From owner-software@net.bio.net Tue Apr 01 23:00:00 1997 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software Subject: T cell epitope prediction ? Date: 2 Apr 1997 07:58:34 GMT Organization: Belgian EMBnet Node Lines: 5 Message-ID: <5ht3ja$odd@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] Does someone know of a software to predict T cell epitopes or maybe a public Server where a protein can be submitted to such a program ? Dr. Guy Bottu From owner-software@net.bio.net Tue Apr 01 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!www.nntp.primenet.com!nntp.primenet.com!news.maxwell.syr.edu!ais.net!ameritech.net!uunet!in1.uu.net!208.200.248.2!news.olypen.com!not-for-mail From: "dtw" Newsgroups: bionet.software Subject: E-MAIL BLASTER WANTED Date: 2 Apr 1997 08:51:38 GMT Organization: OLYPEN.COM Lines: 19 Message-ID: <01bc3f43$107086e0$39f8c8d0@dtw.olypen.com> NNTP-Posting-Host: annex-s1-47.olypen.com Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_01BC3F00.024D46E0" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Internet News 4.70.1161 This is a multi-part message in MIME format. ------=_NextPart_000_01BC3F00.024D46E0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit FULL VERSION dtw@olypen.com ------=_NextPart_000_01BC3F00.024D46E0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

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------=_NextPart_000_01BC3F00.024D46E0-- From owner-software@net.bio.net Tue Apr 01 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news-xfer.netaxs.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsserver.jvnc.net!princeton!cnn.Princeton.EDU!usenet From: "Nike" Newsgroups: bionet.software Subject: Amplify? Date: 1 Apr 1997 05:41:51 GMT Organization: Princeton University Lines: 7 Message-ID: <01bc3e5f$60ca09c0$0387b48c@swoosh.student.Princeton.EDU> NNTP-Posting-Host: nike.student.princeton.edu X-Newsreader: Microsoft Internet News 4.70.1161 Can anyone direct me where to find the program "Amplify"? Thanks, Thom Knowles Princeton University nike@cs.princeton.edu From owner-software@net.bio.net Tue Apr 01 23:00:00 1997 Path: biosci!agate!howland.erols.net!worldnet.att.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.nacamar.de!news-kar1.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!swidir.switch.ch!news.belwue.de!news.uni-freiburg.de!sun2.ruf.uni-freiburg.de!menendez From: menendez@sun2.ruf.uni-freiburg.de (Castor Menendez) Newsgroups: bionet.software Subject: Looking for software Date: 2 Apr 1997 09:41:57 GMT Organization: Rechenzentrum der Universitaet Freiburg, Germany Lines: 11 Message-ID: <5ht9l5$acg@n.ruf.uni-freiburg.de> NNTP-Posting-Host: sun2.ruf.uni-freiburg.de X-Newsreader: TIN [version 1.2 PL2] Dear Netters, I would like to improve my typewritting. Does anyone knows of a PC-IBM compatible software to train these skills. A freeware or shareware would be welcomed. Thanks, CM -- Castor Menendez From owner-software@net.bio.net Tue Apr 01 23:00:00 1997 Path: biosci!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!cc122 From: C Coward Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Manipulating ABI Chromatogram files Date: 2 Apr 1997 14:04:09 GMT Organization: University of Cambridge, England Lines: 25 Message-ID: <5htp0p$9f6@lyra.csx.cam.ac.uk> Reply-To: C Coward NNTP-Posting-Host: mole.bio.cam.ac.uk X-Newsreader: NN version 6.5.0 #3 (NOV) Originator: cc122@mole.bio.cam.ac.uk Xref: biosci bionet.molbio.methds-reagnts:56286 bionet.software:18259 Greetings to the world..... I have numerous chromatogram sequence files generated from an ABI automatic sequencing machine. I want to be able to make figures using parts of the chromatograms to point out features alongside the chromatogram traces. Does anyone know a way of doing this? I have access to the ABI Macintosh programs on the machine used for sequencing and the Sequencher v3.0 sequence analysis program from GeneCodes. Cheers in advance. Chris ------------------------------------------------------------------------------ Chris Coward | Tel: +44 1223 333545 University of Cambridge | Fax: +44 1223 333346 Department of Pathology | E-mail: cc122@mole.bio.cam.ac.uk Tennis Court Road, Cambridge. | (MIME compliant) CB2 1QP | ------------------------------------------------------------------------------ PGP 2.6ui Key Fingerprint F0 C2 D7 8F 23 DB 03 7E EF 5D A3 15 BF 46 10 0A ------------------------------------------------------------------------------ From owner-software@net.bio.net Tue Apr 01 23:00:00 1997 Path: biosci!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!cc122 From: C Coward Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Re: Manipulating ABI Chromatogram files Date: 2 Apr 1997 16:14:24 GMT Organization: University of Cambridge, England Lines: 21 Message-ID: <5hu0l0$dse@lyra.csx.cam.ac.uk> References: <5htp0p$9f6@lyra.csx.cam.ac.uk> Reply-To: C Coward NNTP-Posting-Host: mole.bio.cam.ac.uk X-Newsreader: NN version 6.5.0 #3 (NOV) Originator: cc122@mole.bio.cam.ac.uk Xref: biosci bionet.molbio.methds-reagnts:56298 bionet.software:18261 "Dr. Duncan Clark" writes: >Try Chromas on a PC >http://trishul.sci.gu.edu.au/~conor/chromas.html >I use it to capture any part of the chromatogram using LviewPro to then >manipulate the graphic size and format etc Cheers - unfortunately I don't have access to a PC....... ------------------------------------------------------------------------------ Chris Coward | Tel: +44 1223 333545 University of Cambridge | Fax: +44 1223 333346 Department of Pathology | E-mail: cc122@mole.bio.cam.ac.uk Tennis Court Road, Cambridge. | (MIME compliant) CB2 1QP | ------------------------------------------------------------------------------ PGP 2.6ui Key Fingerprint F0 C2 D7 8F 23 DB 03 7E EF 5D A3 15 BF 46 10 0A ------------------------------------------------------------------------------ From owner-software@net.bio.net Tue Apr 01 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!ais.net!cdc2.cdc.net!newsfeed.concentric.net!news-master!news From: Ketchup@cris.com (ketchup) Newsgroups: bionet.software Subject: Re: protein sequence analysis Date: Wed, 02 Apr 1997 19:12:02 GMT Organization: Concentric Internet Services Lines: 33 Message-ID: <5huatr$lq1@chronicle.concentric.net> References: NNTP-Posting-Host: cnc50179.concentric.net X-Newsreader: Forte Free Agent 1.0.82 If you can run a PC/Windows program, GeneDoc may be of some help. While it will not automatically align sequences for you, it will shade sequences with secondary structure information and allow you to manually align the shaded sequences. Perhaps the initial alignment can be made with the 'usual' program and then tuned for structure considerations with GeneDoc. Also, Structural Alignments done by the Argos Goup with the 3d_ali effort can be downloaded viewed from the GeneDoc home page. Hope this helps. http://www.cris.com/~ketchup/genedoc.shtml Karl Nicholas. tnorris@molbio.uoregon.edu (Tracy B Norris) wrote: >I am looking for a software program that will allow me to do specialized >alignments of protein sequence. I would like to align structural elements >of one sequence with another protein sequence. I have tried alignments in >MegAlign, but as a consequence of alignment the program puts gaps in the >structural elements of the first sequence (it's shorter than the other). >Any ideas? >Thanks, >Tracy From owner-software@net.bio.net Tue Apr 01 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeeds.sol.net!worldnet.att.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!dispatch.news.demon.net!demon!genesys.demon.co.uk!genesys.demon.co.uk!duncan From: "Dr. Duncan Clark" Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Re: Manipulating ABI Chromatogram files Date: Wed, 2 Apr 1997 16:34:27 +0100 Organization: GeneSys Ltd Distribution: world Message-ID: References: <5htp0p$9f6@lyra.csx.cam.ac.uk> NNTP-Posting-Host: genesys.demon.co.uk X-NNTP-Posting-Host: genesys.demon.co.uk MIME-Version: 1.0 X-Newsreader: Turnpike Version 3.03 Lines: 29 Xref: biosci bionet.molbio.methds-reagnts:56293 bionet.software:18260 In article <5htp0p$9f6@lyra.csx.cam.ac.uk>, C Coward writes >Greetings to the world..... > >I have numerous chromatogram sequence files generated from an ABI >automatic sequencing machine. I want to be able to make figures using >parts of the chromatograms to point out features alongside the >chromatogram traces. Does anyone know a way of doing this? I have access >to the ABI Macintosh programs on the machine used for sequencing and the >Sequencher v3.0 sequence analysis program from GeneCodes. > Try Chromas on a PC http://trishul.sci.gu.edu.au/~conor/chromas.html I use it to capture any part of the chromatogram using LviewPro to then manipulate the graphic size and format etc Duncan -- The problem with being on the cutting edge is that you occasionally get sliced from time to time.... Duncan Clark DNAmp Ltd. TEl/FAX 01252376288 http://www.dnamp.com http://www.genesys.demon.co.uk From owner-software@net.bio.net Tue Apr 01 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!EU.net!Norway.EU.net!nntp.uio.no!news.uoregon.edu!neonlights.uoregon.edu!fp1-chemistry-4.uoregon.edu!user From: tnorris@molbio.uoregon.edu (Tracy B Norris) Newsgroups: bionet.software Subject: protein sequence analysis Date: 2 Apr 1997 04:42:35 GMT Organization: University of Oregon Lines: 11 Message-ID: NNTP-Posting-Host: fp1-chemistry-4.uoregon.edu I am looking for a software program that will allow me to do specialized alignments of protein sequence. I would like to align structural elements of one sequence with another protein sequence. I have tried alignments in MegAlign, but as a consequence of alignment the program puts gaps in the structural elements of the first sequence (it's shorter than the other). Any ideas? Thanks, Tracy From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!news.idt.net!enews.sgi.com!news.corp.sgi.com!news.sgi.com!news1.best.com!nntp1.ba.best.com!nntp2.ba.best.com!shellx!jquinn From: jquinn@best.com (Greg) Newsgroups: bionet.software Subject: Re: C++ on unix Date: 3 Apr 1997 20:30:43 GMT Lines: 21 Message-ID: <5i141j$23j$1@nntp2.ba.best.com> References: <3343918E.167E@techno.sanbi.ac.za> NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] You'll need to include code, Joe, for anyone to be able to help. Joe Oppon (joe@techno.sanbi.ac.za) wrote: : Hi everyone, : I have a problem with compiling my C++ program on SGI that : I am using. A test program which runs oerfectly well on : an IDE enviroment comes up with a lot of "mistakes" on the unix : system running on SGI. : Is there something that I am not doing right ? : Desperado !! From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!cyclic.gsl.net!news.gsl.net!news.maxwell.syr.edu!worldnet.att.net!newsadm From: "Douglas Ward" Newsgroups: bionet.software Subject: Re: Clone Manager? Date: 3 Apr 1997 21:00:50 GMT Organization: Sci-Ed Software Lines: 31 Message-ID: <01bc4070$4512dc30$01010101@douglas> References: <5hrep0$pjl$1@hermes-x.louisville.edu> NNTP-Posting-Host: 207.146.33.175 X-Newsreader: Microsoft Internet News 4.70.1155 caw@SPAM@bcc.louisville.edu wrote in article <5hrep0$pjl$1@hermes-x.louisville.edu>... > Does anybody know if there is a version of Clone Manager beyond version 4.0? > and if so where I can get it? I can't find Scientific and Educational Software(the > company) to save my life. > Scientific and Educational Software moved to Durham, NC last year. Registered users of our software were notified. We are sorry that your notice must have been lost in the mail. You can contact us at: Mail: PO Box 72045, Durham, NC 27722-2045, USA Phone: (919)-471-6064 FAX: (919)-471-0311 URL: www.scied.com Email sciedsoft@msn.com The current version of Clone Manager is 4.1 and provides full compatibility and molecule sharing with our Primer Designer V3 software. It is also compatible with our Align Plus V3 program which will be released next week. Sincerely Douglas Ward, Ph.D. Scientific and Educational Software From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!news-out.communique.net!communique!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!newsfeeds.sol.net!uwm.edu!newsspool.doit.wisc.edu!news.doit.wisc.edu!thaliana From: trichmon@students.wisc.edu (Todd Richmond) Newsgroups: bionet.software Subject: Re: Amplify? Date: Thu, 03 Apr 97 16:11:02 GMT Organization: UW-Madison Dept of Botany Lines: 14 Message-ID: <5i0ktd$4h6e@news.doit.wisc.edu> References: <01bc3e5f$60ca09c0$0387b48c@swoosh.student.Princeton.EDU> NNTP-Posting-Host: thaliana.botany.wisc.edu X-Newsreader: News Xpress 2.0 In article <01bc3e5f$60ca09c0$0387b48c@swoosh.student.Princeton.EDU>, "Nike" wrote: >Can anyone direct me where to find the program "Amplify"? Try the Amplify page at: http://www.wisc.edu/genetics/CATG/amplify/index.html Todd ********************************************************* Todd Richmond UW-Madison Dept of Botany B129 Birge Hall trichmon@students.wisc.edu 430 Lincoln Drive Phone: 608-262-4008 Madison, WI 53706 Fax: 608-262-7509 From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!EU.net!Norway.EU.net!sn.no!nntp.uio.no!newsfeed.nacamar.de!wuff.mayn.de!wuff.franken.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software Subject: Re: ReadSeq Bug Date: Thu, 3 Apr 1997 17:33:49 +0200 Organization: University of Wuerzburg, Germany Lines: 120 Message-ID: References: <860029387.2018@dejanews.com> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Michael Yasayko (yasayko@darwin.com) wrote: > I've discovered a potentially fatal bug in the Feb 1 1993 release of > "ReadSeq". ReadSeq, authored by Don Gilbert of Indiana University, > conveniently converts between most of the major sequence file types that > people have developed over the years. ReadSeq is available at: > > ftp://ftp.bio.indiana.edu/molbio/readseq/ I found a file in my distribution of readseq which contains this patch and a couple of others. I have no idea who did these patches apart from where noted. The patches have the following effects on my Linux machine: a) Better recognition of PIR files as obtained from the server at the NCBI. b) Correct calculation of 32-bit checksum (this seems a really serious bug to me; maybe on other platforms compilers behave differently?). c) No warnings during compilation. d) No more problems with sequence lines which don't end with line feeds (first published by jip@helix.nih.gov (John Powell)). To apply the patches (which are in a so-called "unified diff" format), do the following (on Unix machines): 1) Extract the following file (between the ---snip--- signs) into a separate text file. Let's call it patch-PL3 (that's what it is called on my harddisk :-). Put this file in the same directory where your readseq sources are located. 2) Change to the directory where your readseq sources are located and do a patch < patch-PL3 This will modify your source files and generate a couple of files called blabla.c.orig. These contain your original source code. 3) Compile readseq as usual. ---snip--- --- readseq.c.orig Thu Jan 5 00:28:51 1995 +++ readseq.c Thu Jan 5 00:29:02 1995 @@ -180,7 +180,7 @@ static char inputfilestore[256], *inputfile = inputfilestore; -const char *formats[kMaxFormat+1] = { +char *formats[kMaxFormat+1] = { " 1. IG/Stanford", " 2. GenBank/GB", " 3. NBRF", --- ureadseq.c.orig Thu Dec 22 19:28:59 1994 +++ ureadseq.c Sat Jan 7 14:00:54 1995 @@ -297,7 +297,12 @@ { /*PIR -- many seqs/file */ while (!V->allDone) { + /* Skip header */ + /* ENTRY or SEQUENCE has to be the first word in a line while (! (feof(V->f) || strstr(V->s,"ENTRY") || strstr(V->s,"SEQUENCE")) ) + */ + /* ENTRY or SEQUENCE has to be the only word in a line */ + while (! (feof(V->f) || !strcmp(V->s,"ENTRY") || !strcmp(V->s,"SEQUENCE")) ) getline(V); strcpy(V->seqid, (V->s)+16); while (! (feof(V->f) || strstr(V->s,"SEQUENCE") == V->s)) @@ -1477,7 +1482,9 @@ register unsigned long c = 0xffffffffL; register long n = seqlen; - while (n--) c = crctab[((int)c ^ (to_upper(*seq++))) & 0xff] ^ (c >> 8); + while (n--) { + c = crctab[((int)c ^ (to_upper(*seq))) & 0xff] ^ (c >> 8); *seq++; + } c= c ^ 0xffffffffL; *checktotal += c; return c; @@ -1634,7 +1641,8 @@ fprintf(outf,"ENTRY %s \n", idword); fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); /* fprintf(outf,"ACCESSION %s\n", accnum); */ - fprintf(outf,"SEQUENCE \n"); + /* fprintf(outf,"SEQUENCE \n"); */ + fprintf(outf,"SEQUENCE\n"); numwidth = 7; width= 30; spacer = kSpaceAll; --- ureadseq.c.orig Fri Nov 24 18:01:24 1995 +++ ureadseq.c Fri Nov 24 18:01:09 1995 @@ -133,6 +133,11 @@ else { cp = strchr(s, '\n'); if (cp != NULL) *cp = 0; + /* + * Following line fixes BUG when last line in the input does not have + * an EOL character + */ + if (feof(f)) clearerr(f); } } --- readseq.c.orig Fri Nov 24 17:46:34 1995 +++ readseq.c Fri Nov 24 17:47:09 1995 @@ -19,7 +19,7 @@ */ const char *title - = "readSeq (1Feb93), multi-format molbio sequence reader.\n"; + = "readSeq (1Feb93) PL3 (24Nov95), multi-format molbio sequence reader.\n"; /* History 27 Feb 90. 1st release to public. ---snip--- If you don't have "patch", unified diffs are fairly easy to comprehend. Look at the first character in a line. If you find a minus sign, it means that this line has to be "subtracted" from your original source code. If you find a plus sign, you have to "add" the line to your source code. --Cornelius. -- /* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */ /* D-97078 Wuerzburg, Germany email: phak004@rzbox.uni-wuerzburg.de SP3 */ /* "Science is the game we play with God to find out what His rules are." */ From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeeds.sol.net!newspump.sol.net!howland.erols.net!rill.news.pipex.net!pipex!tank.news.pipex.net!pipex!iafrica.com!not-for-mail From: Joe Oppon Newsgroups: bionet.software Subject: Compiler for C++ Date: Thu, 03 Apr 1997 13:37:11 +0200 Organization: sanbi Lines: 16 Message-ID: <33439667.2781@techno.sanbi.ac.za> NNTP-Posting-Host: techno.sanbi.ac.za Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) Hi everyone, I have a problem with compiling my C++ program on SGI that I am using. A test program which runs oerfectly well on an IDE enviroment comes up with a lot of "mistakes" on the unix system running on SGI. Is there something that I am not doing right ? Desperado !! From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!newsfeeds.sol.net!news.maxwell.syr.edu!news.bc.net!info.ucla.edu!psgrain!iafrica.com!not-for-mail From: Joe Oppon Newsgroups: bionet.software Subject: C++ on unix Date: Thu, 03 Apr 1997 13:16:30 +0200 Organization: sanbi Lines: 18 Message-ID: <3343918E.167E@techno.sanbi.ac.za> NNTP-Posting-Host: techno.sanbi.ac.za Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) Hi everyone, I have a problem with compiling my C++ program on SGI that I am using. A test program which runs oerfectly well on an IDE enviroment comes up with a lot of "mistakes" on the unix system running on SGI. Is there something that I am not doing right ? Desperado !! From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!mindspring!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!cs.utexas.edu!news.eng.convex.com!news.ecn.uoknor.edu!munnari.OZ.AU!harbinger.cc.monash.edu.au!news.uwa.edu.au!not-for-mail From: Steve Woods Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Re: Manipulating ABI Chromatogram files Date: Thu, 03 Apr 1997 11:26:04 +0800 Organization: Biochem UWA Lines: 14 Message-ID: <3343234C.49CE@cyllene.uwa.edu.au> References: <5htp0p$9f6@lyra.csx.cam.ac.uk> <5hu0l0$dse@lyra.csx.cam.ac.uk> Reply-To: swoods@cyllene.uwa.edu.au NNTP-Posting-Host: pc2.biochem.uwa.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) To: C Coward Xref: biosci bionet.molbio.methds-reagnts:56314 bionet.software:18265 There is a similar program for the Mac. Try looking for SeqED (I forget where from - email me if you need me to find it). It does multiple alignments and can display all or part of the original chromatograms. Hope this helps. -- ,-_|\ Steve Woods email: swoods@cyllene.uwa.edu.au / \ PhD Student phone: 380 1394 fax: 380 1148 *_,-._/ Department of Biochemistry, UWA v http://www.general.uwa.edu.au/u/swoods/ From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!agate!howland.erols.net!cam-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!ais.net!ameritech.net!uunet!in3.uu.net!204.238.120.21!jump.net!grunt.dejanews.com!not-for-mail Date: Wed, 02 Apr 1997 19:21:43 -0600 From: yasayko@darwin.com (Michael Yasayko) Subject: ReadSeq Bug Newsgroups: bionet.software Message-ID: <860029387.2018@dejanews.com> Reply-To: yasayko@darwin.com Organization: Darwin Molecular Corporation To: yasayko@darwin.com X-Article-Creation-Date: Thu Apr 03 01:03:07 1997 GMT X-Originating-IP-Addr: 199.238.223.1 (gateway.darwin.com) X-Http-User-Agent: Mozilla/3.01Gold (X11; I; SunOS 5.4 sun4m) X-Authenticated-Sender: yasayko@darwin.com (Michael Yasayko) Lines: 55 I've discovered a potentially fatal bug in the Feb 1 1993 release of "ReadSeq". ReadSeq, authored by Don Gilbert of Indiana University, conveniently converts between most of the major sequence file types that people have developed over the years. ReadSeq is available at: ftp://ftp.bio.indiana.edu/molbio/readseq/ On modern machines, the bug typically shows up only in large sequence files. Nonetheless, the bug can theoretically affect files of any length. The most common manifestation of the bug on our Solaris 2.4 machines is a "segmentation fault". The bug is in "ureadseq.c" line 1480. The following changes will fix it; the diff command line was: diff "original" "fixed" In other words, the code lines following the "<"s needs to be replaced with the code lines following the ">"s: ] diff ureadseq.c ../../readseqd/ureadseq.c 1480c1480,1483 < while (n--) c = crctab[((int)c ^ (to_upper(*seq++))) & 0xff] ^ (c >> 8); --- > while (n--) { > c = crctab[((int)c ^ (to_upper(*seq))) & 0xff] ^ (c >> 8); > seq++; > } Technical notes on why this is a bug: "to_upper" is a preprocessor macro, not a function. The macro makes use of the argument parameter twice within the macro body: #define to_upper(c) ((char)(is_lower(c) ? (c)-' ' : (c))) Hence, placing a variable along with the increment operator (*seq++) into the macro arg list yields code which increments "seq" twice per iteration of the "while" loop, not just once as intended. Hence, the code skips over every second character in the sequence, eventually running past the end of the allocated memory for "char *seq". My guess is that the bug is also making the "checksum" results invalid, although I could be mistaken as I don't know how this particular "checksum" really works. --Mike __________________________________________________________________________ Mike Yasayko, Scientific Programmer, Darwin Molecular Corporation E-mail: yasayko@darwin.com -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Pat Thoyts Newsgroups: bionet.software Subject: Re: Compiler for C++ Date: Thu, 03 Apr 1997 21:20:51 +0100 Organization: IACR-Long Ashton Research Station Lines: 17 Message-ID: <33441123.798AA28D@bsa.bristol.ac.uk> References: <33439667.2781@techno.sanbi.ac.za> NNTP-Posting-Host: pc0652.lars.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; Linux 2.0.29 i486) Joe Oppon wrote: > > Hi everyone, > > I have a problem with compiling my C++ program on SGI that > I am using. A test program which runs oerfectly well on > an IDE enviroment comes up with a lot of "mistakes" on the unix > system running on SGI. > Is there something that I am not doing right ? > > Desperado !! Without knowing what messages were produced I couldn't even guess! -- Pat Thoyts mailto:thoyts@bsa.bristol.ac.uk http://pc0652.lars.bbsrc.ac.uk/~pat/home.shtml From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Pat Thoyts Newsgroups: bionet.software Subject: Re: ReadSeq Bug Date: Thu, 03 Apr 1997 21:19:32 +0100 Organization: IACR-Long Ashton Research Station Lines: 14 Message-ID: <334410D4.8EE13C@bsa.bristol.ac.uk> References: <860029387.2018@dejanews.com> NNTP-Posting-Host: pc0652.lars.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; Linux 2.0.29 i486) To: yasayko@darwin.com I think readseq got itself wrapped up in the seqio library. The new version comes under the name fmtseq but does the same job. The version that I have is seqio-1.2.2 and mentions in the README This software uses the SEQIO package for reading and writing sequences. Copyright (c) 1996 by James Knight at Univ. of California, Davis. So it's a bit more recent than readseq. I don't know if the bug you mention is in there though. -- Pat Thoyts mailto:thoyts@bsa.bristol.ac.uk http://pc0652.lars.bbsrc.ac.uk/~pat/home.shtml From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!MAIL.UTEXAS.EDU!kbrowning From: kbrowning@MAIL.UTEXAS.EDU (Karen Browning) Newsgroups: bionet.software Subject: Windows DNA/Protein analysis programs Date: 3 Apr 1997 11:28:24 -0800 Organization: University of Texas at Austin Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <334407FF.3D1E@mail.utexas.edu> NNTP-Posting-Host: net.bio.net Here we go again. GeneRunner is apparently out of business. Does anyone know of a user friendly, inexpensive DNA/protein analysis program for Windows that does what GeneRunner did. I would also like to be able to do contigs for DNA sequencing, etc. Can anyone explain to me why this is so difficult? From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Newsgroups: bionet.molbio.methds-reagnts,bionet.software Path: biosci!daresbury!uninett.no!hermod.uio.no!nntp.uio.no!newsfeeds.sol.net!news-xfer.netaxs.com!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!hermes.sovam.com!sovam!demos!news.stealth.net!news.ibm.net.il!news.ibm.net!news.biu.ac.il!news.huji.ac.il!wisipc.weizmann.ac.il!gustavo-pm8200.weizmann.ac.il!bmgustav From: Gustavo Glusman Subject: Re: Manipulating ABI Chromatogram files Content-Type: text/plain; charset=ISO-8859-1 Message-ID: <1997Apr3.190748.18166@wisipc.weizmann.ac.il> X-Xxmessage-Id: X-Xxdate: Thu, 3 Apr 1997 18:10:23 GMT Sender: news@wisipc.weizmann.ac.il (News User) Content-Transfer-Encoding: 8bit Organization: Weizmann Institute of Science X-Newsreader: Nuntius 2.0.4_PPC References: <5htp0p$9f6@lyra.csx.cam.ac.uk> Mime-Version: 1.0 Date: Thu, 3 Apr 1997 19:07:48 GMT Lines: 28 Xref: biosci bionet.molbio.methds-reagnts:56343 bionet.software:18272 In article <5htp0p$9f6@lyra.csx.cam.ac.uk> C Coward, cc122@mole.bio.cam.ac.uk.trim.the.last.five.items writes: >I have numerous chromatogram sequence files generated from an ABI >automatic sequencing machine. I want to be able to make figures using >parts of the chromatograms to point out features alongside the >chromatogram traces. Does anyone know a way of doing this? I have access >to the ABI Macintosh programs on the machine used for sequencing and the >Sequencher v3.0 sequence analysis program from GeneCodes. The simplest way: - Display the chromatogram using Sequencher - Capture the screen (command-shift-3, or use some utility like Flash-It for capturing only part of the screen) - If you captured the whole screen, double-click on the resulting picture file on your hard-drive, it will open with SimpleText. Select what you need from it, and copy. - Paste into Canvas or some other graphical program. - Add other stuff to point out features, etc. Is this what you needed? ____________________________________________________________ Gustavo Glusman Founder/administrator of BioMOO Gustavo@bioinfo.weizmann.ac.il (public PGP key available) http://bioinfo.weizmann.ac.il/Gustavo Visit BioMOO, the biologists' virtual meeting place, at ___________ http://bioinfo.weizmann.ac.il/BioMOO ___________ From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news.icm.edu.pl!newsfeed.nacamar.de!azure.xara.net!xara.net!rill.news.pipex.net!pipex!uunet!in1.uu.net!199.232.56.18!news.ultranet.com!not-for-mail From: "carlg" Newsgroups: bionet.software Subject: peak detection macro for Excel Date: 3 Apr 1997 21:03:54 GMT Organization: Avitar Technologies Lines: 18 Message-ID: <01bc4072$372a4de0$100406d1@pete> NNTP-Posting-Host: d16.dial-1.met.ma.ultra.net X-Newsreader: Microsoft Internet News 4.70.1161 Hi, I need a peak detection macro for Excel. It should work on a column of numbers to identify peaks and provide a peak height or area. Does anyone know of one. Thanks for your help -- Dr. Carl M. Good III, Ph.D. Vice President Research and Development Avitar Inc. 65 Dan Road Canton, MA 02021, USA Phone (617) 821-2440, FAX (617) 821-4458 Email = carlg@ultranet.com Web Page = http://www.ultranet.com/~carlg From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!cyclic.gsl.net!news.gsl.net!newsfeed.nacamar.de!worldnet.att.net!newsadm From: "Douglas Ward" Newsgroups: bionet.software Subject: Re: Clone Manager? Date: 3 Apr 1997 21:00:52 GMT Organization: Sci-Ed Software Lines: 32 Message-ID: <01bc4071$c88df580$01010101@douglas> References: <5hrep0$pjl$1@hermes-x.louisville.edu> NNTP-Posting-Host: 207.146.33.175 X-Newsreader: Microsoft Internet News 4.70.1155 caw@SPAM@bcc.louisville.edu wrote in article <5hrep0$pjl$1@hermes-x.louisville.edu>... > Does anybody know if there is a version of Clone Manager beyond version 4.0? > and if so where I can get it? I can't find Scientific and Educational Software(the > company) to save my life. Scientific and Educational Software moved to Durham, NC last year. Registered users of our software were notified. We are sorry that your notice must have been lost in the mail. You can contact us at: Mail: PO Box 72045, Durham NC 27722-2045, USA Phone: (919) 471-6064 FAX: (919) 471-0311 Email: sciedsoft@msn.com URL: www.scied.com The current version of Clone Manager for Windows is 4.1 and enables full compatibility and molecule sharing with our Primer Designer V3 software. It is also compatible with our Align Plus V3 program to be released next week. Sincerely Douglas Ward, Ph.D. Scientific and Educational Software From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!agate!howland.erols.net!news.nacamar.de!newsfeed.nacamar.de!news-kar1.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!feed1.belnet.be!news.belnet.be!news.vub.ac.be!usenet From: Erik Jongert Newsgroups: alt.mac.games.binaries,alt.hackintosh,bionet.software Subject: Please Post MacPlasmap v2.1 Date: Thu, 03 Apr 1997 15:33:35 +0100 Organization: VUB Lines: 7 Message-ID: <3343BFBF.61F1@is1.vub.ac.be> NNTP-Posting-Host: imolpc35.vub.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) Hi, I'm looking for a NON DEMO version of MacPlasmap v2.1 or higher. Please Post it Erik From owner-software@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!MAIL.TSINGHUA.EDU.CN!congjy From: congjy@MAIL.TSINGHUA.EDU.CN (Jinyang Cong) Newsgroups: bionet.software Subject: software for predicting antigenesity Date: 3 Apr 1997 14:49:01 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <9704032246.AB13112@mail> NNTP-Posting-Host: net.bio.net Hi, I would appreciate very much if someone can tell me where I can get a software to analyze a amino acid sequence of any protein to predict its antigenic epitopes. I am working at using synthetic peptides as antigens to make monoclonal antibodies. This kind of software is very useful for me. Any information would be welcome. Cong, JY From owner-software@net.bio.net Thu Apr 03 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news.icm.edu.pl!newsfeed.nacamar.de!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!ais.net!ix.netcom.com!tday From: tday@netcom.com (Tony Day) Newsgroups: bionet.software Subject: Expert in Bioinformatics? - Earn Extra Cash!! Date: Thu, 03 Apr 1997 18:25:30 -0700 Organization: Netcom Lines: 14 Message-ID: NNTP-Posting-Host: tday.slip.netcom.com Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-NETCOM-Date: Thu Apr 03 8:25:35 PM CST 1997 X-Newsreader: Yet Another NewsWatcher 2.3.1 Sorry if this is a repost, I have been having server trouble. We are a biotech company in the San Francisco Bay area looking for someone to spend a few days helping us to do some sequence searches, and alignments using GCG and using internet resources. If you have EXPERT knowledge of GCG and internet databases and would like to earn some extra money for a few days work, please email me at: TDAY@GENENCOR.COM or call me at 415-846-5822. Tony Day From owner-software@net.bio.net Thu Apr 03 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!worldnet.att.net!news.maxwell.syr.edu!news.apfel.de!news-fra1.dfn.de!news-ge.switch.ch!feed1.belnet.be!news.belnet.be!news.vub.ac.be!usenet From: plebrun@fysp1.vub.ac.be (Philippe Lebrun) Newsgroups: bionet.software Subject: statistics and pharmacology Date: 4 Apr 1997 11:21:46 GMT Organization: Brussels Free Universities VUB/ULB Lines: 8 Message-ID: <5i2o8a$jj8@rc1.vub.ac.be> NNTP-Posting-Host: fysp1.vub.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 0.9.8 Does anyone know of software that will calculate regerssion parameters and ED50 value of dose-response curves? Currently I'm doing it by hand (by hand in Excel, that is) but I'm not sure at all of my results. Thanks, Philippe From owner-software@net.bio.net Thu Apr 03 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!uwm.edu!news-peer.gsl.net!news-peer.sprintlink.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!azure.xara.net!xara.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!newsfeed.ed.ac.uk!Aberdeen!mac3.marlab.ac.uk!user From: cunninghamc@marlab.ac.uk Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Re: Manipulating ABI Chromatogram files Date: Thu, 03 Apr 1997 10:00:40 +0100 Organization: University of Aberdeen, Scotland Lines: 26 Message-ID: References: <5htp0p$9f6@lyra.csx.cam.ac.uk> NNTP-Posting-Host: mac3.marlab.ac.uk Xref: biosci bionet.molbio.methds-reagnts:56365 bionet.software:18283 In article <5htp0p$9f6@lyra.csx.cam.ac.uk>, C Coward wrote: > Greetings to the world..... > > I have numerous chromatogram sequence files generated from an ABI > automatic sequencing machine. I want to be able to make figures using > parts of the chromatograms to point out features alongside the > chromatogram traces. Does anyone know a way of doing this? I have access > to the ABI Macintosh programs on the machine used for sequencing and the > Sequencher v3.0 sequence analysis program from GeneCodes. > > Cheers in advance. > > Chris > Chris, I haven't used Sequencher yet, so I'm not sure if it's capable of this sort of thing. Previously, I've had to resort to filling the screen with the required segment of chromatogram (in the relevant ABI application), then taking a 'snapshot' of the screen (command - shift - 3) to creat a PICT file on the hard disk which can then be imported and labelled etc. in a graphics package. It's a bit basic but did the job. I'll be interested in any more sophisticated ways of doing this. Good luck Carey From owner-software@net.bio.net Thu Apr 03 23:00:00 1997 Path: biosci!HERCULES.SDSC.EDU!bourne From: bourne@HERCULES.SDSC.EDU (Philip Bourne) Newsgroups: bionet.software Subject: Proceedings of Crystallographic Computing 7 Date: 4 Apr 1997 13:23:34 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 149 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: Philip Bourne NNTP-Posting-Host: net.bio.net The electronic version of the Proceedings of Crystallographic Computing 7 are now available at http://www.sdsc.edu/Xtal/IUCr/CC/School96/ or via anonymous ftp from ftp.sdsc.edu in the directory pub/sdsc/societies/IUCr/School96/ This meeting was sponsored by the Computing Commission of the International Union of Crystallography (IUCr) and covered all aspects of macromolecular crystallographic computing. A list of the papers is appended. Philip E. Bourne Chairman, IUCr Computing Commission. ---------------------------------------------------------------------------- Editorial Phil Bourne and Keith Watenpaugh Acknowledgments Introduction Jim Stewart and Phil Bourne Contents Macromolecular Crystallographic Data Quality and Quantity The Protein Data Bank: Current Status and Future Challenges Joel Sussman, Enrique Abola, Nancy Manning and Jaime Prilusky Methods to Assess and Classify Protein Structure Coordinates Janet Thornton, A. Michie, E. Hutchinson, R. Laskowski, and C. Orengo Procedures for Assessing the Quality of X-ray Structures of Macromolecules Shoshana Wodak, Joan Pontius, Alexei Vaguine, and Jean Richelle Databases Development of Crystallization Strategies using the Biological Macromolecule Crystallization Database Gary Gilliland, Michael Tung and Jane Ladner The Network Interface to the Nucleic Acid Database Helen Berman, Lester Clowney, Anke Gelbin, Christine Zardecki and John Westbrook Structure Comparison Structural Neighbors and Structural Alignments: The Science behind Entrez/3D Steve Bryant and Christopher Hogue Real-Time Substructure Searching using the Conformational Likeness Method Misha Ponomarenko, Ilya Shindyalov and Phil Bourne Methodology Data Processing Data Processing in Macromolecular Crystallography Andrew Howard Advances in Accuracy and Automation of Data Collection and Processing Wladek Minor and Zbyszek Otwinowski Data Acquisition and Analysis at the Structural Biology Center Mary Westbrook and Jim Pflugrath Phasing Plenary Lecture The Phase Problem: a Problem in Constrained Global Optimization Herb Hauptman Maximum-Likelihood Refinement of Incomplete Models with BUSTER and TNT John Irwin and Gerard Bricogne Optimization of Electron Density Cross-Correlation with Its Square: Relationships for Phase Extension and Refinement Douglas Collins, John Konnert and James Stewart Integration of Direct Method with Macromolecular Crystallographic Techniques Carmelo Giacovazzo, D. Siliqi and J. Gonzalez-Platas SnB: Applying Shake-and-Bake to Proteins A Rotation Function that uses Phases Richard Leggott and Peter Main Refinement High-resolution Structure Refinement George Sheldrick Full Matrix Least Squares Lynn Ten Eyck Electron Density Representation and Real Space Refinement E. Blanc, G. Zhou, Z. Chen, Q. Zie, J. Tang, J. Wang and Michael Chapman The Joint Refinement of Inhibitors of Thermolysin Dale Tronrud Model Building LORE: A Tool for Manipulating Known Structural Information in Protein Modeling and Crystallography Barry Finzel A Semi-automated Map Fitting Procedure Thomas Oldfield Visualization Considerations in the Design of Graphical User Interfaces for Macromolecular Crystallography Robert Sweet and John Skinner Surface Lexicography Anthony Nicholls An AVS/Express Interface to CCP4 David Wild and S. Choe Student Presentation: Sysabs - A program for the Visualization of Crystal Data Symmetry in Reciprocal Space. Craig Taverner Software Updates XtalView Duncan McRee and Mark Israel The PROTEIN System: Real Space Techniques using Patterson and Fourier Maps Wolfgang Steigemann A Collaborative Computational Project, Number 4 CCP-4: Providing Programs for Protein Crystallography Eleanor Dodson SHELX for Macromolecules George Sheldrick MAIN Dusan Turk SHARP Eric de La Fortelle, John Irwin, and Gerard Bricogne New Approaches Crystallographic Topology and its Applications Carroll Johnson and Michael Burnett The Macromolecular CIF Dictionary Paula Fitzgerald, Helen Berman, Phil Bourne, Brian McMahon, Keith Watenpaugh and John Westbrook mmCIF Software Tools Shu-Hsin Hsieh, Steven Schirripa and John Westbrook Supporting Technologies Internet for Crystallographers - Beginners and Advanced Howard Flack Object Oriented Programming in Crystallography David Moss and William Pitt Modification of Crystallographic Codes for Parallel Architectures M.Ramanadham ---------------------------------------------------------------------------- From owner-software@net.bio.net Thu Apr 03 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!news-peer.gsl.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!ais.net!ameritech.net!uunet!in1.uu.net!152.163.170.17!newstf01.news.aol.com!audrey01.news.aol.com!not-for-mail From: haroldb786@aol.com (HaroldB786) Newsgroups: bionet.software Subject: Re: Windows DNA/Protein analysis programs Date: 4 Apr 1997 20:49:13 GMT Organization: AOL http://www.aol.com Lines: 8 Message-ID: <19970404204801.PAA02718@ladder01.news.aol.com> References: <334407FF.3D1E@mail.utexas.edu> NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com First try www.ebi.ac.uk-- lots of software...... GeneDoc can be useful for aligned sequences. MACAW also. Pardon my ignorance, "contigs for DNA sequencing?" Hope this helps, harold From owner-software@net.bio.net Thu Apr 03 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!EU.net!sun4nl!uva.nl!nol.amc.uva.nl!news From: "Jan Filip Hellings (staff)" Newsgroups: bionet.software Subject: Re: ReadSeq Bug Date: Fri, 04 Apr 1997 14:22:52 +0200 Organization: AMC/ADIV/CRS Lines: 45 Message-ID: <3344F29C.5914@amc.uva.nl> References: <860029387.2018@dejanews.com> NNTP-Posting-Host: eland.amc.uva.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; SunOS 5.4 sun4d) Michael Yasayko wrote: > > I've discovered a potentially fatal bug in the Feb 1 1993 release of > "ReadSeq". ReadSeq, authored by Don Gilbert of Indiana University, > conveniently converts between most of the major sequence file types that > people have developed over the years. ReadSeq is available at: > > ftp://ftp.bio.indiana.edu/molbio/readseq/ With Readseq I couldn't read files of raw format with only one line so I changed the code a little. I hope it won't affect any other functionality. ---cut here for the patch file---------------- *** ureadseq.c.orig Fri Apr 4 13:27:19 1997 --- ureadseq.c Fri Apr 4 14:09:30 1997 *************** short seqFileFormatFp( *** 1330,1336 **** else if (foundFitch) format= kFitch; /* no format chars: */ else if (otherlines > 0) format= kUnknown; ! else if (dnalines > 1) format= kPlain; else if (aminolines > 1) format= kPlain; else format= kUnknown; --- 1330,1336 ---- else if (foundFitch) format= kFitch; /* no format chars: */ else if (otherlines > 0) format= kUnknown; ! else if (dnalines >= 1) format= kPlain; else if (aminolines > 1) format= kPlain; else format= kUnknown; ----------cut-------------------------------------- save this file and run: patch < patchfile make all Yours -- ***************************Jan Hellings********************************* * Academic hospital of the Phone: (+31) 20 5667371 * * University of Amsterdam/AMC/G02-209 FAX : (+31) 20 5664440 * * Meibergdreef 9 * * 1105 AZ Amsterdam/Holland Email : j.f.hellings@amc.uva.nl * ************************************************************************ From owner-software@net.bio.net Thu Apr 03 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news-xfer.netaxs.com!news.maxwell.syr.edu!news.apfel.de!news-fra1.dfn.de!news-ge.switch.ch!feed1.belnet.be!news.belnet.be!alpha.luc.ac.be!pstn11.luc.ac.be!user From: ghermans@luc.ac.be (Guy Hermans) Newsgroups: bionet.software Subject: Re: T cell epitope prediction ? Date: Fri, 04 Apr 1997 13:21:56 +0100 Organization: Dr. L. Willems-Instituut Lines: 33 Message-ID: References: <5ht3ja$odd@rc1.vub.ac.be> NNTP-Posting-Host: pstn11.luc.ac.be In article <5ht3ja$odd@rc1.vub.ac.be>, gbottu@ben.vub.ac.be (Guy Bottu) wrote: > Does someone know of a software to predict T cell epitopes or > maybe a public Server where a protein can be submitted to such > a program ? > > Dr. Guy Bottu Sure! A number of methods has been proposed and evaluated. One Mac program, called T-sites, incorporates a number of such methods. It is freeware, and new versions could be obtained from the company where the authors worked _at the time_. I tried to contact them for a new version, but to no avail. I'll include the program in a personal e-mail to you, so I won't have to overload newsservers all over the planet. If someone out here wishes to get a copy, please let me know personally. Greetings to all Guy -- Guy Hermans, PhD student Ms research Unit Immunology research group Dr. L. Willems-Institute Dept. of Physiology, LUC University Campus University Campus B-3590 Diepenbeek B-3590 Diepenbeek Belgium Belgium Voice ++32(0)11/26.92.07 Fax ++32(0)11/26.92.09 From owner-software@net.bio.net Thu Apr 03 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!EU.net!news-peer.sprintlink.net!cs.utexas.edu!news.eng.convex.com!news.ecn.uoknor.edu!munnari.OZ.AU!news.mel.connect.com.au!news.mel.aone.net.au!usenet From: "Phuc Hoang" Newsgroups: bionet.software Subject: Software for FREE Date: 4 Apr 1997 06:21:11 GMT Organization: Customer of Access One Pty Ltd, Melbourne, Australia Lines: 1 Message-ID: <01bc40c0$9f725520$8c143ccb@default> NNTP-Posting-Host: ip140.ans.com.au Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Internet News 4.70.1155 Only at : http://www.ans.com.au/~hoang/software From owner-software@net.bio.net Thu Apr 03 23:00:00 1997 Path: biosci!agate!howland.erols.net!newsserver.jvnc.net!news.merck.com!internal.merck.com!user From: mark_yeager@merck.com (Mark Yeager) Newsgroups: bionet.molbio.methds-reagnts,bionet.software Subject: Re: Manipulating ABI Chromatogram files Date: Thu, 03 Apr 1997 14:06:14 -0500 Organization: Merck & Co. Lines: 25 Message-ID: References: <5htp0p$9f6@lyra.csx.cam.ac.uk> <5hu0l0$dse@lyra.csx.cam.ac.uk> <3343234C.49CE@cyllene.uwa.edu.au> Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Xref: biosci bionet.molbio.methds-reagnts:56382 bionet.software:18289 In article <3343234C.49CE@cyllene.uwa.edu.au>, swoods@cyllene.uwa.edu.au wrote: > There is a similar program for the Mac. > > Try looking for SeqED (I forget where from - email me if you need me to > find it). > > It does multiple alignments and can display all or part of the original > chromatograms. The program EditView is free from Perkin Elmer/ABI -- Mark Yeager -> mark_yeager@merck.com WP16-107, Dept. of Virus & Cell Biology Merck Research Labs, West Point, PA 19486 The contents of this message express only the sender's opinion. This message does not necessarily reflect the policy or views of my employer, Merck & Co., Inc. All responsibility for the statements made in this Usenet posting resides solely and completely with the sender. From owner-software@net.bio.net Fri Apr 04 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!news.visi.net!mur2.odyssey.on.ca!news3.sprint-canada.net!roger.interlynx.net!not-for-mail From: Lars Thomsen Newsgroups: bionet.software Subject: Curvefitting in Preader (free patch clamp analysis software) soon to come... Date: Fri, 04 Apr 1997 19:45:01 -0800 Organization: Interlynx Lines: 62 Message-ID: <3345CABD.7DCD@interlynx.net> NNTP-Posting-Host: port14.hm.interlynx.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.0b2 (Win95; I) X-Priority: 3 (Normal) Hi Our freeware program Preader for analysis of patch clamp data will soon be include all the possible fitting routines that you can think of in terms of pharmacological and electrophysiological analysis. We got a very kind offer from GraphPad who will allow us to use the trial version of their software in our program. This is really good because it takes a lot of time to develop the curve fitting routines and now we can concentrate on the more direct analysis. We also asked Jandel Software (the maker of SigmaPlot) if there was a possibility to get a restricted version of their software or something, but they said no. Until recently I didn't know that GraphPad had such a good curve fitting program as far as I can see it matches SigmaPlot pretty well and it beats MicroCal Origin which I regret that I bought. So we are really excited about this because we this will soon give us the analysis program that we want. The reason why we make it is that we are PC users and we do not want to jump to the Mac where AxoGraph is available. I really like that program. We will make some things that you not will find in AxoGraph which is a pretty smart database function utilizing SQL language to sort/find the data. It means that one time you have entered the information from your logbook (or used Preaders automatic features for peaks and soon rise times, time constants etc.) then you can perform the statistics that you want. This basically means that you do not have to work yourself to dead by paging back and forth in your logbooks. Recently I made 4 abstracts to the ISAN meeting in Cairns and it took me the whole weekend to sort out the data from the logbook. If I had finished that feature in Preader then I would have finished in one hour. Example : Find all concentrations of GABA=1000 µM give me the mean peak current, 50% rise time ± SD and ± SE. Preader currently have a peak detector but version 1.7 (not released yet) will improve this feature a lot. Preader also offers automatic transfer to the database of the numbers returned from the analysis. I think its smart...(but I also made it, so Im quite uncritical) Please give some response if you think this is worth pursuing We have just got VB5 and we will make the transition from VB4, which should make the program faster. We are also working very hard on getting the support for Cambridge Electronic Designs file format CFS into our program. CED has also been very helpful with the support for their file format. You can go to the download page of Preader beta version 1.6 : http://home.interlynx.net/~lthomsen/preader You can mail me to obtain a password : lthomsen@interlynx.net or thomsenl@fhs.mcmaster.ca Please note that we haven't incorporated GraphPad Prism in our program yet, but you can try the trial version by going to : http://www.graphpad.com/www/welcome.html -- Lars Thomsen, MSc Ph.D. 115 South Oval, Hamilton, L8S1R2 Ontario, Canada tlp +1 905 777 0720 fax +1 905 777 0738 email lthomsen@interlynx.net homepage http://home.interlynx.net/~lthomsen From owner-software@net.bio.net Fri Apr 04 23:00:00 1997 Path: biosci!ACCEFYN.ORG!acad From: acad@ACCEFYN.ORG (acad) Newsgroups: bionet.software Subject: help Date: 5 Apr 1997 06:00:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net How can I subscribe to this listserv, what other list does it handle? thanks From owner-software@net.bio.net Fri Apr 04 23:00:00 1997 Path: biosci!agate!howland.erols.net!ix.netcom.com!super.zippo.com!zdc!news.onramp.net!news From: jdean@scscomm.com (John D. Eanust) Newsgroups: bionet.software Subject: ANNOUNCE: Get Newsgroup Binaries Automatically Date: Sat, 05 Apr 1997 04:09:25 GMT Organization: OnRamp Technologies, Inc.; ISP Lines: 12 Message-ID: <5i4ieo$iqm@newnews.onramp.net> Reply-To: jdean@scscomm.com NNTP-Posting-Host: ppp1-09.ftwotx.onramp.net X-Newsreader: Forte Free Agent 1.0.82 The new software named "Pluckit" from www.pluckit.com intelligently and automatically scans and downloads binary attachments from newsgroups postings, based upon your interests. Just select the groups of interest and press "start plucking" and then while you watch, hundreds or thousands of binary attachments (fonts, pictures, sound files, etc.) will flood into your hard drive. Try the FREE evaluation copy of Pluckit from www.pluckit.com. From owner-software@net.bio.net Sat Apr 05 23:00:00 1997 Path: biosci!MAIL.TSINGHUA.EDU.CN!congjy From: congjy@MAIL.TSINGHUA.EDU.CN (Jinyang Cong) Newsgroups: bionet.software Subject: software for predicting antigenesity Date: 6 Apr 1997 15:43:21 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <9704062241.AB28999@mail> NNTP-Posting-Host: net.bio.net Hi, I would appreciate very much if someone can tell me where I can get a software to analyze a amino acid sequence of any protein to predict its antigenic epitopes. I am working at using synthetic peptides as antigens to make monoclonal antibodies. This kind of software is very useful for me. Any information would be welcome. Cong, JY From owner-software@net.bio.net Sat Apr 05 23:00:00 1997 Path: biosci!lmb.uni-muenchen!bmeister From: bmeister@lmb.uni-muenchen (Ralf Baumeister) Newsgroups: bionet.software Subject: Sequence analysis software Date: 6 Apr 1997 09:21:23 -0700 Organization: Genzentrum Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: <5i0e0j$ait$1@sparcserver.lrz-muenchen.de> NNTP-Posting-Host: net.bio.net Dear all, we are looking for a DNA sequence analysis program, similar to the MAC program DNA Strider, which runs under Windows and is public domain or not overly expensive. Any suggestions? Thanks Ralf Baumeister bmeister@lmb.uni-muenchen.de From owner-software@net.bio.net Sat Apr 05 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news-xfer.netaxs.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.nacamar.de!news1.best.com!nntp1.ba.best.com!nntp2.ba.best.com!shellx!jquinn From: jquinn@best.com (Greg) Newsgroups: bionet.software Subject: Re: Windows DNA/Protein analysis programs Date: 6 Apr 1997 02:14:29 GMT Lines: 21 Distribution: world Message-ID: <5i70u5$83q$1@nntp2.ba.best.com> References: <334407FF.3D1E@mail.utexas.edu> NNTP-Posting-Host: shellx.best.com X-Newsreader: TIN [version 1.2 PL2] Karen Browning (kbrowning@MAIL.UTEXAS.EDU) wrote: : Here we go again. GeneRunner is apparently out of business. Does : anyone know of a user friendly, inexpensive DNA/protein analysis program : for Windows that does what GeneRunner did. I would also like to be able : to do contigs for DNA sequencing, etc. : Can anyone explain to me why this is so difficult? It's not that difficult, given that windows has a massive backup in terms of compilers, IDE's etc. However, it is time consuming to construct a natty interface to the algorithms, and debug the stuff to a reasonable degree, such that many people now try and sell their hard work rather than distributing freely. If you check back in this group you'll see several posts from people offering demo software of their sequence analysis software. This whole thing may be circumvented soonish by the serious use of Java, and since this is more or less platform independent (I say more or less because I am one of many who are encountering platform problems with Java) it would only take one kind soul to distribute a serious Java app (not just a collection of relatively trivial applets) and it would run on Windows, a Mac etc. etc. I am sure that will come from one serious minded individual and/or research group in the near future. From owner-software@net.bio.net Sun Apr 06 23:00:00 1997 Path: biosci!agate!howland.erols.net!rill.news.pipex.net!pipex!tank.news.pipex.net!pipex!iafrica.com!not-for-mail From: Joe Oppon Newsgroups: bionet.software Subject: Correction ! Nucleotide seqs to Aminoacids Date: Mon, 07 Apr 1997 14:16:01 +0300 Organization: sanbi Lines: 26 Message-ID: <3348D771.59E2@techno.sanbi.ac.za> NNTP-Posting-Host: techno.sanbi.ac.za Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) -- Should have read "which translates nucleotide seq to aminoacids" Very sorry. ************************************************ * Joseph Cruick_Shank Oppon * South African Bioinformatics Institute * University of The Western Cape * Bellville. South Africa * Tel: 0027 (021) 959 3645 * http://techno.sanbi.ac.za/~joe ************************************************ From owner-software@net.bio.net Sun Apr 06 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!nntp.uio.no!uninett.no!due.unit.no!usenet From: Ingar Pareliussen Newsgroups: bionet.plants,bionet.software,comp.sys.handhelds,comp.sys.palmtops Subject: Using handheld computers in ecological field work Date: Mon, 07 Apr 1997 15:04:44 +0200 Organization: The Norwegian University of Science and Technology Lines: 7 Distribution: inet Message-ID: <3348F0EC.2AA9@nvg.ntnu.no> NNTP-Posting-Host: mn6604.mnfak.unit.no Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win95; I) Xref: biosci bionet.plants:14958 bionet.software:18300 comp.sys.handhelds:19320 comp.sys.palmtops:71059 I wonder if there was anyone that had used Psion 3c, USR pilot or similar computers in ecological field work. This summer I am going to perform a plant abundance mesurements and need a reliable palmtop that can run a simple spreadsheet program, (one colomn with latin name and 18 columns behind for ecological data and about 100 sutch entries pr. day), easy to use, low power consumption and weather hardy. From owner-software@net.bio.net Sun Apr 06 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!ais.net!uunet!in3.uu.net!137.208.127.3!newsfeed.wu-wien.ac.at!usenet From: bunka@i112pc09.vu-wien.ac.at (Sebastian Bunka) Newsgroups: bionet.software Subject: Re: software for predicting antigenesity Date: 7 Apr 1997 07:53:55 GMT Organization: Vet. University Vienna Lines: 45 Message-ID: <5ia96j$hji@cantine.wu-wien.ac.at> References: <9704062241.AB28999@mail> NNTP-Posting-Host: i112pc09.vu-wien.ac.at Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 0.9.8 In article <9704062241.AB28999@mail>, congjy@MAIL.TSINGHUA.EDU.CN (Jinyang Cong) writes: > Hi, I would appreciate very much if someone can tell me where I can get a > software to analyze a amino acid sequence of any protein to predict its > antigenic epitopes. I am working at using synthetic peptides as antigens to > make monoclonal antibodies. This kind of software is very useful for me. Any > information would be welcome. > Cong, JY > I know of 2 or three DOS programs that analyse an AA sequence using the Chou and Frasman algorythms. You can find 1 or two at ftp.bio.indiana.edu in the pub/molbio... subdirs, ibmpc, "seqaid.uue", "sqaid381.zip" and maybe prograph. see also (91)sunsite.unc.edu 91 /pub/academic/biology/molbio/ibmpc -r--r--r-- 4788 23:00:00 12 May 1993 GMT prograph.zip (113)bioinformatics.weizmann.ac.il 113 /pub/software/dos -r--r--r-- 83354 01:00:00 02 Nov 1993 GMT predict.exe (134)ftp.jussieu.fr 134 /pub16/pc/garbo/math -r--r--r-- 26785 23:00:00 20 May 1989 GMT predict.zip (135)ftp.cnr.it 135 /pub/PC-IBM/garbo.uwasa.fi/math -r--r--r-- 1289220 21:05:00 03 Aug 1996 GMT predict.zip Hope this helps, SWB -- ;-) ------------------------------------------------------------------------ Sebastian Bunka ph. (+43-1) 250 77 4208 Institute of FAX (+43-1) 250 77 4290 Medical Chemistry email: Sebastian.Bunka@vu-wien.ac.at University of Veterinary Medicine - Vienna - Austria ------------------------------------------------------------------------ From owner-software@net.bio.net Sun Apr 06 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!news-out.communique.net!communique!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!dispatch.news.demon.net!demon!fido.news.demon.net!demon!newsgate.unisource.nl!news.unisource.nl!xs4all!not-for-mail From: marker@xs4all.nl (Niels Groot) Newsgroups: bionet.software Subject: Re: Sequence analysis software Date: 7 Apr 1997 20:45:43 GMT Organization: XS4ALL, networking for the masses Distribution: world Message-ID: <5ibmdn$hio$1@news1.xs4all.nl> References: <5i0e0j$ait$1@sparcserver.lrz-muenchen.de> NNTP-Posting-Host: asd05-17.dial.xs4all.nl Mime-Version: 1.0 Content-Type: Text/Plain; charset=US-ASCII X-XS4ALL-Date: Mon, 07 Apr 1997 22:45:43 CEST X-Newsreader: WinVN 0.99.7 Lines: 26 In article <5i0e0j$ait$1@sparcserver.lrz-muenchen.de>, bmeister@lmb.uni-muenchen says... > >Dear all, > >we are looking for a DNA sequence analysis program, similar to the MAC >program DNA Strider, which runs under Windows and is public domain or >not overly expensive. > >Any suggestions? > >Thanks > >Ralf Baumeister > >bmeister@lmb.uni-muenchen.de > You could take a look at SeqSearch v1.1 for Windows at http://www.xs4all.nl/~marker. I should include a disclaimer since I'm one of the authors.. Regards Niels Groot From owner-software@net.bio.net Sun Apr 06 23:00:00 1997 Path: biosci!CIFN.UNAM.MX!amedrano From: amedrano@CIFN.UNAM.MX (Arturo Medrano) Newsgroups: bionet.software Subject: Re: Code for nucleotide translation to ptn. Date: 7 Apr 1997 08:17:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 67 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3348D527.15FB@techno.sanbi.ac.za> Reply-To: Arturo Medrano NNTP-Posting-Host: net.bio.net What platform do you want the source code for? I wrote a C++ code for windows 3.1, which obtains an amino acid sequence from a DNA sequence stored in a data base FoxPro-compatible. Is this useful to you? Best regards Arturo ___ Luis Arturo Medrano Soto Computational Biology Nitrogen Fixation Research Center CIFN-UNAM P.O Box 565-A Cuernavaca, Morelos Mexico 62100 Tels: (VOICE) 527-313-2063 ( FAX ) 527-317-5581 E-mail: AMedrano@cifn.unam.mx WWWS: http://www.cifn.unam.mx _/_/_/ _/_/_/ _/_/_/_/ _/ _/ _/ _/ _/ _/_/ _/ _/ _/ _/_/_/ _/ _/ _/ _/ _/ _/ _/ _/_/ _/_/_/ _/_/_/ _/ _/ _/ _____________________________________________ On Mon, 7 Apr 1997, Joe Oppon wrote: > -- I am looking for a source coder for any program ...could be > > the gcg program which translates amino seq to protein seq or vice > > versa. The simpler , the better. Meanwhile anything goes. > > > Ooops ! I forgot; better still if it is in C or C++ > > Thanks. > > > > > > > > > > > > > > ************************************************ > * Joseph Cruick_Shank Oppon > * South African Bioinformatics Institute > * University of The Western Cape > * Bellville. South Africa > * Tel: 0027 (021) 959 3645 > * http://techno.sanbi.ac.za/~joe > ************************************************ > > From owner-software@net.bio.net Sun Apr 06 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!dispatch.news.demon.net!demon!fido.news.demon.net!demon!news2.euro.net!news.euro.net!usenet From: mbleeker@euronet.nl (Marco Bleeker) Newsgroups: bionet.plants,bionet.software,comp.sys.handhelds,comp.sys.palmtops Subject: Re: Using handheld computers in ecological field work Date: 7 Apr 1997 22:24:49 GMT Organization: EuroNet Internet Distribution: inet Message-ID: <334972a1.3323460@news.euro.net> References: <3348F0EC.2AA9@nvg.ntnu.no> NNTP-Posting-Host: p105.asd.euronet.nl X-Newsreader: Forte Free Agent 1.1/32.230 Lines: 18 Xref: biosci bionet.plants:14965 bionet.software:18303 comp.sys.handhelds:19333 comp.sys.palmtops:71094 On Mon, 07 Apr 1997 15:04:44 +0200, Ingar Pareliussen wrote: >I wonder I use a Psion series 3A (2 MB RAM) with a database of 2100 species names. That is about the max the database can handle at a (barely) acceptable performance. I haven't tried the spreadsheet yet with such a large number of lines, but I suppose the max would be about the same. The spreadsheet is quite powerfull (as opposed to the database) and the 18 columns you mention should not be a problem I think. The Psion 3A is perhaps not very waterproof. Battery life is great though. Success, Marco -- ------------------ --- ------------------------------ From owner-software@net.bio.net Sun Apr 06 23:00:00 1997 Path: biosci!agate!howland.erols.net!rill.news.pipex.net!pipex!tank.news.pipex.net!pipex!iafrica.com!not-for-mail From: Joe Oppon Newsgroups: bionet.software Subject: Code for nucleotide translation to ptn. Date: Mon, 07 Apr 1997 14:06:15 +0300 Organization: sanbi Lines: 31 Message-ID: <3348D527.15FB@techno.sanbi.ac.za> NNTP-Posting-Host: techno.sanbi.ac.za Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) -- I am looking for a source coder for any program ...could be the gcg program which translates amino seq to protein seq or vice versa. The simpler , the better. Meanwhile anything goes. Ooops ! I forgot; better still if it is in C or C++ Thanks. ************************************************ * Joseph Cruick_Shank Oppon * South African Bioinformatics Institute * University of The Western Cape * Bellville. South Africa * Tel: 0027 (021) 959 3645 * http://techno.sanbi.ac.za/~joe ************************************************ From owner-software@net.bio.net Mon Apr 07 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news.maxwell.syr.edu!news.apfel.de!news-fra1.dfn.de!news-ge.switch.ch!news-zh.switch.ch!rzunews.unizh.ch!newsadm From: Rolf Kocherhans Newsgroups: bionet.software Subject: Free practical programs for molecular biologists !!! Date: Tue, 08 Apr 1997 15:19:21 +0100 Organization: University of Zurich Lines: 49 Message-ID: <334A53E9.4677@vetvir.unizh.ch> Reply-To: rolfk@vetvir.unizh.ch NNTP-Posting-Host: 130.60.22.38 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Macintosh; I; PPC) I wrote a few practical and simple to use programs which facilitate your daily work in the lab such as predicting the size of DNA fragments after digestion (graphical) with restriction enzymes. I would like to make these programs accessible to a broad user group by the Internet. All programs have been tested on MacOS and Windows95. My programs are accessible over the WWW and made functional using Netscape 2.x or Internet Explorer 2.x or higher in association with a free plugin which you have to download and install first. This is what you do: - Download the Roadster plugin http://www.unizh.ch/vetvir/plugin.html) install it on your computer. - Then connect to: http://www.unizh.ch/vetvir/programs.html That's it !! These are my programs which make your live as a molecular biologist easier ! Find here a few more examples or my programs: a. Digest Preview: Enter the size(s) of your DNA fragment(s) and see their migration pattern in a virtual gel in comparison to a 1 kb ladder. b. Adapter Design: Helps to create in frame adapters in order to link incompatible DNA ends together. c. Dilution Calculator: Does all the calculations when you have to make up solutions There are many other programs such as Oligo Tm, Compatible ends etc. Please have a look, comments are welcome! Have fun Rolf Kocherhans mailto:rolfk@vetvir.unizh.ch From owner-software@net.bio.net Mon Apr 07 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!ais.net!news.stealth.net!newsfeed.de.ibm.net!ibm.net!02-newsfeed.univie.ac.at!03-newsfeed.univie.ac.at!mail.boku.ac.at!news From: Andreas Wernitznig Newsgroups: bionet.software Subject: Re: Phyllip Interleave Format? Date: Tue, 08 Apr 1997 17:37:23 +0200 Organization: Univ. for Agriculture Lines: 9 Message-ID: <334A6633.24AA@edv1.boku.ac.at> References: Reply-To: h8760592@edv1.boku.ac.at NNTP-Posting-Host: 141.244.88.51 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (WinNT; I) Marc A. Goldstein wrote: > Could someone please direct me to a reference that would describe > the Phyllip Interleave format used by various sequence alignment > programs? I am curious to know how to build a file in this format. Have a look in the Phylip manual. There is a short description of the Interleave format. Andreas Wernitznig From owner-software@net.bio.net Mon Apr 07 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news.maxwell.syr.edu!news.apfel.de!news-fra1.dfn.de!news-koe1.dfn.de!main.Germany.EU.net!Dortmund.Germany.EU.net!news.gsf.de!news From: Kerstin Quandt Newsgroups: bionet.software Subject: SW to detect correlated TF binding sites Date: Tue, 08 Apr 1997 17:07:22 +0200 Organization: GSF Forschungszentrum Lines: 36 Message-ID: <334A5F2A.167E@gsf.de> NNTP-Posting-Host: atlantis.gsf.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; OSF1 V3.2 alpha) We would like to announce the availability of the online version of the programs FastM and ModelInspector, tools for detection of correlated transcription factor binding sites in DNA sequences (including databases). FastM builds a so-called model from the information of - which two binding sites are involved - their strand orientation (with respect to each other) - and a distance range between the two binding sites. ModelInspector then uses this FastM-model to scan either a given DNA sequence or a selected GenBank section for matches to the model. This allows fast verification whether a pair of binding sites is really characteristic for the sequence you are analyzing. You can use FastM/ModelInspector interactively via WWW at http://www.gsf.de/cgi-bin/fastm.pl More information and an example can be found at http://www.gsf.de/biodv/fastm.html All parameters for the programs can be set via the WWW-form, you can select a GenBank section or enter your own sequence to be scanned for matches. The resulting output will be mailed to you. The binding site library used by FastM is based on the latest release 3.1 of the TRANSFAC database (http://transfac.gbf-braunschweig.de/TRANSFAC). -- Kerstin Quandt | email: quandt@gsf.de GSF - National Research Centre for Environment and Health 85764 Neuherberg, F.R.Germany From owner-software@net.bio.net Mon Apr 07 23:00:00 1997 Path: biosci!GENECODES.COM!jimgalt From: jimgalt@GENECODES.COM (Jim Galt) Newsgroups: bionet.software Subject: Manipulating ABI Chromatogram files Date: 8 Apr 1997 13:32:18 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 41 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net To Chris Cunningham: In response to your query about capturing ABI trace file images for making figures, I would recommend the following technique, which I have been using recently: Go to the Ambrosia Software shareware web site at http://www.ambrosiasw.com and download a demo copy of "Snapz Pro". This screen capture utility allows much more flexibility than the standard Macintosh cmd-shift-3 screen capture. For instance, you can capture just a selection of the window by dragging a marquee (which is what you will probably want to do). It can also capture windows or menus. Install this control panel, and restart your Mac. (Don't forget to pay your shareware fees!) 1. Using Sequencher, select the region of the trace file(s) you want to view by highlighting the DNA sequence. 2. Click on the "Show Chromatograms" button in the menubar. 3. Alter the size of the viewing window and the scaling of the peaks on the trace file to suit your needs. 4. I would then click on a base outwith the region of interest, to remove the highlighting from the selected sequence. 5. Type the keystroke to activate Snapz Pro (I think it is cmd-shift-3 by default) and choose the "Selection" tool. 6. Decide how you want the picture to be captured - I have had variable success with "Clipboard", and more reliable results with "Screen Snapz". The latter saves it as a SimpleText file, which you then open up, select all, copy and paste into a drawing program (I use Superpaint, for instance). 7. Then you can erase parts of the picture, add legends, etc. and prepare the final figure the way you want. I hope this helps you get what you want. Please let me know if it does, or if you have any questions. Sincerely, Jim Galt P.S. - I should also mention that I am originally from Glasgow, and I have been in the US for 9 years now. From owner-software@net.bio.net Mon Apr 07 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news.maxwell.syr.edu!news.apfel.de!fu-berlin.de!unlisys!blackbush.xlink.net!news-ge.switch.ch!news.bme.hu!news.iif.hu!kokiux.koki.hu!f-guest From: Guest of Freund Group Newsgroups: bionet.software Subject: Patch clamp software Date: Tue, 8 Apr 1997 19:25:29 +0200 Organization: IIF Lines: 17 Message-ID: NNTP-Posting-Host: kokiux.koki.hu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Did anyone heard something about the patch clamp acquisitioning and analyzing software DEMPSTER. If my infos are correct, thats probably the best FREE software in the 'market', but I can't find it on the net :( By the way, does anyone have a cool software of the type and FREE ? Any info is waited with open arms at RANCZ@LUDENS.ELTE.HU or F-GUEST@KOKIUX.KOKI.HU Thanx From owner-software@net.bio.net Mon Apr 07 23:00:00 1997 Path: biosci!daresbury!uninett.no!hermod.uio.no!nntp.uio.no!newsfeed.nacamar.de!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!wap18.zi.biologie.uni-muenchen.de!strimmer From: Korbinian Strimmer Newsgroups: bionet.software Subject: Version 3.1 of PUZZLE available Date: Tue, 8 Apr 1997 10:37:23 +0200 Organization: [posted via] Leibniz-Rechenzentrum, Muenchen (Germany) Lines: 52 Distribution: world Message-ID: NNTP-Posting-Host: wap18.zi.biologie.uni-muenchen.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII P U Z Z L E Maximum likelihood analysis for nucleotide and amino acid alignments Version 3.1 April 1997 Copyright 1995-97 by Korbinian Strimmer and Arndt von Haeseler Zoologisches Institut, Universitaet Muenchen, Muenchen, Germany What's new in PUZZLE 3.1: * Much improved user interface to rate heterogeneity (less confusing menu, rearranged outfile, additional out-of-range check). * Possibility to read rooted input trees (automatic removal of basal bifurcation). * Computation of average distance between all pairs of sequences. * Fix of a bug that caused PUZZLE 3.0 to crash on some systems (DEC Alpha). * Cosmetic changes in program and documentation. PUZZLE is an application to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm (quartet puzzling) that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Rate heterogeneity (invariable sites plus Gamma distributed rates) is incorporated in all models of substitution available (nucleotides: TN, HKY, F84, and submodels; amino acids: Dayhoff, JTT, mtREV24). All model parameters including rate heterogeneity can be estimated from the data by maximum likelihood. PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. In addition, PUZZLE offers a novel method, likelihood mapping, to investigate the support of internal branches without computing an overall tree. PUZZLE is available free of charge from http://www.zi.biologie.uni-muenchen.de/~strimmer/puzzle.html (PUZZLE home page) ftp://ftp.ebi.ac.uk/pub/software (European Bioinformatics Institute) ftp://ftp.pasteur.fr/pub/GenSoft (Institut Pasteur) PUZZLE is written as an ANSI C program. This means that it will run on most personal computers and workstations if compiled by an appropriate C compiler. Precompiled executables are available for MacOS and MS-DOS. UNIX and VMS makefiles are also provided. From owner-software@net.bio.net Mon Apr 07 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!supernews.com!news From: "Rob Halvorson" Newsgroups: bionet.plants,bionet.software,comp.sys.handhelds Subject: Re: Using handheld computers in ecological field work Date: 8 Apr 1997 20:33:41 GMT Organization: All USENET -- http://www.Supernews.com Lines: 12 Distribution: inet Message-ID: <01bc4424$f7aaab40$LocalHost@prefferc> References: <3348F0EC.2AA9@nvg.ntnu.no> NNTP-Posting-Host: p30.delrio.com X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.plants:14977 bionet.software:18310 comp.sys.handhelds:19365 put an HP200LX in a ziplock bag. Meets all your requirements. Ingar Pareliussen wrote in article <3348F0EC.2AA9@nvg.ntnu.no>... > I wonder if there was anyone that had used Psion 3c, USR pilot or > similar computers in ecological field work. > This summer I am going to perform a plant abundance mesurements and > need a reliable palmtop that can run a simple spreadsheet program, > (one colomn with latin name and 18 columns behind for ecological data > and about 100 sutch entries pr. day), easy to use, low power consumption > and weather hardy. > From owner-software@net.bio.net Tue Apr 08 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!hermes.sovam.com!sovam!demos!news.rcom.ru!infopro!not-for-mail From: "Yuriy Eizner" Newsgroups: bionet.software Subject: Re: statistics and pharmacology Date: 9 Apr 1997 07:37:17 GMT Organization: WinWare Unlimited Lines: 21 Message-ID: <01bc43d9$25b95b40$af01f2c3@eizner> References: <5i2o8a$jj8@rc1.vub.ac.be> NNTP-Posting-Host: dialup-126.infopro.spb.su X-Newsreader: Microsoft Internet News 4.70.1155 Philipp Lebran wrote: > Does anyone know of software that will calculate regerssion parameters and > ED50 value of dose-response curves? > > Currently I'm doing it by hand (by hand in Excel, that is) but I'm not sure > at all of my results. > > Thanks, > Philippe > Hi, Philipp Try to use "Origin" . This product is convenient. Yurii From owner-software@net.bio.net Tue Apr 08 23:00:00 1997 Path: biosci!agate!howland.erols.net!cam-news-hub1.bbnplanet.com!cpk-news-feed3.bbnplanet.com!news.bbnplanet.com!es.dupont.com!topgun.es.dupont.com!millermac.es.dupont.com!user From: millertj@esvax.dnet.dupont.com (T Miller) Newsgroups: bionet.software Subject: Re: Manipulating ABI Chromatogram files Date: Wed, 09 Apr 1997 10:19:03 -0400 Organization: Dupont Lines: 26 Distribution: world Message-ID: References: NNTP-Posting-Host: millermac.es.dupont.com In article , jimgalt@GENECODES.COM (Jim Galt) wrote: > To Chris Cunningham: > > In response to your query about capturing ABI trace file images for making > figures, I would recommend the following technique, which I have been using > recently: > > Go to the Ambrosia Software shareware web site at http://www.ambrosiasw.com > and download a demo copy of "Snapz Pro". This screen capture utility allows > much more flexibility than the standard Macintosh cmd-shift-3 screen > capture. For instance, you can capture just a selection of the window by > dragging a marquee (which is what you will probably want to do). It can > also capture windows or menus. Install this control panel, and restart your > Mac. (Don't forget to pay your shareware fees!) > You might want to try Mainstay's Capture (now called Captivate, I think). It is a commercial package and used for screen captures and later viewing/saving. Regards, Tom. Standard disclaimers.... -- Opinions are my own and not of my employer. From owner-software@net.bio.net Tue Apr 08 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!news.sgi.com!news.maxwell.syr.edu!ott.istar!news.istar.net!tor.istar!east.istar!ftn.net!passport.ca!news From: Ryan Burns Newsgroups: bionet.plants,bionet.software,comp.sys.handhelds,comp.sys.palmtops Subject: Re: Using handheld computers in ecological field work Date: Wed, 09 Apr 1997 09:59:23 -0400 Organization: Fieldworker Lines: 18 Message-ID: <334BA0BB.5166@fieldworker.com> References: <3348F0EC.2AA9@nvg.ntnu.no> Reply-To: webmaster@fieldworker.com NNTP-Posting-Host: pm1-24.passport.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Xref: biosci bionet.plants:14989 bionet.software:18313 comp.sys.handhelds:19394 comp.sys.palmtops:71227 FieldWorker software running on a Newton allows you to collect all your field data and link it to GPS position readings. You can customize your database and easily export the data to any desktop program on a PC or MAC. Multiple data types include sliders, pick lists, and check boxes. In the upcoming Pro version, a sketch pad will also be available, as well as a full relational database. Contact me at webmaster@fieldworker.com or visit our website at http://www.fieldworker.com/ for more information. -- ================================================ Ryan Burns, Webmaster Download FieldWorker 2.3 Demo!..at http://www.fieldworker.com Navigation, Differential GPS, Offset, Relational Map, Multi-lingual! FieldWorker - Handheld PC data collection linked to GPS -- FieldWorker Products Ltd.-- Tel: +1 416 483 3485 ================================================ From owner-software@net.bio.net Tue Apr 08 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!newsin.iconnet.net!news-xfer.netaxs.com!news.maxwell.syr.edu!nntp.uio.no!uninett.no!due.unit.no!usenet From: Hans Stenöien Newsgroups: bionet.software Subject: Arlequin ver.1.0 and RAPD-PCR Date: Wed, 09 Apr 1997 12:57:21 +0200 Organization: The Norwegian University of Science and Technology Lines: 17 Message-ID: <334B7611.5105@vm.unit.no> NNTP-Posting-Host: vm238.ubt.unit.no Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0Gold (Win95; I) Dear all: I am doing RAPD-PCR analyses on two Sphagnum (peat-moss) species. I am using the haploid gametophores in the analyses. The software Arlequin ver. 1.0 does not accept RAPD-PCR data from diploids. However, shouldn't it be possible to define my data as "RFLP haplotypic data" and carry out ordinary population genetic analyses using this software? Thank you. Sincerely, Hans Stenøien Inst. of Natl. Hist. Museum of Natl. Hist. & Arch. Norwegian University of Science and Technology N-7004 Trondheim, Norway From owner-software@net.bio.net Tue Apr 08 23:00:00 1997 Path: biosci!uthct.edu!wu From: wu@uthct.edu Newsgroups: bionet.software Subject: ANNOUNCE: GeneFIND Server for protein family identification Date: 9 Apr 1997 08:45:01 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <9704091546.AA18297@diana.uthct.edu> NNTP-Posting-Host: net.bio.net The Bioinformatics Research Group of the University of Texas Health Center at Tyler is pleased to announce the availability of its GeneFIND Server for protein family identification at: http://diana.uthct.edu/genefind.html GeneFIND (Gene Family Identification Network Design) is an integrated database search system that combines several search/alignment tools and ProClass database (http://diana.uthct.edu/proclass.html) to provide rapid and sensitive search results with enriched family information. Multi-level filters are used, starting with the fastest MOTIFIND neural networks, followed by BLAST search, SSEARCH (Smith-Waterman) sequence alignment, and motif pattern search. The server currently provides large-scale on-line identification of query sequences for 942 protein families. Search results are returned as HTML documents showing global and motif scores, alignment to best matched members of all possible ProSite protein groups and PIR superfamilies, motif pattern match, as well as links to corresponding ProClass family records. Please cite the following reference in publications that benefit from the GeneFIND family identification system: Wu, C. H., Zhao, S., Chen, H. L., Lo, C. J. and McLarty, J. (1996). Motif identification neural design for rapid and sensitive protein family search. CABIOS, 12(2), 109-118. Please visit our site and send suggestions and comments to me at wu@uthct.edu. Also contact me directly if you are interested in obtaining a copy of the GeneFIND software program. I am looking forward to hearing from you! Cathy Wu, Ph.D. Associate Professor of Biomathematics University of Texas Health Center at Tyler P. O. Box 2003, Tyler, TX 75710 E-Mail : wu@uthct.edu Fax : (903) 877-5914 Phone : (903) 877-7962 WWW URL : http://diana.uthct.edu/~wu From owner-software@net.bio.net Tue Apr 08 23:00:00 1997 Path: biosci!agate!howland.erols.net!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!metro.atlanta.com!cssun.mathcs.emory.edu!hubcap.clemson.edu!sc.edu!usenet From: Dean Pentcheff Newsgroups: bionet.plants,bionet.software,comp.sys.handhelds,comp.sys.palmtops Subject: Re: Using handheld computers in ecological field work Date: 09 Apr 1997 18:30:48 -0400 Organization: Univ. of South Carolina, Columbia Lines: 40 Sender: dean@nauplius.psc.sc.edu Distribution: inet Message-ID: References: <3348F0EC.2AA9@nvg.ntnu.no> NNTP-Posting-Host: nauplius.psc.sc.edu X-Newsreader: Gnus v5.3/Emacs 19.34 Xref: biosci bionet.plants:14996 bionet.software:18316 comp.sys.handhelds:19429 comp.sys.palmtops:71284 Ingar Pareliussen writes: > I wonder if there was anyone that had used Psion 3c, USR pilot or > similar computers in ecological field work. > This summer I am going to perform a plant abundance mesurements and > need a reliable palmtop that can run a simple spreadsheet program, > (one colomn with latin name and 18 columns behind for ecological data > and about 100 sutch entries pr. day), easy to use, low power consumption > and weather hardy. I recently (4 months ago) set up an HP200LX (1 Mb memory) for use by people collection bird abundance observations from shipboard in Antarctica. I was very impressed with it. It's a little DOS machine, with a built-in copy of Lotus 1-2-3. There's a layer of HP graphical software which can be disabled, saving memory. You can repartition the 1 Mb of memory between program RAM and RAM disk as appropriate for your use. The unit is small and quite rugged. It has a small but usable keyboard (not for touch-typing, but fine for data entry, particularly if you set up useful one-key spreadsheet macros). It runs off two AA batteries for several weeks. Communications are over a serial port (signals are standard RS232, but the cable connector is weird - buy HP's "Connectivity Kit", or build your own cable and use standard old DOS serial communications packages). It's also got a PCMCIA (PC Card) slot that can use memory cards. All in all, quite a useful little beastie. I recommend it - particularly since it's now a model or two behind the most recent releases, you can probably buy two or three used ones and have spares (which is a MUST for field work). -Dean -- N. Dean Pentcheff WWW: http://tbone.biol.sc.edu/~dean/ Biological Sciences, Univ. of South Carolina, Columbia SC 29208 (803-777-3936) PGP ID=768/22A1A015 Keyprint=2D 53 87 53 72 4A F2 83 A0 BF CB C0 D1 0E 76 C0 Get PGP keys and information with the command: "finger dean@tbone.biol.sc.edu" From owner-software@net.bio.net Wed Apr 09 23:00:00 1997 Path: biosci!biochem.umass.edu!bscott From: bscott@biochem.umass.edu (Brian Scott) Newsgroups: bionet.software Subject: Free molecular visualization workshops for profs Date: 9 Apr 1997 17:34:28 -0700 Organization: University of Massachusetts Lines: 54 Sender: daemon@net.bio.net Distribution: world Message-ID: <334C354C.6136@biochem.umass.edu> Reply-To: bscott@biochem.umass.edu NNTP-Posting-Host: net.bio.net Free Workshops on Molecular Visualization for Undergraduate Bioscience Teaching Amherst MA -- Summer, 1997-8 Understanding the three-dimensional structures of proteins, DNA, RNA, and their interactions is difficult from flat pictures, yet grasping structure is important to understanding function. Free software is now available which displays attention-grabbing 3D animated images of biological molecules in depth-cued spacefilling color. RasMol (http://www.umass.edu/microbio/rasmol), which works on Windows or Macs, encourages self-directed exploration. Chime (http://www.umass.edu/microbio/chime) allows annotated preset views of molecules to be delivered as web tutorials. Free, hands-on workshops will be held this summer at the University of Massachusetts in Amherst to prepare college faculty with no prior experience to use molecular visualization in their classes. Participants will travel to the Amherst campus on three separate days (two this summer, one the following summer), and are responsible for their own travel expenses (and therefore are expected primarily from the Northeastern USA). Overnight accomodations will be provided free to those needing them (based on distance traveled). Participants will be expected to incorporate molecular visualization into their teaching, and to mentor two faculty colleagues at their home institution. The workshops will be led by Eric Martz, a Professor in the Department of Microbiology. Martz has innovated molecular structure tutorials which are in use throughout the USA and in dozens of other countries. The web site he created (see above) was visited by 40,000 people in 1996. 1997 dates are June 17 and 30 (workshop A), or June 19 and July 2 (workshop B). Workshops A and B also meet for one day in late June 1998. To obtain more detailed information and a REGISTRATION FORM, visit http://www.umass.edu/microbio/rasmol/workshop.htm or FAX a request to 413-545-1578, or email a request to emartz@microbio.umass.edu. Supported by the National Science Foundation (Undergraduate Faculty Enhancement, Division of Undergraduate Education) and the University of Massachusetts. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol Other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/  From owner-software@net.bio.net Wed Apr 09 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: "Holger Scheib" Newsgroups: bionet.software Subject: Some questions Date: 10 Apr 1997 12:00:22 +0100 Lines: 56 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5iih86$sq@mserv1.dl.ac.uk> Original-To: molmodel@dl.ac.uk, comp-bio@dl.ac.uk, bio-www@dl.ac.uk, bio-soft@dl.ac.uk, hscheib@tebio1.biologie.uni-stuttgart.de Dear collegues, my name is Holger Scheib and I am working at the Institute of Technical Biochemistry at the University of Stuttgart, Germany. Recently, we decided to get your Grasp software which is a real nice and handy tool and well suited for my research interests. I am investigating lipase-triglyceride complexes and would like to calculate 1st the total accessible surface and 2nd the accessible surface for polar as well as for hydrophobic amino acid residues. So far, I performed several calculations leading to the following results: total surface unpolar surface polar surface 11007 (4220) 3548 (1721) 3434 (1434) 11002 (4220) 3519 (1721) 3551 (1434) 10945 (4220) 3540 (1721) 3463 (1434) 11086 (4220) 3554 (1721) 3454 (1434) The values on the left of each column are the surface sizes in squared angstroems. The values in brackets represent the number of atoms that have been considered for the surface calculation. I performed the calculations as mentioned in your Manual. Here my questions in detail: Why isn't the accessible total surface the sum of accessible polar and unpolar surface? Or why are roughly 1000 atoms ignored for these calculations? What happens to the rest? Are Hydrogens used for the calculation of a surface or will Grasp sort them out before calculating the surface? Is the accessible surface calculated from the center of the (standard) 1.4 A probe or from the probe surface? Are substrate VdW radii automatically set or accepted by Grasp or will I have to manually adding them to some file? Is there a possibility to color the surface by hydrophobicity? It would be great to hear from you soon. Thanx a bunch in advance. Sincerely, Holger -- ******************************************************* * Dipl. Chem. M. Sc. Holger Scheib * * Institut fuer Technische Biochemie * * Universitaet Stuttgart * * Allmandring 31 * * 70569 Stuttgart * * * * Tel.: (0711) 685-7481 * * Fax.: (0711) 685-3196 * * email: hscheib@tebio1.biologie.uni-stuttgart.de * * www: http://www.itb.uni-stuttgart.de:8080/home.html * ******************************************************* From owner-software@net.bio.net Wed Apr 09 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!news-peer.gsl.net!howland.erols.net!rill.news.pipex.net!pipex!oleane!jussieu.fr!not-for-mail From: Michel SEIGNEURET Newsgroups: bionet.software Subject: alignment software Date: 10 Apr 1997 09:30:57 GMT Organization: Universites Paris VI/Paris VII - France Lines: 16 Message-ID: <5iic0h$39s$1@vishnu.jussieu.fr> NNTP-Posting-Host: mood.biophy.jussieu.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP20) X-URL: news:bionet.software Dear Collegues. My question is probably trivial but I am a newcomer to this field and I could not find a FAQ on this. I currently often do BLAST or FASTA searches of particular protein sequences against the SWISSPROT or PIR databases though the WWW. The problem is that the internet connection of my lab is slow. I am thus thinking of doing such searches locally after downloading the complete database. Could somebody suggest me a freely available software that allows one to do a BLAST or FASTA alignment search locally ? Thank you in advance. Michel Seigneuret Lab. de Biophysique Cellulaire et RMN Universite Paris 7 France From owner-software@net.bio.net Wed Apr 09 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!newsfeed.nacamar.de!uunet!in1.uu.net!205.229.48.18!news.fdt.net!news.gwi.net!web.ddp.state.me.us!sol.caps.maine.edu!dartvax.dartmouth.edu!atgw-kip-2-157.dartmouth.edu!user From: Nick.Morris@Dartmouth.Edu (Nick Morris) Newsgroups: bionet.software Subject: Re: alignment software Date: Thu, 10 Apr 1997 11:34:52 +0100 Organization: Dartmouth College Lines: 32 Message-ID: References: <5iic0h$39s$1@vishnu.jussieu.fr> NNTP-Posting-Host: atgw-kip-2-157.dartmouth.edu In article <5iic0h$39s$1@vishnu.jussieu.fr>, Michel SEIGNEURET wrote: > Dear Collegues. > My question is probably trivial but I am a newcomer to this field and > I could not find a FAQ on this. > I currently often do BLAST or FASTA searches of particular protein sequences > against the SWISSPROT or PIR databases though the WWW. The problem is that the > internet connection of my lab is slow. I am thus thinking of doing such > searches locally after downloading the complete database. Could somebody > suggest me a freely available software that allows one to do a BLAST or FASTA > alignment search locally ? > Thank you in advance. > > Michel Seigneuret > Lab. de Biophysique Cellulaire et RMN > Universite Paris 7 > France If your internet connection is so slow that you can't do BLAST by WWW then dowloading the database (if possible?) may take days! My suggestion would be to do the BLAST searches by e-mail, the results would then be returned by e-mail. It may not be quite as user friendly as the WWW but at least you won't have to sit at the computer waiting for things to happen. Also, the e-mail can be formatted so that an HTML document is returned so you can still make use of the direct links to the protein/DNA entry in the database. I hope this helps, Nick From owner-software@net.bio.net Wed Apr 09 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!ix.netcom.com!news.webspan.net!news-out.internetmci.com!newsfeed.internetmci.com!news.net-master.net!usenet From: lankford@net-master.net (C. L. Lankford) Newsgroups: bionet.software Subject: LANKFORD SCREEN COPY UTILITY v1.7 Date: Thu, 10 Apr 1997 15:51:46 GMT Organization: NetMaster Internet Services Lines: 20 Message-ID: <5ij24s$61u@tiger.net-master.net> NNTP-Posting-Host: s32.net-master.net X-Newsreader: Forte Free Agent 1.0.82 http://www.net-master.net/~lankford/ LANKFORD SCREEN COPY UTILITY v1.7 - THE must have utility for automating capture/saving of screen images with the press of a key. Support for Windows/CD-ROM/Games/Internet/ OnLine Services to quickly and easily save ANYTHING you can see to a file, print, etc. In short, if you can see it on a monitor display, then this utility can acquire it, save it to a file, print it, etc. Designed for Windows 3.1x/W95. Requires VBRUN300.DLL Package includes an uninstall program, so that you can remove the software easily, if you don't want to keep it. You can download this package from: http://www.net-master.net/~lankford/ From owner-software@net.bio.net Wed Apr 09 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: James McInerney Newsgroups: bionet.software Subject: Re: alignment software Date: 10 Apr 1997 14:17:26 +0100 Organization: The Natural History Museum Lines: 33 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5iip96$ah5@mserv1.dl.ac.uk> References: <9741010320.~INN-PPBa00253.bionet-news@dl.ac.uk> Reply-To: J.McInerney@nhm.ac.uk MIME-Version: 1.0 Original-To: Bionet Software Michel SEIGNEURET wrote: > > Dear Collegues. > My question is probably trivial but I am a newcomer to this field and > I could not find a FAQ on this. > I currently often do BLAST or FASTA searches of particular protein sequences > against the SWISSPROT or PIR databases though the WWW. The problem is that the > internet connection of my lab is slow. I am thus thinking of doing such > searches locally after downloading the complete database. Could somebody > suggest me a freely available software that allows one to do a BLAST or FASTA > alignment search locally ? > Thank you in advance. > You can get FastA from: ftp://ftp.virginia.edu/pub/ you are going to need a beefy computer for big searches, but I like the package and it does quite a lot of cool things. regards, James -- ========= James O. McInerney email: J.mcinerney@nhm.ac.uk Senior Scientific Officer, phone: +44 171 938 9247 Department of Zoology, Fax: +44 171 938 9158 The Natural History Museum, Cromwell Road, London SW7 5BD. ========= From owner-software@net.bio.net Wed Apr 09 23:00:00 1997 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!sprint!news.maxwell.syr.edu!news.visi.net!mur2.odyssey.on.ca!news3.sprint-canada.net!roger.interlynx.net!not-for-mail From: Lars Thomsen Newsgroups: bionet.software Subject: Re: statistics and pharmacology Date: Mon, 07 Apr 1997 17:33:22 -0700 Organization: Interlynx Lines: 24 Message-ID: <33499252.F37@interlynx.net> References: <5i2o8a$jj8@rc1.vub.ac.be> NNTP-Posting-Host: port11.hm.interlynx.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.0b2 (Win95; I) X-Priority: 3 (Normal) GraphPad Prism and you can download a trial version that will run for 30 days from their webpages. http://www.graphpad.com/www/welcome.html You could also try Microcal Origin, but I have both but I think the other is doing a better job and its easier to use (and its free for 30 days) SigmaPlot is another possibility I dont know if they have builtin functions for pharmacology, but I would think so because one of their commercials is that the have tons and tons of inbuilt equations. If you are doing whole cell measurements then I am developing freeware that will be integrated with GraphPad Prism. Best Regards -- Lars Thomsen, MSc PhD 115 South Oval, Hamilton, L8S1R2 Ontario, Canada tlp +1 905 777 0720 fax +1 905 777 0738 email lthomsen@interlynx.net homepage http://home.interlynx.net/~lthomsen From owner-software@net.bio.net Thu Apr 10 23:00:00 1997 Path: biosci!kazusa.or.jp!miyajima From: miyajima@kazusa.or.jp (Nobuyuki Miyajima) Newsgroups: bionet.software Subject: JMGD:Java-based User Interface to the Microbial Genome Database Date: 11 Apr 1997 00:22:24 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 62 Sender: daemon@net.bio.net Distribution: world Message-ID: <199704110723.QAA06335@not1.kazusa.or.jp> NNTP-Posting-Host: net.bio.net Dear colleagues, I'd like to introduce you our Java based WWW-Genome tool, JMGD. You can see examples (Haemophilus influenzae, Mycoplasma genitalium, Methanococcus jannaschii) in http://www.kazusa.or.jp/jmgd/ Source codes are available. ============================================================================ JMGD:Java-based User Interface to the Microbial Genome Database ============================================================================ As the rate of progress in the determination of the whole genome sequencing of microbial organisms increases, we will need to have efficient, ready-to-use tools to publicize the data through WWW as soon as we finish the work. Java-based user interface to the microbial genome database (JMGD) can be used for almost any kind of circular microbial organisms. We use JMGD for the genome sequencing of cyanobacterium we published recently (http://www.kazusa.or.jp/cyanobase/map/java/cmap_small/cmap_sm.html). Java-based highlight-image techniques that were originally developed y Jim Graham(Sun Microsystem) are used in JMGD. JMGD includes all the Java source codes, perl scripts and the cgi scripts that are also used to blink the selected ORFs. The platform-independent aspect of Java makes it easily implemented in any machines used such as UNIX workstations, Macintosh or Windows computers. JMGD has been developed under Sybase, but any other database management systems can be applied to without substantial modifications. JMGD is available from: ftp://ftp.kazusa.or.jp/pub/JMGD/ http://www.kazusa.or.jp/jmgd/ 0. Prerequisites: * software perl 5.003 or later JDK 1.02 (1.1 is not supported in the current release) sybperl 2.06 or later (http://www.perl.com/perl/CPAN/authors/id/MEWP) * OS Solaris 2.5 or later OSF1 3.2 or later * DBMS (Database Management System) SQL Server 10/11 or any other DBMSs can be used. ----------------------------------------------- Nobuyuki Miyajima Kazusa DNA Research Institute Department of Genome Informatics, Chief Researcher 1532-3 Yana, Kisarazu, Chiba 292, Japan TEL: +81-438-52-3917 FAX: +81-438-52-3918 E-mail: miyajima@kazusa.or.jp From owner-software@net.bio.net Thu Apr 10 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news-peer.gsl.net!news-peer.sprintlink.net!news.sprintlink.net!sprint!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!paladin.american.edu!news.ecn.uoknor.edu!munnari.OZ.AU!metro!metro!news From: Phillip Robinson Newsgroups: bionet.software Subject: Re: alignment software Date: Fri, 11 Apr 1997 17:15:35 +1000 Organization: Information Technology Services, The University of Sydney, NSW, Australia Lines: 19 Distribution: inet Message-ID: <334DE517.35F9@mail.usyd.edu.au> References: <5iic0h$39s$1@vishnu.jussieu.fr> NNTP-Posting-Host: modem-b-56.mp.usyd.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Michel SEIGNEURET wrote: > > Dear Collegues. > My question is probably trivial but I am a newcomer to this field and > I could not find a FAQ on this. > I currently often do BLAST or FASTA searches of particular protein sequences > against the SWISSPROT or PIR databases though the WWW. The problem is that the > internet connection of my lab is slow. I am thus thinking of doing such > searches locally after downloading the complete database. Could somebody > suggest me a freely available software that allows one to do a BLAST or FASTA > alignment search locally ? > Thank you in advance. I believe you need the PC-based Windows program AnTheProt. Available from: http://www.ibcp.fr:80/antheprot.html At least, I use it and think it is magic. Phil Sydney, Australia From owner-software@net.bio.net Thu Apr 10 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!newsfeeds.sol.net!news.maxwell.syr.edu!news.msfc.nasa.gov!bcm.tmc.edu!news From: Kim Worley Newsgroups: bionet.software Subject: Re: alignment software Date: Fri, 11 Apr 1997 09:33:05 -0500 Organization: Baylor College of Medicine Lines: 31 Message-ID: <334E4BA1.20CA@bcm.tmc.edu> References: <5iic0h$39s$1@vishnu.jussieu.fr> NNTP-Posting-Host: dot.imgen.bcm.tmc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5 sun4m) To: Michel SEIGNEURET To avoid having to wait for the Web searches to complete, I recommend the Search Launcher Batch Client, a Unix and Macintosh application that automatically 1) reads-in sequences from one or more input files, 2) runs a specified search in the background for each sequence, and 3) stores each of the search output files as individual HTML documents directly on a user's system. The result files can be browsed at any later date using Mosaic or Netscape. For users who wish to perform a particular search on a number of sequences at a time, the batch client provides complete access to the Search Launcher with the convenience of batch submission and background operation, greatly simplifying and expediting the search process. Accessing Web based search tools via the Search Launcher Batch Client provides access to the (very) large sequence databases that are changing daily, without having to store and maintain the databases or maintain the search tools locally. Each time the Batch Client is used, it queries the BCM Search Launcher for the most up-to-date list of search tools. The Search Launcher Batch Client v. 2.5 is available from a link (A Batch Client...) on the BCM Search Launcher home page. The BCM Search Launcher (http://gc.bcm.tmc.edu:8088/search-launcher/launcher.html) is an enhanced, integrated, and easy-to-use interface that provides access to a number of different web based sequence analysis services. The Search Launcher extends the functionality of other WWW services by adding additional hypertext links which can be extremely helpful when analyzing database search results. ---------------------------------------------------------------- Kim C. Worley, Ph.D. kworley@bcm.tmc.edu P 713-798-8292 Baylor College of Medicine, Houston, TX 77030 F 713-798-5386 http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html ---------------------------------------------------------------- From owner-software@net.bio.net Thu Apr 10 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news-peer.gsl.net!news-peer.sprintlink.net!news.sprintlink.net!sprint!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!paladin.american.edu!news.ecn.uoknor.edu!munnari.OZ.AU!metro!metro!news From: Phillip Robinson Newsgroups: bionet.software Subject: Re: alignment software Date: Fri, 11 Apr 1997 17:15:23 +1000 Organization: Information Technology Services, The University of Sydney, NSW, Australia Lines: 19 Distribution: inet Message-ID: <334DE50B.25F4@mail.usyd.edu.au> References: <5iic0h$39s$1@vishnu.jussieu.fr> NNTP-Posting-Host: modem-b-56.mp.usyd.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Michel SEIGNEURET wrote: > > Dear Collegues. > My question is probably trivial but I am a newcomer to this field and > I could not find a FAQ on this. > I currently often do BLAST or FASTA searches of particular protein sequences > against the SWISSPROT or PIR databases though the WWW. The problem is that the > internet connection of my lab is slow. I am thus thinking of doing such > searches locally after downloading the complete database. Could somebody > suggest me a freely available software that allows one to do a BLAST or FASTA > alignment search locally ? > Thank you in advance. I believe you need the PC-based Windows program AnTheProt. Available from: http://www.ibcp.fr:80/antheprot.html At least, I use it and think it is magic. Phil Sydnay, Australia From owner-software@net.bio.net Fri Apr 11 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.uth.tmc.edu!news.uh.edu!swrinde!howland.erols.net!europa.clark.net!news.maxwell.syr.edu!newsfeeder.toronto.ican.net!nnrp1.toronto.ican.net!newsfeeder From: ppang@ican.net (Patrick Pang) Newsgroups: bionet.software Subject: Read non-English site with Netscape(3-4) & Internet Explorer(3-4) WITHOUT external viewer Date: Fri, 11 Apr 1997 01:56:41 GMT Organization: Patrick Cyber Domain µê¤Û»â°ì http://ppang.home.ml.org Lines: 17 Message-ID: <33bf95c6.12775944@news.ican.net> NNTP-Posting-Host: ppp-138.toronto-03.ican.net Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Forte Agent 1.0/32.390 Find out how to configure Chinese, Japanese, Korean & PanEuro as well) viewing with Netscape(3.0-4.0 PR3) and Internet Explorer (3.0-4.0 Beta1) under English Windows 95/NT WITHOUT external viewer. Also, find out how to use IE4.0 Outlook Express & Netscape 4.0 Collabra/Messenger to read non-English mail/news. http://ppang.home.ml.org Besdies, the FREE section contains many Free Internet Resources such as free counter, e-mail a/c, guestbook, web space and more. __________ __ \______ \_____ _/ |_ Find out how to setup Netscape & MSIE | ___/\__ \ \ __\ to display Chinese, Japanese, Korean & | | / __ \_ | | Pan Euro without external viewer in |____| (____ / |__| Patrick Cyber Domain µê¤Û»â°ì, ½Ð¦h¦h«ü±Ð \/ Web Page: http://ppang.home.ml.org From owner-software@net.bio.net Sat Apr 12 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!news.apfel.de!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news.sprintlink.net!sprint!news.maxwell.syr.edu!news.visi.net!mur2.odyssey.on.ca!news3.sprint-canada.net!roger.interlynx.net!not-for-mail From: Lars Thomsen Newsgroups: bionet.software Subject: Re: Patch clamp software Date: Sat, 12 Apr 1997 14:23:54 -0700 Organization: Interlynx Lines: 19 Message-ID: <334FFD6A.2F4C@interlynx.net> References: NNTP-Posting-Host: port144.hm.interlynx.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.0b2 (Win95; I) X-Priority: 3 (Normal) Get the whole cell version here : http://physiology.cup.cam.ac.uk/Software/ftp.html Im also working on some patch clamp analysis software and you can get it at : http://home.interlynx.net/~lthomsen/preader Password for zipped file : preader17 My program reads the Axon file format and needs Win95 and a screen resolution of 800x600 -- Lars Thomsen, MSc PhD 115 South Oval, Hamilton, L8S1R2 Ontario, Canada tlp +1 905 777 0720 fax +1 905 777 0738 email lthomsen@interlynx.net homepage http://home.interlynx.net/~lthomsen From owner-software@net.bio.net Sat Apr 12 23:00:00 1997 Path: biosci!roche.com!takeshi.komatani From: takeshi.komatani@roche.com (Zicke Zacke) Newsgroups: bionet.software Subject: medline Date: 13 Apr 1997 08:49:07 -0700 Organization: F.Hoffmann - La Roche Ltd Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <334C9AE9.4560@roche.com> Reply-To: takeshi.komatani@roche.com NNTP-Posting-Host: net.bio.net does anybody know how to import medline data from http://www4.ncbi.nlm.nih.gov/PubMed/ Thanks in advance ======= KOMATANI, Takeshi $B6pC+9d;V(J takeshi.komatani@roche.com PhD candidate(Pharmaceutical Sciences) From owner-software@net.bio.net Sun Apr 13 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!news.uoregon.edu!tezcat!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!ott.istar!news.istar.net!tor.istar!east.istar!ftn.net!passport.ca!news From: Ryan Burns Newsgroups: bionet.agroforestry,bionet.plants,bionet.software,sci.bio.botany Subject: Field Data Collection Date: Mon, 14 Apr 1997 09:32:44 -0400 Organization: Fieldworker Lines: 14 Message-ID: <335231FC.36AE@fieldworker.com> Reply-To: webmaster@fieldworker.com NNTP-Posting-Host: pm3-tor-05.passport.ca Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0Gold (Win95; I) Xref: biosci bionet.agroforestry:5274 bionet.plants:15052 bionet.software:18338 sci.bio.botany:4467 FieldWorker is data collection software which runs on a handheld computer. We now support UTM coordinates for your field data collection, in addition to latitude and longitude from GPS receivers Export collected data into any desktop mapping or GIS package. Need more info on this portable affordable solution? FieldWorker’s website now features an interactive online demo at http://www.fieldworker.com/ -- ==================================================================== Ryan Burns, Webmaster Download FieldWorker 2.3 Demo!..at http://www.fieldworker.com Navigation, Differential GPS, Offset, Relational Map, Multi-lingual! FieldWorker - Handheld PC data collection linked to GPS -- FieldWorker Products Ltd.-- Tel: +1 416 483 3485 ==================================================================== From owner-software@net.bio.net Sun Apr 13 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!gatech!smash.gatech.edu!news From: Jing Li Newsgroups: bionet.software Subject: Postscript file Date: Mon, 14 Apr 1997 18:10:12 -0400 Organization: Georgia Institute of Technology Lines: 11 Message-ID: <3352AB44.67E7@prism.gatech.edu> NNTP-Posting-Host: acmex.gatech.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) Is any one can tell me what program to use for creating a postscript file so that the postscript file can be printed out on any postscript printer, and no just the specified printer. The reason is that I need to put the postscript file onto my home page in the world wide web so that others can download it and print it. Thank you very much. Jing Li mailto:jl98@prism.gatech.edu From owner-software@net.bio.net Sun Apr 13 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!gatech!smash.gatech.edu!news From: Jing Li Newsgroups: bionet.software Subject: Postscript file Date: Mon, 14 Apr 1997 18:07:57 -0400 Organization: Georgia Institute of Technology Lines: 13 Message-ID: <3352AABD.5F0@prism.gatech.edu> NNTP-Posting-Host: acmex.gatech.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) Dear Friends: Is any one can tell me what program to use for creating a postscript file so that the postscript file can be printed out on any postscript printer, and no just the specified printer. The reason is that I need to put the postscript file onto my home page in the world wide web so that others can download it and print it. Thank you very much. Jing Li mailto: jl98@prism.gatech.edu From owner-software@net.bio.net Sun Apr 13 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!nih.gov!usenet From: bernard@elsie.nci.nih.gov (Bernard Murray) Newsgroups: bionet.software Subject: Re: Free practical programs for molecular biologists !!! Date: 14 Apr 1997 20:43:50 GMT Organization: National Institutes of Health, Bethesda, MD Lines: 17 Message-ID: <5iu4u6$ib4@light.nih.gov> References: <3351ECE2.44DA@vetvir.unizh.ch> NNTP-Posting-Host: ermintrude.nci.nih.gov X-Newsreader: WinVN 0.99.7 In article <3351ECE2.44DA@vetvir.unizh.ch>, rolfk@vetvir.unizh.ch says... > >I wrote a few practical and simple to use programs [snip] Rolf, I think you have a problem with your news submission software as I am receiving this message at least once a week and I doubt if you are updating your software so frequently (actually I'm not personally interested in it). Could you make the necessary change(s) to cut down on the traffic? Much appreciated, 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 13 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.maxwell.syr.edu!news.magicnet.net!magicnet.magicnet.net!pmod From: pmod@magicnet.net (Peter M. O'Donnell) Newsgroups: bionet.software.gcg,bionet.software,comp.sys.sun.wanted,comp.sys.sun.hardware Subject: Re: Solaris 2.x on a Pentium? Followup-To: bionet.software.gcg,bionet.software,comp.sys.sun.wanted,comp.sys.sun.hardware Date: 14 Apr 1997 21:07:09 GMT Organization: MagicNet, Inc. Lines: 24 Distribution: world Message-ID: <5iu69t$403$1@comet3.magicnet.net> References: NNTP-Posting-Host: magicnet.magicnet.net X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.software.gcg:2360 bionet.software:18345 comp.sys.sun.wanted:19891 comp.sys.sun.hardware:46096 Albert Gold (bgold@ktb.net) wrote: : I know that SUN apparently makes an OS which clearly will run : upon Pentium machines, called X86, but that system is : NOT Solaris. nope. it is indeed solaris. there is solaris for the sparc family, and there is solaris for the x86 (intels). : Has anybody tried running Solaris on a Pentium machine? Does it work? it absolutely does, and work very very well. bang the search engines to get a clue^H^H^H^Hfaq. [silly glossary chopped] uh, a lot of that was either wrong, or misleading. like i said, check out the faqs. -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Peter M. O'Donnell } pmod@magicnet.net { "If you are going to A.U. Student,CNA,MCP { pmod@abs.net } walk on thin ice, you "Clickity-Clickity" } po0115a@american.edu { might as well dance!" From owner-software@net.bio.net Sun Apr 13 23:00:00 1997 Path: biosci!agate!dog.ee.lbl.gov!overload.lbl.gov!news.emf.net!gatech!smash.gatech.edu!news From: Jing Li Newsgroups: bionet.software,comp.ai,comp.groupware,comp.infosystems,comp.misc Subject: Postscript file: help me please!!! Date: Mon, 14 Apr 1997 18:21:57 -0400 Organization: Georgia Institute of Technology Lines: 10 Message-ID: <3352AE05.1DA9@prism.gatech.edu> NNTP-Posting-Host: acmex.gatech.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (Win95; I) Xref: biosci bionet.software:18349 comp.ai:30411 comp.groupware:8000 comp.infosystems:8578 comp.misc:29018 Is any one can tell me how to create a postscript file so that the file can be printed out on any postscript printer, and no just a specified printer. The reason is that I need to put some documents onto my home page in the world wide web so that others can download it and print it. Thank you very much. Jing Li mailto:jl98@prism.gatech.edu From owner-software@net.bio.net Sun Apr 13 23:00:00 1997 Path: biosci!biosci!not-for-mail From: Albert Gold Newsgroups: bionet.software.gcg,bionet.software,comp.sys.sun.wanted,comp.sys.sun.hardware Subject: Solaris 2.x on a Pentium? Date: 14 Apr 1997 12:48:36 -0700 Organization: KTB Internet Online Lines: 45 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: Albert Gold NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software.gcg:2358 bionet.software:18342 comp.sys.sun.wanted:19890 comp.sys.sun.hardware:46095 Readers of this note probably know that GCG's Wisconsin Package is supported by only a limited number of Operating Systems. None of these to my knowledge runs on an inexpensive Pentium or Power-Mac. machine. Reading the back of one of the 'Partition Magic' -like software boxes today (boot level OS option), I came upon the word 'Solaris' as an OS possibility. I know that SUN apparently makes an OS which clearly will run upon Pentium machines, called X86, but that system is NOT Solaris. I know from taking these newsgroups seriously that SunOS was originally based upon BSD, but apparently 'Solaris' departed from this initiative and moved to incorporate several DEC Fortran extensions, which GCG relies upon. Solaris 2.3 and 2.4 are supportable GCG Operating Systems. Has anybody tried running Solaris on a Pentium machine? Does it work? [Short Glossary] GCG= Genetics Computer Group Sun= Sun Microsystems Inc. DEC= Digital Equipment Corporation Solaris= Unix operating system incorporating C shells, Korn Shells and Bourne shells with old Berkeley Unix (with AT&T Bell Labs) specifically designed? for Sun Microsystem computers. OS or OSs= Operating Systems BSD= Berkeley Software Design, a form of unix of which one is apparently free and available for downloading all over the net, commonly called Free BSD, and one is costly and available from Berkeley Software Design Incorporated of Colorado (1-800-800-BSDI). X86= A form of Unix sold by Sun Microsystems which apparently runs on Pentium machines. SunOS= An early form of the Sun Microsystems Operating System which was based on the unix designed by authors at U. Cal. at Berkeley and those