From owner-software@net.bio.net Sun Jun 01 23:00:00 1997 Path: biosci!peg.it!difonzog From: difonzog@peg.it ("Prof. Giuseppe Di Fonzo") Newsgroups: bionet.software Subject: Information Date: 2 Jun 1997 14:43:32 -0700 Organization: Lynx Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <3393AC14.76D@peg.it> NNTP-Posting-Host: net.bio.net Prof. Giuseppe Di Fonzo e-mail: difonzog@peg.it I would like to know if there is a free software to recording EEG signals with PC Windows, and if there is an schematic electronic of hardware for this EEG. Thank you From owner-software@net.bio.net Sun Jun 01 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!newsfeed.internetmci.com!news-peer.gsl.net!howland.erols.net!usc!usc!not-for-mail From: Li Tian Newsgroups: bionet.software Subject: read DNA sequence automatically? Date: 2 Jun 1997 10:59:37 -0700 Organization: University of Southern California, Los Angeles, CA Lines: 11 Message-ID: NNTP-Posting-Host: hsc.usc.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Is there any software that can read a DNA sequence from a scanned image, like tif file format automatically? Thanks in advance for any information. Dr. Li Tian ltian@hsc.usc.edu -- Dr. Li Tian ltian@hsc.usc.edu From owner-software@net.bio.net Sun Jun 01 23:00:00 1997 Newsgroups: bionet.software Path: biosci!agate!howland.erols.net!newshub2.home.com!news.home.com!su-news-hub1.bbnplanet.com!su-news-feed4.bbnplanet.com!news.bbnplanet.com!enews.sgi.com!decwrl!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!alan From: alan@ebi.ac.uk (Alan Robinson) Subject: FINAL ANNOUNCE: Bioinformatics Conference at European Bioinformatics Institute Sender: news@ebi.ac.uk (usenet news) Message-ID: Date: Mon, 2 Jun 1997 17:04:14 GMT Organization: EBI - European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 103 This is the final announcement and call for participation in 'Objects in Bioinformatics' to be held at the European Bioinformatics Institute in Cambridge (UK) on the 18th and 19th of June, 1997. Currently, there are 185 registered delegates, 22 speakers talking on a variety of object-oriented and distributed computing topics of relevance to the biological sciences and bioinformatics, and over 25 poster presentations. [Abstracts are now available online]. Further information may be found at - http://www.ebi.ac.uk/~alan/Meeting/ The original mailing is included below. For those who have not registered, but are interested in attending, late registration is now in operation at 60 GBP (This includes all meals over the two days, and conference handouts, etc). Yours sincerely, Alan Robinson. ============================================================ Alan J. Robinson Tel:+44-(0)1223 494625 EMBL Outstation Fax:+44-(0)1223 494468 European Bioinformatics Institute Email: alan@ebi.ac.uk Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1RQ, UK http://industry.ebi.ac.uk/~alan/ ============================================================ -- [The full schedule for OiB-97 is now on-line at http://www.ebi.ac.uk/~alan/Meeting/speakers.html ]. --ooOOoo-- Objects in Bioinformatics- Reusable Software Components and Distributed Computing for the Biological Sciences. 18th and 19th June 1997, European Bioinformatics Institute, Cambridge, UK. http://www.ebi.ac.uk/~alan/Meeting/OiB.html Announcing a two day meeting on the role of reusable object-oriented software components and distributed objects in bioinformatics and the biological sciences. The widget and object-oriented approach is a powerful paradigm in which new applications are developed by utilising pre-existing components interacting in concert, and offers the possibility of a new generation of bioinformatic tools. In this way development time is reduced and greater time is spent on data analysis and knowledge discovery. The meeting is aimed at those who are interested in, are developing, or have developed reusable software components that will be of use to the bioinformatics and biological community. It will also address the implication and application of distributed object technology to biology and bioinformatics. The meeting will include lectures, presentations, poster sessions and discussion groups on the rapidly expanding and developing fields of software components and distributed computing from both an academic and industrial perspective. Invited talks will cover the application of reusable components, software libraries, distributed object technology, data visualisation and the bioWidget Consortium. Poster stands, each with a dedicated networked computer, are available upon which delegates may showcase their work and projects. Participants are encouraged to submit a brief abstract for a poster relevant to the meeting themes. There will be prizes for the best poster presentations. Full details about the meeting may be accessed at - http://www.ebi.ac.uk/~alan/Meeting/OiB.html The meeting is organised by the European Bioinformatics Institute in association with the bioWidget Consortium. The meeting will be held in the newly completed conference facilities at the Wellcome Trust Genome Campus in the grounds of Hinxton Hall, Cambridge, UK. -- ============================================================ Alan J. Robinson Tel:+44-(0)1223 494625 EMBL Outstation Fax:+44-(0)1223 494468 European Bioinformatics Institute Email: alan@ebi.ac.uk Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1RQ, UK http://industry.ebi.ac.uk/~alan/ ============================================================ From owner-software@net.bio.net Sun Jun 01 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!worldnet.att.net!news.u.washington.edu!mnr From: mnr@u.washington.edu (Mark N. Rand) Newsgroups: bionet.software Subject: PTI ImageMaster 2 Software Date: Mon, 02 Jun 1997 12:12:53 -0700 Organization: University of Washington Lines: 15 Message-ID: NNTP-Posting-Host: 128.95.211.102 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.1 We'd appreciate hearing from anyone who has recently purchased a PTI ratiometric imaging system. We own two PTI systems which use DeltaRAM monochromators and Photometrics Sensys 1400 CCD cameras controlled by ImageMaster 2.0 software. It would be useful to "compare notes" with other users of this system, especially with regard to the software. Thanks for any and all replies. Cheers, Mark N. Rand, Ph.D. Neurology Department, U.W. Seattle, WA email: mnr@u.washington.edu From owner-software@net.bio.net Mon Jun 02 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!news.bc.net!mongol.sasknet.sk.ca!dragon.sk.sympatico.ca!canopus.cc.umanitoba.ca!not-for-mail From: Brian Fristensky Newsgroups: bionet.software Subject: Re: PC/Gene for UNIX Date: Mon, 02 Jun 1997 16:25:25 -0500 Organization: University of Manitoba Lines: 48 Message-ID: <33933A45.EF0@cc.umanitoba.ca> References: NNTP-Posting-Host: brassica.cc.umanitoba.ca Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------13F81C738B" X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5.1 sun4u) This is a multi-part message in MIME format. --------------13F81C738B Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Berke, Tamas wrote: > > Hello Everibody: > I use PC/Gene 6.85 for basic sequence manipulation on PC. I am going to > switch to UNIX environment soon. Is there a UNIX version of PC/Gene > (UNIX/Gene ;-)? Or what would be closest equivalent of PC/Gene for UNIX? > Thanks. > > Tamas Berke > Norfolk, VA Depending on your budget, the GCG package is probably the best commercial package. See http://www.gcg.com/ It you have a small or nonexistant budget, but have some knowledge of programming, you can put together a comprehensive package using publicly available programs. That's exactly what I've done on our Sun Unix system. See the BIRCH Web site at http://home.cc.umanitoba.ca/~psgendb/ --------------13F81C738B Content-Type: text/plain; charset=us-ascii; name="signature" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="signature" =============================================================================== Brian Fristensky | Department of Plant Science | To really appreciate the magnitude of University of Manitoba | 1997 Red River Valley flood, Winnipeg, MB R3T 2N2 CANADA | consider this: not even CANADA CUSTOMS frist@cc.umanitoba.ca | could stop it from crossing the border! Office phone: 204-474-6085 | FAX: 204-261-5732 | http://home.cc.umanitoba.ca/~frist/ =============================================================================== --------------13F81C738B-- From owner-software@net.bio.net Mon Jun 02 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!cam-news-feed3.bbnplanet.com!news.bbnplanet.com!news.inc.net!news.itis.com!pkuzmic From: pkuzmic@biokin.com (Petr Kuzmic) Newsgroups: bionet.software Subject: Freeware for kinetic data analysis Date: Tue, 03 Jun 1997 08:59:31 GMT Organization: BioKin Consulting Lines: 25 Sender: reguser@wa9.itis.com Message-ID: <5n0m37$6j9$1@bill.itis.com> Reply-To: Petr Kuzmic NNTP-Posting-Host: wa9.itis.com X-Newsreader: News Xpress 2.01 Program DYNAFIT for statistical analysis of biochemical kinetic data (enzymology, receptor-ligand interactions) was updated to ver. 2.16. It is a freeware, reviewed this week in a Software Alert column in http://biomednet.com/hmsbeagle/ The program runs under DOS, Win95(DOS box), MacOS7.5(PowerMac), SGI, DEC Alpha, and IBM-RISC/System-6000. To quote the reviewer from the Software Alert, "If you do any kind of kinetic data analysis as part of your research program, be sure to download DynaFit from the BioKin Web site" http://biokin.com See also the original report in Anal. Biochem. 237, 260-273 (1996). Petr Kuzmic ------------------------------------------------------- Petr Kuzmic, Ph.D. * http://www.biokin.com B i o K i n, Ltd. * P.O. Box 8336 * Madison WI 53708 voice 608.256.4790 * fax 608.256.1269 From owner-software@net.bio.net Mon Jun 02 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!news.maxwell.syr.edu!news.apfel.de!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news-koe1.dfn.de!news.ruhr-uni-bochum.de!not-for-mail From: Marc.Saric@rz.ruhr-uni-bochum.de (Marc Saric) Newsgroups: bionet.software Subject: Re: Richard Dawkins Date: Tue, 03 Jun 1997 19:15:52 GMT Organization: Ruhr-Universitaet Bochum, Rechenzentrum Lines: 13 Message-ID: <33946d51.5205415@news.ruhr-uni-bochum.de> References: <338EA20E.633D@dial.pipex.com> NNTP-Posting-Host: dialppp-1-11.rz.ruhr-uni-bochum.de X-Newsreader: Forte Free Agent 1.1/32.230 On Fri, 30 May 1997 10:46:54 +0100, Spencer wrote: >There is some interesting software based on Dawkins Biomorphs program at >http://www.nottinghillcom/cyber. It is 3D Alife that allows you to breed The mentioned URL does not work for me -are you sure it is ok??? Bye, Marc Saric Internet/Fidonet/FsFan-Net/Gernet Visit http://www.rat.de/marc_saric/ From owner-software@net.bio.net Mon Jun 02 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!xfer.kren.nm.kr!nntp.kreonet.re.kr!newsfeed.dacom.co.kr!newsfeed.internetmci.com!in3.uu.net!202.82.1.1!bull.hkstar.net!hkstar2!news From: "=?BIG5?B?qvel1aT0?=" Newsgroups: bionet.software Subject: Help, please Date: 3 Jun 1997 15:22:32 GMT Organization: =?BIG5?B?pL2lcaZXutmlvKq+?= Lines: 3 Message-ID: <01bc702f$e28879e0$LocalHost@default> NNTP-Posting-Host: ip-55-124.dialup.hkstar.com Mime-Version: 1.0 Content-Type: text/plain; charset=BIG5 Content-Transfer-Encoding: 8bit X-Newsreader: Microsoft Internet News 4.70.1157 ½Ð°Ý¦³¨S¦³¤Hª¾¹D¨ºùئ³¤@¨Ç¼sªF¸Ü©Î´¶³q¸Üµo­µªºsoftware¥i¥H download °Ú? ª¾¹Dªº¸Ü, ½ÐÂà§i¤@Án, ÁÂÁ I lookng forward from you soon!! From owner-software@net.bio.net Mon Jun 02 23:00:00 1997 Newsgroups: bionet.software Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!EU.net!CERN.ch!news From: bics1 Subject: Secondary Structure Prediction Software X-Nntp-Posting-Host: tifrc4.tifr.res.in Content-Type: text/plain; charset=us-ascii Message-ID: <33949710.1C93@158.144.26.18> Sender: news@news.cern.ch (USENET News System) Reply-To: bics1@158.144.26.18 Content-Transfer-Encoding: 7bit Organization: T.I.F.R. References: <5n0m37$6j9$1@bill.itis.com> Mime-Version: 1.0 Date: Tue, 3 Jun 1997 22:13:36 GMT X-Mailer: Mozilla 3.01Gold (Win95; I) Lines: 7 I am looking for a software which can predict protein secondary structure from circular dichroism data. Can anybody please help me? Please mail me in the following address: krish@tifrvax.tifr.res.in Krishnananda Chattopadhyay India From owner-software@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!newsfeed.internetmci.com!news.chatlink.com!not-for-mail From: "Jeremiah Tilley" Newsgroups: alt.binaries.w-software,alt.comp.software.financial,amiga.software,at.tuwien.software,att.software-dev,att.software-dev.metatool,bfm.programmers.software.bondcalc,bionet.software,bionet.software.acedb,bionet.software.gcg,bionet.software.pc,bion Subject: Digital Mail Date: 3 Jun 1997 21:40:33 GMT Organization: - Lines: 5 Message-ID: <01bc709f$fc90f2c0$de698bcd@default> NNTP-Posting-Host: cl3-p4.chatlink.com X-Newsreader: Microsoft Internet News 4.70.1161 Xref: biosci bionet.software:18731 bionet.software.acedb:1253 bionet.software.gcg:2538 Try out this new software that allows you to communicate digitally with friends and family who don't have e-mail, but yet have a computer. Visit: http://www.chatlink.com/~pioneer/ From owner-software@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!xfer.kren.nm.kr!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!rill.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!server6.netnews.ja.net!str-ccsun!singer.cent.gla.ac.uk!lenzie.cent.gla.ac.uk!8904741e From: Andrew Elwell <8904741e@udcf.gla.ac.uk> Newsgroups: bionet.software,bionet.general Subject: Shimadzu LC10 Problems Date: Tue, 3 Jun 1997 12:52:27 +0100 Organization: University of Glasgow Lines: 15 Message-ID: NNTP-Posting-Host: lenzie.cent.gla.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: 8904741e@lenzie.cent.gla.ac.uk Xref: biosci bionet.software:18732 bionet.general:27048 Howdy all, we have a Shimadzu LC10 HPLC system with a SPD-M10AV diode-array detector. only recently have we started using this in the visible range, but there is NO spectra being recorded by the class software. Has anyone else had this problem (spectra up to 300nm are fine) Any help would be appreciated, especially replying by email. Ta Andrew Elwell http://www.enzyme.gla.ac.uk/~andrew/ From owner-software@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!ukrv.de!jea From: jea@ukrv.de Newsgroups: bionet.software Subject: hardy weinberg equilibrium Date: 4 Jun 1997 08:00:37 -0700 Organization: dhzb Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: <3395F2CD.1CBF@ukrv.de> NNTP-Posting-Host: net.bio.net looking for a program to look for Hardy Weinberg equilibrium. Please help. thanks J. Erdmann From owner-software@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!nntp0.brunel.ac.uk!strath-cs!news.qub.ac.uk!not-for-mail From: Dr Peter Hamilton Newsgroups: bionet.software Subject: pathology Date: Wed, 04 Jun 1997 17:37:43 +0100 Organization: The Queen's University of Belfast Lines: 8 Message-ID: <339599D7.646D@qub.ac.uk> Reply-To: p.hamilton@qub.ac.uk NNTP-Posting-Host: quan1.pt.qub.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Announcing the International Congress of Diagnostic Quantitative Pathology - Sienna, Italy 2-4 October 1997 Anyone interested in attending please contact Dr Peter Hamilton (p.hamilton@qub.ac.uk) More information can be found at: http://quan8.pt.qub.ac.uk/society/conf97_1.htm From owner-software@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!ais.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!server3.netnews.ja.net!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!willow.cc.kcl.ac.uk!not-for-mail From: foop@sg4.pcy.kcl.ac.uk (Chris Richardson) Newsgroups: bionet.software Subject: Re: Richard Dawkins Date: 4 Jun 1997 09:50:30 +0100 Organization: King's College London Lines: 23 Message-ID: <5n3a8m$ir4$1@sg4.pcy.kcl.ac.uk> References: <338EA20E.633D@dial.pipex.com> <33946d51.5205415@news.ruhr-uni-bochum.de> Reply-To: foop@sg2.pcy.kcl.ac.uk NNTP-Posting-Host: sg4.pcy.kcl.ac.uk , the entity called Marc Saric, wrote: >On Fri, 30 May 1997 10:46:54 +0100, Spencer >wrote: >>There is some interesting software based on Dawkins Biomorphs program at >>http://www.nottinghillcom/cyber. It is 3D Alife that allows you to breed >The mentioned URL does not work for me -are you sure it is ok??? I had the same problem: try www.nottinghill.com. It also took me a few seconds to realise that it requires that you have JavaScript turned on in your browser. Whether you want to activate this, given the rather patchy nature of its security, is left as an exercise to the reader. However, the text only pages seem to work okay. It might also be useful to point out that the free software is only for Win32 and Win95. Not much use for me and my SG Indy. -- -- foop (fu:p):n. [Pharmacy, King's College London] Departmental PostDoc Geek. "I hate broccoli, and yet, in a certain sense, I am broccoli." -- The Tick From owner-software@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!feed1.news.erols.com!newsfeed.internetmci.com!in2.uu.net!138.133.17.7!amgen!usenet From: John Philo Newsgroups: bionet.software Subject: Re: Secondary Structure Prediction Software Date: Wed, 04 Jun 1997 13:45:00 -0700 Organization: Amgen Inc. Lines: 23 Message-ID: <3395D3CC.1DC5@amgen.com> References: <5n0m37$6j9$1@bill.itis.com> <33949710.1C93@158.144.26.18> Reply-To: jphilo@amgen.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) To: bics1@158.144.26.18 bics1 wrote: > > I am looking for a software which can predict protein secondary > structure from circular dichroism data. > Can anybody please help me? > Please mail me in the following address: > krish@tifrvax.tifr.res.in > Krishnananda Chattopadhyay > India All the CD instrument manufacturers supply programs that will do this. One public domain program I know of is available at http://www-structure.llnl.gov/cd/cdtutorial.htm I haven't tried it myself. I believe Gerald Fasman (Brandeis) also has a program he has released into the public domain. You could try e-mailing him at fasman@binah.cc.brandeis.edu 'Hope this helps. John Philo, Protein Chemistry, Amgen *** Disclaimer: These are the opinions of the poster not Amgen Inc.*** From owner-software@net.bio.net Tue Jun 03 23:00:00 1997 Newsgroups: bionet.software Path: biosci!daresbury!uninett.no!Norway.EU.net!EU.net!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!129.174.1.8!portal.gmu.edu!hearst.acc.Virginia.EDU!murdoch!usenet From: wrp@alpha0.bioch.virginia.edu (William R. Pearson) Subject: Medlars to refer format X-Nntp-Posting-Host: alpha0.bioch.virginia.edu Message-ID: Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia X-Newsreader: Gnus v5.3/Emacs 19.34 Date: Wed, 4 Jun 1997 20:37:18 GMT Lines: 8 I am looking for a perl script that will convert Entrez or Ovid (they are slightly different) Medlars tagged format to unix refer/bib format. Something that would make it easy to include or exclude abstracts would be helpful. Bill Pearson From owner-software@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!news.maxwell.syr.edu!howland.erols.net!newsfeed.internetmci.com!news1.bellglobal.com!sunqbc.risq.qc.ca!news.microtec.net!news3.sprint-canada.net!roger.interlynx.net!not-for-mail From: Lars Thomsen Newsgroups: bionet.software Subject: Entrez browser helper tool Date: Wed, 04 Jun 1997 00:59:02 -0400 Organization: Interlynx Lines: 26 Message-ID: <3394F616.ACC0CB9D@interlynx.net> NNTP-Posting-Host: port85.hm.interlynx.net Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 X-Mailer: Mozilla 4.0b4 [en] (Win95; I) X-Priority: 3 (Normal) When I have downloaded from the Entrez browser most of my programs does not display the full filename and that is a pain. Another thing that was irritating was whenever I had to paste my sequences into e.g. the FASTA search form. I therefore made a file utility that finds all sequence formats downloaded from the Entrez browser and sorts them into different lists by fileformat. The first line of the file format is displayed for each imported sequence (works pretty good, because all the important info is in this line) and then you can copy the list or selected items from it to the clipboard just by pressing a button. The program have several other features and it saves me a lot of time. You can get the program for free if you mail me or maybe you have some server space where it can reside...I have only 15 MB and that is already filled up with my patch clamp analysis program PREADER http://home.interlynx.net/~lthomsen/preader -- Lars Thomsen, MSc PhD 115 South Oval, Hamilton, L8S1R2 Ontario, Canada tlp +1 905 777 0720 fax +1 905 777 0738 email lthomsen@interlynx.net homepage http://home.interlynx.net/~lthomsen From owner-software@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!ais.net!europa.clark.net!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!baron.netcom.net.uk!netcom.net.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news.ox.ac.uk!worf.molbiol.ox.ac.uk!rgrant From: rgrant@see.sig.for.address (Richard P Grant) Newsgroups: bionet.software Subject: Re: Richard Dawkins Date: 4 Jun 1997 12:26:18 GMT Organization: Oxford University Message-ID: <5n3mta$cf7@news.ox.ac.uk> References: <338EA20E.633D@dial.pipex.com> <33946d51.5205415@news.ruhr-uni-bochum.de> <5n3a8m$ir4$1@sg4.pcy.kcl.ac.uk> NNTP-Posting-Host: worf.molbiol.ox.ac.uk X-Newsreader: TIN [version 1.2 PL2] Lines: 22 Chris Richardson (foop@sg4.pcy.kcl.ac.uk) wrote: } It also took me a few seconds to realise that it requires that you have } JavaScript turned on in your browser. Whether you want to activate this, } given the rather patchy nature of its security, is left as an exercise to } the reader. However, the text only pages seem to work okay. Downer #1 } It might also be useful to point out that the free software is only for } Win32 and Win95. Not much use for me and my SG Indy. Downer #2 Not much use for me and my Mac. Thanks for saving me the trouble, Chris. -- Richard P. Grant MA DPhil University of Oxford | rgrant@molbiol http://www.molbiol.ox.ac.uk/~rgrant FFPGP | .ox.ac.uk ----------------# Set your thermonuclear devices on stun #---------------- From owner-software@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!MARLIN.UTMB.EDU!tjiffar From: tjiffar@MARLIN.UTMB.EDU Newsgroups: bionet.software Subject: T-cell epitope prediction ? Date: 4 Jun 1997 12:32:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: <3395DF05.5451@marlin.utmb.edu> NNTP-Posting-Host: net.bio.net Is there a software for T-cell epitope prediction based on a gene sequence? Thanks From owner-software@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!NATURE.BERKELEY.EDU!bosborne From: bosborne@NATURE.BERKELEY.EDU (Brian Osborne) Newsgroups: bionet.software Subject: Good books for student of "informatics"? Date: 4 Jun 1997 11:05:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <9706041106.ZM13086@ultra170.pw.usda.gov> NNTP-Posting-Host: net.bio.net To the group, I'm probably going to buy : Computer methods for macromolecular sequence analysis Doolittle, R. F., editor, 1996 which is volume 266 of the Methods of Enzymology series, (Academic Press). Are there any other books that you like? Brian O. -- Brian I. Osborne bosborne@nature.berkeley.edu Plant Gene Expression Center TEL 510 559 5924 800 Buchanan St. FAX 510 559 5678 Albany CA 94710 USA From owner-software@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Dmitrij Frishman Newsgroups: bionet.software Subject: GCB '97 Extended Deadline Date: 4 Jun 1997 10:34:48 -0700 Organization: Max-Planck-Institute for Biochemistry Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: <33959099.167E@mips.biochem.mpg.de> NNTP-Posting-Host: net.bio.net German Conference on Bioinformatics GCB '97 http://www.mips.biochem.mpg.de Extended deadline for full paper submissions: June 15th 1997 Full Papers should be 12 pages, single-spaced and set in 12 point type, including title, abstract, figures, tables, and bibliography. Submissions to be considered for CABIOS publication must follow authors instructions which can be downloaded from our WWW page. Abstracts for oral presentations should be a minimum of 2 pages. Poster and software demonstration abstracts should be a maximum of 2 pages. Postal and electronic mailing addresses, telephone, and fax numbers must be included. Processing of submissions can be facilitated by sending postscript files via e-mail to gcb97@mips.embnet.org. Deadline for poster and software demonstration submissions: July 20th 1997 From owner-software@net.bio.net Tue Jun 03 23:00:00 1997 From: Lars Thomsen Newsgroups: bionet.software Subject: Conc1 x Vol1 = Conc2 x Vol...I have made a little tool Date: Wed, 04 Jun 1997 00:51:38 -0400 Organization: Interlynx Lines: 18 Message-ID: <3394F459.44677BD7@interlynx.net> NNTP-Posting-Host: port85.hm.interlynx.net Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 X-Mailer: Mozilla 4.0b4 [en] (Win95; I) X-Priority: 3 (Normal) Path: biosci!rutgers.rutgers.edu!gatech!news1.mid-ga.com!news.hom.net!nntp.mid-ga.com!news.oru.edu!news.uoregon.edu!hammer.uoregon.edu!ais.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!news1.bellglobal.com!sunqbc.risq.qc.ca!news.microtec.net!news3.sprint-canada.net!roger.interlynx.net!not-for-mail I do this calculations tons of times every day and I got tired of it...so here is the tool : http://home.interlynx.net/~lthomsen/Dilution.ZIP Download zip file and unpack with Winzip or Pkunzip in a directory and then click SETUP.EXE (zipfile = 1.38 MB) Please send me your comments Best Regards -- Lars Thomsen, MSc PhD 115 South Oval, Hamilton, L8S1R2 Ontario, Canada tlp +1 905 777 0720 fax +1 905 777 0738 email lthomsen@interlynx.net homepage http://home.interlynx.net/~lthomsen From owner-software@net.bio.net Wed Jun 04 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!newsfeed.internetmci.com!worldnet.att.net!news.u.washington.edu!evolution.genetics.washington.edu!joe From: joe@evolution.genetics.washington.edu (Joe Felsenstein) Newsgroups: bionet.software Subject: Re: hardy weinberg equilibrium Date: 5 Jun 1997 13:39:21 GMT Organization: University of Washington Genetics Lines: 15 Message-ID: <5n6fi9$aua@nntp3.u.washington.edu> References: <3395F2CD.1CBF@ukrv.de> NNTP-Posting-Host: evolution.genetics.washington.edu Summary: Hardy-Weinberg In article <3395F2CD.1CBF@ukrv.de>, wrote: >looking for a program to look for Hardy Weinberg equilibrium. >J. Erdmann If you mean testing for Hardy-Weinberg proportions, there are a number of packages that do that, such as GDA. Check Patrick Phillips's very useful evolutionary genetics web site EP-GED: http://wbar.uta.edu which has lists of evolutionary genetics software. ----- 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 Wed Jun 04 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!news-out.communique.net!communique!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!news-was.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!in2p3.fr!univ-lyon1.fr!cnusc.fr!ciril.fr!u-strasbg.fr!news From: pingouin@crystal.u-strasbg.fr (Francois JEANMOUGIN) Newsgroups: bionet.software Subject: Re: Adding to mult. alignment ? Date: 5 Jun 1997 14:56:20 GMT Organization: IGBMC Lines: 29 Message-ID: <5n6k2k$qco@news.u-strasbg.fr> References: <5n6aj9$9on@n.ruf.uni-freiburg.de> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 0.9.8 In article <5n6aj9$9on@n.ruf.uni-freiburg.de>, vonrhein@bio6.chemie.uni-freiburg.de (Clemens Vonrhein) writes: > Is there a (free?) alignment software which can use an existing > multiple alignment - and keep it fixed - to align several other > sequences to? > > I *think* MSA can handle this? But it's sloooow ... Well, I'm not using a bulk mail programme but... ClustalW and ClustalX can do that. Using the profile alignment system, you input an alignment which is used as a profile, and you can easily (very easily with ClustalX) add new sequences to a fixed alignment. Note that if the new sequence diverge, you will have to add gaps to your existing profile, but the alignement between original sequences is maintained. Just try ClustalX and let us know: ftp://ftp-igbmc.u-strasbg.fr/ClustalX/ Hope this helps, Francois. P.S.: The profile alignement method from Clustal is not so slow, it depends of the machine and system you have. -- Francois Jeanmougin | groupe de bioinformatique / bioinformatics groupe tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France e-mail : jeanmougin@igbmc.u-strasbg.fr "C'est pas parcequ'on monte au banc, qu'il faut descendre a jeun."(Thiefaine) From owner-software@net.bio.net Wed Jun 04 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!newsfeed.internetmci.com!howland.erols.net!newsfeed.nacamar.de!fu-berlin.de!news.belwue.de!news.uni-freiburg.de!bio6.chemie.uni-freiburg.de!vonrhein From: vonrhein@bio6.chemie.uni-freiburg.de (Clemens Vonrhein) Newsgroups: bionet.software Subject: Adding to mult. alignment ? Date: 5 Jun 1997 12:14:33 GMT Organization: Uni Freiburg Lines: 21 Message-ID: <5n6aj9$9on@n.ruf.uni-freiburg.de> NNTP-Posting-Host: bio6.chemie.uni-freiburg.de Keywords: alignment software Is there a (free?) alignment software which can use an existing multiple alignment - and keep it fixed - to align several other sequences to? I *think* MSA can handle this? But it's sloooow ... Thanks anyway Clemens *************************************************************************** * Clemens Vonrhein email vonrhein@bio5.chemie.uni-freiburg.de * * WWW http://bio5.chemie.uni-freiburg.de/~vonrhein/ * * * * Institut f. Org. Chemie u. Biochemie * * Albertstr.21 * * D-79104 Freiburg i.Br. (Germany) * * Tel.: 761/203-6061 FAX: 761/203-5987 * *************************************************************************** From owner-software@net.bio.net Wed Jun 04 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!feeder.chicago.cic.net!news.maxwell.syr.edu!news-was.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!feed2.belnet.be!news.belnet.be!inf6serv.rug.ac.be!not-for-mail From: Laury Chaerle Newsgroups: sci.stat.consult,sci.stat.edu,comp.soft-sys.sas,comp.soft-sys.stat.spss,comp.soft-sys.stat.systat,bionet.software Subject: split split plot analysis Date: Thu, 05 Jun 1997 11:40:10 +0200 Organization: University of Ghent, Belgium Lines: 6 Message-ID: <3396897A.7446@gengenp.rug.ac.be> NNTP-Posting-Host: mata.rug.ac.be 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 i86pc) Which software other than SAS can perform a split split plot analysis? -- Laury CHAERLE ==================================================== Vlaams Instituut voor Biotechnologie VIB LABORATORY OF GENETICS UNIVERSITY OF GENT, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium From owner-software@net.bio.net Wed Jun 04 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsout1.alt.net!news1.alt.net!news.aros.net!not-for-mail From: "DAVID G. JENSON" Newsgroups: bionet.software Subject: MUST READ Date: 5 Jun 1997 07:30:50 GMT Organization: ArosNet Inc. Lines: 14 Message-ID: <01bc718a$f0b12ce0$6e19adcf@default> NNTP-Posting-Host: dm1-35.slc.aros.net X-Newsreader: Microsoft Internet News 4.70.1155 I just found a web site that offers 7.9¢/min long distance and 14.9¢/min PhoneCards (with no hidden fees!) This is a great deal for those of us who make a lot of long distance calls at home and on the road. (They make Customized cards too!) They gave me a FREE phonecard just for visiting them. Click on: http://www.unikey.net D. Jenson From owner-software@net.bio.net Wed Jun 04 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!199.2.96.62!news.rain.net!news.teleport.com!ip-pdx03-06.teleport.com!user From: dave@rsd.com_!rem!ove!this (Dave Goldman) Newsgroups: bionet.software Subject: Re: Medlars to refer format Date: Wed, 04 Jun 1997 23:23:23 -0800 Organization: Research Software Design Lines: 26 Message-ID: References: NNTP-Posting-Host: ip-pdx03-06.teleport.com In article , wrp@alpha0.bioch.virginia.edu (William R. Pearson) wrote: > I am looking for a perl script that will convert Entrez or Ovid (they > are slightly different) Medlars tagged format to unix refer/bib > format. Something that would make it easy to include or exclude > abstracts would be helpful. Bill -- It's not a perl script, and it's not free, but if you can't come up with an easy solution you might consider our PAPYRUS bibliographic database program. It only costs $99, can import Entrez, Ovid, or pretty much any other source of bibliographic references, and can reformat and output the data any way you like, including refer/bib. If you're interested, please take a look at our Web site, or e-mail me for more information. -- Dave Goldman (dave@rsd.com) Research Software Design 503/796-1368, fax 503-241-4260 2718 SW Kelly Street, Suite 181 The PAPYRUS Bibliography System Portland OR 97201 (U.S.A.) Technical Support: support@rsd.com Other Questions: info@rsd.com WWW Site: http://www.rsd.com/~rsd/ From owner-software@net.bio.net Wed Jun 04 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!nntprelay.mathworks.com!news.mathworks.com!news.maxwell.syr.edu!news.cis.ohio-state.edu!magnus.acs.ohio-state.edu!bertbishop!bishop.11 From: bishop.11@osu.edu (Bert Bishop) Newsgroups: sci.stat.consult,sci.stat.edu,comp.soft-sys.sas,comp.soft-sys.stat.spss,comp.soft-sys.stat.systat,bionet.software Subject: Re: split split plot analysis Date: Thu, 5 Jun 1997 12:48:56 GMT Organization: The Ohio State University Lines: 7 Message-ID: References: <3396897A.7446@gengenp.rug.ac.be> NNTP-Posting-Host: rs131c.oardc.ohio-state.edu X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #1] In article <3396897A.7446@gengenp.rug.ac.be> Laury Chaerle writes: >Which software other than SAS can perform a split split plot analysis? MINITAB can do the analysis of variance at least. Bert Bishop From owner-software@net.bio.net Wed Jun 04 23:00:00 1997 Path: biosci!biosci!not-for-mail From: btsmith@mit.edu (Bradley T. Smith) Newsgroups: bionet.software Subject: Searching DNA Seq. for promoter elements, binding sites, etc.? Date: 5 Jun 1997 13:15:34 -0700 Organization: M.I.T. Department of Biology Lines: 22 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello! As my subject line indictaes, I am interested in any advice or information concerning the searching of DNA sequences for various motifs such as protein binding sites, promoter elements, etc. I am hoping that there is some sort of software package that uses a large database of such motifs to scan query sequences. I have heard of something called "Motif" which may or may not be what I am looking for. Although, I think that it may be a a part of GCG, which I'd like to avoid if at all possible. However, if that is my only choice, I'll just have to grin and bear it! Thank you, in advance, for you help... -Bradley T. Smith btsmith@mit.edu M.I.T. Biology Department - Walker Laboratory From owner-software@net.bio.net Wed Jun 04 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!newsfeed.internetmci.com!in3.uu.net!151.99.250.2!server-b.cs.interbusiness.it!news.tin.it!news From: "Omar Marin" Newsgroups: bionet.software Subject: GP2 MANAGER Date: 2 Jun 1997 08:41:12 GMT Organization: PC TO WIN Lines: 4 Message-ID: <01bc6f31$0703c720$46851fc3@p-166> NNTP-Posting-Host: bassano2-7.tin.it X-Newsreader: Microsoft Internet News 4.70.1157 I'M LOOKING TO FINDE SOME HELP HOW TO PALY IN THE GP2 AGME AND HAVE A LOT OF MONEY AND WIN THE CHAMPION. REPLY TO ME pctowin@tin.it From owner-software@net.bio.net Wed Jun 04 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!news-out.communique.net!communique!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!howland.erols.net!torn!ccshst05.cs.uoguelph.ca!ccshst01!wyu From: wyu@uoguelph.ca (Wenjin Yu) Newsgroups: bionet.software Subject: Plasmid drawing program for windows Date: 5 Jun 1997 16:10:12 GMT Organization: University of Guelph Lines: 19 Message-ID: <5n6od4$6lf@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: ccshst01.cs.uoguelph.ca X-Newsreader: TIN [version 1.2 PL2] Dear netters, Does anyone know where there is a plasmid-drawing program for windows for sale at a reasonable price ($400-500)? Thanks in advance for your reply. Wenjin Yu -- ================================================================== || Wen-Jin Yu * E-Mail: wyu@uoguelph.ca || || Dept. Crop Science * Tel.(home): (519)836-2868 || || University of Guelph * Tel.(work): (519)824-4120, x6089 || || Guelph, Ont. Canada * Fax: (519)763-8933 || || N1G 2W1 * URL: http://www.uoguelph.ca/~wyu || ================================================================== From owner-software@net.bio.net Thu Jun 05 23:00:00 1997 Path: biosci!fn.csa.ru!bios From: bios@fn.csa.ru (Bioinformation systems Laboratory) Newsgroups: bionet.software Subject: JAVA applet for presentation of information about genetic networks Date: 6 Jun 1997 03:08:31 -0700 Organization: Institute of High-Performance Computing and Databases Lines: 53 Sender: daemon@net.bio.net Distribution: world Message-ID: <3397E1A1.3B1A@fn.csa.ru> Reply-To: bios@fn.csa.ru NNTP-Posting-Host: net.bio.net JAVA APPLET FOR PRESENTATION OF KNOWLEDGES ON GENETIC NETWORKS. The essential progress in study of the molecular mechanisms of organisms individual development results in discovery of a hundreds genes, which sole function consist in the control and regulation of other genes activity. These genes comprise so called "genetic networks". As the genes networks consist of tens of genes involved in complex regulatory interactions it is necessary to develop a special tools for their graphical presentation. We develop Java applet for graphical presentation of information on gap genetic network in fruit fly Drosophila melanogaster. Our program (http://www.csa.ru/Inst/gorb_dep/inbios/genet/Graph/genes.html) represents genes as rectangles. The interacting genes are connected by arrows. Clicking on gene leads to its activation and bringing out its relations with other genes. Red arrows connect gene with upstream genes of network, blue arrows - with downstream genes. Filled and hollow arrows reflect the mode of gene action - activation and repression correspondingly. It is possible to drag genes for better visualization of links between them. In parallel to emphasizing the links clicking on gene activates the appearance of lists of upstream and downstream genes in pop-up menu windows. These genes are linked to GeNet database (http://www.csa.ru/Inst/gorb_dep/inbios/genet/genet.htm) entries, containing the information about them. Thus the selection of the gene from the menu calls out the information about it. Special filters permit selective visualization of the interaction of genes controlling different parts of the embryo body. The applet source code is available. We highly appreciate any suggestions and comments. Maria Samsonova Bioinformation Systems Laboratory Institute of High-Performance Computing and Databases St.Petersburg, Russia e-mail samson@fn.csa.ru http://www.csa.ru/Inst/gorb_dep/inbios/lab.htm From owner-software@net.bio.net Thu Jun 05 23:00:00 1997 Path: biosci!fn.csa.ru!bios From: bios@fn.csa.ru (Bioinformation systems Laboratory) Newsgroups: bionet.software Subject: Java applet for presentation of information about genetic networks Date: 6 Jun 1997 02:53:39 -0700 Organization: Institute of High-Performance Computing and Databases Lines: 85 Sender: daemon@net.bio.net Distribution: world Message-ID: <3397DE19.21FD@fn.csa.ru> Reply-To: bios@fn.csa.ru NNTP-Posting-Host: net.bio.net Java applet for presentation of knowledges on genetic networks. The essential progress in study of the molecular mechanisms of organisms individual development results in discovery of a hundreds genes, which sole function consist in the control and regulation of other genes activity. These genes comprise so called "genetic networks". As the genes networks consist of tens of genes involved in complex regulatory interactions it is necessary to develop a special tools for their graphical presentation. We develop Java applet for graphical presentation of information on gap genetic network in fruit fly Drosophila melanogaster. Our program (http://www.csa.ru/Inst/gorb_dep/inbios/genet/Graph/genes.html) represents genes as rectangles. The interacting genes are connected by arrows. Clicking on gene leads to its activation and bringing out its relations with other genes. Red arrows connect gene with upstream genes of network, blue arrows - with downstream genes. Filled and hollow arrows reflect the mode of gene action - activation and repression correspondingly. It is possible to drag genes for better visualization of links between them. In parallel to emphasizing the links clicking on gene activates the appearance of lists of upstream and downstream genes in pop-up menu windows. These genes are linked to GeNet database (http://www.csa.ru/Inst/gorb_dep/inbios/genet/genet.htm) entries, containing the information about them. Thus the selection of the gene from the menu calls out the information about it. Special filters permit selective visualization of the interaction of genes controlling different parts of the embryo body. The applet source code is available. We highly appreciate any suggestions and comments. Maria Samsonova Bioinformation Systems Laboratory Institute of High-Performance Computing and Databases St.Petersburg, Russia e-mail samson@fn.csa.ru http://www.csa.ru/Inst/gorb_dep/inbios/lab.htm \subsection {Development of tools for presentation of knowledge on gene networks} The essential progress in study of the molecular mechanisms of organisms individual development results in discovery of a hundreds genes, which sole function consist in the control and regulation of other genes activity. These genes comprise so called "genes networks". Gene networks serve to orchestrate the genome activity during embryo development. As the genes networks consist of tens of genes involved in complex regulatory interactions it is necessary to develop a special tools for their graphical presentation. We design such a tool using Java programming language. Our program (http://www.csa.ru/Inst/gorb\_dep/inbios/genet/Graph/genes.html) represents genes as rectangles (fig.1). The interacting genes are connected by arrows. Clicking on gene leads to its activation and bringing out its relations with other genes. Red arrows connect gene with upstream genes of network, blue arrows - with downstream genes. Filled and hollow arrows reflect the mode of gene action - activation and repression correspondingly. It is possible to drag genes for better visualization of links between them. In parallel to emphasizing the links clicking on gene activates the appearance of lists of upstream and downstream genes in pop-up menu windows. These genes are linked to GeNet database entries, containing the information about them. Thus the selection of the gene from the menu calls out the information about it. Special filters permit selective visualization of the interaction of genes controlling different parts of the embryo body. From owner-software@net.bio.net Thu Jun 05 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.nacamar.de!news-kar1.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!news.unige.ch!news From: grandcha@cmu.unige.ch (Kenneth Grandchamp) Newsgroups: bionet.software Subject: Re: Plasmid drawing program for windows Date: 6 Jun 1997 07:39:32 GMT Organization: Centre Medical Universitaire Lines: 21 Message-ID: <5n8erk$t49@uni2f.unige.ch> References: <5n6od4$6lf@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: 129.194.97.221 Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.6 In article <5n6od4$6lf@ccshst05.cs.uoguelph.ca>, wyu@uoguelph.ca says... > >Dear netters, > Does anyone know where there is a plasmid-drawing program for >windows for sale at a reasonable price ($400-500)? Thanks in advance for >your reply. > >Wenjin Yu you can find PC versions at: - Clone Manager 4: http://www.scied.com/sescat.htm - WinPlas 2.5 at: http://www.webaxis.com/goldstein/winplas.html Ken. From owner-software@net.bio.net Thu Jun 05 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!nntprelay.mathworks.com!news.mathworks.com!howland.erols.net!newsfeed.internetmci.com!in3.uu.net!132.158.82.102!hearye.mlb.semi.harris.com!usenet From: Jim Zalnoski Newsgroups: sci.stat.consult,sci.stat.edu,comp.soft-sys.sas,comp.soft-sys.stat.spss,comp.soft-sys.stat.systat,bionet.software Subject: Re: split split plot analysis Date: Fri, 06 Jun 1997 07:32:30 -0400 Organization: Harris Semiconductor, Melbourne, FL Lines: 16 Message-ID: <3397F54E.1E35@harris.com> References: <3396897A.7446@gengenp.rug.ac.be> NNTP-Posting-Host: jzalnoski.mis.semi.harris.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) SAS can perform this analysis because it allows you to specify the correct error term for each factor. Any software that can specify error terms will therefore also 'perform' split split plot analysis. A PC based software I use that can do this is Statistica. Jim Zalnoski Statistician Harris Semiconductor Laury Chaerle wrote: > > Which software other than SAS can perform a split split plot analysis? > -- > Laury CHAERLE ==================================================== > Vlaams Instituut voor Biotechnologie VIB > LABORATORY OF GENETICS > UNIVERSITY OF GENT, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium From owner-software@net.bio.net Thu Jun 05 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!newsfeed.nacamar.de!news-feed.inet.tele.dk!uninett.no!news.uni-c.dk!balder.adm.ku.dk!not-for-mail From: Søren Schandorff Newsgroups: bionet.software Subject: Which DNA analysis programs? Date: Fri, 06 Jun 1997 11:51:49 +0200 Organization: Zoological Institute Lines: 10 Message-ID: <3397DDB5.A7A@aki.ku.dk> Reply-To: sschandorf@aki.ku.dk NNTP-Posting-Host: pc197.zi.ku.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (WinNT; I) Hi, I am working on Impala population genetics, and need a window (PC) program for manual aligning. A program that have colors for each base (as in Seq Pub) and that have other features such as; consensus, show complement string and which can deal with different sequence formats. All in all a program similar to seq pub (for example a PC version of seq app), but without the bugs of Seq Pub for windows. Thanks, Louise, Dept of Population Biology, University of Copenhagen Please also reply directly; E-mail: lgrau@zi.ku.dk From owner-software@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!feed.nntp.acc.ca!newsfeeder.toronto.ican.net!news.ican.net!newsfeeder From: The Free Stuff Webring Newsgroups: bionet.software Subject: Free Stuff to give away!? Date: Fri, 06 Jun 1997 16:47:37 -0300 Organization: ACC TelEnterprises Ltd. Lines: 4 Message-ID: <33986959.1190@chebucto.ns.ca> Reply-To: as280@chebucto.ns.ca NNTP-Posting-Host: ppp-180.halifax-01.ican.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win95; I) Let people know about it by joining the FREE STUFF webring! Sign up today and let people know what you're giving away! http://chebucto.ns.ca/~as280/fswebring.html From owner-software@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!vixen.cso.uiuc.edu!uwm.edu!news.cse.psu.edu!news.ece.nwu.edu!newsfeed.acns.nwu.edu!news.acns.nwu.edu!news From: "Steve Glaum" Newsgroups: bionet.software Subject: Axoscope won't use free IRQ Date: 6 Jun 1997 16:57:04 GMT Organization: Northwestern University, Evanston, IL, US Lines: 13 Message-ID: <01bc729a$855c9ae0$506f7ca5@glaum.physio.nwu.edu> NNTP-Posting-Host: pc080.physio.nwu.edu X-Newsreader: Microsoft Internet News 4.70.1161 We just installed a digidata 1200B board in our new Dell Pentium Pro 200 and Axoscope will not accept IRQ 15, saying it is in use by something else. Win95 system properties reports IRQ as being free. Freeing other IRQs (10, 11) and trying them also failed to work. This board worked fine on IRQ15 on our older Dimension 150. pClamp6, which needs no IRQ, also works, so the board is fine. Any ideas? s-glaum@nwu.edu Dr. Steven R. Glaum Assistant Professor Northwestern University Medical School From owner-software@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!199.3.12.173!newsfeed.concentric.net!news-master!news From: Ketchup@cris.com (ketchup) Newsgroups: bionet.software Subject: Re: Which DNA analysis programs? Date: Fri, 06 Jun 1997 17:03:22 GMT Organization: Concentric Internet Services Lines: 27 Message-ID: <5n9fqm$b7u@chronicle.concentric.net> References: <3397DDB5.A7A@aki.ku.dk> NNTP-Posting-Host: ts035d01.cup-ca.concentric.net X-Newsreader: Forte Free Agent 1.0.82 The next version of GeneDoc will have import/export support for multiple file formats and will be able to compliment and reverse DNA sequences. Its due out next week. If you want to get the current version and try out these features on a beta basis, get the program from the below website and get the update patch from the below ftp site: http://www.cris.com/~ketchup/genedoc.shtml ftp://ftp.netcom.com/pub/ka/karl/GD322008.EXE (32 bit version) ftp://ftp.netcom.com/pub/ka/karl/GD162008.EXE (16 bit version) Søren Schandorff wrote: >Hi, >I am working on Impala population genetics, and need a window (PC) >program for manual aligning. A program that have colors for each base >(as in Seq Pub) and that have other features such as; consensus, show >complement string and which can deal with different sequence formats. >All in all a program similar to seq pub (for example a PC version of seq >app), but without the bugs of Seq Pub for windows. >Thanks, Louise, Dept of Population Biology, University of Copenhagen >Please also reply directly; E-mail: lgrau@zi.ku.dk From owner-software@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!in3.uu.net!205.230.7.55!whowhere.com!charnel.ecst.csuchico.edu!waldorf.csc.calpoly.edu!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software,bionet.software.gcg Subject: facility charges Date: 3 Jun 1997 16:34:14 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 16 Message-ID: <5n1h26$ceh@gap.cco.caltech.edu> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu Xref: biosci bionet.software:18767 bionet.software.gcg:2543 The Biology division is once again reviewing how it does facility chargebacks, and as part of that the powers that be want to know how at least two other Universities recover costs for their Protein/DNA analysis facilities. As is typical of such things, they allotted me a total of two days to gather this information :-(. So, I would greatly appreciate it if any of you who run a central GCG (or Staden, or whatever) analysis facility would share your billing methods with me. (FYI: currently we charge $3.00/hour for connect/batch time, and make up the remainder of costs from general Division funds.) Thank you, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!feed1.news.erols.com!tipu4.cwix.net!h1-news1.mcl.net!sun1.mcmail.com!berrall From: berrall@mcmail.com (Nick Berrall) Newsgroups: bionet.software Subject: Visit The Windows Goodies Website Date: Sat, 07 Jun 1997 18:21:26 GMT Organization: CWC - Internet Dial News Server Lines: 15 Message-ID: <5nc8mj$mo53@sun1.mcmail.com> NNTP-Posting-Host: asn17-120.mcmail.com X-Newsreader: News Xpress 2.01 Visit The Windows Goodies Website At: http://www.windows-goodies.mcmail.com/ For: Software (Shareware and Freeware), Wallpaper Images for your Windows Desktop, webpage bacgrounds, Various Sound Files and free Internet services. Also free Java scripts for your Homepages and you can submit your own software to my website. From owner-software@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-feed.inet.tele.dk!uninett.no!news.uni-c.dk!news.uni-c.dk!not-for-mail From: Peter Lindum Newsgroups: bionet.software Subject: Need to check my oligos/primers Date: Sat, 07 Jun 1997 16:57:02 +0200 Organization: Dept. of Microbiology, DTU, Denmark Lines: 11 Message-ID: <339976BE.56@im.dtu.dk> Reply-To: pwl@im.dtu.dk NNTP-Posting-Host: clint.im.dtu.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) I've heard of an easy to use, small, freeware program, which is able to determine if a given PCR- or sequencing-primer is any good. It should check inhibitory factors like dimers, stem-loop structures etc. which may impair proper hybridization. Please respond to me directly, and thanks in advance. Peter W. Lindum, Dept. of Microbiology, DTU, Denmark. pwl@im.dtu.dk From owner-software@net.bio.net Sun Jun 08 23:00:00 1997 Newsgroups: bionet.software Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!news.idsc.gov.eg!not-for-mail From: Sherif Safwatt Subject: Re: Axoscope won't use free IRQ Message-ID: <33988FE3.7721@iec.egnet.net> Date: Sat, 07 Jun 1997 01:32:03 +0300 References: <01bc729a$855c9ae0$506f7ca5@glaum.physio.nwu.edu> Organization: Home X-Mailer: Mozilla 3.0Gold (Win95; I) MIME-Version: 1.0 To: Steve Glaum Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 12 Dear Dr.Steve ; IRQ 15 is used by IDE2 on motherboard to work with it you may disable secondry IDE option from the motherboard setup utility or setup software , but be sure that you do not have any other divice use IRQ 15 like CD-drive connected to secondary IDE ......... ======================================================================= Yours : Sherif Safwat Biophysist From owner-software@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!enzyme.demon.co.uk!enzyme.demon.co.uk!not-for-mail From: pedro@enzyme.demon.co.uk (Pedro Mendes) Newsgroups: bionet.software Subject: Re: Public domain source code for fast fourier transforms and/or spectral analysis... Date: Sun, 08 Jun 1997 23:34:56 GMT Organization: Home Message-ID: <687cd$172238.22d@enzyme.demon.co.uk> References: <5net75$q2f@kew.globalnet.co.uk> NNTP-Posting-Host: enzyme.demon.co.uk X-NNTP-Posting-Host: enzyme.demon.co.uk [158.152.78.15] X-Newsreader: WinVN 0.99.8 (x86 32bit) Lines: 26 In article <5net75$q2f@kew.globalnet.co.uk>, aida@globalnet.co.uk says... > >I am looking for some public domain source code for performing fast >fourier transforms and/or spectral analysis for a medical application. >A pointer to a software library would be very much appreciated. You will find routines for FFT and many other numerical methods in the netlib archive. You can access a UK mirror of netlib at: http://sunsite.doc.ic.ac.uk/packages/netlib/ The original is at http://netlib.bell-labs.com/netlib/master/readme.html -- Pedro Mendes home: pedro@enzyme.demon.co.uk , work: prm@aber.ac.uk | Aberystwyth, http://www.enzyme.demon.co.uk/pedro.html | Wales, U.K. Author of GEPASI, a biochemical kinetics simulator | European Union http://gepasi.dbs.aber.ac.uk/softw/Gepasi.html From owner-software@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!news.bbnplanet.com!theplanet.net!knews.uk0.vbc.net!vbcnet-gb!azure.xara.net!xara.net!news-feed1.globalnet.co.uk!kew.globalnet.co.uk!usenet From: aida@globalnet.co.uk (Dr. Eldon D. Lehmann) Newsgroups: bionet.software Subject: Public domain source code for fast fourier transforms and/or spectral analysis... Date: Mon, 09 Jun 1997 02:24:39 GMT Lines: 28 Message-ID: <5net75$q2f@kew.globalnet.co.uk> NNTP-Posting-Host: client86dd.globalnet.co.uk X-Newsreader: Forte Free Agent 1.0.82 8th June 1997 - pm Hi there - I am new to this group - but I wonder if someone might be able to help. I am looking for some public domain source code for performing fast fourier transforms and/or spectral analysis for a medical application. A pointer to a software library would be very much appreciated. Thanks in anticipation. With best wishes, Dr. Eldon Lehmann London, UK From: Dr. Eldon D. Lehmann, London, UK E-mail: aida@globalnet.co.uk Over 5500 visitors and over 2500 users can't all be wrong! Check out the *free*ware DOS-based AIDA interactive diabetes simulator at the Diabetes UK site: http://www.diabetic.org.uk/aida.htm From owner-software@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gsl.net!uwm.edu!news.cse.psu.edu!news.ece.nwu.edu!newsfeed.acns.nwu.edu!news.acns.nwu.edu!news From: "Steve Glaum" Newsgroups: bionet.software Subject: Re: Axoscope won't use free IRQ Date: 9 Jun 1997 18:32:06 GMT Organization: Northwestern University, Evanston, IL, US Lines: 18 Message-ID: <01bc7503$4b714f40$506f7ca5@glaum.physio.nwu.edu> References: <01bc729a$855c9ae0$506f7ca5@glaum.physio.nwu.edu> <33988FE3.7721@iec.egnet.net> NNTP-Posting-Host: pc080.physio.nwu.edu X-Newsreader: Microsoft Internet News 4.70.1161 This was freed, but still doesn't work. Sherif Safwatt wrote in article <33988FE3.7721@iec.egnet.net>... > Dear Dr.Steve ; > > IRQ 15 is used by IDE2 on motherboard to work with it you may disable > secondry IDE option from the motherboard setup utility or setup software > , but be sure that you do not have any other divice use IRQ 15 like > CD-drive connected to secondary IDE ......... > > ======================================================================= > > Yours : > Sherif Safwat > Biophysist > > From owner-software@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.nacamar.de!news-kar1.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!swsbe6.switch.ch!news.vub.ac.be!usenet From: plebrun@fysp1.vub.ac.be (Philippe Lebrun) Newsgroups: bionet.software Subject: Re: Public domain source code for fast fourier transforms and/or spectral analysis... Date: 9 Jun 1997 11:28:14 GMT Organization: Brussels Free Universities VUB/ULB Lines: 14 Message-ID: <5ngpce$r58@rc1.vub.ac.be> References: <5net75$q2f@kew.globalnet.co.uk> NNTP-Posting-Host: fysp1.vub.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 0.9.8 In article <5net75$q2f@kew.globalnet.co.uk>, aida@globalnet.co.uk (Dr. Eldon D. Lehmann) writes: > > I am looking for some public domain source code for performing fast > fourier transforms and/or spectral analysis for a medical application. > A pointer to a software library would be very much appreciated. > Try "Numerical Recipes in [C Pascal Fortan ...]" by Press, Flannery,Teukolsky, and Vetterling Cambridge University Press. All you need, and quite well explained. -Philippe From owner-software@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!nntp.uio.no!not-for-mail From: Kaare Gärtner Newsgroups: alt.image.medical,bionet.software,comp.dsp,comp.graphics.visualization,sci.image.processing,sci.med.radiology Subject: Image processing SW Date: Mon, 09 Jun 1997 13:20:11 +0200 Organization: The Norwgian Radiumhospital, Dept. of Biophysics Lines: 16 Message-ID: <339BE6EB.2C7B@radium.uio.no> Reply-To: kaareg@radium.uio.no NNTP-Posting-Host: pcdnr130.uio.no Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.01 (Win95; I) CC: kaareg@radium.uio.no Hi, I need a comment from You on image processing software. Anyone of You have strong feelings 'bout some particular package ? I'd be thankful if You'd also give me some hints 'bout market leadership. Thank you, --kaare -------------------------------------------------------------- | Kaare Gärtner | The Norwegian Radium Hospital | | kaareg@radium.uio.no| Dep. of biophysics | | fax:+47 22934270 | Montebello | | tlf:+47 22934276 | 0310 OSLO | -------------------------------------------------------------- From owner-software@net.bio.net Mon Jun 09 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!su-news-feed4.bbnplanet.com!news.bbnplanet.com!enews.sgi.com!decwrl!tribune.usask.ca!rover.ucs.ualberta.ca!not-for-mail From: "Dr. D. J. Pehowich" Newsgroups: bionet.software Subject: Calcium Buffers Date: Mon, 09 Jun 1997 09:31:43 -0600 Organization: University of Alberta Lines: 6 Message-ID: <339C21DF.CE6@gpu.srv.ualberta.ca> NNTP-Posting-Host: physi2.dent.ualberta.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win95; I) There was a program titled CABUFFER by Dr. J. Kleinschmidt at NYU that was on bionet.software at one time. Does anyone have this program? If you do could you please send me an email with the files attached. D.J. Pehowich dpehowic@gpu.srv.ualbertra.ca From owner-software@net.bio.net Mon Jun 09 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!jump.net!grunt.dejanews.com!not-for-mail Date: Mon, 09 Jun 1997 19:36:14 -0600 From: ftir@hotmail.com Subject: Re: Shimadzu Class VP software Newsgroups: bionet.software Message-ID: <865646201.18964@dejanews.com> Reply-To: Andrew Elwell <8904741e@udcf.gla.ac.uk> Organization: Deja News Usenet Posting Service To: ftir@hotmail.com References: X-Article-Creation-Date: Sat Jun 07 01:16:42 1997 GMT X-Originating-IP-Addr: 198.76.201.196 (sailor.lib.md.us) X-Http-User-Agent: Lynx/2.7.1ac-0.24 libwww-FM/ X-Authenticated-Sender: ftir@hotmail.com Lines: 20 In response to Andrew Elwell email regarding Shimadzu LC-10 Problems ftir@hotmail.com wrote: > > Considering that it apparently only took 18 months to get Class VP > software to market according to info at http://members.tripod.com/~alerts, > what could you be complaining about? Where is your Shimadzu tech > support specialist? Where is your Shimadzu sales representative? > Contact Shimadzu and see if they'll buy back your LC-10 system. > This will probably save you some future headaches! BUYER BEWARE after reading about the OTHER side of Shimadzu! > GOOD LUCK! > > > > > http://members.tripod.com/~alerts -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-software@net.bio.net Mon Jun 09 23:00:00 1997 Path: biosci!rutgers!gatech!EU.net!Norway.EU.net!online.no!not-for-mail From: "Tor Egon Mikkelsen" Newsgroups: alt.comp.shareware,alt.comp.shareware.programmer,alt.rec.camping,bionet.software,chinese.comp.software,comp.mail.list-admin.software,comp.software-eng,de.comm.internet.software,de.comp.shareware,rec.outdoors.camping Subject: Program for ma Camping Site Date: 10 Jun 1997 18:47:46 GMT Organization: Telenor Online Public Access Lines: 15 Message-ID: <01bc75cf$b40c0d20$a6584382@tjuke> NNTP-Posting-Host: ti11a02-0038.dialup.online.no X-Newsreader: Microsoft Internet News 4.70.1157 We need a small prgram dos / windows to admin a small camping site because we must make list over all guests every day Is there anyone who can give us a hint ?? Pls answer by mail Yours faithfully Tor Egon Mikkelsen Drammen .Norway Mailto: sleepy@mail.link.no From owner-software@net.bio.net Mon Jun 09 23:00:00 1997 Path: biosci!rutgers!dziuxsolim.rutgers.edu!uunet!in3.uu.net!128.230.129.106!news.maxwell.syr.edu!europa.clark.net!newsfeeds.sol.net!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Re: pairwise alignment program wanted Followup-To: bionet.software Date: 10 Jun 1997 11:29:07 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 23 Message-ID: References: Reply-To: aiyar@ebv.oncology.wisc.edu NNTP-Posting-Host: ebv.oncology.wisc.edu X-Newsreader: slrn (0.9.4.0 UNIX) Xref: biosci bionet.molbio.methds-reagnts:58466 bionet.software:18778 On 10 Jun 1997 09:46:39 GMT, Xavier De Bolle (Xavier.DeBolle@fundp.ac.be) wrote: >We currently need a simple program (free of charge, if possible) that >aligns two DNA sequences The programs "align" and "align0" that are part of the FASTA distribution will let you align two DNA sequences. It is free, and Macintosh binaries of the FASTA programs are available. You can retrieve the fasta programs from: ftp://ftp.virginia.edu/pub/fasta For multiple alignments on a Mac, you might consider using ClustalX, available from ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX. Mac68k and PowerPC binaries are available. Later, Ashok -- Ashok Aiyar, Ph.D. McArdle Laboratory for Cancer Research aiyar@ebv.oncology.wisc.edu From owner-software@net.bio.net Mon Jun 09 23:00:00 1997 Newsgroups: bionet.software Path: biosci!rutgers!gatech!howland.erols.net!europa.clark.net!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!server6.netnews.ja.net!str-ccsun!strath-cs!liv!news From: len bell Subject: Wanted: Calcium buffer program. Content-Type: text/plain; charset=us-ascii Message-ID: <339D3E99.7581@liverpool.ac.uk> Sender: news@liverpool.ac.uk (News System) Nntp-Posting-Host: pc028022.med.liv.ac.uk Content-Transfer-Encoding: 7bit Organization: The University of Liverpool Mime-Version: 1.0 Date: Tue, 10 Jun 1997 11:46:33 GMT X-Mailer: Mozilla 2.02 (Win16; I) Lines: 9 Does anyone know of a good program for calculating free calcium (Ca2+) levels in buffers containing [ATP/ADP], [EGTA], pH etc. Would the CABUFFER program reffered to in D J Pehowich post do the job? Thanks for your help, Len Bell. lgbell@liv.ac.uk From owner-software@net.bio.net Mon Jun 09 23:00:00 1997 Path: biosci!rutgers!uwm.edu!news-peer.gsl.net!europa.clark.net!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!server5.netnews.ja.net!server3.netnews.ja.net!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!charlie.lif.icnet.uk!not-for-mail From: islam Newsgroups: alt.image.medical,bionet.software,comp.dsp,comp.graphics.visualization,sci.image.processing,sci.med.radiology Subject: Re: Image processing SW Date: Tue, 10 Jun 1997 02:52:54 -0700 Organization: Imperial Cancer Research Fund Message-ID: <339D23F6.167E@icrf.icnet.uk> References: <339BE6EB.2C7B@radium.uio.no> NNTP-Posting-Host: palm.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) Lines: 21 Hi , Perhaps you can say what type of use (e.g. 3D reconstruction, 2D image processing)/computer systems you have in mind. Examples of 2D tools are NIH image (sorry cant recall reference). Also look at http://biocomp.arc.nasa.gov/3dreconstruction/software/ Kaare Gärtner wrote: > I need a comment from You on image processing software. > Anyone of You have strong feelings 'bout some particular package ? > I'd be thankful if You'd also give me some hints 'bout market > leadership. ____________________________________________ 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/ ____________________________________________ From owner-software@net.bio.net Mon Jun 09 23:00:00 1997 From: stu30142@mail.uni-kiel.d400.de (Kai Lehmann) Newsgroups: alt.image.medical,bionet.software,comp.dsp,comp.graphics.visualization,sci.image.processing,sci.med.radiology Subject: Re: Image processing SW Date: Tue, 10 Jun 1997 22:29:35 GMT Organization: University of Kiel / FRG Lines: 18 Message-ID: <339dd46c.8080568@news.rz.uni-kiel.de> References: <339BE6EB.2C7B@radium.uio.no> NNTP-Posting-Host: 134.245.99.229 X-Newsreader: Forte Agent .99e/32.227 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.nacamar.de!fu-berlin.de!news.rz.uni-hildesheim.de!newsserver.rrzn.uni-hannover.de!infosrv.rz.uni-kiel.de!not-for-mail Kaare Gärtner wrote: >Hi, > >I need a comment from You on image processing software. >Anyone of You have strong feelings 'bout some particular package ? >I'd be thankful if You'd also give me some hints 'bout market >leadership. Try ImageTool (http://ddsdx.uthscsa.edu/dig/itdesc.html) or NIH-Image (Mac: http://rsb.info.nih.gov/nih-image/) (IBM-PC: NIH-Homepage/News/Scion-Image-PC). Both are well tested programms and you get them for free. - Kai Lehmann stu30142@mail.uni-kiel.d400.de From owner-software@net.bio.net Mon Jun 09 23:00:00 1997 From: Lu.Do@Home.DiVa.nl (L.P.J.J. Noldus) Newsgroups: alt.image.medical,bionet.software,comp.dsp,comp.graphics.visualization,sci.image.processing,sci.med.radiology Subject: Re: Image processing SW Date: Tue, 10 Jun 1997 22:29:26 GMT Organization: Noldus Information Technology b.v. Reply-To: Lu.Do@Home.DiVa.nl Message-ID: <339dd4f4.7334378@News.DiVa.NL> References: <339BE6EB.2C7B@radium.uio.no> X-Newsreader: Forte Free Agent 1.11/32.235 NNTP-Posting-Host: wg04.diva.nl Path: biosci!rutgers!gatech!www.nntp.primenet.com!nntp.primenet.com!news.mathworks.com!europa.clark.net!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!fido.news.demon.net!demon!newsgate.unisource.nl!surfnet.nl!wau.nl!wg04.diva.nl Lines: 24 Kaare Gärtner wrote: >I need a comment from You on image processing software. >Anyone of You have strong feelings 'bout some particular package ? >I'd be thankful if You'd also give me some hints 'bout market >leadership. We use Image-Pro Plus from Media Cybernetics. It is a very flexible toolbox for analysis of static 2D images. For dynamic analysis of moving images, we use EthoVision (our own development). Feel free to contact me directly if you need more details. Lucas Noldus Noldus Information Technology b.v. Costerweg 5 P.O. Box 268 6700 AG Wageningen The Netherlands Phone: +31-(0)317-497677 Fax: +31-(0)317-424496 E-mail: info@noldus.nl Web: http://www.noldus.com From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!ais.net!howland.erols.net!newsfeed.internetmci.com!news.dti.ad.jp!news.dtinet.or.jp!ppp7!aisoai From: aisoai@agc.co.jp (ISOAI Atsushi) Newsgroups: bionet.software Subject: Re: Need to check my oligos/primers Date: Wed, 11 Jun 1997 22:10:07 +0900 Organization: Asahi Glass Co.LTD. Lines: 23 Message-ID: References: <339976BE.56@im.dtu.dk> NNTP-Posting-Host: ppp7.yokohama2.dtinet.or.jp Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Newsreader: NewsWatcher-J18 (2.1.6) In article <339976BE.56@im.dtu.dk>, pwl@im.dtu.dk wrote: >I've heard of an easy to use, small, freeware program, which is able to >determine if a given PCR- or sequencing-primer is any good. > >It should check inhibitory factors like dimers, stem-loop structures >etc. which may impair proper hybridization. ... Hi, Peter, You can get a useful software "Amplify" for PCR from; url: http://www.wisc.edu/genetics/CATG/amplify/index.html. And I suggest good Web site; url: http://genome-www2.stanford.edu/cgi-bin/SGD/web-primer for designing PCR and sequencing primers. Please try. Good luck! Bye. -- =================================================== Atsushi Isoai, Ph.D. | Research Center, Asahi Glass Co.LTD., JAPAN URL: http://www.yk.rim.or.jp/~aisoai/molbio-j.html =================================================== From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!rutgers!uwm.edu!newsfeeds.sol.net!news.maxwell.syr.edu!EU.net!news.eunet.fi!news2.funet.fi!voxopm!jsaarela From: jsaarela@csc.fi (Janne Saarela) Newsgroups: bionet.software Subject: Re: Plasmid drawing program for windows Date: 11 Jun 97 08:28:37 GMT Organization: Centre for Scientific Computing, Finland (CSC) Lines: 38 Distribution: sfnet Message-ID: References: <5n6od4$6lf@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: 128.214.248.23 X-Newsreader: NN version 6.5.1 (NOV) In <5n6od4$6lf@ccshst05.cs.uoguelph.ca> wyu@uoguelph.ca (Wenjin Yu) writes: >Dear netters, > Does anyone know where there is a plasmid-drawing program for >windows for sale at a reasonable price ($400-500)? Thanks in advance for >your reply. >Wenjin Yu >-- HI! Take a look at: http://www.hytti.uku.fi/~kiviraum/plasmid/plasmid.html Plasmid Processor is a simple tool for plasmid presentation for scientific and educational purposes. Plasmid Processor is freeware, so you can use and distribute it freely. You can download full executable version of Plasmid Processor 1.02 for Windows at http://www.uku.fi/~kiviraum/plasmid/plasp102.zip With regards, Janne Saarela -- saarela@messi.uku.fi http://www.uku.fi/~saarela From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!IR2CBM.CNRS-MRS.FR!athel From: athel@IR2CBM.CNRS-MRS.FR (Athel) Newsgroups: bionet.software Subject: Re: Wanted: Calcium buffer program. Date: 11 Jun 1997 05:28:01 -0700 Organization: CNRS Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <339E99BF.290A@ibsm.cnrs-mrs.fr> Reply-To: athel@ir2cbm.cnrs-mrs.fr NNTP-Posting-Host: net.bio.net Len Bell asked: >Does anyone know of a good program for calculating free calcium (Ca2+) levels in buffers containing [ATP/ADP], [EGTA], pH etc. Your colleague John Easterby (jse@liverpool.ac.uk) should be able to help you on this one! Take a look at his pages at http://www.liv.ac.uk/~jse/software.html and http://www.bi.umist.ac.uk/Staff/Academia/RJB/Buffers/Bufbook.html. I haven't yet looked at his book myself, but I read a very complimentary review of it recently. It seems to be mainly (or exclusively) concerned with pH, but the same principles apply to pCa, and I don't see any obvious reason why the program couldn't be modified to calculate pCa. My own program described in Biochem. J. (1976) 159, 1-5 could certainly do these calculations, but as it is a Fortran program for running on mainframes (and not at all friendly by modern standards), I doubt if it would satisfy you. In any case, I'm not sure how easily I could dig out a copy. I mention it here only because it wouldn't be especially difficult to rewrite it to modern standards, and I could probably be persuaded to do it if there were a demand. Athel From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!199.232.56.18!news.ultranet.com!not-for-mail From: Williamstone Enterprises Newsgroups: bionet.software Subject: ANNOUNCE: Free primer design online Date: Wed, 11 Jun 1997 09:27:17 -0400 Organization: Williamstone Enterprises Lines: 11 Message-ID: <339EA7B5.3507@williamstone.com> Reply-To: rjr@williamstone.com NNTP-Posting-Host: gonzo.worksystems.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Macintosh; I; PPC) Dear Colleagues, Please enjoy our free oligonucleotide design applications online. We welcome any comments or suggestions on how to make the software a better tool for the molecular biology community. http://www.williamstone.com/primers Many thanks for your time. Williamstone Enterprises, Inc. From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!www.nntp.primenet.com!nntp.primenet.com!europa.clark.net!ais.net!vixen.cso.uiuc.edu!news.indiana.edu!sunflower.bio.indiana.edu!not-for-mail From: wfischer@sunflower.bio.indiana.edu (Will Fischer) Newsgroups: bionet.software Subject: Re: multiple alignment Date: 11 Jun 1997 17:47:40 GMT Organization: Biology, Indiana University - Bloomington Lines: 17 Distribution: world Message-ID: <5nmobs$5qg$1@dismay.ucs.indiana.edu> References: NNTP-Posting-Host: sunflower.bio.indiana.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Berke, Tamas (TBerke@CHKD.COM) wrote: : Could any of you name a program (PC or UNIX) which can help me to align : corresponding nucleic acid sequences to the already aligned (Clustal) : amino acid sequences? "align2aa", a perl program to do this, is available via my web page (below). It reads input via readseq, and should work 'most anywhere Perl is installed. See http://www.bio.indiana.edu/~wfischer/Perl_Scripts/ -- ____________________________________________________________ Will Fischer (to reply, remove smiley after username) Biology Department wfischer;-)@indiana.edu Jordan Hall http://www.bio.indiana.edu/~wfischer Indiana University Lab: 812-855-2549 Bloomington, Indiana 47405 USA FAX: 812-855-6705 From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!agate!howland.erols.net!newsxfer.itd.umich.edu!news2.acs.oakland.edu!jobone!lynx.unm.edu!bubba.NMSU.Edu!dkim From: dkim@nmsu.edu (D. KIM) Newsgroups: bionet.software Subject: Re: Plasmid drawing program for windows Date: 11 Jun 1997 16:43:16 GMT Organization: New Mexico State University, Las Cruces, NM Lines: 6 Distribution: sfnet Message-ID: <5nmkj4$sd2@bubba.NMSU.Edu> References: <5n6od4$6lf@ccshst05.cs.uoguelph.ca> NNTP-Posting-Host: verdi.nmsu.edu WRT recommendation for Plasmid Processor. I must concur that this is a really nice program. In spite of its limitations, it produces a very nice plasmid schematic without a lot of fuss. I highly recommend it as well. Daniel Kim From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: James McInerney Newsgroups: bionet.software Subject: Re: multiple alignment Date: 11 Jun 1997 16:07:28 +0100 Organization: The Natural History Museum Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5nmevg$4bb@mserv1.dl.ac.uk> References: <97611145355.~INN-UTQa00195.bionet-news@dl.ac.uk> Reply-To: jamm@nhm.ac.uk MIME-Version: 1.0 Original-To: "Berke, Tamas" Lines: 38 Berke, Tamas wrote: > > Dear Colleagues: > Could any of you name a program (PC or UNIX) which can help me to align > corresponding nucleic acid sequences to the already aligned (Clustal) > amino acid sequences? > Your assistance is appreciated. > Tamas Berke I have coded a little program that should compile on most unix machines for introducing gaps into DNA sequences according to where they appear in an amino acid alignment. It is available as C source code or compiled for the PowerPC at: ftp://ftp.nhm.ac.uk/pub/gcua/Putgaps Its neither elegant nor fancy (none of my code is!) and I cannot provide any guarantees, but... Bill Pearson also distributes a program called mrtrans (I think) which also does this. It is available from: ftp://ftp.virginia.edu/ (I hope that's correct). regards, James. p.s. read the documentation with putgaps!!! -- ========= James O. McInerney email: J.mcinerney@nhm.ac.uk Senior Scientific Officer, phone: +44 171 938 9247 Department of Zoology, Fax: +44 171 938 9158 The Natural History Museum, Cromwell Road, London SW7 5BD. ========= From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!FINGON.NORLINK.NET!jsm From: jsm@FINGON.NORLINK.NET Newsgroups: bionet.software Subject: HELP URGENTLY NEEDED PLEASE Date: 10 Jun 1997 22:01:06 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 43 Sender: daemon@net.bio.net Distribution: world Message-ID: <3.0.2.32.19970610004443.007af100@norlink.net> NNTP-Posting-Host: net.bio.net YOUR HELP IS URGENTLY NEEDED PLEASE Dear friend, My name is Mike Chenard, and I am a student here in Thunder Bay, Ontario, Canada, with another year to go before graduating with my college diploma. I am sending you this e-mail because I urgently and desperately need your HELP. The summer job opportunities for students in my community are less than adequate, and are caused by an extremely slow economic recovery from our recent recession. For every summer job available for a student, approximately 60 applications are received. I have personally submitted 87 resumes for minimum wage jobs' without even receiving a response. The total cost for my last year at the college will cost me $14,000. Without the possibility of obtaining a summer job to help me finance this cost, I will not be able to complete my last year of education. Therefore, I will not be able to fulfill my dream of graduating with a college diploma. Face with this situation, I am appealing for your help and generosity. Although my pride will suffer from this request, I need to keep my education as my priority. I am asking you (more like begging you) to help me by sending me $5, or whatever you feel you can afford, to help finance my last year at the college. I figure that your generosity plus all others who help me, will allow me to fulfill my dream of obtaining my college diploma. Please send $5 or whatever amount you feel you can afford to: Mike Chenard 337 Lark Street Thunder Bay, Ontario Canada, P7B 1P4 I wish to express my sincere thank's for your support toward my education. Please feel happy and full of pride with the knowledge that you have help a student fulfill his dream of completing his education. Let me sincerely thank you for your help. Mike Chenard From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!CHKD.COM!TBerke From: TBerke@CHKD.COM ("Berke, Tamas") Newsgroups: bionet.software Subject: (none) Date: 11 Jun 1997 06:45:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Colleagues: Could any of you name a program (PC or UNIX) which can help me to align corresponding nucleic acid sequences to already aligned (Clustal) amino acid sequences? Your assistance is appreciated. Tamas Berke From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!sol.ctr.columbia.edu!news.columbia.edu!sawasdee.cc.columbia.edu!sa176 From: Steve Albanese Newsgroups: bionet.software Subject: Software for college biology? Date: Wed, 11 Jun 1997 14:26:46 -0400 Organization: Columbia University Lines: 8 Message-ID: NNTP-Posting-Host: sawasdee.cc.columbia.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am looking for biology software that simulates animal dissection. Any tips or suggestions greatly appreciated. The student level is freshman/sophmore college. Thank you. From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!rutgers!gatech!nntprelay.mathworks.com!news.mathworks.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!news.apfel.de!univ-lyon1.fr!jussieu.fr!oleane!weld.news.pipex.net!pipex!warm.news.pipex.net!pipex!tank.news.pipex.net!pipex!bbc!news From: "BBC" Newsgroups: alt.image.medical,bionet.software,comp.graphics.visualization,comp.protocols.dicom,sci.image.processing,sci.med.informatics,sci.med.radiology,sci.techniques.mag-resonance Subject: Loading MRI & CT scans onto a SGI Date: 11 Jun 1997 17:45:22 GMT Organization: British Broadcasting Corp. Lines: 13 Message-ID: <01bc768f$6fe7e2c0$9c3cb984@pc-215079> NNTP-Posting-Host: 132.185.60.156 X-Newsreader: Microsoft Internet News 4.70.1161 I am trying to find a way of loading scan data onto an SGI machine for volume rendering. The data is obtained from both MRI & CT scanners, mainly Siemens & General Electric, from various hospitals. The SGI is an Indigo2 High Impact R10,000 in a fairly isolated environment, where FTP or ISDN probably won't be practical. Ideally I would like to able to hook up a magneto-optical drive to the SGI which would read the mo disks. However, nobody I have spoken to seems to be able to know of such a device. It seems likely that a Pioneer SH7101 or SH9101 will load Siemens data on a Sun Sparc workstation, which might be an option if I can get access to a Sun, but it seems unlikely that these drives will talk to a SGI. Does anybody know of any solutions to this problem ? From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!ais.net!europa.clark.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.apfel.de!fu-berlin.de!rag3.rz-berlin.mpg.DE!not-for-mail From: andy@rag3.RZ-Berlin.MPG.DE (Andrei Grigoriev) Newsgroups: bionet.molbio.yeast,bionet.software,bionet.general Subject: genome navigator: yeast Date: 11 Jun 1997 18:54:20 GMT Lines: 13 Message-ID: <5nms8s$8v2@fu-berlin.de> NNTP-Posting-Host: rag3.rz-berlin.mpg.de (141.14.130.162) X-Access: 16 25 816 X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.yeast:7193 bionet.software:18797 bionet.general:27126 Two more data sources have been added to the interactive yeast genome display at the Genome Navigator site: PEDANT by Dmitrij Frishman and Yeast Gene Duplications by Ken Wolfe and Denis Shields. http://www.mpimg-berlin-dahlem.mpg.de/~andy/GN/S.cerevisiae/ Please have a look and let me know if you have any suggestions, criticisms, etc. Andrei Grigoriev Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin-Dahlem, Germany E-mail: andy@rag3.rz-berlin.mpg.de From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!199.2.96.62!news.rain.net!news.teleport.com!ip-pdx03-14.teleport.com!user From: dave@rsd.com_!rem!ove!this (Dave Goldman) Newsgroups: bionet.software Subject: Re: HELP URGENTLY NEEDED PLEASE Date: Wed, 11 Jun 1997 11:56:54 -0800 Organization: Research Software Design Lines: 9 Distribution: world Message-ID: References: <3.0.2.32.19970610004443.007af100@norlink.net> NNTP-Posting-Host: ip-pdx03-14.teleport.com Mike -- Please post the name and address of your college so that would-be donors to your education can confirm with the college registrar that you are indeed enrolled there. -- Dave Goldman Research Software Design From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 From: mreanj@singtao.com Newsgroups: alt.comp.shareware,alt.comp.shareware.programmer,alt.rec.camping,bionet.software,chinese.comp.software,comp.mail.list-admin.software,comp.software-eng,de.comm.internet.software,de.comp.shareware,rec.outdoors.camping Subject: Re: Program for ma Camping Site Date: Wed, 11 Jun 1997 01:34:19 +0800 Organization: STED Lines: 16 Message-ID: <339D901B.12D1@singtao.com> References: <01bc75cf$b40c0d20$a6584382@tjuke> NNTP-Posting-Host: ppp37.singtao.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win95; I) To: Tor Egon Mikkelsen Path: biosci!rutgers!gatech!news.akorn.net!nntprelay.mathworks.com!news.mathworks.com!News1.Vancouver.iSTAR.net!news.istar.net!hammer.uoregon.edu!newsgate.cuhk.edu.hk!news2.hkt.net!news.singtao.com!daniel@singtao.com Tor Egon Mikkelsen wrote: > > We need a small prgram dos / windows > to admin a small camping site > because we must make list over all guests every day > > Is there anyone who can give us a hint ?? > > Pls answer by mail > > Yours faithfully > > Tor Egon Mikkelsen > Drammen .Norway > Mailto: sleepy@mail.link.no fgfd From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!CHKD.COM!TBerke From: TBerke@CHKD.COM ("Berke, Tamas") Newsgroups: bionet.software Subject: multiple alignment Date: 11 Jun 1997 06:45:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Colleagues: Could any of you name a program (PC or UNIX) which can help me to align corresponding nucleic acid sequences to the already aligned (Clustal) amino acid sequences? Your assistance is appreciated. Tamas Berke From owner-software@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!199.3.12.173!newsfeed.concentric.net!news-master!news From: Ketchup@cris.com (ketchup) Newsgroups: bionet.software Subject: Re: multiple alignment Date: Wed, 11 Jun 1997 17:50:35 GMT Organization: Concentric Internet Services Lines: 20 Message-ID: <5nmofc$khb@chronicle.concentric.net> References: NNTP-Posting-Host: ts028d12.cup-ca.concentric.net X-Newsreader: Forte Free Agent 1.0.82 GeneDoc allows you to import new sequences to an alignment file manually align them. Hope this helps. Available for PC/Windows. http://www.cris.com/~ketchup/genedoc.shtml Karl Nicholas. TBerke@CHKD.COM ("Berke, Tamas") wrote: >Dear Colleagues: >Could any of you name a program (PC or UNIX) which can help me to align >corresponding nucleic acid sequences to the already aligned (Clustal) >amino acid sequences? >Your assistance is appreciated. >Tamas Berke From owner-software@net.bio.net Wed Jun 11 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!130.207.244.18!gatech!news.jax.bellsouth.net!news.rdu.bellsouth.net!news.sdf.bellsouth.net!news.atl.bellsouth.net!news.cha.bellsouth.net!not-for-mail From: John Newsgroups: alt.image.medical,bionet.software,comp.graphics.visualization,comp.protocols.dicom,sci.image.processing,sci.med.informatics,sci.med.radiology,sci.techniques.mag-resonance Subject: Re: Loading MRI & CT scans onto a SGI Date: Thu, 12 Jun 1997 17:22:00 -0400 Lines: 17 Message-ID: <33A06878.2A30@bellsouth.net> References: <01bc768f$6fe7e2c0$9c3cb984@pc-215079> Reply-To: jjance@bellsouth.net NNTP-Posting-Host: host-32-96-81-194.cha.bellsouth.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01C-BLS20 (Win95; I) BBC wrote: > > I am trying to find a way of loading scan data onto an SGI machine for > volume rendering. The data is obtained from both MRI & CT scanners, mainly > Siemens & General Electric, from various hospitals. The SGI is an Indigo2 > High Impact R10,000 in a fairly isolated environment, where FTP or ISDN > probably won't be practical. > Ideally I would like to able to hook up a magneto-optical drive to the SGI > which would read the mo disks. However, nobody I have spoken to seems to > be able to know of such a device. It seems likely that a Pioneer SH7101 or > SH9101 will load Siemens data on a Sun Sparc workstation, which might be an > option if I can get access to a Sun, but it seems unlikely that these > drives will talk to a SGI. > > Does anybody know of any solutions to this problem ? I don't know the whole answer but the images would have to be DICOM compliant. From owner-software@net.bio.net Wed Jun 11 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!news-peer.gsl.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-feed.inet.tele.dk!uninett.no!news.uni-c.dk!news.uni-c.dk!not-for-mail From: Jan Hansen Newsgroups: bionet.software Subject: Re: T-cell epitope prediction ? Date: Thu, 12 Jun 1997 13:57:18 +0200 Organization: News Server at UNI-C, Danish Computing Centre for Research and Education. Lines: 30 Message-ID: <339FE41E.1372@cbs.dtu.dk> References: <3395DF05.5451@marlin.utmb.edu> NNTP-Posting-Host: dna.cbs.dtu.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.2 IP22) To: tjiffar@MARLIN.UTMB.EDU tjiffar@MARLIN.UTMB.EDU wrote: > > Is there a software for T-cell epitope prediction based on > a gene sequence? > > Thanks Please see: http://www-bimas.dcrt.nih.gov/molbio/hla_bind/index.html http://www.epimatrix.com/hiv -- Jan Hansen Center for Biological Sequence Analysis Department of Physical Chemistry The Technical University of Denmark Building 206 DK-2800 Lyngby Denmark Phone: +45 4525 2485 Fax: +45 4593 4808 E-mail: janhan@cbs.dtu.dk WWW: http://www.cbs.dtu.dk/janhan/homepage.html From owner-software@net.bio.net Wed Jun 11 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Peter Kulmburg Newsgroups: bionet.software Subject: problems with open transport - modifier, tuner requested Date: 12 Jun 1997 13:43:38 +0100 Lines: 22 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5noqtq$3rf@mserv1.dl.ac.uk> X-Authentication-Warning: skl1.ukl.uni-freiburg.de: smap set sender to using -f Original-To: bio-software@dl.ac.uk Dear collegues, I am using my internet connection quite a lot. Until now I have been working on a PowerMac 6100/60 using the classic network protocol with system 7.5.5 to go to internet. Some days ago I changed to system 7.6.1 and now I have to use OpenTransport 1.1.2. However, I have great problems to go over our firewall with it, something is wrong during daytime although it works perfectly during the night and on weekends. I have heard that there was somewhere a OT tuner or modifier or something that influences IP package sending. Has anybody heard about it or seen a similar problem? Please feel free to send this mail to perhaps more adequate mailing lists, asking them to send the answer to my personal mail address. Thank you very much in advance! Sincerely Peter Peter KULMBURG at home Tel./Fax:+49 761 80 84 39 at work: Tel.: +49 761 270/7208 or 7207 Fax: /7217 From owner-software@net.bio.net Wed Jun 11 23:00:00 1997 Path: biosci!cigb.edu.cu!Mariaelena.Ochagavia From: Mariaelena.Ochagavia@cigb.edu.cu ("Ma. Elena Ochagavia") Newsgroups: bionet.software Subject: viral capsids, 3D coord. Date: 11 Jun 1997 17:23:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <54319EE6EF9@serverdos.cigb.edu.cu> NNTP-Posting-Host: net.bio.net Dear Netters: I need to calculate, using the transformation matrices, the spatial coordinates of the whole viral capsids for a group of virus. Unfortunally, in PDB files the transformation matrices are not uniformily written, and I cannot extract them automatically. Somebody knows about any other alternative database or program to perform this task? Any other suggestion will be appreciated. Maria Elena CIGB. HAVANA. CUBA From owner-software@net.bio.net Wed Jun 11 23:00:00 1997 Path: biosci!rutgers!usenet.logical.net!Gamma.RU!srcc!news.maxwell.syr.edu!feed1.news.erols.com!news.voicenet.com!not-for-mail From: "Visionary Solutions, Inc" Newsgroups: alt.image.medical,bionet.software,comp.dsp,comp.graphics.visualization,sci.image.processing,sci.med.radiology Subject: Re: Image processing SW Date: 12 Jun 1997 00:20:33 GMT Organization: Voicenet - Internet Access - (215)674-9290 Lines: 22 Message-ID: <01bc76bd$0fc81a80$9b1f67cf@g6-266> References: <339BE6EB.2C7B@radium.uio.no> NNTP-Posting-Host: phila227-pri.voicenet.com X-Newsreader: Microsoft Internet News 4.70.1161 Kaare Gärtner wrote in article <339BE6EB.2C7B@radium.uio.no>... > Hi, > > I need a comment from You on image processing software. > Anyone of You have strong feelings 'bout some particular package ? > I'd be thankful if You'd also give me some hints 'bout market > leadership. > > What kind of Image Processing software are yo looking for. You amy want to take a look at VisImage from Visionary Solutions, Inc. You can obtain (download) the VisImage toolkit from www.visolu.com. I hope this helps. Visionary Solutions, Inc. From owner-software@net.bio.net Wed Jun 11 23:00:00 1997 Path: biosci!IRCM.UMontreal.CA!duhaimj From: duhaimj@IRCM.UMontreal.CA ("SI-Johanne Duhaime") Newsgroups: bionet.software Subject: Blast in eukaryotes Date: 12 Jun 1997 13:36:10 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <970612163652.ZM12518@si05.IRCM.UMontreal.CA> NNTP-Posting-Host: net.bio.net Good day Is there any www site where we can compare a sequence to eukaryote sequences only? Thank you -- Johanne Duhaime IRCM 110 Ave des Pins O Montreal, Quebec 987-5556 (tel) 987-5644 (fax) Duhaimj@ircm.umontreal.ca http://www.ircm.umontreal.ca From owner-software@net.bio.net Wed Jun 11 23:00:00 1997 Path: biosci!rutgers!gatech!news.akorn.net!nntprelay.mathworks.com!news.mathworks.com!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!167.142.225.6!newsrelay.netins.net!news.spss.com!news From: nichols@spss.com (David Nichols) Newsgroups: sci.stat.consult,sci.stat.edu,comp.soft-sys.sas,comp.soft-sys.stat.spss,comp.soft-sys.stat.systat,bionet.software Subject: Re: split split plot analysis Date: 12 Jun 1997 20:20:25 GMT Organization: SPSS, Inc. Lines: 20 Message-ID: <5nplm9$5nj@netsrv2.spss.com> References: <3396897A.7446@gengenp.rug.ac.be> NNTP-Posting-Host: sseq1.spss.com In article <3396897A.7446@gengenp.rug.ac.be>, Laury Chaerle wrote: >Which software other than SAS can perform a split split plot analysis? >-- >Laury CHAERLE ==================================================== >Vlaams Instituut voor Biotechnologie VIB > LABORATORY OF GENETICS >UNIVERSITY OF GENT, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium Most statistical software would probably be able to do it. SPSS will do it, most easily in recent releases (7.0 and above). It's unlikely that software will have commands specialized so that they're called anything like this, but the model would be estimable in many procedures that to ANOVA models. -- ----------------------------------------------------------------------------- David Nichols Senior Support Statistician SPSS, Inc. Phone: (312) 329-3684 Internet: nichols@spss.com Fax: (312) 329-3668 ----------------------------------------------------------------------------- From owner-software@net.bio.net Wed Jun 11 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!spool.mu.edu!uwm.edu!chi-news.cic.net!feeder.chicago.cic.net!ftpbox.mot.com!newsfeed.acns.nwu.edu!news.acns.nwu.edu!smallpox1 From: clolson@casbah.acns.nwu.edu (Cheryl Olson) Newsgroups: bionet.software Subject: EST database management Date: Thu, 12 Jun 97 19:04:04 GMT Organization: Northwestern University, Evanston, IL. USA Lines: 6 Message-ID: <5nph74$br0_001@pathology.nwu.edu> NNTP-Posting-Host: smallpox1.pathology.nwu.edu X-Newsreader: News Xpress Version 1.0 Beta #4 Does anyone know or use an EST database management program. We are windows-based and would like to compare new sequences against previous sequences to remove duplicates. Thanks for your help. Bill pcola@merle.acns.nwu.edu From owner-software@net.bio.net Wed Jun 11 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!129.174.1.8!portal.gmu.edu!hearst.acc.Virginia.EDU!mercury.vcu.edu!kguyre From: Max V Myakishev Newsgroups: bionet.software,bionet.molbio.methds-reagnts Subject: Pairwise alignment of 200,000 and 20,000 bp sequences Date: Thu, 12 Jun 1997 14:19:36 -0400 Organization: MCV Lines: 12 Distribution: world Message-ID: <33A03DB8.BB58B5CA@scientist.com> NNTP-Posting-Host: 128.172.85.18 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.0b5 [en] (Win95; I) X-Priority: 3 (Normal) Xref: biosci bionet.software:18807 bionet.molbio.methds-reagnts:58573 I am looking for the tool to perform pairwise alignment of 200,000 and 20,000 bp sequences. Preferable computer platforms: WWW > PC > Mac > UNIX. I already tried many programs and most of them are limited by the input sequence size 32000. Thanks Max V Myakishev, Ph.D. Email: max@scientist.com From owner-software@net.bio.net Wed Jun 11 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!news-feed1.tiac.net!uunet!in1.uu.net!151.99.250.2!server-b.cs.interbusiness.it!usenet From: Sergio Newsgroups: bionet.software Subject: ECG data needed Date: Thu, 05 Jun 1997 19:57:12 +0200 Organization: Centro Servizi Interbusiness Lines: 12 Message-ID: <3396FDF8.778F@elis.interbusiness.it> NNTP-Posting-Host: 151.99.239.60 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Hi, is there anyone who has ECG data (normal and pathological) in ASCII format ? Where can i find it or a program which simulates ECG signals with a digital data output ? Thanks in advance. From owner-software@net.bio.net Wed Jun 11 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!howland.erols.net!psinntp!news.columbia.edu!kiaora.cc.columbia.edu!sa176 From: Steve Albanese Newsgroups: bionet.software Subject: Trying to locate biology software Date: Thu, 12 Jun 1997 08:41:11 -0400 Organization: Columbia University Lines: 8 Message-ID: NNTP-Posting-Host: kiaora.cc.columbia.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am looking for biology software that simulates animal dissection. Any tips or suggestions greatly appreciated. The student level is freshman/sophmore college. Thank you. From owner-software@net.bio.net Wed Jun 11 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!feed1.news.erols.com!tipu4.cwix.net!h1-news1.mcl.net!sun1.mcmail.com!berrall From: berrall@mcmail.com (Nick Berrall) Newsgroups: bionet.software Subject: Test Date: Wed, 11 Jun 1997 22:49:26 GMT Organization: CWC - Internet Dial News Server Lines: 1 Message-ID: <5nn9u0$6nu2@sun1.mcmail.com> NNTP-Posting-Host: asn17-99.mcmail.com X-Newsreader: News Xpress 2.01 test From owner-software@net.bio.net Thu Jun 12 23:00:00 1997 Path: biosci!IR2CBM.CNRS-MRS.FR!athel From: athel@IR2CBM.CNRS-MRS.FR (Athel) Newsgroups: bionet.software Subject: Re: Public domain source code for fast fourier transforms and/or spectral analysis... Date: 13 Jun 1997 01:11:52 -0700 Organization: CNRS Lines: 25 Sender: daemon@net.bio.net Distribution: world Message-ID: <33A1012E.66F4@ibsm.cnrs-mrs.fr> Reply-To: athel@ir2cbm.cnrs-mrs.fr NNTP-Posting-Host: net.bio.net Sean Eddy wrote: >Except that Numerical Recipes source code is emphatically *not* in the public domain. True enough, if the original questioner meant public domain in the strict legal sense. But if he just meant stuff he could use for his own purposes (without passing it on to others) then the Preface to Numerical Recipes explicitly allows this (p. xiii in the 1986 Fortran/Pascal edition): "Although this book and its programs are copyrighted, we specifically authorize you, a reader of the book, to make one machine-readable copy of each program for your own use...". Personally I find the discussion of numerical methods in the book excellent, but the programs themselves virtually incomprehensible because of the meaningless names given to most of the variables. So what I do is to read the text carefully and then write programs that I can understand on that basis rather than try to use the programs as supplied. (Legalists may like to note that that procedure is likewise authorized and even recommended by the authors: "If you analyze the ideas contained in a program, and then express those ideas in your own distinct implementation, then that new program implementation belongs to you.") Athel From owner-software@net.bio.net Thu Jun 12 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!surfnet.nl!ruu.nl!not-for-mail From: nospam-m.r.hoeksma@far.ruu.nl ( Marco Hoeksma) Newsgroups: alt.image.medical,bionet.software,comp.graphics.visualization,comp.protocols.dicom,sci.image.processing,sci.med.informatics,sci.med.radiology,sci.techniques.mag-resonance Subject: Re: Loading MRI & CT scans onto a SGI Date: Fri, 13 Jun 1997 08:18:23 GMT Organization: Academic Computer Centre Utrecht, (ACCU) Lines: 34 Message-ID: <33a0f766.1806016@news.cc.ruu.nl> References: <01bc768f$6fe7e2c0$9c3cb984@pc-215079> <33A06878.2A30@bellsouth.net> Reply-To: m.r.hoeksma@far.ruu.nl NNTP-Posting-Host: psycpc39.far.ruu.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Forte Agent 1.0/32.354 On Thu, 12 Jun 1997 17:22:00 -0400, John wrote: >Quote>BBC wrote: >Quote>> >Quote>> I am trying to find a way of loading scan data onto an SGI machine for >Quote>> volume rendering. The data is obtained from both MRI & CT scanners, mainly >Quote>> Siemens & General Electric, from various hospitals. The SGI is an Indigo2 >Quote>> High Impact R10,000 in a fairly isolated environment, where FTP or ISDN >Quote>> probably won't be practical. >Quote>> Ideally I would like to able to hook up a magneto-optical drive to the SGI >Quote>> which would read the mo disks. However, nobody I have spoken to seems to >Quote>> be able to know of such a device. It seems likely that a Pioneer SH7101 or >Quote>> SH9101 will load Siemens data on a Sun Sparc workstation, which might be an >Quote>> option if I can get access to a Sun, but it seems unlikely that these >Quote>> drives will talk to a SGI. >Quote>> >Quote>> Does anybody know of any solutions to this problem ? >Quote>I don't know the whole answer but the images would have to be DICOM >Quote>compliant. I don't think the image format has anything to do with being able to read the images or not. You only need a MO drive that can talk to your Indigo. As far as I know, you have one external SCSI-2 connector on your Indigo to which you can connect your MO. Ask SGI for a list of drives that are compatible with your system. DICOM is the file format, it is not critical for reading /writing the MO. You should check what filesystem is used when the disk is written however. Regards, Marco Standard disclaimer etc. and standard anti-spam: e-mail: remove 'nospam-' from my address when you reply by email. From owner-software@net.bio.net Thu Jun 12 23:00:00 1997 Path: biosci!daresbury!uninett.no!news-feed.inet.tele.dk!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gsl.net!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!ebv.oncology.wisc.edu!aiyar From: aiyar@ebv.oncology.wisc.edu (Ashok Aiyar) Newsgroups: bionet.software,bionet.molbio.methds-reagnts Subject: Re: Pairwise alignment of 200,000 and 20,000 bp sequences Followup-To: bionet.software Date: 12 Jun 1997 21:47:56 GMT Organization: Sugden Lab, McArdle Laboratory for Cancer Research, UW-Madison Lines: 22 Distribution: world Message-ID: References: <33A03DB8.BB58B5CA@scientist.com> Reply-To: aiyar@ebv.oncology.wisc.edu NNTP-Posting-Host: ebv.oncology.wisc.edu X-Newsreader: slrn (0.9.4.0 UNIX) Xref: biosci bionet.software:18813 bionet.molbio.methds-reagnts:58589 On Thu, 12 Jun 1997 14:19:36 -0400, Max V Myakishev (max@scientist.com) wrote: >I am looking for the tool to perform >pairwise alignment of 200,000 and 20,000 bp sequences. > >Preferable computer platforms: WWW > PC > Mac > UNIX. > >I already tried many programs and most of them >are limited by the input sequence size 32000. Get the FASTA source from ftp.virginia.edu. It is trivial to modify the source for the ALIGN program within the FASTA package to use input sequences of any desired length. Note that Bill Pearson doesn't recommend that this be done - as smaller alignments will likely be missed. However I regularly use ALIGN for pairwise alignments of sequences that are in the range of 100 - 200 kb. Ashok -- Ashok Aiyar, Ph.D. McArdle Laboratory for Cancer Research aiyar@ebv.oncology.wisc.edu From owner-software@net.bio.net Thu Jun 12 23:00:00 1997 Path: biosci!rutgers!gatech!www.nntp.primenet.com!nntp.primenet.com!news.maxwell.syr.edu!howland.erols.net!newsxfer.itd.umich.edu!gumby!newspump.wustl.edu!newsreader.wustl.edu!not-for-mail From: eddy@wol.wustl.edu (Sean Eddy) Newsgroups: bionet.software Subject: Re: Public domain source code for fast fourier transforms and/or spectral analysis... Date: 12 Jun 1997 19:20:27 -0500 Organization: Washington University in St. Louis Lines: 22 Message-ID: References: <5net75$q2f@kew.globalnet.co.uk> <5ngpce$r58@rc1.vub.ac.be> NNTP-Posting-Host: wol.wustl.edu In-reply-to: plebrun@fysp1.vub.ac.be's message of 9 Jun 1997 11:28:14 GMT X-Newsreader: Gnus v5.1 In article <5ngpce$r58@rc1.vub.ac.be> plebrun@fysp1.vub.ac.be (Philippe Lebrun) writes: >> I am looking for some public domain source code for performing fast >> fourier transforms and/or spectral analysis for a medical application. >> A pointer to a software library would be very much appreciated. >Try "Numerical Recipes in [C Pascal Fortan ...]" by Press, Flannery,Teukolsky, >and Vetterling Cambridge University Press. > >All you need, and quite well explained. Except that Numerical Recipes source code is emphatically *not* in the public domain. Try NETLIB (http://netlib2.cs.utk.edu/) for public domain Fortran implementations of numerical code, including FFTs. -- - Sean Eddy, Ph.D. - Dept. of Genetics, Washington University School of Medicine - 660 S. Euclid Box 8232, St. Louis MO 63110, USA - mailto://eddy@genetics.wustl.edu http://genome.wustl.edu/eddy From owner-software@net.bio.net Thu Jun 12 23:00:00 1997 Path: biosci!daresbury!uninett.no!Norway.EU.net!EU.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!peernews.ftech.net!telehouse1.frontier-networks.co.uk!Aladdin!aladdin.net!ns2.aladdin.net!RMplc!rmplc.co.uk!yama.mcc.ac.uk!hydraulix.bangor.ac.uk!manager From: Keith James Newsgroups: bionet.software Subject: Linux GDE problems Date: 13 Jun 1997 18:13:57 +0100 Organization: University of Wales, Bangor. Lines: 28 Sender: bss194@pwilliams.bangor.ac.uk Message-ID: Reply-To: k.james@bangor.ac.uk NNTP-Posting-Host: pwilliams.bangor.ac.uk X-Newsreader: Gnus v5.3/Emacs 19.34 Hi all, I have the GDE 2 binaries installed on an Intel box running RedHat Linux 4.1 (ELF). I installed the required X libraries and put the binaries in /usr/local/bin/GDE and the help/data files in /usr/local/lib/GDE. When I run GDE all seems fine- the window appears and the menus look fine, but creating a new sequence causes a crash with the message: UniqueID(): Failed to get host name. Also, when I open an existing sequence nothing appears in the editor window. I would be interested in hearing how anyone has set GDE up on their Linux system. I have considered building new binaries from the source myself, but the download always stalls before completion. Maybe there is a European mirror? Thanks for any advice. -- Keith James Ph.D. - k.james@bangor.ac.uk PGP 2.6.2i Key ID 469A9FA1 Biodegradation Group *Encrypt and Survive* School of Biological Sciences Guvf znl znxr ab frafr vs bar bs gur University of Wales, Bangor, UK vasvavgr ahzore bs zbaxrlf vf bssyvar From owner-software@net.bio.net Thu Jun 12 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!worf.molbiol.ox.ac.uk!rgrant From: rgrant@see.sig.for.address (Richard P Grant) Newsgroups: bionet.software,bionet.molbio.proteins Subject: Structure similarity search Followup-To: bionet.software Date: 13 Jun 1997 16:06:12 GMT Organization: Oxford University Lines: 20 Message-ID: <5nrr5k$h9c@news.ox.ac.uk> NNTP-Posting-Host: worf.molbiol.ox.ac.uk X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software:18821 bionet.molbio.proteins:10959 Hi people, Given a protein domain structure (100 amino acids) we would like to search for similar domains in (a) 1 protein (b) the entire sequence databases. The problem is of course that there is no solved structure for (a) and most of (b).... so some form of prediction, threading or modelling will have to be done as part of the search/comparison. Ideas? I can't find exactly what I want on the Web, although the most excellent PredictProtein service in Heidelberg may do what we want. We're looking for either an internet-based resource, or a standalone that will run under Unix or MacOS. Thanks, please followup to bionet.software so that everyone can see if there is a solution. -- Richard P. Grant MA DPhil University of Oxford | rgrant@molbiol http://www.molbiol.ox.ac.uk/~rgrant FFPGP | .ox.ac.uk -----------------------# Trust me - I'm a doctor. #----------------------- From owner-software@net.bio.net Thu Jun 12 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!supernews.com!Supernews!not-for-mail From: Ray Smith Newsgroups: alt.image.medical,bionet.software,comp.dsp,comp.graphics.visualization,sci.image.processing,sci.med.radiology Subject: Re: Image processing SW Date: Fri, 13 Jun 1997 10:51:15 -0400 Organization: Media Cybernetics, L.P. Lines: 31 Message-ID: <33A15E63.3733@mediacy.com> References: <339BE6EB.2C7B@radium.uio.no> <339dd4f4.7334378@News.DiVa.NL> Reply-To: ray@mediacy.com NNTP-Posting-Host: dialup22.atlantech.net Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0Gold (Win95; I) To: Lu.Do@Home.DiVa.nl CC: rita.skare.peaker@login.eunet.no L.P.J.J. Noldus wrote: > > Kaare Gärtner wrote: > > >I need a comment from You on image processing software. > >Anyone of You have strong feelings 'bout some particular package ? > >I'd be thankful if You'd also give me some hints 'bout market > >leadership. > > We use Image-Pro Plus from Media Cybernetics. It is a very flexible > toolbox for analysis of static 2D images. For dynamic analysis of > moving images, we use EthoVision (our own development). Feel free to > contact me directly if you need more details. > > Lucas Noldus For more information on Image-Pro in Norway, contact: Scan Marketing Ms. Rita Skare Peaker Strandkaien 18-20 5013 Bergen, NORWAY Tel: 5-53-25-225 Fax: 5-52-34-379 Email: rita.skare.peaker@login.eunet.no or visit Media Cybernetics' site. Ray Smith Media Cybernetics, L.P. http://www.mediacy.com From owner-software@net.bio.net Thu Jun 12 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software Subject: Re: Wanted: Calcium buffer program. Date: 13 Jun 1997 12:50:43 GMT Organization: Biology, Indiana University - Bloomington Lines: 33 Message-ID: <5nrfn3$kpt$1@dismay.ucs.indiana.edu> References: <339D3E99.7581@liverpool.ac.uk> <33a5c0c3.23134684@newsserver.cc.monash.edu.au> NNTP-Posting-Host: chipmunk.bio.indiana.edu CABUFFER software is available at IUBio archive, in folder /molbio/ibmpc/ as cabufzip.exe. It works on MSDOS systems. IUBio archive is {ftp,http}://iubio.bio.indiana.edu/ From the readme files --- This program allows you to calculate the concentrations of all ionic species present in a mixture of up to four divalent cations (e.g. Mg, Ca, Sr, Ba) and four ligands ("buffers") for these ions. Examples of such buffers are EDTA, EGTA, NTA, HEDTA, citrate, Ca-binding proteins, etc. Corrections for temperature, ionic stength and pH are provided. The CABUFFER program, Basic source code files, data files, and explanatory text files all reside in one self-extracting, compressed archive file named cabufzip.exe. Author: Jochen Kleinschmidt, Ph.D. Dept. of Ophthalmology NYU Medical Center Internet: kleinschmidt@mcclb0.med.nyu.edu > >>Does anyone know of a good program for calculating free calcium (Ca2+) >>levels in buffers containing [ATP/ADP], [EGTA], pH etc. >> >>Would the CABUFFER program reffered to in D J Pehowich post do the job? >> >CABUFFER seems to have vanished into thin air. ... -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-software@net.bio.net Thu Jun 12 23:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.apfel.de!univ-lyon1.fr!news.ujf-grenoble.fr!grenet.fr!news.imag.fr!macjesior.imag.fr!user From: jean-claude.jesior@imag.fr (J.C. Jesior) Newsgroups: bionet.software Subject: Protein modelling freeware Date: Fri, 13 Jun 1997 14:42:43 +0100 Organization: Institut Albert Bonniot, CNRS Lines: 102 Message-ID: NNTP-Posting-Host: macjesior.imag.fr Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit ANNOUNCING THE NEW PPC VERSION OF 'FOLDIT (LIGHT) v.4.2.6¹ a molecular modelling freeware for MacOS compatible computers. €€€€€€€€€€€€€€€€€€€€€ FREEWARE €€€€€€€€€€€€€€€€€€€€€ Enhanced PPC version DOWNLOAD * ŒFoldIt (light) v.4.2.6¹ can be downloaded from the following address: ftp://ftp.imag.fr/pub/TIMC/FoldIt.html * ŒFoldIt (light) Files¹ can also be downloaded from the same address (it contains a set of 20 protein structure files). WHAT 'FOLDIT (LIGHT)' DOES? 'FoldIt (light)' is a molecular modelling program to visualize and manipulate proteins. 'FoldIt (light)' is an interactive program with a user friendly interface. The goal of this program was to build an integrated environment in which statistical analysis as well 3D observations could be realized on PDB files without having to transfer files or swap machines. Our major underlying research project is still to try to improve the folding prediction methods (hence the name 'FoldIt'). This is also the sole desactivated feature in this released version (hence the adjective '(light)'). 'FoldIt (light)' is intented to provide the possibility to analyze proteins up to 1600 residues in size, to visualize and manipulate them interactively. It can directly read any protein coordinate text file from the Brookhaven Protein Data Bank (PDB) (Bernstein et al., 1977) including hetero-atoms and water molecules. 'FoldIt (light)' has two main windows: a color image window to display the protein structure and a text window to record the result of all operations requested by the user. The protein structure can be manipulated easily in real time with the mouse, zoomed or observed in stereo. Structure movement can also occur stepwise for a more precise control. Animations can be created. Steric conflicts, disulfide bonds, hydrogen and ionic interactions can be located and displayed in the protein structure. These interactions are also reported in the text window. Atoms and residues can be tagged individually (or globally) and structural information can then be extracted. Portions of a structure can be read into memory or displayed. Two structures can be read at the same time in memory and can be overlapped automatically. The second structure can be manipulated independently of the first. Bonds can be rotated and atomic parameters can be changed. The sequential folding of a protein can be simulated. It is possible to create a protein de novo from the menu or by entering the sequence from the keyboard. Structures can then be manipulated locally or forced into helices. Site directed mutations can be simulated. The application can process structures in the batch mode to extract a number of structural features: Ramachandran plots, SS-bond plots, H-bond plots. Statistics on atomic parameters are displayed as histograms. The content of image and text windows as well as histograms can be saved to disk. SOFTWARE ENVIRONMENT 'FoldIt (light)' can only work on Macintosh computers running under system 7.0 and higher. It has been developed with Symantec Think Pascal and includes 55000 lines of code. The application can run in the background which is convenient for lengthy statistical procedures. 'FoldIt (light)' does not support printing but can save the content of its text window (report of different operations and data analysis) and the content of the image window (result of graphic operations) in TEXT or PICT formats. These files can then be manipulated by other specialized applications and printed. HARDWARE ENVIRONMENT 'FoldIt (light)' runs only on MacOs compatible computers equipped with a PPC processor. The application itself requires 2 MB of memory; 3.3 KB of additional memory are required for each read residue: this means that 660 KB of extra RAM are necessary to read a typical 200-residue protein. Color monitors are preferred to give a better depth perception but black & white monitors may also be used. DOCUMENTATION On-line help as well as balloon help are supported, and a printable stand alone document is provided. Several small size protein structures are included as example. ****************************************************** FoldIt (light) freeware by Jean-Claude JESIOR / CNRS, Grenoble, France e-mail: jean-claude.jesior@imag.fr Version 4.2.6 - 11 june 1997 developed in Pascal with Symantec Think & Metrowerks Code Warrior. ****************************************************** -- Jean-Claude Jesior jean-claude.jesior@imag.fr From owner-software@net.bio.net Thu Jun 12 23:00:00 1997 Path: biosci!rutgers!dziuxsolim.rutgers.edu!uunet!in3.uu.net!206.252.192.28!news.stealth.net!news.ibm.net.il!news.ibm.net!news.biu.ac.il!news.huji.ac.il!usenet From: Iddo Friedberg Newsgroups: bionet.software Subject: Re: Trying to locate biology software Date: Fri, 13 Jun 1997 13:45:18 +0300 Organization: The Hebrew University of Jerusalem Lines: 24 Message-ID: <33A124BE.59E2@cc.huji.ac.il> References: NNTP-Posting-Host: bishop.md.huji.ac.il Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.2 IP22) Steve Albanese wrote: > > I am looking for biology software that simulates > animal dissection. Any tips or suggestions greatly appreciated. > The student level is freshman/sophmore college. > > Thank you. Try looking at: http://www.yahoo.com/Science/Zoology/Anima