbacher A New Method for modeling and solving the protein fold recognition problem. PAPER 038 Z. Zhang, P. Berman, W. Miller Alignments Without Low-Scoring Regions. If you do NOT want to be in our mailing list, please reply with Subject line "Recomb98: remove". Sorry, if you get this mail twice. From owner-software@net.bio.net Thu Dec 11 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!205.252.116.205!howland.erols.net!feed2.news.erols.com!winter.news.erols.com!not-for-mail From: "Jeff Reidler" Newsgroups: bionet.software Subject: FREE Image Acquisition and Analysis Software Date: Thu, 11 Dec 1997 21:56:47 -0200 Organization: Erol's Internet Services Lines: 5 Message-ID: <66q9a2$vl$2@winter.news.erols.com> NNTP-Posting-Host: fdk-as1s