From owner-software@net.bio.net Wed May 01 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!news.cac.psu.edu!news.cse.psu.edu!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!news2.cais.net!news.cais.net!van-bc!unixg.ubc.ca!news.bc.net!news.sfu.ca!trog.mbb.sfu.ca!jbryer From: jbryer@trog.mbb.sfu.ca (Jeff Bryer) Newsgroups: bionet.software Subject: Molecular Biology Programs on CD-ROM Date: 2 May 1996 17:55:26 GMT Organization: IMBB, Simon Fraser University Lines: 27 Distribution: world Message-ID: <4masue$28q@morgoth.sfu.ca> NNTP-Posting-Host: trog.mbb.sfu.ca I am considering putting together a CD-ROM that would contain public-domain, freeware, and shareware molecular biology/biology/ chemistry/etc type programs (for example clustalw, Phylip, fasta, GDE, treetool). I wanted to find out what people thought of the idea. This is completely a non-profit project. The cost of the CD (which I haven't set yet) will be just to recoup the cost of the media and shipping. Thanks to Don Gilbert, I plan on putting the ftp.bio.indiana.edu archive onto the CD. If people are interested in such a CD and the project goes ahead, I will create a WWW page which will list what software will go onto the CD. And I hope to get feedback from people for suggestions of additional software to go on to the CD and how best to organize it. Thanks, Jeff Bryer -- ------- Jeff Bryer | "Maybe VR.12 turns you into Fabio." jbryer@darwin.mbb.sfu.ca | -Duncan in Parallel Lives (VR.5) From owner-software@net.bio.net Wed May 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!surfnet.nl!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!news.dfn.de!news.embl-heidelberg.de!usenet From: "Luca Ida Giovanni TOLDO (Ph.D.)" Newsgroups: bionet.software Subject: Re: WWW interfaces to GCG Date: Thu, 02 May 1996 21:25:11 +0200 Organization: European Molecular Biology Laboratory Lines: 49 Distribution: world Message-ID: <31890C17.7A1D@embl-heidelberg.de> References: <4m92ij$nko@itssrv1.ucsf.edu> Reply-To: toldo@embl-heidelberg.de NNTP-Posting-Host: toldo1.lt.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b3 (Macintosh; I; PPC) Cristopher Botka wrote: > > I am looking for any info about WWW interfaces to GCG. I've already seen the > ones at http://genome.dkfz-heidelberg.de/w2hdemo/index.html and > http://ben.vub.ac.be I'd appreciate pointers to source, demos or URLs if > you've got them. Respond by email please. I'll gladly to post a summary of > what I get to the group. > > Thanks much. > > CWB > > botka@cgl.ucsf.edu Those are the only two WWW Interfaces to GCG which exist. W2H is based on JavaScript and is the work of Marting SENGER WWW2GCG is instead "plain" c and perl programs and is wht work of Marc COLET. Each of them had advantages and disadvantages. WWW2GCG is a joint project of the EMBNet.ORG and as such is sponsored by the EU. Its use is encouraged by EMBNet nodes. W2H is a 2 months old project but inspite of that it decreases considerably network connections compared with WWW2GCG. I have used the WWW2GCG since long time, but I am also in tight contact with W2H developers, and as soon as one of the two will be really fully stable I will then use them for "production purposes" for the EMBL-Heidelberg (where I manage the GCG and the central WWW facilities). None of them is yet at my opinion fully stable, unfortunately. None of them is yet fully capable of offering a full fledge service as the WPI interface does, unfortunately. If you have interest in WWW-based tools for doing GCG-like (and more) operations, please return me your feedback on the Java Based Molecular Biology Workbench that I am developing / summing ... at the url: http://www.embl-heidelberg.de/~toldo/JaMBW.html regards Dr. Luca Ida Giovanni TOLDO (Ph.D.) European Molecular Biology Laboratory Computer Group Heidelberg Germany From owner-software@net.bio.net Wed May 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!swrinde!howland.reston.ans.net!surfnet.nl!swsbe6.switch.ch!scsing.switch.ch!ubaclu.unibas.ch!burglin From: burglin@ubaclu.unibas.ch Newsgroups: bionet.software Subject: MACAW probems on MacIntosh. Message-ID: <1996May2.160513.46394@yogi.urz.unibas.ch> Date: 2 May 96 16:05:13 MET Organization: University of Basel, Switzerland Lines: 22 Hi, is anybody out there supporting MACAW, a multiple sequence alignment package with blocks features? I have tried in on the macintosh in 68k mode (with or without cache), and in PowerPc mode, running on Quadra 650 with PPC card and System 7.5.1. and as soon as I try to do something after loading in sequences, the thing crashes with an error 1 (even though I gave it 6 meg of RAM). Anybody knows a bug fix? Are there other multiple sequence alignment programs out there? (that don't cost a fortune). Thank you very much. Thomas Burglin burglin@ubaclu.unibas.ch From owner-software@net.bio.net Wed May 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!surfnet.nl!swsbe6.switch.ch!news.belnet.be!news.sri.ucl.ac.be!jussieu.fr!univ-lyon1.fr!news From: Nicolas Galtier Newsgroups: bionet.software Subject: available tools for alignment and phylogeny Date: 2 May 1996 09:31:25 GMT Organization: Universite Claude Bernard - Lyon 1 Lines: 51 Distribution: world Message-ID: <4m9vdd$len@tempo.univ-lyon1.fr> Reply-To: galtier@biomserv.univ-lyon1.fr NNTP-Posting-Host: acnuc.univ-lyon1.fr SEAVIEW and PHYLO_WIN, two graphic tools dedicated to sequence alignment and molecular phylogenetics are available by anonymous ftp to : biom3.univ-lyon1.fr (pub/mol_phylogeny). SEAVIEW (Manolo Gouy) is an efficient multiple alignment editor. It allows easy gap insertions/deletions into/from selectable groups of sequences. Alignment program clustalw (Des Higgins) can be called on-line, so that (parts of) the sequences may be automatically aligned. A dot-plot routine allows an easy matching of similar regions. PHYLO_WIN (Nicolas Galtier) is a graphic interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony and maximum likelihood methods and bootstrap with any of them. Many distances can be used including Jukes & Cantor, Kimura, Tajima & Nei, Galtier & Gouy (1995), LogDet for nucleotidic sequences, Poisson correction for proteic sequences, Ka and Ks for codon sequences. Species and sites to include in the analysis are selected by mouse. Reconstructed trees can be drawn, edited, printed, stored, evaluated according to numerous criteria. Taxonomic species groups and sets of conserved regions can be defined by mouse in both tools and stored into sequence files, thus avoiding multiple data files. Both are entirely mouse-driven. On-line help makes them easy to use. Most usual sequence file formats are read : CLUSTAL, FASTA, PHYLIP, MASE. They run on many Unix WorkStations including Sun (SunOS and Solaris), Silicon Graphics, IBM, DEC alpha, HP. For any comment, question, help needed to install, etc... please contact N. Galtier (galtier@biomserv.univ-lyon1.fr). Manolo GOUY and Nicolas GALTIER C.N.R.S. UMR 5558 Universite C.Bernard Lyon 1 Laboratoire de Biometrie, Genetique et Biologie des Populations 43, Bd du 11 novembre 1918 69622 VILLEURBANNE cedex FRANCE galtier@biomserv.univ-lyon1.fr mgouy@biomserv.univ-lyon1.fr From owner-software@net.bio.net Wed May 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!ixnews1.ix.netcom.com!netcom.com!netcom.net.uk!ix.netcom.com!news From: nccrsrch@ix.netcom.com(Nemours Research) Newsgroups: bionet.software Subject: graphing error bars Date: 1 May 1996 20:30:36 GMT Organization: Netcom Lines: 6 Message-ID: <4m8hlc$979@dfw-ixnews1.ix.netcom.com> NNTP-Posting-Host: jac-fl4-14.ix.netcom.com X-NETCOM-Date: Wed May 01 3:30:36 PM CDT 1996 Can anyone suggest a graphing package that interfaces with Microsoft Office Products and SPSS? We currently have some pretty simple requirements in terms of stats (means, standard deviations; bar graphs, line graphs.) My main concern is the ability to EASILY graph error bars. Excel works okay, but is there anything ELSE out there? From owner-software@net.bio.net Wed May 01 23:00:00 1996 Path: biosci!agate!cgl!itssrv1.ucsf.edu!usenet From: botka@cgl.ucsf.edu (Cristopher Botka) Newsgroups: bionet.software Subject: WWW interfaces to GCG Date: 2 May 1996 01:19:15 GMT Organization: UCSF, ITS Lines: 14 Message-ID: <4m92ij$nko@itssrv1.ucsf.edu> NNTP-Posting-Host: russell.ucsf.edu X-Newsreader: Alexandra.app (Version 0.82) I am looking for any info about WWW interfaces to GCG. I've already seen the ones at http://genome.dkfz-heidelberg.de/w2hdemo/index.html and http://ben.vub.ac.be. I'd appreciate pointers to source, demos or URLs if you've got them. Respond by email please. I'll gladly to post a summary of what I get to the group. Thanks much. CWB botka@cgl.ucsf.edu From owner-software@net.bio.net Wed May 01 23:00:00 1996 Path: biosci!rutgers!oitnews.harvard.edu!oitnews.harvard.edu!nagle From: nagle@yuri.harvard.edu (Robert J. Nagle) Newsgroups: bionet.software Subject: CHARMM now available for OS/2 platforms. Date: 02 May 1996 22:43:20 GMT Organization: Harvard Chemistry Department Lines: 45 Message-ID: NNTP-Posting-Host: yuri.harvard.edu The widely used molecular dynamics package, {CHARMM}, is now available for platforms running OS/2 Warp. This version includes support for all of the commonly used features of CHARMM 24 (except for the QM/MM interface). The OS/2 support is available in two different distributions - an executable only (with the necessary parameter files etc.) and a complete source tape. The former is available on a set of floppies or via FTP and requires about 5MB of disk space to install. The latter will be available either by FTP, cartridge tape or DAT. As usual, in order to obtain a copy of CHARMM, a {license agreement} must first be executed with the CHARMM Development Project at Harvard University. The cost for the executable is $220 At least 16MB of RAM are required to run CHARMM under OS/2 - we recommend 24MB or more. On 24MB systems we have succesfully simulated systems up to 14,000 atoms. Performance for molecular dynamics simulations on a 75 MHz Pentium (24 MB) compared with an HP 735 workstation is System #atoms time(PC)/time(HP) alawat 2940 3.85 barnase 10124 4.08 bpti 892 4.16 crambin 396 5.03 mbco 14026 3.94 4.21 More information can be obtained from {http://yuri.harvard.edu/charmm} or by emailing marci@tammy.harvard.edu -- ------------------------------------------------------------------------------- Robert J. Nagle nagle@tammy.harvard.edu Dept. of Chemistry, M/S 223, Harvard University (617) 495-0787 12 Oxford Street, Cambridge, MA 02138, USA From owner-software@net.bio.net Wed May 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!brighton.openmarket.com!decwrl!pacbell.com!well!nh1.well.com!usenet From: robg@well.com (Rob Griffith) Newsgroups: bionet.software,comp.publish.cdrom.software,comp.software.testing,misc.forsale.computers.pc-specific.software Subject: Re: What kind of software is this, please give me advise! Date: Thu, 02 May 1996 04:50:22 GMT Organization: The WELL Lines: 66 Message-ID: <4m9e5i$q0c@nh1.well.com> References: NNTP-Posting-Host: sf-tty36-ppp.well.com X-Newsreader: Forte Free Agent v0.71 Xref: biosci bionet.software:15361 comp.publish.cdrom.software:8048 comp.software.testing:9278 misc.forsale.computers.pc-specific.software:30969 I have a friend who got a similar CD, but unfortunately it contained a virus which wiped out her hard disk entirely. It ended up costing her about 30 hours of time and around $3000 to replace stuff, except some files that are lost forever. I recommend that you just load everything from that CD onto your hard drive and see what happens!!! Maybe you will be lucky, and your CD won't have any viruses. veloo@worldaccess.nl (Ronald / Sonja) wrote: >Hello out there, >Here is my story .................. >Via some friends I got a CD-rom from the Middle East which contains about 600 >Mb of valuable software. Of course, I know, this is not a legal copy and you >won't find it in a normal store in the western countries like Europe, Australia >and US. Anyway, I don't mind of course about this. After installation of the >most valuable software like Windows95 (& Plus Options), MS Backoffice products >and Corel Draw 6 (yes, it's true, all on one CD!) there were some 30 other >applications left of which I regocnized a few and did intall some of them. >However, after installation of one of these other products (Delrina Fax Pro) I >got very bad troubles with my system and after a few hours of sweating and lots >of frustration I decided to reinstall all the software. >And here are my questions ................ >As I've told you, there were a lot of other applications of which I haven't got >the slightest idea what it is, and what I can do with it. Here are the names: >1. Quicken >2. Super Base 95 >3. Side Kick >4. Soft Ram >5. Dashboard for Win95 >6. Drag & File >7. Visual Foxpro >8. MacFee Scan >9. Power Builder 95 (+ Toolkits) >10. Caligari Truespace >11. Smart Page >12. Novell Perfect Office >13. Power Manager >14. PC File V >15. Fractal Design Painter >16. Adobe Type Manager >17. Avery Label Pro >18. Code Wright v3.1 >19. Music Time v2.0 >Can you please e-mail me personally if you know one or more of these programs, >and you think it is worth intalling it. Of course I do not feel like intalling >useless programs and taking the risk to have problems again. I still take that >risk if I install one of the programs you hopefully will advice to me, but that >risk I want to take if the chance of getting new, usefull, programs is excists. >Any advice on this is wellcome, also if you disadvice to install one of these >applications. >Thanks a lot, and greetings from the Netherlands! >Ronald From owner-software@net.bio.net Wed May 01 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!brighton.openmarket.com!decwrl!tribune.usask.ca!rover.ucs.ualberta.ca!fliegel-2.cvascular.med.ualberta.ca!user From: lfliegel@gpu.srv.ualberta.ca (L. Fliegel) Newsgroups: bionet.software Subject: kinetic software Followup-To: bionet.software Date: 2 May 1996 21:01:01 GMT Organization: University of Alberta, Edmonton, Canada Lines: 10 Message-ID: NNTP-Posting-Host: fliegel-2.cvascular.med.ualberta.ca If anyone knows of any good software or programs which can be used for analysis of multiple inhibitors can they give me a call at the address below. (Mac versions especially). We have have examined the effect of inhibitors on a cell type which has 2 forms of a protein, a resistant and a sensitive protein. We would like to try and fit the data and analyze inhibitory constants presumably by using something that can fit data to nonlinear least squares regression. We would be willing to purchase software for this purpose. lfliegel@gpu.srv.ualberta.ca From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!ra.nrl.navy.mil!news.math.psu.edu!news.cse.psu.edu!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in2.uu.net!newsfeed.pitt.edu!godot.cc.duq.edu!usenet From: "Frank R. Gorga" Newsgroups: bionet.software Subject: Re: graphing error bars Date: Fri, 03 May 1996 11:25:12 -0700 Organization: Duquesne University Lines: 28 Message-ID: <318A4F88.7DC1@next.duq.edu> References: <4m8hlc$979@dfw-ixnews1.ix.netcom.com> NNTP-Posting-Host: phosphorus.chemistry.duq.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) Nemours Research wrote: > > Can anyone suggest a graphing package that interfaces with Microsoft > Office Products and SPSS? We currently have some pretty simple > requirements in terms of stats (means, standard deviations; bar graphs, > line graphs.) My > main concern is the ability to EASILY graph error bars. Excel works > okay, but is there anything ELSE out there? We have been using DeltaGraph Pro published by DeltaPoint (http://www.deltapoint.com) for over a year now, one major reason we chose it was its handling of error bars. It is very flexible in a most areas. Standard disclaimer: I have no connection to DeltaPoint, other than as a satisifed customer. -- F.R.G. *********************************** Frank R. Gorga, Ph.D. Dept. of Chemistry & Biochemistry Duquesne University Pittsburgh, PA 15282 412-396-5858 / 412-396-5683 (fax) gorga@next.duq.edu From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!usenet.eel.ufl.edu!arclight.uoregon.edu!enews.sgi.com!decwrl!tribune.usask.ca!rover.ucs.ualberta.ca!mongol.sasknet.sk.ca!io.innovplace.saskatoon.sk.ca!news From: "Dr. Mohamad Morsey" Newsgroups: bionet.software Subject: Re: graphing error bars Date: Fri, 03 May 1996 03:48:53 -0700 Organization: Biostar Inc Lines: 9 Message-ID: <3189E495.7803@nnovplace.saskatoon.sk.ca> References: <4m8hlc$979@dfw-ixnews1.ix.netcom.com> NNTP-Posting-Host: biostar5.innovplace.saskatoon.sk.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win95; I) Nemours Research wrote: > > Can anyone suggest a graphing package that interfaces with Microsoft > Office Products and SPSS? We currently have some pretty simple > requirements in terms of stats (means, standard deviations; bar graphs, > line graphs.) My > main concern is the ability to EASILY graph error bars. Excel works > okay, but is there anything ELSE out there?Try Sigmaplot. It does what you want and it interfaces really nice with EXCEL From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!ng-mac1.gen.cam.ac.uk!strimmer From: Korbinian Strimmer Newsgroups: bionet.software Subject: Re: Molecular Biology Programs on CD-ROM Date: 3 May 1996 11:15:14 GMT Organization: LMU Munich Lines: 6 Distribution: world Message-ID: <4mcps2$b9s@lyra.csx.cam.ac.uk> References: <4masue$28q@morgoth.sfu.ca> NNTP-Posting-Host: ng-mac1.gen.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.3_PPC X-XXMessage-ID: X-XXDate: Fri, 3 May 1996 11:15:01 GMT You probably might check the EBI software CD first. I haven't seen it but at least I know how to order it ;-) : http://www.ebi.ac.uk/ebi_docs/subscription.html Korbinian Strimmer From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!swrinde!news.uh.edu!news.uth.tmc.edu!bmb155.med.uth.tmc.edu!user From: tliang@utmmg.med.uth.tmc.edu (T. Chyau Liang) Newsgroups: bionet.software Subject: Re: MACAW probems on MacIntosh. Date: Fri, 03 May 1996 09:26:41 +0100 Organization: U. Texas-Houston Lines: 17 Message-ID: References: <1996May2.160513.46394@yogi.urz.unibas.ch> NNTP-Posting-Host: bmb155.med.uth.tmc.edu Mime-Version: 1.0 Content-Type: text/plain;charset=US-ASCII Content-Transfer-Encoding: 7bit In article <1996May2.160513.46394@yogi.urz.unibas.ch>, burglin@ubaclu.unibas.ch wrote: [snip] > I have tried in on the macintosh in 68k mode (with or > without cache), and in PowerPc mode, running on > Quadra 650 with PPC card and System 7.5.1. > and as soon as I try to do something after loading in > sequences, the thing crashes with an error 1 > (even though I gave it 6 meg of RAM). FWIW: Type 1 error is bus error. This will seem to indicate that the hardware is not compatible with this software. Did you try it on other machine (e.g. original 68K or original PPC without add-on cards)? Just a thought. Hope this helps. From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!hobyah.cc.uq.oz.au!bunyip.cc.uq.oz.au!harbinger.cc.monash.edu.au!calcium.med.monash.edu.au!Ian.Musgrave From: Ian.Musgrave@med.monash.edu.au (Ian Musgrave) Newsgroups: bionet.software Subject: Calcium Buffer Software Date: Fri, 3 May 1996 08:42:22 GMT Organization: PHIMR at Monash Medical Center Lines: 14 Message-ID: NNTP-Posting-Host: calcium.med.monash.edu.au X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] G'Day All Does anyone know of a public domain/shareware program to calculate appropriate calcium/edta buffers for precise calcium concentrations. There was a program called CABUFFER listed in the IUBIO archives, but it appears to have been removed from the server, and my searches have turned up nothing else. Cheers! Ian --------------------------------------------- Ian Musgrave Ph.D Prince Henry's Institue of Medical Research PO Box 5152, Clayton 3168, Australia. Phone +61 3 550 4286 FAX +61 3 550 6125 Lab: Ian.Musgrave@med.monash.edu.au Private: Reynella@werple.mira.net.au From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!lade.news.pipex.net!pipex!tube.news.pipex.net!pipex!hole.news.pipex.net!pipex!oleane!jussieu.fr!news.sri.ucl.ac.be!news.belnet.be!swsbe6.switch.ch!scsing.switch.ch!elna.ethz.ch!retrograde.ethz.ch!user From: mantei@neuro.biol.ethz.ch (Ned Mantei) Newsgroups: bionet.software Subject: Re: Signal peptide sequence Date: Fri, 03 May 1996 08:47:25 +0200 Organization: Dept. of Neurobiology, ETH-Zurich Lines: 23 Distribution: world Message-ID: References: <4mc0hj$3oh@woodstock.socs.uts.EDU.AU> NNTP-Posting-Host: retrograde.ethz.ch In article <4mc0hj$3oh@woodstock.socs.uts.EDU.AU>, Slavica Masina wrote: > Does anybody know any methods, preferably recent, for the identification > of protein secretory sequences and for prediciting the site of cleavage > between a signal sequence and the mature exported protein. I currently > have the paper of G. von Heljne (1986) Nucleic acids research, 14(11), > but I would prefer computer program that performs the analysis. In the University of Indiana biology archive, at GOPHER://ftp.bio.indiana.edu:70/11 in the section on Macintosh programs there is a (Macintosh) program called AnalyseSignalase that applies the von Heijne method for eukaryotes (I know because I wrote the program). I also have a version for prokaryotes. There are surely PC versions available, but I don't know where. There may have been neural net approaches to this problem, which you might find by looking through CABIOS. -- Ned Mantei Dept. of Neurobiology, Swiss Federal Institute of Technology CH-8093 Zurich, Switzerland mantei@neuro.biol.ethz.ch Fax: +41-1-633-1046 From owner-software@net.bio.net Thu May 02 23:00:00 1996 Newsgroups: bionet.software Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!world!oravaxcm From: oravaxcm@world.std.com (Charles A Miller) Subject: Looking for a DNA/Protein signal Database and Program.. Message-ID: Organization: The World Public Access UNIX, Brookline, MA X-Newsreader: TIN [version 1.2 PL2] Date: Fri, 3 May 1996 06:40:38 GMT Lines: 18 [ Article crossposted from bionet.molbio.proteins ] [ Author was Charles A Miller ] [ Posted on Fri, 3 May 1996 06:39:56 GMT ] Hello, I am trying to locate a database of signal sequences and motifs for DNA and/or Amino Acids. I would like to also locate a MAC or PC program that allows one to create a database of sequences which can then be searched for these signals. If anyone one knows where I could find such a program (we have Lasergene's Geneman, but it doesn't yet allow one to create custom databases using one's own sequences). Thanks for the help! Chuck oravaxcm@world.std.com From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!swrinde!sgigate.sgi.com!enews.sgi.com!news.uoregon.edu!arclight.uoregon.edu!dispatch.news.demon.net!demon!peer.news.xara.net!xara.net!netcom.net.uk!ix.netcom.com!news From: pjraval@ix.netcom.com(P. Raval ) Newsgroups: bionet.software Subject: Looking for Electronic Forms software (Scanner based) Date: 3 May 1996 04:40:02 GMT Organization: Netcom Lines: 7 Message-ID: <4mc2n2$94t@dfw-ixnews5.ix.netcom.com> NNTP-Posting-Host: irv-ca14-13.ix.netcom.com X-NETCOM-Date: Thu May 02 11:40:02 PM CDT 1996 Are there any Windows based software packages that allow scanned paper forms to be saved as Postscript (PS, not EPS) files, or files that could be converted to such format, for later editing and printing? If so, who publishes them and how much are they? Thanks. PJR pjraval@ix.netcom.com From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!BGUMAIL.BGU.AC.IL!aflaloc From: aflaloc@BGUMAIL.BGU.AC.IL (Claude Aflalo) Newsgroups: bionet.software Subject: Re: MACAW probems on MacIntosh. Date: 2 May 1996 23:00:32 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <1996May2.160513.46394@yogi.urz.unibas.ch> NNTP-Posting-Host: net.bio.net The first thing I would check BEFORE loading a sequence is the sequence type in the preferences. MACAW will crash if it is configured for DNA and you load a protein seqence, and vive versa. Hope this help... Claude Aflalo ######################### Phones: Office 972-7-472118 #### Dept. of Life Sciences Lab 972-7-472119 Ben Gurion University of the Negev **New**Fax 972-7-472890 P.O.Box 653 email: aflaloc@bgumail.bgu.ac.il Beer Sheva 84105 Israel URL: http://www.bgu.ac.il/life/aflalo.html From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!metro!metro!socs.uts.edu.au!ib_lc630.bio.uts.edu.au!smasina From: Slavica Masina Newsgroups: bionet.software Subject: Signal peptide sequence Date: 3 May 1996 04:02:59 GMT Organization: University of Technology, Sydney Australia. Lines: 8 Distribution: world Message-ID: <4mc0hj$3oh@woodstock.socs.uts.EDU.AU> NNTP-Posting-Host: 138.25.241.85 X-Newsreader: Nuntius Version 1.2 X-XXMessage-ID: X-XXDate: Fri, 3 May 1996 22:09:38 GMT Does anybody know any methods, preferably recent, for the identification of protein secretory sequences and for prediciting the site of cleavage between a signal sequence and the mature exported protein. I currently have the paper of G. von Heljne (1986) Nucleic acids research, 14(11), but I would prefer computer program that performs the analysis. Can anyone help? Thanks in advance, S. Masina. From owner-software@net.bio.net Thu May 02 23:00:00 1996 Newsgroups: bionet.software Path: biosci!daresbury!sunsite.doc.ic.ac.uk!warwick!bradford.ac.uk!leeds.ac.uk!news From: BGYCSW@leeds.ac.uk ("C.S. WILDING") Subject: genepop Message-ID: <318A1245.5247@leeds.ac.uk> NNTP-Posting-Host: pab_pc007.leeds.ac.uk X-Mailer: Mozilla 2.0 (Win16; I) Content-Type: text/plain; charset=us-ascii Organization: University of Leeds MIME-Version: 1.0 Date: Fri, 3 May 1996 15:02:23 +0100 (BST) Lines: 6 Content-Transfer-Encoding: 7bit Anyone know where to get Michel Raymond and Francois Rousset's Genepop program? They are/were at Montpelier, France but haven't replied to e-mails so maybe have moved. Craig WIlding Leeds University From owner-software@net.bio.net Thu May 02 23:00:00 1996 Newsgroups: bionet.software Path: biosci!daresbury!sunsite.doc.ic.ac.uk!warwick!bradford.ac.uk!leeds.ac.uk!news From: BGYCSW@leeds.ac.uk ("C.S. WILDING") Subject: excoffier's AMOVA Message-ID: <318A11B1.34BE@leeds.ac.uk> NNTP-Posting-Host: pab_pc007.leeds.ac.uk X-Mailer: Mozilla 2.0 (Win16; I) Content-Type: text/plain; charset=us-ascii Organization: University of Leeds MIME-Version: 1.0 Date: Fri, 3 May 1996 14:59:55 +0100 (BST) Lines: 5 Content-Transfer-Encoding: 7bit Does anyone know how to get a copy of the program for analysis of molecular variance (Excoffier et al. Genetics 131p479). Thanks Craig Wilding From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.cais.net!newsfeed.internetmci.com!in1.uu.net!nwnews.wa.com!news.halcyon.com!usenet From: you@somehost.somedomain (Your Name Here) Newsgroups: bionet.software Subject: Re: kinetic software Date: 3 May 1996 21:30:04 GMT Organization: Your Organization Lines: 23 Message-ID: <4mdtss$rmo@news.halcyon.com> References: NNTP-Posting-Host: blv-pm10-ip9.halcyon.com X-Newsreader: WinVN 0.90.3 Have you tried KineCyte for Macintosh, turns concepts into predictions RainTown Biotech, PO Box 31263, Seattle WA 98103-1263 (206) 547-3289 email raintown@halcyon.com Create by Dr Dan Cook regards, Eugene Nutt In article , lfliegel@gpu.srv.ualberta.ca (L. Fliegel) says: > >If anyone knows of any good software or programs which can be used for >analysis of multiple inhibitors can they give me a call at the address >below. (Mac versions especially). We have have examined the effect of >inhibitors on a cell type which has 2 forms of a protein, a resistant and a >sensitive protein. We would like to try and fit the data and analyze >inhibitory constants presumably by using something that can fit data to >nonlinear least squares regression. We would be willing to purchase >software for this purpose. > >lfliegel@gpu.srv.ualberta.ca From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!hobyah.cc.uq.oz.au!bunyip.cc.uq.oz.au!news From: John.Harrison@mailbox.uq.oz.au (John Harrison) Newsgroups: bionet.software Subject: Software for managing references from medline (mainly)??? Date: Fri, 03 May 1996 20:10:46 GMT Organization: University of Queensland Lines: 4 Message-ID: <4mdp6b$btp@hobyah.cc.uq.oz.au> NNTP-Posting-Host: sujharri.slip.cc.uq.oz.au X-Newsreader: Forte Free Agent 1.0.82 Anyone got good shareware to do all this in some easy manner. I am jus trying out REFS but am having trouble importing the medline downloads into it. From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.cais.net!van-bc!unixg.ubc.ca!news From: lance@neuro.pharmacology.ubc.ca (Lance Corey) Newsgroups: bionet.software Subject: Re: Calcium Buffer Software Date: Fri, 03 May 1996 20:15:12 GMT Organization: University of British Columbia Lines: 35 Message-ID: <318a68a7.85104200@news.ucs.ubc.ca> References: Reply-To: lance@neuro.pharmacology.ubc.ca NNTP-Posting-Host: alpha.pharmacology.ubc.ca X-Newsreader: Forte Free Agent 1.1/16.198 There is a program called MAXCHELATOR by Chris Patton that will do what you wish. You can obtain a copy from his WWW homepage. The following is part of the message he sent me. ______________ The latest versions of MAXCHELATOR for DOS and Windows can now be downloaded from the World Wide Web site: http://www-leland.stanford.edu/~cpatton The math for ionic contributions has been significantly improved, especially on the Windows version. Lance Ian.Musgrave@med.monash.edu.au (Ian Musgrave) wrote: >G'Day All > >Does anyone know of a public domain/shareware program to calculate appropriate >calcium/edta buffers for precise calcium concentrations. There was a program >called CABUFFER listed in the IUBIO archives, but it appears to have been >removed from the server, and my searches have turned up nothing else. > >Cheers! Ian >--------------------------------------------- >Ian Musgrave Ph.D Prince Henry's Institue of Medical Research >PO Box 5152, Clayton 3168, Australia. >Phone +61 3 550 4286 FAX +61 3 550 6125 >Lab: Ian.Musgrave@med.monash.edu.au >Private: Reynella@werple.mira.net.au Lance Corey Dept. Pharmacology & Therapeutics University of British Columbia From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!newsxfer.itd.umich.edu!jobone!fiesta.srl.ford.com!eccdb1.pms.ford.com!mhughes From: mhughes@pms104.pms.ford.com (Mark Hughes) Newsgroups: bionet.software,comp.publish.cdrom.software,comp.software.testing,misc.forsale.computers.pc-specific.software Subject: Re: What kind of software is this, please give me advise! Date: 3 May 1996 19:45:51 GMT Organization: Ford Motor Company Lines: 36 Sender: mhughes@pms104 (Mark Hughes) Distribution: world Message-ID: <4mdnpf$qn3@eccdb1.pms.ford.com> References: <4m9e5i$q0c@nh1.well.com> NNTP-Posting-Host: pms104.pms.ford.com Xref: biosci bionet.software:15383 comp.publish.cdrom.software:8077 comp.software.testing:9293 misc.forsale.computers.pc-specific.software:31054 veloo@worldaccess.nl (Ronald / Sonja) wrote: > I got a CD-rom from the Middle East which contains about 600 Mb of > valuable software. Of course, I know, this is not a legal copy... > ... I don't mind of course about this. > However, after installation of one of these other products (Delrina > Fax Pro) I got very bad troubles with my system ... I don't believe this. There are alot of people who will ask questions that they have spent zero effort trying to figure out themselves because they are profoundly lazy and their access to newsgroups is free. There are also people who will pester thousands of people to try to save a trivial amount of money (e.g. "Where can I the best price on a ___ ?"). These people are bad enough. Here we have a jerk who wants our help installing an illegal copy of software. There seems to be no limit to just how incredibly stupid and selfish people can be. > Can you please e-mail me personally if you know one or more of these He wants help with his illegal software but he's too damn lazy to even read the newsgroup for answers. Jerk. robg@well.com (Rob Griffith) writes: > I have a friend who got a similar CD, but unfortunately it contained a > virus which wiped out her hard disk entirely. It ended up costing her > about 30 hours of time and around $3000 to replace stuff, except some > files that are lost forever. Good. I hope the same thing happens to Ronald / Sonja. Mark -- mhughes@pms104.pms.ford.com (Mark Hughes) No Web page. I have better things to do. So do you. Visit a library. From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!bloom-beacon.mit.edu!gatech!news.jsums.edu!news2.cais.net!news.cais.net!newsfeed.internetmci.com!howland.reston.ans.net!torn!nott!nrcnet0.nrc.ca!ratilal From: ASH@BIOTECH.LAN.NRC.CA (Ash, JosŽe) Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Re: Software for strain collections Date: 3 May 1996 17:40:23 GMT Organization: BRI-NRCC Lines: 9 Sender: -Not-Authenticated-[3406] Message-ID: <4mdge7$3p0@nrcnet0.nrc.ca> References: <3183B4C9.48EB@micro.biol.ethz.ch> NNTP-Posting-Host: 132.246.220.242 X-Posted-From: InterNews 1.0.7@132.246.220.242 Xdisclaimer: No attempt was made to authenticate the sender's name. Xref: biosci bionet.molbio.methds-reagnts:44039 bionet.software:15382 FilemakerPro (Claris) is a good one, but I am not sure if it does the formating you need. JosŽe Ash NRC-IRB MontrŽal ash@biotech.lan.nrc.ca I am not associated with Claris, just a happy user. From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.cais.net!newsfeed.internetmci.com!in2.uu.net!interaccess!d180.nb.interaccess.com!crabtree From: crabtree@interaccess.com (Crabtree Electronic Publishing, Inc.) Newsgroups: bionet.software,comp.publish.cdrom.software,comp.software.testing,misc.forsale.computers.pc-specific.software Subject: Re: What kind of software is this, please give me advise! Date: Fri, 3 May 1996 13:11:05 Organization: InterAccess,Chicagoland's Full Service Internet Provider Lines: 31 Message-ID: References: <4m9e5i$q0c@nh1.well.com> NNTP-Posting-Host: d180.nb.interaccess.com X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #4] Xref: biosci bionet.software:15381 comp.publish.cdrom.software:8075 comp.software.testing:9291 misc.forsale.computers.pc-specific.software:31043 In article <4m9e5i$q0c@nh1.well.com> robg@well.com (Rob Griffith) writes: >From: robg@well.com (Rob Griffith) >>Of course, I know, this is not a legal copy and you won't find it in a >>normal store in the western countries like Europe, Australia and US. Anyway, >>I don't mind of course about this. Rob: So, you don't mind about stealing? I suppose you're the type that figures reality is optional. What you're doing is nothing less than taking food out of the mouths of honest working people around the world. Then you have the intestinal fortitude to ask netizens which is the best of your stolen software? Get real! My advice? Throw out the pirated software, and go buy what you can truly afford. Terry Gallagher ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + CrabTree InterActive, Inc. + + + + MagNet Interactive Catalogs + + + + Multimedia Brochures, Annual Reports, Presentations and Training + + + + (708)577-5935 F (708)577-5985 + + + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!swrinde!news.uh.edu!news.uth.tmc.edu!bmb155.med.uth.tmc.edu!user From: tliang@utmmg.med.uth.tmc.edu (T. Chyau Liang) Newsgroups: bionet.software Subject: Re: kinetic software Date: Fri, 03 May 1996 09:46:49 +0100 Organization: U. Texas-Houston Lines: 22 Message-ID: References: NNTP-Posting-Host: bmb155.med.uth.tmc.edu Mime-Version: 1.0 Content-Type: text/plain;charset=US-ASCII Content-Transfer-Encoding: 7bit In article , lfliegel@gpu.srv.ualberta.ca (L. Fliegel) wrote: > If anyone knows of any good software or programs which can be used for > analysis of multiple inhibitors can they give me a call at the address > below. (Mac versions especially). We have have examined the effect of > inhibitors on a cell type which has 2 forms of a protein, a resistant and a > sensitive protein. We would like to try and fit the data and analyze > inhibitory constants presumably by using something that can fit data to > nonlinear least squares regression. We would be willing to purchase > software for this purpose. > > lfliegel@gpu.srv.ualberta.ca If you are intereted in simulating the kinetic mechanism, I strongly recommend KinSim, which is a VAX program, or its Mac version, HopKinSim, which was ported to Mac by people at Johns Hopkins U. This is a very nice program and is a postcard ware. Unfortunately, I don't have the URL on hand, but I found it with Web search. Give it a try. If you have difficulty, E_mail me. Good luck. From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!SERVIDOR.DGSCA.UNAM.MX!Apartado.Postal.811,=?iso-8859-1?Q?Mazatl=E1n?=,Sinaloa,MEXICO.82000 From: Apartado.Postal.811,=?iso-8859-1?Q?Mazatl=E1n?=,Sinaloa,MEXICO.82000@SERVIDOR.DGSCA.UNAM.MX (Alberto Abreu Grobois) Newsgroups: bionet.software Subject: (none) Date: 3 May 1996 15:46:54 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <9605032343.AA29101@servidor.dgsca.unam.mx> NNTP-Posting-Host: net.bio.net Can anyone tell me of a freeware programme or internet site which I can access which can identify restriction enzyme sites in polymorphic DNA sequences? ************************************************************************* Dr. F. Alberto Abreu Grobois Banco de Informacion sobre Tortugas Marinas (BITMAR) Estacion Mazatlan Instituto de Ciencias del Mar y Limnologia UNAM tel. 52 (69) 85-28-45,-46,-47,-48 Apartado Postal 811 fax. 52 (69) 82-61-33 Mazatlan, Sinaloa 82000 e-mail abreu@servidor.unam.mx MEXICO priv. 52 (69) 81-22-94 street address: Calz. Joel Montes Camarena S/N Mazatlan, Sinaloa MEXICO 82040 ************************************************************************* From owner-software@net.bio.net Thu May 02 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!surfnet.nl!swsbe6.switch.ch!news.belnet.be!news.sri.ucl.ac.be!jussieu.fr!pasteur.fr!usenet From: Hassan Badrane Newsgroups: bionet.software Subject: Re: Signal peptide sequence Date: 3 May 1996 09:18:14 GMT Organization: Institut Pasteur Lines: 25 Message-ID: <4mcj0m$gdg@montespan.pasteur.fr> References: <4mc0hj$3oh@woodstock.socs.uts.EDU.AU> NNTP-Posting-Host: cleopatre.pasteur.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; OSF1 V3.2 alpha) To: smasina@uts.edu.au X-URL: news:4mc0hj$3oh@woodstock.socs.uts.EDU.AU Slavica Masina wrote: >Does anybody know any methods, preferably recent, for the identification >of protein secretory sequences and for prediciting the site of cleavage >between a signal sequence and the mature exported protein. I currently >have the paper of G. von Heljne (1986) Nucleic acids research, 14(11), >but I would prefer computer program that performs the analysis. Can >anyone help? > >Thanks in advance, S. Masina. I've used PSORT I don't know if it answer you request, but I think so. you can use it at the URL: http://psort.nibb.ac.jp/ good luck. -- ########################################################################### # BADRANE Hassan tele : 331 45688978 ### #### # # Institut Pasteur fax : 331 40613256 # # # # # Laboratoire des Lyssavirus e-mail: hbadrane@pasteur.fr # #### # # 25, rue du Dr. ROUX # # # # 75724 Paris cedex 15, ### # PARIS # # FRANCE http://www.dsg.ki.se/pasteur/ # ########################################################################### From owner-software@net.bio.net Fri May 03 23:00:00 1996 Newsgroups: bionet.software,comp.publish.cdrom.software,comp.software.testing,misc.forsale.computers.pc-specific.software Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!news.inc.net!arclight.uoregon.edu!dispatch.news.demon.net!demon!netcom.net.uk!netcom.com!cemkaner From: cemkaner@netcom.com (Cem Kaner) Subject: Re: What kind of software is this, please give me advise! Message-ID: Followup-To: bionet.software,comp.publish.cdrom.software,comp.software.testing,misc.forsale.computers.pc-specific.software Organization: NETCOM On-line Communication Services (408 261-4700 guest) X-Newsreader: TIN [version 1.2 PL1] References: Date: Sat, 4 May 1996 01:28:51 GMT Lines: 27 Sender: cemkaner@netcom14.netcom.com Xref: biosci bionet.software:15391 comp.publish.cdrom.software:8088 comp.software.testing:9311 misc.forsale.computers.pc-specific.software:31109 This guy is obviously trolling for flames. Now that I see (in comp.software.testing, anyway) that some people are getting hooked, please. Spare your fingers, and our bandwidth. Breath deeply. Spend your time on something useful instead. Ronald / Sonja (veloo@worldaccess.nl) wrote: : Hello out there, : Here is my story .................. : Via some friends I got a CD-rom from the Middle East which contains about 600 : Mb of valuable software. Of course, I know, this is not a legal copy and you : won't find it in a normal store in the western countries like Europe, Australia : and US. Anyway, I don't mind of course about this. After installation of the : most valuable software like Windows95 (& Plus Options), MS Backoffice products : and Corel Draw 6 (yes, it's true, all on one CD!) there were some 30 other -- ----------------------------------------------------------------- CEM KANER JD, PhD. Attorney / ASQC-Certified Quality Engineer read Kaner, Falk & Nguyen, TESTING COMPUTER SOFTWARE (2d Ed. VNR) 1060 Highland Court #4, Santa Clara 95050 408-244-7000 ----------------------------------------------------------------- From owner-software@net.bio.net Fri May 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!newsfeed.internetmci.com!vixen.cso.uiuc.edu!ks.uiuc.edu!dalke From: dalke@ks.uiuc.edu (Andrew Dalke) Newsgroups: bionet.software,comp.publish.cdrom.software,comp.software.testing,misc.forsale.computers.pc-specific.software Subject: Re: What kind of software is this, please give me advise! Date: 4 May 1996 04:48:47 GMT Organization: TB BI Lines: 12 Distribution: world Message-ID: <4menjf$j7v@vixen.cso.uiuc.edu> References: <4m9e5i$q0c@nh1.well.com> <4mdnpf$qn3@eccdb1.pms.ford.com> NNTP-Posting-Host: ophelia.ks.uiuc.edu Xref: biosci bionet.software:15389 comp.publish.cdrom.software:8083 comp.software.testing:9305 misc.forsale.computers.pc-specific.software:31096 Mark Hughes justifiably complained: > Here we have a jerk who wants our help installing an illegal copy of > software. There seems to be no limit to just how incredibly stupid and > selfish people can be. It is even worse than that. This asinine simpleton really asked which of the listed pirated software he should _try_ to install. Andrew Dalke dalke@ks.uiuc.edu P.S. Does the SPA have any offices in the Netherlands? From owner-software@net.bio.net Fri May 03 23:00:00 1996 Path: biosci!rutgers!csn!news-1.csn.net!magnus.acs.ohio-state.edu!math.ohio-state.edu!howland.reston.ans.net!newsfeed.internetmci.com!in1.uu.net!sun.sirius.com!usenet From: wizkid@sirius.com Newsgroups: bionet.software,comp.publish.cdrom.software,comp.software.testing,misc.forsale.computers.pc-specific.software Subject: Re: What kind of software is this, please give me advise! Date: Fri, 03 May 1996 17:16:44 -0700 Organization: Sirius Connections Lines: 40 Message-ID: <318AA1EC.63AE@sirius.com> References: <4m9e5i$q0c@nh1.well.com> NNTP-Posting-Host: ppp032-sf2.sirius.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win95; I) Xref: biosci bionet.software:15388 comp.publish.cdrom.software:8081 comp.software.testing:9302 misc.forsale.computers.pc-specific.software:31084 Crabtree Electronic Publishing, Inc. wrote: > > In article <4m9e5i$q0c@nh1.well.com> robg@well.com (Rob Griffith) writes: > >From: robg@well.com (Rob Griffith) > > > >>Of course, I know, this is not a legal copy and you won't find it in a > >>normal store in the western countries like Europe, Australia and US. Anyway, > >>I don't mind of course about this. > > Rob: > > So, you don't mind about stealing? I suppose you're the type that figures > reality is optional. What you're doing is nothing less than taking food out of > the mouths of honest working people around the world. Then you have the > intestinal fortitude to ask netizens which is the best of your stolen > software? Get real! > > My advice? Throw out the pirated software, and go buy what you can truly > afford. > > Terry Gallagher > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > + CrabTree InterActive, Inc. + > + + > + MagNet Interactive Catalogs + > + + > + Multimedia Brochures, Annual Reports, Presentations and Training + > + + > + (708)577-5935 F (708)577-5985 + > + + > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Don't buy anything from the software companies! $500 for Pagemaker or Adobe Photoshop. All we pay for is the damn advertisting that they do. Support pirate software!!! They blame that they lose money from pirating. yeah right. Look at how much they make. people can't affored to buy 5 disk for $500. Damn software manufactures rip us off, and we let them, what a joke!!! From owner-software@net.bio.net Fri May 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!howland.reston.ans.net!newsfeed.internetmci.com!news.inc.net!trellis.wwnet.com!news.bconnex.net!news.clic.net!mixnews2!rcogate.rco.qc.ca!altitude!usenet From: Achim Recktenwald Newsgroups: bionet.software Subject: Re: Looking for enzfitter Date: Fri, 03 May 1996 11:34:12 -0500 Organization: IBEX Technologies, Inc. Lines: 31 Message-ID: <318A3584.149E@ibex.ca> References: <4m5iuo$1u8@lilith.uab.es> NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) Francisco Mata Rodr=CCguez wrote: > = > Hi, i am looking for any version (linux, dos, or Windows) of > the enzfitter package. > = > I'll be very pleased if I found a free, shareware or gnu one. > = > Do you know where could I found it??? > = > Note: any similar program would be fine. > = > Thanks. > = > -- > Francisco Mata franma@hp-bpo.bpo.hp.com Enzfitter (DOS) is a commercial product; you can buy it from SIGMA. I would recommend GraFit 3 for Windows, from Erithacus = (http://www.erithacus.co.uk/). The programmer is the same one who made = Enzfitter, but the program is newer and also more powerful. Achim From owner-software@net.bio.net Fri May 03 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!csn!news-1.csn.net!decwrl!amd!netcomsv!uu4news.netcom.com!sr0!netcomsv!uu3news.netcom.com!ixnews1.ix.netcom.com!netcom.com!fadden From: fadden@netcom.com (Andy McFadden) Newsgroups: bionet.software,comp.publish.cdrom.software,comp.software.testing,misc.forsale.computers.pc-specific.software Subject: Re: What kind of software is this, please give me advise! Message-ID: Date: 4 May 96 04:37:59 GMT References: <4m9e5i$q0c@nh1.well.com> <318AA1EC.63AE@sirius.com> Sender: fadden@netcom4.netcom.com Followup-To: alt.dev-null Organization: Lipless Rattling Crankbait Lines: 21 Xref: biosci bionet.software:15397 comp.publish.cdrom.software:8098 comp.software.testing:9317 misc.forsale.computers.pc-specific.software:31152 In article <318AA1EC.63AE@sirius.com>, wrote: >Don't buy anything from the software companies! $500 for Pagemaker or >Adobe Photoshop. All we pay for is the damn advertisting that they do. >Support pirate software!!! They blame that they lose money from >pirating. yeah right. Look at how much they make. people can't affored >to buy 5 disk for $500. Damn software manufactures rip us off, and we >let them, what a joke!!! I think the net is better off without discussion #582795 about software piracy. Nobody has managed to convince the other side of anything yet. Please keep one thing in mind: whatever else you want to say about it, software piracy is illegal, and asking for support for pirated software on Usenet is, at best, stupid. Please refrain. -- fadden@netcom.com (Andy McFadden) [These are strictly my opinions.] PGP Anyone can do any amount of work provided it isn't the work he is supposed to be doing at the moment. -- Robert Benchley From owner-software@net.bio.net Fri May 03 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!ks.uiuc.edu!dalke From: dalke@ks.uiuc.edu (Andrew Dalke) Newsgroups: bionet.software,comp.publish.cdrom.software,comp.software.testing,misc.forsale.computers.pc-specific.software Subject: Re: What kind of software is this, please give me advise! Date: 4 May 1996 05:45:40 GMT Organization: TB BI Lines: 65 Distribution: world Message-ID: <4mequ4$j7v@vixen.cso.uiuc.edu> References: <4m9e5i$q0c@nh1.well.com> <318AA1EC.63AE@sirius.com> NNTP-Posting-Host: ophelia.ks.uiuc.edu Xref: biosci bionet.software:15390 comp.publish.cdrom.software:8085 comp.software.testing:9309 misc.forsale.computers.pc-specific.software:31098 In a bizarre fit of financial ignorance wizkid@sirius.com babbled: > Don't buy anything from the software companies! $500 for Pagemaker or > Adobe Photoshop. All we pay for is the damn advertisting that they do. > Support pirate software!!! They blame that they lose money from > pirating. yeah right. Look at how much they make. people can't affored > to buy 5 disk for $500. Damn software manufactures rip us off, and we > let them, what a joke!!! Ever hear of economics? A budget? Since you are a "kid", let me give you a simple lesson: 1) To give you an idea of the costs involved in software publishing, we produce software (it is free software, paid for by a grant from the US National Institutes of Health). We have 1 1/2 programmers and support staff. We spend about $125,000/year in salaries and overhead. We only advertise by our web site and usenet. During the last year we have had about 800 downloads, of which about 100 are users (others found that the progam wasn't useful for their work). Hence, if we required payment, it would cost $1,250. Please point out to me where the advertising cost comes in and how we can reduce our costs by advertising less. I'm sure our funding agency would love to learn about this idea. 2) there's this thing called "supply and demand". If Pagemaker isn't worth $500, why buy it? Since it is being sold for $500, obviously, someone is buying it. You could always do your layout with scissors and glue -- maybe $20 total! 3) Another priciple - "economy of scale". If more people buy software, the overall price can be reduced, especially since producing another unit of software is cheap. If you thives didn't steal the software, more would be sold, and the price to you lessened. But you may be right. If thieves like you would never actually buy software at any price, then the companies wouldn't loose money to you. On the other hand, how many thieves are opportunistic and would have bought the software if they didn't scam it from someone else. If there is even one, the company lost money. 4) there's this thing called a "free economy". If software publishers are ripping you off, make your own version of the program and undersell them. You'll make money selling cheap and useful software. Of course, that would be joining the system, wouldn't it -- so make better software and give it away free! Choice of the GNU generation. But of course, you've probably never written anything more complicated than "Hello, world" or a class project. If you had, you would have known how much time was needed to make a good commercial product and wouldn't have rushed to support your neighborhood crook. 5) This is a different form of economics. Laws against illegal copying of software are slowly coming into effect, and companies are becoming more savvy at figuring out when their software is being used. Imagine the days when your computer is always connected to the net, and every 100th time you start a program, it contacts the main server for the company. If you aren't registered, you get this nice letter from their attorney. Think something like this won't happen? It already does. The economics here is the tradeoff in "free" illegal software vs. a fine or jail time. Andrew Dalke dalke@ks.uiuc.edu From owner-software@net.bio.net Fri May 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!EU.net!sun4nl!uva.nl!amc!ka2-05.amc.uva.nl!user From: a.jonker@amc.uva.nl (Ard Jonker) Newsgroups: bionet.software Subject: Re: kinetic software Date: Sat, 04 May 1996 17:25:05 +0300 Organization: University of Amsterdam Lines: 30 Message-ID: References: NNTP-Posting-Host: ka2-05.amc.uva.nl In article , lfliegel@gpu.srv.ualberta.ca (L. Fliegel) wrote: >If anyone knows of any good software or programs which can be used for >analysis of multiple inhibitors can they give me a call at the address >below. (Mac versions especially). We have have examined the effect of >inhibitors on a cell type which has 2 forms of a protein, a resistant and a >sensitive protein. We would like to try and fit the data and analyze >inhibitory constants presumably by using something that can fit data to >nonlinear least squares regression. We would be willing to purchase >software for this purpose. > >lfliegel@gpu.srv.ualberta.ca If it is only for the curve fit, where you can apply your own formula to fit the data (i.e. you know how the kinetics of multiple inhibitors are mathematically modelled), I highly recommend MacCurveFit, shareware ($25 or so) by Kevin Raner. Most recent version 1.2.1. V2.0 is developed at the moment. The program fits a curve (which you describe mathematically) to data (you feed it) and graphs it for you. Multiple parameters can be fit simultaneous. ard -- Ard Jonker |Meibergdreef 15 Dept of Anatomy & Embryology |1105 AZ Amsterdam Dept of Histology and Cell Biology |The Netherlands Faculty of Medicine |tel +31 20 566 5396 University of Amsterdam |a337ard@horus.sara.nl From owner-software@net.bio.net Fri May 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news.cse.psu.edu!news.ecn.bgu.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!iglou!bubba.emanon.com!usenet From: Scott Morris Newsgroups: bionet.software,comp.publish.cdrom.software,comp.software.testing,misc.forsale.computers.pc-specific.software Subject: Re: What kind of software is this, please give me advise! Date: Sat, 04 May 1996 08:43:50 -0400 Organization: emanon.com Lines: 37 Message-ID: <318B5106.26F5@emanon.com> References: <4m9e5i$q0c@nh1.well.com> <318AA1EC.63AE@sirius.com> NNTP-Posting-Host: blah.emanon.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win95; I) To: wizkid@sirius.com Xref: biosci bionet.software:15394 comp.publish.cdrom.software:8092 comp.software.testing:9312 misc.forsale.computers.pc-specific.software:31120 wizkid@sirius.com wrote: > Don't buy anything from the software companies! $500 for Pagemaker or > Adobe Photoshop. All we pay for is the damn advertisting that they do. > Support pirate software!!! They blame that they lose money from > pirating. yeah right. Look at how much they make. people can't affored > to buy 5 disk for $500. Damn software manufactures rip us off, and we > let them, what a joke!!! Be real... Even people who happen to be "real" pirates have a particular code of honor. You're one of the slimy types apparantly who always will use pirated software. Even though the software industy whines about how many pirates there are, a good number of them in the utilities scenes have a code of honor. Use piracy to test software to determine whether it truly suits your needs or not, and if it does, buy it! If it's worth enough to you that you gain a benefit from using it, then you should also pay for it. They sunk all the money into creating something that you apparantly like enough to hunt it down, so be a real man and pirate. I can agree with you on some things about software companies, but the more competition, they've been getting better about things. Some companies, you still cannot get your hands on the full software for a demo/eval for a period of time while deciding whether to buy it or not... I agree with you that it's a waste to buy the software only when you find out that it doesn't do what was promised and you have no recourse in terms of returning opened software for a refund. Many companies are starting to do 60-120 days of evaluation on full product (not crippled software) which is a GREAT answer to this. IF the software meets your needs though, you should still go and buy the damn thing, that way you aren't guilty of the same logic of screwing people that you accuse the software companies of.... Scott PS. I know the scene, and I also know the code of honor that MOST of the utility-oriented people have. Gamers are different, but we won't get into that.... From owner-software@net.bio.net Fri May 03 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!news.cac.psu.edu!news.cse.psu.edu!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!oleane!jussieu.fr!news.forth.gr!news.auth.gr!usenet From: Zanos Stavros Newsgroups: bionet.software Subject: Looking for Brain Structure and Function Multimedia Software Date: 3 May 1996 06:01:03 GMT Organization: Medical School, Aristotle University of Salonica, Greece Lines: 16 Message-ID: <4mc7ev$p49@evia.ccf.auth.gr> NNTP-Posting-Host: antigoni.med.auth.gr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.2N (Windows; I; 16bit) In order to use it for a graduate course on the structure and function of the CNS, a professor of Psychology (Dr. Vasiliadis) would like to know some multimedia titles on the subject. The level of analysis should be as high as possible. I would appreciate every reference. -- Zanos Stavros Aristotle Univ School of Medicine Thessaloniki, Macedonia, Greece "If I had more time, I would have written you a shorter letter" Pascal From owner-software@net.bio.net Fri May 03 23:00:00 1996 Path: biosci!aol.com!Jeanchev From: Jeanchev@aol.com Newsgroups: bionet.software Subject: CRaZy Complimentary Offer........ Date: 4 May 1996 12:44:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 228 Sender: daemon@net.bio.net Distribution: world Message-ID: <960504152552_287138076@emout08.mail.aol.com> NNTP-Posting-Host: net.bio.net --------------------- Forwarded message: Subj: CRaZy Complimentary Offer........ Date: 96-05-04 14:44:00 EDT From: Jeanchev To: free_offer_news.reflector@usenet.vax1.zer2.co.np -----> NOTE: Please first read my note which appears below the "Request for more info Form." Then, to get more info, just fill out the "Request for More Info" form completely and *FAX* or *SMAIL* it back to the company. You will get a quick reply via email within 1 business day of receipt of the info request form below. IMPORTANT NOTICE FOR THOSE FAXING IN THEIR REPLY: Please make sure you return *only* the below form and *no part* of this message other than the actual form below. If you do not know how to cut and paste the below form onto a fresh clean blank page for faxing, then you may re-type the below form, as long as you copy it line for line *exactly.* This is necessary in order for them to be able to process the tremendous number of replies that they get daily. Your fax goes directly onto their 4.2 gigabyte computer hard drive, not paper, and all incoming fax calls are set-up to be *auto-terminated* and/or *auto-deleted* from the incoming queue of faxes to be read, if your fax: 1. has a cover page; 2. is more than one page 3. is sent more than one time 4. does not begin with the "cut here/begin" line from the below form 5. does not end with the "cut here/end" line from the below form. 6. has any handwritten info. on it (info must must be filled out *only* with your computer keyboard or typewriter keyboard). This last provision re: no handwriting on the form applies to requests sent in via smail also. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ NOTE: Their fax line is open 24 hrs. per day / 7 days per week. However, if you have trouble getting through due to the high volume of overseas faxes coming in during the early morning and late night hours, please note that the best time to get through to their fax is Monday-Friday, 9 am - 5 pm EST (New York Time). If you have trouble getting through to their fax, or do not have a fax machine at work or at home, just drop the below form to them via smail (airmail or first class mail). ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ *------------cut here/begin-------------------------------------------* REQUEST FOR MORE INFO: please return *only* this section (with no cover page) via 1-page fax to: 718-967-1550 in the USA or via smail (first class mail or airmail) to: Magazine Club Inquiry Center Att. FREE Catalogue-by-email Dept. PO Box 990 Staten Island NY 10312-0990 Sorry, but incomplete forms *will not* be acknowledged. If you do not have an email address, or access to one, they will not be able to help you until you do have one. If you saw this message, then you should have one. :) ---> SORRY, BUT NO HANDWRITTEN FORMS WILL BE ACKNOWLEDGED. MUST BE TYPED-OUT ON YOUR COMPUTER OR TYPEWRITER. <--- Name: Internet email address: Smail home address: City-State-Zip: Country: Work Tel. #: Work Fax #: Home Tel. #: Home Fax #: How did you hear about us (name of person who referred you or the area of the internet that you saw us mentioned in): Referral by: Jean Chevalier. 05046-l-cco Name of USA mags you currently get on the newsstand or in the store: Name of USA mags you currently get on a subscription basis, through the mail: Name of USA mags you would like price quotes on when we call you: Catalogue format desired (list "1," "2," "3" or "4"): *------------cut here/end--------------------------------------------* Catalogue Format Options: 1. 19-Part email- can be read by EVERYONE (~525 K Total). 2. For more advanced computer users: attached text file ~525K - you must know how to download an attached text file and then be able to open it with your word processor. If in doubt, don't ask for this version. This isn't for internet *newbies.* Better to order option 1 and spend a few minutes pasting them into one whole text document with your word processor, than to waste hours trying to figure how to deal with this option. 3. For more advanced Macintosh computer users: compressed attached text file, created with a Stuffit(tm) self-extracting archive (.sea), ~133K. Can be decompressed by any Macintosh computer user; no special expansion software or knowledge of Stuffit (tm) needed. You just double-click on the file icon and it automatically expands (unstuffs). This is for more advanced mac computer users only, as you still have to know how to deal with an attached file. It will cut your download time by 75%. Expands out to the same ~525K file in option #2. See option #2 for more info on what you will need to be able to do. 4. For expert computer users: compressed attached text file, created with Stuffit(tm), ~114K. Can be decompressed by any computer user who has expansion software to decompress (expand) Stuffit(tm) (.sit) files. This is for more advanced computer users only and will cut your download time by 78%. Expands out to the same ~525K file in option #2. See option #2 for more info on what you will need to be able to do. Hi fellow 'netters, My name is Jean Chevalier and I recently started using a magazine subscription club in the USA that has a FREE 1 yr. magazine subscription deal with your first paid order- and I have been very pleased with them. They have over 1,500 different USA titles that they can ship to any country on a subscription basis. As for computer magazines from the USA, they more of a selection than I ever knew even existed. They have magazines for most every area of interest in their list of 1,500 titles. Within the USA, for their USA members, they are cheaper than all their competitors and even the publishers themselves. This is their price guarantee. Overseas, on the average, they are generally around one-fourth to one-half of what the newsstands overseas charge locally for USA magazines. On some titles they are as little as one-tenth of what the newsstands charge. They feel that mgazines should not be a luxury overseas. In the USA, people buy magazines and then toss them after reading them for just a few minutes or hours. They are so cheap in the USA! Well, this company would like to make it the same way for their overseas members. They are also cheaper than all their competitors in the USA and overseas, including the publishers themselves! This is their price guarantee. Around one-half their business comes from overseas, so they are very patient with new members who only speak limited English as a 2nd language. Their prices are so cheap because they deal direct with each publisher and cut-out all the middlemen. They will send you their DELUXE EMAIL CATALOGUE (around 525K-big and juicey) !)...if you completely fill out the form above. It has lists of all the freebies, lists of all the titles they sell, titles broken down by categories and detailed descriptions on nearly 1,200 of the titles that they sell. Please do not email me as I am just a happy customer and a *busy* student. I don't have time to even complete my thesis in time, let alone run my part-time software business! Please fill out the above form and carefully follow the intructions above to get it to them via fax or smail. They guarantee to beat all their competitors' prices. Sometimes they are less than half of the next best deal I have been able to find and other times, just a little cheaper - but I have never found a lower rate yet. They assured me that if I ever do, they will beat it. They have been very helpful and helped me with all my address changes as I haved moved from one country to another. They have a deal where you can get a free 1 yr. sub to a new magazine from a special list of over 270 popular titles published in the USA. They will give you this free 1 yr. sub when you place your first paid order with them to a renewal or new subscription to any of the over 1,500 different popular USA titles they sell. They can arrange delivery to virtually any country and I think they have clients in around 45 or 46 countries now. Outside the USA there is a charge for FPH (foreign postage and handling) (on both paid and freebie subs) that varies from magazine to magazine. I have found their staff to be very friendly and courteous. They even helped me with an address change when I moved from one country to another. The owner thinks of his service as a "club" and his clients as "members" (even though there is no extra fee to become a member - your first purchase automatically makes you a member) and he is real picky about who he accepts as a new member. When he sets you up as a new member, he himself calls you personally on the phone to explain how he works his deal, or sometimes he has one of his assistants call. He is kind of quirky sometimes - he insists on setting up new members by phone so he can say hi to everyone (I sure wouldn't want to have his phone bills!), but you can place future orders (after your first order) via E-mail. He has some really friendly young ladies working for him, who seem to know just as much as he does about this magazine stuff. If you live overseas, he will even call you there, as long as you are interested, but I think he still makes all his overseas calls on the weekends, I guess cause the long distance rates are cheaper then. He only likes to take new members from referrals from satisfied existing members and he does virtually no advertising. When I got set-up, they had a 2-3 week waiting list for new members to be called back so that they could join up. (Once you are an existing member, they help you immediately when you call. ) I think they are able to get back to prospective new members the same day or within a few days now, as they have increased their staff. I am not sure about this.........but if you email the above form to them, that is the way to get started! They will send you their DELUXE EMAIL CATALOGUE (around 525K-big and juicey) !)...if you completely fill out the form above. It has lists of all the freebies, lists of all the titles they sell, titles broken down by categories and detailed descriptions on nearly 1,200 of the titles that they sell. They then send you email that outlines how his club works and the list of free choices that you can choose from, as well as the entire list of what he sells; and then they will give you a quick (3-5 minute) friendly, no-pressure no-obligation call to explain everything to you personally and answer all your questions. Once you get in, you'll love them. I do. Sincerely, Jean Chevalier From owner-software@net.bio.net Sat May 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!howland.reston.ans.net!paladin.american.edu!news.jhu.edu!news From: kfurata@welchlink.welch.jhu.edu (Koh Furuta) Newsgroups: bionet.software Subject: Software for making slides Date: 4 May 1996 17:01:59 GMT Organization: HCF - Johns Hopkins University, Baltimore, Maryland, USA Lines: 11 Sender: -Not-Authenticated-[3656] Message-ID: <4mg2i7$q7d@news.jhu.edu> NNTP-Posting-Host: 128.220.62.142 X-Posted-From: InterNews 1.1@128.220.62.142 Xdisclaimer: No attempt was made to authenticate the sender's name. Hi, Does anybody out there recommeded good software (Macintosh) for making presentation slides? Some of my friends recommended me to use "Powerpoint", and "AdobePhotoshop". If anybody has an experience of using them, pleaes let me know of it. Thanks in advance. Koh Furuta kfurata@welchlink.welch.jhu.edu From owner-software@net.bio.net Sat May 04 23:00:00 1996 Newsgroups: bionet.software Path: biosci!news.Stanford.EDU!nntp-hub2.barrnet.net!sgigate.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!sangam!iitb!powai!sasidhar From: sasidhar@powai.cc.iitb.ernet.in (dr y u sasidhar) Subject: pdb input for peptides Message-ID: Date: Sun, 5 May 1996 06:11:43 GMT Organization: Computer Centre, Indian Institute of Technology, Bombay X-Newsreader: TIN [version 1.2 PL2] Lines: 14 dear netters, is there a program which can take the amino acid sequence with backbone and side chain dihedral angle informtion and generate a coordinate file in PDB format which can be used as input for RASMOL/KINEMAGE Thanks in advance -Sasidhar ********************************************** Dr. Y. U. Sasidhar Assistant Professor Dept. of Chemistry Indian Institute of Technology Bombay 400 076 India From owner-software@net.bio.net Sat May 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!newsfeed.internetmci.com!newshub.csu.net!csulb.edu!usenet From: "Chen, Hui-Lin" Newsgroups: bionet.software Subject: Help Date: Sun, 05 May 1996 13:14:27 -0700 Organization: cal state u. long beach Lines: 9 Message-ID: <318D0C23.1D11@csulb.edu> NNTP-Posting-Host: 134.139.77.27 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win16; I) CC: chhuilin@csulb.edu Hi, This is Hui-Lin Chen, a student at Cal. State U. Long Beach. I am working on my Information System project related to the topic of lotus notes. Can anyone give me information about the major function of lotus notes and the benefit that it can bring to the organization? Thanks HuiLin Chen From owner-software@net.bio.net Sat May 04 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!newsxfer2.itd.umich.edu!news.itd.umich.edu!centipede.rs.itd.umich.edu!tdib From: tdib@umich.edu (Thomas K. Dibenedetto) Newsgroups: bionet.software,sci.bio.systematics Subject: Re: Program for testing incongruences Followup-To: bionet.software,sci.bio.systematics Date: 5 May 1996 12:46:32 GMT Organization: University of Michigan Lines: 73 Message-ID: <4mi7v8$qin@lastactionhero.rs.itd.umich.edu> NNTP-Posting-Host: centipede.rs.itd.umich.edu X-Newsreader: TIN [version 1.2 PL2] X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software:15399 sci.bio.systematics:953 Andrew J. Roger (aroger@ac.dal.ca) wrote: : Have you heard of lateral gene transfer? In case you haven't,,,,, Howdy Andrew! Long time, no read! Yeah, I sorta, kinda heard about this stuff. But you know, it _still_ doesnt strike me as all that much different from any other character which may be misleading.... : Now if you were trying to work out the phylogenetic position of an organism : and you used all of the genes available from this organism and related : ones, _all_ the genes available? then you would probably not be misled by a case of lateral transfer... Glad to see you inching up on the "total evidence" bandwagon! :) : including a gene which this organism picked up from another lineage : (which the other taxa in the dataset did not), you would be including : a datum which will be positively misleading about the phylogenetic : relationships of this organism (if you were interested in the : relationships which are the result of vertical descent rather than : lateral transfer of one of its genes). : The need to keep data like these separate seems so obvious to me : that I cannot conceive why you might object to it. Can you enlighten me? Well gee, if I could _know_ that a gene came from elsewhere, I might go along, but how do you get to know this, before you do the analysis? The original poster had two conflicting (or potentially conflicting) datasets and wondered if they should be combined. If they were "significantly different", would this necessarily indicate lateral transfer? Partitions of a single dataset (one gene) can be different right? Thus, there must be other reasons why one discovers incongruence, no? Do you think conflicting data should never be combined, irrespective of the reason? : If we are dealing at the level of molecular data then one must try to : think of what patterns of conflicting data will be indicative of true : chimaerism as opposed to "noisy" data. Well, noisy data (as you point out) is unpatterned. I am asking you, are there other factors which might pattern data besides "chimaerism" or the true history? : Thus it is clear in principle and in practice in this case how you : would destinguish between noisy data and real gene chimaerism. You may be distinguishing noise from pattern, but why must it be chimaerism? I guess it just strikes me as a backwards approach. You start with a process, predict a pattern it may produce, then identify any such discovered patterns as resulting from that process. This doesnt really consider alternative explanations for the pattern. In my little corner of systematics, we usually nail down the patterns first, then go searching for explanations. re. my total evidence, lump it all together argument: : This would be fine if you could be certain that a significant portion : of your dataset were derived from vertical descent only. But it is : possible that your total dataset may contain a large portion of : data which is postively conflicting. The result may be a phylogeny : which makes no sense at all because it is derived from multiple : datasets which had different histories. : The success of total evidence depends on the anomalous phylogenies : being in the minority...and that the true phylogeny will "come out : in the wash". I wouldn't be comfortable with this assumption. Well, I dont know why not. Would you care to point me toward those sources of evidence which have led you to conclude that "anomolous" gene trees are anywhere near as common as would be necessary to upset a total evidence analysis? -- Tom diBenedetto Fish Division University of Michigan Museum of Zoology From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!newsfeeder.servtech.com!murphy2.servtech.com!news From: Kim Pruitt Newsgroups: bionet.software Subject: Free Demo Available Date: 6 May 1996 00:02:57 GMT Organization: Salt City Software Lines: 22 Message-ID: <4mjfjh$3lv@murphy2.servtech.com> NNTP-Posting-Host: saltcitysw.syr.servtech.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22KIT (Windows; U; 16bit) Hi, I thought some of you might be interested in knowing we have added a free demonstration version of Genome Tracker to our home page (http://www.servtech.com/public/saltcity). Genome Tracker is an inventory database, for Macintosh users, designed to keep track of your stocks of'your-favorate-organism'. In addition it can be used to keep track of different experiments including genetic experiments (each record includes information on parent stocks used in a cross and a family tree can be generated). We welcome any comments you may have. Thank you. Sincerely, Kim D. Pruitt, Ph.D. Salt City Software 7744 Sotherden Dr. Liverpool, NY 13090 e-mail: 70761.2216@compuserve.com www: http://www.servtech.com/public/saltcity From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!xmission!news.cc.utah.edu!news.cs.utah.edu!swen.emba.uvm.edu!brianf From: brianf@med.uvm.edu (Brian Foley) Newsgroups: bionet.software,bionet.molbio.evolution,bionet.molbio.hiv Subject: Re: Massive Multiple Sequence Alignment tools? Date: 3 May 1996 23:46:51 GMT Organization: EMBA Computer Facility, The University of Vermont Lines: 56 Message-ID: <4me5tb$1vi@swen.emba.uvm.edu> References: <4lmb4n$905@swen.emba.uvm.edu> NNTP-Posting-Host: salus.med.uvm.edu X-Newsreader: TIN [version 1.2 PL1] Xref: biosci bionet.software:15410 bionet.molbio.evolution:4514 bionet.molbio.hiv:2153 Thank you very much for ideas on tools such as AMPS. In addition to performing an alignment on sequences, once I have all of the sequences ready for alignment, I was hoping to find a tool that would use the information obtained in a BLAST or FASTA run to help me obtain the sequences and clip out the region withhigh similarity to my query sequence. There are some 6,000 HIV sequences in the GenBank database and it is easy to obtain the accession numberds for all 6,000. The problem is that some are complete genomes, some contain only the 5' half of the region I want to align (the envelope gene), some conatin only the 3' half, and some are only fragments in the middle. I'd like to automate the process of retrieving the GenBank entry, and either clipping the env gene out of complete genomes, or padding the ends of incomplete sequences until all of the sequences are in approximate alignment. The results of a BLAST search give me almost all the information, I would need to write a script to do this. However, BLAST does not allow gaps, and often gives me several fragmentary alignments for a single sequence paired to my query. I suspect that FASTA will do better, but I have not gotten FASTA running locally, and I have not found a FASTA server which will return the best 7,000 matches to me (most FASTA servers are limited to less than 100 "hits" via e-mail). I do have some tools for dealing with the final product alignment. I have already aligned over 1,000 HIV-1 env V3 region sequences. I have tools to count the frequency of ocurrance of each base (or amino acid in a protein alignment) at each position. This then shows me the relative variability at each position in the gene or protein. Two opposing forces are at work on the evolution of the HIV-1 env gene. Conservative forces are selecting for envelope protein which can function well in binding to the CD4 receptors on host cells. Diversifying forces are selecting for envelope proteins which can evade the host's immune system. Forgive the unscientific use of "forces" there. We need to develop vaccines based on conserved regions. The variable regions will diverge too quickly. By the time we have a HIV-1 subtype B vaccine generated, tested and approved, the subtype B will have moved on. We have some good information about which regions of the envelope protein are immunogenic. Are any of the immunogenic regions conserved? -- ******************************************************************** * Brian Foley * btf@t10.lanl.gov * * T-10, MS-K710, LANL * http://hiv-web.lanl.gov * * Los Alamos, NM 87545 USA * http://hiv-web.lanl.gov/~btf * ******************************************************************** From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!biosci!not-for-mail From: syoung@unix5.netaxs.com (Resampling; syoung) Newsgroups: bionet.plants,bionet.info-theory,bionet.software,bionet.population-bio,bionet.molbio-evolution Subject: Short Course in Resampling Statistics (p04306) Followup-To: poster Date: 5 May 1996 19:24:53 -0700 Organization: Philadelphia's Complete Internet Provider Lines: 24 Sender: biohelp@net.bio.net Distribution: world Message-ID: <4m4guc$a0r@netaxs.com> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.plants:11180 bionet.info-theory:4114 bionet.software:15403 bionet.population-bio:1925 Course in Resampling Statistics An introduction to the "new statistics" of resampling will be offered June 3-5 in Washington, DC. Resampling - bootstrap, permutation, and other tests - has revolutionized the field of statistics. Resampling is now the method of choice for confidence limits, hypothesis tests, and other everyday inferential problems. Resampling is for both experts and non-statisticians. With resampling procedures you use the given sample data to repeatedly simulate hypothetical "re-samples", recalculating the statistic of interest. No "black-box" formulas will hide the underlying statistical procedure. This is an introductory course, with no specific pre- requisites, though a familiarity with basic probability and descriptive statistics will help. For information reply by email to: syoung@netaxs.com Resampling Project Fax: (703) 522-5846 From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!newsfeed.internetmci.com!in1.uu.net!news-in.tiac.net!news-central.tiac.net!djhatzi.tiac.net!user From: djhatzi@tiac.net (paul h) Newsgroups: bionet.software Subject: DNA model available Date: Mon, 06 May 1996 03:12:04 -0500 Organization: - Lines: 16 Message-ID: NNTP-Posting-Host: djhatzi.tiac.net Need a DNA model for your medical animation, textbook render, or current project? No need to model it yourself, save your time for something more artistic. A quality representation is available for $150, for your use (half what Viewpoint charges for the same model). It can be e-mailed in virtually any 3D format. Request a .jpg of a render of the model by email. Paul Hatziiliades From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.ksu.ksu.edu!news.cis.okstate.edu!news.ecn.uoknor.edu!munnari.OZ.AU!metro!metro!news From: glenn holden Newsgroups: bionet.software Subject: Re: available tools for alignment and phylogeny Date: 6 May 1996 05:03:34 GMT Organization: Information Services, The University of Sydney, NSW, Australia Lines: 8 Distribution: inet Message-ID: <4mk176$k4c@metro.usyd.edu.au> References: <4m9vdd$len@tempo.univ-lyon1.fr> NNTP-Posting-Host: 129.78.38.21 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: galtier@biomserv.univ-lyon1.fr X-URL: news:4m9vdd$len@tempo.univ-lyon1.fr How big is Seaview and how much data can it hold, i.e. how many sequences of what length? Brendan Scott Dep. Pathology Sydney Uni Australia From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.ksu.ksu.edu!news.cis.okstate.edu!news.ecn.uoknor.edu!munnari.OZ.AU!metro!metro!news From: glenn holden Newsgroups: bionet.software Subject: Re: available tools for alignment and phylogeny Date: 6 May 1996 05:03:33 GMT Organization: Information Services, The University of Sydney, NSW, Australia Lines: 8 Distribution: inet Message-ID: <4mk175$k2m@metro.usyd.edu.au> References: <4m9vdd$len@tempo.univ-lyon1.fr> NNTP-Posting-Host: 129.78.38.21 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: galtier@biomserv.univ-lyon1.fr X-URL: news:4m9vdd$len@tempo.univ-lyon1.fr How big is Seaview and how much data can it hold, i.e. how many sequences of what length? Brendan Scott Dep. Pathology Sydney Uni Australia From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.ksu.ksu.edu!news.cis.okstate.edu!news.ecn.uoknor.edu!munnari.OZ.AU!metro!metro!news From: glenn holden Newsgroups: bionet.software Subject: Re: available tools for alignment and phylogeny Date: 6 May 1996 05:01:54 GMT Organization: Information Services, The University of Sydney, NSW, Australia Lines: 8 Distribution: inet Message-ID: <4mk142$jnq@metro.usyd.edu.au> References: <4m9vdd$len@tempo.univ-lyon1.fr> NNTP-Posting-Host: 129.78.38.21 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: galtier@biomserv.univ-lyon1.fr X-URL: news:4m9vdd$len@tempo.univ-lyon1.fr How big is Seaview and how much data can it hold, i.e. how many sequences of what length? Brendan Scott Dep. Pathology Sydney Uni Australia From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!swrinde!sgigate.sgi.com!nntp.coast.net!torn!newshost.uwo.ca!jkiernan.anatomy.uwo.ca!jkiernan From: jkiernan@julian.uwo.ca (J. A. Kiernan) Newsgroups: bionet.software Subject: Re: Software for managing references from medline (mainly)??? Date: Mon, 6 May 1996 16:41:01 GMT Organization: ITS, University of Western Ontario Lines: 14 Message-ID: References: <4mdp6b$btp@hobyah.cc.uq.oz.au> NNTP-Posting-Host: jkiernan.anatomy.uwo.ca In article <4mdp6b$btp@hobyah.cc.uq.oz.au> John.Harrison@mailbox.uq.oz.au (John Harrison) writes: >Anyone got good shareware to do all this in some easy manner. PAPYRUS is excellent. It accepts all the formats in which references are downloaded. It will even index all the words in the abstracts (if you want it to). The best $100 I ever spent! John A. Kiernan Department of Anatomy Univ. of Western Ontario LONDON, Canada N6A 5C1 e-mail: kiernan@uwo.ca From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!decwrl!tribune.usask.ca!rover.ucs.ualberta.ca!news.ucalgary.ca!news From: dchurchi@acs.ucalgary.ca (Dennis Churchill) Newsgroups: bionet.software Subject: re: calcium buffer software Date: 6 May 1996 15:58:15 GMT Organization: University of Calgary Lines: 34 Message-ID: <4ml7io$12v4@ds2.acs.ucalgary.ca> NNTP-Posting-Host: @pc4.macvicar.ucalgary.ca Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 I posted concerning this topic a month ago and haven't got around to posting a summary post. So here it is. Thanks to all those who responded to my original post (as Caren Helbing by accident). This is a copy of the mail I received from Theo Schoenmakers who gave a complete summary of what is generally available. -Fabiato & Fabiato. Classic program in use since beginning of the 80's. Don't know on what systems it runs now, but was designed for something big like the old PDP-11. Correspondingly archaic design, but correct calculations. -Chelator, by myself. DOS, freeware. Menus-and-windows interface plus mouse. No help menu, just a thin paper manual. Complete freedom of entering chelator, metals and their stability constants (comes with some sets predefined). Is designed to take some less common binding equilibria into account. Send me an email if you want it. Schoenmakers,TJM; Visser,GJ; Flik,G; Theuvenet,APR (1992): CHELATOR: An improved method for computing metal ion concentrations in physiological solutions. Biotechniques 12, 870-879. -BAD, Bound and Determined, by Brooks and Storey. DOS, freeware. Comes with some predefined constants. Have to get used to its interface... Brooks,SPJ; Storey,KB (1992): Bound and determined: a computer program for making buffers of defined ion concentrations. Anal.Biochem. 201, 119-126. -MaxChelator, by Chris Patton. In a DOS and a Windows flavour. Very well documented with a help file. Easy to use. Comes with several predefined sets of stability constants, but will only calculate the basic binding reactions. Nice additional features, such as graphs for interpreting the effect of buffering as a function of [chelator] etc. Grab it at his WWW-page: http://www-leland.stanford.edu/~cpatton/ Bers,DM; Patton,CW; Nuccitelli,R (1994): A practical guide to the preparation of Ca{+2+} buffers. Chap. 1. In: A practical guide to the study of calcium in living cells. (Ed: Nuccitelli,R) (Methods in Cell Biology, 40.) Academic Press, San Diego, USA, 3-29. From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!nntp.coast.net!howland.reston.ans.net!swrinde!cssun.mathcs.emory.edu!hobbes.cc.uga.edu!news From: russell@dogwood.botany.uga.edu (Russell L. Malmberg) Newsgroups: bionet.software Subject: web page - alpha NT biology software Date: 6 May 1996 12:17:02 GMT Organization: Botany Department, University of Georgia Lines: 36 Distribution: world Message-ID: <4mkqju$ph7@hobbes.cc.uga.edu> Reply-To: russell@dogwood.botany.uga.edu NNTP-Posting-Host: twopaths.botany.uga.edu X-Newsreader: News for Windows NT X1.0-87 Some molecular biology programs compiled for the alpha NT platform: ============================= http://dogwood.botany.uga.edu/malmberg/software.html I have set up a web page of software that I compiled for DEC alphas running Windows NT. These are (mostly) not programs written by me, but rather are the fine programs that many bionet.software contributors have written. I have just compiled them for this specific platorm, and (with the author's permissions) put them on this one web page. I hope they might be useful to the small, but fortunate, number of biologists who have an alpha running Windows NT. Note: These programs, in this form, will not run on Windows NT on an Intel CPU. Most of them are available at other archive sites for Intel CPUs. Some programs are command-line, some are windowed. ClustalWA.zip -- Multiple sequence alignment program original source authors Des Higgins, Julie Thompson, Toby Gibson GeneDocA.zip -- Sequence alignment viewer original source author Karl Nicholas Molphy22.alpha.zip -- Phylogenetic analysis original source author Jun Adachi, Masami Hasegawa NCBIprog.alpha.tar.gz -- Nentrez, Blast, Sequin: Sequence database searches multiply authored from NCBI Peaks05.alpha.zip -- Integrates areas in HPLC data source author Russell Malmberg Phylip.alpha.zip -- Phylogenetic analysis source author Joe Felsenstein readseqA.exe -- DNA/Protein Sequence format conversions source author Don Gilbert SeqPup.alpha.tar.gz -- DNA/Protein Sequence analysis source author Don Gilbert Russell L. Malmberg russell@dogwood.botany.uga.edu From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!psinntp!psinntp!psinntp!psinntp!prophet.unoverica.com!mikasa.iol.it!peroni.ita.tip.net!news.vol.it!news From: Deirdré Straughan <74431.2004@compuserve.com> Newsgroups: bionet.software,comp.publish.cdrom.software,comp.software.testing,misc.forsale.computers.pc-specific.software Subject: Re: What kind of software is this, please give me advise! Date: Sun, 05 May 1996 13:00:15 +0200 Organization: Incat Systems, an Adaptec company Lines: 24 Message-ID: <318C8A3F.44B6@compuserve.com> References: <4m9e5i$q0c@nh1.well.com> <318AA1EC.63AE@sirius.com> <318B5106.26F5@emanon.com> NNTP-Posting-Host: timi48.vol.it Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Win95; I) Xref: biosci bionet.software:15412 comp.publish.cdrom.software:8113 comp.software.testing:9330 misc.forsale.computers.pc-specific.software:31274 Scott Morris wrote: > > I agree with you that it's a waste to buy the software only when > you find out that it doesn't do what was promised and you have no > recourse in terms of returning opened software for a refund. Many > companies are starting to do 60-120 days of evaluation on full product > (not crippled software) which is a GREAT answer to this. IF the > software meets your needs though, you should still go and buy the damn > thing, that way you aren't guilty of the same logic of screwing people > that you accuse the software companies of.... > What would you think of buying it upfront, with a money-back guarantee, no questions asked, if you then discover it's not what you need? -- Best regards, Deirdre' Straughan Adaptec Software Products Group ** 74431.2004@compuserve.com Web site: http://www.adaptec.com/incat ** demo software: ftp.adaptec.com/pub/bbs/incat "Largo al factotum del CD-R" From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: "Menczel Laszlo" Newsgroups: bionet.software Subject: Re: debate on pirated software Date: 6 May 1996 09:59:15 +0100 Organization: Biological Research Center Lines: 33 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4mkf13$h91@mserv1.dl.ac.uk> X-Confirm-Reading-To: "Menczel L szl˘" Original-To: bio-software@dl.ac.uk X-Pmrqc: 1 wizkid@sirius.com wrote: > Don't buy anything from the software companies! $500 for Pagemaker > or Adobe Photoshop. All we pay for is the damn advertisting that > they do. Support pirate software!!! They blame that they lose money > from pirating. yeah right. Look at how much they make. people can't > affored to buy 5 disk for $500. Damn software manufactures rip us > off, and we let them, what a joke!!! Hi, Basically I agree that a certain degree of rip-off is happening. Not to mention that the 'high quality' software offered is many times nothing else but a huge lot of unwanted 'features' crammed into a big, impossible to undertstand program (see e.g. Microsoft Word for Windows). Why people pay a lot of money for such software is a mistery to me. However, the solution is not stealing software, but to make better ones -- and give them away free. I suggest that you look up what the Free Software Foundation is (and does). If you are a 'wizkid', join them and make us happy by writing a few wonderful programs! Also you might want to protest when software companies try to prevent universities from releasing the software they developed using public money. (This really happened, and they had the temerity to say it was unfair competition.) Laszlo Menczel Biological Research Center Szeged, Hungary E-mail: menczel@szbk.u-szeged.hu From owner-software@net.bio.net Sun May 05 23:00:00 1996 Newsgroups: bionet.molbio.methds-reagnts,bionet.software Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!news.cais.net!newsfeed.internetmci.com!news.sprintlink.net!rockyd!notes From: =?ISO-8859-1?Q?Sigur=F0ur E. Vilhelmsson?= Subject: Re: Software for strain collections X-Nntp-Posting-Host: masurer-pc.rockefeller.edu Content-Type: multipart/alternative; boundary="Cyberdog-AltBoundary-000537F2" Message-ID: X-Newsgroups-To: nntp://news/bionet.molbio.methds-reagnts, nntp://news/bionet.software Sender: notes@rockyd.rockefeller.edu (News Administrator) Content-Transfer-Encoding: 7bit Organization: Rockefeller University References: <4mdge7$3p0@nrcnet0.nrc.ca> Mime-Version: 1.0 Date: Mon, 6 May 1996 15:32:34 GMT X-Mailer: Cyberdog/1.0 X-News-Servers: news Lines: 105 Xref: biosci bionet.molbio.methds-reagnts:44132 bionet.software:15416 --Cyberdog-AltBoundary-000537F2 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable >FilemakerPro (Claris) is a good one, but I am not sure if it does the >formating you need. Yup, it does >Jos=8Ee Ash >NRC-IRB >Montr=8Eal >ash@biotech.lan.nrc.ca ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Sigurdur E. Vilhelmsson Guest Investigator Microbiology laboratory, box 152 The Rockefeller University 1230 York Avenue New York, NY 10021-6399 tel: (212)-327-8278 fax: (212)-327-8688 e-mail: vilhels@rockvax.rockefeller.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >I am not associated with Claris, just a happy user. Same here --------------------------------------------------- This message was created and sent using the Cyberdog Mail System --------------------------------------------------- --Cyberdog-AltBoundary-000537F2 Content-Type: multipart/mixed; boundary="Cyberdog-MixedBoundary-000537F3" Content-Transfer-Encoding: 7bit --Cyberdog-MixedBoundary-000537F3 Content-Type: text/enriched; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Helvetica>FilemakerPro (Claris) is a good one, but I am not sure if it does the >formating you need. Yup, it does >Jos=8Ee Ash >NRC-IRB >Montr=8Eal >ash@biotech.lan.nrc.ca ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Sigurdur E. Vilhelmsson Guest Investigator Microbiology laboratory, box 152 The Rockefeller University 1230 York Avenue New York, NY 10021-6399 tel: (212)-327-8278 fax: (212)-327-8688 e-mail: vilhels@rockvax.rockefeller.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >I am not associated with Claris, just a happy user.10Geneva GenevaSa= me here --------------------------------------------------- This message was created and sent using the Cyberdog Mail System --------------------------------------------------- --Cyberdog-MixedBoundary-000537F3-- --Cyberdog-AltBoundary-000537F2-- From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!info.ucla.edu!psgrain!quagga.ru.ac.za!inet.up.ac.za!crimson!fourie From: fourie@crimson (Fourie Joubert) Newsgroups: bionet.software Subject: SEQPUP on SPARC? Date: 6 May 1996 08:24:43 GMT Organization: University of Pretoria Lines: 21 Message-ID: <4mkd0b$fj0@inet.up.ac.za> Reply-To: fourie@scientia.up.ac.za NNTP-Posting-Host: crimson.up.ac.za X-Newsreader: TIN [version 1.2 PL2] Hi I am trying to run the Motif-static version of SEQPUP on our Sparc with Solaris 2.1. It just comes up saying Vibrant apps require X-windows... Nothing wrong with my X-display seeing that SEQPUP from our SGI runs happily. Any advice would be sincerely appreciated! -------------- Fourie Joubert Department of Biochemistry University of Pretoria fourie@scientia.up.ac.za http://suntiger.ee.up.ac.za/biodocs/home.html +27-12-420-2011 From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!news.sprintlink.net!tezcat.com!imci5!pull-feed.internetmci.com!news.internetMCI.com!newsfeed.internetmci.com!uwm.edu!news.cse.psu.edu!news.cc.swarthmore.edu!netnews.upenn.edu!dsinc!ub!newsstand.cit.cornell.edu!NewsWatcher!user From: brucec@arthur.bio.cornell.edu (Bruce W. Church ) Newsgroups: bionet.software Subject: rDNA software we wish to make available to any software archives Date: 6 May 1996 19:39:28 GMT Organization: Mens Rugby Football Club at Cornell Lines: 7 Sender: mhd2@cornell.edu (Verified) Message-ID: NNTP-Posting-Host: 128 Our lab has developed an MS-DOS program to help a lab manage its recombinant DNAs and perform restriction enzyme mapping on them. It can be downloaded from http://www.communique.net/~biosci/bs_home.htm, and we are also planning to send it to the MBCRR and bio.indiana.edu archives. Are there any other archives that people would particularly recommend we contribute it to? Please email me at mhd2@cornell.edu rather than posting a reply here. From owner-software@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!news.service.uci.edu!buggus.bio.uci.edu!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: DNA model available Date: Mon, 06 May 1996 14:32:18 -0800 Organization: Microbiology and Molecular Genetics, UC Irvine Lines: 15 Message-ID: References: NNTP-Posting-Host: buggus.bio.uci.edu I know this is silly and I shouldn't be wasting time, but ... In article , djhatzi@tiac.net (paul h) wrote: > A quality representation is available for $150, for your use (half what > Viewpoint charges for the same model). Or even slightly cheaper... get it from PDB (http://www.pdb.bnl.gov/)for free, (already complexed with various proteins, with the added bonus that it has been validated by at least some kind of peer review... Cheers Harry -- Harry J Mangalam, MolBio+Biochem / Dev+Cell Bio, Rm 4201, BioSciII UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 From owner-software@net.bio.net Mon May 06 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.mel.connect.com.au!harbinger.cc.monash.edu.au!calcium.med.monash.edu.au!Ian.Musgrave From: Ian.Musgrave@med.monash.edu.au (Ian Musgrave) Newsgroups: bionet.software Subject: Re: re: calcium buffer software Date: Tue, 7 May 1996 01:05:57 GMT Organization: PHIMR at Monash Medical Center Lines: 27 Message-ID: References: <4ml7io$12v4@ds2.acs.ucalgary.ca> NNTP-Posting-Host: calcium.med.monash.edu.au X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] G'Day All dchurchi@acs.ucalgary.ca (Dennis Churchill) writes: >From: dchurchi@acs.ucalgary.ca (Dennis Churchill) >Subject: re: calcium buffer software >Date: 6 May 1996 15:58:15 GMT >I posted concerning this topic a month ago and haven't got around to posting a summary post. >So here it is. Thanks to all those who responded to my original post (as Caren Helbing by >accident). This is a copy of the mail I received from Theo Schoenmakers who gave a complete >summary of what is generally available. [Very useful summary, which saves me the effort, snipped] Thanks Dennis, and all those who replied to me. I now have MaxChelator, a nice little program indeed. On a related topic, is there some way to notify the IUBIO archives that the CABUFFER program is nolonger on the listed server? Cheers! Ian --------------------------------------------- Ian Musgrave Ph.D Prince Henry's Institue of Medical Research PO Box 5152, Clayton 3168, Australia. Phone +61 3 550 4286 FAX +61 3 550 6125 Lab: Ian.Musgrave@med.monash.edu.au Private: Reynella@werple.mira.net.au From owner-software@net.bio.net Mon May 06 23:00:00 1996 Newsgroups: bionet.software Path: biosci!rutgers!umdnj!news From: "Michael D. Ward" Subject: Cell line database management Content-Type: text/plain; charset=us-ascii Message-ID: <318E6493.6841@umdnj.edu> Sender: news@umdnj.edu () Content-Transfer-Encoding: 7bit Organization: Univ. of Medicine and Dentistry of NJ Mime-Version: 1.0 Date: Mon, 6 May 1996 20:44:03 GMT X-Mailer: Mozilla 3.0b3 (Win95; I) Lines: 21 Dear bionet, I have written a MS Access database program for the management of large tissue and cell line repositories. It was written for computer semi-illiterates so is very easy to use yet is capable of very sophisticated management. Much of the credit goes to Microsoft though, for developing such a great program. If you would like a copy to use and/or evaluate, please email me at: mward@umdnj.edu I would also greatly appreciate any improvement suggestions once you try it out. Some of the features include: beinag able to add, delete and view stocks from a screen that resembles the inside of a freezer box, which shows the relative position and identification of the sample within the box. Thank you M. Ward From owner-software@net.bio.net Mon May 06 23:00:00 1996 Path: biosci!rutgers!uwm.edu!newsfeed.internetmci.com!news.msfc.nasa.gov!pendragon!tricia!uwvax!newssinet!news.nc.u-tokyo.ac.jp!wnoc-tyo-news!infoweb-news!news.tokyo.infoweb.or.jp!usenet From: Fujisawa Newsgroups: bionet.software Subject: Re: ligand-receptor binding Date: 7 May 1996 09:30:32 GMT Organization: Fujisawa Pharm. Co., Ltd. Lines: 14 Message-ID: <4mn57o$1kg@fs.tokyo.web.ad.jp> References: <4m5ecl$74j@dfw-ixnews5.ix.netcom.com> NNTP-Posting-Host: dialup07.tokyo.infoweb.or.jp Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) To: jolleren@ix.netcom.comtion X-URL: news:4m5ecl$74j@dfw-ixnews5.ix.netcom.com Dear Jeremy, You may want to try SigmaPlot for Windows from Jandel. It has a very easy curve fitting function. You can modify or type equations you use. To calculate ED50, "Logistic Functions" should be used. I think Jandel has their own WWW page.... Good luck. Taku. From owner-software@net.bio.net Mon May 06 23:00:00 1996 Path: biosci!rutgers!uwm.edu!lll-winken.llnl.gov!fnnews.fnal.gov!nntp-server.caltech.edu!news From: yukim@cco.caltech.edu (yukim) Newsgroups: bionet.software,alt.comp.shareware,sci.chem,de.comm.internet.software,de.comp.shareware,sci.chem.organomet Subject: ANNOUNCE : AutoRef, v1.1.1 Date: 7 May 1996 10:26:34 GMT Organization: Caltech Lines: 10 Sender: yukim@piccolo.cco.caltech.edu Message-ID: <4mn8gq$lse@gap.cco.caltech.edu> Reply-To: yukim@cco.caltech.edu NNTP-Posting-Host: yukim-ppp.caltech.edu Keywords: AutoRef X-Posted-From: InterNews 1.0.4@yukim-ppp.caltech.edu X-Authenticated: yukim on POP host piccolo.cco.caltech.edu Xref: biosci bionet.software:15425 sci.chem:55588 sci.chem.organomet:2052 This version was given several functions to cover more formats used in other fields as requested by some people (biology, etc..) 1) Kim, Y. (year) Journal, volume, page. 2) &, et, und in addition to and 3) ',', '.', ';', ':' in either plain or bold style It's downloadable at www.cco.caltech.edu/~yukim/ Yuntae Kim From owner-software@net.bio.net Mon May 06 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!metro!metro!unsw.edu.au!NewsWatcher!user From: m.hill@unsw.edu.au (Mark Hill) Newsgroups: bionet.software Subject: Re: Looking for Brain Structure and Function Multimedia Software Date: Tue, 07 May 1996 19:22:29 +1000 Organization: Cell Biology Lab, Anatomy, UNSW Lines: 20 Message-ID: References: <4mc7ev$p49@evia.ccf.auth.gr> NNTP-Posting-Host: 129.94.18.86 In article <4mc7ev$p49@evia.ccf.auth.gr>, Zanos Stavros wrote: > In order to use it for a graduate course on the structure and function of the > CNS, a professor of Psychology (Dr. Vasiliadis) would like to know some > multimedia titles on the subject. The level of analysis should be as high as > possible. > I would appreciate every reference. > > -- > Zanos Stavros > Aristotle Univ School of Medicine > Thessaloniki, Macedonia, Greece > > "If I had more time, I would have written you a shorter letter" > > Pascal I can recommend "Brainstorm" as a teaching program for undergraduates. From owner-software@net.bio.net Mon May 06 23:00:00 1996 Newsgroups: bionet.software Path: biosci!lhc.nlm.nih.gov!nih-csl!postman From: bernard@elsie.nci.nih.gov (Bernard Murray) Subject: Re: Software for managing references from medline (mainly)??? Message-ID: <1996May7.070825.18543@alw.nih.gov> Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: ermintrude.nci.nih.gov Organization: National Institutes of Health, Bethesda, MD X-Newsreader: WinVN 0.99.7 References: <4mdp6b$btp@hobyah.cc.uq.oz.au> Date: Tue, 7 May 1996 07:08:25 GMT Lines: 32 In article , jkiernan@julian.uwo.ca says... > >In article <4mdp6b$btp@hobyah.cc.uq.oz.au> John.Harrison@mailbox.uq.oz.au (John >Harrison) writes: > >>Anyone got good shareware to do all this in some easy manner. > > PAPYRUS is excellent. It accepts all the formats in which > references are downloaded. It will even index all the words > in the abstracts (if you want it to). The best $100 I ever > spent! I wholeheartedly agree. The craziest (good) thing about it is the licence agreement eg. the free (functional) demo that comes with it, and the policy that allows as many copies of the referencing program as you need and only limits you as to the number of distinct databases that you can maintain. Dave Goldman must have had a vocation for this. I don't pretend to understand why, I'm just glad he did. I suppose for a balanced point of view Papyrus may not be to everyone's tastes as it tends to go for functionality rather than bells and whistles. At the end of the day you pays your money... Bernard [No affiliation with Research Software Design except as a customer] Bernard Murray, Ph.D. bernard@elsie.nci.nih.gov (National Cancer Institute, NIH, Bethesda MD, USA) From owner-software@net.bio.net Mon May 06 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.mel.connect.com.au!harbinger.cc.monash.edu.au!newshost.anu.edu.au!newsmaster From: John Armstrong Newsgroups: bionet.software Subject: Re: excoffier's AMOVA Date: 7 May 1996 02:52:38 GMT Organization: Australian National University Lines: 2 Message-ID: <4mmdtm$r31@manuel.anu.edu.au> References: <318A11B1.34BE@leeds.ac.uk> NNTP-Posting-Host: 150.203.38.97 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) To: BGYCSW@leeds.ac.uk ftp://anthropologie.unige.ch/pub/comp/win/amova/ From owner-software@net.bio.net Mon May 06 23:00:00 1996 Newsgroups: bionet.software,bionet.molbio.evolution,bionet.molbio.hiv Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!news.ycc.yale.edu!yale!gumby!newspump.wustl.edu!news.cellbio.wustl.edu!not-for-mail From: eddy@wol.wustl.edu (Sean Eddy) Subject: Re: Massive Multiple Sequence Alignment tools? Sender: eddy@wol.wustl.edu Message-ID: Date: 07 May 1996 07:14:42 -0500 References: <4lmb4n$905@swen.emba.uvm.edu> <4me5tb$1vi@swen.emba.uvm.edu> In-reply-to: brianf@med.uvm.edu's message of 3 May 1996 23:46:51 GMT X-Newsreader: Gnus v5.1 Lines: 42 Xref: biosci bionet.software:15427 bionet.molbio.evolution:4518 bionet.molbio.hiv:2158 In article <4me5tb$1vi@swen.emba.uvm.edu> brianf@med.uvm.edu (Brian Foley) writes: >Thank you very much for ideas on tools such as AMPS. >In addition to performing an alignment on sequences, once >I have all of the sequences ready for alignment, I was >hoping to find a tool that would use the information obtained >in a BLAST or FASTA run to help me obtain the sequences and >clip out the region withhigh similarity to my query sequence. You might check out hidden Markov model software. Two packages are publicly distributed that I know of: SAM from UC Santa Cruz (http://www.cse.ucsc.edu/research/compbio/sam.html) and HMMER from myself at Washington University (http://genome.wustl.edu/eddy/hmmer.html). HMM multiple alignment algorithms are O(N) instead of O(N^2) in the number of sequences, so they are much more efficient for huge sequence sets. They also (in my hands) tend to be more accurate than other popular methods for large sequence sets (though for more reasonable numbers of sequences (10-50) I still prefer Clustal). We've aligned sets as large as 2000+ sequences. Your 6000 would pose no problem. HMMs can also allow you to align to a previous smaller multiple alignment. You can carefully hand-craft an alignment of a representative set of sequences, then align the rest of your 6000 relative to that. You can use an HMM built from your alignment to search for matches in other sequences. HMMER includes four different search algorithms: one for complete global alignment; one for Smith/Waterman local alignment; one for finding complete matches to the HMM in longer sequences (say, if you're trying to find several complete copies of immunoglobulin domains in a neural cell adhesion molecule sequence), and one for finding multiple non-overlapping Smith/Waterman local alignments. We often use HMMER in tasks like what you seem to be describing. Make a small seed alignment by hand, by ClustalW, or by HMM training. Build an HMM. Search a bunch of extracted GenBank sequences with that HMM. Use a Perl script to parse out the coordinates of the matching subsequences and fetch the subsequences from GenBank. Make a new alignment, and new HMM. Re-iterate if necessary until you've got all the sequences you want. -- - Sean Eddy - 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 Mon May 06 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!oslonett.no!sn.no!Norway.EU.net!EU.net!news.kreonet.re.kr!news.dacom.co.kr!arclight.uoregon.edu!usenet.eel.ufl.edu!eng.ufl.edu!usenet.cis.ufl.edu!caen!newsxfer2.itd.umich.edu!newsfeed.internetmci.com!news.mathworks.com!fu-berlin.de!zrz.TU-Berlin.DE!zib-berlin.de!gmdtub!cs1.FTA-Berlin.de!news From: rottmann@hermes.fmp.fta-berlin.de (Rottmann) Newsgroups: de.comp.shareware,alt.comp.shareware,bionet.software,sci.chem,de.comm.internet.software Subject: Re: Where I can find "Ligand", a plot program from NIH? Keywords: "LIGAND", DOS program, receptor Message-ID: <4mn1sp$7po@cs1.FTA-Berlin.de> Date: 7 May 96 18:33:13 GMT References: <4lpihi$o06@gap.cco.caltech.edu> <31811678.6EBE@uic.edu> Reply-To: hbae1@uic.edu Organization: FMP Lines: 27 NNTP-Posting-Host: ropc01.fmp.fta-berlin.de Mime-Version: 1.0 X-Newsreader: WinVN 0.93.0 Xref: biosci bionet.software:15432 sci.chem:55601 In article <31811678.6EBE@uic.edu>, hbae1@uic.edu says... > >For some reason we need the program named "ligand" from NIH. I got it >long time ago and the one I got is for DOS. Does anyone knows where to >get it? >Any help is appreciated. > >Take it easy. I might not be the first one to send a reply, but, nevertheless, I'd guess I've some experience in using "LIGAND". For quite some time it is commercially available from BIOSOFT, P.O.B. 10938, Ferguson, MO 63135, U.S.A., phone: (314)524-8029, fax: (314)524-8129, e-mail: ab47@cityscape.co.uk (there should be another address in the U.S. and there IS definitely a WWW-Site of BIOSOFT; which I don't remember, so go and find out!). The program you are longing for is now a package called KELL (Kinetic, EBDA, LIGAND and Lowry) and was sold for US$ 500 two years ago (please inquire ---> WWW-Site!). Working with 3 different versions of LIGAND for a couple of years (among them probably the old one you had),I found out that each of them has its own advantages and disadvantages, which we could discuss after you specified your task. The package still consists of pure DOS-programs. Curve-fitting features are excellent (though you need some experience!), but graphics not the state of the art. If you've further questions, don't hesitate to contact me Matthias Rottmann From owner-software@net.bio.net Mon May 06 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!in1.uu.net!nectec!news.mahidol.ac.th!mucc!g3421101 From: g3421101@mucc.mahidol.ac.th (Enrique Jose Labadan Frio - SCBC - 3421101) Newsgroups: bionet.software Subject: libf77? Date: 4 May 1996 19:30:21 GMT Organization: Mahidol University, Thailand Lines: 14 Message-ID: <4mgb8d$orr@mars.mahidol.ac.th> NNTP-Posting-Host: 202.14.162.1 X-Newsreader: TIN [version 1.2 PL2] Dear all, Our Sun Sparc gives a library not found error when I try to run a program: ld.so: libF77.so.1: not found Can this lib be obtained somewhere? Thanks 10^6! Sincerely yours, Querix g3421101@mucc.mahidol.ac.th From owner-software@net.bio.net Mon May 06 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!nntp.coast.net!torn!news.dal.ca!news From: "Andrew J. Roger" Newsgroups: bionet.software,sci.bio.systematics Subject: Re: Program for testing incongruences Date: 7 May 1996 18:03:34 GMT Organization: Dalhousie Biochemistry Lines: 117 Message-ID: <4mo39m$f9f@News.Dal.Ca> References: <4mi7v8$qin@lastactionhero.rs.itd.umich.edu> NNTP-Posting-Host: samiam.biochem.dal.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:4mi7v8$qin@lastactionhero.rs.itd.umich.edu Xref: biosci bionet.software:15430 sci.bio.systematics:959 tdib@umich.edu (Thomas K. Dibenedetto) wrote: >Andrew J. Roger (aroger@ac.dal.ca) wrote: >: Have you heard of lateral gene transfer? In case you haven't,,,,, > >Howdy Andrew! Long time, no read! >Yeah, I sorta, kinda heard about this stuff. But you know, it _still_ >doesnt strike me as all that much different from any other character >which may be misleading.... Well, its different on a theoretical level. Other characters might mislead one because of homoplasy. A laterally transferred gene could be full of historically true synapomorphies but still be misleading about the phylogeny of the organism in which it currently resides. > >: Now if you were trying to work out the phylogenetic position of an organism >: and you used all of the genes available from this organism and related >: ones, snip >: including a gene which this organism picked up from another lineage >: (which the other taxa in the dataset did not), you would be including >: a datum which will be positively misleading about the phylogenetic >: relationships of this organism (if you were interested in the >: relationships which are the result of vertical descent rather than >: lateral transfer of one of its genes). >: The need to keep data like these separate seems so obvious to me >: that I cannot conceive why you might object to it. Can you enlighten me? > >Well gee, if I could _know_ that a gene came from elsewhere, I might go >along, but how do you get to know this, before you do the analysis? Your point is well taken. In the absence of knowledge about the organism's phylogenetic position, you cannot distinguish lateral transfer from vertical descent. Fortunately, most of the time one has some idea of phylogenetic position. For instance, I may not know whether Trichoplax adhaerens (to quote an example mentioned in this newsgroup) falls within the metazoa or is an unrelated multicellular protist. But I do know that it is definitely a eukaryote. So, if I were cloning genes from this organism and one gene showed a mysteriously strong affinity for a gram positive eubacterium whereas all others showed affinities for eukaryotes, I would be pretty justified in assuming that the gene I have is not indicative of a relationship of Trichoplax with gram positive eubacteria. I can know this because there are dozens of eukaryotic character states that Trichoplax possesses...it cannot be specifically related to bacteria. The fact is, it is rare that we know NOTHING about the phylogenetic position of an extant organism in the tree of life. Usually, we know a little about it (whether it is eubacterial, eukaryotic or archaebacterial). In cases where genes tell us things about relationships which conflict with this knowledge, then you can be reasonably certain that you are dealing with lateral transfer or a case of gene paralogy. In many other cases, as you correctly imply, we cannot differentiate between lateral transfer and direct descent. >The original poster had two conflicting (or potentially conflicting) >datasets and wondered if they should be combined. If they were >"significantly different", would this necessarily indicate lateral >transfer? Partitions of a single dataset (one gene) can be different right? >Thus, there must be other reasons why one discovers incongruence, no? >Do you think conflicting data should never be combined, irrespective of >the reason? > >: If we are dealing at the level of molecular data then one must try to >: think of what patterns of conflicting data will be indicative of true >: chimaerism as opposed to "noisy" data. > >Well, noisy data (as you point out) is unpatterned. I am asking you, are >there other factors which might pattern data besides "chimaerism" or the >true history? This is a good point. It could be that portions of a gene (consecutive codons for instance) all display similarly misleading patterns. This set of codons could all be susceptible to the same force (biased substitution pattern for instance) and appear to conflict with the dataset as a whole in a consistent way. But once again, there would be implications which distinguish this from gene chimaerism which could be used to resolve the issue. > >: Thus it is clear in principle and in practice in this case how you >: would destinguish between noisy data and real gene chimaerism. snip >re. my total evidence, lump it all together argument: >: This would be fine if you could be certain that a significant portion >: of your dataset were derived from vertical descent only. But it is >: possible that your total dataset may contain a large portion of >: data which is postively conflicting. The result may be a phylogeny >: which makes no sense at all because it is derived from multiple >: datasets which had different histories. >: The success of total evidence depends on the anomalous phylogenies >: being in the minority...and that the true phylogeny will "come out >: in the wash". I wouldn't be comfortable with this assumption. > >Well, I dont know why not. Would you care to point me toward those >sources of evidence which have led you to conclude >that "anomolous" gene trees are anywhere near as common as would be >necessary to upset a total evidence analysis? They are probably not very common in a lot of cases. There is one fundamental case where they might be. Recently Golding and Gupta published a paperin Molecular Biology and Evolution where they described comparisons of eukaryote/archaebacteria/gram positive/ gram negative homologs of roughly 2 dozen genes. They found that about 1/3 of the genes gave a significantly different relatioship of these groups to roughly 1/2 of the dataset. The rest of the genes did not resolve relationships very well. However, the point is that the fundamental relationships between eukaryotes, archaebacteria and eubacterial groups are unknown and the data significantly conflict in their answers. Total evidence on this dataset would mean nothing. Cheers Andrew Roger aroger@ac.dal.ca From