From owner-gcg@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Iosif Vaisman Newsgroups: bionet.general,bionet.biophysics,bionet.molbio.proteins,bionet.molec-model,bionet.molbio.methds-reagnts,bionet.software,bionet.structural-nmr,bionet.xtallography,bionet.cellbiol,bionet.jobs,bionet.software.gcg,bionet.molbio.bio-matrix Subject: Computational Molecular Biology Workshop, October 15-19, 1996 Date: 5 Sep 1996 15:03:54 -0700 Organization: The University of North Carolina at Chapel Hill Lines: 47 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.general:23165 bionet.biophysics:2276 bionet.molbio.proteins:8677 bionet.molec-model:1132 bionet.molbio.methds-reagnts:48854 bionet.software:16470 bionet.structural-nmr:1480 bionet.xtallography:2850 bionet.cellbiol:5405 bionet.software.gcg:1978 bionet.molbio.bio-matrix:755 CAROLINA WORKSHOPS University of North Carolina at Chapel Hill Computational Molecular Biology October 15 - 19, 1996 This course is designed for scientists with limited prior experience in computational molecular biology. The topics to be covered include: biomolecular informatics and databases, protein and nucleic acid sequence analysis and alignment, 3D protein structure analysis and prediction, molecular modeling and dynamic simulations of proteins and nucleic acids, and structure-based drug design. The workshop will consist of the in-depth theoretical lectures and intensive hands-on laboratory sessions. CAROLINA WORKSHOPS are intensive hands-on courses designed to teach cutting edge methods in molecular biology and biotechnology. Four or five courses on different topics in molecular biology and/or biotechnology are offered each year. The courses are designed for novice students as well as for individuals with prior experience. All students benefit from in-depth interaction with instructors. To apply, send a curriculum vitae and a brief letter describing your research interests and their relevance to the Workshop. Applicants should contact the program office as soon as possible. Please indicate your complete mailing address and telephone/fax number. Application Deadline-September 7, 1996. Tuition - $ 1,200.00. Participation is limited to 15 people. COURSE DIRECTOR: Alexander Tropsha, Ph.D., University of North Carolina at Chapel Hill INSTRUCTORS: Frank K. Brown (Oxford Molecular) David C. Richardson (Duke University) Wayne Litaker (UNC-Chapel Hill) Alexander Tropsha (UNC-Chapel Hill) Michael Mitchell (UNC-Chapel Hill) Iosif I. Vaisman (UNC-Chapel Hill) For further information or to apply, contact: Dr. Wayne Litaker, Facility Director University of North Carolina at Chapel Hill Program in Molecular Biology & Biotechnology 442 Taylor Hall CB 7100 Chapel Hill, North Carolina 27599-7100 TELEPHONE (919) 966-1730, FAX (919) 966-6821 E-MAIL litaker@med.unc.edu From owner-gcg@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!news3.cac.psu.edu!news.cse.psu.edu!rutgers!mcrcr6!cmcl2!news.nyu.edu!mcrcr1.med.nyu.edu!user Newsgroups: bionet.software.gcg Subject: New GCG version 9 Message-ID: From: browns02@mcrcr.med.nyu.edu (Stuart M. Brown) Date: Thu, 05 Sep 1996 13:23:17 -0500 Organization: NYU-MC Research Computing Resource NNTP-Posting-Host: mcrcr1.med.nyu.edu Lines: 11 I am working with a Beta version of GCG v9 and having some problems getting it configured- especailly the SRS stuff. Has anyone successfully got this installed this on a VMS machine? If so, please e-mail me, I could use some help. -- Stuart M. Brown, Molecular Biology Consultant NYU-MC Research Computing Resource, Dept. of Cell Biology 550 First Ave, New York, NY 10016 Phone: (212)263-7689 FAX: (212)263-8139 From owner-gcg@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!CCR.DSI.UANL.MX!pearl From: pearl@CCR.DSI.UANL.MX ("Dr. Paul R.Earl") Newsgroups: bionet.software.gcg Subject: BIOMX, ELECTRONIC JOURNAL Date: 5 Sep 1996 15:13:19 -0700 Organization: UANL Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <322F6D78.3C68@ccr.dsi.uanl.mx> NNTP-Posting-Host: net.bio.net Please see http://www.uanl.mx/biomx or enter Biomx in Yahoo search to get the HomePage. Thank you for your kind attention. Best Wishes, Dr Paul R Earl From owner-gcg@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!Norway.EU.net!mcsun!EU.net!www.nntp.primenet.com!nntp.primenet.com!newspump.sol.net!uwm.edu!lll-winken.llnl.gov!usenet From: Chris Barry Newsgroups: bionet.software.gcg Subject: GCG-->FASTA Date: Fri, 06 Sep 1996 08:50:06 -0700 Organization: Lawrence Livermore National Lab Lines: 4 Message-ID: <3230482E.4061621@llnl.gov> NNTP-Posting-Host: mackiller.llnl.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; Linux 1.1.72 i486) How do you convert a GCG sequence to a FASTA sequence? or save a sequence as a FASTA sequence from GCG? Chris From owner-gcg@net.bio.net Thu Sep 05 23:00:00 1996 Newsgroups: bionet.software.gcg Path: biosci!daresbury!hgmp.mrc.ac.uk!ebi.ac.uk!stoehr From: stoehr@ebi.ac.uk (Peter Stoehr) Subject: re: FETCH wont find............ Sender: news@ebi.ac.uk (Mr news) Message-ID: <1996Aug28.133730@ebi.ac.uk> Date: Wed, 28 Aug 1996 13:37:30 GMT Lines: 20 References: <321C9D26.537@bbsrc.ac.uk> Organization: European BioInformatics Institute In article <321C9D26.537@bbsrc.ac.uk>, Aengus Stewart writes: > > I was under the impression that accession numbers were unique across both protein and DNA > but today completely at random I selected A25909 and pulled entries from embl and PIR. > > I take it that acc nums are only unique within one type of sequence? > They are unique between the nucleotide databases (EMBL/GenBank/DDBJ) and SWISS-PROT. 'A' accession numbers are assigned to sequences taken from patent applications at EMBL. All single letter accession number prefixes are used by the nucleotide databases, except O, P and Q. P and Q are used by SWISS-PROT, and when they are all used up SWISS-PROT will use accession numbers which do not conflict with nucleotide ones. Regards, Peter Stoehr EMBL - EBI From owner-gcg@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!rsvs.ulaval.ca!proy From: proy@rsvs.ulaval.ca (Paul Roy) Newsgroups: bionet.software.gcg Subject: Re: GCG-->FASTA Date: 6 Sep 1996 09:59:16 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 23 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <3230482E.4061621@llnl.gov> NNTP-Posting-Host: net.bio.net On Fri, 6 Sep 1996, Chris Barry wrote: > How do you convert a GCG sequence to a FASTA sequence? or save a > sequence as a FASTA sequence from GCG? > > Chris > > There is a specific GCG program just for this : TOFASTA ****************************************************************************** Paul H. Roy Phone: +1 418 654 2705 Departement de biochimie,FSG FAX: +1 418 654 2715 Universite Laval E-mail: proy@rsvs.ulaval.ca Quebec, QC G1K 7P4 CANADA ****************************************************************************** From owner-gcg@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!cam-news-hub1.bbnplanet.com!cpk-news-feed2.bbnplanet.com!cpk-news-hub1.bbnplanet.com!newsserver.jvnc.net!crick.bms.com!usenet From: John Watson Newsgroups: bionet.software.gcg Subject: Re: GCG-->FASTA Date: Fri, 06 Sep 1996 13:58:31 -0400 Organization: Bristol-Myers Squibb Company Lines: 14 Message-ID: <32306647.12E2@bms.com> References: <3230482E.4061621@llnl.gov> Reply-To: watson_j@bms.com NNTP-Posting-Host: s107_static_223.wf.bms.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) Chris Barry wrote: > > How do you convert a GCG sequence to a FASTA sequence? or save a > sequence as a FASTA sequence from GCG? You can use the TOFASTA command to convert GCG Files to FastA files. Use the FROMFASTA command to go the other way. ---------------- John Watson Bristol-Myers Squibb Co. watson_j@bms.com --------------------------------------------------------------------- "If you're not part of the solution, you're part of the precipitate." --------------------------------------------------------------------- From owner-gcg@net.bio.net Sat Sep 07 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!brighton.openmarket.com!wizard.pn.com!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.gcg Subject: Re: New GCG version 9 Date: 8 Sep 1996 12:43:24 GMT Organization: EMBL Heidelberg Lines: 14 Distribution: world Message-ID: <50uf1c$qua@lion.embl-heidelberg.de> References: NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) X-URL: news:browns02-0509961323170001@mcrcr1.med.nyu.edu SRS installation should be easy compare to gcg. Could you tell what kind problems you have ? Ramu -- =============================================================== Ramu C | EMBL E-mail: chenna@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 356229 (Res) | 69012 Heidelberg Fax: (49) 6221 387517 | Germany http://www.embl-heidelberg.de/~chenna/ ------------------------------------------------------------- From owner-gcg@net.bio.net Sat Sep 07 23:00:00 1996 Path: biosci!agate!newsgate.duke.edu!solaris.cc.vt.edu!homer.alpha.net!uwm.edu!lll-winken.llnl.gov!fnnews.fnal.gov!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software.gcg Subject: Re: GCG-->FASTA Date: 8 Sep 1996 16:42:41 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 16 Message-ID: <50ut21$def@gap.cco.caltech.edu> References: <3230482E.4061621@llnl.gov> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu In article <3230482E.4061621@llnl.gov>, Chris Barry writes: >How do you convert a GCG sequence to a FASTA sequence? or save a >sequence as a FASTA sequence from GCG? > Use TOFASTA to convert (part of GCG). You could also use "readseq" from W. Pearson, I think I picked that up from ftp.bio.indiana.edu. There is no switch to use with the other GCG programs that will have them output in FASTA format. Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-gcg@net.bio.net Sat Sep 07 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!mr.net!newshub.tc.umn.edu!fu-berlin.de!news.th-darmstadt.de!uni-erlangen.de!winx03!wpxx02!not-for-mail From: krasel@wpxx02.toxi.uni-wuerzburg.de (Cornelius Krasel) Newsgroups: bionet.software.gcg Subject: Re: GCG-->FASTA Date: 8 Sep 1996 17:44:44 GMT Organization: University of Wuerzburg, Germany Lines: 17 Message-ID: <50v0mc$3mu@winx03.informatik.uni-wuerzburg.de> References: <3230482E.4061621@llnl.gov> <50ut21$def@gap.cco.caltech.edu> NNTP-Posting-Host: wpxx02.toxi.uni-wuerzburg.de X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] mathog@seqaxp.bio.caltech.edu wrote: > In article <3230482E.4061621@llnl.gov>, Chris Barry writes: > >How do you convert a GCG sequence to a FASTA sequence? or save a > >sequence as a FASTA sequence from GCG? > > Use TOFASTA to convert (part of GCG). You could also use "readseq" from > W. Pearson, I think I picked that up from ftp.bio.indiana.edu. Minor correction: "readseq" is by Don Gilbert, maintainer of ftp.bio.indiana.edu. --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-gcg@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!ken.baker From: ken.baker@bbsrc.ac.uk (Ken Baker) Newsgroups: bionet.software.gcg Subject: Prettybox on A3 Date: Mon, 09 Sep 1996 18:19:08 +0000 Organization: BBSRC Lines: 23 Message-ID: NNTP-Posting-Host: tr0010.cc.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.2.0b13 Does anybody know how to force prettybox to use A3 sized output? We've got output which occupies 2 landscape A4 pages, and we want to print it onto portrait A3. (For those unfamiliar with European paper sizes, A4 is roughly letter-sized, A3 is like two A4's stuck together along their long edges.) The photocopier won't reproduce all those nice halftones 8-(, and we don't have access to a postscript editing package. Anybody got any bright ideas? Thanks in advance, Ken. -- Dr Ken Baker Internet:ken.baker@bbsrc.ac.uk B.I.T.S. BBSRC Computing Centre BritishTelecomnet: (+44)1582 762271 West Common Faxnet: (+44)1582 761710 Harpenden AL5 2JE ICBMnet: 51'48'N 00'21'W From owner-gcg@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Andy Phillips Newsgroups: bionet.software.gcg Subject: Re: Prettybox on A3 Date: Tue, 10 Sep 1996 09:41:02 +0100 Organization: BBSRC, Institute of Arable Crops Research, LARS Lines: 69 Message-ID: <3235299E.69A9@bbsrc.ac.uk> References: NNTP-Posting-Host: pc0628.lars.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01Gold (Win95; I) To: Ken Baker Ken Baker wrote: > > Does anybody know how to force prettybox to use A3 sized output? We've got > output which occupies 2 landscape A4 pages, and we want to print it onto > portrait A3. (For those unfamiliar with European paper sizes, A4 is > roughly letter-sized, A3 is like two A4's stuck together along their long > edges.) > > The photocopier won't reproduce all those nice halftones 8-(, and we don't > have access to a postscript editing package. > > Anybody got any bright ideas? > > Thanks in advance, > > Ken. > > -- > Dr Ken Baker Internet:ken.baker@bbsrc.ac.uk > B.I.T.S. > BBSRC Computing Centre BritishTelecomnet: (+44)1582 762271 > West Common Faxnet: (+44)1582 761710 > Harpenden AL5 2JE ICBMnet: 51'48'N 00'21'W Ken, You don't need a PS editing package - PS files are just text, so you can use a text editor. One of the first postscript commands in the output file (after the list of procedures) is X Y SCALE. This, no surprise, sets the scale of the output, in points, so when you specify 10 point in PRETTYBOX this generates 10 10 SCALE in the output. So one way to produce A3 output is to set the point size in prettybox to generate a portrait A4, then edit the PS file and change the SCALE command to increase scaling: to change A4 to A3, multiply both X and Y scaleings by 1.414 (square root of 2). You can get the postscript interpreter to do this (note that postscript uses reverse notation): X 2 sqrt mul Y 2 sqrt mul scale (I think: I'm not the most competent programmer) This will scale everything up to A3 size. The next problem is that this will scale everything from the origin (bottom left, I think), and it may move your output so it's no longer centred on the page (or even off the page alltogether). To move the output on the page, insert the command X Y translate after the scale command. This will move your output by X scale units (as specified by the scale command) right and Y scale units left. You may have to fiddle with different values of X and Y to get your output centred on the page. I'd recommend using ghostscript to monitor progress: most PS printers don't give error messages by default, you just don't get any output. The Windows front end, ghostview, lets you set the page size (under media). Ghostscript will also tell you what's wrong (or at least you'll get some incomprehensble garbage that will give a hint as to the problem). I wouldn't print from ghostscript as a PS printer will probably do a better job. Give me a ring/email if you run into problems. Andy ------------------------------------------------------------------------ Email : andy.phillips@bbsrc.ac.uk : University of Bristol Home : andy@cycad.demon.co.uk : IACR Long Ashton Research Station Phone : +44-1275-549257 : Long Ashton Fax : +44-1275-394281 : Bristol, BS18 9AF, UK WWW : http://www.lars.bbsrc.ac.uk/plantsci/molbiol/andy.html ------------------------------------------------------------------------ From owner-gcg@net.bio.net Mon Sep 09 23:00:00 1996 Newsgroups: bionet.software.gcg Path: biosci!agate!newsgate.duke.edu!solaris.cc.vt.edu!homer.alpha.net!uwm.edu!news-peer.gsl.net!news.gsl.net!swrinde!cs.utexas.edu!howland.erols.net!vixen.cso.uiuc.edu!newsfeed.internetmci.com!in3.uu.net!EU.net!sun4nl!sci.kun.nl!caos.kun.nl!root From: Jack Leunissen Subject: Embl2Nbrf update Content-Type: text/plain; charset=us-ascii Message-ID: <32356BD3.41C6@caos.kun.nl> Sender: root@caos.kun.nl (System PRIVILEGED Account) Nntp-Posting-Host: cammsg3.caos.kun.nl Content-Transfer-Encoding: 7bit Organization: CAOS/CAMM Center Mime-Version: 1.0 Date: Tue, 10 Sep 1996 13:23:31 GMT X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP22) Lines: 20 Dear Collegues, For the ones that use EMBL2NBRF to generate GCG-compatible sequence libraries from the EMBL flatfiles, a new version of the program has been made available on the CAOS/CAMM FTP server. The new version in- cludes support for the new "GSS" section in EMBL. The URL is "ftp://ftp.caos.kun.nl/pub/molbio/embl2nbrf/" Best regards, Jack -- +--------------------------------------------------------------+ Jack A.M. Leunissen, PhD | CAOS/CAMM Center Email: jackl@caos.kun.nl | University of Nijmegen Tel. : +31 24 365 22 48 | Toernooiveld 1 Fax : +31 24 365 29 77 | 6525 ED Nijmegen, The Netherlands | URL=http://www.caos.kun.nl/ +------- CAOS/CAMM is the Dutch National Node in EMBnet -------+ From owner-gcg@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Andy Phillips Newsgroups: bionet.software.gcg Subject: Re: Prettybox on A3 (PS) Date: Tue, 10 Sep 1996 09:48:19 +0100 Organization: BBSRC, Institute of Arable Crops Research, LARS Lines: 71 Message-ID: <32352B53.3505@bbsrc.ac.uk> References: NNTP-Posting-Host: pc0628.lars.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01Gold (Win95; I) To: Ken Baker Ken Baker wrote: > > Does anybody know how to force prettybox to use A3 sized output? We've got > output which occupies 2 landscape A4 pages, and we want to print it onto > portrait A3. (For those unfamiliar with European paper sizes, A4 is > roughly letter-sized, A3 is like two A4's stuck together along their long > edges.) > > The photocopier won't reproduce all those nice halftones 8-(, and we don't > have access to a postscript editing package. > > Anybody got any bright ideas? > > Thanks in advance, > > Ken. > > -- > Dr Ken Baker Internet:ken.baker@bbsrc.ac.uk > B.I.T.S. > BBSRC Computing Centre BritishTelecomnet: (+44)1582 762271 > West Common Faxnet: (+44)1582 761710 > Harpenden AL5 2JE ICBMnet: 51'48'N 00'21'W P.S. (pun intended) You can also use the postscript language to put colour into your prettybox files. I wrote the enclosed routines to replace the existing ones in the prettybox output. You can specific the colour of boxes using RGB notation, then output to a Deskjet (or even a slidemaker) using Ghostview. /docolor { %do coloured boxes with black letters newpath setrgbcolor 2 copy moveto box moveto 0 setgray .22 .2 rmoveto show } def /black { %red box, black letter 1 0.1 0.1 docolor } def /white { %white box, black letter 1 doblack } def /dark { %dark pink box, black letter 1.0 0.3 0.3 docolor } def /light { %pink box, black letter 1.0 0.5 0.5 docolor } def /pale { %pale pink box, black letter 1 0.7 0.7 docolor } def Andy ------------------------------------------------------------------------ Email : andy.phillips@bbsrc.ac.uk : University of Bristol Home : andy@cycad.demon.co.uk : IACR Long Ashton Research Station Phone : +44-1275-549257 : Long Ashton Fax : +44-1275-394281 : Bristol, BS18 9AF, UK WWW : http://www.lars.bbsrc.ac.uk/plantsci/molbiol/andy.html ------------------------------------------------------------------------ From owner-gcg@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!ken.baker From: ken.baker@bbsrc.ac.uk (Ken Baker) Newsgroups: bionet.software.gcg Subject: Re: Prettybox on A3 Date: Wed, 11 Sep 1996 16:09:32 +0000 Organization: BBSRC Lines: 90 Message-ID: References: <3235299E.69A9@bbsrc.ac.uk> NNTP-Posting-Host: tr0010.cc.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.2.0b13 In article <3235299E.69A9@bbsrc.ac.uk>, Andy Phillips wrote: > Ken Baker wrote: > > > > Does anybody know how to force prettybox to use A3 sized output? We've got > > output which occupies 2 landscape A4 pages, and we want to print it onto > > portrait A3. (For those unfamiliar with European paper sizes, A4 is > > roughly letter-sized, A3 is like two A4's stuck together along their long > > edges.) > > > > The photocopier won't reproduce all those nice halftones 8-(, and we don't > > have access to a postscript editing package. > > > > Anybody got any bright ideas? > > > > Thanks in advance, > > > > Ken. > > > > -- > > Dr Ken Baker Internet:ken.baker@bbsrc.ac.uk > > B.I.T.S. > > BBSRC Computing Centre BritishTelecomnet: (+44)1582 762271 > > West Common Faxnet: (+44)1582 761710 > > Harpenden AL5 2JE ICBMnet: 51'48'N 00'21'W > > Ken, > > You don't need a PS editing package - PS files are just text, so you can use a text editor. > > One of the first postscript commands in the output file (after the list of procedures) is X Y > SCALE. This, no surprise, sets the scale of the output, in points, so when you specify 10 point > in PRETTYBOX this generates > > 10 10 SCALE > > in the output. So one way to produce A3 output is to set the point size in prettybox to generate > a portrait A4, then edit the PS file and change the SCALE command to increase scaling: to change > A4 to A3, multiply both X and Y scaleings by 1.414 (square root of 2). You can get the > postscript interpreter to do this (note that postscript uses reverse notation): [edit] > Andy Yep, Andy is right. Actually I knew that postscript is text; what I didn't know was which bits to edit. Anyway, with Andy's help we've now cracked it. In case anybody else get the same problem: here's the answer:- Prettybox/linesize=60/fontsize=7 and select portrait That sets the scale line in the postscript output to 7 7 scale edit it to read 10 10 scale (10 being about 1.414 x 7) and print to an A3 printer. What you get is the output which formerly occupied 2 landscape pages of A4 on one landscape page of A3. It wasn't necessary to translate it positionally. Presumably something analogous could be be done if the output was larger. Cheers, Ken. -- Dr Ken Baker Internet:ken.baker@bbsrc.ac.uk B.I.T.S. BBSRC Computing Centre BritishTelecomnet: (+44)1582 762271 West Common Faxnet: (+44)1582 761710 Harpenden AL5 2JE ICBMnet: 51'48'N 00'21'W From owner-gcg@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!faseb.org!cpk-news-feed1.bbnplanet.com!cpk-news-feed2.bbnplanet.com!cam-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!newsfeed.randomc.com!news.miracle.net!usenet From: Thomas Zucker-Scharff Newsgroups: bionet.software.gcg Subject: mycobacteria codon table? Date: Wed, 11 Sep 1996 14:57:27 +0500 Organization: Albert Einstein College of Medicine Lines: 12 Message-ID: <32368D07.42A2@leper1.ca.aecom.yu.edu> Reply-To: zucker@aecom.yu.edu NNTP-Posting-Host: slug.ca.aecom.yu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b6Gold (Win16; I) One of my users asked for a mycobacteria codon table. I have not found one yet, does anyone know where I could get such an animal? Tom -- ___________________________________________________________________________________ | Thomas Zucker-Scharff | VOICE: 718-430-3512 | | Director, Scientific Computing Facility | FAX: 718-822-6538 | | Albert Einstein College of Medicine | BEEPER: 917-632-6416 | | 1300 Morris Park Ave. | E-MAIL: gcghelp@aecom.yu.edu | | Bronx, New York 10461 | WWW: http://www.ca.aecom.yu.edu | ----------------------------------------------------------------------------------- From owner-gcg@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!aecom.yu.edu!zucker From: zucker@aecom.yu.edu (Thomas Zucker-Scharff) Newsgroups: bionet.software.gcg Subject: mycobacteria codon usage table Date: 11 Sep 1996 11:39:04 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 15 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Does anybody know of a codon usage table for mycobacteria? One of my users just requested it. --------------------------------------------------------------------------- Thomas Zucker-Scharff | PH: 718-430-3512 Director, Scientific Computer Facility | FAX: 718-430-8550 Albert Einstein Cancer Center | BEEPER: 917-632-6416 Albert Einstein College of Medicine | EMAIL: scicomp@aecom.yu.edu 1300 Morris Park Avenue | WWW: http://www.ca.aecom.yu.edu Bronx, New York 10461 | --------------------------------------------------------------------------- From owner-gcg@net.bio.net Wed Sep 11 23:00:00 1996 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.gcg Subject: Re: mycobacteria codon table? Date: Wed, 11 Sep 1996 05:22:31 +0100 Organization: SEQNET Lines: 32 Distribution: bionet Message-ID: <32363E87.41C6@dl.ac.uk> References: <32368D07.42A2@leper1.ca.aecom.yu.edu> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) Thomas Zucker-Scharff wrote: > > One of my users asked for a mycobacteria codon table. I have not found > one yet, does anyone know where I could get such an animal? > > Tom > -- > The SRS-server (http://www.seqnet.dl.ac.uk/srs/srsc )at SEQNET allows access to the cutg (codon usage tables tabulated from genbank), reformatted in gcg-format. From the SRS start page, select cutg from the 'Search libraries of bioinformatics information' option. A search for the organism name mycobacterium will give you codon usage tables for a variety of mycobacteria Martin -- --------------------------------------------------------------------------- | Martin Hilbers | E-mail: m.p.hilbers@dl.ac.uk | | SEQNET | Tel: +44-1925-603492 | | Daresbury Laboratory | Fax: +44-1925-603100 | | Daresbury, Warrington |----------------------------------------------| | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.dl.ac.uk/SEQNET/home.html | --------------------------------------------------------------------------- From owner-gcg@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.gov!fnnews.fnal.gov!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software.gcg Subject: Re: Migrating to Unix: SGI vs. SUN Date: 13 Sep 1996 18:47:35 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 70 Message-ID: <51ca87$88c@gap.cco.caltech.edu> References: <1996Sep12.155933@bphvax> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu In article <1996Sep12.155933@bphvax>, caal@bphvax.biophysics.rochester.edu (Charles A. Alexander) writes: >Hello > >We're presently evaluating the pros and cons of migrating our GCG >package to a UNIX platform. It seems like a lot of the freeware >biocomputing apps are being written for UNIX and though I love my VAX >and VMS System Management, it seems like I would be doing my users a >disservice by not providing at least the option of other software. > >We also want to provide molecular modelling tools for the people we >support and it seems that SGI and SUNS have a lot of tools available for >these applications as well. If you're going to be doing molecular modeling you need an SGI that isn't going to be used for anything else. It pretty much has to be an SGI because all the molecular modeling software runs on them, but only a few packages run on each of the other platforms. Until such time as all of this software gets rewritten to OpenGL I don't see much likelihood of that changing. I don't know about your users, but 95% of mine hate Unix as much as VMS. They aren't so fond of GCG either ("You mean we need to remember the name of the program to run? It uses a what, command line interface???") but when they use it enough, generally come to appreciate that it works quite well. Still, for the last couple of years, up until about a year ago, they were demanding something that was Mac or Windows native (as appropriate). Now, they pretty much expect everything to pop up in Netscape. Lord only knows what will be trendy next year :-(. Bottom line, most of them won't like GCG on Unix any more than they like it now on VMS. after all it's the same thing except for the minor interface change of "/" vs. "-" and the case sensitivity problems. You will find that more software runs out of the box on Unix systems, primarily because somebody else has already made the OS specific changes that the programs need. Well written ANSI C compliant code runs on anything, but you won't find as much of that in the public domain as you might wish. I've ported scads of "Unix" programs to OpenVMS, rarely is it much work, there are usually fewer "ifdefs" for OpenVMS than between the Unix variants. For instance, I added practically nothing to get the last version of the NCBI toolbox running. In other words, for most things, the fact that a program was written on a Unix system is irrelevant - it just processes data, and it will do that with small changes on any other platform. However, I do still run into programs that are not in ANSI C, or worse, are Sun or SGI specific (usually for no good reason, just lazy programming.) On the other hand, WNT is clearly winning the OS wars, and if you have a lot of PCs around (we don't, almost all Macs) you *will* eventually be running WNT servers. If you have enough cash, go and buy that SGI for modeling. Then buy an Alpha, go with OpenVMS (if you don't want to retrain your users) or Digital Unix (if having a bit more software matters). Then later on you can shift the thing over to WNT if you need to. That should keep you in business for about 5 years, which is the prediction limit anyway. If you want a pure SGI shop (which would simplify your life) buy a second one to run GCG on, but get a server with minimal graphics (you don't want people modeling and database crunching on the same machine). Hint, since SGI changed around their licenses you should more seriously consider getting an SMP capable machine, since otherwise you have to buy extra licenses for extra capacity. SMP works great on our two processor 2100. Odd that in industry HP seems to be the most common Unix platform, but they are rare in academia. GCG doesn't even support it, either not enough demand, or maybe some major incompatibility with the GCG software? Regards, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-gcg@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Andy Phillips Newsgroups: bionet.software.gcg Subject: Re: GCG version 9 under VMS? Date: Fri, 13 Sep 1996 17:22:20 +0100 Organization: BBSRC, Institute of Arable Crops Research, LARS Lines: 23 Message-ID: <32398A3C.208F@bbsrc.ac.uk> References: <3239177E.4F3A@bbsrc.ac.uk> NNTP-Posting-Host: pc0628.lars.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01Gold (Win95; I) Andy Phillips wrote: > > A while ago I heard that the next version (9) of the GCG package will run > only on Unix machines and not under VAX/VMS. However, I can find no > information about this on the GCG Web page. Is there any truth in this > rumour? > > Thanks for any info. > > Andy I've now had a number of emails/news that indicate that this rumour is completely untrue. Thanks for all the info. Andy ------------------------------------------------------------------------ Email : andy.phillips@bbsrc.ac.uk : University of Bristol Home : andy@cycad.demon.co.uk : IACR Long Ashton Research Station Phone : +44-1275-549257 : Long Ashton Fax : +44-1275-394281 : Bristol, BS18 9AF, UK WWW : http://www.lars.bbsrc.ac.uk/plantsci/molbiol/andy.html ------------------------------------------------------------------------ From owner-gcg@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!daresbury!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.gcg Subject: Re: GCG version 9 under VMS? Date: 13 Sep 1996 15:42:37 GMT Organization: The Sanger Centre Lines: 23 Message-ID: References: <3239177E.4F3A@bbsrc.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: Andy Phillips's message of Fri, 13 Sep 1996 09:12:46 +0100 In article <3239177E.4F3A@bbsrc.ac.uk> Andy Phillips writes: > A while ago I heard that the next version (9) of the GCG package will run > only on Unix machines and not under VAX/VMS. However, I can find no > information about this on the GCG Web page. Is there any truth in this > rumour? See the latest Transcript Newsletter on the GCG Web pages: http://www.gcg.com/pub/newsletter/vol4_no1_jun96.html VMS *is* still supported. VAX/VMS 5.5-2 and 6.1 are dropped. VAX/VMS 6.2 is supported. It is ULTRIX that has vanished from the supported Digital OS list. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division, E-mail: pmr@sanger.ac.uk | The Sanger Centre, Tel: (44) 1223 494967 | Wellcome Trust Genome Campus, Fax: (44) 1223 494919 | Hinxton, Cambridge, CB10 1SA, URL: http://www.sanger.ac.uk/~pmr/ | England From owner-gcg@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!nntp.primenet.com!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-angers.fr!ciril.fr!usenet From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software.gcg Subject: Re: Migrating to Unix: SGI vs. SUN Date: 13 Sep 1996 08:32:37 GMT Organization: IGBMC Lines: 59 Message-ID: <51b675$21d@arcturus.ciril.fr> References: <1996Sep12.155933@bphvax> NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.6 In article <1996Sep12.155933@bphvax>, caal@bphvax.biophysics.rochester.edu (Charles A. Alexander) writes: >Hello > [...]> >We also want to provide molecular modelling tools for the people we >support and it seems that SGI and SUNS have a lot of tools available for >these applications as well. Don't try to run molecular modelling tools on a server! I mean, if you want to use one of Whatif, Quanta, o, setor, molscript and so on to do molecular modelling, it's better to dedicate a Indigo2 or an SGI like that (that's what we do), else you will make interactives remote processes really slow. >Anybody have any recommendations on what kind of machines would be >able to handle the kind of processing power required for both these >applications for a peak load of about 10-15 users simultaneously. We >have a total of about 50 users and growing. We have about 600 users, with pics at 30-40 users. we use a Sparc server 1000 E (4 processors). I think, it's better to use a multiprocessor machine. Note that we build our SRS indexes on a DEC calculator (from Xtallography group, thanks ;-) >I don't want to start a holy war but should we look at Suns or SGIs ? >Anybody care to share their experiences ? How stable are the OS' and >how difficult are they to manage. My limited experience tells me that >SGIs are easier to handle. I'll apologize in advance if my ignorance >is showing. I use or used GCG on all of those machines, and I "feel" the better configuration to be a DEC server with 2 or 3 processors. An Indigo for molecular modelling. We also recently put our external server (for SRS, GCGdoc and so on) on another Sparc server (sparc20). >Thanks in advance. BTW, anybody have an updated spec sheet on how GCG >performs on various platforms ? Of course, all of this depends of the money you have, because a DEC 2500, 3 proc, is quite expensive... If this helps, Francois. P.S.: I don't think that a UNIX system is secure, and it gives some problems to users to understand how it works...Sorry. -- Francois Jeanmougin Service de bioinformatique / bioinformatics service IGBMC BP 163 67404 Illkirch France tel : (33) 88 65 32 71 e-mail : jeanmougin@igbmc.u-strasbg.fr "Si les choses ne sont pas ce qu'elles sont, c'est qu'elles ne sont pas ce qu'elles devraient etre" Pierre Dac "citant" De Gaulle. From owner-gcg@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Andy Phillips Newsgroups: bionet.software.gcg Subject: GCG version 9 under VMS? Date: Fri, 13 Sep 1996 09:12:46 +0100 Organization: BBSRC, Institute of Arable Crops Research, LARS Lines: 15 Message-ID: <3239177E.4F3A@bbsrc.ac.uk> NNTP-Posting-Host: pc0628.lars.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01Gold (Win95; I) A while ago I heard that the next version (9) of the GCG package will run only on Unix machines and not under VAX/VMS. However, I can find no information about this on the GCG Web page. Is there any truth in this rumour? Thanks for any info. Andy ------------------------------------------------------------------------ Email : andy.phillips@bbsrc.ac.uk : University of Bristol Home : andy@cycad.demon.co.uk : IACR Long Ashton Research Station Phone : +44-1275-549257 : Long Ashton Fax : +44-1275-394281 : Bristol, BS18 9AF, UK WWW : http://www.lars.bbsrc.ac.uk/plantsci/molbiol/andy.html ------------------------------------------------------------------------ From owner-gcg@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!www.nntp.primenet.com!nntp.primenet.com!arclight.uoregon.edu!usenet.eel.ufl.edu!warwick!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!tjrc1 From: tjrc1@mole.bio.cam.ac.uk (Tim Cutts) Newsgroups: bionet.software.gcg Subject: Re: Migrating to Unix: SGI vs. SUN Date: 13 Sep 1996 07:17:31 GMT Organization: University of Cambridge Lines: 86 Message-ID: <51b1qb$mj8@lyra.csx.cam.ac.uk> References: <1996Sep12.155933@bphvax> NNTP-Posting-Host: mole.bio.cam.ac.uk In article <1996Sep12.155933@bphvax>, Charles A. Alexander wrote: >Hello > >We're presently evaluating the pros and cons of migrating our GCG >package to a UNIX platform. It seems like a lot of the freeware >biocomputing apps are being written for UNIX and though I love my VAX >and VMS System Management, it seems like I would be doing my users a >disservice by not providing at least the option of other software. > >We also want to provide molecular modelling tools for the people we >support and it seems that SGI and SUNS have a lot of tools available for >these applications as well. > >Anybody have any recommendations on what kind of machines would be >able to handle the kind of processing power required for both these >applications for a peak load of about 10-15 users simultaneously. We >have a total of about 50 users and growing. mole.bio.cam.ac.uk is a three year-old SGI Indigo2 with a 150MHz R4400 and 128Mb RAM. Not a stupendous machine at all, and we are looking to replace it soon. However, we are trying to do what you are doing, but on a rather larger scale; mole has 1,500 users, with usually 30-40 logged in at any one time during the day. FASTA searches are getting a bit slow these days, which is why we want a more powerful machine. However, it seems that an SGI workstation would probably suit you quite well. However, *don't* to molecular visualisation on the same machine; you will kill the interactive performance of the remote users. Our protein modelling group uses SGI Indigo2 machines as well for their NMR work, and are very happy with them. I can't speak for Sun machines really, but it seems that the majority of the bioinformatics world are either using SGI or DEC. We have a Digital Alpha machine on loan at the moment for evaluation. A 250MHz ev5 Alpha processor seems to be about on a par with a 195 MHz R10000, although the R10000 might have a slight edge in our tests. Having said that, so far I prefer IRIX to DEC Unix. IRIX seems to have more flexible process sheduling, and this is very important if you buy a single processor machine which is also going to handle interactive tasks such as e-mail (which ours does). With multi-processor machines this is less of a problem because you can restrict certain functions to certain processors. >I don't want to start a holy war but should we look at Suns or SGIs ? You should definitely consider DEC as well. It also gives you the flexibility to run OpenVMS if your users (or you) decide they loathe UNIX :-) Or even Windows NT; a fair bit of software seems to be being ported to it these days. >Anybody care to share their experiences ? How stable are the OS' and >how difficult are they to manage. We used to use VAXen, although this was before I joined. In many ways UNIX is much more messy than VMS (according to my boss/predecessor), and it's probably less secure. However, IRIX is pretty stable (as long as you use a 'standard' version, which at the moment means 5.3 or 6.2). mole runs quite happily for months without a reboot. I only had to shut it down last week because a hard disk failed (joy!). >My limited experience tells me that >SGIs are easier to handle. I'll apologize in advance if my ignorance >is showing. Well, I know very little about VMS, so I can't really compare. >Thanks in advance. BTW, anybody have an updated spec sheet on how GCG >performs on various platforms ? Don't trust these things. The comparisons are always totally ludicrous. In our tests so far, on a Dec AlphaServer 2100 5/250 and an SGI Indigo2 with a 195MHz R10000 processor, both machines are about 3x as fast as the 150MHz R4400 doing either GCG or Pearson FASTA searches. From the SGI data I have seen, performance scales rather better with multiple processors on SGIs than on DECs, but you'd expect SGI benchmarks to say that, of course. Tim. -- -------------------------------------------------------------------------- Dept. of Biochemistry Tel: +44 1223 333596 Tennis Court Rd. Cambridge, CB2 1QW, UK From owner-gcg@net.bio.net Thu Sep 12 23:00:00 1996 Newsgroups: bionet.software.gcg Path: biosci!rutgers!uwm.edu!news.sol.net!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!arclight.uoregon.edu!news.sprintlink.net!news-peer.sprintlink.net!news-peer.gsl.net!news.gsl.net!portc01.blue.aol.com!newsstand.cit.cornell.edu!newstand.syr.edu!hood.cc.rochester.edu!bphvax!caal From: caal@bphvax.biophysics.rochester.edu (Charles A. Alexander) Subject: Migrating to Unix: SGI vs. SUN Message-ID: <1996Sep12.155933@bphvax> Followup-To: bionet.software.gcg Lines: 27 Sender: news@galileo.cc.rochester.edu Nntp-Posting-Host: bphvax.biophysics.rochester.edu Reply-To: caal@bphvax.biophysics.rochester.edu Organization: University of Rochester, Rochester, New York Date: 12 Sep 96 15:59:33 EST Lines: 27 Hello We're presently evaluating the pros and cons of migrating our GCG package to a UNIX platform. It seems like a lot of the freeware biocomputing apps are being written for UNIX and though I love my VAX and VMS System Management, it seems like I would be doing my users a disservice by not providing at least the option of other software. We also want to provide molecular modelling tools for the people we support and it seems that SGI and SUNS have a lot of tools available for these applications as well. Anybody have any recommendations on what kind of machines would be able to handle the kind of processing power required for both these applications for a peak load of about 10-15 users simultaneously. We have a total of about 50 users and growing. I don't want to start a holy war but should we look at Suns or SGIs ? Anybody care to share their experiences ? How stable are the OS' and how difficult are they to manage. My limited experience tells me that SGIs are easier to handle. I'll apologize in advance if my ignorance is showing. Thanks in advance. BTW, anybody have an updated spec sheet on how GCG performs on various platforms ? - Charles Alexander From owner-gcg@net.bio.net Sun Sep 15 23:00:00 1996 Path: biosci!MIMER.SCS.UIUC.EDU!cole From: cole@MIMER.SCS.UIUC.EDU (Ronald N. Cole) Newsgroups: bionet.software.gcg Subject: Hello GCG Gurus. Date: 15 Sep 1996 18:38:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <199609151815.NAA17395@mimer.scs.uiuc.edu> NNTP-Posting-Host: net.bio.net Hi, I am faced with a simple, but labor intensive task. I have a large list of pdb files (466 to be exact). I would like to turn this list into a list of accession numbers. I then want to do a pileup on all of these sequences. Does anyone know of an automated or even semi-automated way of doing this? I can write scripts or do any programming necessary. I just want to know the best way to approach this. Thanks in Advance, Skip Cole ************************************************************************** * Skip Cole (aka Ron Cole) * Calculation performed; * * cole@mimer.scs.uiuc.edu * Fast, Reliable or Meaningful. * * (217)355-5308 * Pick any 2 * ************************************************************************** From owner-gcg@net.bio.net Sun Sep 15 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.uoregon.edu!news-peer.gsl.net!news.gsl.net!news-dc.gsl.net!news.gsl.net!hookup!news.nstn.ca!newsflash.concordia.ca!torn!resunix.sickkids.on.ca!resunix.sickkids.on.ca!not-for-mail From: greig@resunix.sickkids.on.ca (David Iain Greig) Newsgroups: bionet.software.gcg Subject: Re: Migrating to Unix: SGI vs. SUN Date: 15 Sep 1996 10:29:03 -0400 Organization: NMR Core Facility, Dept. of Biochemistry, University of Ediacara Lines: 33 Message-ID: <51h3rf$71j@resunix.sickkids.on.ca> References: <1996Sep12.155933@bphvax> NNTP-Posting-Host: resunix.sickkids.on.ca X-Newsreader: TIN [version 1.2 PL2] Charles A. Alexander (caal@bphvax.biophysics.rochester.edu) wrote: : Hello : We're presently evaluating the pros and cons of migrating our GCG : package to a UNIX platform. It seems like a lot of the freeware ... [snip] Personally, having worked extensively with both Sun and SGI hardware, I'd go (now) with Suns, get an UltraSparc system. Solaris 2.5 is much better than previous versions, the hardware is cheaper, you can attach just about anything to a Sun and expect it to work, etc. SGI's look cooler, have better graphics, and have a nifty bunch of networked games like BattleZone and dogfight. They do tend to be fussier about peripherals. An R10000 Power Challenge or Indigo2 R10k is faster than an UltraSparc[*], (but not a ton faster) so if price isn't an obstacle, go wild. All of the above is just my opinion, mind. =] [*] based on the latest benchmark summary obtainable from ftp://ftp.cdf.utoronto.ca/pub/spectable --D. ---- David Iain Greig, UNIX System Administrator Tel: (416) 813-5013 Research Computing Services Fax: (416) 813-7099 Hospital for Sick Children, 555 University Ave, Toronto, Ont. M5G 1X8 greig@sickkids.on.ca "Arbor plena allouatarum" From owner-gcg@net.bio.net Sun Sep 15 23:00:00 1996 Path: biosci!faseb.org!cpk-news-feed1.bbnplanet.com!cpk-news-feed2.bbnplanet.com!cpk-news-hub1.bbnplanet.com!www.nntp.primenet.com!nntp.primenet.com!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!in3.uu.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.gcg Subject: Re: Migrating to Unix: SGI vs. SUN Date: 16 Sep 1996 08:22:01 GMT Organization: The Sanger Centre Lines: 35 Message-ID: References: <1996Sep12.155933@bphvax> <51ca87$88c@gap.cco.caltech.edu> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: mathog@seqaxp.bio.caltech.edu's message of 13 Sep 1996 18:47:35 GMT David Mathog writes: >Odd that in industry HP seems to be the most common Unix platform, but they >are rare in academia. GCG doesn't even support it, either not enough >demand, or maybe some major incompatibility with the GCG software? There is indeed a major incompatibility. HP Fortran behaves quite differently to *all* the GCG-supported Unix Fortrans. To port EGCG programs to HP (the German Cancer Research Centre support HP versions somewhere) I would have to add "//Char(0)" to every character string constant in every program. It's still standard Fortran of course, but I would much rather forget about HP. Even AIX was easier than this. The worst one in AIX was changing '???' to '?'//'?'//'?' because the preprocessor wants to treat ??? as a triptych. Oops, I forgot. Also I had to convert TAB-delimited Fortran continuation lines to spaces because AIX, alone of the GCG-supported systems, tabs to a different column. All these are Fortran problems of course. I fully agree that plain ANSI C is not too difficult to support across platforms, at least when converting Unix to VMS. The other way round is often trickier. ------------------------------------------------------------------------ Peter Rice | Informatics Division, E-mail: pmr@sanger.ac.uk | The Sanger Centre, Tel: (44) 1223 494967 | Wellcome Trust Genome Campus, Fax: (44) 1223 494919 | Hinxton, Cambridge, CB10 1SA, URL: http://www.sanger.ac.uk/~pmr/ | England -- ------------------------------------------------------------------------ Peter Rice | Informatics Division, E-mail: pmr@sanger.ac.uk | The Sanger Centre, Tel: (44) 1223 494967 | Wellcome Trust Genome Campus, Fax: (44) 1223 494919 | Hinxton, Cambridge, CB10 1SA, URL: http://www.sanger.ac.uk/~pmr/ | England From owner-gcg@net.bio.net Tue Sep 17 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!gondor!newsfeeder.sdsu.edu!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!panix!cmcl2!news.nyu.edu!mcrcr1.med.nyu.edu!user From: browns02@mcrcr.med.nyu.edu (Stuart M. Brown) Newsgroups: bionet.software.gcg Subject: Re: Hello GCG Gurus. Date: Tue, 17 Sep 1996 13:19:02 -0500 Organization: NYU-MC Research Computing Resource Lines: 43 Distribution: world Message-ID: References: <199609151815.NAA17395@mimer.scs.uiuc.edu> NNTP-Posting-Host: mcrcr1.med.nyu.edu In article <199609151815.NAA17395@mimer.scs.uiuc.edu>, cole@MIMER.SCS.UIUC.EDU (Ronald N. Cole) wrote: > Hi, > I am faced with a simple, but labor intensive task. I have a large > list of pdb files (466 to be exact). I would like to turn this list into a > list of accession numbers. I then want to do a pileup on all of these > sequences. I would be very interested to learn your solution to this problem. I have figured out a very clumsy workaround. First, I edit a list of seq. names (produced by FASTA/NoHis/NoAlign) to get a pure list of names with no extra text, then I use DATASET to turn the list into a GCG data library. Then I use TOFASTA to create a concatenated list of all sequences. Then I use CLUSTAL to do the alignment. I have not been able to use PILEUP on more than about 20 sequences of varying length due to the 2000 gap limitation. The only way around this is to limit each seq. to the region that will align well (begin and end #'s). > > Does anyone know of an automated or even semi-automated way of doing > this? I can write scripts or do any programming necessary. I just want to > know the best way to approach this. > > > Thanks in Advance, > Skip Cole > > ************************************************************************** > * Skip Cole (aka Ron Cole) * Calculation performed; * > * cole@mimer.scs.uiuc.edu * Fast, Reliable or Meaningful. * > * (217)355-5308 * Pick any 2 * > ************************************************************************** -- Stuart M. Brown, Molecular Biology Consultant NYU-MC Research Computing Resource, Dept. of Cell Biology 550 First Ave, New York, NY 10016 Phone: (212)263-7689 FAX: (212)263-8139 From owner-gcg@net.bio.net Tue Sep 17 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!gondor!newsfeeder.sdsu.edu!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!panix!cmcl2!news.nyu.edu!mcrcr1.med.nyu.edu!user From: browns02@mcrcr.med.nyu.edu (Stuart M. Brown) Newsgroups: bionet.software.gcg Subject: Re: GCG version 9 under VMS? Date: Tue, 17 Sep 1996 13:12:44 -0500 Organization: NYU-MC Research Computing Resource Lines: 27 Message-ID: References: <3239177E.4F3A@bbsrc.ac.uk> NNTP-Posting-Host: mcrcr1.med.nyu.edu In article <3239177E.4F3A@bbsrc.ac.uk>, Andy Phillips wrote: > A while ago I heard that the next version (9) of the GCG package will run > only on Unix machines and not under VAX/VMS. However, I can find no > information about this on the GCG Web page. Is there any truth in this > rumour? > > Thanks for any info. > > Andy > ------------------------------------------------------------------------ > Email : andy.phillips@bbsrc.ac.uk : University of Bristol > Home : andy@cycad.demon.co.uk : IACR Long Ashton Research Station > Phone : +44-1275-549257 : Long Ashton > Fax : +44-1275-394281 : Bristol, BS18 9AF, UK > WWW : http://www.lars.bbsrc.ac.uk/plantsci/molbiol/andy.html > ------------------------------------------------------------------------ GCG v9 will support both UNIX and VMS versions. I am running a Beta test version of GCG v9 on a DEC 2100 VMS machine. -- Stuart M. Brown, Molecular Biology Consultant NYU-MC Research Computing Resource, Dept. of Cell Biology 550 First Ave, New York, NY 10016 Phone: (212)263-7689 FAX: (212)263-8139 From owner-gcg@net.bio.net Tue Sep 17 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!nntp.primenet.com!cpk-news-hub1.bbnplanet.com!newsfeed.internetmci.com!in1.uu.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.gcg Subject: Re: Hello GCG Gurus. Date: 18 Sep 1996 08:02:59 GMT Organization: The Sanger Centre Lines: 40 Distribution: world Message-ID: References: <199609151815.NAA17395@mimer.scs.uiuc.edu> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: cole@MIMER.SCS.UIUC.EDU's message of 15 Sep 1996 18:38:09 -0700 In article <199609151815.NAA17395@mimer.scs.uiuc.edu> cole@MIMER.SCS.UIUC.EDU (Ronald N. Cole) writes: > I am faced with a simple, but labor intensive task. I have a large > list of pdb files (466 to be exact). I would like to turn this list into a > list of accession numbers. I then want to do a pileup on all of these > sequences. > > Does anyone know of an automated or even semi-automated way of doing > this? I can write scripts or do any programming necessary. I just want to > know the best way to approach this. Clearly a task for SRS. No, not the lame version in GCG 8.x - you need the real SRS for this. 1. Make a list of PDB entries in a file 2. Use this as a query (@filename) in SRS 3. Link it to SwissProt and (nagically) you have the full set of sequences you need: % getz "@filename > SWISSPROT" I guess what you really want to do is to use PileUp to get the tree of related sequences, rather than a full alignment - or maybe they really do align. Anyway, you can try further tests in SRS, like looking for PROSITE motifs to see whether your PDB entries share a common motif - then you could of course just align around that part. If you have HSSP, you can also look for alignments directly from your PDB entries. You can try the bionet.software.srs for more help on SRS. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division, E-mail: pmr@sanger.ac.uk | The Sanger Centre, Tel: (44) 1223 494967 | Wellcome Trust Genome Campus, Fax: (44) 1223 494919 | Hinxton, Cambridge, CB10 1SA, URL: http://www.sanger.ac.uk/~pmr/ | England From owner-gcg@net.bio.net Tue Sep 17 23:00:00 1996 Path: biosci!COURRIER.USHERB.CA!jp.perre From: jp.perre@COURRIER.USHERB.CA (Jean-Pierre Perreault) Newsgroups: bionet.software.gcg Subject: (none) Date: 18 Sep 1996 10:37:42 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net unsuscribe Laboratoire Jean-Pierre Perreault Departement de Biochimie Centre Universitaire de Sant=E9 de l'Estrie From owner-gcg@net.bio.net Tue Sep 17 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!gondor!newsfeeder.sdsu.edu!news.sgi.com!enews.sgi.com!arclight.uoregon.edu!news.sprintlink.net!news-peer.sprintlink.net!howland.erols.net!cam-news-hub1.bbnplanet.com!cam-news-feed5.bbnplanet.com!umass.edu!nic.umass.edu!titan.oit.umass.edu!not-for-mail From: stacy@titan.oit.umass.edu (STACY A CIUFO) Newsgroups: bionet.software.gcg Subject: GCG access available Date: 16 Sep 1996 23:29:36 GMT Organization: University of Massachusetts, Amherst Lines: 29 Message-ID: <51knt0$sgl@nic.umass.edu> NNTP-Posting-Host: titan.oit.umass.edu X-Newsreader: TIN [UNIX 1.3 950824BETA PL0] Dear Researchers, Access to the GCG package is now available to educational and other nonprofit groups. Our UNIX system runs Solaris (SUNOS 5.3) and maintains daily updated databases. Access to the system is via telnet. A standard account includes 2.5 meg disk space, unlimited access, and unlimited user help. The yearly fee for educational and nonprofit groups is a modest $250/year. Additional disk space is also available is desired, and we handle all GCG lisencing considerations. Need custom work done? Ask about our nucleotide and protein data analysis services. For more information, contact: Stacy Ciufo Molecular Biology / Biotechnology Computing Center Department of Microbiology University of Massachusetts Amherst, MA 01003 (413) 545-1936 ciufo@rna.micro.umass.edu From owner-gcg@net.bio.net Wed Sep 18 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!www.nntp.primenet.com!nntp.primenet.com!cpk-news-hub1.bbnplanet.com!newsserver.jvnc.net!weblizard.bms.com!usenet From: John Watson Newsgroups: bionet.software.gcg Subject: GCG on a Multiprocessor SGI? Date: Thu, 19 Sep 1996 11:29:47 -0400 Organization: Bristol-Myers Squibb Company Lines: 23 Message-ID: <324166EB.213F@bms.com> Reply-To: watson_j@bms.com NNTP-Posting-Host: s107_static_223.wf.bms.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) My company has just decided to start a bioinformatics group (better late than never ;-> ). Anyway I am told that the bioinformatics stuff will run on a multiprocessor SGI system. I assume this means a SGI Power Challenge System, or are there other multiprocessor SGI's out there? I'm also assuming that there are plans to run molecular modelling stuff on the same machine. As an end-user who relies heavily on GCG and related molecular biology computing applications, I'd like to know -- is this a good system for running all this stuff on? Oh, and I am told that the equipment budget is on the order of $250K. Does this sound right? Thanks for any input. AJW ---------------- John Watson Bristol-Myers Squibb Co. watson_j@bms.com --------------------------------------------------------------------- "If you're not part of the solution, you're part of the precipitate." --------------------------------------------------------------------- From owner-gcg@net.bio.net Wed Sep 18 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!news.sprintlink.net!news-peer.sprintlink.net!EU.net!Austria.EU.net!01-newsfeed.univie.ac.at!swidir.switch.ch!in2p3.fr!univ-lyon1.fr!ws41.cnusc.fr!ciril.fr!u-strasbg.fr!news From: Frederic PLEWNIAK Newsgroups: bionet.software.gcg Subject: Re: Hello GCG Gurus. Date: Thu, 19 Sep 1996 16:57:22 +0200 Organization: IGBMC Lines: 19 Message-ID: <32415F52.5579@igbmc.u-strasbg.fr> References: <199609151815.NAA17395@mimer.scs.uiuc.edu> NNTP-Posting-Host: didon.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b7 (X11; I; SunOS 5.5 sun4m) Hi, > > Hi, > I am faced with a simple, but labor intensive task. I have a large >list of pdb files (466 to be exact). I would like to turn this list into a >list of accession numbers. I then want to do a pileup on all of these >sequences. > Some time ago I turned a copy of GCG's 'Dataset' into 'PDBToGCG'. It is able to read PDB files (provided there is a SEQRES field in there ;o) ) and create a GCG type protein sequence database. You may have it if you wish. I made it available at : ftp://ftp-igbmc.u-strasbg.fr/pub/PDBToGCG Best regards, Fred From owner-gcg@net.bio.net Thu Sep 19 23:00:00 1996 Path: biosci!rutgers!uwm.edu!cs.utexas.edu!swrinde!news.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!sun4nl!uva.nl!amc!news From: "J.F.Hellings" Newsgroups: bionet.software.gcg Subject: Q:Running EGCG8.1 on Solaris 2.4 Date: Wed, 18 Sep 1996 18:28:44 +0200 Organization: AMC Lines: 15 Message-ID: <3240233C.112D@amc.uva.nl> NNTP-Posting-Host: divg-janpc.amc.uva.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02Gold (Win95; I) CC: j.f.hellings@amc.uva.nl, M.huijberts@amc.uva.nl Dear GCG users Is there anybody out there how succeed in getting EGCG running with Solaris 2.4. The problem is linking Fortran compiled files with C compiled files I have tried it with a simple program but I failed. What exact versions of Fortran and C do you need to get the things runnig. Is it possible to get the executables from someone who succeed in installing EGCG on Solaris 2.4? Thanks for all the help Yours ***************************Jan Hellings********************************** Academic hospital of the Phone: (+31) 20 5665067 ** 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-gcg@net.bio.net Thu Sep 19 23:00:00 1996 Path: biosci!biosci!not-for-mail From: pingouin@crystal.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software,bionet.software.gcg,bionet.molbio.evolution Subject: ClustalW on-line help Date: 20 Sep 1996 13:44:50 -0700 Organization: IGBMC Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <51tp8l$7c8@arcturus.ciril.fr> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.software:16585 bionet.software.gcg:2015 bionet.molbio.evolution:5039 Hi all, I'm pleased to announce an html version of the clustalw 1.6 documentation and on-line help. This is experimental and any suggestions are welcome. The URL is : http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/ For those who are using our website regularly, please note the new address (old address will be out of date soon): Home Page: http://www-igbmc.u-strasbg.fr/ Bioinformatics pages: http://www-igbmc.u-strasbg.fr/BioInfo/ Francois. -- Francois Jeanmougin Service de bioinformatique / bioinformatics service IGBMC BP 163 67404 Illkirch France tel : (33) 88 65 32 71 e-mail : jeanmougin@igbmc.u-strasbg.fr "Si les choses ne sont pas ce qu'elles sont, c'est qu'elles ne sont pas ce qu'elles devraient etre" Pierre Dac "citant" De Gaulle. From owner-gcg@net.bio.net Fri Sep 20 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.gcg Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 21 Sep 1996 02:00:40 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199609210900.CAA07229@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-gcg@net.bio.net Sun Sep 22 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.gcg Subject: Re: Q:Running EGCG8.1 on Solaris 2.4 Date: 23 Sep 1996 08:10:59 GMT Organization: The Sanger Centre Lines: 47 Message-ID: References: <3240233C.112D@amc.uva.nl> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: "J.F.Hellings"'s message of Wed, 18 Sep 1996 18:28:44 +0200 In article <3240233C.112D@amc.uva.nl> "J.F.Hellings" writes: > Is there anybody out there how succeed in getting EGCG running with Solaris > 2.4. The problem is linking Fortran compiled files with C compiled files > I have tried it with a simple program but I failed. > What exact versions of Fortran and C do you need to get the things runnig. > Is it possible to get the executables from someone who succeed in > installing EGCG on Solaris 2.4? It is more a question of which compiler versions you have, rather then the Solaris version. Sun added a new library from release 3.0 onwards of the compilers. The 000readme.unix file in EGCG 8.1 was not quite right on this. We actually put the old version of the makefiles in the release, and you have to make the change for the latest versions of Solaris compilers. This was because our Solaris test site still has the old versions. 7a. *** Solaris users only *** If you are using the Solaris 3.0 compilers, you must have the Solaris 3.0.1 versions, and apply Patch #101911 to Fortran. (These are required to build GCG anyway). After some sites reported problems, we now know why the patch is needed :-) If you are using Solaris 3.0 compilers you must edit one of the makefiles to add a Solaris 3.0 library: % to egenmakefiles then edit eoptions.mm and change lines to add "-lsunmath" : STDCLIBS = $stdClibs CEXLIBS = $esharedLib $sharedLib $sharedCFlags $stdClibs to: STDCLIBS = $stdClibs -lsunmath CEXLIBS = $esharedLib $sharedLib $sharedCFlags -lsunmath $stdClibs *** end of Solaris special instructions *** -- ------------------------------------------------------------------------ Peter Rice | Informatics Division, E-mail: pmr@sanger.ac.uk | The Sanger Centre, Tel: (44) 1223 494967 | Wellcome Trust Genome Campus, Fax: (44) 1223 494919 | Hinxton, Cambridge, CB10 1SA, URL: http://www.sanger.ac.uk/~pmr/ | England