From owner-software@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news01.sunet.se!sunic!mn6.swip.net!plug.news.pipex.net!pipex!tube.news.pipex.net!pipex!lade.news.pipex.net!pipex!tank.news.pipex.net!pipex!newsfeed.internetmci.com!newsserver.jvnc.net!crick.bms.com!usenet From: "Nicholas D. Garigliano" Newsgroups: bionet.software Subject: Data Analysis Software Date: Tue, 02 Apr 1996 11:45:16 -0500 Organization: Bristol-Myers Squibb Company Lines: 8 Message-ID: <3161599C.22A@bms.com> References: <4j77rm$lc6@voyager.iii.org.tw> NNTP-Posting-Host: bar_hp_a.wf.bms.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) CC: bionet.general I'm looking for info on software for doing data analysis of cell based and ELISA type assays. It would need to be able to perform various curve fits, spline, quadratic, 4-P etc., without extensive programing or macro making and provide relevant information about the curve. I am I just wishing here or is there anyting out there?? Could you also replay to my e-mail as I'm buried with work and usually fall quickly behind on reading the news. Thanks. From owner-software@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!news.belnet.be!swsbe6.switch.ch!swidir.switch.ch!in2p3.fr!oleane!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!newsfeed.internetmci.com!newsserver.jvnc.net!crick.bms.com!usenet From: "Nicholas D. Garigliano" Newsgroups: bionet.software Subject: Data Analysis Software Date: Tue, 02 Apr 1996 11:45:57 -0500 Organization: Bristol-Myers Squibb Company Lines: 8 Message-ID: <316159C5.61B2@bms.com> References: <4j77rm$lc6@voyager.iii.org.tw> NNTP-Posting-Host: bar_hp_a.wf.bms.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) I'm looking for info on software for doing data analysis of cell based and ELISA type assays. It would need to be able to perform various curve fits, spline, quadratic, 4-P etc., without extensive programing or macro making and provide relevant information about the curve. I am I just wishing here or is there anyting out there?? Could you also replay to my e-mail as I'm buried with work and usually fall quickly behind on reading the news. Thanks. From owner-software@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!in2.uu.net!news.cais.net!peer.news.xara.net!xara.net!netcom.net.uk!ix.netcom.com!ix.netcom.com!news From: rbrady@ix.netcom.com(Richard Brady) Newsgroups: bionet.software Subject: Looking for clone & primer design software Date: 1 Apr 1996 23:19:18 GMT Organization: Netcom Lines: 13 Message-ID: <4jpo9m$ch9@dfw-ixnews5.ix.netcom.com> NNTP-Posting-Host: lax-ca20-21.ix.netcom.com X-NETCOM-Date: Mon Apr 01 5:19:18 PM CST 1996 Netters, Would appreciate any information on commercial or freeware software that can be used for cloning and primer design-analysis. Am trying to find something that works well, is intuitive and under a thousand bucks. CloneWorks by Anteater Software looks good (http://www.cloneworks.com/anteater). Would like to download eval and/or demos for similar packages. Suggestions, URLs, would be appreciated. R.B. From owner-software@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!daresbury!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!brenner From: brenner@mole.bio.cam.ac.uk (Steven Brenner) Newsgroups: bionet.software Subject: Re: software for sequential downloading of software after line breaks? Date: 2 Apr 1996 19:37:02 GMT Organization: University of Cambridge, England Lines: 21 Message-ID: <4jrvku$6f7@lyra.csx.cam.ac.uk> References: <4jo7eh$kej@winx03.informatik.uni-wuerzburg.de> NNTP-Posting-Host: mole.bio.cam.ac.uk X-Newsreader: NN version 6.5.0 #3 (NOV) humberto@momo.uthscsa.edu (Humberto Ortiz Zuazaga) writes: > CK> I don't think that it is possible with the current ftp > CK> server/client software to just fetch parts of files. >NcFtp, a UNIX ftp client optimized for annonymous ftp will skip over >the start of files which have been partially transferred. It also has >a command line mode which makes it great for scheduling automated >transfers at night. Virtually any unix ftp client can do partial-downloads. The command is 'reget' which is used just like 'get'. As noted in previous messages, truely difficult transfers are best done at unusual hour. Steve -- Steven E. Brenner | S.E.Brenner@bioc.cam.ac.uk MRC Laboratory of Molecular Biology | Hills Road | Office: +44 1223 248011 Cambridge CB2 2QH, UK | Fax: +44 1223 213556 From owner-software@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!info.ucla.edu!nnrp.info.ucla.edu!usenet From: Paul Morcos Newsgroups: bionet.software Subject: Re: CloneWorks Date: Mon, 01 Apr 1996 20:03:18 -0800 Organization: University of California, Los Angeles Lines: 27 Message-ID: <3160A706.625@ucla.edu> References: <4jpo9m$ch9@dfw-ixnews5.ix.netcom.com> NNTP-Posting-Host: ts21-1.wla.ts.ucla.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win95; I) Richard Brady wrote: Thanks for the post R.B., We downloaded CloneWorks this morning (all 1.4 megs) and thought it was awesome! I like the fact that they don't over analyze and they spend more time on generating primers and helping you clone. I've never seen a cloning package like this. We called this morning and since we have PC gene it only costs $795. It's the fastest decision my boss ever made! Thanks, P.M. U.C.L.A. p.s. I didn't remember the web site, but i found it by searching for Cloneworks using netscape's net search. > Netters, > > Would appreciate any information on commercial or freeware software > that can be used for cloning and primer design-analysis. Am trying to > find something that works well, is intuitive and under a thousand > bucks. CloneWorks by Anteater Software looks good > (http://www.cloneworks.com/anteater). Would like to download eval > and/or demos for similar packages. Suggestions, URLs, would be > appreciated. > > R.B. From owner-software@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!news.belnet.be!swsbe6.switch.ch!surfnet.nl!howland.reston.ans.net!gatech!willis.cis.uab.edu!nntp.msstate.edu!Sunmuw1.MUW.Edu!mat From: Mark Tidwell Newsgroups: bionet.software Subject: gnuplot Date: Tue, 2 Apr 1996 13:21:17 -0600 Organization: Mississippi State University Lines: 12 Message-ID: NNTP-Posting-Host: sunmuw1.muw.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I'm looking for a shareware copy of gnuplot.exe for use with GEPASI 2.0. I've done some searching but come up empty for the actual .exe file. I would appreciate any ftp or http site known. Thank you in advance. ############################################################ # Mark Tidwell \ "Oh, beware the other head of # # mat@sunmuw1.muw.edu \ science Arthur! It bites!" # # http://www.muw.edu/~mat \ -The Tick # ############################################################ From owner-software@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!data-transport.com!scott_jokerst From: scott_jokerst@data-transport.com (R. Scott Jokerst) Newsgroups: bionet.software Subject: Re: Data Analysis Software Date: 2 Apr 1996 12:31:38 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hello Nicholas, A search of Biological Data Transport's resources at http://www.data-transport.com for the terms software and curve finds two companies, one or both of whom may have what you are looking for. Jandel Scientific Graphpad Scientific Software Another query for data analysis turned up several, among them: Statware, Inc. Of course, simply querying for software will get you many more. Let me know if any of these help, Scott *********** At 8:45 AM 4/2/96, Nicholas D. Garigliano wrote: >I'm looking for info on software for doing data analysis of >cell based and ELISA type assays. It would need to be able >to perform various curve fits, spline, quadratic, 4-P etc., >without extensive programing or macro making and provide >relevant information about the curve. I am I just wishing >here or is there anyting out there?? Could you also replay >to my e-mail as I'm buried with work and usually fall >quickly behind on reading the news. Thanks. R. Scott Jokerst scott_jokerst@data-transport.com Biological Data Transport http://www.data-transport.com "Life sciences informatics, product, and services resources" From owner-software@net.bio.net Mon Apr 01 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!in1.uu.net!news.magicnet.net!news.supernet.net!news.iosphere.net!grumpy.insinc.net!roger.interlynx.net!news From: lthomsen@interlynx.net (Lars Thomsen) Newsgroups: bionet.software Subject: Image-one - problems with software settings of 340nm, 380 ok Date: Tue, 02 Apr 1996 16:29:00 GMT Organization: Interlynx Lines: 12 Message-ID: <4js676$kcr@roger.interlynx.net> NNTP-Posting-Host: ppp05_max2.interlynx.net X-Newsreader: Forte Free Agent 1.0.82 I want to use the dual-wavelength method to measure Ca2+ with Fura2 in my cells. The cells are loading nicely - the filter settings look allright. I tried to add a lot of Fura2 and then some CaCl2 and I got bright fluorescence at both wavelengths (seen through the eyepieces). However I can't see any signal via the software on wavelenght 1 (=340nm). Wavelenght 2 (=380nm) is clearly visuable in the analog settings - any suggestions !! From owner-software@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!ra.nrl.navy.mil!news.math.psu.edu!psuvax1!news.cc.swarthmore.edu!netnews.upenn.edu!dsinc!newsfeed.pitt.edu!gatech!newsfeed.internetmci.com!info.ucla.edu!news.ucdavis.edu!quad!knight From: knight@quad.cs.ucdavis.edu (James Knight) Newsgroups: bionet.software Subject: ANNOUNCE: The SEQIO Package, version 1.1 is now Available Date: 3 Apr 1996 03:44:36 GMT Organization: University of California, Davis Lines: 46 Message-ID: <4jss74$pr7@mark.ucdavis.edu> NNTP-Posting-Host: quad.cs.ucdavis.edu X-Newsreader: TIN [version 1.2 PL2] The SEQIO package is a software package in C (or a C library, if you prefer) which reads and writes the major biological sequence file formats and databases. It has been designed so that the programmer interface is as close to the stdio library as possible, given the more complex I/O performed by this package. The package supports the GenBank, EMBL, Swiss-Prot, PIR/CODATA, PIR/NBRF, FASTA, IG/Stanford, PHYLIP, Clustal and ASN.1 file formats, along with plain text and the output produced by the FASTA programs (FASTA, TFASTA, SSEARCH, LFASTA, LALIGN and ALIGN). It can be compiled and used with C and C++ programs on most of the Unix variants and Windows NT. This message is to announce the release of version 1.1 of the SEQIO package. Major changes from version 1.0: * Added the PHYLIP, Clustal and FASTA output formats. The NBRF format now conforms completely to the format for the VMS version of the PIR database. * The program was ported to Windows NT, was compiled on Solaris, and was compiled with g++. * Added fmtseq, a file format conversion problem that reimplements and extends Don Gilbert's readseq program, with a more robust interactive mode and with the ability to parse FASTA program output and construct a big alignment from the pairwise alignments. * Added keyword, a program which searches files and databases for exact and approximate matches to a fixed-width motif. * Converted all of the program documentation into HTML files. The package is freely available to anyone and can be ftp'ed from the following FTP site: ftp://ftp.cs.ucdavis.edu/pub/strings/seqio.tar.gz It is a gzip'ed, tar file (181K compressed) containing the package code and documentation files. I've also set up a web site for the package at http://wwwcsif.cs.ucdavis.edu/~knight/seqio.html From owner-software@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news01.sunet.se!sunic!news99.sunet.se!news.uni-c.dk!news From: "Ulrik Skands (phd.- be/kc)" Newsgroups: bionet.software Subject: ANNOUNCE: Short Course on Computer-Assisted Image Analysis Date: Wed, 03 Apr 1996 14:56:36 +0200 Organization: IMM Lines: 39 Message-ID: <31627584.7CBF@imm.dtu.dk> NNTP-Posting-Host: serv1.imm.dtu.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; HP-UX A.09.05 9000/755) Content-Disposition: inline; filename="ipcourse" ANNOUNCEMENT of 4th European Short Course and Workshop on ============================================== COMPUTER-ASSISTED IMAGE ANALYSIS & MEASUREMENT ============================================== Copenhagen, 17th-20th June 1996 Organized by: Professor John C. Russ, Materials Science and Engineering Department, N. C. State University, Author of "Practical Stereology", "Computer-Assisted Microscopy", and "The Image Processing Handbook". Professor H. J. G. Gundersen, Stereological Research Laboratory, University of Aarhus, Denmark. Gundersen is the author of a number of papers and review articles on new stereological methods. Dr. Leif Hoejslet Christensen, Course Manager, Department of Chemistry, Danish Technological Institute (DTI). Registration: The registration fee for the 3 1/2 day seminar is Dkr. 10,500. The fee is Dkr. 7,500 for students. Advance registration is requested to assist the institute in making plans for the group. The registration fee includes meeting facilities, all course materials (incl. "The Image Processing Handbook" and CD-ROM), refreshments and lunch each day. Information on registration, tuition and lodging is available from Ms. Linda M. Gertz, Department of Enviroment, Danish Technological Institute, tel.: +45 43 50 46 03 or fax: +45 43 50 71 50, e-mail: LHC@svane.dti.dk, US Web-page: http://vims.ncsu.edu/matsci/IPCourse.html DK Web-page: http://193.88.23.34/sem-dti.htm, From owner-software@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!agate!spool.mu.edu!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!gatech!concert!news-server.ncren.net!taco.cc.ncsu.edu!news From: Susan Jane Hogarth Newsgroups: bionet.software Subject: primer tracking software? Date: Tue, 02 Apr 1996 11:15:12 -0500 Organization: North Carolina State University Lines: 28 Message-ID: <31615290.40F2@unity.ncsu.edu> NNTP-Posting-Host: sparc5c-2203gardnr.ppath.ncsu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.4 sun4m) Hello, I'm looking for (free?) software to keep track of RAPD primers. Please respond by email. Thanks -- Susan Jane Hogarth "Luck is the residue of design." -- Freddy the Fish "Personally, I'm always ready to learn, although I do not always like being taught." -- Winston Churchill http://www4.ncsu.edu/~sjhogart/public/home.html . .-~\ / `-'\.' `- : | / `._ | | .-. { \ | `-' `. . \ | / ~-.`. \| .-~_ `.\-.\ .-~ \ `-'/~~ -.~ / .-~/|`-._ /~~-.~ -- ~ / | \ ~- . _\ From owner-software@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!PEASTMS.PKU.EDU.CN!lxzyx From: lxzyx@PEASTMS.PKU.EDU.CN Newsgroups: bionet.software Subject: Clustal Plus?? Date: 3 Apr 1996 02:11:25 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604030908.AA22671@peastms.pku.edu.cn> NNTP-Posting-Host: net.bio.net I am now using Clustal with Pcgene, the pragram is useful. However, it has a limit to compare no more than 25 sequencen at a time. Can anyone tell me wether I can find any program that can do the same task(multiple alignment, and building phylogenetic trees) and can compare more protein sequence at a time?? Thank you very much Sincerely Yours Chunhui Mo College of Life Sciences Peking University Beijing P.R.China. email lxzyx@peastms.pku.edu.cn From owner-software@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: "Lennart Nilsson (Karolinska institutet)" Newsgroups: bionet.software Subject: ANNOUNCEMENT: Understanding Protein Structure Determination Date: 3 Apr 1996 12:19:42 +0100 Lines: 28 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4jtmse$hup@mserv1.dl.ac.uk> X-Mts: smtp Original-To: pdb-l@pdb.pdb.bnl.gov, bioforum@dl.ac.uk, bionews@dl.ac.uk, biophys@dl.ac.uk, bio-soft@dl.ac.uk, comp-bio@dl.ac.uk, methods@dl.ac.uk, molmodel@dl.ac.uk, proteins@dl.ac.uk, xtal-log@dl.ac.uk, str-nmr@dl.ac.uk Posted-Date: Wed, 03 Apr 96 13:18:43 +0200 The Karolinska Institute's Center for Structural Biochemistry will hold its 6th summer school, entitled "Understanding Protein Structure Determination" on September 1-6, 1996. This is one of a series of short graduate courses organized each summer by the Summer University of Southern Stockholm at NOVUM Research Park, located about 15 km south of Stockholm. As usual we are aiming for an informal format with students on the graduate and postdoc levels. A fair amount of time will be set aside for discussions and social activities. The topic of the 1996 summer school is intended to cover the two major protein structure determination techniques: X-ray crystallography and NMR spectroscopy. Topics such as the physical basis, experimental aspects, computational and software aspects, quality assessment of determined structures, and effects of structural heterogeneity and dynamics will be addressed. Emphasis will be put on the complementarity of the two techniques. Course fee: SEK 2500 (academic), SEK 5000 (non academic) Deadlines: Application June 14, 1996; poster abstract August 2, 1996. For further information/application forms please contact Ms. Aila Holappa at FAX +46-8-608 9290 or e-mail Aila.Holappa@cbt.ki.se More information is available at http://www.csb.ki.se/events/summer96.html Organizing committee: Hans Hebert, Torleif Hard, Rudolf Ladenstein, Lennart Nilsson From owner-software@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!news.Stanford.EDU!nntp-hub2.barrnet.net!newsfeed.internetmci.com!in2.uu.net!info-server.bbn.com!news5.ner.bbnplanet.net!news.ner.bbnplanet.net!news3.near.net!bigboote.WPI.EDU!news.ultranet.com!usenet From: Ken Brady Newsgroups: bionet.software Subject: Re: gnuplot Date: Wed, 3 Apr 1996 00:35:00 GMT Organization: UltraNet Communications, Inc. Lines: 14 Message-ID: <4jsgv6$rgb@caesar.ultra.net> References: NNTP-Posting-Host: kbrady.ultranet.com X-Newsreader: Post Road News Reader 1.01f > > I'm looking for a shareware copy of gnuplot.exe for use with > GEPASI 2.0. I've done some searching but come up empty for the actual > ..exe file. I would appreciate any ftp or http site known. Thank you in > advance. > I just recently downloaded the OS/2 version from hobbes.nmsu.edu. I assume versions for other platforms can be found there as well. Ken Brady kbrady@ultranet.com From owner-software@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!taurus!news From: kenc@adnc.com (Kenc) Newsgroups: bionet.software Subject: FREE Disk Space Management Utility Date: 3 Apr 1996 04:08:17 GMT Organization: Sedona Software Lines: 8 Message-ID: <4jstjh$34q@taurus.adnc.com> NNTP-Posting-Host: 205.216.157.2 Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-Newsreader: WinVN 0.99.7 Check out a free disk space management utility for Windows that my company, Sedona Software, wrote. It's FREE on the web at http://www.adnc.com/web/sedona Look for Disk Space Finder. If you like it let me know Ken From owner-software@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news01.sunet.se!sunic!news99.sunet.se!columba.udac.uu.se!nostromo.bmc.uu.se!user From: gerard@xray.bmc.uu.se (Gerard Kleywegt) Newsgroups: bionet.software Subject: Re: MOLGEN Date: 3 Apr 1996 21:54:55 GMT Organization: Biomedical Centre, Uppsala University Lines: 58 Message-ID: References: NNTP-Posting-Host: nostromo.bmc.uu.se X-Newsreader: Value-Added NewsWatcher 2.0d31h+ In article , friedric@techfak.uni-bielefeld.de (Friedrich Ackermann) wrote: ?> Dear Netters, ?> ?> I am putting together a list of topics I want to present ?> in a seminary called "`Informatik in der Molekularbiologie"' ?> (german translation of "`Molecular Bioinformatics"' or ?> "`Computing for Molecular Biology"'). ?> Among the topics I have found to be interesting there is ?> a program called MOLGEN by M. Stefik (see for example ?> Stefik, M., Planning with Constraints (MOLGEN: Part 1), ?> Artificial Intelligence 1981(16), 111-140 or the dicussion in ?> Schulze-Kremer, S., Molecular Bioinformatics, Berlin 1996). ?> Since I am working on the protein docking problem I am not an ?> expert neither for Artificial Intelligence nor for cloning experiments ?> (the application domain of MOLGEN). ?> ?> Therefore I would appreciate any answers on the following questions: ?> ?> 1. Is MOLGEN still in use? Can it be downloaded? Ist it ?> supported by an institution or do commercial versions exist? ?> What are the current versions? How do they differ from the ?> originally described ones? ?> ?> 2. Do any successors of MOLGEN or other programs with a ?> similar application goal exist? (Remark: MOLGEN's goal is ?> to develop automatically plans for producing genetically ?> modified bacteriums using methods from Artifical Intelligence.) ?> Where can they be found? Which references should be read? ?> ?> Beside this any hints about lists of topics or curriculae for molecular ?> bioinformatics are appreciated. ?> ?> Best regards, ?> Friedrich Ackermann hmm, a couple of years ago i threw away all my aritificial intelligence- related papers ;-) most AI projects in the life sciences were "demonstration" projects which were not actually used much by the people in the field (despite inflated claims to the contrary from some AI people; dendral springs to mind immediately; crysalis looked promising but was never used in any real cases as far as i know; the stanford protein nmr system is used mostly in stanford i think; etc etc) i seem to remember vaguely that molgen was actually marketed commercially, probably by IntelliGenetics (which, i further seem to remember, was bought up by another company a few years ago); whether or not it was a success i don't know - maybe a web or literature search will help you further --gerard -------------------------------------------------------------------- Gerard J. Kleywegt Department of Molecular Biology, Biomedical Centre Uppsala University, Uppsala, SWEDEN From owner-software@net.bio.net Tue Apr 02 23:00:00 1996 Newsgroups: bionet.software Path: biosci!rutgers!news.iag.net!news.math.psu.edu!psuvax1!uwm.edu!newsfeed.internetmci.com!howland.reston.ans.net!EU.net!ieunet!maths.tcd.ie!news.tcd.ie!acer!smulcahy From: smulcahy@acer.gen.tcd.ie (Stephen Mulcahy) Subject: Prettybox Message-ID: Sender: usenet@news.tcd.ie (TCD News System ) Reply-To: 9224076@ul.ie Organization: University of Dublin, Trinity College X-Newsreader: TIN [version 1.2 PL2] Date: Wed, 3 Apr 1996 14:02:08 GMT Lines: 21 I wazs wondering if anyone out there has got this successfully installed on an osf/1 machine. We don't have egcg installed on the machine I'm working on, but a copy of the prettybox program would be very useful to me write now. I have the vax fortran source which the author of the original version was kind enough to send me, but this will not cleanly compile with f77 on osf/1. Has anyone got a binary or hacked osf/1 compatible source that they'd like to share? thanks -stephen -- Stephen Mulcahy 4th Industrial Biochemistry Undergraduate University of Limerick, Ireland www: http://skynet.ul.ie/~stephen From owner-software@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!mn6.swip.net!seunet!news2.swip.net!inet-1.pharmacia.se!usenet From: Kjell Madsen Newsgroups: bionet.software Subject: Re: Data Analysis Software Date: 3 Apr 1996 08:16:56 GMT Organization: Pharmacia Lines: 8 Message-ID: <4jtc5o$lme@inet-1.pharmacia.se> References: <4j77rm$lc6@voyager.iii.org.tw> <3161599C.22A@bms.com> NNTP-Posting-Host: pcmakj.upp.se.pnu.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1 (Windows; I; 16bit) To: gariglia@bms.com For a Windows program, try GraphPad Prism from GraphPad Software, Inc., 10855 Sorrento Vally Rd #203, San Diego, CA 92121. Email: sales@graphpad.com URL: http://www.graphpad.com/www/welcome.html Kjell From owner-software@net.bio.net Tue Apr 02 23:00:00 1996 Path: biosci!biosci!not-for-mail From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software Subject: Re: MOLGEN Date: 3 Apr 1996 15:21:38 -0800 Organization: BIOSCI International Newsgroups for Biology Lines: 33 Distribution: world Message-ID: <4jv162$91r@net.bio.net> References: NNTP-Posting-Host: net.bio.net In article , Gerard Kleywegt wrote: >In article , >friedric@techfak.uni-bielefeld.de (Friedrich Ackermann) wrote: > >?> I am putting together a list of topics I want to present >?> in a seminary called "`Informatik in der Molekularbiologie"' >?> (german translation of "`Molecular Bioinformatics"' or >?> "`Computing for Molecular Biology"'). >?> Among the topics I have found to be interesting there is >?> a program called MOLGEN by M. Stefik (see for example >i seem to remember vaguely that molgen was actually marketed commercially, >probably by IntelliGenetics (which, i further seem to remember, was bought >up by another company a few years ago); whether or not it was a success >i don't know - maybe a web or literature search will help you further > >--gerard I worked previously for IntelliGenetics (no longer have any affiliation there) and do know that the MOLGEN software was the precursor for the "IG Suite" of Sun and VAX molbiol programs which was IG's first product line in the 80s. If you want the early history of MOLGEN, you can probably get this from Doug Brutlag at Stanford (brutlag@cmgm.stanford.edu). Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-software@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!oxpath!hugh From: hugh@molbiol.ox.ac.uk (Hugh Salter) Newsgroups: bionet.software Subject: Protein representation software? Date: 4 Apr 96 10:48:35 GMT Organization: Oxford University Molecular Biology Data Centre Lines: 16 Message-ID: <1996Apr4.104835@molbiol.ox.ac.uk> NNTP-Posting-Host: ania.path.ox.ac.uk Hi... Can anyone suggest a program (any platform) that will make (or help to make) a pepnet-style representation of a complete protein sequence, drawing out the loops as some sort of thread (made of alphanumeric characters) as well as any transmembrane spans? Hugh ----------------------------------------------------------------------------- Hugh Salter Oxford University Molecular Biology Data Centre hugh@molbiol.ox.ac.uk Tel: (01865) 2-75507 (Univ) "Hell hath no fury like a vested interest disguised as a moral principle" (R4) ----------------------------------------------------------------------------- From owner-software@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!uwm.edu!fnnews.fnal.gov!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software Subject: Re: Introducing silent restriction sites Date: 4 Apr 1996 18:09:13 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 17 Message-ID: <4k1389$23r@gap.cco.caltech.edu> References: <315F9C11.507F@mrc-lmb.cam.ac.uk> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu In article <315F9C11.507F@mrc-lmb.cam.ac.uk>, Tony Hodge writes: >Hi, > >we are looking for some (preferably Mac) software to identify the >positions where 'silent' restriction sites can be introduced by >mutagenesis into DNA sequence. > >Anyone help? GCG's MAP programs will do this, if you have access to that on OpenVMS or Unix. No Mac version, sorry. Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-software@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!agate!usenet From: abbas@mendel.berkeley.edu (Alex Abbas) Newsgroups: bionet.software,bionet.molbio.proteins Subject: Antigenicity Prediction Software? Date: 4 Apr 1996 17:51:52 GMT Organization: U.C. Berkeley Lines: 10 Message-ID: <4k127o$21p@agate.berkeley.edu> NNTP-Posting-Host: bark2mac30.berkeley.edu X-Posted-From: InterNews 1.0.6@bark2mac30.berkeley.edu X-Authenticated: abbas on POP host mendel.berkeley.edu Xref: biosci bionet.software:15166 bionet.molbio.proteins:7512 I'm looking for mac software to generate theoretical predictions of the antigenicity of regions along a protein sequence... I'm trying to figure out what peptide to try to raise antibodies against. If anyone knows of anything, please drop me a line. Thanks in advance, Alex Alex Abbas http://mendel.berkeley.edu/~abbas/ From owner-software@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!tank.news.pipex.net!pipex!oleane!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!fu-berlin.de!cs.tu-berlin.de!uni-erlangen.de!gs.dfn.de!immunbio.mpg.de!immunbio.mpg.de!nntp Newsgroups: bionet.software Subject: Re: Introducing silent restriction sites Message-ID: <1996Apr2.103924.232@immunbio.mpg.de> From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Date: 2 Apr 96 10:39:23 +0100 References: <315F9C11.507F@mrc-lmb.cam.ac.uk> Distribution: world Organization: Max-Planck-Institut fuer Immunbiologie Nntp-Posting-Host: mpi2.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24 In-Reply-To: Tony's message of Mon, 01 Apr 1996 09:04:17 +0000 Lines: 21 In <315F9C11.507F@mrc-lmb.cam.ac.uk> Tony writes: > we are looking for some (preferably Mac) software to identify the > positions where 'silent' restriction sites can be introduced by > mutagenesis into DNA sequence. If you have access to GCG you may use MAP/SILENT (VMS) or map -silent (UNIX). In conjunction with additional switches like /MAXCUTS=1 and the program MAPSORT it shouldn't be to difficult to find a suitable restriticon site that can easily be detected on a gel. Regards, Christoph Gartmann +----------------------------------------------------------------------------+ | Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 | | Immunbiologie | | Postfach 1169 Internet: gartmann@immunbio.mpg.de | | D-79011 Freiburg, FRG | +----------- Do you know MENUE, the user environment for OpenVMS? -----------+ From owner-software@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!biosci!not-for-mail From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software Subject: Re: New Home Page Date: 4 Apr 1996 14:41:12 -0800 Organization: BIOSCI International Newsgroups for Biology Lines: 107 Distribution: world Message-ID: <4k1j68$7pl@net.bio.net> References: <4k1ap4$oih@murphy2.servtech.com> NNTP-Posting-Host: net.bio.net In article <4k1ap4$oih@murphy2.servtech.com>, Kim Pruitt wrote: >Hi, > >I thought some of you might be interested in our new HOME PAGE describing Sorry, but posting notices about commercial software or about home pages for commercial companies is against BIOSCI/bionet policy. Please do not do this again. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net ---------------------------------------------------------------------- WHAT ARE THE RESTRICTIONS ON COMMERCIAL ACTIVITIES IN THE BIOSCI/bionet NEWSGROUPS? The BIOSCI/bionet newsgroups system is a public service which provides research discussion forums for the community of biological scientists. Commercial advertisements are not allowed on the newsgroups because there is a high risk that the volume of resulting ads would drive away readers who use their valuable time and participate in the newsgroups solely for research purposes. While we do not distribute ads posted to our moderated newsgroups, we unfortunately have no effective way to regulate advertising on our unmoderated groups other than to publicly chastise those who try to break our rules. We will publicly denounce violations brought to our attention. The BIOSCI project is a non-profit service which must now cover its own costs of operation. Internet "spammers" who attempt to use the newsgroups for free advertising are in effect stealing from us whether or not their ads are for products of relevance to the biological sciences. It is BIOSCI's effort and cash which maintains the system (the central computer systems, archives, network connections and tech support) that spammers attempt to exploit for commercial gain without doing anything to support us in return. The appropriate means of reaching our readership is to advertise on the BIOSCI/bionet WWW pages. This is a high traffic Web site and visitors to the site have the option of viewing the advertisements instead of having them sent unsolicited to their personal mail files. For details, please contact biosci-help@net.bio.net. Commercial postings/activities on the BIOSCI/bionet newsgroups are in general prohibited except as noted below. People at for-profit organizations are free to read all postings made to the BIOSCI/bionet newsgroups, but must ensure that their postings to the newsgroups do not violate our guidelines. Commercial organizations may post job openings on EMPLOYMENT/bionet.jobs.offered free of charge. Please consult the guidelines in the newsgroup charter on the WWW at http://net.bio.net/bioarchives/EMPLOYMENT/CHARTER before posting your message. BIOSCI readers without any financial connections to a company or a product may discuss and/or post endorsements of a commercial product. However, it is standard Internet practice to include in the posting a disclaimer of any financial interest in the product/company. Note that postings to newsgroups are subject to libel laws. BIOSCI advises readers to think twice before taking potshots at products that they do not like. BIOSCI users often post general questions about problems that might be solved through the use of a commercial product. It is *extremely important*, however, that such general questions *not* be answered publicly by people affiliated with the product or company that might stand to gain a sale as a result. Private e-mail replies to the poster of the question are permissible since they do not impact our system by broadcasting to the entire newsgroup readership. For example, user X may ask, "Is there a product that will allow me to separate protein A from protein B given the following properties ...?", but, if user Y works at company Z which sells a product that can accomplish this task, user Y does *NOT* have permission to respond to the question publicly. Public responses can only be posted by other scientists who might have experience in solving the problem in question and who do not stand to gain financially by promoting the product in question, i.e., they are not employees, consultants, or connected to the company via other financial ties. As noted above, postings endorsing commercial products should contain a customary disclaimer stating the absence of financial ties of the poster to the product/company. Commercial companies *may* respond to a public BIOSCI newsgroup if a BIOSCI user asks a question directly about one of their products, e.g., mentions it by name. The response should be limited to a factual answer of the question posed and should avoid any hint of advertising hype. Comparisons with competitors' products should be avoided completely. Finally, as a general rule, if you are unsure about the appropriateness of your posting, before you post anything please send a copy of what you propose to post to the BIOSCI adminstrator at biosci-help@net.bio.net for review. BIOSCI and its readership appreciate adherence to these policies by our users in the commercial domain. Good corporate citizens who assist us in providing this free service to biologists make a positive impression on our readers. We will take action against people who attempt to exploit our resources without providing support for BIOSCI. ---------------------------------------------------------------------- From owner-software@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!qns3.qns.com!imci4!newsfeed.internetmci.com!news.sprintlink.net!new-news.sprintlink.net!news-res.gsl.net!news.sprintlink.co.za!usenet From: Karl Kansen Newsgroups: bionet.software Subject: Label Printing Softwar Date: 4 Apr 1996 12:07:04 GMT Organization: Sprint Communications South Africa Lines: 2 Message-ID: <4k0e18$deg@johan.sprintlink.co.za> NNTP-Posting-Host: 206.49.48.41 Anyone know where I can find above. Robin Computers in Sandton, Hide park Corner marketed something like that. Where can I fin them? From owner-software@net.bio.net Wed Apr 03 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!gatech!newsfeed.internetmci.com!newsfeeder.servtech.com!murphy2.servtech.com!news From: Kim Pruitt Newsgroups: bionet.software Subject: New Home Page Date: 4 Apr 1996 20:17:40 GMT Organization: Salt City Software Lines: 13 Message-ID: <4k1ap4$oih@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 our new HOME PAGE describing organizational software. A description of Genome Tracker, a plant/animal stock database can be found at URL: http://www.servtech.com/public/saltcity Coming soon: Plasmid Tracker. A bacterial stock database program which will generate a restriction map for each record. Kim D. Pruitt From owner-software@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!park.uvsc.edu!news.cc.utah.edu!howard!patrick From: Patrick Newsgroups: bionet.software Subject: No-brainer Date: Thu, 4 Apr 1996 21:17:31 -0700 Organization: University of Utah Computer Center Lines: 16 Message-ID: NNTP-Posting-Host: howard.genetics.utah.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: patrick@howard I am interested OS/2 software for DNA, RNA, and protein analysis (not necessarily the same program). Protein analysis would include the works, folding predictions, protease cleavage predictions, putative kinase site prediction, SH2 and SH3 domain prediction, etc. RNA program need only be simple folding predition program and the DNA program would be for oligo analysis, restriction mapping, open reading frame search. I just know these programs don't exist for OS/2 but I wish to ask anyway... Windows 3.1 or DOS-based programs do run under OS/2 but I'd prefer native software. Thanks, poneil@genetics.utah.edu From owner-software@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!gatech!gt-news!james From: james@amber.biology.gatech.edu (James McIninch) Newsgroups: bionet.software Subject: Re: Linux MolBio Software Date: 5 Apr 1996 18:25:28 GMT Organization: Georgia Institute of Technology Lines: 16 Distribution: bionet Message-ID: <4k3oio$o6h@mordred.gatech.edu> References: <4ikpgc$igg@usenet.ucs.indiana.edu> NNTP-Posting-Host: exon.biology.gatech.edu X-Newsreader: TIN [version 1.2 PL2] Dave Love (d.love@dl.ac.uk) wrote: : >>>> On Thu, 28 Mar 1996 22:42:59 GMT, aimania@airmail.net (Walter Rothe) said: : Walter> bernard@elsie.nci.nih.gov (Bernard Murray) wrote: : >> In article <4ivauu$oda@news-f.iadfw.net>, aimania@airmail.net says... : >>> : >>> mangalam@uci.edu (Harry Mangalam) wrote: : >>> : >>>> (altho, some would say that GNU is better than commercial quality :) : Indeed. Gcc is, anyway, a commercial product. It is not. As a matter of fact, the GNU public license under which the GCC compiler is distributed expressly prohibits the sale of GCC (I believe that the license permits distributors to charge $3.00 above the actual media cost as a copying fee). From owner-software@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!news.belnet.be!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-stuttgart.de!uni-regensburg.de!lrz-muenchen.de!informatik.tu-muenchen.de!Germany.EU.net!howland.reston.ans.net!cs.utexas.edu!newshost.convex.com!news.onramp.net!news.tcst.com!news.spectrum.titan.com!research-01.ski.mskcc.org!nntp.mskcc.org!phil From: phil@xtreme1.mskcc.org (Phil Jeffrey) Newsgroups: bionet.software Subject: Re: MOLGEN (& slurs about Artificial Intelligence) Date: 5 Apr 96 12:28:18 Organization: Memorial Sloan-Kettering Cancer Center Lines: 29 Message-ID: References: NNTP-Posting-Host: xtreme1.ski.mskcc.org In-reply-to: gerard@xray.bmc.uu.se's message of 3 Apr 1996 21:54:55 GMT In article gerard@xray.bmc.uu.se (Gerard Kleywegt) writes: >> hmm, a couple of years ago i threw away all my aritificial intelligence- >> related papers ;-) Such cynicism, Gerard ;) Actually Mitch Lewis and Geoff Chang at the University of Pennsylvania have done some interesting stuff with the Genetic Algorithm and its application to crystallographic searches (see in particular the methods used to solve the Lac repressor structure recently published in Science). My personal tinkerings with GA have indicated some impressive search speed-ups, but I remain forever nervous about algorithms driven by random number generators and I think I'd prefer just to buy a faster computer and do it the hard (systematic) way ;) I'm not sure I believe that GA can do anything that conventional methods cannot, in the Macromolecular Crystallography field. Just my 2c Phil -- ------------------------------------------------------------------------------- | Phil Jeffrey | | | Crystallography Facility Manager | If you lie to the compiler, | | Memorial Sloan-Kettering Cancer Center, NYC | it will get its revenge | | phil@xray2.mskcc.org, p-jeffrey@ski.mskcc.org | - Henry Spencer | | Voice: (212) 639 2189 Fax: (212) 717 3066 | | ------------------------------------------------------------------------------- From owner-software@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!mn6.swip.net!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!newsfeed.internetmci.com!news.internetMCI.com!darwin.sura.net!blaze.cs.jhu.edu!RacerX.mse.jhu.edu!news.jhu.edu!welchlink.welch.jhu.edu!lilu From: LI LU Newsgroups: bionet.molbio.proteins,bionet.software,bionet.molbio.proteins,bionet.cellbiol Subject: Phosphorylation sites Date: Fri, 5 Apr 1996 16:22:50 -0500 Organization: HCF - Johns Hopkins University, Baltimore, Maryland, USA Lines: 5 Message-ID: References: NNTP-Posting-Host: 128.220.59.78 Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: Xref: biosci bionet.molbio.proteins:7518 bionet.software:15178 bionet.cellbiol:4448 Hi, there. I'd like to ask where can I find a list or o program to search for phosphoylation site in a protein sequence, by different kinases. Any ftp site or web site are welcome. Thanks a lot. Please reply to my email address: lilu@welchlink.welch.jhu.edu From owner-software@net.bio.net Thu Apr 04 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!mn6.swip.net!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!newsfeed.internetmci.com!in2.uu.net!newsfeed.pitt.edu!bb3.andrew.cmu.edu!andrew.cmu.edu!bm2t+ From: Brian Timothy Mcnally Newsgroups: bionet.software Subject: homology Date: Fri, 5 Apr 1996 15:53:39 -0500 Organization: Senior, Biology, Carnegie Mellon, Pittsburgh, PA Lines: 9 Message-ID: NNTP-Posting-Host: po9.andrew.cmu.edu I am currently in search of an internet site or an application where I can import DNA sequences from multiple sources and then perform homology analysison them. The sources are various databases as well as sequences that have to be entered in by hand. If you could respond to this account, I would appreciate it greatly. Oh, a footnote not involving the GCG would be preferable. TIA Brian McNally From owner-software@net.bio.net Fri Apr 05 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!mn6.swip.net!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!newsfeed.internetmci.com!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!repressor.pharmacy.wisc.edu!ross From: "Ross J. Reedstrom" Newsgroups: bionet.software Subject: Re: Linux MolBio Software Date: Fri, 5 Apr 1996 17:34:01 -0600 Organization: University of Wisconsin, Madison Lines: 40 Message-ID: References: <4ikpgc$igg@usenet.ucs.indiana.edu> <4k3oio$o6h@mordred.gatech.edu> NNTP-Posting-Host: repressor.pharmacy.wisc.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <4k3oio$o6h@mordred.gatech.edu> On 5 Apr 1996, James McIninch wrote: > Dave Love (d.love@dl.ac.uk) wrote: > : >>>> On Thu, 28 Mar 1996 22:42:59 GMT, aimania@airmail.net (Walter Rothe) said: > > : Walter> bernard@elsie.nci.nih.gov (Bernard Murray) wrote: > : >> In article <4ivauu$oda@news-f.iadfw.net>, aimania@airmail.net says... > : >>> > : >>> mangalam@uci.edu (Harry Mangalam) wrote: > : >>> > : >>>> (altho, some would say that GNU is better than commercial quality :) > > : Indeed. Gcc is, anyway, a commercial product. > > It is not. As a matter of fact, the GNU public license under which the GCC > compiler is distributed expressly prohibits the sale of GCC (I believe that > the license permits distributors to charge $3.00 above the actual media cost > as a copying fee). > Sigh - no, that's _not_ what the GPL says. if you've ever looked at it at all you'd know that it explicitly _allows_ sale of any GPLed software for whatever you can get for it.. but you have to give your customers the source code as well! Including any improvements/changes you've made. And your customers are free to go ahead and sell copies of whatever you've sold them. The original comment about commercial product perhaps refers to Cygnus Software, who sell GCC and offer support to their customers. Essentially, they sell support. They've also contributed many improvements to GCC back to the free software community. Ross ---------------- Ross J. Reedstrom rjr@pharmacy.wisc.edu (608) 265-5591 School of Pharmacy or University of Wisconsin-Madison (608) 265-2599 425 N. Charter St. Madison, WI 53706 From owner-software@net.bio.net Fri Apr 05 23:00:00 1996 Path: biosci!data-transport.com!scott_jokerst From: scott_jokerst@data-transport.com (R. Scott Jokerst) Newsgroups: bionet.software Subject: Re: homology Date: 5 Apr 1996 19:42:44 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Brian, I'd be interested in the responses you get, in case any reply privately. Would you forward any of the good leads you get to: scott_jokerst@data-transport.com or perhaps repost to the newsgroup? Thanks Scott ************ At 12:53 PM 4/5/96, Brian Timothy Mcnally wrote: >I am currently in search of an internet site or an application where I >can import DNA sequences from multiple sources and then perform homology >analysison them. The sources are various databases as well as sequences >that have to be entered in by hand. If you could respond to this >account, I would appreciate it greatly. Oh, a footnote not involving >the GCG would be preferable. TIA > >Brian McNally R. Scott Jokerst scott_jokerst@data-transport.com Biological Data Transport http://www.data-transport.com "Life sciences informatics, product, and services resources" From owner-software@net.bio.net Sat Apr 06 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!in1.uu.net!electriciti.com!ppp16 From: johnC@electriciti.com (John Collins/UCSD) Newsgroups: bionet.software Subject: RE: CloneWorks Date: 7 Apr 1996 04:16:28 GMT Organization: ElectriCiti, Inc. Lines: 13 Message-ID: <4k7fis$che@watt.electriciti.com> NNTP-Posting-Host: ppp16.nwla.electriciti.com X-Newsreader: News Xpress Version 1.0 Beta #3 My lab and I have checked out CloneWorks. It's really great for those of you who want to keep track of your constructs. I found the primer tools to be better than anything I've seen yet. The version I downloaded from their site (www.cloneworks.com/anteater) was a beta, and they emailed me that it would be available next week. I noticed that I couldn't edit a molecules sequence easily...but I can see a tool for molecule editing that is greyed out. If they do as good a job on that one as the rest of the tools...it should be a very nice addition to all of us doing mol. bio. Just thought you should have my opinion :) John Collins, post-doc From owner-software@net.bio.net Sat Apr 06 23:00:00 1996 Path: biosci!agate!sunsite.doc.ic.ac.uk!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news01.sunet.se!sunic!mn6.swip.net!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!iol!imci2!imci3!imci4!newsfeed.internetmci.com!news.compuserve.com!news.production.compuserve.com!news From: Bob Obar <102063.2640@CompuServe.COM> Newsgroups: bionet.software Subject: Re: Introducing silent restriction sites Date: 7 Apr 1996 06:33:38 GMT Organization: Matritech, Inc. Lines: 3 Message-ID: <4k7nk2$9l2$1@mhadg.production.compuserve.com> References: <315F9C11.507F@mrc-lmb.cam.ac.uk> "DNA Inspector" (a Mac program) will do this; I don't know where you can get it from though - perhaps someone will post it. Good luck. ---Bob Obar From owner-software@net.bio.net Sat Apr 06 23:00:00 1996 Newsgroups: bionet.software Path: biosci!rutgers!gatech!newsfeed.internetmci.com!in1.uu.net!nih-csl!postman From: bernard@elsie.nci.nih.gov (Bernard Murray) Subject: Re: No-brainer Message-ID: <1996Apr7.075840.21799@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: Date: Sun, 7 Apr 1996 07:58:40 GMT Lines: 24 In article , patrick@corona.med.utah.edu says... > >I am interested OS/2 software for DNA, RNA, and protein analysis (not >necessarily the same program). [snip] >I just know these programs don't exist for OS/2 but I wish to ask anyway... >Windows 3.1 or DOS-based programs do run under OS/2 but I'd prefer native >software. >poneil@genetics.utah.edu Since gcc has been ported to OS/2 I suggest you grab a copy and then follow the "Linux molecular biology software" threads and grab the source code for anything that sounds interesting. After compilation the programs may not make full use of the GUI/WIMP environment but they should be "native". I don't think I've seen any OS/2 native binaries for molbio software on any of the usual sites so please post/e-mail if you find any. Good luck, Bernard Bernard Murray, Ph.D. bernard@elsie.nci.nih.gov (National Cancer Institute, NIH, Bethesda MD, USA) From owner-software@net.bio.net Sun Apr 07 23:00:00 1996 Path: biosci!WICCMAIL.WEIZMANN.AC.IL!cobogin From: cobogin@WICCMAIL.WEIZMANN.AC.IL ("cobogin") Newsgroups: bionet.software Subject: (none) Date: 8 Apr 1996 02:44:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604080940.CAA29013@net.bio.net> NNTP-Posting-Host: net.bio.net Hello, does anyone know where I might find PowerMac compatible software (free or shareware) which can model proteins? ie. you input the sequence and a 3D structure is rendered, or that minimizes a mutation of a known structure. Thanks in advance, Oren cobogin@weizmann.weizmann.ac.il From owner-software@net.bio.net Sun Apr 07 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!news.exodus.net!news.alt.net!newspost1.alt.net!usenet From: jmcmahon@bright.net (Joe McMahon) Newsgroups: bionet.software Subject: Re: Label Printing Softwar Date: Mon, 08 Apr 1996 13:58:54 GMT Organization: AltNet - Affordable Usenet Access - http://www.alt.net Lines: 15 Message-ID: <4kb2f4$jt8@tofu.alt.net> References: <4k0e18$deg@johan.sprintlink.co.za> X-Newsreader: Forte Agent .99c/32.126 On 4 Apr 1996 12:07:04 GMT, Karl Kansen wrote: >Anyone know where I can find above. Robin Computers in Sandton, Hide park Corner marketed something like that. >Where can I fin them? THere are a lot of good label makers around. SOme are shareware and some are not. I don't have my list handy, but if you haven't had any luck, E-Mail me (jmcmahon@bright.net), and I'll get you some names. Some of the new word processors have pretty sophisticated label capacity. I use Winword 7.0 and it supports a complete series of Avery Labels as well as other brands. Joe From owner-software@net.bio.net Sun Apr 07 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!oxpath!rpgrant From: rpgrant@molbiol.ox.ac.uk (Richard P. Grant) Newsgroups: bionet.software Subject: Re: Interesting Free Offer........ Date: 8 Apr 96 10:12:58 GMT Organization: Oxford University Molecular Biology Data Centre Lines: 60 Distribution: world Message-ID: <1996Apr8.101258@molbiol.ox.ac.uk> References: <960408034457_266463134@mail06> NNTP-Posting-Host: ania.path.ox.ac.uk Sorry to be flippant but these insults to intelligence warrant a closer look. I was frankly shocked at the categories "advanced" and "expert". If anyone would rather receive a 19-part email and piece it together rather than take the 15 seconds to learn how to access a compressed attachment, then they're welcome to it. Of course, those without Macs can still receive attachments, and what's more, if the file had been zipped then both Mac users and IBM-compatible users would be able to save 78% download time. _And_ those who have to use Unix or VMS systems to read mail. Serious note: is there software for DOS/windoze/unix/vms that will unstuff .sit files? I think we should be told, in the interests of cross-platform compatibility. In article <960408034457_266463134@mail06>, JohnChen00@aol.com writes: > 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. !!!!!! (hey, did you know you can get attachments with Eudora?) > 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 > 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. There is a wonderful piece of software called "Stuffit Expander" which does this for you, it's at info-mac in the cmp directory and it's FREE. > 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. Is there an adjective that remains for those who can _make_ a self-extracting stuffit archive _and_ mail it as an attachment? Good grief. Maybe I'm getting old. -- Richard P. Grant MA DPhil rpgrant@molbiol.ox.ac.uk Nuffield Department of Obstetrics and Gynaecology, University of Oxford. http://sable.ox.ac.uk/~lady0266 Fax +44 1 865 69141 Walk softly..... and carry an armoured tank division From owner-software@net.bio.net Sun Apr 07 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!oxpath!rpgrant From: rpgrant@molbiol.ox.ac.uk (Richard P. Grant) Newsgroups: bionet.software Subject: Re: Protein modelling software for PowerMacs (was: (none)) Date: 8 Apr 96 20:49:32 GMT Organization: Oxford University Molecular Biology Data Centre Lines: 29 Distribution: world Message-ID: <1996Apr8.204932@molbiol.ox.ac.uk> References: <199604080940.CAA29013@net.bio.net> <4kbe18$kdj@winx03.informatik.uni-wuerzburg.de> NNTP-Posting-Host: ania.path.ox.ac.uk In article <4kbe18$kdj@winx03.informatik.uni-wuerzburg.de>, krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) writes: > You might have seen on this newsgroup an announcement for the program > "FoldIt Light" which should do what you want (I have never tried it). > However, do not expect any program to get a sequence as input and > spew out a structure. The protein folding problem isn't yet solved. > > Rasmol, mentioned by somebody else, can only render existing structures, > but not calculate new ones. It is a (really nifty!) program for looking > at molecules, not constructing new ones. You are 100% correct Cornelius. I would it were that simple to determine structure! There are a number of ways of predicting secondary structure, if you have good homology with another proteins you can do this to about 80% accuracy with a program whose name escapes me, but I can look it up for you. It's better rated than the stuff within GCG, but maybe that dooes not say much... PredictProtein@embl-heidelberg.de is possibly what I'm thinkin - Sanders and Rost did the algorithms. Please correct me if I'm wrong. > /* "Science is the game we play with God to find out what His rules are." */ Well, that and for paying the bills ;-) Richard -- Richard P. Grant MA DPhil rpgrant@molbiol.ox.ac.uk Nuffield Department of Obstetrics and Gynaecology, University of Oxford. http://sable.ox.ac.uk/~lady0266 Fax +44 1 865 69141 Walk softly..... and carry an armoured tank division From owner-software@net.bio.net Sun Apr 07 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!oxpath!rpgrant From: rpgrant@molbiol.ox.ac.uk (Richard P. Grant) Newsgroups: bionet.software Subject: Re: (none) Date: 8 Apr 96 11:33:21 GMT Organization: Oxford University Molecular Biology Data Centre Lines: 18 Distribution: world Message-ID: <1996Apr8.113321@molbiol.ox.ac.uk> References: <199604080940.CAA29013@net.bio.net> NNTP-Posting-Host: ania.path.ox.ac.uk A lovely little app is RasMac - Ras Mol for the Mac. Available from Info-mac in the /sci Directory. Have fun. In article <199604080940.CAA29013@net.bio.net>, cobogin@WICCMAIL.WEIZMANN.AC.IL ("cobogin") writes: > Hello, > does anyone know where I might find PowerMac compatible software (free or > shareware) which can model proteins? ie. you input the sequence > and a 3D structure is rendered, or that minimizes a mutation of a known > structure. -- Richard P. Grant MA DPhil rpgrant@molbiol.ox.ac.uk Nuffield Department of Obstetrics and Gynaecology, University of Oxford. http://sable.ox.ac.uk/~lady0266 Fax +44 1 865 69141 Walk softly..... and carry an armoured tank division From owner-software@net.bio.net Sun Apr 07 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!mn6.swip.net!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!newsfeed.internetmci.com!in1.uu.net!fu-berlin.de!news.belwue.de!news.uni-stuttgart.de!uni-regensburg.de!lrz-muenchen.de!uni-erlangen.de!winx03!wpxx02.toxi.uni-wuerzburg.de!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: Interesting Free Offer........ Date: 8 Apr 1996 16:16:05 GMT Organization: University of Wuerzburg, Germany Lines: 13 Distribution: world Message-ID: <4kbe45$kdj@winx03.informatik.uni-wuerzburg.de> References: <960408034457_266463134@mail06> <1996Apr8.101258@molbiol.ox.ac.uk> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Richard P. Grant (rpgrant@molbiol.ox.ac.uk) wrote: > Is there an adjective that remains for those who can _make_ a self-extracting > stuffit archive _and_ mail it as an attachment? Genius? (It's not an adjective, but you could use it in the context of "computer genius", something like "wizard hacker" or whatever :-) --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Sun Apr 07 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news00.sunet.se!sunic!mn6.swip.net!plug.news.pipex.net!pipex!weld.news.pipex.net!pipex!rail.news.pipex.net!pipex!tube.news.pipex.net!pipex!dish.news.pipex.net!pipex!tank.news.pipex.net!pipex!newsfeed.internetmci.com!in1.uu.net!fu-berlin.de!news.belwue.de!news.uni-stuttgart.de!uni-regensburg.de!lrz-muenchen.de!uni-erlangen.de!winx03!wpxx02.toxi.uni-wuerzburg.de!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: Protein modelling software for PowerMacs (was: (none)) Date: 8 Apr 1996 16:14:32 GMT Organization: University of Wuerzburg, Germany Lines: 26 Distribution: world Message-ID: <4kbe18$kdj@winx03.informatik.uni-wuerzburg.de> References: <199604080940.CAA29013@net.bio.net> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] cobogin (cobogin@WICCMAIL.WEIZMANN.AC.IL) wrote: > does anyone know where I might find PowerMac compatible software (free or > shareware) which can model proteins? ie. you input the sequence > and a 3D structure is rendered, or that minimizes a mutation of a known > structure. You might have seen on this newsgroup an announcement for the program "FoldIt Light" which should do what you want (I have never tried it). However, do not expect any program to get a sequence as input and spew out a structure. The protein folding problem isn't yet solved. Rasmol, mentioned by somebody else, can only render existing structures, but not calculate new ones. It is a (really nifty!) program for looking at molecules, not constructing new ones. To search for old postings on bionet.software (e.g. for finding the "FoldIt Light" announcements), look at http://www.bio.net/ Hope that helps, --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news01.sunet.se!sunic!mn6.swip.net!plug.news.pipex.net!pipex!weld.news.pipex.net!pipex!rail.news.pipex.net!pipex!tube.news.pipex.net!pipex!lade.news.pipex.net!pipex!tank.news.pipex.net!pipex!iol!imci2!imci3!imci4!newsfeed.internetmci.com!news.compuserve.com!news.production.compuserve.com!news From: Mr Nothing <100712.2127@CompuServe.COM> Newsgroups: bionet.software Subject: new neural network WEB page Date: 9 Apr 1996 00:11:12 GMT Organization: NothingLand Lines: 7 Message-ID: <4kc9v0$3i3$2@mhadg.production.compuserve.com> There is a new WEB site with information on neural networks, as well as a multimedia product explaining how they work. There is also a free introductory chapter on neural networks to download. http://www.abas.co.uk Please pass this message on to anyone you think might be interested. From owner-software@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Matteo diTommaso Newsgroups: hinxton.announce,embnet.general,ebi.general,bionet.software,bionet.molbio.embldatabank Subject: "SynCron" - Tools for EMBL Database Update Date: 8 Apr 1996 21:39:21 -0700 Organization: European Bioinformatics Institute Lines: 72 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:15195 bionet.molbio.embldatabank:625 Subj="SynCron" tools for maintaining synchronised copies of the EMBL Nucleotide Sequence Database Looking at the statistics for access to the EMBL Nucleotide Sequence Database update files on the EBI ftp site (ftp://ftp.ebi.ac.uk/pub/databases/embl/new/) we observe that many people download the full cumulative data file (cumulative.dat) rather than the daily update files. In an attempt to make daily update files more useful and to provide a reliable mechanism for re-generating the cumulative.dat file locally from daily updates, the EBI and the Swiss EMBNet node have jointly developed a set of tools which can be used to fetch the daily updates and update the local database. The programs make use of 'transaction listings' made available on the EBI ftp site. These transaction listings are now supplied with every update file and include a record of each update, insert and delete operation to the EMBL Nucleotide Sequence Database as represented in the flat-file updates. The naming scheme for transaction listings is the same as for daily, weekly, and cumulative updates with the extension ".lis". The transaction listings are found in: ftp://ftp.ebi.ac.uk/pub/databases/embl/new/list/ and look like: Acc# ID Action DateStamp Ver# Division T58328 AA328 U 19951108232958 3 EST T58329 AA329 C 19951108233007 3 EST T58330 AA330 D 19951108233015 3 EST R67977 AA977 U 19951108230600 3 EST R67978 AA978 U 19951108230611 3 EST where U=Update C=Create D=Delete Using the tools it is possible to regenerate the cumulative.dat file (at a remote site) reliably from daily updates. Validation of the new cumulative.dat file is also possible using the transaction listing provided at the EBI. Using these programs it should be possible to keep a copy of the EMBL Nucleotide Sequence Database that exactly matches the contents of the database in operation at the EBI for external services with manual intervention required only in the event of some failure in network transfer of the file - etc. These programs are available by anonymous ftp from (the _002 version number will change as the programs are updated): UNIX Version: ftp://ftp.ebi.ac.uk/pub/software/unix/listtools/SynCron_002.tar.gz VMS Version: (backup/gzip) ftp://ftp.ebi.ac.uk/pub/software/vms/listtools/SynCron_002.bck-gz OR (tar/compress) ftp://ftp.ebi.ac.uk/pub/software/vms/listtools/SynCron_002.tar_Z Matteo diTommaso Database Programming Group EMBL Outstation The European Bioinformatics Institute E-mail: ditommaso@ebi.ac.uk Nicole Redaschi and Reinhard Doelz Biozentrum - University of Basel EMBnet Node Switzerland E-Mail: embnet@comp.bioz.unibas.ch From owner-software@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!in1.uu.net!news.euro.net!usenet From: mbleeker@euronet.nl (Marco_Bleeker) Newsgroups: bionet.software Subject: Veldbiologische Software Checklist (WWW page) Date: Tue, 09 Apr 1996 21:36:17 GMT Organization: Euronet Internet Lines: 38 Message-ID: <4kel4n$oqo@news.euro.net> NNTP-Posting-Host: p205.asd.euronet.nl X-Newsreader: Forte Free Agent 1.0.82 Software for ecology, taxonomy, and management of collections. The Fieldwork Software Checklist at Chez Marco's has been thoroughly updated. I'd say that especially the *Dutch* language version could be accused of approaching completeness... But well, please tell me otherwise, and it's certainly a good reference: http://www.euronet.nl/users/mbleeker/prog/soflis_n.html Also the English language version of the page is a good starter for someone who is looking out for software in this area - to use, or to review before you perhaps decide to program something yourself: http://www.euronet.nl/users/mbleeker/prog/soflis_e.html I welcome you all on my pages, and more, would appreciate any help, further information, criticisms, etc. While you're at it, please feel free to nose around the other Chez Marco's pages: botanical pictures, a multimedia tour through the rainforest, list of botany URLs, and much more. Thank you for your kind attention, sincerely, Marco -- ------------------ --- ------------------------------ <-------------------------------------------------------------------> Help mee bij de oprichting van een nieuwe Newsgroup: NL.TUINEN. Neem nu deel aan de discussie in NL.NEWSGROUPS, en breng tussen 14 april 5 mei je stem uit. Er zijn 50 stemmen nodig. <-----This was a call for votes for a Dutch gardening newsgroup-----> <-------------------------------------------------------------------> YES!!! It has arrived: CIVILIZATION II. The CD-ROM sequel to the best strategic computergame ever! You'll be sorry if you miss it! <-------------------------------------------------------------------> From owner-software@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!MKG.COM!MAJOHNS From: MAJOHNS@MKG.COM ("Johnson, Michael A") Newsgroups: bionet.software Subject: Peak-fitting programs Date: 9 Apr 1996 08:28:47 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Can anyone recommend a good DOS/Windows (shareware) program for plotting ASCI data and determining the area under the curve? Thanks, Michael Johnson From owner-software@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!daresbury!usenet From: Dave Love Newsgroups: bionet.software Subject: Re: Linux MolBio Software Date: 09 Apr 1996 18:24:28 +0100 Organization: Daresbury Laboratory, Warrington WA4 4AD, UK Lines: 22 Sender: fx@djlvig.dl.ac.uk Distribution: bionet Message-ID: References: <4ikpgc$igg@usenet.ucs.indiana.edu> <4k3oio$o6h@mordred.gatech.edu> NNTP-Posting-Host: djlvig.dl.ac.uk X-Plaque: Raised by Men of Liverpool for the Advancement of Learning and the Enoblement of Life In-reply-to: "Ross J. Reedstrom"'s message of Fri, 5 Apr 1996 17:34:01 -0600 X-Newsreader: Gnus v5.1 >>>>> On Fri, 5 Apr 1996 17:34:01 -0600, "Ross J. Reedstrom" said: Ross> On 5 Apr 1996, James McIninch wrote: >> : Indeed. Gcc is, anyway, a commercial product. >> >> It is not. As a matter of fact, the GNU public license under which the GCC >> compiler is distributed expressly prohibits the sale of GCC (I believe >> that the license permits distributors to charge $3.00 above the actual >> media cost as a copying fee). [Correct response elided.] The Free Software Foundation itself sells GCC. Ross> The original comment about commercial product perhaps refers to Ross> Cygnus Software, [Cygnus *Support*,] in particular, but not only them. Ross> who sell GCC and offer support to their customers. Essentially, Ross> they sell support. Yes. http://www.cygnus.com and the GCC `SERVICE' file. From owner-software@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!gatech!newsfeed.internetmci.com!info.ucla.edu!csulb.edu!drivel.ics.uci.edu!news.service.uci.edu!NewsWatcher!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: Protein modelling software for PowerMacs (was: (none)) Date: Tue, 09 Apr 1996 08:11:57 -0800 Organization: Microbiology and Molecular Genetics, UC Irvine Lines: 68 Distribution: world Message-ID: References: <199604080940.CAA29013@net.bio.net> <4kbe18$kdj@winx03.informatik.uni-wuerzburg.de> <1996Apr8.204932@molbiol.ox.ac.uk> NNTP-Posting-Host: 128.200.169.26 > In article <4kbe18$kdj@winx03.informatik.uni-wuerzburg.de>, krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) writes: > > You might have seen on this newsgroup an announcement for the program > > "FoldIt Light" which should do what you want (I have never tried it). > > However, do not expect any program to get a sequence as input and > > spew out a structure. The protein folding problem isn't yet solved. To which (Richard P. Grant) replied: > You are 100% correct Cornelius. I would it were that simple to determine > structure! There are a number of ways of predicting secondary structure, if > you have good homology with another proteins you can do this to about 80% > accuracy with a program whose name escapes me, but I can look it up for you. > It's better rated than the stuff within GCG, but maybe that dooes not say > much... > > PredictProtein@embl-heidelberg.de is possibly what I'm thinkin - Sanders and > Rost did the algorithms. Please correct me if I'm wrong. And Harry chipped in with his 2 bits... There are a number of secondary structure prediction sites available on the web (BMERC, phd, SSPROT, Deleage's SOPM email service). Try my page that describes my first go thru them: http://hornet.mmg.uci.edu/~hjm/projects/biocomp/structure.html (altho the IP# and machine name will change shortly, email if the URL doesn't work) As well, anyone interested in protein folding with a PowerMac or SGI in hand should check out Mark Surles' Sculpt from Interactive Simulations: htttp://www.intsim.com which is one of the more astonishing pieces of software that I've ever dealt with (yeah, yeah, yeah, heard that before..). Near real-time minimization of surprisingly large molecules, as well as nice interface, easy to learn and a very good educational tool (see all those bewildering formulae spring to life in fast 3D). Handles Van der Waals and electrostatics, freeze/thaw different parts, complete interactivity or set reps to a high # to relax the structure and have a few sips of coffee. I'm not sure about the final accuracy relative to approaches avaiable via BIOSYM/MSI's DIscover, but they appear to be pretty close and the validation tools available to me (ProsaII, Profiles 3D, etc) seem not to mind. Mark has just ported what was an SGI-only SW to the PMac and found (to MY surprise) that a 100MHz 601 runs about 3/4 the speed of an 150MHz R4400 on the pure computational code; I'd expect parity or better with a evenly-clocked PPC604 Much slower and grungier graphics (but then that extra $25,000 to SGI has to go for something). Nevertheless, it is WELL worth looking at. Disclaimer: I've known Mark Surles professionally for several years and have been a sporadic beta tester for both SGI and PMac versions, but have no financial interest in his company. But he's a terrific scientist, programmer and interface designer. Cheers Harry -- Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 http://hornet.mmg.uci.edu/~hjm/hjm.html Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW From owner-software@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!uwm.edu!lll-winken.llnl.gov!enews.sgi.com!sgigate.sgi.com!news1.best.com!nntp1.best.com!jquinn From: jquinn@nntp.best.com (Dr.Greg Quinn) Newsgroups: bionet.software Subject: Re: CloneWorks Date: 9 Apr 1996 17:54:28 GMT Organization: Best Internet Communications Lines: 46 Message-ID: <4ke88k$i8l@nntp1.best.com> References: <4k7fis$che@watt.electriciti.com> NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] John Collins/UCSD (johnC@electriciti.com) wrote: : My lab and I have checked out CloneWorks. It's really great for those of you : who want to keep track of your constructs. I found the primer tools to be : better than anything I've seen yet. The version I downloaded from their site : (www.cloneworks.com/anteater) was a beta, and they emailed me that it would be : available next week. I noticed that I couldn't edit a molecules sequence : easily...but I can see a tool for molecule editing that is greyed out. If : they do as good a job on that one as the rest of the tools...it should be a : very nice addition to all of us doing mol. bio. : Just thought you should have my opinion :) : : John Collins, : post-doc Well, this is a bit strange; 'johnC@electriciti.com' is a non-existant email address (a direct connection to their email server, and also bounced email indicates this). A check on 'cloneworks .com' using 'whois' shows: Anteater Software Inc. (CLONEWORKS-DOM) 12442 Stanwood Place Los Angeles, CA 90066 Domain Name: CLONEWORKS.COM Administrative Contact: Morocs, Dr. Paul (DPM6) clone@ELECTRICITI.COM 310 937 8873 Technical Contact, Zone Contact: Staff, Domain Registration (DRS16) domain@ELECTRICITI.COM (619)-338-9000 ext 19 Record last updated on 17-Jan-96. Record created on 17-Jan-96. Domain servers in listed order: POWERGRID.ELECTRICITI.COM 198.5.212.8 ARC.ELECTRICITI.COM 198.5.212.97 eg. CloneWorks is a virtual domain hosted at Electriciti.com, ie the same internet address indicated as the host address of 'John Collins'. A check through to the UCSD web server fails to show a listing for a 'John Collins') I thought that it was against Bionet regulations for companies to post directly here? From owner-software@net.bio.net Mon Apr 08 23:00:00 1996 Path: biosci!rutgers!uwm.edu!msunews!harbinger.cc.monash.edu.au!newshost.anu.edu.au!newshost.telstra.net!news.ci.com.au!metro!metro!news From: glenn holden Newsgroups: bionet.software Subject: CPrimer Date: 9 Apr 1996 00:22:28 GMT Organization: Information Services, The University of Sydney, NSW, Australia Lines: 12 Distribution: inet Message-ID: <4kcak4$nlh@metro.usyd.edu.au> 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) X-URL: news:bionet.software I am trying to find a manual for the primer designing program CPrimer. Alternatively, I am trying to get in contact with the alleged authors of CPrimer, Greg Bristol and Robert Anderson, allegedly from UCLA, but UCLA refuses to provide me with email addresses or their present whereabouts. I would appreciate it if anyone could be of any help. Brendan Scott Department of Pathology University of Sydney Sydney, Australia From owner-software@net.bio.net Tue Apr 09 23:00:00 1996 Path: biosci!PEASTMS.PKU.EDU.CN!lxzyx From: lxzyx@PEASTMS.PKU.EDU.CN Newsgroups: bionet.software Subject: About Sigmaplot Date: 9 Apr 1996 21:14:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604100305.AA20810@peastms.pku.edu.cn> NNTP-Posting-Host: net.bio.net Can anyone tell me, where can I find user guidence of Sigmaplot? Chunhui Mo From owner-software@net.bio.net Tue Apr 09 23:00:00 1996 Path: biosci!rutgers!gatech!newsjunkie.ans.net!newsfeeds.ans.net!rcogate.rco.qc.ca!altitude!usenet From: Achim Recktenwald Newsgroups: bionet.molbio.proteins,bionet.software,bionet.molbio.proteins,bionet.cellbiol Subject: Re: Phosphorylation sites Date: Wed, 10 Apr 1996 09:15:13 -0500 Organization: IBEX Technologies, Inc. Lines: 13 Message-ID: <316BC271.63AF@ibex.ca> References: NNTP-Posting-Host: ibex.hip.cam.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) Xref: biosci bionet.molbio.proteins:7545 bionet.software:15206 bionet.cellbiol:4470 LI LU wrote: > > Hi, there. > I'd like to ask where can I find a list or o program to search for > phosphoylation site in a protein sequence, by different kinases. Any ftp > site or web site are welcome. Thanks a lot. Please reply to my email > address: lilu@welchlink.welch.jhu.edu This would interest me, as well. Please, also post the reply to this newsgroup. Achim From owner-software@net.bio.net Tue Apr 09 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!univ-lyon1.fr!news From: perriere@biomserv.univ-lyon1.fr (Guy Perriere) Newsgroups: bionet.software Subject: Pairwise alignment computing and visualization Date: 10 Apr 1996 07:25:20 GMT Organization: Universite Claude Bernard - Lyon 1 Lines: 51 Distribution: world Message-ID: <4kfnp0$6gk@tempo.univ-lyon1.fr> Reply-To: perriere@biomserv.univ-lyon1.fr NNTP-Posting-Host: evol10.univ-lyon1.fr Keywords: Pairwise alignment, SIM, LFASTA, WWW It is now possible to perform pairwise local alignments on proteins and on nucleic acids on the two World Wide Web servers ExPASy and WWW-Query. Alignments are computed with the SIM (proteins) and LFASTA (nucleic acids) algorithms. To ease the interpretation of the results returned by SIM and LFASTA, the users may use the LALNVIEW program. LALNVIEW allows to represent sequences by colored rectangles that give an overall picture of the similarities between the two sequences. Blocks containing similar fragments are colored according to the degree of similarity between the two segments. Also, when aligning sequences from SWISS-PROT, EMBL, GenBank or Hovergen data banks, it is possible to include in the alignment a graphical view of the sequences features. LALNVIEW can be used as a standalone application or as a helper application when using ExPASy or WWW-Query. In this case, prospective users must configure their World Wide Web browser in a way to make it able to recognize the MIME-type associated to the data returned by LALNVIEW: chemical/ x-aln2. For instance, UNIX users have to modify the .mailcap file located in their home directory by adding the following line: chemical/x-aln2; lalnview %s Binaries of LALNVIEW for Macintosh, PC and compatibles, SUN, DEC Alpha, IBM RS/6000, SGI and HP computers are available at URL: ftp://expasy.hcuge.ch/pub/lalnview The page on the ExPASy server allowing to align protein sequences can be reached at URL: http://expasy.hcuge.ch/sprot/sim-prot.html The page on the WWW-Query server allowing to align nucleic acids sequences can be reached at URL: http://acnuc.univ-lyon1.fr/lfasta.html -- Guy Perriere Laboratoire BGBP - UMR CNRS 5558 Universite Claude Bernard - Lyon 1 F-69622 Villeurbanne Cedex From owner-software@net.bio.net Tue Apr 09 23:00:00 1996 Path: biosci!biosci!not-for-mail From: djt2@po.cwru.edu (Dennis Templeton) Newsgroups: bionet.molbio.methds-reagnts,bionet.cellbiol,bionet.immunology,bionet.software Subject: NIH grant templates for Mac Word 5 and Excel available Date: 9 Apr 1996 21:45:37 -0700 Organization: CWRU School of Medicine Lines: 46 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molbio.methds-reagnts:42853 bionet.cellbiol:4466 bionet.immunology:8489 bionet.software:15204 Mac users preparing for the upcoming NIH grant cycle will want to check out our templates for the PHS 398 application form. They are available at: http://129.22.87.13 There are pointers on our page to archives at SUMEX-AIM and IUBio. While you are there, please check out our post-doctoral position that is available in signal transduction. These forms are updates of the templates I distributed in 1991, which were modifications of some done by others. I have incorporated the changes for the revised PHS398 application, dated 5/95, for use after 1/1/96. I don't have the non-comp or the NRSA forms yet. If you make them send them along to me at djt2@po.cwru.edu and I'll post them. The templates are in Word 5 and Excel 4 format. I have not, and do not intend to update them to Word 6 or Excel 5 format. The documents are in Stationary form for your own protection. PLEASE COPY THE COMPLETE FOLDER BEFORE MODIFYING THEM. This is because the Excel files are linked (the 5 year automatically updates when the 1 year is modified) and separated files will be frustrated. Note that in most cases salaries and raw data get input in the non-printing part of the sheet, to the right. By the way, I do not have similar sheets for those attached to the Micro$oft umbilicus. These may translate well to MS Word4Win, but there are no guarantees. Almost all of the Emails for help I get are from PC users who expect me to have PC-based templates. I do not. Do not ask me where to get them. You can probably find some by querying a web indexer with "NIH grant templates PC". Don't expect the results on a PC to be as nice as the Mac templates. Best of luck with your proposals. Dennis Templeton Institute of Pathology CWRU School of Medicine djt2@po.cwru.edu From owner-software@net.bio.net Tue Apr 09 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!salliemae!europa.chnt.gtegsc.com!wlbr!news.cerf.net!nic.cerf.net!strand From: strand@nic.cerf.net (Parallel Performance Group) Newsgroups: alt.dcom.telecom,bionet.software,comp.dcom.telecom.tech Subject: Software Announcement Date: 10 Apr 1996 21:28:51 GMT Organization: CERFnet Dial n' CERF Customer Lines: 22 Message-ID: <4kh96j$6ce@news.cerf.net> NNTP-Posting-Host: nic.cerf.net Xref: biosci bionet.software:15209 comp.dcom.telecom.tech:22569 Parallel Performance Group, of Sedona, AZ, announces a Series of FREE E-Mail Newsletters on high-tech software topics. Below is a list of the topics discussed in the Newsletter Series: Business Process Reengineering Real-Time Multiprocessing/Uniprocessing DSP Multiprocessing Neural Networks/Fuzzy Logic/Fuzzy Control Parallel Processing Animation/Solid Modelling Distributed Processing Mechanical Design Automation Object-Oriented CASE Tools CAD for Industrial and Architectural Design Project Management Discrete and Continuous Simulation Image Processing Medical Imaging Graphical Application Interfaces Virtual Reality Statistical Analysis Volume Visualization To receive more information, send any e-mail to info@ppgsoft.com; this will return a detailed listing of the Newsletters, and instructions on how to re- ceive sample copies and subscriptions. Visit Our Web site at http://www.ppgsoft.com/ on high-tech software products, presented with pleasing professional graphics. From owner-software@net.bio.net Tue Apr 09 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!info.ucla.edu!library.ucla.edu!csulb.edu!drivel.ics.uci.edu!news.service.uci.edu!NewsWatcher!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: CloneWorks Date: Wed, 10 Apr 1996 10:14:36 -0800 Organization: Microbiology and Molecular Genetics, UC Irvine Lines: 25 Message-ID: References: <4k7fis$che@watt.electriciti.com> <4ke88k$i8l@nntp1.best.com> NNTP-Posting-Host: 128.200.169.26 Good work. I verify this. Looks like a spoofed advert to me. If not, could we have a reply from the mysterious John Collins, with a real email/phone number AND suitable disclaimer? I'm just about to test this program but if this is what they have to stoop to, perhaps the program will not stand on it's own. Cheers Harry Disclaimer: I do not work for Cloneworks, and if I did, I wouldn't be anymore B). > > eg. CloneWorks is a virtual domain hosted at Electriciti.com, ie the same > internet address indicated as the host address of 'John Collins'. A check > through to the UCSD web server fails to show a listing for a 'John Collins') > > I thought that it was against Bionet regulations for companies to post > directly here? -- Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 http://hornet.mmg.uci.edu/~hjm/hjm.html Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW From owner-software@net.bio.net Tue Apr 09 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!newsserver.jvnc.net!stevens-tech.edu!s97299 From: abrunner@attila.stevens-tech.edu (Andy Brunner) Newsgroups: alt.amateur-comp,alt.america.online,alt.authorware,bionet.software,comp.os.ms-windows.apps.utilities.win95,comp.os.ms-windows.win95.misc,comp.software.international,comp.software.testing,misc.forsale.computers.pc-specific.software,news.software.b,pa.lv.forsale Subject: ******DarkStar Stickits 32 Bit and 16 Bit Versions available****** Date: Wed, 10 Apr 96 18:28:11 GMT Organization: DarkStar Computers Lines: 12 Message-ID: <4kgugr$qc7@apocalypse.dmi.stevens-tech.edu> NNTP-Posting-Host: s97299.u97.stevens-tech.edu Summary: Stickits Reminder Program X-Newsreader: News Xpress 2.0 Beta #0 Keyword: Reminder Xref: biosci bionet.software:15207 comp.os.ms-windows.apps.utilities.win95:8523 comp.os.ms-windows.win95.misc:123266 comp.software.international:3682 comp.software.testing:8965 misc.forsale.computers.pc-specific.software:29167 news.software.b:7863 Are you looking for the best reminder for a competetive price? Stickits has many features, options, and the appearance of a top of the line application. Stop by and check it out... http://attila.stevens-tech.edu/~abrunner/stickits/ DarkStar Computers 209 Castle Point Hoboken NJ, 07030 From owner-software@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!news.service.uci.edu!NewsWatcher!user From: mangalam@uci.edu (Harry Mangalam) Newsgroups: bionet.software Subject: Re: CloneWorks Date: Wed, 10 Apr 1996 17:06:11 -0800 Organization: Microbiology and Molecular Genetics, UC Irvine Lines: 30 Distribution: world Message-ID: References: NNTP-Posting-Host: 128.200.169.26 Not at all - just that it seemed an unusually strong recommendation AND his email is bogus AND UCSD phonebook doesn't list him (and it's usually pretty good) AND it's odd that he used a non-'ucsd.edu' account AND he hasn't replied (to this point anyway) AND I was getting bombarded with fax and phone messages from Cloneworks trying to drum up $. I've nothing against them advert'ing on newsgroups as a matter of fact, but I really can't abide this kind of sneakiness, if that's what it is. If it turns out that it's above-board, I'll be happy to apologize. Cheers Harry In article , scott_jokerst@data-transport.com (R. Scott Jokerst) wrote: > Just my two unsolicited cents, but I do fail to see how one concludes that > an email domain with electriciti.com leads to the conclusion that John > Collins works for CloneWorks. > > electriciti.com is an internet access provider in the San Diego area. I > have seen several individuals associated with it who have nothing to do > with CloneWorks. -- Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 http://hornet.mmg.uci.edu/~hjm/hjm.html Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW From owner-software@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!data-transport.com!scott_jokerst From: scott_jokerst@data-transport.com (R. Scott Jokerst) Newsgroups: bionet.software Subject: Re: CloneWorks Date: 10 Apr 1996 17:38:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 45 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Just my two unsolicited cents, but I do fail to see how one concludes that an email domain with electriciti.com leads to the conclusion that John Collins works for CloneWorks. electriciti.com is an internet access provider in the San Diego area. I have seen several individuals associated with it who have nothing to do with CloneWorks. Scott http://www.data-transport.com ************ At 11:14 AM 4/10/96, Harry Mangalam wrote: >Good work. I verify this. Looks like a spoofed advert to me. If not, >could we have a reply from the mysterious John Collins, with a real >email/phone number AND suitable disclaimer? > >I'm just about to test this program but if this is what they have to stoop >to, perhaps the program will not stand on it's own. > >Cheers >Harry > >Disclaimer: I do not work for Cloneworks, and if I did, I wouldn't be >anymore B). > >> >> eg. CloneWorks is a virtual domain hosted at Electriciti.com, ie the same >> internet address indicated as the host address of 'John Collins'. A check >> through to the UCSD web server fails to show a listing for a 'John Collins') >> >> I thought that it was against Bionet regulations for companies to post >> directly here? >-- >Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine, > Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598 > http://hornet.mmg.uci.edu/~hjm/hjm.html > Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW R. Scott Jokerst scott_jokerst@data-transport.com Biological Data Transport http://www.data-transport.com "Life sciences informatics, product, and services resources" From owner-software@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!pasteur.fr!univ-lyon1.fr!in2p3.fr!oleane!tank.news.pipex.net!pipex!swrinde!newsfeed.internetmci.com!in2.uu.net!news.glink.net.hk!taiwan From: taiwan@glink.net.hk (·sÄ_®q¼Ö¶é ¡À=) Newsgroups: bionet.software Subject: Are there any PMC S/W out there ? Date: 11 Apr 1996 15:10:13 GMT Organization: Global Link Information Services Ltd. Lines: 11 Message-ID: <4kj7cl$jrp@unix2.glink.net.hk> NNTP-Posting-Host: earth.glink.net.hk X-Newsreader: TIN [version 1.2 PL2] Hi, I post this topic on behalf of my relative. He is a planning engineer so that he wants to know are there any PMC S/W either for dos/windows avail. -- < ·sÄ_®q¼Ö¶é > From owner-software@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: "Simon M. Brocklehurst" Newsgroups: bionet.software Subject: ANNOUNCE: NAOMI Version 2.4c Date: Thu, 11 Apr 1996 13:38:27 +0100 Organization: University of Oxford Lines: 33 Message-ID: <316CFD43.2781E494@bioch.ox.ac.uk> NNTP-Posting-Host: nmrv.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; SunOS 4.1.3_U1 sun4m) NAOMI - Version Upgrade Announcement (Please note, NAOMI is provided at zero charge for academic use) (e-mail contact smb@bioch.ox.ac.uk) _____________________________________________________________________________ NAOMI Version 2.4c is available as of now from the NAOMI Web site at: http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html or via anonymous ftp ftp://nmrz.ocms.ox.ac.uk/pub/smb/naomi i.e. at nmrz.ocms.ox.ac.uk in directory pub/smb/naomi/ Users of versions older than 2.10 will need new license keys to allow the upgrade to work (please contact the author in this case). _____________________________________________________________________________ NB NAOMI currently works only on Silicon Graphics workstations running IRIX 5.* or IRIX 6.* _____________________________________________________________________________ | | ,_ o Simon M. Brocklehurst, | / //\, Oxford Centre for Molecular Sciences, Department of Biochemistry, | \>> | University of Oxford, Oxford, UK. | \\, E-mail: smb@bioch.ox.ac.uk | WWW: http://www.ocms.ox.ac.uk/~smb/ |____________________________________________________________________________ From owner-software@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!news.msfc.nasa.gov!sgigate.sgi.com!news1.best.com!nntp1.best.com!jquinn From: jquinn@nntp.best.com (Dr.Greg Quinn) Newsgroups: bionet.software Subject: Re: CloneWorks Date: 11 Apr 1996 02:03:40 GMT Organization: Best Internet Communications Lines: 78 Distribution: world Message-ID: <4khp9s$iqs@nntp1.best.com> References: NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] R. Scott Jokerst (scott_jokerst@data-transport.com) wrote: : Just my two unsolicited cents, but I do fail to see how one concludes that : an email domain with electriciti.com leads to the conclusion that John : Collins works for CloneWorks. : electriciti.com is an internet access provider in the San Diego area. I : have seen several individuals associated with it who have nothing to do : with CloneWorks. I think the point that I was trying to make is that the email address was either removed in the two days between the post being made and my checking it, or the possibility exists that it was a non-existant address fabricated for the purposes of hyping software in a newsgroup which is meant to be for discussion about 'things biosoftware'. Look, I really didn't want to hammer this one home because any young, enterprising software outfit needs to get some support and have some room, even if they do make mistakes. But it wasn't just the last post; from a previous 'unsolicited testimonial' about CloneWorks in this newsgroup, you can find this one in the Bionet archives: > From: Paul Morcos > Newsgroups: bionet.software > Subject:Re: CloneWorks > Date: Mon, 01 Apr 1996 20:03:18 -0800 > Organization:University of California, Los Angeles > Lines: 27 > Message-ID:<3160A706.625@ucla.edu> > References: <4jpo9m$ch9@dfw-ixnews5.ix.netcom.com> > NNTP-Posting-Host: ts21-1.wla.ts.ucla.edu > Mime-Version: 1.0 > Content-Type:text/plain; charset=us-ascii > Content-Transfer-Encoding: 7bit > X-Mailer:Mozilla 2.0 (Win95; I) > > Richard Brady wrote: Thanks for the post R.B., We downloaded CloneWorks > this morning (all 1.4 megs) and thought it was awesome! I like the fact > that they don't over analyze and they spend more time on generating > primers and helping you clone. I've never seen a cloning package like > this. We called this morning and since we have PC gene it only costs > $795. It's the fastest decision my boss ever made! > Thanks, > P.M. > U.C.L.A. > p.s. I didn't remember the web site, but > i found it by searching for Cloneworks using netscape's net search. > The signature of 'PM' refers to the sender of this post, given as: "From: Paul Morcos ". A campus search at the UCLA Web site shows up two people called Morcos, though none with this email address or first name. A 'whois' Internic database search shows that the contact (ie 'owner') of the the internet domain 'Cloneworks.com' is a Dr. Paul Morcos. The poster is apparently reticent about making a direct statement regarding the internet address of Cloneworks (he doesn't even know the address of his own domain??!!). Yes, I agree that it could be pure coincidence that: 1) The posts regarding CloneWorks sound they were written by total pricks ("it was awesome!" ??!! Sounds more like a 16 year old describing a 'Thrashing Pumpkins' concert than a Postdoc describing sequence analysis software; "It's the fastest decision my boss ever made!", again sounds more like an outsiders impression of what goes in a DNA lab ). 2) Posts are being made about the product from non-existant email addresses, whose host domain coincides with that of CloneWorks. 3) posts are being made by people with exactly the same name as the person who runs the domain Cloneworks.com. Yes, coming to think of it, I am wrong. From owner-software@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!CGL.UCSF.EDU!lonetto From: lonetto@CGL.UCSF.EDU Newsgroups: bionet.software Subject: Re: CloneWorks Date: 11 Apr 1996 14:53:30 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <199604112114.OAA10162@socrates.ucsf.EDU> NNTP-Posting-Host: net.bio.net Hi, I'd also like to see this discussion stop, but I can't resist putting in my own two cents :-) It is possible that the original poster of the message in question made up the name and is really from cloneworks. Deplorable behavior if true. I noticed, however, that in the original message he referred to himself as a post doc. If THIS is true, then the fact that he doesn't seem to exist in his university phonebook is not surprising. Try finding any of the post docs you know at UCSF, Davis or Stanford through their University phone books and you'll see what I mean. Post docs are treated as non-existant by many universities: They are not registered (like students), they aren't on payroll (like staff and faculty), thus they don't exist. The non-existent email address is another problem, but since the message was posted from another system (apparently a public access ISP) it COULD be a typo. And if this person really is a post doc, then they probably have better things to do than getting entangled in this thread, I know I do :-) Mike -=-=-=-=-=-=- Mike Lonetto lonetto@cgl.ucsf.edu UCSF Dept of Stomatology, 513 Parnassus Avenue, San Francisco, CA 94143-0512 =-=-=-=-=-=-=- From owner-software@net.bio.net Wed Apr 10 23:00:00 1996 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!munnari.OZ.AU!news.unimelb.EDU.AU!news.rmit.EDU.AU!harbinger.cc.monash.edu.au!news.mira.net.au!vic.news.telstra.net!act.news.telstra.net!imci3!imci4!imci5!pull-feed.internetmci.com!news.internetMCI.com!newsfeed.internetmci.com!in1.uu.net!fu-berlin.de!news.dfn.de!news.embl-heidelberg.de!usenet From: "Luca Ida Giovanni TOLDO (Ph.D.)" Newsgroups: bionet.software Subject: [APPLET] Window Composition, JaMBW Date: 11 Apr 1996 19:19:15 GMT Organization: EMBL Heidelberg Lines: 55 Distribution: world Message-ID: <4kjlvj$c67@lion.embl-heidelberg.de> NNTP-Posting-Host: mac-ara4.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) To: toldo@EMBL-Heidelberg.DE X-URL: news:bionet.software Dear Collegues, another applet had been developed and added in the Java based Molecular Biologists Workbench (JaMBW) set. http://www.embl-heidelberg.de/~toldo/JaMBW.html This one really starts using the Java graphical capabilities and not only the mere character i/o. It is called WindowComposition and can be used for any kind of sequences in order to know the running percentage composition in the defined set of symbols. http://www.embl-heidelberg.de/~toldo/WindowComposition html The output is obviously graphical ... Variables: sequence (dna or protein does not matter) window size symbols to use Examples of its use are for answering questions as: which are the regions reacher in xxxx ? e.g. "hydrophilic regions of protein sequence" "hydrophobic regions of protein sequence" "acidic regions of prein sequence" "AT reach regions of nucleic acids ..." and so on Feedback (mailto:Luca.Toldo@EMBL-Heidelberg.DE) is welcome and extremely appreciated ! (e.g. which mol-bio applet would you appreciate next?) More applets are appearing on the JaMBW set written by also other contributors: The JavaScript Oligo Calculator of Eugen BUEHLER The Java applet Helical Wheel by Marcel TURCOTTE and more are coming ... Dr. Luca Ida Giovanni TOLDO (Ph.D.) European Molecular Biology Laboratory Computer Group User Consultant, WebMaster, GCGManager Heidelberg Germany From owner-software@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!hamblin.math.byu.edu!acs2.byu.edu!news.cuny.edu!caen!uwm.edu!cs.utexas.edu!howland.reston.ans.net!surfnet.nl!ruu.nl!news From: I.nijman@vetmic.dgk.ruu.nl (I.Nijman) Newsgroups: bionet.software Subject: LOOKING FOR PRIMERDESIGN SOFTWARE Date: 12 Apr 1996 12:33:53 GMT Organization: RUU Lines: 18 Message-ID: <4klijh$i1a@newshost.cc.ruu.nl> Reply-To: I.Nijman@vetmic.dgk.ruu.nl NNTP-Posting-Host: bac023.vetmic.dgk.ruu.nl X-Newsreader: WinVN 0.92.6+ Does anybody know a software package which can develop multiplex primersets? Please send me an Email with info! Thanks, Ies Nijman I.J. Nijman Institute of Infectious Diseases and Immunology Department of Bacteriology, Faculty of Veterinary Medicine Yalelaan 1 3585 CL Utrecht The Netherlands Private: Phone: (31) (0) 30 2 53 39 43 (31)(0)35 6 24 79 32 Fax : (31) (0) 30 2 54 07 84 Prins Bernhardstraat 35 Email: I.Nijman@vetmic.dgk.ruu.nl 1211 GJ Hilversum The Netherlands From owner-software@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!biosci!not-for-mail From: BIOSCI Administrator Newsgroups: bionet.software Subject: IMPORTANT - Sun Microsystems and Academic Press sponsor BIOSCI!! Date: 11 Apr 1996 18:00:39 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: biohelp@net.bio.net Distribution: world Message-ID: <4kk9vn$fua@net.bio.net> NNTP-Posting-Host: net.bio.net I am extremely pleased to announce two new major BIOSCI sponsors: Sun Microsystems, Inc., a leading provider of solutions for open network computing environments. Academic Press, a leading scientific publisher for more than 50 years. Sun is a main home page sponsor on http://www.bio.net/ and will be providing BIOSCI with a new computing system to replace our aging machine. Once it is up and running, users of our archive site should experience much better archive search performance. Academic Press is helping BIOSCI by sponsoring our BIO-JOURNALS and METHODS-AND-REAGENTS newsgroups. If you contact representatives of either of these companies, please thank them for supporting BIOSCI. Both of these companies are major sponsors and are a big step forward for us in reaching our funding goal. We are still a long way, however, from reaching our goal of building a $100,000 operating reserve, having raised about half of that to date, so we can not stop fundraising yet. We currently have enough money to ensure continued operation of the project at a minimal level after our DOE grant runs out in a few months, i.e., we can keep the existing system running with little or no enhancements and limited user support. We would not relish having to cut back on personal service and are continuing to seek advertisers. We appreciate readers who refer sponsors to us at biosci-help@net.bio.net. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-software@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!ns1.faseb.org!lamarck.sura.net!newsfeed.internetmci.com!swrinde!cs.utexas.edu!howland.reston.ans.net!surfnet.nl!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-stuttgart.de!uni-regensburg.de!uni-erlangen.de!winx03!wpxx02.toxi.uni-wuerzburg.de!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: CloneWorks Date: 12 Apr 1996 13:31:43 GMT Organization: University of Wuerzburg, Germany Lines: 29 Distribution: world Message-ID: <4kllvv$n5c@winx03.informatik.uni-wuerzburg.de> References: <199604112114.OAA10162@socrates.ucsf.EDU> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] lonetto@CGL.UCSF.EDU wrote: > The non-existent email address is another problem, but since the message > was posted from another system (apparently a public access ISP) it > COULD be a typo. I would think that it is fairly unlikely misconfigure a newsreader by mistake if you are on an ISP (correct me when I'm wrong). I have no idea how difficult or easy it is to configure News Xpress Version 1.0 Beta #3. A search at altavista failed to show up other postings made by johnc@electriciti.com. It also failed to turn up postings by a John Collins originating from electriciti.com or ucsd.edu. iaf.net also failed to find a Jo* Collins at ucsd.edu or electriciti.com. Neither would whowhere or Four11 find John Collins at electriciti.com or ucsd.edu. It would be fairly easy to track down the poster (knowing that the posting originated from ppp16.nwla.electriciti.com and the date of the post most probably was 7 Apr 1996 04:16:28 GMT), but I think unless Dave K. wants to go after this, it does not make much sense. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news01.sunet.se!sunic!news99.sunet.se!news.uni-c.dk!iesd.auc.dk!news From: su1kj@but.auc.dk (Karsten Jensen) Newsgroups: bionet.software Subject: Re: gnuplot Date: Fri, 12 Apr 1996 13:47:08 GMT Organization: Aalborg University Lines: 57 Message-ID: <4klmt0$gc@news.iesd.auc.dk> References: NNTP-Posting-Host: pc23-404.but.auc.dk X-Newsreader: Forte Free Agent 1.0.82 Version: 3.5 This information is from the ReadMe file I got with my version of gnuplot: In general, GNUPLOT 3.5 is available as the file gnuplot3.5.tar.Z. There will patches to bring 3.4 to 3.5 as well called gp34to35.shar.Z. (Version 3.3 was skipped because of possible confusion with the numerous BETA releases.) It will be made available to simtel20 and its mirrors in ZIP format, along with a DOS, MS-Windows 3.1 and OS/2 2.0 executables. Also, some sites will have gpdoc_ps.zip which contains PostScript versions of the manuals and tutorials. Please obtain gnuplot from the site nearest you. USENET users: GNUPLOT 3.5 will posted to comp.sources.misc. NORTH AMERICA: Anonymous ftp to ftp.dartmouth.edu (129.170.16.4) Fetch pub/gnuplot/gnuplot3.5.tar.Z in binary mode. Users without ftp capability can obtain it through a mail ftp server. Send a mail message saying 'help' to BITFTP@pucc.princeton.edu for instructions. For a uuencoded copy of the gnuplot sources (compressed tar file), send this message to BITFTP@pucc.princeton.edu: FTP DARTMOUTH.EDU UUENCODE USER ANONYMOUS CD pub/gnuplot BINARY GET gnuplot3.5.tar.Z QUIT AUSTRALIA: Anonymous ftp to monu1.cc.monash.edu.au (130.194.1.101). Fetch pub/gnuplot3.5.tar.Z in binary mode. EUROPE: Anonymous ftp to irisa.irisa.fr (131.254.2.3). Fetch pub/gnuplot3.5.tar.Z in binary mode. From owner-software@net.bio.net Thu Apr 11 23:00:00 1996 Path: biosci!rutgers!csn!news-1.csn.net!imci3!imci2!news.internetMCI.com!newsfeed.internetmci.com!tank.news.pipex.net!pipex!oleane!in2p3.fr!univ-lyon1.fr!jussieu.fr!uvsq.fr!Newsmaster From: risler@genetique.uvsq.fr (J-L. Risler) Newsgroups: bionet.software Subject: Mol. Weight and pI's Date: 12 Apr 1996 10:57:16 GMT Organization: C.N.R.S./U.V.S.Q Lines: 23 Message-ID: <4klcuc$9sl@soleil.uvsq.fr> NNTP-Posting-Host: jlr.genetique.uvsq.fr Mime-Version: 1.0 X-Newsreader: WinVN 0.93.14 Dear all, I would like to search a protein databank (SwissProt or PIR) with queries such as: - find all the proteins whose Mol. Weights lie between 123 and 135 kDA - find all the proteins whose (calculated) pI's lie between 5.7 and 6.1 I'm pretty sure that such a service does exist on the net ... but where? Thank you for your help, Jean-Loup -- ------------------------------- Jean-Loup RISLER risler@genetique.uvsq.fr Universite de Versailles 45 Avenue des Etats-Unis 78035 Versailles Cedex France ------------------------------- From owner-software@net.bio.net Fri Apr 12 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!cdc2.cdc.net!news.texas.net!news1.best.com!nntp1.best.com!biosoft From: sales@PremierBiosoft.com (Kay Brown) Newsgroups: bionet.software Subject: Re: LOOKING FOR PRIMERDESIGN SOFTWARE Date: Fri, 12 Apr 96 21:34:09 GMT Organization: Premier Biosoft International Lines: 48 Message-ID: <4kmslq$n3s@nntp1.best.com> References: <4klijh$i1a@newshost.cc.ruu.nl> NNTP-Posting-Host: biosoft.vip.best.com X-Newsreader: News Xpress Version 1.0 Beta #4 In article <4klijh$i1a@newshost.cc.ruu.nl>, I.nijman@vetmic.dgk.ruu.nl (I.Nijman) wrote: >Does anybody know a software package which can develop multiplex primersets? >Please send me an Email with info! > >Thanks, > >Ies Nijman > >I.J. Nijman >Institute of Infectious Diseases and Immunology >Department of Bacteriology, Faculty of Veterinary Medicine >Yalelaan 1 >3585 CL Utrecht >The Netherlands > Private: >Phone: (31) (0) 30 2 53 39 43 (31)(0)35 6 24 79 32 >Fax : (31) (0) 30 2 54 07 84 Prins Bernhardstraat 35 >Email: I.Nijman@vetmic.dgk.ruu.nl 1211 GJ Hilversum > The Netherlands Primer Premier 4 from Premier Biosoft International supports multiplex/nested primers. The program helps you find a set of highly specific, high yield primers free of secondary structures automatically. Cross homologies among primers result in poor yield. The program locates a set of multiplex primers, free of cross homologies. The program is available for Windows 3.1, 95, NT and Power Macintosh. FREE demo version can be downloaded from: http://www.PremierBiosoftl.com Sincerely, Kay Brown V.P. Sales and Marketing ==================================================================== Premier Biosoft International 3786 Corina Way Palo Alto, CA 94303-4504 Phone: 415.856.2703 Fax: 415.843.1250 http://www.PremierBiosoft.com ===================================================================== From owner-software@net.bio.net Fri Apr 12 23:00:00 1996 Path: biosci!rutgers!gatech!swrinde!tank.news.pipex.net!pipex!oleane!in2p3.fr!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news.uni-stuttgart.de!news.urz.uni-heidelberg.de!usenet From: Christoph.Lorra@urz.uni-heidelberg.de Newsgroups: bionet.molbio.proteins,bionet.software,bionet.molbio.proteins,bionet.cellbiol Subject: Re: Phosphorylation sites Date: 13 Apr 1996 00:37:35 GMT Organization: University of Heidelberg, Germany Lines: 25 Message-ID: <4kmt0f$fmn@sun0.urz.uni-heidelberg.de> References: <316BC271.63AF@ibex.ca> Reply-To: Christoph.Lorra@urz.uni-heidelberg.de NNTP-Posting-Host: modem.urz.uni-heidelberg.de X-Newsreader: IBM NewsReader/2 v1.09 Xref: biosci bionet.molbio.proteins:7561 bionet.software:15223 bionet.cellbiol:4485 In <316BC271.63AF@ibex.ca>, Achim Recktenwald writes: >LI LU wrote: >> >> Hi, there. >> I'd like to ask where can I find a list or o program to search for >> phosphoylation site in a protein sequence, by different kinases. Any ftp >> site or web site are welcome. Thanks a lot. Please reply to my email >> address: lilu@welchlink.welch.jhu.edu > > >This would interest me, as well. Please, also post the reply to this >newsgroup. > >Achim I donïknow if this will help you but i have a paper describing phosphorylation sites, which is an article in: Methods in Enzymology, Vol. 200, 1991, 62 - 81. The title is " Protein kinase phosphorylation site sequences and consensus specifity motifs: Tabulations" by R.P. Pearson and B.E Kemp. A source for a program would be at least PCGENE from Intelligenetics which is able to find at least PKA and PKC-sides I hope this will help you Christoph From owner-software@net.bio.net Fri Apr 12 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!tank.news.pipex.net!pipex!howland.reston.ans.net!ix.netcom.com!news From: rbrady@ix.netcom.com(Richard Brady) Newsgroups: bionet.software Subject: CloneWorks apology Date: 13 Apr 1996 07:30:48 GMT Organization: Netcom Lines: 21 Message-ID: <4knl78$itb@dfw-ixnews2.ix.netcom.com> NNTP-Posting-Host: lbx-ca16-10.ix.netcom.com X-NETCOM-Date: Sat Apr 13 2:30:48 AM CDT 1996 I noticed today a series of messages regarding a disguise posting to bionet.software. We have looked into the matter and do apologize for a fictitious posting from one of our own, an individual acting on his own initiative. This was not company policy and we have addressed the matter promptly so that it does not happen again. The Company has presented a beta version of CloneWorks to faculty at UC Irvine and was referred to Harry Mangalem for a possible site license. I have personally sent one fax and left one phone message in reference to any feedback regarding the beta. Anteater Software stands firmly behind our product with utmost integrity. We apologize for any inconvenience or hard feelings and affirm that your forum will not be used in such a manner again. It is Company policy to communicate with prospective users only via our legitimate e-mail account and Web site. best regards, Richard L. Brady Anteater Software From owner-software@net.bio.net Fri Apr 12 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!oslonett.no!sn.no!newsfeed.tip.net!peroni.ita.tip.net!mikasa.iol.it!news From: edoardo.shockwav@iol.it (Edoardo Razzetti) Newsgroups: bionet.software Subject: Statistical software Date: Thu, 11 Apr 1996 18:01:48 GMT Organization: Italia Online Lines: 6 Message-ID: <316ceb5c.3057642@news.iol.it> NNTP-Posting-Host: sw24-165.iol.it X-Newsreader: Forte Agent .99d/32.182 I am looking for shareware software for statistical analisys of data is there anything that is useful for multivariate analisys? Thank you Edoardo From owner-software@net.bio.net Fri Apr 12 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!tech.cftnet.com!ns2.mainstreet.net!bug.rahul.net!rahul.net!a2i!kaiwan.kaiwan.com!not-for-mail From: bayers@kaiwan009.kaiwan.com (Jim) Newsgroups: bionet.software Subject: Keyout Beta Second Build Date: 13 Apr 1996 14:55:30 -0700 Organization: KAIWAN Internet (310-527-4279,818-756-0180,909-785-9712,714-638-4133,805-294-9338) Lines: 95 Message-ID: <4kp7si$rfh@kaiwan009.kaiwan.com> NNTP-Posting-Host: kaiwan009.kaiwan.com X-Newsreader: TIN [version 1.2 PL2] Just finish the second build of the Keyout beta. Thanks to your bug reports and comments, it's a much more stable and usable product. * Rewrote the best-question and proctor algorithms to make them faster and better. * Simplified and rewrote the help files. (Hey! How can you use it if you can understand the instructions?) * Improved the sample database. * Made inumerable fixes to several cosmetic and not so cosmetic bugs. ===================================================== As alwayes, I'm looking for some brave souls willing to beta test some automated dichotomous key software I've written. It's called Keyout and it is in the beta stage of development. Features: * Designers can include graphics and text to explain what they mean. * Since all the data is stored in a database, the size of the key is limited only by the space on your harddrive. * Has algorithm to determine the best question to ask. * Has algorithm to rapidly eliminate choices. * Easily edited, updated, and modified. * Takes full advantage of the Windows GUI environment. * Code is available. * You get me for tech support: bayers@kaiwan.com * Comes with a sample database key to adult insect orders. Downside: * It's big, 3 meg zipped. Hey! Blame Microsoft. Part of that is the insect orders database. * Since the key is on a database, I relied on SQL statements to manipulate the data. It's a little slow. * The graphics were a bit of a trade off. I wanted graphics big enough to be usable, but small so that the database wouldn't be so big. * I built the graphics editor myself, it's no Correl Draw; however, you can use the Windows clipboard to import graphics from other programs. The deal: You test the software and report back to me any changes you'd like to see or bugs you found. I make changes and release new beta versions. When the product is refined enough, I release the final version. Requirements: You'll need a PC capable of running Windows 3.1. It was tested on a 486DX/66 with 16 meg of RAM, a P100 with 16 meg of RAM and a 486SX/33 with 8 meg of RAM. The first two were running Win95, the last one had Windows 3.1. It ran best on the Pentium. :) Installation: 1. FTP it from ftp.kaiwan.com It's in the /user/bayers directory. Download it to your PC's root directory, i.e. C:\ 2. Unzip it with the -d switch to make a temporty directory. For example: pkunzip -d ko_02b.zip 3. If you are updating keyout, deltree the old keyout directory. Otherwise Windows won't let you install it. 4. Start Windows. DON'T START ANY OTHER PROGRAMS! Click on the FILE menu item. Then click on the RUN menu item. Browse for \kotemp\setup.exe. Run it. Follow the prompts. NOTE! If you're using 3.1 you'll have to exit then restart Windows to enable the share driver. If you don't, you'll get an error. 4. Start Keyout and read HELP by pressing the F1 key. - Jim -- - Jim From owner-software@net.bio.net Sat Apr 13 23:00:00 1996 Newsgroups: bionet.software Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!pasteur.fr!univ-lyon1.fr!in2p3.fr!oleane!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!swrinde!newsfeed.internetmci.com!newsxfer2.itd.umich.edu!newsxfer.itd.umich.edu!news.join.ad.jp!news.imnet.ad.jp!ripspost.aist.go.jp!news.tisn.ad.jp!news.nips.ac.jp!nips087003!kai From: kai@nips.ac.jp (Nobuyuki Kai) Subject: PEST-find Sender: news@nips.ac.jp Message-ID: Date: Sun, 14 Apr 1996 14:22:49 GMT Content-Type: text/plain; charset=iso-2022-jp Nntp-Posting-Host: cccs Mime-Version: 1.0 Organization: National Insitute for Physiological Siences X-Newsreader: NewsWatcher-J 2.0J16 Lines: 8 I'm looking for info on Macintosh software doing automatic serches for PEST regions. Can anyone help me? Thanks a lot. Nobuyuki Kai e-mail: kai@nips.ac.jp From owner-software@net.bio.net Sat Apr 13 23:00:00 1996 Path: biosci!agate!hpg30a.csc.cuhk.hk!news.cuhk.edu.hk!hkusuc.hku.hk!pc From: h8914664@hkusub.hku.hk (Wong Yim Wah) Newsgroups: bionet.software Subject: multivariate analysis tool? Date: Sat, 13 Apr 96 16:21:45 GMT Organization: The University of Hong Kong Lines: 8 Message-ID: <4kokap$bc4_001@news.hku.hk> NNTP-Posting-Host: 147.8.189.115 X-Newsreader: News Xpress Version 1.0 Beta #4 hi,I've of there is a software call" Discri... " something that can work with TWINSPAN to perform an indirect gradient analysis using the environmental variable. Can someone show me the full name of this software and where I can get the catalogue or ordering information. Thanks. (If posible, please reply through e-mail) From owner-software@net.bio.net Sat Apr 13 23:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!pasteur.fr!univ-lyon1.fr!in2p3.fr!oleane!plug.news.pipex.net!pipex!tank.news.pipex.net!pipex!newsfeed.internetmci.com!in2.uu.net!demos!news1.best.com!nntp1.best.com!jquinn From: jquinn@nntp.best.com (Dr.Greg Quinn) Newsgroups: bionet.software Subject: Re: CloneWorks apology Date: 14 Apr 1996 07:37:54 GMT Organization: Best Internet Communications Lines: 40 Message-ID: <4kqa0i$qvq@nntp1.best.com> References: <4knl78$itb@dfw-ixnews2.ix.netcom.com> NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] Richard Brady (rbrady@ix.netcom.com) wrote: : I noticed today a series of messages regarding a disguise posting to : bionet.software. We have looked into the matter and do apologize for a : fictitious posting from one of our own, an individual acting on his own : initiative. This was not company policy and we have addressed the : matter promptly so that it does not happen again. Richard, This individual who was 'acting on his own' apparently has access to your Netcom Email account, since this 'hype thread' appears to have been started by a letter from you!!? (see below from the bionet news archives). Also, I would comment that this was not just one posting but several, including posts in bionet.software and bionet.microbiology (in the guise of a reply to a genuine post). > From rbrady@ix.netcom.com(Richard Brady) > Organization Netcom > Date 1 Apr 1996 23:19:18 GMT > Newsgroups bionet.software > Message-ID <4jpo9m$ch9@dfw-ixnews5.ix.netcom.com> > > Netters, > Would appreciate any information on commercial or freeware software > that can be used for cloning and primer design-analysis. Am trying to > find something that works well, is intuitive and under a thousand > bucks. CloneWorks by Anteater Software looks good > (http://www.cloneworks.com/anteater). Would like to download eval > and/or demos for similar packages. Suggestions, URLs, would be > appreciated. > > R.B. From owner-software@net.bio.net Sat Apr 13 23:00:00 1996 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!swrinde!newsfeed.internetmci.com!news.vivanet.com!usenet From: vonbuskr@vivanet.com (R. VonBuskirk) Newsgroups: bionet.softwa