From owner-srs@net.bio.net Mon Jan 01 22:00:00 1996 Newsgroups: bionet.molbio.embldatabank,bionet.software.srs Path: biosci!bloom-beacon.mit.edu!newsfeed.internetmci.com!news.sprintlink.net!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!stoehr From: stoehr@ebi.ac.uk (Peter Stoehr) Subject: Re: trembl and EMBL 45 Sender: news@ebi.ac.uk (Mr news) Message-ID: <1995Dec31.144120@ebi.ac.uk> Date: Sun, 31 Dec 1995 13:41:20 GMT Lines: 21 References: <4btvtm$9qk@lovelace.infobiogen.fr> Organization: European BioInformatics Institute Xref: biosci bionet.molbio.embldatabank:584 bionet.software.srs:207 In article <4btvtm$9qk@lovelace.infobiogen.fr>, Jean-Marc Plaza writes: > Sorry, I forgot the subjecty so I post it again: > > > Hi, > there are several problems with EMBL 45 when you > run trembl (Thure Etzold) on it. > First, in CDS complement , trembl does a core dump when it finds : > "complememt(>" instead of "complememt(" > Secondly, The codon start for HSACTSG7 is /codon_start!29 in EMBL 45 > instead of 1, 2 or 3. And trembl does not like it -core dump. :-) > In Genbank the codon start is /codon_start=1 for HUMACTSG7 and > the translated sequence is different. Jean-Marc, We have corrected the /codon_start value in the EMBL entry, from 2129 to 1. I realise that doesn't immediately help with trembling EMBL 45... Regards, Peter Stoehr EMBL - EBI From owner-srs@net.bio.net Fri Jan 05 22:00:00 1996 Path: biosci!agate!newsxfer2.itd.umich.edu!newsfeed.internetmci.com!in1.uu.net!zib-berlin.de!fu-berlin.de!news.dfn.de!gs.dfn.de!immunbio.mpg.de!immunbio.mpg.de!news Newsgroups: bionet.software.srs Subject: General error or specific for my setup? Message-ID: <1996Jan6.152333.209@immunbio.mpg.de> From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Date: 6 Jan 96 15:23:32 +0100 Distribution: world Organization: Max-Planck-Institut fuer Immunbiologie Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24Lines: 21 Lines: 21 Hello, we have SRS V4.08 under VAX-VMS, the sequences are in GCG format, the GCG databases have been created as "novmsonly". Now I do a getz -d "[SWISSPROT-ID:cra2_mesau]" to view the sequence data. Result: the comment line in the GCG .SEQ-file is treated as sequence characters and the sequence itself is truncated. Question: does this happen on other sites? Under Unix, VMS-VAX, VMS-AXP, with or without "novmsonly"? Regards, Christoph Gartmann +----------------------------------------------------------------------------+ | Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 | | Immunbiologie PSI : PSI%(0262)45050160374::GARTMANN | | Postfach 1169 Internet: gartmann@immunbio.mpg.de | | D-79011 Freiburg, FRG | +----------- Do you know MENUE, the user environment for OpenVMS? -----------+ From owner-srs@net.bio.net Mon Jan 08 22:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!dec5!palard From: palard@dec5 (Philippe Alard) Newsgroups: bionet.software.srs Subject: Re: General error or specific for my setup? Date: 9 Jan 1996 15:27:01 GMT Organization: Brussels Free Universities VUB/ULB Lines: 19 Distribution: world Message-ID: <4cu1g5$7bb@rc1.vub.ac.be> References: <1996Jan6.152333.209@immunbio.mpg.de> NNTP-Posting-Host: dbmdec5.ulb.ac.be. X-Newsreader: TIN [version 1.2 PL0] Christoph Gartmann (GARTMANN@IMMUNBIO.MPG.DE) wrote: : we have SRS V4.08 under VAX-VMS, the sequences are in GCG format, the GCG : databases have been created as "novmsonly". Now I do a : getz -d "[SWISSPROT-ID:cra2_mesau]" : to view the sequence data. Result: the comment line in the GCG .SEQ-file is : treated as sequence characters and the sequence itself is truncated. : Question: does this happen on other sites? Under Unix, VMS-VAX, VMS-AXP, : with or without "novmsonly"? Yes we have the same problem under Unix. We also run srs v4.08. In the GCG .seq files most of the nucleic sequences are compressed, this is marked by 2BIT in the title. All the protein seqences + nucleic sequences which don't use ATGC are not compressed and marked ASCII. There is no problem with the compressed sequences but well with the non compressed. Philippe Alard From owner-srs@net.bio.net Mon Jan 08 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!tank.news.pipex.net!pipex!peer-news.britain.eu.net!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: General error or specific for my setup? Date: 09 Jan 1996 20:42:00 GMT Organization: The Sanger Centre Lines: 27 Distribution: world Message-ID: References: <1996Jan6.152333.209@immunbio.mpg.de> <4cu1g5$7bb@rc1.vub.ac.be> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: palard@dec5's message of 9 Jan 1996 15:27:01 GMT In article <4cu1g5$7bb@rc1.vub.ac.be> palard@dec5 (Philippe Alard) writes: > Christoph Gartmann (GARTMANN@IMMUNBIO.MPG.DE) wrote: > : we have SRS V4.08 under VAX-VMS, the sequences are in GCG format, the GCG > : databases have been created as "novmsonly". Now I do a > : getz -d "[SWISSPROT-ID:cra2_mesau]" > : to view the sequence data. Result: the comment line in the GCG .SEQ-file is > : treated as sequence characters and the sequence itself is truncated. > > : Question: does this happen on other sites? Under Unix, VMS-VAX, VMS-AXP, > : with or without "novmsonly"? > > Yes we have the same problem under Unix. We also run srs v4.08. Just to counter these two sites - we run srs 4.08 on Unix (Irix 5.2) and have no problems like this. Is this only with "novmsonly" VMS formatting of databases, or is this also happening to some pure Unix sites? -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr/ | England From owner-srs@net.bio.net Tue Jan 09 22:00:00 1996 Path: biosci!bloom-beacon.mit.edu!newsfeed.internetmci.com!vixen.cso.uiuc.edu!howland.reston.ans.net!nntp.coast.net!swidir.switch.ch!scsing.switch.ch!news.belwue.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: General error or specific for my setup? Date: Wed, 10 Jan 1996 13:52:52 +0100 Organization: EMBL Lines: 18 Distribution: world Message-ID: <30F3B6A4.6EEA@embl-heidelberg.de> References: <1996Jan6.152333.209@immunbio.mpg.de> <4cu1g5$7bb@rc1.vub.ac.be> <4cvt1e$7hq@ankka.csc.fi> <4d05bf$i4@rc1.vub.ac.be> NNTP-Posting-Host: falcon.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b4 (X11; I; IRIX 5.3 IP20) To: Guy Bottu Guy Bottu wrote: > > I have found the cause of the problem at the BEN site : The EMBL has 3 > sequences of more than 350000 bases long and from GCG 8.1 on, the way > GCG splits these sequences has changed. To allow SRS to recompose the > sequences, I modified the file srsgeneral.sdl, I replaced ... after doing these changes it is not necessary to rebuild all indices of embl. the following command rebuilds only the file 'embl_id.idx' which has the pointers to the flat files: srsbuild -r embl ...the 'r' means relocate regards thure From owner-srs@net.bio.net Tue Jan 09 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!fu-berlin.de!news.dfn.de!gs.dfn.de!immunbio.mpg.de!immunbio.mpg.de!news Newsgroups: bionet.software.srs Subject: Re: General error or specific for my setup? Message-ID: <1996Jan10.101910.210@immunbio.mpg.de> From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Date: 10 Jan 96 10:19:09 +0100 References: <1996Jan6.152333.209@immunbio.mpg.de> <4cu1g5$7bb@rc1.vub.ac.be> Distribution: world Organization: Max-Planck-Institut fuer Immunbiologie Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24In-Reply-To: pmr@sanger.ac.uk's message of 09 Jan 1996 20:42:00 GMTLines: 36 Lines: 36 In pmr@sanger.ac.uk writes: > In article <4cu1g5$7bb@rc1.vub.ac.be> palard@dec5 (Philippe Alard) writes: > > Christoph Gartmann (GARTMANN@IMMUNBIO.MPG.DE) wrote: > > : we have SRS V4.08 under VAX-VMS, the sequences are in GCG format, the GCG > > : databases have been created as "novmsonly". Now I do a > > : getz -d "[SWISSPROT-ID:cra2_mesau]" > > : to view the sequence data. Result: the comment line in the GCG .SEQ-file is > > : treated as sequence characters and the sequence itself is truncated. > > > > : Question: does this happen on other sites? Under Unix, VMS-VAX, VMS-AXP, > > : with or without "novmsonly"? > > > > Yes we have the same problem under Unix. We also run srs v4.08. > > Just to counter these two sites - we run srs 4.08 on Unix (Irix 5.2) > and have no problems like this. > > Is this only with "novmsonly" VMS formatting of databases, or is > this also happening to some pure Unix sites? I looked a bit deeper into it: it happens independent of the "novmsonly" switch. It depends on the format of the sequence - 2BIT or ASCII. With 2BIT things are fine but with ASCII the error occurs. Example: EM_PAT A00674 (2BIT) and A00709 (ASCII). But of course, I can only check the VMS version. Regards, Christoph Gartmann +----------------------------------------------------------------------------+ | Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 | | Immunbiologie PSI : PSI%(0262)45050160374::GARTMANN | | Postfach 1169 Internet: gartmann@immunbio.mpg.de | | D-79011 Freiburg, FRG | +----------- Do you know MENUE, the user environment for OpenVMS? -----------+ From owner-srs@net.bio.net Tue Jan 09 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!peer-news.britain.eu.net!yama.mcc.ac.uk!daresbury!bioftp.unibas.ch!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Re: General error or specific for my setup? Date: 10 Jan 1996 10:45:03 GMT Organization: Belgian EMBnet Node Lines: 29 Message-ID: <4d05bf$i4@rc1.vub.ac.be> References: <1996Jan6.152333.209@immunbio.mpg.de> <4cu1g5$7bb@rc1.vub.ac.be> <4cvt1e$7hq@ankka.csc.fi> NNTP-Posting-Host: ben.vub.ac.be. X-Newsreader: TIN [version 1.2 PL2] I have found the cause of the problem at the BEN site : The EMBL has 3 sequences of more than 350000 bases long and from GCG 8.1 on, the way GCG splits these sequences has changed. To allow SRS to recompose the sequences, I modified the file srsgeneral.sdl, I replaced ! gcg sequence file #filetype /ID=%GCGSEQ_FILE /typename=seq /maxline=20000 /begstr=">>>>" /advance=0 /exitstr=">>>>" /find=id /iscont="-" by ! gcg sequence file #filetype /ID=%GCGSEQ_FILE /typename=seq /maxline=20000 /begstr=">>>>" /advance=0 /exitstr=">>>>" /seqtype=gcg8_1 I had not reindexed. Changing srsgeneral.sdl back to its old form cures the problem of the faulty sequence retrieval, except of course that the long sequences are not handled well. I do not know if remaking all the indexes after the change would have helped (since this takes a whole weekend, I did not try it just now). I also have no idea if the problem of Christoph Gartmann has the same cause or is entirely different. Guy Bottu From owner-srs@net.bio.net Tue Jan 09 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!cdc2.cdc.net!news1.cris.com!news2.acs.oakland.edu!nntp.coast.net!news00.sunet.se!sunic!news99.sunet.se!news.funet.fi!news.csc.fi!usenet From: "Heikki LehvŠslaiho" Newsgroups: bionet.software.srs Subject: Re: General error or specific for my setup? Date: 10 Jan 1996 08:23:10 GMT Organization: CSC - Center for Scientific Computing Lines: 42 Message-ID: <4cvt1e$7hq@ankka.csc.fi> References: <1996Jan6.152333.209@immunbio.mpg.de> <4cu1g5$7bb@rc1.vub.ac.be> NNTP-Posting-Host: siru.csc.fi Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 1.12(Macintosh; I; PPC) X-URL: news:PMR.96Jan9204201@unst.sanger.ac.uk pmr@sanger.ac.uk (Peter Rice) wrote: >In article <4cu1g5$7bb@rc1.vub.ac.be> palard@dec5 (Philippe Alard) writes: >> Christoph Gartmann (GARTMANN@IMMUNBIO.MPG.DE) wrote: >> : we have SRS V4.08 under VAX-VMS, the sequences are in GCG format, the GCG >> : databases have been created as "novmsonly". Now I do a >> : getz -d "[SWISSPROT-ID:cra2_mesau]" >> : to view the sequence data. Result: the comment line in the GCG .SEQ-file is >> : treated as sequence characters and the sequence itself is truncated. >> >> : Question: does this happen on other sites? Under Unix, VMS-VAX, VMS-AXP, >> : with or without "novmsonly"? >> >> Yes we have the same problem under Unix. We also run srs v4.08. > >Just to counter these two sites - we run srs 4.08 on Unix (Irix 5.2) >and have no problems like this. > >Is this only with "novmsonly" VMS formatting of databases, or is >this also happening to some pure Unix sites? I had the same problem while I was running SRS v. 4.07 under IRIX 6.0.1 with GCG version 8.1 data files. Upgrading to 4.08 helped. Later, I got a message from Thure saying that the problem lies in the changing format of GCG datafiles. Accorging to him, the file format is defined in file srsgeneral.sdl. Check that or contact Thure for details. Sorry for not posting this earlier, -Heikki ______ _/ _/____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehväslaiho _/_/_/_/_/ CSC Scientific Computing _/ _/ _/ Tietotie 6, P.O. Box 405, FIN-02101 Espoo FINLAND _/ _/ _/ Phone: +358 0 457 2076 FAX: +358 0 457 2302 _/ The Finnish EMBnet node __ _/_/_/_/_/________________________________________________________ From owner-srs@net.bio.net Tue Jan 09 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!vixen.cso.uiuc.edu!howland.reston.ans.net!nntp.coast.net!swidir.switch.ch!swsbe6.switch.ch!scsing.switch.ch!news.belwue.de!news.dfn.de!gs.dfn.de!immunbio.mpg.de!immunbio.mpg.de!news Newsgroups: bionet.software.srs Subject: Re: General error or specific for my setup? Message-ID: <1996Jan10.151539.211@immunbio.mpg.de> From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Date: 10 Jan 96 15:15:36 +0100 References: <1996Jan6.152333.209@immunbio.mpg.de> <4cu1g5$7bb@rc1.vub.ac.be> <4cvt1e$7hq@ankka.csc.fi> <4d05bf$i4@rc1.vub.ac.be> Distribution: world Organization: Max-Planck-Institut fuer Immunbiologie Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24In-Reply-To: gbottu@ben.vub.ac.be's message of 10 Jan 1996 10:45:03 GMTLines: 44 Lines: 44 In <4d05bf$i4@rc1.vub.ac.be> gbottu@ben.vub.ac.be writes: > I have found the cause of the problem at the BEN site : The EMBL has 3 > sequences of more than 350000 bases long and from GCG 8.1 on, the way > GCG splits these sequences has changed. To allow SRS to recompose the > sequences, I modified the file srsgeneral.sdl, I replaced > > ! gcg sequence file > #filetype /ID=%GCGSEQ_FILE > /typename=seq /maxline=20000 > /begstr=">>>>" /advance=0 /exitstr=">>>>" > /find=id /iscont="-" > > by > > ! gcg sequence file > #filetype /ID=%GCGSEQ_FILE > /typename=seq /maxline=20000 > /begstr=">>>>" /advance=0 /exitstr=">>>>" > /seqtype=gcg8_1 > > I had not reindexed. Changing srsgeneral.sdl back to its old form > cures the problem of the faulty sequence retrieval, except of course > that the long sequences are not handled well. > > I do not know if remaking all the indexes after the change would have > helped (since this takes a whole weekend, I did not try it just now). > I also have no idea if the problem of Christoph Gartmann has the > same cause or is entirely different. All my indices were created with /seqtype=gcg8_1 . Now I changed the SDL back to its original state and I experience the same as Guy. So I think reindexing won't help, it is more a matter of a correct SDL. Regards, Christoph Gartmann +----------------------------------------------------------------------------+ | Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 | | Immunbiologie PSI : PSI%(0262)45050160374::GARTMANN | | Postfach 1169 Internet: gartmann@immunbio.mpg.de | | D-79011 Freiburg, FRG | +----------- Do you know MENUE, the user environment for OpenVMS? -----------+ From owner-srs@net.bio.net Fri Jan 12 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!nntp.coast.net!oleane!jussieu.fr!infobiogen.fr!lovelace.infobiogen.fr!dessen From: dessen@lovelace.infobiogen.fr (Philippe Dessen) Newsgroups: bionet.software.srs Subject: SRS heidelberg address Date: 13 Jan 1996 09:59:35 GMT Organization: GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France Lines: 20 Message-ID: <4d7vq7$kle@lovelace.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] On several sites there is a error in the address of SRS servers : There is often : http://www.embl-heidelberg.de/srs/status.html instead of http://www.embl-heidelberg.de/srs/src/status.html Particular on the Basel WWW server : http://beta.embnet.unibas.ch/#europe -- ------------------------------------------------------- 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 Fri Jan 12 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!vixen.cso.uiuc.edu!howland.reston.ans.net!EU.net!peer-news.britain.eu.net!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: SRS heidelberg address Date: 13 Jan 1996 20:55:25 GMT Organization: The Sanger Centre Lines: 25 Message-ID: References: <4d7vq7$kle@lovelace.infobiogen.fr> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: dessen@lovelace.infobiogen.fr's message of 13 Jan 1996 09:59:35 GMT In article <4d7vq7$kle@lovelace.infobiogen.fr> dessen@lovelace.infobiogen.fr (Philippe Dessen) writes: > On several sites there is a error in the address of SRS servers : > > There is often : > http://www.embl-heidelberg.de/srs/status.html > instead of > http://www.embl-heidelberg.de/srs/src/status.html The first address is normally correct. With the current release some sites have a different URL /srsdoc/status.html (at Sanger /srs and /srsdoc are the same, which seems sensible until all sites are using /srsdoc in URLs). Perhaps /srs/srsc is where Thure has moved it, but /srsdoc is the "correct" URL: http://www.embl-heidelberg.de/srsdoc/status.html Perhaps this could have been clearer in the SRS release information. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr/ | England From owner-srs@net.bio.net Sat Jan 13 22:00:00 1996 Path: biosci!daresbury!s-crim1!mph From: mph@s-crim1.dl.ac.uk (M.P. Hilbers) Newsgroups: bionet.software.srs Subject: SEQNET SRS-server address change Date: 14 Jan 1996 18:39:23 GMT Organization: SERC Daresbury Lab, Warrington, U.K. Lines: 24 Distribution: world Message-ID: <4dbikr$53f@mserv1.dl.ac.uk> NNTP-Posting-Host: s-crim1.dl.ac.uk X-Newsreader: TIN [version 1.2 PL2] [ Article crossposted from bionet.announce ] [ Author was Martin Hilbers ] [ Posted on 12 Jan 1996 18:57:50 -0800 ] The internet address of the SEQNET SRS-server has changed. It can now be reached at http://www.seqnet.dl.ac.uk/srs/srsc. The old SRS-server address (http://seqnet.dl.ac.uk/srs/srsc or http://s-crim1.dl.ac.uk/srs/srsc ) will no longer function from 19 Jan 1996, so please adapt links in your html pages. As the SRS-server then no longer runs on our heavily used main computer, response times for SRS queries should be much better. --------------------------------------------------------------------------- | 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-srs@net.bio.net Thu Jan 18 22:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI miniFAQ, ver. 14-DEC-95 Date: 19 Jan 1996 02:42:14 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 199 Sender: daemon@net.bio.net Distribution: world Message-ID: <199601191000.CAA17654@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 14-DEC-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/. Contents: -------- 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. 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 in addition to the master index for the entire set. 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-srs@net.bio.net Mon Jan 22 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!oleane!jussieu.fr!infobiogen.fr!lovelace.infobiogen.fr!dessen From: dessen@lovelace.infobiogen.fr (Philippe Dessen) Newsgroups: bionet.software.srs Subject: REPBASE on SRS Date: 23 Jan 1996 18:50:38 GMT Organization: GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France Lines: 24 Message-ID: <4e3alu$dqo@lovelace.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] The REPBASE database is now online on SRS at INFOBIOGEN: http://www.infobiogen.fr/srs/srsc REPBASE (release 96.01) has 25538 entries in EMBL format and contains repetitive DNA sequences compiled by : P.I. Jerzy Jurka Linus Pauling Institute of Science and Medicine 440 Page Mill Rd Palo Alto, CA 94306 tel. (415) 327 4064 FAX (415) 327 8564 email jurek@ncbi.nlm.nih.gov Flat files are from ncbi.nlm.nih.gov (/repository/repbase). -- ------------------------------------------------------- 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 Thu Jan 25 22:00:00 1996 Path: biosci!biosci!not-for-mail From: malik@ebi.ac.uk (Ansar Malik) Newsgroups: bionet.immunology,sci.med.immunology,sci.med,bionet.software.srs,bionet.molbio.embldatabank,bionet.molbio.genbank,sci.med.informatics Subject: ANNOUNCE: IMGT Immunogenetics Database Release 2 Date: 25 Jan 1996 20:26:09 -0800 Organization: European Bioinformatics Institute (EMBL) - UK Lines: 55 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: malik@ebi.ac.uk (Ansar Malik) NNTP-Posting-Host: net.bio.net Keywords: Immunogenetics,Database,Immunoglobulin,T Cell Receptor,DNA sequence,sequences annotation Xref: biosci bionet.immunology:7357 sci.med.immunology:4390 sci.med:107739 bionet.software.srs:221 bionet.molbio.embldatabank:596 bionet.molbio.genbank:2211 sci.med.informatics:4997 IMMUNOGENETICS IMGT DATABASE ============================= Professor Marie-Paule LEFRANC Laboratoire d'ImmunoGenetique Moleculaire, LIGM UMR CNRS 9942, Institut de Genetique Moleculaire BP 5051, 1919 route de Mende, 34033 MONTPELLIER Cedex 1 FRANCE Telephone: (33) 67 61 36 34 FAX : (33) 67 04 02 31/67 04 02 45 e-mail : lefranc@ligm.crbm.cnrs-mop.fr INTRODUCTION ============ The ImMunoGeneTics database, IMGT, is an integrated specialised database containing nucleotide sequence information of genes important in the function of the immune system. It collects and annotates sequences belonging to the immunoglobulin superfamily which are involved in immune recognition, these are the B cell antigen receptor (Immunoglobulin or Ig), the T cell antigen receptor (TCR) (LIGM-database) and the class I and class II molecules of the Human Leucocyte Antigens (HLA) system (HLA-database). Release 2 (December 1995) contains 3149 fully annotated sequence entries. IMGT/LIGM DATABASE ================== An integrated immumogenetics database (IMGT/LIGM) specialising in Ig and TcR is under development through collaboration between LIGM, IFG and EMBL oustation EBI. This database consists of the Ig and TcR sequence entries. Collaborators: LIGM Montpellier :Marie-Paule Lefranc (coordinator) Veronique Giudicelli,Denys Chaume EMBL-EBI :Ansar Malik IFG :Werner Mueller MRC :Ian Tomlinson ACCESS/DATA DISTRIBUTION ======================== WWW server: http://www.ebi.ac.uk/contrib/imgt/ FTP server: ftp.ebi.ac.uk/pub/databases/imgt This database is available on CD-ROM as an acompanying database to the EMBL Nucleotide Sequence Database at nominal cost. ======================================================================= Ansar Malik Ph.D | Email:Malik@ebi.ac.uk EBI - European Bioinformatics Institute | URL: http://www.ebi.ac.uk Hinxton Hall, Hinxton | Tel: +44 (1223) 494417 Cambridge CB10 1RQ, UK | Fax: +44 (1223) 494968 ======================================================================== From owner-srs@net.bio.net Fri Jan 26 22:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!howland.reston.ans.net!Germany.EU.net!zib-berlin.de!fu-berlin.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: indexing gcg formatted sequence files Date: Fri, 26 Jan 1996 21:46:38 +0100 Organization: EMBL Lines: 32 Distribution: world Message-ID: <31093DAE.41C6@embl-heidelberg.de> NNTP-Posting-Host: kappa.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b4 (X11; I; OSF1 V2.0 alpha) (1) once more for all those who still have indexing the embl (or genbank) databanks in gcg 8.1 format - this is how the filetype record should be. please make sure that it is defined exactly like this in your file "srsgeneral.sdl" #filetype /ID=%GCGSEQ_FILE /typename=seq /maxline=20000 /begstr=">>>>" /advance=0 /exitstr=">>>>" /find="%s" /iscont="-" /seqtype=gcg8_1 (2) i fixed the program trembl - it works on our site and the two databanks "trembl" and "tremblnew" (built daily) can be obtained via ftp (felix.embl-heidelberg.de in the directory "pub/databases/trembl" regards thure -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-srs@net.bio.net Sun Jan 28 22:00:00 1996 Path: biosci!daresbury!hgmp.mrc.ac.uk!news From: pwoollar@hgmp.mrc.ac.uk (Peter M. Woollard x4523) Newsgroups: bionet.software.srs Subject: EMBL Indexing Date: 29 Jan 1996 15:19:10 GMT Organization: UK MRC Human Genome Mapping Project Lines: 44 Message-ID: <4eiohe$c5q@mercury.hgmp.mrc.ac.uk> Reply-To: pwoollar@hgmp.mrc.ac.uk NNTP-Posting-Host: iron.hgmp.mrc.ac.uk Hello, I am getting an error building the ID indeces for EMBL, has anyone ideas on how to convince SRS that there is space? Unix % srsbuild -i EMNEW EMBL -xdir 'SRSINX:' -odir 'SRSINX:' -env 'unix' e__settoosmall, set has not enough space for IDs attempt to copy 1890 IDs where only for 1000 is space Segmentation Fault (core dumped) Unix% I have tried the following: 1) altered the sdl file for embl (and similarly the emnew part), embl.sdl: /format=@EMBL_FORMAT /cachesize=2048 /maxIndexSizeKb=6400 2) srssection 3) srsbuild -i EMNEW EMBL -xdir 'SRSINX:' -odir 'SRSINX:' -env 'unix' This appeared to have no effect, so I forced an srsmake for all the binaries and then repeated the above. This also had apparently no effect. There is currently sufficient physical disc space. Any other ideas? (I checked through any documentation files and WWW refs. I could find, but could not see anything of relevance. ) TIA Best Regards, Peter Woollard ----------------------------------------------------------------------- Computing Services Section, Internet: p.woollard@hgmp.mrc.ac.uk MRC Human Genome Mapping Project http://www.hgmp.mrc.ac.uk/ Resource Centre, Hinxton Hall, Hinxton, Cambridge, CB10 1RQ, UK Tel: ++44 (0)1223 494 523 ---------------------------------------------------------------------- From owner-srs@net.bio.net Mon Jan 29 22:00:00 1996 Path: biosci!daresbury!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: EMBL Indexing Date: 30 Jan 1996 09:54:26 GMT Organization: The Sanger Centre Lines: 36 Message-ID: References: <4eiohe$c5q@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: pwoollar@hgmp.mrc.ac.uk's message of 29 Jan 1996 15:19:10 GMT In article <4eiohe$c5q@mercury.hgmp.mrc.ac.uk> pwoollar@hgmp.mrc.ac.uk (Peter M. Woollard x4523) writes: > I am getting an error building the ID indeces for EMBL, has anyone ideas > on how to convince SRS that there is space? > > Unix % srsbuild -i EMNEW EMBL -xdir 'SRSINX:' -odir 'SRSINX:' -env 'unix' > e__settoosmall, set has not enough space for IDs > attempt to copy 1890 IDs where only for 1000 is space > > Segmentation Fault (core dumped) > Unix% It's those H.influenzae entries again I suspect - lots of cross references in EMBL and EMNEW when they change. The problam is in srsbuild.c: change: #define BLDxMAXTMPSETSIZE 1000 to: #define BLDxMAXTMPSETSIZE 3000 and remake the srsbuild program. Fixed in the next release. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr/ | England From owner-srs@net.bio.net Tue Jan 30 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!EU.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: EMBL Indexing Date: Tue, 30 Jan 1996 14:22:31 +0100 Organization: EMBL Lines: 39 Distribution: world Message-ID: <310E1B97.41C6@embl-heidelberg.de> References: <4eiohe$c5q@mercury.hgmp.mrc.ac.uk> NNTP-Posting-Host: hawk.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0b6a (X11; I; IRIX 5.3 IP7) To: pwoollar@hgmp.mrc.ac.uk Peter M. Woollard x4523 wrote: > > Hello, > I am getting an error building the ID indeces for EMBL, has anyone ideas > on how to convince SRS that there is space? > > Unix % srsbuild -i EMNEW EMBL -xdir 'SRSINX:' -odir 'SRSINX:' -env 'unix' > e__settoosmall, set has not enough space for IDs > attempt to copy 1890 IDs where only for 1000 is space > the link between EMNEW and EMBL uses accession numbers - both primary and secondary - which can result in an 'explosion' of links if there are many entries sharing the same secondary accession number which seems to be more often the case - it is possible to set the limit to a higher value in srsbuild.c #define BLDxMAXTMPSETSIZE 3000 ...or higher a better solution is to change the link so that it uses the entry names instead of the accession number - this assumes that entries once renamed are sufficiently different to be treated as new entries - any comments on that? here is the modified link from EMNEW to EMBL (in embl.sdl) #link /id=%EMNEW_EMBL_LINK /lib1=@EMBLNEW_DB /lib2=@EMBL_DB /type=index /field1=@EMNEW_ID_FIELD /field2=@EMBL_ID_FIELD /idtype1=@SRSxSEQID /idtype2=@SRSxSEQID another and possibly the best solution would be to create at least for one of the two the accession index with only the primary accession number ...i am not sure how important it is to make the secondary accession number searchable anyway ....for the 'normal' user that is regards thure From owner-srs@net.bio.net Tue Jan 30 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!EU.net!peer-news.britain.eu.net!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: EMBL Indexing Date: 31 Jan 1996 15:37:57 GMT Organization: The Sanger Centre Lines: 22 Distribution: world Message-ID: References: <4eiohe$c5q@mercury.hgmp.mrc.ac.uk> <310E1B97.41C6@embl-heidelberg.de> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: Thure Etzold's message of Tue, 30 Jan 1996 14:22:31 +0100 In article <310E1B97.41C6@embl-heidelberg.de> Thure Etzold writes: > > I am getting an error building the ID indeces for EMBL, has anyone ideas > > on how to convince SRS that there is space? > a better solution is to change the link so that it uses the entry names instead of > the accession number - this assumes that entries once renamed are sufficiently > different to be treated as new entries - any comments on that? For the Haemophilus entries this makes much more sense. These share a common secondary accession number (for the entire genome) which is not much use for the cross-referencing (a Haemophilus entry in EMNEW would pick up *all* Haemophilus entries in EMBL by cross-reference this way. These would be better linked by entry name (which I will switch to for now at Sanger) or primary accession number (sounds like a job for ICARUS) -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr/ | England