From owner-srs@net.bio.net Fri Dec 06 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!online.no!sn.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!EU.net!main.Germany.EU.net!news-koe1.dfn.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs,bionet.software Subject: New release 5.0 of SRS Date: Sat, 07 Dec 1996 01:25:48 +0100 Organization: EMBL Lines: 57 Distribution: world Message-ID: <32A8B98C.41C6@embl-heidelberg.de> NNTP-Posting-Host: kappa.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V2.0 alpha) Xref: biosci bionet.software.srs:357 bionet.software:17303 Dear all, SRS5 is finally out! ...this time it is the full release and not a 'beta' you can get it from ftp://ftp.embl-heidelberg.de/pub/databases/trembl/srs5_0.tar.gz Those are the changes since the last beta (srs5.04b): o The indexing works now with databanks in native or GCG format. o There is now support for sequence features o srscheck and srsbuild have been revised and work as in SRS4. This includes the -r, -t and -rel options of srsbuild. o Parsers have been written for many more databanks. o Documentation is much better (Icarus manual, Guided tour). o All installation scripts have been rewritten as Bourne shell scripts. SRS5 is much more powerful but also more complicated as SRS4. A lot of parsers have still to be written, but those that are there can be used as templates for 'cut and paste' programming. Adding a new databank needs now three files that describe the structure (format, data-fields, links), the syntax and the databank itself (Source, ftp address, contact address, etc). This is described in the "Guided Tour" that comes with the distribution. We would like to invite you to write Icarus files and post them to the newsgroup bionet.software.srs to make them available to others. We will then put the files into future releases of SRS. For the installation of the SRSWWW server an Alias and a ScriptAlias are needed. Following the discussion in this newsgroup about notifying the proxies not to cache we use now the ScriptAlias /srs5bin/cgi-bin/. Please tell us if that works. ...more in the release notes regards and happy installation Giorgio Verde verde@embl-heidelberg.de Johnathon Weare weare@embl-heidelberg.de Thure Etzold etzold@embl-heidelberg.de -- =============================================================================== 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 Mon Dec 09 22:00:00 1996 Newsgroups: bionet.software.srs Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!howland.erols.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!ebi.ac.uk!news From: Tao Jiang Subject: question about SRS5.0 Sender: news@ebi.ac.uk (usenet news) Message-ID: <32ACBDA7.57D9066B@pku.edu.cn> Date: Tue, 10 Dec 1996 01:32:23 GMT Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 X-Mailer: Mozilla 3.01Gold (X11; I; Linux 2.0.0 i586) Organization: Network Center Lines: 18 I downloaded the SRS version 5.0, and had a small test yesterday. I installed only a very small part of EMBL : phg.dat, and try to index it. To my surprising, I found it would take me over 12 hours to index it (in fact, the indexing hasn't finished yet), and too many index files were generated: embl_fts_1.inx, embl_fts_2.inx, ... , embl_569.inx, ... (I have modified srsdb.i and embl.i to include only phg.dat of EMBL). However, if I test it with swissprot, it seems to work well (only one index file for every index). Any suggestions and help are greatly appreciated. -- Tao Jiang Fax: 86-10-62751982 Network Center Homepage: http://jiangt.pku.edu.cn/~jiangt/ Peking University Email: jiangt@pku.edu.cn From owner-srs@net.bio.net Mon Dec 09 22:00:00 1996 Path: biosci!agate!howland.erols.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.srs Subject: Re: question about SRS5.0 Date: 10 Dec 1996 09:43:30 GMT Organization: The Sanger Centre Lines: 42 Message-ID: References: <32ACBDA7.57D9066B@pku.edu.cn> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: Tao Jiang's message of Tue, 10 Dec 1996 01:32:23 GMT In article <32ACBDA7.57D9066B@pku.edu.cn> Tao Jiang writes: > I downloaded the SRS version 5.0, and had a small test > yesterday. I installed only a very small part of EMBL > : phg.dat, and try to index it. To my surprising, I > found it would take me over 12 hours to index it (in fact, > the indexing hasn't finished yet), and too many index > files were generated: embl_fts_1.inx, embl_fts_2.inx, ... > , embl_569.inx, ... (I have modified srsdb.i and embl.i to > include only phg.dat of EMBL). > > However, if I test it with swissprot, it seems to work well > (only one index file for every index). The multiple index files are not a bug - they are a feature of SRS 5.0 (and a very welcome feature too). SRS 4.0 needed to index all of EMBL in one go, which consumed terrible amounts of memory. SRS 5.0 splits EMBL into smaller chunks (defined in embl.i as partSize:100000 for 100000 entries), and builds a separate index for each. There is a new "srsbuild -m" step which merges these smaller indices together once they have been compressed. Having said that, I seem to have problems with the EMBL indexing too, so I am still checking on what is happening. After 82500+ entries from est1, I get: > SRSDB:embl.is:70: error: insufficient memory - error during malloc, > could not allocate "Cursor object" This was indexing the EMBL flat files. Of course, we have both been editing the embl.i file (and some others) so maybe we did something wrong. -- ------------------------------------------------------------------------ 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-srs@net.bio.net Mon Dec 09 22:00:00 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.srs Subject: Re: question about SRS5.0 Date: 10 Dec 1996 13:22:18 GMT Organization: The Sanger Centre Lines: 39 Message-ID: References: <32ACBDA7.57D9066B@pku.edu.cn> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: pmr@sanger.ac.uk's message of 10 Dec 1996 09:43:30 GMT In article pmr@sanger.ac.uk (Peter Rice) writes: >In article <32ACBDA7.57D9066B@pku.edu.cn> Tao Jiang writes: >> I downloaded the SRS version 5.0, and had a small test >> yesterday. I installed only a very small part of EMBL >> : phg.dat, and try to index it. To my surprising, I >> found it would take me over 12 hours to index it (in fact, > the indexing hasn't finished yet) > > SRS 5.0 splits EMBL into smaller chunks (defined in embl.i as > partSize:100000 for 100000 entries), and builds a separate index for > each. There is a new "srsbuild -m" step which merges these smaller > indices together once they have been compressed. > > Having said that, I seem to have problems with the EMBL indexing > too, so I am still checking on what is happening. After 82500+ entries > from est1, I get: > > > SRSDB:embl.is:70: error: insufficient memory - error during malloc, > > could not allocate "Cursor object" I tracked down the problem. It was caused by srsbuild using more memory (131Mb) than I had available. Even reducing "partSize:100000" in embl.i failed to reduce this by much. I have increased the limits (unlimit datasize) on the machine I used. For your very slow runs, I assume that srsbuild is using more memory than the machine has, and it has been swapping like crazy. I guess this is connected with changes in EMBL indexing since the last beta release (there have been several changes that could trigger it), but that is something Thure is best able to answer. -- ------------------------------------------------------------------------ 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-srs@net.bio.net Tue Dec 10 22:00:00 1996 Newsgroups: bionet.software.srs Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!news From: Thure Subject: Re: question about SRS5.0 Sender: news@ebi.ac.uk (usenet news) Message-ID: <32AEA3C2.41C6@embl-heidelberg.de> Date: Wed, 11 Dec 1996 12:06:26 GMT To: Tao Jiang Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii References: <32ACBDA7.57D9066B@pku.edu.cn> Mime-Version: 1.0 X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) Organization: EMBL Lines: 39 Tao Jiang wrote: > > I downloaded the SRS version 5.0, and had a small test > yesterday. I installed only a very small part of EMBL > : phg.dat, and try to index it. To my surprising, I > found it would take me over 12 hours to index it (in fact, > the indexing hasn't finished yet), and too many index > files were generated: embl_fts_1.inx, embl_fts_2.inx, ... > , embl_569.inx, ... (I have modified srsdb.i and embl.i to > include only phg.dat of EMBL). > I am having with indexing GCG formatted EMBL as well and will fix it this week. However, there seem to be no problems with the original flat file version. To switch from gcg format to distributed flat file edit embl.i and search all lines with a comment 'GCG format' # fileType:{@DAT_FILE @SEQ_FILE} #orig format fileType:{@GCGREF_FILE @GCGSEQ_FILE} #GCG format flip around the comments so that you get fileType:{@DAT_FILE @SEQ_FILE} #orig format # fileType:{@GCGREF_FILE @GCGSEQ_FILE} #GCG format then you must change the file names at the beginning of the file $file:pro will have to change to $file:em_pro I included lists of both gcg file names and original names where one list is always outcommented regards thure From owner-srs@net.bio.net Tue Dec 10 22:00:00 1996 Path: biosci!agate!howland.erols.net!news-peer.gsl.net!news.gsl.net!EU.net!Ireland.EU.net!web3.tcd.ie!gen035.gen.tcd.ie!user From: atlloyd@acer.gen.tcd.ie (Andrew T. Lloyd) Newsgroups: bionet.software.srs Subject: SRS 5_0 srsinstall all fails Date: Wed, 11 Dec 1996 12:17:15 +0000 Organization: INCBI, Trinity College, Dublin 2, Ireland. Lines: 24 Message-ID: NNTP-Posting-Host: gen035.gen.tcd.ie Hi Folks, I get a rather strange error trying to srsinstall all: (cc -Dosf -I/data/du5/srs/bin/osf -g -D__ODD -DSRSINCLUDE=\"srs5.h\" -c -o \/ta /du5/srs/bin/osf/seqdb.o seqdb.c; ar r /data/du5/srs/bin/osf/libsrs.a \/datdu5/ srs/bin/osf/seqdb.o; ) /: write failed, file system is full ar: error writing archive member contents: No such file or directory *** Exit 1 Stop. There is an error: Stopping make procedure. Surely 4GB is big enough, or is it some other file system which is choked ? variables: OSF1 v.3.2 make cc Any ideas gratefully considered. Andrew -- Andrew T. Lloyd Irish National Centre for BioInformatics INCBI atlloyd@acer.gen.tcd.ie http://acer.gen.tcd.ie Tel: (+353)-1-608-1969 EMBnet Ireland Fax: (+353)-679-8558 From owner-srs@net.bio.net Tue Dec 10 22:00:00 1996 Newsgroups: bionet.software.srs Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!news From: Thure Subject: Re: question about SRS5.0 Sender: news@ebi.ac.uk (usenet news) Message-ID: <32AEC9DA.2781@embl-heidelberg.de> Date: Wed, 11 Dec 1996 14:48:58 GMT To: Tao Jiang Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii References: <32ACBDA7.57D9066B@pku.edu.cn> Mime-Version: 1.0 X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) Organization: EMBL Lines: 47 Tao Jiang wrote: > > I downloaded the SRS version 5.0, and had a small test > yesterday. I installed only a very small part of EMBL > : phg.dat, and try to index it. To my surprising, I > found it would take me over 12 hours to index it (in fact, > the indexing hasn't finished yet), and too many index > files were generated: embl_fts_1.inx, embl_fts_2.inx, ... > , embl_569.inx, ... (I have modified srsdb.i and embl.i to > include only phg.dat of EMBL). > > However, if I test it with swissprot, it seems to work well > (only one index file for every index). > > Any suggestions and help are greatly appreciated. I found the bug, in fact there were two: 1) edit file src/icarus.c after line 670 you find if (!IcaCursorIsInput (job->inCursor, job->cursor)) { /* CursorDelete (&job->cursor); */ job->cursor = NULL; } remove the comments and rebuild srsbuild: srsmake srsbuild 2) edit icarus/db/embl.is around line 55 you find seq: ~ (/.*2BIT *Len:/ /[0-9]+/ {$len=$Ct} ln ln {$s=$SeqGet2Bit:[$s file:$File len:$len]} ('>>>>'{$Not} ln)*| /.*ASCII/ ln ln ('>>>>' {$Not} /.*/ {$SeqApp:[$s s:$Ct]})+) ~ change '$s=$SeqGet2Bit' to '$SeqGet2Bit' regards thure From owner-srs@net.bio.net Tue Dec 10 22:00:00 1996 Newsgroups: bionet.software.srs Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!news From: Thure Subject: Re: SRS 5_0 srsinstall all fails Sender: news@ebi.ac.uk (usenet news) Message-ID: <32AEC7F0.167E@embl-heidelberg.de> Date: Wed, 11 Dec 1996 14:40:48 GMT To: "Andrew T. Lloyd" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii References: Mime-Version: 1.0 X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) Organization: EMBL Lines: 31 Andrew T. Lloyd wrote: > > Hi Folks, > > I get a rather strange error trying to srsinstall all: > > (cc -Dosf -I/data/du5/srs/bin/osf -g -D__ODD -DSRSINCLUDE=\"srs5.h\" -c -o \/ta > /du5/srs/bin/osf/seqdb.o seqdb.c; ar r /data/du5/srs/bin/osf/libsrs.a \/datdu5/ > srs/bin/osf/seqdb.o; ) > > /: write failed, file system is full > ar: error writing archive member contents: No such file or directory > *** Exit 1 > Stop. > There is an error: Stopping make procedure. > > Surely 4GB is big enough, or is it some other file system which > is choked ? variables: OSF1 v.3.2 make cc > Any ideas gratefully considered. hi andrew, the 'ar' command writes temporary files into the /tmp directory and it didn't find enough space there - you tell ar to write these files somewhere else by defining the environment variable TMPDIR, eg, setenv TMPDIR /trash/tmp regards thure From owner-srs@net.bio.net Wed Dec 11 22:00:00 1996 Path: biosci!rutgers!uwm.edu!news-peer.gsl.net!news.gsl.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.srs Subject: Re: question about SRS5.0 Date: 12 Dec 1996 10:34:59 GMT Organization: The Sanger Centre Lines: 22 Message-ID: References: <32ACBDA7.57D9066B@pku.edu.cn> <32AEC9DA.2781@embl-heidelberg.de> <32AF65E2.36601FB1@pku.edu.cn> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: Tao Jiang's message of Thu, 12 Dec 1996 01:54:42 GMT In article <32AF65E2.36601FB1@pku.edu.cn> Tao Jiang writes: > I modified the file icarus.c, embl.i and embl.is just > as Thure suggested and compiled icarus.c and run 'srssection' > and 'srsupdate', but it still blocks (maybe it will ends > after a very long time?). The changes worked for me. Memory usage dropped dramatically, at least in the early stages (then I went home, and it was finished this morning). Maybe something went wrong with the "srsmake srsbuild" step? Or else you really have very little memory on your system. Our SRS 5.0 server will be available next week. I am still busy exploring the icarus files. I expect to be changing the indexing methods, and adding new databases, frequently for some time yet. -- ------------------------------------------------------------------------ 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-srs@net.bio.net Wed Dec 11 22:00:00 1996 Newsgroups: bionet.software.srs Path: biosci!rutgers!uwm.edu!cs.utexas.edu!www.nntp.primenet.com!nntp.primenet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!news From: Tao Jiang Subject: Re: question about SRS5.0 Sender: news@ebi.ac.uk (usenet news) Message-ID: <32AF65E2.36601FB1@pku.edu.cn> Date: Thu, 12 Dec 1996 01:54:42 GMT To: Thure Content-Type: multipart/mixed; boundary="------------1357101B5F987D624118B159" References: <32ACBDA7.57D9066B@pku.edu.cn> <32AEC9DA.2781@embl-heidelberg.de> Mime-Version: 1.0 X-Mailer: Mozilla 3.01Gold (X11; I; Linux 2.0.0 i586) Organization: Network Center Lines: 419 This is a multi-part message in MIME format. --------------1357101B5F987D624118B159 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am not sure if I am missing something here, but I always have problems with SRS5.0. I want to test with only phg.dat of EMBL, which is a very small data file. With SRS4.08, indexing takes only 1 min., while with SRS5.0, it will take too long for me to wait it ends. I modified the file icarus.c, embl.i and embl.is just as Thure suggested and compiled icarus.c and run 'srssection' and 'srsupdate', but it still blocks (maybe it will ends after a very long time?). I attach my embl.i, embl.is at the end, and any suggestions are greatly appreciated. -- Tao Jiang Fax: 86-10-62751982 Network Center Homepage: http://jiangt.pku.edu.cn/~jiangt/ Peking University Email: jiangt@pku.edu.cn --------------1357101B5F987D624118B159 Content-Type: text/plain; charset=us-ascii; name="embl.i" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="embl.i" #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # # $RCSfile: embl.i,v $ # $Revision: 1.11 $ # $Date: 1996/12/06 22:17:37 $ # $Author: etzold $ # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #EMBLNEW_DB:$library:[EMBLNEW group:@SEQUENCE_LIBS # format:@EMBL_FORMAT cachesize:2048 maxNameLen:15 # subentries:@EmblnewFeatures_DB # files:$file:emnew #] EMBL_DB:$library:[EMBL group:@SEQUENCE_LIBS partSize:1000000 comment:" Nucleotide Sequence Database from EBML" subentries:@EmblFeatures_DB format:@EMBL_FORMAT cachesize:2048 maxNameLen:30 files:{ # $file:est1 # $file:est2 # $file:est3 # $file:est4 # $file:est5 # $file:est6 # $file:est7 # $file:fun # $file:gss # $file:hum1 # $file:hum2 # $file:inv # $file:mam # $file:org # $file:patent # $file:phg # $file:pln # $file:pro # $file:rod # $file:sts # $file:syn # $file:unc # $file:vrl # $file:vrt # $file:em_est1 # $file:em_est2 # $file:em_est3 # $file:em_est4 # $file:em_est5 # $file:em_est6 # $file:em_est7 # $file:em_ba # $file:em_fun # $file:em_gss # $file:em_hum1 # $file:em_hum2 # $file:em_in # $file:em_om # $file:em_or # $file:em_ov # $file:em_pat $file:em_ph # $file:em_pl # $file:em_pr # $file:em_ro # $file:em_sts # $file:em_sy # $file:em_un # $file:em_vi } ] EMBL_FORMAT:$libformat:[syntax:@EMBL_SYNTAX fileType:{@DAT_FILE @SEQ_FILE} #orig format # fileType:{@GCGREF_FILE @GCGSEQ_FILE} #GCG format fields:{ $field:[@DF_ID code:id index:id indexToken:id] $field:@DF_ALL $field:[@DF_Accession code:acc index:str indexToken:acc tableToken:acc tableFormat:left] $field:[@DF_Division code:id index:str indexToken:div tableToken:div tableFormat:left] $field:[@DF_Molecule code:id index:str indexToken:mol tableToken:mol tableFormat:left] # $field:[@DF_DBOrigin code:acc index:str indexToken:dbOri # tableToken:dbOri tableFormat:left] # $field:[@DF_AccessionKey code:acc index:str indexToken:accKey # tableToken:accKey tableFormat:center] $field:[@DF_Description code:des index:str indexToken:des tableToken:t_des tableFormat:left] $field:[@DF_Keywords code:key index:str indexToken:key tableToken:key tableFormat:left] $field:[@DF_Organism code:org index:str indexToken:org] $field:[@DF_Authors code:ra index:str indexToken:authors tableToken:authors tableFormat:left] $field:[@DF_Date code:date index:int indexToken:date tableToken:date tableFormat:center] $field:[@DF_SeqLength code:sq index:int indexToken:seqLen tableToken:seqLen tableFormat:right] $field:[@DF_LINK code:dr] # $field:[@DF_DNASequence token:gcgseq format:embl] #GCG format $field:[@DF_DNASequence token:sequence format:embl] #orig format $field:[@DF_HeaderField name:'Feature Table Fields'] $field:[@DF_FtKey code:ft index:str indexToken:ftKey indexId:@SUBENTRY_ID tableToken:ftKey tableFormat:left] $field:[@DF_FtQualifier code:ft index:str indexToken:ftQual indexId:@SUBENTRY_ID] $field:[@DF_PID code:ft index:str indexToken:pid indexId:@SUBENTRY_ID] $field:[@DF_FtDescription code:ft index:str indexToken:ftDes indexId:@SUBENTRY_ID] $field:[@DF_FtSource code:ft index:str indexToken:ftSrc indexId:@SUBENTRY_ID] $field:[@DF_ChrsNo code:ft index:str indexToken:chrsNo indexId:@SUBENTRY_ID] $field:[@DF_FtMap code:ft index:str indexToken:map indexId:@SUBENTRY_ID] } ] EMBL_SYNTAX:$syntax:[file:"SRSDB:embl.is" ignore:" \t"] $syntax:[name:ftseq file:"SRSDB:ftseq.is" ignore:" \t\n"] #$link:[@EMBL_DB to:@?GENBANK_DB toField:@DF_ACCNO] #$link:[@EMBL_DB to:@?PIR_DB toField:@DF_ACCNO] #$link:[@EMBL_DB to:@?REBASE_DB toField:@DF_ID] #$link:[@EMBL_DB to:@?OMIM_DB toField:@DF_ID] #$link:[@EMBL_DB to:@?MEDLINE_DB toField:@DF_ID] EmblFeatures_DB:$library:[EMBL_features format:@EmblFeature_Format] EmblnewFeatures_DB:$library:[EMBLNEW_features format:@EmblFeature_Format] EmblFeature_Format:$libformat:[syntax:@EMBL_SYNTAX #idType:@SUBENTRY_ID tableFormat:left fields:{ $field:[@DF_ID token:ftId] # $field:[@DF_Accession code:acc fromParent:y] # $field:[@DF_Description code:des fromParent:y] $field:[@DF_FtKey token:ft tableToken:'t_ft|key'] $field:[@DF_FtQualifier token:ft tableToken:'t_ft|qual'] $field:[@DF_PID token:ft tableToken:'t_ft|db_xref'] $field:[@DF_FtDescription token:ft tableToken:'t_ft|note'] $field:[@DF_FtGene token:ft tableToken:'t_ft|gene'] $field:[@DF_FtProduct token:ft tableToken:'t_ft|product'] $field:[@DF_FtPartial token:ft tableToken:'t_ft|partial'] $field:[@DF_FtPseudo token:ft tableToken:'t_ft|pseudo'] $field:[@DF_FtNumber token:ft tableToken:'t_ft|number'] $field:[@DF_FtSource token:ft tableToken:ftSrc] $field:[@DF_ChrsNo token:ft tableToken:'t_ft|chromosome'] $field:[@DF_FtMap token:ft tableToken:'t_ft|map'] $field:[@DF_DNALocation token:ftLocat tableFormat:listing] } ] DF_FtGene:$srsfield:[Gene short:gen] DF_FtProduct:$srsfield:[Product short:pro] DF_FtPartial:$srsfield:[Partial short:par] DF_FtPseudo:$srsfield:[Pseudo short:pse] DF_FtNumber:$srsfield:[Number short:num] --------------1357101B5F987D624118B159 Content-Type: text/plain; charset=us-ascii; name="embl.is" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="embl.is" #!/bin/env icarus #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # $RCSfile: embl.is,v $ # $Revision: 1.10 $ # $Date: 1996/12/06 22:17:38 $ # $Author: etzold $ # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ $rules={ entry: ~ {$In:[file:text] $Out pre $Skip:0} ('ID ' {$not} ln)* ('ID '{$entryFip=$Fip $Wrt} ln {$App} (/( |ID|>>)/ {$Not} ln {$App})+ )? ~ # data fields fields: ~ {$In:entry $Out $Skip:1} id sep acc sep nid sep date sep f_des sep f_key sep (src tax? sep f_org? sep)+ (rn rc? rp? rx? ra rt? rl? sep)* link? sep (cmnt sep)* (fh f_ft*)? sep sq ~ sep: ~ {$Wrt:sep} ('XX' ln)* ~ id: ~ {$Wrt:id} 'ID' / *([A-Z0-9_]+)/ {$entryName=$1} ln ~ acc: ~ {$Wrt:acc} ('AC' ln)+ ~ nid: ~ {$Wrt:nid} ('NI' ln)* ~ date: ~ {$Wrt:date} ('DT' ln)+ ~ f_des: ~ {$Wrt:des} ('DE' ln)+ ~ src: ~ {$Wrt:org} ('OS' ln)+ ~ tax: ~ {$Wrt:org} ('OC' ln)+ ~ f_org: ~ {$Wrt:org} ('OG' ln)+ ~ rn: ~ {$Wrt:rn} ('RN' ln)+ ~ rc: ~ {$Wrt:rc} ('RC' ln)+ ~ rp: ~ {$Wrt:rp} ('RP' ln)+ ~ rx: ~ {$Wrt:rx} ('RX' ln)+ ~ ra: ~ {$Wrt:ra} ('RA' ln)+ ~ rt: ~ {$Wrt:rt} ('RT' ln)+ ~ rl: ~ {$Wrt:rl} ('RL' ln)+ ~ cmnt: ~ {$Wrt:cmnt} ('CC' ln)+ ~ link: ~ {$Wrt:link} ('DR' ln)+ ~ f_key: ~ {$Wrt:key} ('KW' ln)* ~ fh: ~ {$Wrt:fh} ('FH' ln)+ ~ f_ft: ~ {$Wrt:ft} 'FT' ln ('FT ' ln)* ~ sq: ~ {$Wrt:sq} 'SQ' ln ~ # parsing the sequence part from separate stream gcgseq: ~ { $In:[file:seq] $Out pre $s=$SeqNew $SeqMake:$s $Wrt:[s:$entryName] } '>>>>' {$seqFip=$Fip} (/[A-Z0-9]+/ seq | /[A-Z0-9]+_0/ seq (/>>>>[A-Z0-9]+_[1-9]+/ {$SeqTrunc:[$s len:10000]} seq)+) ~ seq: ~ (/.*2BIT *Len:/ /[0-9]+/ {$len=$Ct} ln ln {$SeqGet2Bit:[$s file:$File len:$len]} ('>>>>'{$Not} ln)*| /.*ASCII/ ln ln ('>>>>' {$Not} /.*/ {$SeqApp:[$s s:$Ct]})+) ~ sequence: ~ {$In:[file:seq share:text] $Out pre {$s=$SeqNew $seqFip=$Fip} $Wrt:[s:$entryName] $SeqMake:$s} ('ID' {$Not} ln {$SeqApp:[$s s:$Ct]})* ~ # for indexing i_id: ~ {$In:[entry] $Out:id} /ID +/ name {$Wrt} ~ i_div: ~ {$In:[fields c:id] $Out:div} /ID +/ name /[^;]+/ ';' /[^;]+/ ';' name {$Wrt} ~ i_mol: ~ {$In:[fields c:id] $Out:mol} /ID +/ name /[^;]+/ ';' /[^;]+/ {$Wrt} ~ i_acc: ~ {$In:[fields c:acc] $Out:acc} ('AC' (name {$Wrt} ';')+)+ ~ i_nid: ~ {$In:[fields c:nid] $Out:nid} 'NI' name {$Wrt} ~ i_dates: ~ { $In:[fields c:date] $Out:date init $month={JAN:1 FEB:2 MAR:3 APR:4 MAY:5 JUN:6 JUL:7 AUG:8 SEP:9 OCT:10 NOV:11 DEC:12} } /.* ([0-9]+)-([A-Z]+)-([0-9]+)[^\n]+Cre/ {$Wrt:[credate s:($1 + $month.$2*100 + $3*10000)]} ~ des: ~ {$In:[fields c:des] $Out} ('DE' (/\\(EC *([0-9]+\\.[0-9]+\\.[0-9]+\\.[0-9]+)/ {$Wrt:[s:$1]}| word{$Wrt} | sp)+ ln)+ ~ org: ~ {$In:[fields c:org] $Out} ('OC' (/[^;.\n]+/ {$Wrt} | /[^\n]/)*)+ | 'OS' /[^(\n]+/ {$Wrt:[s:$Trim:$Ct]} ('(' (/[^ \n)]+/ | /[^)]/)+)? | 'OG' /[^\n;.]+/ {$Wrt} ~ key: ~ {$In:[fields c:key] $Out} ('KW' (/[^\n;.]+/ {$Wrt} | /[^\n]/)+)+ ~ i_authors: ~ {$In:[fields c:ra] $Out:authors} (/RA/ (/([^.,\n]+) +([^,;\n]+)/ {$Uniq:[s:"$1,$2"]} /[,;]/)* ln)* ~ i_accKey: ~ {$In:[fields c:acc] $Out:accKey} 'AC' /[A-Z]+/ {$Wrt} ~ i_dbOri: ~ {$In:[fields c:acc] $Out:dbOri init { $dbOriN={ A:1 F:1 V:1 X:1 Y:1 Z:1 AA:2 AC:2 AD:2 B:2 G:2 H:2 I:2 J:2 K:2 L:2 M:2 N:2 R:2 S:2 T:2 U:2 W:2 AB:3 C:3 D:3 E:3} $dbName={1:EMBL 2:GenBank 3:DDBJ} } } 'AC' /[A-Z]+/ {$Wrt:[s:$dbName.$dbOriN.$Ct]} ~ i_seqLen: ~ {$In:[fields c:sq] $Out:seqLen} 'SQ Sequence' /[0-9]+/ {$Wrt} ~ # indexing features ftWord: ~ /[^" ,;:()\n.-]+/ ~ #" ftSep: ~ /[ ,;.:()-]+/ ~ ftKey: ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out} 'FT' /[^ ]+/ {$Wrt:[n:$ftN]} ~ ftQual: ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out} /[^\/]+/ (/\/([a-zA-Z0-9_]+)/ {$Wrt:[s:$1 n:$ftN]} (/=[a-zA-Z0-9_]+/ | /="[^"]+"/)? /[^\/]+/)* ~ #" chrsNo: ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out} /.+\/chromosome="?/ (/[^\n\" ]+/ {$Uniq:[n:$ftN n:0]} | '\nFT' | ' ')+ ~ #" ftSrc: ~ {$In:[fields c:ft count:ft var:$ftN] $Out} (/[^\/]+\/(tissue_type|cell_line|organism|strain|dev_stage|sex|clone_lib)="/ ('\nFT' | ftWord {$Uniq:[n:$ftN]} | ftSep)+ | '/')* ~ ftDes: ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out} (/[^\/]+\/(product|note|gene)="/ ('\nFT' | /NCBI gi: *[0-9]+/ | ftWord {$Uniq:[n:$ftN]} | ftSep)+ | '/')* ~ map: ~ {$In:[fields c:ft count:ft var:$ftN] $Out} /.+\/map="/ (/[^a-zA-Z0-9"]+/|/[a-zA-Z0-9]+/{$Wrt:[n:$ftN]})+ #" ~ pid: ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out} (/db_xref="?PID:([0-9a-zA-Z]+)/ {$Wrt:[n:$ftN s:$1]} | /[^\/]+\// )+ ~ # displaying features ftClean: ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out } 'FT' ln {$Wrt} ('FT' ln {$App})* ~ ftLoc: ~ {$In:ftClean $Out} /[^ ]+/ /[^\/]+/ {$Wrt} ~ ft: ~ {$In:[fields c:ft count:ft var:$ftN select:$subEntryN] $Out} /.*/ {$Wrt} ~ ftId: ~ {$In:[fields c:id] $Out} /.. *([A-Z0-9]+)/ {$Wrt:[s:"ID $1\_$subEntryN; parent: $1"]}~ h_ftId: ~ {$In:[ftId t:html]} /.*parent: */ /[A-Z0-9]+/ {$Rep:{$ParStr:emblIdR $Ct $Ct}} ~ t_ft: ~ {$In:ftClean $Out} /(]*>/ ~ h_links: ~ {$In:[fields c:link t:html] init{$hl={ 'SWISS-PROT': swissR DICTYDB: dictydbR GCRDB: gcrdbR MAIZEDB: maizedbR WORMPEP: wormpepR LISTA: listaR PIR: pirR YEPD: yepdR SGD: sgdR STYGENE: stygeneR HIV: hivR ECOGENE: ecogeneR ECO2DBASE: eco2dbaseR MIM: mimR SUBTILIST: subtilistR FLYBASE: flybaseR TRANSFAC: transfacR REBASE: rebaseR } } } (/DR/ dbName {$db=$Ct} ';' accno {$Rep:{$ParStr:$hl.$db $Ct $Ct}} ln)* ~ # other stuff word: ~ /[^" ,;:()\/=\n.-]+/ ~ sp: ~ /[ ,;.:()\/=-]+/ ~ lnCode: ~ /\n[A-Z][A-Z]/ ~ ln: ~ /[^\n]*\n/ ~ accno: ~ /[A-Z0-9]+/ ~ num: ~ /(<|>)?[0-9?]+/ ~ name: ~ /[a-zA-Z0-9_-]+/ ~ dbName: ~ /[^;]+/ ~ } if:$TestMode { $job = $JobNew:[prod:$rules skip:" " fileName:'/data/embl_dna/mam.dat'] while:$JobHasInput:$job { $JobTokens:[$job name:acc print:0] $JobTokens:[$job name:t_ft print:1] $JobNext:$job #$print:"-------->entry\n" } } --------------1357101B5F987D624118B159-- From owner-srs@net.bio.net Wed Dec 11 22:00:00 1996 Path: biosci!rutgers!uwm.edu!www.nntp.primenet.com!nntp.primenet.com!usenet.eel.ufl.edu!warwick!lyra.csx.cam.ac.uk!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: srs 5.0 - srscheck Date: Thu, 12 Dec 1996 14:51:49 +0000 Organization: SEQNET Lines: 50 Distribution: bionet Message-ID: <32B01C05.1CFB@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) Hello folks, I noted a few odd things with srscheck in the new SRS 5.0 If a library is up to date, it still puts a line like srsbuild PIR -f '' -xdir 'SRSINX:' -odir 'SRSINX:' -env 'unix' in the srsupdate file, which gives an error message when you run it. Sometimes commands for the compression (and merging) of up to date databases are inserted. As far as I could find out this occurs if one or more of its indices contain 0 entries. The fssp database at our site consists of a directory filled with symbolic links to the real fssp data, and the "suppos" and "comp3D" alternative fssp data. It indexes allright, but srscheck keeps on thinking that there are 0 entries in that directory, and orders a reindexing since the index contains 1090 entries. Another thing which causes some problems is that for single entry databases getz apparently expects entries to be in a file called "id.ext" ("id" the id of the entry, and "ext" the extension for the files in this database.) This works nice if you have a your pdb files named this way (e.g. 1azu.pdb), but at our site we have names like "pdb1azu.ent". Indexing goes fine, but retrieving the data is impossible. A similar problem exists with fssp, were a filename may have an additional character indicating a different chain. For the curious people - the experimental (and very much incomplete) SEQNET srs5.0 server can be found at http://www.seqnet.dl.ac.uk/srs5.0 - but don't expect things to work there yet..... Until we have all the icarus files sorted out for all the databases we have on our srs4 server (http://www.seqnet.dl.ac.uk/srs/srsc) we will not switch to srs5. Cheers, 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-srs@net.bio.net Thu Dec 12 22:00:00 1996 Newsgroups: bionet.software.srs Path: biosci!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!warwick!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!news From: Tao Jiang Subject: Re: question about SRS5.0 Sender: news@ebi.ac.uk (usenet news) Message-ID: <32B0B1D7.7C88435F@pku.edu.cn> Date: Fri, 13 Dec 1996 01:31:03 GMT To: Peter Rice Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii References: <32ACBDA7.57D9066B@pku.edu.cn> <32AEC9DA.2781@embl-heidelberg.de> <32AF65E2.36601FB1@pku.edu.cn> Mime-Version: 1.0 X-Mailer: Mozilla 3.01Gold (X11; I; Linux 2.0.0 i586) Organization: Network Center Lines: 23 Peter Rice wrote: > The changes worked for me. Memory usage dropped dramatically, at least > in the early stages (then I went home, and it was finished this morning). > Maybe something went wrong with the "srsmake srsbuild" step? Or else you > really have very little memory on your system. > > Our SRS 5.0 server will be available next week. > > I am still busy exploring the icarus files. I expect to be changing the > indexing methods, and adding new databases, frequently for some time yet. > -- > Well, in fact I have pnly 32M in my system. Then how much memory is proper for SRS5.0?? regards, -- Tao Jiang Fax: 86-10-62751982 Network Center Homepage: http://jiangt.pku.edu.cn/~jiangt/ Peking University Email: jiangt@pku.edu.cn From owner-srs@net.bio.net Thu Dec 12 22:00:00 1996 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: question about SRS5.0 Date: Fri, 13 Dec 1996 10:03:08 +0000 Organization: SEQNET Lines: 23 Distribution: bionet Message-ID: <32B129DB.41C6@dl.ac.uk> References: <32ACBDA7.57D9066B@pku.edu.cn> <32AEC9DA.2781@embl-heidelberg.de> <32AF65E2.36601FB1@pku.edu.cn> <32B0B1D7.7C88435F@pku.edu.cn> 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) Tao Jiang wrote: > > > Well, in fact I have pnly 32M in my system. Then how much > memory is proper for SRS5.0?? > > regards, > The DEC alpha on which I have our SRS server also has only 32 M, (and 155 M swapspace), and indexing the embl phage section takes only a few minutes. (although it is considerable slower than srs4) -- ----------------------------------------------------------------- | 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 Sun Dec 15 22:00:00 1996 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: question about SRS5.0 Date: Mon, 16 Dec 1996 13:28:33 +0000 Organization: SEQNET Lines: 69 Distribution: bionet Message-ID: <32B54E81.41C6@dl.ac.uk> References: <32ACBDA7.57D9066B@pku.edu.cn> <32AEC9DA.2781@embl-heidelberg.de> 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) Thure wrote: > > I found the bug, in fact there were two: > > 1) edit file src/icarus.c > > after line 670 you find > > if (!IcaCursorIsInput (job->inCursor, job->cursor)) { > /* CursorDelete (&job->cursor); */ > job->cursor = NULL; > > } > > remove the comments and rebuild srsbuild: > > srsmake srsbuild > > 2) edit icarus/db/embl.is > > around line 55 you find > > seq: ~ (/.*2BIT *Len:/ /[0-9]+/ {$len=$Ct} ln ln > {$s=$SeqGet2Bit:[$s file:$File len:$len]} ('>>>>'{$Not} ln)*| > /.*ASCII/ ln ln ('>>>>' {$Not} /.*/ {$SeqApp:[$s > s:$Ct]})+) ~ > > change '$s=$SeqGet2Bit' to '$SeqGet2Bit' > > regards > thure Despite the changes, I seem to have a memory problem. I tried to index the new EMBL release this weekend, and it crashed with this message: ...no. 720600, MJU67483 SRSDB:embl.is:72: error: insufficient memory - error during malloc, could not allocate "sequence" I retried, but now tracked memory usage during srsbuild, and it appears that after writing a subindex (*_1.inx etc), memory usage hardly decreases, and continues to increase when srsbuild works further through the database. I would expect that a significant amount of memory would be freed after writing an index file, or that memory usage almost stops growing after writing the first one. Is it possible there is a problem with freeing/reallocating memory after a subindexfile has been written ? This was with gcg formatted embl. I also made changes to the embl.i and embl.is files, but I don't really think that causes the problem (Ofcourse I might be completely wrong with that :-)) Cheers, 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-srs@net.bio.net Mon Dec 16 22:00:00 1996 Newsgroups: bionet.software.srs Path: biosci!rutgers!uwm.edu!news-peer.gsl.net!news.gsl.net!howland.erols.net!agate!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!news From: Tao Jiang Subject: Re: question about SRS5.0 Sender: news@ebi.ac.uk (usenet news) Message-ID: <32B5FAE8.4E059D36@pku.edu.cn> Date: Tue, 17 Dec 1996 01:44:08 GMT To: Thure Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii References: <32ACBDA7.57D9066B@pku.edu.cn> <32AEA3C2.41C6@embl-heidelberg.de> Mime-Version: 1.0 X-Mailer: Mozilla 3.01Gold (X11; I; Linux 2.0.0 i586) Organization: Network Center Lines: 25 Thure wrote: > then you must change the file names at the beginning of the file > > $file:pro > > will have to change to > > $file:em_pro > Is $file:pro means the gcg format while $file:em_pro means the original format? In my CD the file name is pro with original format, and should I need to change its name to em_pro after I copy it to hard disk? > regards > thure -- Tao Jiang Fax: 86-10-62751982 Network Center Homepage: http://jiangt.pku.edu.cn/~jiangt/ Peking University Email: jiangt@pku.edu.cn From owner-srs@net.bio.net Tue Dec 17 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!nntp.uio.no!news.apfel.de!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: srs5.01 Date: Wed, 18 Dec 1996 23:56:03 +0100 Organization: EMBL Lines: 29 Distribution: world Message-ID: <32B87683.167E@embl-heidelberg.de> NNTP-Posting-Host: kappa.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V2.0 alpha) Dear folks, this is to announce version 5.01 of SRS. The main difference is the fix of the memory fragmentation problem with srsbuild and EMBL indices. A few minor things got fixed too: o "download page" is now functional. o swissprot and embl entries have no longer duplicated SQ lines o added the Citation index for both Swissprot and EMBL o the install procedure produces by default optimized code (O2) the distribution is available as ftp://www.embl-heidelberg.de/pub/databases/trembl/srs5_01.tar.gz regards Thure Etzold Jonny Weare -- =============================================================================== 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 Tue Dec 17 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!voskovec.radio.cz!btnet-feed2!unlisys!cs.tu-berlin.de!zrz.TU-Berlin.DE!news-ber1.dfn.de!news-lei1.dfn.de!news-nue1.dfn.de!news-mue1.dfn.de!news-stu1.dfn.de!news-kar1.dfn.de!news-koe1.dfn.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: question about SRS5.0 Date: Wed, 18 Dec 1996 11:16:39 +0100 Organization: EMBL Lines: 45 Distribution: world Message-ID: <32B7C487.41C6@embl-heidelberg.de> References: <32ACBDA7.57D9066B@pku.edu.cn> <32AEC9DA.2781@embl-heidelberg.de> <32B54E81.41C6@dl.ac.uk> NNTP-Posting-Host: kappa.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V2.0 alpha) To: Martin Hilbers CC: Tao Jiang Martin Hilbers wrote: > > Despite the changes, I seem to have a memory problem. I tried to > index the new EMBL release this weekend, and it crashed with this > message: > > ...no. 720600, MJU67483 > SRSDB:embl.is:72: error: insufficient memory - error during malloc, > could not allocate "sequence" > sorry for the long silence - I was sick for a couple of days. I found the problem with index building for EMBL. It is not caused by a memory leak but by memory fragmentation. Building the index chunks iteratively requires large chunks of memory to be freed and allocated at each run and for some reason the program gets new memory from the system instead of reclaiming freed blocks. This behaviour is much more pronounced on irix than osf1. srsbuild does now the memory management for these large chunks itself which seems to solve the problem. I managed to build EMBL with less than 50 mbyte virtual memory Tao, since you have only 32mb you should really try to upgrade your machine but in the meantime you could try to set the partition size to 60000 EMBL_DB:$library:[EMBL group:@SEQUENCE_LIBS partSize:60000 ... We hope to create a new version with these changes by the end of the day which will be announced. 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 Wed Dec 18 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!nntp.uio.no!news.apfel.de!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news-koe1.dfn.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Johnathon Weare Newsgroups: bionet.software.srs Subject: Re: srs5.01 Date: 19 Dec 1996 18:39:19 +0100 Organization: EMBL Heidelberg Lines: 11 Distribution: world Message-ID: References: <32B87683.167E@embl-heidelberg.de> NNTP-Posting-Host: dove.embl-heidelberg.de X-Newsreader: Gnus v5.3/Emacs 19.32 Instead of ftp://www.embl-heidelberg.de/pub/databases/trembl/srs5_01.tar.gz read ftp://ftp.embl-heidelberg.de/pub/databases/trembl/srs5_01.tar.gz Johnny From owner-srs@net.bio.net Wed Dec 18 22:00:00 1996 Path: biosci!britbio.co.uk!dudgeon From: dudgeon@britbio.co.uk (Tim Dudgeon) Newsgroups: bionet.software.srs Subject: hssp swissprot links Date: 19 Dec 1996 09:08:55 -0800 Organization: British Biotech Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <32B96831.6231@britbio.co.uk> NNTP-Posting-Host: net.bio.net Dear SRS-folk, I'm having problems building the hssp-swissprot link with SRS4.08. When I do: srsbuild HSSP -l -xdir 'SRSINX:' -odir 'SRSINX:' -env 'unix' I (eventually) get: e__settoosmall, set has not enough space for IDs attempt to copy 300001 IDs where only for 300000 is space Looks like I need to reparameterise something. Any suggestions? Tim -- Dr. Tim Dudgeon Phone: 01865 748747 British Biotech Pharmaceuticals Ltd. FAX: 01865 717598 Watlington Road, Oxford, OX4 5LY, UK email: dudgeon@britbio.co.uk From owner-srs@net.bio.net Fri Dec 20 22:00:00 1996 Path: biosci!biosci!not-for-mail From: malik@uranus.ebi.ac.uk (Ansar Malik) Newsgroups: bionet.immunology,bionet.molbio.embldatabank,bionet.software.srs Subject: ANNOUNCEMENT: Immunogenetics IMGT database - update Date: 21 Dec 1996 13:45:31 -0800 Organization: European Bioinformatics Institute (EMBL) - UK Lines: 62 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: malik@uranus.ebi.ac.uk (Ansar Malik) NNTP-Posting-Host: net.bio.net Keywords: database, immunogenetics, immunoglobulin, T cell receptor cell,sequences annotation, DNA sequence Xref: biosci bionet.immunology:10503 bionet.molbio.embldatabank:738 bionet.software.srs:383 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). 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: Release 96.11 contains 7937 fully annotated sequence entries. LIGM Montpellier :Marie-Paule Lefranc (coordinator) Veronique Giudicelli,Denys Chaume EMBL-EBI :Ansar Malik IFG :Werner Mueller ACCESS/DATA DISTRIBUTION ======================== SRS server: http://www.ebi/srs/srsc NOTE: Selecting this option will bring you to the SRS qerry interface page, where you have to select "search Sequence Libraries" WWW server: http://www.ebi.ac.uk/imgt/ FTP server: ftp.ebi.ac.uk/pub/databases/imgt E_MAIL server: email netserv@ebi.ac.uk -- send "help IMGT" in the mail body. 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 Mon Dec 23 22:00:00 1996 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!arclight.uoregon.edu!news.ibm.net.il!news.biu.ac.il!news.tau.ac.il!usenet From: yoav_ab@netvision.net.il (yoav abrahami) Newsgroups: bionet.software.srs Subject: looking for beaker Date: Tue, 24 Dec 1996 18:33:33 GMT Organization: Tel-Aviv University Computation Center Lines: 8 Message-ID: <32c021e2.13313563@news.tau.ac.il> NNTP-Posting-Host: slip-303.tau.ac.il X-Newsreader: Forte Free Agent 1.1/32.230 Hello there! Maybe someone has a version of the sottware "Beaker" for PC?( not for mac!!!) I will be greatfull if someone can send me a copy or even information on a ftp site i can download it from. my e-mail is: yoav_ab@netvision.net.il thanx, yoav. (israel) From owner-srs@net.bio.net Thu Dec 26 22:00:00 1996 Path: biosci!news.artemis.com!uunet!in1.uu.net!206.229.87.25!news.sprintlink.net!news-peer.sprintlink.net!nntp.coast.net!oleane!pasteur.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: swissprot and embl under SRS5_01 Date: Fri, 27 Dec 1996 11:24:51 +0100 Organization: INFOBIOGEN Lines: 19 Message-ID: <32C3A3F3.642C@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 sun4d) Hello all, I find some problems in srs5_01 with embl and swissprot I have message like : unknown object input file type "seq" does not exist It was the same error message as in version srs5_0 The changes were made in icarus.c and embl.is Thanks for your help in advance -- --------------------------------------------------- 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 Thu Dec 26 22:00:00 1996 Path: biosci!newshost.lanl.gov!biosci!rutgers!iag.net!www.nntp.primenet.com!nntp.primenet.com!nntp.coast.net!oleane!pasteur.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: swissprot and embl under SRS5_01 Date: Fri, 27 Dec 1996 11:24:51 +0100 Organization: INFOBIOGEN Lines: 19 Message-ID: <32C3A3F3.642C@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 sun4d) Hello all, I find some problems in srs5_01 with embl and swissprot I have message like : unknown object input file type "seq" does not exist It was the same error message as in version srs5_0 The changes were made in icarus.c and embl.is Thanks for your help in advance -- --------------------------------------------------- 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 Thu Dec 26 22:00:00 1996 Path: biosci!lhc.nlm.nih.gov!biosci!rutgers!iag.net!www.nntp.primenet.com!nntp.primenet.com!nntp.coast.net!oleane!pasteur.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: swissprot and embl under SRS5_01 Date: Fri, 27 Dec 1996 11:24:51 +0100 Organization: INFOBIOGEN Lines: 19 Message-ID: <32C3A3F3.642C@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 sun4d) Hello all, I find some problems in srs5_01 with embl and swissprot I have message like : unknown object input file type "seq" does not exist It was the same error message as in version srs5_0 The changes were made in icarus.c and embl.is Thanks for your help in advance -- --------------------------------------------------- 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 Thu Dec 26 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!www.nntp.primenet.com!nntp.primenet.com!nntp.coast.net!oleane!pasteur.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: swissprot and embl under SRS5_01 Date: Fri, 27 Dec 1996 11:24:51 +0100 Organization: INFOBIOGEN Lines: 19 Message-ID: <32C3A3F3.642C@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 sun4d) Hello all, I find some problems in srs5_01 with embl and swissprot I have message like : unknown object input file type "seq" does not exist It was the same error message as in version srs5_0 The changes were made in icarus.c and embl.is Thanks for your help in advance -- --------------------------------------------------- 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 Thu Dec 26 22:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!www.nntp.primenet.com!nntp.primenet.com!nntp.coast.net!oleane!pasteur.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: swissprot and embl under SRS5_01 Date: Fri, 27 Dec 1996 11:24:51 +0100 Organization: INFOBIOGEN Lines: 19 Message-ID: <32C3A3F3.642C@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 sun4d) Hello all, I find some problems in srs5_01 with embl and swissprot I have message like : unknown object input file type "seq" does not exist It was the same error message as in version srs5_0 The changes were made in icarus.c and embl.is Thanks for your help in advance -- --------------------------------------------------- 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 Thu Dec 26 22:00:00 1996 Path: biosci!agate!howland.erols.net!nntp.coast.net!oleane!pasteur.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: swissprot and embl under SRS5_01 Date: Fri, 27 Dec 1996 11:24:51 +0100 Organization: INFOBIOGEN Lines: 19 Message-ID: <32C3A3F3.642C@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 sun4d) Hello all, I find some problems in srs5_01 with embl and swissprot I have message like : unknown object input file type "seq" does not exist It was the same error message as in version srs5_0 The changes were made in icarus.c and embl.is Thanks for your help in advance -- --------------------------------------------------- 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 Thu Dec 26 22:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!nntp.coast.net!oleane!pasteur.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: swissprot and embl under SRS5_01 Date: Fri, 27 Dec 1996 11:24:51 +0100 Organization: INFOBIOGEN Lines: 19 Message-ID: <32C3A3F3.642C@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 sun4d) Hello all, I find some problems in srs5_01 with embl and swissprot I have message like : unknown object input file type "seq" does not exist It was the same error message as in version srs5_0 The changes were made in icarus.c and embl.is Thanks for your help in advance -- --------------------------------------------------- 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 Thu Dec 26 22:00:00 1996 Path: biosci!rutgers!iag.net!www.nntp.primenet.com!nntp.primenet.com!nntp.coast.net!oleane!pasteur.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: swissprot and embl under SRS5_01 Date: Fri, 27 Dec 1996 11:24:51 +0100 Organization: INFOBIOGEN Lines: 19 Message-ID: <32C3A3F3.642C@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 sun4d) Hello all, I find some problems in srs5_01 with embl and swissprot I have message like : unknown object input file type "seq" does not exist It was the same error message as in version srs5_0 The changes were made in icarus.c and embl.is Thanks for your help in advance -- --------------------------------------------------- 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 Thu Dec 26 22:00:00 1996 Path: biosci!rutgers!cnn.Princeton.EDU!udel-eecis!gatech!news.sprintlink.net!news-peer.sprintlink.net!voskovec.radio.cz!btnet-feed2!unlisys!cs.tu-berlin.de!zrz.TU-Berlin.DE!news-ber1.dfn.de!news-lei1.dfn.de!news-nue1.dfn.de!news-mue1.dfn.de!news-stu1.dfn.de!news-kar1.dfn.de!news-koe1.dfn.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: question about SRS5.0 Date: Wed, 18 Dec 1996 11:16:39 +0100 Organization: EMBL Lines: 45 Distribution: world Message-ID: <32B7C487.41C6@embl-heidelberg.de> References: <32ACBDA7.57D9066B@pku.edu.cn> <32AEC9DA.2781@embl-heidelberg.de> <32B54E81.41C6@dl.ac.uk> NNTP-Posting-Host: kappa.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V2.0 alpha) To: Martin Hilbers CC: Tao Jiang Martin Hilbers wrote: > > Despite the changes, I seem to have a memory problem. I tried to > index the new EMBL release this weekend, and it crashed with this > message: > > ...no. 720600, MJU67483 > SRSDB:embl.is:72: error: insufficient memory - error during malloc, > could not allocate "sequence" > sorry for the long silence - I was sick for a couple of days. I found the problem with index building for EMBL. It is not caused by a memory leak but by memory fragmentation. Building the index chunks iteratively requires large chunks of memory to be freed and allocated at each run and for some reason the program gets new memory from the system instead of reclaiming freed blocks. This behaviour is much more pronounced on irix than osf1. srsbuild does now the memory management for these large chunks itself which seems to solve the problem. I managed to build EMBL with less than 50 mbyte virtual memory Tao, since you have only 32mb you should really try to upgrade your machine but in the meantime you could try to set the partition size to 60000 EMBL_DB:$library:[EMBL group:@SEQUENCE_LIBS partSize:60000 ... We hope to create a new version with these changes by the end of the day which will be announced. 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 Thu Dec 26 22:00:00 1996 Path: biosci!bloom-beacon.mit.edu!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!su-news-hub1.bbnplanet.com!arclight.uoregon.edu!news.ibm.net.il!news.biu.ac.il!news.tau.ac.il!usenet From: yoav_ab@netvision.net.il (yoav abrahami) Newsgroups: bionet.software.srs Subject: looking for beaker Date: Tue, 24 Dec 1996 18:33:33 GMT Organization: Tel-Aviv University Computation Center Lines: 8 Message-ID: <32c021e2.13313563@news.tau.ac.il> NNTP-Posting-Host: slip-303.tau.ac.il X-Newsreader: Forte Free Agent 1.1/32.230 Hello there! Maybe someone has a version of the sottware "Beaker" for PC?( not for mac!!!) I will be greatfull if someone can send me a copy or even information on a ftp site i can download it from. my e-mail is: yoav_ab@netvision.net.il thanx, yoav. (israel) From owner-srs@net.bio.net Thu Dec 26 22:00:00 1996 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!uunet!in1.uu.net!206.229.87.25!news.sprintlink.net!news-peer.sprintlink.net!nntp.coast.net!oleane!pasteur.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: swissprot and embl under SRS5_01 Date: Fri, 27 Dec 1996 11:24:51 +0100 Organization: INFOBIOGEN Lines: 19 Message-ID: <32C3A3F3.642C@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 sun4d) Hello all, I find some problems in srs5_01 with embl and swissprot I have message like : unknown object input file type "seq" does not exist It was the same error message as in version srs5_0 The changes were made in icarus.c and embl.is Thanks for your help in advance -- --------------------------------------------------- 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 Thu Dec 26 22:00:00 1996 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.sprintlink.net!news-peer.sprintlink.net!nntp.coast.net!oleane!pasteur.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: swissprot and embl under SRS5_01 Date: Fri, 27 Dec 1996 11:24:51 +0100 Organization: INFOBIOGEN Lines: 19 Message-ID: <32C3A3F3.642C@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 sun4d) Hello all, I find some problems in srs5_01 with embl and swissprot I have message like : unknown object input file type "seq" does not exist It was the same error message as in version srs5_0 The changes were made in icarus.c and embl.is Thanks for your help in advance -- --------------------------------------------------- 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 Dec 27 22:00:00 1996 Path: biosci!rutgers!igor.rutgers.edu!newsserver.jvnc.net!news.merck.com!cam-news-feed1.bbnplanet.com!delphi.com!news-feed.iguide.com!news.uoregon.edu!arclight.uoregon.edu!feed1.news.erols.com!howland.erols.net!usc!news.cerf.net!news1.ni.net!news From: polo@haha.com (polo) Newsgroups: bionet.software.srs Subject: ***** http://206.103.186.160 ***** Date: Wed, 18 Dec 1996 06:04:11 GMT Organization: Network Intensive Lines: 1 Sender: BatMan Message-ID: <32be895a.505995@news.ni.net> Reply-To: polo@haha.com NNTP-Posting-Host: yyuen.newgeneration.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit From owner-srs@net.bio.net Sun Dec 29 22:00:00 1996 Path: biosci!rutgers!iag.net!news.sgi.com!esiee.fr!jussieu.fr!oleane!pasteur.fr!univ-lyon1.fr!news.imag.fr!ciril.fr!univ-angers.fr!univ-rennes1.fr!cict.fr!news From: Lionel Mourey Newsgroups: bionet.software.srs Subject: Professor position at Toulouse University Date: Mon, 30 Dec 1996 16:12:37 +0100 Organization: CNRS-IPBS Lines: 50 Message-ID: <32C7DBE5.15FB@ecstasy.cemes.fr> NNTP-Posting-Host: ecstasy.cemes.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; OSF1 V3.2 alpha) ----------------------------------------- PROFESSOR POSITION AT TOULOUSE UNIVERSITY ----------------------------------------- A Professor position is opened at Toulouse University in 1997. The area of scientific expertise is Biocomputing. Teaching will start in October 1997. Research will be held at the CNRS Institute of Pharmacology and Structural Biology (IPBS) in the areas of protein structure, protein-protein and protein-ligand interactions with special emphasis in sequence and structure similariry searching, human and microbial genome analysis, computer sciences. Completed applications must be received by January 17, 1997 at: UPS, Service du personnel enseignant 118 route de Narbonne 31058 - TOULOUSE FRANCE Additional informations can be obtained from: Pr. Jean CROS, IPBS, Tel: 33 05 61 17 59 18 Fax: 33 05 61 17 59 94 email: cros@ipbs.fr Dr. J. P. Samama, IPBS Tel: 33 05 62 25 78 08 Fax: 33 05 62 25 79 60 email: samama@ipbs.fr or samama@ecstasy.cemes.fr Dr. G. Puzo, IPBS Tel: 33 05 61 33 59 10 Fax: 33 05 61 33 58 86 email: germain@lptf.biotoul.fr Institut de Pharmacologie et de Biologie Structurale CNRS, UPR 9062 205 Route de Narbonne 31 077 - Toulouse, France ------------------------------------------------------------------- Lionel MOUREY Groupe de Cristallographie Biologique de l'IPBS CEMES-LOE/CNRS 29 rue Jeanne Marvig Tel (33 or 0) 5 62 25 79 63 BP 4347 Fax (33 or 0) 5 62 25 79 60 31055 TOULOUSE CEDEX e-mail mourey@ipbs.fr France -------------------------------------------------------------------