From owner-srs@net.bio.net Sun Nov 02 22:00:00 1997 Path: biosci!rutgers!news-relay.ncren.net!newsgate.duke.edu!news.eng.convex.com!cs.utexas.edu!howland.erols.net!ix.netcom.com!news From: IntimateSVC@GetPaid.com Newsgroups: bionet.software.srs Subject: Women Pay You For Intimate Services Date: Sun, 2 Nov 1997 22:13:32 Organization: Netcom Lines: 12 Message-ID: <63jfgf$iqe@dfw-ixnews11.ix.netcom.com> NNTP-Posting-Host: haw-ak1-04.ix.netcom.com X-NETCOM-Date: Sun Nov 02 9:13:19 PM CST 1997 GIRLS PAY YOU FOR YOUR SPECIAL INTIMATE SERVICES Men around the country are making $500 plus weekly in their spare time providing services to lonely women in need. This service can be provided by men just like you. Anyone can provide these services, race, age (over18) , and looks do not matter. Send $2.00 cash for details via Snail Mail, or send $1 cash for details via your E-Mail address. Services, 811 Flushing Ave. Brooklyn, NY 11206 C/O Jeffrey Hardman From owner-srs@net.bio.net Sun Nov 02 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!news.idt.net!ix.netcom.com!news From: IntimateSVC@GetPaid.com Newsgroups: bionet.software.srs Subject: Women Pay You For Intimate Services Date: Sun, 2 Nov 1997 22:13:36 Organization: Netcom Lines: 12 Message-ID: <63jfgj$iqe@dfw-ixnews11.ix.netcom.com> NNTP-Posting-Host: haw-ak1-04.ix.netcom.com X-NETCOM-Date: Sun Nov 02 9:13:23 PM CST 1997 GIRLS PAY YOU FOR YOUR SPECIAL INTIMATE SERVICES Men around the country are making $500 plus weekly in their spare time providing services to lonely women in need. This service can be provided by men just like you. Anyone can provide these services, race, age (over18) , and looks do not matter. Send $2.00 cash for details via Snail Mail, or send $1 cash for details via your E-Mail address. Services, 811 Flushing Ave. Brooklyn, NY 11206 C/O Jeffrey Hardman From owner-srs@net.bio.net Tue Nov 04 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!192.48.96.123!in1.uu.net!netnews.sbphrd.com!not-for-mail From: Ray Wang Newsgroups: bionet.software.srs Subject: indexing TREMBLNEW Date: Wed, 05 Nov 1997 17:21:24 -0500 Organization: SmithKline Beecham Pharmaceuticals Research & Development Lines: 12 Message-ID: <3460F164.10AB@mh.us.sbphrd.com> NNTP-Posting-Host: phu824.sbphrd.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5.1 sun4u) Hello, I am indexing TREMBLNEW in SRS5.05 using SPTREMBL format. But when I search TREMBLNEW, nothing shows up below "Sequence Format", check the source code of the HTML display, find that the page doesn't finish. Could someone give an answer to the question? Ray SmithKline Beecham R&D From owner-srs@net.bio.net Tue Nov 04 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: Complex query Date: 05 Nov 1997 12:23:25 +0000 Organization: The Sanger Centre Lines: 36 Sender: pmr@unst Message-ID: References: <63pml7$d9p@caroll.infobiogen.fr> NNTP-Posting-Host: unst.sanger.ac.uk Original-Sender: pmr@sanger.ac.uk X-Newsreader: Gnus v5.3/Emacs 19.34 dessen@lovelace.infobiogen.fr (Philippe Dessen) writes: > How is it possible with wwwgetz (SRS 4 or SRS 5) and the Query Form > to have answer to the following (not very complex) query ? > > Description : topoisomerase > Organism : homo sapiens > Keyword : ! EST > > with ! EST => error > with * ! EST very long query and timeout. > >With 2 queries and combining them (in the Query Manager) no problem, >but this is not optimized ! > >[libs={embl emblnew}-Description: topoisomerase*] & [libs-Organism: homo sapiens*] >[libs={embl emblnew}-Keywords: EST*] > >Query "Q1 ! Q2" found 43 entries It works on the command line (SRS 5) getz "([libs={embl emblnew}-des:topoisomerase] &[libs-org:homo sapiens]) \ ! [libs-key:est]" You need the parentheses around the first two queries, then "not" the third. The query form may not cover the construction you need, so your Q1 and Q2 method may be the best for the Web interface. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Tue Nov 04 22:00:00 1997 Path: biosci!rutgers!uwm.edu!news-out.internetmci.com!newsfeed.internetmci.com!206.229.87.25!news-peer.sprintlink.net!news.sprintlink.net!Sprint!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.ecrc.net!newsfeed.nacamar.de!oleane!jussieu.fr!infobiogen.fr!lovelace.infobiogen.fr!dessen From: dessen@lovelace.infobiogen.fr (Philippe Dessen) Newsgroups: bionet.software.srs Subject: Complex query Date: 5 Nov 1997 11:52:07 GMT Organization: GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France Lines: 68 Message-ID: <63pml7$d9p@caroll.infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL2] How is it possible with wwwgetz (SRS 4 or SRS 5) and the Query Form to have answer to the following (not very complex) query ? Description : topoisomerase Organism : homo sapiens Keyword : ! EST with ! EST => error with * ! EST very long query and timeout. Message : While trying to retrieve the URL: http://www.infobiogen.fr/srs5/cgi-bin/wgetz The following error was encountered: No Object Data This means that: The remote server closed the connection before sending any data. With 2 queries and combining them (in the Query Manager) no problem, but this is not optimized ! [libs={embl emblnew}-Description: topoisomerase*] & [libs-Organism: homo sapiens*] [libs={embl emblnew}-Keywords: EST*] Query "Q1 ! Q2" found 43 entries Elsewhere with ACNUC query is relatively quick : $ acnuc -b genbank **** ACNUC Data Base Content **** GenBank Rel. 103 (15 Octoger 1997) Last Updated: Nov 4, 1997 1,200,675,858 bases; 1,828,859 sequences; 229,363 subseqs; 142,660 references. Command? (H for command list) select k=@topoisomerase@II@ et sp=homo sapiens et no k=EST Sequence list named LIST1 contains 15 seqs (among which 6 subseqs) Short description of list: LIST2 D87012 Human (lambda) DNA for immunoglobin light chain. =40083 bp HSDNAT2 H.sapiens mRNA for DNA topoisomerase II. =702 bp HSTIIIAPR H.sapiens DNA for topoisomerase IIa gene promoter region. =607 bp HSTOP2P3 H.sapiens TOP2 mRNA for DNA topoisomerase II (partial). =3432 bp HSTOP2P5 H.sapiens TOP2 mRNA for DNA topoisomerase II (partial). =1200 bp HSTOPIIB H.sapiens topIIb mRNA for topoisomerase IIb. =4866 bp HSTOPIIB2 H.sapiens topIIb gene for topoisomerase II (partial). =360 bp HSU43431 Human DNA topoisomerase III mRNA, complete cds. =3755 bp HSU54831 Human topoisomerase IIb mRNA, partial cds. =1388 bp HSU96765 Homo sapiens topoisomerase II beta gene, partial cds. =1576 bp HUMBGLOBC Human beta-globin cluster gene, enhancers with repeat region. HUMTOPIIX Homo sapiens topoisomerase type II (Topo II) mRNA, partial cds. Regards Philippe Dessen -- ------------------------------------------------------- Philippe Dessen GIS INFOBIOGEN 7 rue Guy Moquet BP8, 94801 VILLEJUIF Cedex, France tel : +33 1 45 59 52 41 fax : +33 1 45 59 52 50 e-mail : dessen@infobiogen.fr http://www.infobiogen.fr ------------------------------------------------------- From owner-srs@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!howland.erols.net!recycled.news.erols.com!nntp.uio.no!not-for-mail From: Alfredo Chinchilla Newsgroups: bionet.software.srs Subject: Re: Applications as sequences Date: Thu, 06 Nov 1997 09:47:25 +0100 Organization: University of Oslo, Norway Lines: 20 Message-ID: <3461841D.94087B76@biotek.uio.no> References: <34576FAC.EC5FF06D@britbio.co.uk> NNTP-Posting-Host: biotek11.uio.no Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: Tim Dudgeon X-Priority: 3 (Normal) hi tim, in fact we encountered this problem ourselves. We added to the blast output entry the field sequence that is taken from the "subject" sequence, the sequence from the sequence databank that blast found to be similar to the query sequence. This field enables to associate "clustalw" and all other methods to blast entries. We took a slightly different strategy in 5.1. The field "ProtSequence" is now linked to the applications and not $libformat. This means as soon as a databank has a field "ProtSequence" methods on that field apply for entries of the databank regards thure ...there will be at least a prerelease available by the end of november From owner-srs@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: Operating system dependant bug in SRS ? Date: Thu, 06 Nov 1997 16:24:37 +0000 Organization: SEQNET Lines: 15 Distribution: bionet Message-ID: <3461EF45.167E@dl.ac.uk> References: <63sot6$2qf@rc1.vub.ac.be> 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) To: Guy Bottu Guy Bottu wrote: > if we knew the operating systems on which all these SRS servers are > running. > SEQNET (bugged) OSF/1 3.2 -- ------------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/Person.asp?m.p.hilbers | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.seqnet.dl.ac.uk/ | ------------------------------------------------------------------- From owner-srs@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!news-peer.gip.net!news.gsl.net!gip.net!news.maxwell.syr.edu!eerie.fr!jussieu.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: Re: Operating system dependant bug in SRS ? Date: Thu, 06 Nov 1997 17:19:05 +0100 Organization: INFOBIOGEN Lines: 32 Message-ID: <3461EDF9.4E78@infobiogen.fr> References: <63sot6$2qf@rc1.vub.ac.be> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; SunOS 5.5.1 sun4u) To: Guy Bottu Guy Bottu wrote: > > that only some show the same problem : > Institut Pasteur, SEQNET, OUMBCD, Weizmann Institute and of course > BEN > Others do not have the problem : > EBI, INFOBIOGEN, EMBL BMC, CSC, DKFZ, GBF, HGMP, INCBI, IUBio, > Peking University, Sanger Centre and WEHI > > I wonder if there is the problem is not dependant on some detail in > the icarus code and on the operating system. It would be intersting > if we knew the operating systems on which all these SRS servers are > running. I will send this message as E-mail to the SRS server managers. > > We at BEN are using OSF/1 4.0 > > Guy Bottu Hi, we are using Sun Solaris 2.5 (Sparc Entreprise) at INFOBIOGEN Regards -- --------------------------------------------------- Jean-Marc PLAZA INFOBIOGEN - CNRS 7, rue Guy Moquet BP8 94801 VILLEJUIF Cedex, France tel: +33 45 59 52 39 fax: +33 45 59 52 50 e-mail: plaza@infobiogen.fr --------------------------------------------------- From owner-srs@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gip.net!news-dc.gip.net!news.gsl.net!gip.net!news.belnet.be!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Operating system dependant bug in SRS ? Date: 6 Nov 1997 15:48:54 GMT Organization: Belgian EMBnet Node Lines: 23 Message-ID: <63sot6$2qf@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] SRS 5 shows some curious and unpleasant misbehaviour : when I do a search in the EMBL databank and select one or more "Include in list" checkboxes, the first entry appears correct, but after the name of the second entry everything is blank. wgetz at the command line displays a Segmentation fault message. The view manager gives an entirely empty screen. This misbehaviour occurs with EMBL, but not with GENBANK, SWISSPROT or PIR. Furthermore, I checked all the public SRS 5 servers and found that only some show the same problem : Institut Pasteur, SEQNET, OUMBCD, Weizmann Institute and of course BEN Others do not have the problem : EBI, INFOBIOGEN, EMBL BMC, CSC, DKFZ, GBF, HGMP, INCBI, IUBio, Peking University, Sanger Centre and WEHI I wonder if there is the problem is not dependant on some detail in the icarus code and on the operating system. It would be intersting if we knew the operating systems on which all these SRS servers are running. I will send this message as E-mail to the SRS server managers. We at BEN are using OSF/1 4.0 Guy Bottu From owner-srs@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: indexing TREMBLNEW Date: Thu, 06 Nov 1997 09:57:57 +0000 Organization: SEQNET Lines: 36 Distribution: bionet Message-ID: <346194A5.41C6@dl.ac.uk> References: <3460F164.10AB@mh.us.sbphrd.com> 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) To: Ray Wang Ray Wang wrote: > > Hello, > > I am indexing TREMBLNEW in SRS5.05 using SPTREMBL format. But when > I search TREMBLNEW, nothing shows up below "Sequence Format", check > the source code of the HTML display, find that the page doesn't > finish. > > Could someone give an answer to the question? > > Ray > > SmithKline Beecham R&D I had a similar problem, and it seems to be caused by the the fact that the Comment_type and Comment indices are completely empty in tremblnew. Apparently srs does not like empty indices when composing a search form. Removing those fields from the format description solved the problem, but you end up with a new tremblnew format (assuming that you don't want to remove the comments fields in sptrembl as well) Cheers, Martin -- ------------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/Person.asp?m.p.hilbers | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.seqnet.dl.ac.uk/ | ------------------------------------------------------------------- From owner-srs@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!news.idt.net!news1.chicago.iagnet.net!iagnet.net!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: Re: Operating system dependant bug in SRS ? Date: 6 Nov 1997 17:24:34 GMT Organization: Biology, Indiana University - Bloomington Lines: 13 Message-ID: <63sugi$b2n$1@dismay.ucs.indiana.edu> References: <63sot6$2qf@rc1.vub.ac.be> NNTP-Posting-Host: chipmunk.bio.indiana.edu IUbio runs under solaris 2.5. We also use SRS v505 in the flybase mirrors running under DEC OSF (ebi), SGI Irix 6 (astorg.u-strasbg.fr), SunOS 4 (cbbridges.harvard.edu and fly.bio.indiana.edu) and Solaris 2.x on two others. This summer/fall we ran into serious site-specific problems -- when the astorg site upgraded from Irix 5 to Irix 6, and we supplied binaries built under Irix 5, we had various segfault type failures. Replacing those binaries with ones built under Irix 6 seems to have cured the problem. -- Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!192.48.96.125!in3.uu.net!netnews.sbphrd.com!not-for-mail From: Ray Wang Newsgroups: bionet.software.srs Subject: Re: Operating system dependant bug in SRS ? Date: Thu, 06 Nov 1997 15:45:17 -0500 Organization: SmithKline Beecham Pharmaceuticals Research & Development Lines: 31 Message-ID: <34622C5D.63B3@mh.us.sbphrd.com> References: <63sot6$2qf@rc1.vub.ac.be> NNTP-Posting-Host: phu824.sbphrd.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5.1 sun4u) Guy Bottu wrote: > > SRS 5 shows some curious and unpleasant misbehaviour : > when I do a search in the EMBL databank and select one or more > "Include in list" checkboxes, the first entry appears correct, but > after the name of the second entry everything is blank. > wgetz at the command line displays a Segmentation fault message. > The view manager gives an entirely empty screen. > This misbehaviour occurs with EMBL, but not with GENBANK, SWISSPROT > or PIR. Furthermore, I checked all the public SRS 5 servers and found > that only some show the same problem : > Institut Pasteur, SEQNET, OUMBCD, Weizmann Institute and of course > BEN > Others do not have the problem : > EBI, INFOBIOGEN, EMBL BMC, CSC, DKFZ, GBF, HGMP, INCBI, IUBio, > Peking University, Sanger Centre and WEHI > > I wonder if there is the problem is not dependant on some detail in > the icarus code and on the operating system. It would be intersting > if we knew the operating systems on which all these SRS servers are > running. I will send this message as E-mail to the SRS server managers. > > We at BEN are using OSF/1 4.0 > > Guy Bottu We are running Sun Solaris 2.5, and don't have such a problem. Ray SmithKline Beecham Pharmaceuticals R&D From owner-srs@net.bio.net Thu Nov 06 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!news.misty.com!news-xfer.netaxs.com!newsfeed.ecrc.net!newsfeed.nacamar.de!eerie.fr!jussieu.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: lookup (gcg9-srs4.08) and fragments Date: Fri, 07 Nov 1997 10:40:52 +0100 Organization: INFOBIOGEN Lines: 18 Message-ID: <3462E224.3B47@infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; SunOS 5.5.1 sun4u) Hi we have problems to extract fragments from cds features (from genbank) with lookup in GCG9.It makes a segmentation fault. We do not use gcg-srs indices for lookup but SRS indices. we compiled GCG9(SDK) with SRS4.08 sources and the only trouble we have is with option -Frag (It's ok with -ANNotate=FEAture) need help Jean-Marc -- --------------------------------------------------- Jean-Marc PLAZA INFOBIOGEN - CNRS 7, rue Guy Moquet BP8 94801 VILLEJUIF Cedex, France tel: +33 45 59 52 39 fax: +33 45 59 52 50 e-mail: plaza@infobiogen.fr --------------------------------------------------- From owner-srs@net.bio.net Fri Nov 07 22:00:00 1997 Path: biosci!agate!howland.erols.net!news-peer.gip.net!news-dc.gip.net!news.gsl.net!gip.net!news.belnet.be!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Re: lookup (gcg9-srs4.08) and fragments Date: 7 Nov 1997 17:23:29 GMT Organization: Belgian EMBnet Node Lines: 5 Message-ID: <63viqh$i6a@rc1.vub.ac.be> References: <3462E224.3B47@infobiogen.fr> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] I noticed the same problem, already from GCG8.1 - SRS 4.08 on. I do not know if it occurs when you use the indexes made by GCG itself. I am afraid I do not know the solution. Guy Bottu From owner-srs@net.bio.net Mon Nov 10 22:00:00 1997 Path: biosci!rutgers!uwm.edu!newsfeeds.sol.net!europa.clark.net!208.134.241.18!newsfeed.internetmci.com!192.48.96.125!in3.uu.net!netnews.sbphrd.com!not-for-mail From: Ray Wang Newsgroups: bionet.software.srs Subject: Indexing REBASE Date: Tue, 11 Nov 1997 15:58:57 -0500 Organization: SmithKline Beecham Pharmaceuticals Research & Development Lines: 11 Message-ID: <3468C711.438D@mh.us.sbphrd.com> NNTP-Posting-Host: phu824.sbphrd.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5.1 sun4u) Hello, I am indexing REBASE, and always meet serious segmentation Fault when SRS5.05 is building the links between REBASE and SWISSPROT, REBASE and SWISSNEW, REBASE and SPTREMBL, which caused core dump. Would anyone has an answer to solve the problem? Ray SmithKline Beecham Pharmaceuticals R&D From owner-srs@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!rutgers!uwm.edu!news-penn.gip.net!news-peer.gip.net!news.gsl.net!gip.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: Indexing REBASE Date: Wed, 12 Nov 1997 13:24:42 +0000 Organization: EMBL-EBI Lines: 20 Message-ID: <3469AE1A.A8A7A50@ebi.ac.uk> References: <3468C711.438D@mh.us.sbphrd.com> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: Ray Wang X-Priority: 3 (Normal) Ray Wang wrote: > > Hello, > > I am indexing REBASE, and always meet serious segmentation Fault when > SRS5.05 is building the links between REBASE and SWISSPROT, REBASE and > SWISSNEW, REBASE and SPTREMBL, which caused core dump. > > Would anyone has an answer to solve the problem? just in case Martin Hilbers is too busy answering on that himself. He has indexed Rebase on his sites and the links seem to work. http://www.seqnet.dl.ac.uk/srs5/ ...have a look at the rebase information page and copy the Icarus files to your site regards thure From owner-srs@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: Indexing REBASE Date: Wed, 12 Nov 1997 20:19:10 +0000 Organization: SEQNET Lines: 54 Distribution: bionet Message-ID: <346A0F3E.819DFC14@mph-home.dl.ac.uk> References: <3468C711.438D@mh.us.sbphrd.com> <3469AE1A.A8A7A50@ebi.ac.uk> Reply-To: mph@dl.ac.uk NNTP-Posting-Host: mph-home.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (X11; I; Linux 2.0.0 i686) Thure Etzold wrote: > > Ray Wang wrote: > > > > Hello, > > > > I am indexing REBASE, and always meet serious segmentation Fault when > > SRS5.05 is building the links between REBASE and SWISSPROT, REBASE and > > SWISSNEW, REBASE and SPTREMBL, which caused core dump. > > > > Would anyone has an answer to solve the problem? > > just in case Martin Hilbers is too busy answering on that himself. > He has indexed Rebase on his sites and the links seem to work. > > http://www.seqnet.dl.ac.uk/srs5/ > > ...have a look at the rebase information page and copy the Icarus > files to your site > > regards > thure Just one warning - I did a "dirty" trick to create the links between rebase and swissprot - I linked the ID of rebase to the description field of swissprot, asssuming that any occurence of a word like BAMHI in that field indicates a protein which has something to do with that restriction enzyme. And the internal rebase links (ie rebase entry to rebase entry) do not work at the moment - got to find some time to fix that, but for the moment it may be better to comment that line out from the rebase.i file. It may be worthwile to have a look at what I have called "rebcom" as well - it indexes the information about restriction enzyme suppliers in the rebase commdata.nnn file. Cheers, Martin -- ------------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/Person.asp?m.p.hilbers | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.seqnet.dl.ac.uk/ | ------------------------------------------------------------------- From owner-srs@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!rutgers!uwm.edu!news-penn.gip.net!news-dc.gip.net!news-peer.gip.net!news.gsl.net!gip.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: Indexing REBASE Date: 12 Nov 1997 10:13:51 +0000 Organization: The Sanger Centre Lines: 23 Sender: pmr@unst Message-ID: References: <3468C711.438D@mh.us.sbphrd.com> NNTP-Posting-Host: unst.sanger.ac.uk X-Newsreader: Gnus v5.3/Emacs 19.34 Ray Wang writes: > I am indexing REBASE, and always meet serious segmentation Fault when > SRS5.05 is building the links between REBASE and SWISSPROT, REBASE and > SWISSNEW, REBASE and SPTREMBL, which caused core dump. I found the links in SwissProt used new accession numbers in REBASE which are one digit short. Amos promised me he would fix this in the next SwissProt release. SRS 5 picks up the accession number field rather than the enzyme name for links. At Sanger, we index REBASE in the "bairoch.nnn" format, where these accession numbers appear. But now I have learned a little more Icarus, I suppose I could fix it too... Done.... Our swissprot.is now adds the zeros to REBASE accession numbers and finds the links. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!news.misty.com!news-xfer.netaxs.com!newsfeed.direct.ca!news-feed1.tiac.net!news-master.tiac.net!news@tiac.net From: propdig Newsgroups: bionet.software.srs Subject: National Biotech Register(NatBio) New Service Date: Thu, 13 Nov 1997 10:25:07 -0500 Organization: propdig Lines: 5 Message-ID: <346B1BD3.4BAD@barryinc.com> Reply-To: propdig@barryinc.com NNTP-Posting-Host: p11.ts4.lowel.ma.tiac.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0C-NSCP (Win95; U) NatBio, http://www.barryinc.com/bio is pleased to introduce a new service on our web site. A Biotech Industry Company profile search. Are you looking for information on a particular Biotech company? We probably have it. We also invite you to check out your own company. If you are not listed, email us the data and we will add it for free. From owner-srs@net.bio.net Tue Nov 18 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 Nov 1997 02:00:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199711191000.CAA17187@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. From owner-srs@net.bio.net Tue Nov 18 22:00:00 1997 Path: biosci!daresbury!uninett.no!news-feed.ifi.uio.no!recycled.news.erols.com!howland.erols.net!newsfeed.internetmci.com!192.48.96.125!in3.uu.net!netnews.sbphrd.com!not-for-mail From: Ray Wang Newsgroups: bionet.software.srs Subject: Operating System and SRS Date: Wed, 19 Nov 1997 16:55:03 -0500 Organization: SmithKline Beecham Pharmaceuticals Research & Development Lines: 37 Message-ID: <34736037.38E5@mh.us.sbphrd.com> NNTP-Posting-Host: phu824.sbphrd.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5.1 sun4u) CC: etzold@ebi.ac.uk Hello, I was wondering whether SRS has a version which could work properly on Sun Solaris. Recently, I compiled SRS5.0.5 in different machines which run Solaris 2.5.1, and 2.6, using gcc compiler(gcc version 2.7.2.3). None of these compilation run smoothly, major error messages are as following: gcc: unrecognized option `-Xa' sdlnew.c:454: warning: initialization makes integer from pointer without a cast ...... I also tried to use cc compiler to compile SRS5.0.5 in a Sun Solaris machine, the compilation was also quite bad. Now we are running SRS5.0.5 server in a Sun Ultra 2 machine, which was compiled using gcc compiler in Solaris 2.5.1. We ignored the warning messages before. But we are sufferring several malfunctions od SRS, such as the table below the three buttons in the View Manager page doesn't show up, etc. I also met problems to index gcg format EMBL databank, the whole GENBANK. Both of these databanks's ID fields could not be indexed, and the process stopped because of core dump. I did try to compile SRS5.0.5 in a SGI IRIX 6.2 machine, which ran quite smoothly without a single error. But quite sadly, that is not our machine, so we couldn't set up a SRS server on that machine. Hope SRS developing team can answer the question whether SRS has a version which could run properly under Sun Solaris. Thanks. Ray SmithKline Beecham Pharmaceuticals R&D From owner-srs@net.bio.net Wed Nov 19 22:00:00 1997 Path: biosci!rutgers!uwm.edu!news1.chicago.iagnet.net!news2.chicago.iagnet.net!iagnet.net!129.79.5.185!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: Re: Operating System and SRS Date: 20 Nov 1997 11:54:23 GMT Organization: Biology, Indiana University - Bloomington Lines: 12 Message-ID: <6518df$rus$1@dismay.ucs.indiana.edu> References: <34736037.38E5@mh.us.sbphrd.com> NNTP-Posting-Host: chipmunk.bio.indiana.edu Ray, I haven't had any problems compiling SRS 505 on a handful of Solaris (2.4/2.5.x) systems, including Solaris on X86, using Sun's C compiler. The -Xa switch is a Sun C switch, but not a GCC switch, I think. I don't recall needing to make any changes to the SRS make/install scripts to compile. - Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Mon Nov 24 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!205.252.116.205!howland.erols.net!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Memory and indexing links Date: Tue, 25 Nov 1997 09:53:17 +0000 Organization: SEQNET Lines: 26 Distribution: bionet Message-ID: <347AA00D.167E@dl.ac.uk> 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) Hi folks, With the latest release of EMBL, I had to increase the LINKxMAXIDN constant in link.c in order to be able to build the (index) link between EMBL and GenBank. Setting this value to 4000000 seemed to do the trick. However, this had an unwelcome side effect: It became impossible to build read links for libraries which are linked to more than 5 databases, due to a lack of memory. I suppose srsbuild allocates an amount of memory proportional to LINKxMAXIDN for each link to be build, even if the library is only very small. Anybody with a (software) solution for this ? Cheers, Martin -- ------------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/Person.asp?m.p.hilbers | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.seqnet.dl.ac.uk/ | -------------------------------------------------------------------