From owner-srs@net.bio.net Tue Jul 01 23:00:00 1997 Newsgroups: bionet.software.srs Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!news From: etzold Subject: [Re: indexing subdirectiories] Sender: news@ebi.ac.uk (usenet news) Message-ID: <33B93604.B28DA1C@ebi.ac.uk> X-Priority: 3 (Normal) Date: Tue, 1 Jul 1997 16:53:24 GMT Content-Type: multipart/mixed; boundary="------------988835B85C2726CC8187CEEE" Mime-Version: 1.0 X-Mailer: Mozilla 4.01 [en] (Win95; I) Organization: EMBL-EBI Lines: 42 This is a multi-part message in MIME format. --------------988835B85C2726CC8187CEEE Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit --------------988835B85C2726CC8187CEEE Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-ID: <33B92256.171AF45A@ebi.ac.uk> Date: Tue, 01 Jul 1997 16:29:26 +0100 From: etzold Organization: EMBL-EBI X-Mailer: Mozilla 4.01 [en] (Win95; I) MIME-Version: 1.0 To: Mike Tennant Subject: Re: indexing subdirectiories X-Priority: 3 (Normal) References: <33B911C9.167E@mh.uk.sbphrd.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Mike Tennant wrote: > > Hi, > I'm trying to index our pdb hierarchy, which has the format > /pdb/dist/*/*.ent.gz, but can't get srs5.05 to get past the first wild > card (which is a set of directories). Does anybody know whether this can > be done? funny! i am working on that right now...which means that it cannot be done at the moment. This will be possible with the next release 5.0.6. regards thure --------------988835B85C2726CC8187CEEE-- From owner-srs@net.bio.net Tue Jul 01 23:00:00 1997 Path: biosci!rutgers!news.sgi.com!news.msfc.nasa.gov!europa.clark.net!newsfeed.internetmci.com!news.wolsi.com!news.aros.net!not-for-mail From: "Chuck Nelson" Newsgroups: bionet.software.srs Subject: Chat with a Tech, Free... Date: 1 Jul 1997 18:19:36 GMT Organization: Free Tech Lines: 5 Message-ID: <01bc8612$46bc2540$4618adcf@chuck> NNTP-Posting-Host: pm3-5.slc.aros.net X-Newsreader: Microsoft Internet News 4.70.1155 Want to ask a tech, a question? PC software, hardware questions.. Free Technical Support. Come to: http://www.free-tech.com From owner-srs@net.bio.net Wed Jul 02 23:00:00 1997 From: "Chuck Nelson" Newsgroups: bionet.software.srs Subject: Want Answers? Date: 2 Jul 1997 23:30:10 GMT Organization: Free Tech Lines: 9 Message-ID: <01bc8706$d3f47c60$0118adcf@chuck> NNTP-Posting-Host: pm1-0.slc.aros.net X-Newsreader: Microsoft Internet News 4.70.1155 Path: biosci!daresbury!lyra.csx.cam.ac.uk!server1.netnews.ja.net!server5.netnews.ja.net!server3.netnews.ja.net!baron.netcom.net.uk!netcom.net.uk!cpk-news-hub1.bbnplanet.com!su-news-feed4.bbnplanet.com!news.bbnplanet.com!gronk.provo.novell.com!news.cs.utah.edu!news.aros.net!not-for-mail Want your questions ansered now? Have "How To" Questions for both hardware and software. Free technical support via form mail and chat. Free Tech, Technical Support Center Come to: http://www.free-tech.com From owner-srs@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: etzold Newsgroups: bionet.software.srs Subject: Re: indexing multiple blast files Date: Thu, 03 Jul 1997 13:21:32 +0100 Organization: EMBL-EBI Message-ID: <33BB994C.6EF46EAA@ebi.ac.uk> References: <33BB73D5.41C6@britbio.co.uk> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: Tim Dudgeon X-Priority: 3 (Normal) Lines: 47 Tim Dudgeon wrote: > I am wanting to set up SRS5 to index multiple blast files (pregenerated > output, not generating the blast output within SRS). > > I've made what I beleive should be the required changes by including a > MULTI_BLAST database, based on what is already in blast.i and on how > hssp.i handles multiple input files, but I'm getting run time errors: > > MULTI_BLAST_DB:$library:[MULTI_BLAST group:@APPLICATION_LIBS > comment:"" > format:@MULTI_BLAST_FORMAT maxNameLen:40 ifiles:{"blast.i" "blast.is"} > type:user > # files:{ > # $file:tmp > # } > ] the problem is that at the moment there is the choice between 1) each entry is in a separate file and 2) entries are contained in one or more flatfiles. in the latter case the file names as attribute "files" of $library MUST be specified. Searching files with a search expression as for hssp (*.hssp) work only for the single entry/file case. That means to fix the problem quickly you need to remove the above comments and write something like files:{ $file:tmp1 $file:tmp2 ... } ...obviously that is not what you want since the names and number fo the blast output files will probably vary quite a lot. To make that a little more flexible you could write a script that generates the 'files' part, inserts it into blast.i and runs srssection ....sorry about that! Since I am working on the problem with the multiple directories for pdb i will probably fix the multiple blast file problem next since the too are quite related (at least as seen from SRS's perspective). regards Thure problems From owner-srs@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!britbio.co.uk!dudgeon From: dudgeon@britbio.co.uk (Tim Dudgeon) Newsgroups: bionet.software.srs Subject: indexing multiple blast files Date: 3 Jul 1997 03:41:39 -0700 Organization: British Biotech Lines: 117 Sender: daemon@net.bio.net Distribution: world Message-ID: <33BB73D5.41C6@britbio.co.uk> NNTP-Posting-Host: net.bio.net Hi, Here's a question for the icarus gurus amongst you. I am wanting to set up SRS5 to index multiple blast files (pregenerated output, not generating the blast output within SRS). I've made what I beleive should be the required changes by including a MULTI_BLAST database, based on what is already in blast.i and on how hssp.i handles multiple input files, but I'm getting run time errors: % $SRSEXE/srsbuild multi_blast ...processing MULTI_BLAST SRSICA:icarus.i:77: error: insufficient memory - error during malloc, could not allocate "library file objects" Can anyone point out the error of my ways. My new blast.i is as follows: #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # $RCSfile: blast.i,v $ # $Revision: 1.4 $ # $Date: 1997/03/03 18:33:46 $ # $Author: srs $ # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BLAST_DB:$library:[BLAST group:@APPLICATION_LIBS comment:"" format:@BLAST_FORMAT maxNameLen:40 ifiles:{"blast.i" "blast.is"} type:user files:{ $file:tmp } ] MULTI_BLAST_DB:$library:[MULTI_BLAST group:@APPLICATION_LIBS comment:"" format:@MULTI_BLAST_FORMAT maxNameLen:40 ifiles:{"blast.i" "blast.is"} type:user # files:{ # $file:tmp # } ] BLAST_FORMAT:$libformat:[fileType:@BLAST_FILE syntax:@BLAST_SYNTAX fields:{ $field:[@DF_ID code:title index:id indexToken:id] $field:[@DF_TopMatch code:tmatch tableToken:t_tmatch tableFormat:left] $field:[@DF_Alignment code:tmatch tableToken:t_entry tableFormat:left] $field:[@DF_TopScore code:tscore1 index:int indexToken:score tableToken:score tableFormat:right] $field:[@DF_PercIdent code:tscore2 index:int indexToken:percIdent tableToken:percIdent tableFormat:right] $field:[@DF_QueryBeg code:tmatch index:int indexToken:queryBeg tableToken:queryBeg tableFormat:right] $field:[@DF_QueryEnd code:tmatch index:int indexToken:queryEnd tableToken:queryEnd tableFormat:right] $field:[@DF_MatchLen code:tmatch index:int indexToken:matchLen tableToken:matchLen tableFormat:right] $field:[@DF_LINK index:link code:link indexToken:link] } ] MULTI_BLAST_FORMAT:$libformat:[fileType:@MULTI_BLAST_FILE syntax:@BLAST_SYNTAX fields:{ $field:[@DF_ID code:title index:id indexToken:id] $field:[@DF_TopMatch code:tmatch tableToken:t_tmatch tableFormat:left] $field:[@DF_Alignment code:tmatch tableToken:t_entry tableFormat:left] $field:[@DF_TopScore code:tscore1 index:int indexToken:score tableToken:score tableFormat:right] $field:[@DF_PercIdent code:tscore2 index:int indexToken:percIdent tableToken:percIdent tableFormat:right] $field:[@DF_QueryBeg code:tmatch index:int indexToken:queryBeg tableToken:queryBeg tableFormat:right] $field:[@DF_QueryEnd code:tmatch index:int indexToken:queryEnd tableToken:queryEnd tableFormat:right] $field:[@DF_MatchLen code:tmatch index:int indexToken:matchLen tableToken:matchLen tableFormat:right] $field:[@DF_LINK index:link code:link indexToken:link] } ] DF_TopMatch:$srsfield:[TopMatch short:tma] DF_TopScore:$srsfield:[TopScore short:tsc] DF_PercIdent:$srsfield:[PercentIdentity short:pid] DF_QueryBeg:$srsfield:[QueryMatchBeginPos short:qbp] DF_QueryEnd:$srsfield:[QueryMatchEndPos short:qep] DF_MatchLen:$srsfield:[MatchLength short:mtl] BLAST_SYNTAX:$syntax:[file:"SRSDB:blast.is" ignore:" "] BLAST_FILE:$filetype:[typename:blast maxline:100] MULTI_BLAST_FILE:$FileType:[ singleEntry:n maxline:100 saveName:file saveNameLength:20 # searchName:'*.blastp' typeName:'blastp' ] $link:[@BLAST_DB to:@?SWISSPROT_DB token:'link|swiss' toField:@DF_Accession] -- Dr. Tim Dudgeon Phone: 01865 748747 British Biotech Pharmaceuticals Ltd. FAX: 01865 717598 Watlington Road, Oxford, OX4 5LY, UK email: dudgeon@britbio.co.uk From owner-srs@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!howland.erols.net!newsfeed.nacamar.de!news-kar1.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!news.rediris.es!news.uam.es!newsmasters From: txomsy@cnb.uam.es (José R. Valverde) Newsgroups: bionet.software.srs Subject: Re: [Re: indexing subdirectiories] Date: 3 Jul 1997 09:33:20 GMT Organization: EMBnet/CNB Lines: 47 Message-ID: <5pfrl0$q4n@acebo.sdi.uam.es> References: <33B93604.B28DA1C@ebi.ac.uk> NNTP-Posting-Host: bossa-nova.cnb.uam.es Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.8 In article <33B93604.B28DA1C@ebi.ac.uk>, etzold writes: > Mike Tennant wrote: >> >> Hi, >> I'm trying to index our pdb hierarchy, which has the format >> /pdb/dist/*/*.ent.gz, but can't get srs5.05 to get past the first wild >> card (which is a set of directories). Does anybody know whether this can >> be done? > > funny! i am working on that right now...which means that it cannot > be done at the moment. This will be possible with the next release > 5.0.6. > Well, meanwhile, maybe it would work to make links to those files in another directory. Mike doesn't say, but I guess the problem he refers to is that he's got the entries sorted by starting letters in corresponding characters. Now, if SRS wants them in a single directory, a paliative solution could be to link the files in a single directory. Something like cd /.../pdb/dist mkdir all_entries cd all_entries ln -s ../*/* . You may even remove the "s" and make those hard-links, wherever the files would be exactly the same as the original ones, only they would not take any more space than the directory entries take, which should be a lot less than the actual files themselves. Of course, you may have some trouble if you update PDB nightly, since you'd already have thousands of old links, and running that nightly would waste a lot of cycles and create many errors. Nothing easier to fix: use 'find' testing for '-ctime -nodays' where 'nodays' is the period with which you update your links. I know, it's a kludge, but works and saves a lot of space and trouble. After all, that's one of the beauties of Unix, isn't it? jr -- Jose R. Valverde EMBnet/CNB From owner-srs@net.bio.net Wed Jul 02 23:00:00 1997 Path: biosci!OBZOR.BIO21.ACAD.BG!ttsonev From: ttsonev@OBZOR.BIO21.ACAD.BG (biofac) Newsgroups: bionet.software.srs Subject: Please, Help! Date: 3 Jul 1997 10:04:13 -0700 Organization: Institute of Plant Physiology Lines: 137 Sender: daemon@net.bio.net Distribution: world Message-ID: <33BBDB4E.D514335A@obzor.bio21.acad.bg> NNTP-Posting-Host: net.bio.net Sofia University "St Kliment Ohridsky"
Faculty of Biology
8, Dragan Tsankov Blvd
1421 Sofia, Bulgaria
Tel: (3592) 63301
Fax (3592) 658079

Dear Sirs,

The  daughter of  a colleague  of  ours,  chief  researcher  in  the
"Cytology,  Histology and  Embriology" at  the Biological Faculty of
the  Sofia University  "St Kliment  Ohridsky" is  suffering from  an
acute  form  of  a  myelloblast  leukaemia.  The  personnel  of  the
Department  and the parents of the girl address you with the request
for  financial funds,  necessary for  bone marrow  transplant to  be
conducted  abroad. The  required sum  amounts to  USD 80  000 - 1000
000.
We  also  appeal  to:  Bulgarian  and  foreign  banks,  foundations,
charity  organisations, private  and state  companies, the  academic
community  and private persons to assist, and we hope that they will
be charitable and will respond to our deeply human call for help.
The  donation account  in the  name of Desislava Plamenova Georgieva
was  opened in  Biochim Ad,  Sredetz Branch,  1 Ivan  Vazov  Street,
Sofia:
BGL 660084225   No. 1003363608
USD 660084225   No. 18323000103363601
DM  660084225   No. 18323010103363608

We  rely on  your charity and on your parental understanding for the
destiny  of the  18-year old  girl who  probably will  be given  the
chance to live thanks to your assistance.

MEMBERS OF THE DEPARTMENT
 

COMMERCIAL BANK "BIOCHIM"
SWIFT CODE: CBBIBGSF
BRANCH "SREDETZ": 1040, SOFIA, 1, IVAN VAZOV STR.
NOSTRO ACCOUNTS ABROAD: (as at 10.10.1996):

BANK                currency    ACCOUNT             SWIFT

AMERICAN EXPRESS    USD         300700823           AEIBUS33
BANK, New York
BANKERS TRUST CO.,  USD         04090904            BKTRUS33
NEW YORK
BANK OF NEW YORK    USD         8900058935          IRVTUS3N
NEW YORK
CITIBANK N.A.,      USD         36017613            CITIUS33
NEW YORK
CREDIT LYONNAIS,    USD         01-19782-0001-00    CRLYUS33
NEW YORK
DEUTSCHE BANK AG,   USD         923 3610 00         DEUTDEFF
FRANKFURT AM MAIN
LLOYDS BANK PLC,    USD         12308436            LOYDGB2L
LONDON
NATIONAL BANK OF    USD         040/504097          ETHNGRAA
GREECE, ATHENS
STOPANSKA BANKA DD, USD         100.840.2           STOBMK2X
SKOPJE
SWISS BANK CORP.,   USD         101-WA-343749-000   SBCOUS33
NEW YORK

AMERICAN EXPRESS BANK   DEM     424-007406906       AEIBDEFX
FRANKFURT AM MAIN
BANKERS TRUST CO.,      DEM     810150027           BKTDDEFF
FRANKFURT AM MAIN
BAYERISCHE HYPOTEKEN    DEM     6450026539000       HYPODEMM
UND WECHSEL BANK
MUNICH
BAYERISCHE VEREINSBANK, DEM     68100470            BVBEDEMM
MUNICH
BfG BANK AG,            DEM     100 34 777 00       BFGFDEFF
FRANKFURT AM MAIN
COMMERZBANK AG,         DEM     400871916300        COBADEFF
FRANKFURT / MAIN
DEUTSCHE BANK AG,       DEM     100 9233610 0000    DEUTDEFF
FRANKFURT AM MAIN
DRESDNER BANK AG,       DEM     499/08021429/00/000 DRESDEFF
FRANKFURT AM MAIN
DG BANK AG,             DEM     11/1000/1632        DGBKDEFF
FRANKFURT AM MAIN
STOPANSKA BANKA DD,     DEM     100.280.3           STOBMK2X
SKOPJE
WESTDEUTSCHE LANDESBANK DEM     55 891              WELADEDD
DUESSELDORF

Correspondent Banking: Phone +359 2/980 4926, Fax +359 2/881147
                        Telex: 23921, 24757
 
  From owner-srs@net.bio.net Thu Jul 03 23:00:00 1997 Path: biosci!agate!howland.erols.net!EU.net!Ireland.EU.net!web3.tcd.ie!gen035.gen.tcd.ie!user From: atlloyd@tcd.ie (Andrew T. Lloyd) Newsgroups: bionet.software.srs Subject: Indexing EMBL 51 Date: Fri, 04 Jul 1997 08:20:31 +0000 Organization: INCBI, TCD, D2, Ireland. Lines: 35 Message-ID: NNTP-Posting-Host: gen035.gen.tcd.ie Hi SRS giants, It would not be strictly true for me to claim that the workings of SRS are totally opaque to me. It would be a close approx tho. I have three questions which probably have obvious answers. Indexing EMBL 51 took 32 HOURS. During this time, my users get disturbingly wrong info, presmably because the partly built indexes point to the old parts of the flatfiles ? Q1. Is it possible to dump the new indexes to a temporary directory, maintaining full functionality with the old DBs and when the indexing is finished switch it all over in say 32 seconds ? At vast (and I mean VAST) expense, I bought another 256MB memory last year. Q2. Is it possible to rejig the indexing protocol so that it uses more than, say, 90MB and thus goes through faster ? And finally on the real noddy level: Q3. Once I've clagged all my SW:reca_* into one list, how do I extract them as, say, a concatenated fasta file which I can zing through clustalW. Thanks for your help, 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 Thu Jul 03 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!205.237.233.10!wesley.videotron.net!walton.videotron.net!not-for-mail From: Pamela Anderson Newsgroups: bionet.software.srs Subject: !!!!!!!Check here for the BEST HARDCORE SITE on the NET!!!!!! Date: 4 Jul 1997 10:04:11 GMT Organization: VTL Lines: 6 Message-ID: <5pihqr$9vh$8370@walton.videotron.net> NNTP-Posting-Host: ppp103.110.mmtl.videotron.net For the BEST HARDCORE site on the WEB, check this MAGNIFICENT SITE!!!!! You won't regret it... Some of the HOTTEST women and men are waiting for you. http://www.lapis.net/bin/adhome?costin13 From owner-srs@net.bio.net Sat Jul 05 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!csulb.edu!gatech!howland.erols.net!europa.clark.net!newsfeed2.aimnet.com!news.internetMCI.com!not-for-mail From: ldqqkrtjftt@etpyyoipir.com Newsgroups: bionet.software.srs Subject: !!ONE NUMBER FOR ALL!!!! Date: 6 Jul 1997 03:43:32 GMT Organization: Internet MCI Lines: 31 Message-ID: <5pn494$86g$2@news.internetmci.com> NNTP-Posting-Host: usr2-dialup3.mix1.bloomington.mci.net One-Number service puts you in control of your calls while ensuring that your calls, messages and faxes reach you regardless of your location. One-Number service does this by linking your existing telephones, cell phones, pagers, and fax machines through a single telephone number. YOUR One-Number ACCOUNT COMES STANDARD WITH THESE FEATURES - Consolidates your phone, fax, voice-mail and paging services - Works with your existing products and services, no need to change - Easily lets you designate yourself as available or unavailable - Rings you at up to three numbers simultaneously - Never-busy number accepts multiple incoming calls and faxes - Call Screening (by name) lets you know who is calling - Call Waiting lets you know somebody else is calling - Call Move lets you easily transfer calls among different phones - Call Conferencing allows conferences with other parties - Fax Notification on your pager for incoming fax messages - Redirect calls to Personal Operator (live person) if desired - AND MUCH MORE Virtual Office Communications Company is not a phone company, a long distance carrier, nor do we sell telephone equipment, cellular phones, cellular service, pager or pager service. Instead, we offer service to integrate your existing products, adding value to what you already have by letting your phones, pagers, fax machines and voice-mail systems work together seamlessly. To learn more please visit our web site at: http://www.mynumber.com Please do not reply by e-mail as we are not set up to respond to e-mail requests. From owner-srs@net.bio.net Sat Jul 05 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!207.20.0.4!newsfeed2.aimnet.com!news.internetMCI.com!not-for-mail From: weyjr@kjphy.com Newsgroups: bionet.software.srs Subject: Your ONENUMBER for everything Date: 6 Jul 1997 09:09:34 GMT Organization: Internet MCI Lines: 31 Message-ID: <5pnnce$rb6$5@news.internetmci.com> NNTP-Posting-Host: usr1-dialup5.mix1.bloomington.mci.net One-Number service puts you in control of your calls while ensuring that your calls, messages and faxes reach you regardless of your location. One-Number service does this by linking your existing telephones, cell phones, pagers, and fax machines through a single telephone number. YOUR One-Number ACCOUNT COMES STANDARD WITH THESE FEATURES - Consolidates your phone, fax, voice-mail and paging services - Works with your existing products and services, no need to change - Easily lets you designate yourself as available or unavailable - Rings you at up to three numbers simultaneously - Never-busy number accepts multiple incoming calls and faxes - Call Screening (by name) lets you know who is calling - Call Waiting lets you know somebody else is calling - Call Move lets you easily transfer calls among different phones - Call Conferencing allows conferences with other parties - Fax Notification on your pager for incoming fax messages - Redirect calls to Personal Operator (live person) if desired - AND MUCH MORE Virtual Office Communications Company is not a phone company, a long distance carrier, nor do we sell telephone equipment, cellular phones, cellular service, pager or pager service. Instead, we offer service to integrate your existing products, adding value to what you already have by letting your phones, pagers, fax machines and voice-mail systems work together seamlessly. To learn more please visit our web site at: http://www.mynumber.com Please do not reply by e-mail as we are not set up to respond to e-mail requests. From owner-srs@net.bio.net Sun Jul 06 23:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!uunet!not-for-mail From: XXXFREEPORN@alpin.or.at Newsgroups: bionet.software.srs Subject: <<>> Date: 7 Jul 1997 17:38:32 GMT Organization: XXX1200+SITESFREE Lines: 12 Message-ID: <5pr9io$dag@news0-alterdial.uu.net> NNTP-Posting-Host: 1cust56.max14.los-angeles.ca.ms.uu.net I found a secret password that lets you into 1800+ of the Hottest Adult Sites on the Web. You can also get FREE UNLIMITED Live Video Sex and FREE XXX Chat Room Access. I no longer pay to get into Adult Sites... you won't either. This secret password gets you into them for FREE. http://38.216.112.100/password From owner-srs@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!agate!howland.erols.net!newshub2.home.com!news.home.com!news-xfer.netaxs.com!hammer.uoregon.edu!azure.xara.net!xara.net!server6.netnews.ja.net!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs,bionet.software.gcg Subject: Re: lookup and SRS5, part two Date: Tue, 08 Jul 1997 13:51:38 +0100 Organization: SEQNET Lines: 34 Distribution: bionet Message-ID: <33C237DA.41C6@dl.ac.uk> References: <5ptbth$jj6@rc1.vub.ac.be> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) To: Guy Bottu Xref: biosci bionet.software.srs:637 bionet.software.gcg:2637 Guy Bottu wrote: > > > It goes wrong however when you ask for the output. The entry names of > the retrieved sequences are correct, but you get often a wrong > definition and database name (e.g. EM_OR instead of EM_VI) or an error > message "* ERROR * end of file encountered". Has the format of the index > *_id.idx that points to the location of the databank entries changed ? > Hi Guy, Just a wild guess.. I once had something which gave similar errors, when I had srs4 running on two machines, with their indices on a shared disk. I had managed to have the order of the database sections different in the .sdl files for those machines, so while it worked perfectly on one machine, it gave errors similar to the ones you got on the other machine.. So maybe that making sure that the order of the various sections is the same in the .i and the .sdl file can solve that problem... Cheers, Martin -- ------------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/Person.asp?m.p.hilbers | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.seqnet.dl.ac.uk/ | ------------------------------------------------------------------- From owner-srs@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.nacamar.de!news-kar1.dfn.de!news-stu1.dfn.de!news-mue1.dfn.de!news-nue1.dfn.de!news-lei1.dfn.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!tubsibr!rzlimes.gbf-braunschweig.de!not-for-mail From: "Dr. Thomas Heinemeyer" Newsgroups: bionet.software.srs Subject: TRANSFAC 3.2 Date: Tue, 08 Jul 1997 08:44:21 +0200 Organization: Ges. f. Biotechn. Forsch. mbH (non profit) Lines: 86 Message-ID: <33C1E1C5.19CD@gbf-braunschweig.de> NNTP-Posting-Host: gen219.gbf-braunschweig.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (WinNT; I) TRANSFAC 3.2 is available now at: http://transfac.gbf.de. On the TRANSFAC server, you will find also the sequence analysis programs PatSearch MatInspector SaGa FastM and Thure Etzold's SRS5 with a large collection of databases. TRANSFAC is a database about eukaryotic transcription factors and their binding sites. It consists of six cross-linked tables: SITE CELL FACTOR CLASS MATRIX GENE It is also cross-linked with TRRD (Transcription Regulatory Region Database) and COMPEL from the ICG, Novosibirsk (N. A. Kolchanov, A. E. Kel). It contains numerous cross-references to external databases such EMBL, SWISSPROT, PIR, FLYBASE, EPD, and PROSITE. For further details see Wingender et al., Nucleic Acids Res. 25:265-268, 1997. NEW FEATURES are: - Additional FACTOR and SITE entries, - cross-references to PDB, - comprehensive linkage of FACTOR entries with a proposed transcription factor classification sytem (http://transfac.gbf.de/TRANSFAC/cl/cl.html). The TRANSFAC database comes along with several sequence analysis tools such as - PatSearch, which uses the sequence information contained in the SITE table for analysis of submitted sequences, - MatInspector, using a library of matrices selected from the TRANSFAC MATRIX table (see Quandt et al., Nucleic Acids Res. 23:4878-4884, 1995). Moreover, the TRANSFAC server provides a new program (SaGa: structural analysis with genetic algorithms, developed by Stefan Meier) which can be used to identify structural characteristics in the environment of aligned functional sites, e.g., transcription factor binding sites. SaGa uses a library of structural parameters developed by H. Sklenar and coworkers (MDC, Berlin; see Karas et al., CABIOS 12:441-446, 1996). The SRS5 system implemented on the TRANSFAC server comprises the following databases, in addition to the TRANSFAC tables: EMBL, EMBLNEW SWISSPROT, SWISSNEW TREMBL REMTREMBL SPTREMBL PIR EPD PDB PROSITE ENZYME EMBLNEW is now updated daily on the TRANSFAC SRS-Site with the new files from European Bioinformatics Institute (EBI) in Hinxton. Edgar Wingender Thomas Heinemeyer -- Dr. Thomas Heinemeyer Tel.: ++49(0)531 6181 295 Ges. f. Biotechn. Forsch. mbH Fax: ++49(0)531 6181 266 Abt. Genomanalyse E-Mail: thh@gbf.de Mascheroder Weg 1 http://transfac.gbf.de/Staff/thh.html D-38124 Braunschweig From owner-srs@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!surfnet.nl!news.belnet.be!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: lookup and SRS5, part two Date: 8 Jul 1997 12:30:41 GMT Organization: Belgian EMBnet Node Lines: 21 Message-ID: <5ptbth$jj6@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] I am trying to make lookup work with the indexes of SRS5. I am however afraid it won't work. I have already discovered the following : lookup can find entries correctly in the indexes made by SRS5, provided the short name is the same. The only name that changed between the distributions of GCG8/SRS4 and SRS5 is Definition(DEF) -> Description (DES). Replacing Definition and DEF in the source code of lookup by Description and DEF and recompiling does not help, lookup still does not retrieve anything. There is however an easy getaround : it is sufficient to make UNIX logical links from embl_def.ids to embl_des.ids,... to make it work. It goes wrong however when you ask for the output. The entry names of the retrieved sequences are correct, but you get often a wrong definition and database name (e.g. EM_OR instead of EM_VI) or an error message "* ERROR * end of file encountered". Has the format of the index *_id.idx that points to the location of the databank entries changed ? Guy Bottu this message has also been posted to : bionet.software.gcg From owner-srs@net.bio.net Mon Jul 07 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!usenet.kornet.nm.kr!howland.erols.net!news.apfel.de!news-fra1.dfn.de!news-ge.switch.ch!news-zh.switch.ch!news.belnet.be!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: srscheck bug Date: 8 Jul 1997 14:32:32 GMT Organization: Belgian EMBnet Node Lines: 24 Message-ID: <5ptj20$jj6@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] In this newslist have already appeared several messages about the problems that arise when you have two databanks that share the same $libformat like EMBL and EMBLNEW. Here is another one : srscheck writes an srsupdate script where the line of the type srsbuild EMBLNEW ' id acc des gen dat ... ' -xdir 'SRSINX:' -odir 'SRSINX:' -s 'unix' is missing. This is not a great problem, since usually the only databanks that share a $libformat are the major release and the updates of the same databank and you do not need to index them together very often. And here is another bug : for big databanks that must be indexed in chunks, the line of the type \rm ../index/embl_id_*.i* is missing. Again, this is not a great problem because you can easily remove the embl_id_1.ids etc. "by hand" and it does not prevent SRS from functionning. Guy Bottu From owner-srs@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!agate!usenet.INS.CWRU.Edu!HSNX.wco.com!newsfeed.dacom.co.kr!newsfeed.internetmci.com!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: EMBL database: parsing problem. Date: 9 Jul 1997 14:31:13 GMT Organization: EMBL Heidelberg Lines: 34 Distribution: world Message-ID: <5q07bh$kp3@lion.embl-heidelberg.de> NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) To: chenna@embl-heidelberg.de X-URL: news:bionet.software.srs?ALL Hello all There is a parsing problem with embl db. It does not parse more than one line in the 'OC OS OG' fields. To correct that insert the following productions for the token table 'org' and rebuild the index. org: ~ {$In:[fields c:org] $Out} (oc | os | og)* ~ oc: ~ ('OC' (/[^;.\n]+/ {$Wrt} /[^\n]/ )+) ln ~ os: ~ 'OS' (/[^(\n]+/ {$Wrt:[s:$Trim:$Ct]})+ ~ og: ~ 'OG' (/[^;.\n]+/ {$Wrt})+ ~ # old code... # ('OC' (/[^;.\n]+/ {$Wrt} | /[^\n]/)*)+ | # 'OS' /[^(\n]+/ {$Wrt:[s:$Trim:$Ct]} # ('(' (/[^ \n)]+/ | /[^)]/)+)? | # 'OG' /[^\n;.]+/ {$Wrt} ~ Ramu -- ________________________________________________________________________________ Chenna Ramu; EMBL; Postfach 10.2209; 69012 Heidelberg; Germany. _/_/_/ _/_/_/ Email: chenna@embl-heidelberg.de _/ _/ _/ Url: http://www.embl-heidelberg.de/~chenna/ _/ . _/_/_/ Tel: (49) 6221 387530 (Off) ; Fax: (49) 6221 387517 _/ _/ _/ _/_/_/ _/ _/ From owner-srs@net.bio.net Tue Jul 08 23:00:00 1997 From: Kris Jacobs Newsgroups: bionet.software.srs Organization: Jake's Home Brew Subject: Try Me! NNTP-Posting-Host: 205.139.183.47 Message-ID: <33c1f73e.1@nntp.kalnet.net> Date: 8 Jul 97 08:15:58 GMT Lines: 12 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.internetmci.com!pull-feed.internetmci.com!nntp.kalnet.net!205.139.183.47 Hello net world are you a beer drinker or maybe a home brewer than this web page is for you! My web page is dedicated to home brewing and beer on the net! If this interests you than go to Jake's Home (brew) Page it is located at http://www.net-link.net/~jtsnake/ I am looking forward to hearing from you soon!!! Kris Jacobs Jake's Home (brew) Page http://www.net-link.net/~jtsnake/ E-Mail To: jtsnake@net-link.net jtsnake@serv01.net-link.net mpinc@SERV01.NET-LINK.NET From owner-srs@net.bio.net Tue Jul 08 23:00:00 1997 From: Damn Yankee Newsgroups: bionet.software.srs Organization: Yankee Inc. Subject: !!!Hello!!! NNTP-Posting-Host: 205.139.183.49 Message-ID: <33c0b456.0@nntp.kalnet.net> Date: 7 Jul 97 09:18:14 GMT Lines: 9 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!pull-feed.internetmci.com!nntp.kalnet.net!205.139.183.49 Are you looking for a great place to find interesting things on the WWW??? Than look no more because you have found the right place!!! The place you are looking for is Yankee Inc.!!! A great Web Site full of interesting links to interesting places!!! Everything from Adult to Xzlyaphone it's here!!! There is something for everyone and then some!!! So give it a try what do you have to lose except some sleep??? Yankee Inc. http://www.kalnet.net/yank714 Yankee Inc. Your Alternative Web Solution!!! Yankee Inc. http://www.kalnet.net/yank714 If you would like to be removed from my mailing list - hit reply and type "REMOVE" and I will promptly remove you from my list!!! Thank You!!! From owner-srs@net.bio.net Tue Jul 08 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!vixen.cso.uiuc.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: Re: srscheck bug Date: 9 Jul 1997 14:35:07 GMT Organization: Biology, Indiana University - Bloomington Lines: 18 Message-ID: <5q07ir$n18$1@dismay.ucs.indiana.edu> References: <5ptj20$jj6@rc1.vub.ac.be> NNTP-Posting-Host: chipmunk.bio.indiana.edu I've noticed this, but have also noticed that the *_id_*.i* files seem to be required to reindex any of the other fields. When I remove them, furthur reindexing, of say the comment field, fails with an error message. In article <5ptj20$jj6@rc1.vub.ac.be>, Guy Bottu wrote: .. >And here is another bug : > >for big databanks that must be indexed in chunks, the line of the type > >\rm ../index/embl_id_*.i* > >is missing. Again, this is not a great problem because you can easily >remove the embl_id_1.ids etc. "by hand" and it does not prevent SRS from >functionning. -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Wed Jul 09 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!server1.netnews.ja.net!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: etzold Newsgroups: bionet.software.srs Subject: Re: Indexing EMBL 51 Date: Thu, 10 Jul 1997 14:54:25 +0100 Organization: EMBL-EBI Lines: 52 Message-ID: <33C4E991.7264559F@ebi.ac.uk> References: NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: "Andrew T. Lloyd" X-Priority: 3 (Normal) Andrew T. Lloyd wrote: > Indexing EMBL 51 took 32 HOURS. During this time, my > users get disturbingly wrong info, presmably because the > partly built indexes point to the old parts of the flatfiles ? i can't say why it took so long to build the indices. The memory requirement is much much lower as with srs4. Since index building is io intensive make sure that the computer creates files on a local disk and does not use nfs. > > Q1. Is it possible to dump the new indexes to a temporary > directory, maintaining full functionality with the old DBs > and when the indexing is finished switch it all over in say > 32 seconds ? we did this at the ebi for the last release of embl. there are two problems: 1) for the duration of the indexing you need to keep two copies of the embl flatfiles ...but this extra amount of disk space is worth paying for! 2) this procedure must be done by hand - srscheck is not clever enough for this kind of thing. > > At vast (and I mean VAST) expense, I bought another 256MB > memory last year. > > Q2. Is it possible to rejig the indexing protocol > so that it uses more than, say, 90MB and thus goes through > faster ? what you could try is to increase .cachesize (embl.i) but it is already quite high. There is no point increasing the .partitionSize of $library. since that makes only merging of the indices (not much) faster. > > And finally on the real noddy level: > > Q3. Once I've clagged all my SW:reca_* into one list, how do > I extract them as, say, a concatenated fasta file which I can > zing through clustalW. try getz '[swissprot-id:reca*]' -f seq -sf regards thure From owner-srs@net.bio.net Wed Jul 09 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!hunter.premier.net!europa.clark.net!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: etzold Newsgroups: bionet.software.srs Subject: Re: srscheck bug Date: Thu, 10 Jul 1997 14:39:42 +0100 Organization: EMBL-EBI Message-ID: <33C4E61D.E9803DA7@ebi.ac.uk> References: <5ptj20$jj6@rc1.vub.ac.be> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: Guy Bottu X-Priority: 3 (Normal) Lines: 86 Guy Bottu wrote: > > In this newslist have already appeared several messages about the > problems that arise when you have two databanks that share the same > $libformat like EMBL and EMBLNEW. Here is another one : srscheck writes > an srsupdate script where the line of the type > > srsbuild EMBLNEW ' id acc des gen dat ... ' -xdir 'SRSINX:' -odir > 'SRSINX:' -s 'unix' > > is missing. This is not a great problem, since usually the only > databanks that share a $libformat are the major release and the updates > of the same databank and you do not need to index them together very > often. I discovered an obvious problem in srscheck (still a 'legacy' from srs4) and suggest to change SRSSOU:srscheck.c in the following way add the function CheckLibInit ------------------------------------------------------------------------------ static void CheckLibInit (SLBo *lib) { SLBoFIELD *field; Int4 k; for (k=0; (field=LibNextField (lib, &k)); k++) { field->done_f=0; field->do_f=0; } } ------------------------------------------------------------------------------ after ------------------------------------------------------------------------------ /******************************************************************************* ** ** Set of functions to set flags of different types for the field object. ** Utilizes flags in the field objects that are normally used in other contexts. ** */ ------------------------------------------------------------------------------ add the prototype of this function ------------------------------------------------------------------------------ static void CheckLibInit (SLBo *lib); ------------------------------------------------------------------------------ after ------------------------------------------------------------------------------ static void CheckInfoDel (CHECKoInfo **ci); ------------------------------------------------------------------------------ and finally call the function ------------------------------------------------------------------------------ CheckLibInit (lib); ------------------------------------------------------------------------------ before ------------------------------------------------------------------------------ ci = CheckInfoNew (lib); ------------------------------------------------------------------------------ and do srsmake srscheck I didn't test whether this really improves anything - please let me know regards thure From owner-srs@net.bio.net Wed Jul 09 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!europa.clark.net!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: etzold Newsgroups: bionet.software.srs Subject: Re: srscheck bug Date: Thu, 10 Jul 1997 13:23:13 +0100 Organization: EMBL-EBI Message-ID: <33C4D431.9B3750E4@ebi.ac.uk> References: <5ptj20$jj6@rc1.vub.ac.be> <5q07ir$n18$1@dismay.ucs.indiana.edu> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: Don Gilbert X-Priority: 3 (Normal) Lines: 31 Don Gilbert wrote: > > I've noticed this, but have also noticed that the *_id_*.i* files > seem to be required to reindex any of the other fields. > When I remove them, furthur reindexing, of say the comment field, > fails with an error message. > > In article <5ptj20$jj6@rc1.vub.ac.be>, Guy Bottu wrote: > .. > >And here is another bug : > > > >for big databanks that must be indexed in chunks, the line of the type > > > >\rm ../index/embl_id_*.i* > > > >is missing. Again, this is not a great problem because you can easily > >remove the embl_id_1.ids etc. "by hand" and it does not prevent SRS from > >functionning. yes, this the embl_id_* files are still necessary since they are used for counting how many index partitions were build. This is necessary, as Don wrote, to build extra indices (non ID indices). This will go away with the next release (btw, most of the features that i announced for the next release are implemented by now;-)) where information such as the number of index partitions will be stored in an extra file ...but for the time being it is safer to keep the *_id_* files regards thure From owner-srs@net.bio.net Wed Jul 09 23:00:00 1997 From: Damn Yankee Newsgroups: bionet.software.srs Organization: Yankee Inc. Subject: I Am Very Sorry!!! NNTP-Posting-Host: 205.139.183.55 Message-ID: <33c2556e.0@nntp.kalnet.net> Date: 8 Jul 97 14:57:50 GMT Lines: 5 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.internetmci.com!pull-feed.internetmci.com!nntp.kalnet.net!205.139.183.55 I would like to apologise to this newsgroup and everyone who reads this newsgroup!!! I promise never to post or send spam to this or any other newsgroup that does not pertain to my posting!!! Please accept my humble apology and again I will never post spam here again!!! Thank You!!! Andrew Schero yank714@kalnet.net From owner-srs@net.bio.net Wed Jul 09 23:00:00 1997 From: randy97 Subject: http://www.love.com Newsgroups: bionet.software.srs NNTP-Posting-Host: pgh.nauticom.net Message-ID: <33c528e9.0@pgh.nauticom.net> Date: 10 Jul 97 18:24:41 GMT Lines: 9 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!newsfeed.internetmci.com!pgh.nauticom.net!pgh.nauticom.net Looking to find people in your area that enjoy the same things as this newsgroup? Check out http://www.love.com It's free, it's new, and it's awesome. Rand From owner-srs@net.bio.net Thu Jul 10 23:00:00 1997 Newsgroups: bionet.software.srs Path: biosci!rutgers!gatech!howland.erols.net!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!server1.netnews.ja.net!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!test.hgmp.mrc.ac.uk!ebi.ac.uk!news From: Giorgio Verde Subject: IMGT parser fix Sender: news@ebi.ac.uk (usenet news) Message-ID: <33C63D71.2781@embl-heidelberg.de> Date: Fri, 11 Jul 1997 14:04:33 GMT Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 X-Mailer: Mozilla 2.0S (X11; I; IRIX 6.2 IP22) Organization: Eurpean Molecular Biology Laboratory Lines: 14 Hi all There are a couple of bugs in the IMGT parser in the current distribution. Please replace your imgt.is and imgt.i files in the $SRSDB directory with the ones downloaded from: http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?-fun+PageIcarusFile+-l+IMGT+-ifile+is http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?-fun+PageIcarusFile+-l+IMGT+-ifile+i NOTE: the configuration is for GCG format An indexing and an access bug are fixed Giorgio Verde From owner-srs@net.bio.net Thu Jul 10 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!bioftp.unibas.ch!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Re: srscheck bug Date: 11 Jul 1997 18:08:45 GMT Organization: Belgian EMBnet Node Lines: 8 Message-ID: <5q5srd$8lj@rc1.vub.ac.be> References: <5ptj20$jj6@rc1.vub.ac.be> <33C4E61D.E9803DA7@ebi.ac.uk> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] > I didn't test whether this really improves anything - please let me know > > thure Yes, it works ! srscheck makes the command lines for both EMBL and EMBLNEW, SWISSPROT and SWISSNEW, ... Guy From owner-srs@net.bio.net Fri Jul 11 23:00:00 1997 Path: biosci!agate!howland.erols.net!ais.net!newsfeed.direct.ca!op.net!not-for-mail From: Dan Harley Newsgroups: bionet.software.srs Subject: Best price on the net CD-R 74 Minute Gold $2.99 Retail package - no rebates no gimmics no surcharges Date: 11 Jul 1997 10:23:48 GMT Organization: NetPro Computer Services, Inc. Lines: 58 Message-ID: <5q51jk$284$4711@picasso.op.net> NNTP-Posting-Host: d7-0f.ppp.op.net NetPro Computer Services, Inc. http://www.netprocs.com The sign of superior service since 1989! Weekly product specials If you don’t see if please email info@netprocs.com for a prompt quotation! SCSI subsystem specialists - let us build yours today Distributor of ACER OPEN SYSTEMS and Components Master distributor DRAM,INTEL processors we will not be undersold on geniune Intel products Dan the Disc and DAT man brings you the best prices on the net: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Wholly KAO ~ best price on the net! KAO 74 Minute CD-R 680MB 2x/4x compatible highest quality. The J & J of Japan! $2.99 kick off special (retail) $2.79 Spindle pack of 50 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Verbatim 74 Minute / 680 MB / 2x / 4x certified White / clear jewel case, white J card, individually wrapped, master case of 50, 5 inner boxes of 10. $3.69 each Memorex 74 Minute GOLD generic package - white j Card, individually wrapped in white/clear jewel case. 25 to a master carton (can break up) $ 3.39 Ricoh ReWritable 74 Minute CD-RW $22.00 HP 6020ES recorder (external SCSI 2x/6x) $529.00 HP 6020 recorder (internal SCSI 2x/6x) $429.00 JVC 2x/6x Internal kit $389.00 + free shipping!!! * Adaptec EZ CD Pro V. 2.11 PC & Mac, Dos Ver 3.5 software * kit includes PressIT CD labler software, 100 CD Blank lables, CD filled with templates, clipart - templates compt. with Pagemaker, Illus, P/S. * 16 bit SCSI controller, cables, drivers * 2 pieces blank media * Highest quality kit COMPAC pales in comparision * your satisfaction assured or you may return for full credit. * JVC Inventor of VHS makes a SUPERIOR mechanism - read the trade mags! Ricoh 6200 spi4 ReWritable Internal kit $519.00 * Authoring software now with variable packet writing - treats R/W as a floppy drive! * Adaptec EZ CD Pro V 2.11, Toast CD for Mac * 16 bit SCSI controller, cables, drivers * one CD-R, one rewritable CD-RW From owner-srs@net.bio.net Fri Jul 11 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!208.216.0.2!news.miracle.net!not-for-mail From: bingo5@micro.net Newsgroups: bionet.software.srs Subject: Writers Seeking Publication Date: 12 Jul 1997 09:21:01 GMT Organization: Woodside International Literary Agency Lines: 35 Message-ID: <5q7i9t$lh$384@roadrunner.miracle.net> NNTP-Posting-Host: ip35.an15-new-york4.ny.pub-ip.psi.net Mime-Version: 1.0 Content-Type: multipart/mixed; boundary=_-=968 This is a multi-part message in MIME format. --_-=968 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7bit This file will become the message body... --_-=968 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7bit 33-29 58 street addressed, stamped envelope (sase). all fiction: send brief synopsis, first chapter, and include a self- all nonfiction: send brief synopsis, first chapter, sase. and previously published writers. writers from around the world are main office please do not submit entire manuscript unless invited to do so. poetry: send 3 poems, sase. sase. screenplays for tv & movies: send brief synopsis, first 20 pages, short stories: brief synopsis, first 3 pages, sase. tele: (718) 651-8145 the woodside international literary agency we are the woodside international literary agency. we are seeking new welcome. two of our offices are in new york and a third is in florida. what to send and where to send it: woodside, new york 11377 ; --_-=968 From owner-srs@net.bio.net Fri Jul 11 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!dispatch.news.demon.net!demon!kinet.demon.co.uk!not-for-mail From: "David Benson" Newsgroups: bionet.software.srs Subject: Medical Web sites can make healthy profits! Date: Sat, 12 Jul 1997 18:33:35 +0100 Message-ID: <868728370.9391.0.nnrp-1.9e989ba8@news.demon.co.uk> NNTP-Posting-Host: kinet.demon.co.uk X-NNTP-Posting-Host: kinet.demon.co.uk [158.152.155.168] X-Newsreader: Microsoft Outlook Express 4.71.0544.0 X-MimeOLE: Produced By Microsoft MimeOLE Engine V4.71.0544.0 Lines: 38 Medical Web sites can make healthy profits! If you run a health related Web site then there is now an opportunity to get some money back for all your hard work and provide a useful service to your readers. The Healthworks Shop Partnership Scheme allows participating Web sites to earn commission on sales of medical information products by just adding an extra page to their sites. Healthworks are one of the worlds leading distributors of electronic medical information products, they are Internet trade veterans with over two years experience of selling CD-ROMs and videotapes from their Web site. The partnership deal enables Web sites to make money and provide a useful service to their visitors. For the smaller sites it can earn them enough to cover all their running costs at the least, the more popular sites can create a substantial income for their organisations. Shop Scheme partners can offer the complete range of over 600 medical information products and gain commission on sales of 7-10%. With the average price of a medical CD-ROM at 300, partners make a good profit on each sale. The scheme utilises a commerce system, specially designed by Information Central Limited, to enable simple set-up and administration by anyone with basic HTML skills. The partnership process is simple: 1.Register your interest with Healthworks and a member of staff will view your Web site. 2. If you are approved you will be given simple instructions on how to set up your shop page. 3. A few minutes of HTML programming and you are up and running. 4. Sit back and wait for your monthly sales commissions. To find out more look at the Healthworks Web site at:http://www.healthworks. co.uk/hw/partner/CDpartner.html or e-mail: partners@d-access.demon.co.uk From owner-srs@net.bio.net Sat Jul 12 23:00:00 1997 Path: biosci!rutgers!gatech!newsxfer3.itd.umich.edu!europa.clark.net!dispatch.news.demon.net!demon!bullseye.news.demon.net!demon!newsgate.unisource.nl!halley.pi.net!news From: jacob Newsgroups: bionet.software.srs Subject: Asian Ladies Date: 13 Jul 1997 18:54:49 GMT Organization: World Access/Planet Internet Message-ID: <5qb89p$rtk@halley.pi.net> NNTP-Posting-Host: 145.220.210.27 Lines: 10 I've found the pefect site with nude Asian ladies. Much more than you can find in any newsgroup. http://home.pi.net/~sappie/playboy.htm From owner-srs@net.bio.net Sat Jul 12 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!ais.net!su-news-hub1.bbnplanet.com!su-news-feed4.bbnplanet.com!news.bbnplanet.com!newsgate.tandem.com!uunet!not-for-mail From: FREESLUTSXXX@alpin.or.at Newsgroups: bionet.software.srs Subject: <<>> Date: 13 Jul 1997 01:58:00 GMT Organization: CUMXXX Lines: 12 Message-ID: <5q9cn8$c1h@news1-alterdial.uu.net> NNTP-Posting-Host: 1cust40.max75.los-angeles.ca.ms.uu.net I found a secret password that lets you into 1800+ of the Hottest Adult Sites on the Web. You can also get FREE UNLIMITED Live Video Sex and FREE XXX Chat Room Access. I no longer pay to get into Adult Sites... you won't either. This secret password gets you into them for FREE. http://38.216.112.100/password From owner-srs@net.bio.net Sat Jul 12 23:00:00 1997 Newsgroups: bionet.software.srs Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!server1.netnews.ja.net!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!test.hgmp.mrc.ac.uk!ebi.ac.uk!news From: etzold Subject: Re: error installing SRS release 5.0.5 on linux Sender: news@ebi.ac.uk (usenet news) Message-ID: <33C66F23.2DE4B29A@ebi.ac.uk> X-Priority: 3 (Normal) Date: Fri, 11 Jul 1997 17:36:35 GMT To: RICARDO BRINGAS Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii References: <6098DD525F@serverdos.cigb.edu.cu> Mime-Version: 1.0 X-Mailer: Mozilla 4.01 [en] (Win95; I) Organization: EMBL-EBI Lines: 33 dear all, some time ago a problem installing srs5.0.5 on linux was reported (srssection crashed). I put an 'early' version 5.0.5 on the ftp server which i replaced a day after ...this was still before the 'official' announcement of the new releaes in the newsgroup. This early version contains a bug in icainit.c. Can you please search for function calls "IopOut (0, NULL)" they need to be converted to IopOut (0, NULL, NULL) there are 4 of them in the same file however, there is another problem in futil.c: edit futil.c and go to FileDelete there delete the two lines if (file->ln) free (file->ln); after these changes do srsmake nodd srssection regards thure From owner-srs@net.bio.net Sun Jul 13 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!xfer.kren.nm.kr!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!not-for-mail From: Aengus Stewart Newsgroups: bionet.software.srs Subject: Linking to queries Date: Mon, 14 Jul 1997 14:40:56 +0100 Organization: Imperial Cancer Research Fund Lines: 44 Message-ID: <33CA2C68.31D2@icrf.icnet.uk> NNTP-Posting-Host: fingermouse.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; OSF1 V4.0 alpha) I am currently trying to link in the results of FASTA and SCANPS(smith-waterman) to the SRS server at the EBI. However the format of the hits does not give the data library from which the sequence was derived only the name and and the accession number, eg ... The best scores are: initn init1 opt z-sc E(473814) BB L32145 Borrelia burgdorferi C62.5 heat ( 236) 1180 1180 1180 892.7 0 ... therefore, http:///srs5bin/cgi-bin/wgetz?[database-id:id]+-e will not work as it goes directly to a single entry. I have tried incorporating the query that is returned when I do the search within a live SRS session eg Query "[libs={embl emblnew}-AccNumber: L32145*] " found 1 entries http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?[libs={embl emblnew}-AccNumber: L32145*]+-e However this returns arguments missing. I have tried variations on this to no avail. Is it possible? Aengus -- ---------------------------------------------------------------------- Aengus Stewart aengus.stewart@icrf.icnet.uk Bioinformatics Support Tel: +44 (0)171 269 3679 Imperial Cancer Research Fund Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ---------------------------------------------------------------------- From owner-srs@net.bio.net Sun Jul 13 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: Re: Linking to queries Date: 14 Jul 1997 22:27:23 GMT Organization: Biology, Indiana University - Bloomington Lines: 10 Message-ID: <5qe94b$i10$1@dismay.ucs.indiana.edu> References: <33CA2C68.31D2@icrf.icnet.uk> NNTP-Posting-Host: chipmunk.bio.indiana.edu it isn't very readable, but it works for me if i url-encode the query string. wgetz's http parser may be eating the '=' before the query parser. http://iubio.bio.indiana.edu/srs/wgetz? [libs%3D%7Bgenbank%20genbanknew%7D-all:esterase] -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Sun Jul 13 23:00:00 1997 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: Linking to queries Date: Mon, 14 Jul 1997 16:44:38 +0100 Organization: SEQNET Lines: 54 Distribution: bionet Message-ID: <33CA4965.41C6@dl.ac.uk> References: <33CA2C68.31D2@icrf.icnet.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) To: Aengus Stewart Aengus Stewart wrote: > > I am currently trying to link in the results of FASTA and > SCANPS(smith-waterman) to the SRS server at the EBI. > > However the format of the hits does not give the data library from which > the sequence was derived only the name and and the accession number, eg > > ... > The best scores are: initn init1 opt z-sc > E(473814) > BB L32145 Borrelia burgdorferi C62.5 heat ( 236) 1180 1180 1180 > 892.7 0 > ... > > therefore, > > http:///srs5bin/cgi-bin/wgetz?[database-id:id]+-e > > will not work as it goes directly to a single entry. > > I have tried incorporating the query that is returned when I do the > search within a live SRS session eg > > Query "[libs={embl emblnew}-AccNumber: L32145*] " found 1 entries > > http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?[libs={embl > emblnew}-AccNumber: L32145*]+-e > > However this returns arguments missing. > I have tried variations on this to no avail. > > Is it possible? > > Aengus > How about: http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?[embl-acc:L32145|emblnew-acc:L32145]+-e Cheers, Martin -- ------------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/Person.asp?m.p.hilbers | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.seqnet.dl.ac.uk/ | ------------------------------------------------------------------- From owner-srs@net.bio.net Sun Jul 13 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!news.apfel.de!howland.erols.net!europa.clark.net!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: etzold Newsgroups: bionet.software.srs Subject: Re: Linking to queries Date: Mon, 14 Jul 1997 16:22:03 +0100 Organization: EMBL-EBI Message-ID: <33CA441B.818B4354@ebi.ac.uk> References: <33CA2C68.31D2@icrf.icnet.uk> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: Aengus Stewart X-Priority: 3 (Normal) Lines: 26 > > Query "[libs={embl emblnew}-AccNumber: L32145*] " found 1 entries > > http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?[libs={embl > emblnew}-AccNumber: L32145*]+-e > > However this returns arguments missing. > I have tried variations on this to no avail. > > Is it possible? you can search as many databanks as you want by including them in a list within { and }. But the databank names must be separated by a space which is interpreted as the end of arguments to the cgi command. A '+' instead of the ' ' doesn't solve the problem either since it occurs within the srs query, which is a single argument which is split into two arguments by the space that replaces the '+'. But there is a solution! use a '_SP_' instead of the ' '. This is the internal encoding for wgetz. So your query should be http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?[libs={embl_SP_emblnew}-AccNumber:L32145*]+-e From owner-srs@net.bio.net Mon Jul 14 23:00:00 1997 Path: biosci!daresbury!uninett.no!news-feed.inet.tele.dk!europa.clark.net!ais.net!vixen.cso.uiuc.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: Re: Linking to queries Date: 15 Jul 1997 20:42:03 GMT Organization: Biology, Indiana University - Bloomington Lines: 12 Message-ID: <5qgnar$f57$1@dismay.ucs.indiana.edu> References: <33CA2C68.31D2@icrf.icnet.uk> <33CA441B.818B4354@ebi.ac.uk> NNTP-Posting-Host: chipmunk.bio.indiana.edu I vote for adding comma ',' to the list of legal library separartors. In article <33CA441B.818B4354@ebi.ac.uk>, etzold wrote: .. >But there is a solution! use a '_SP_' instead of the ' '. This is >the internal encoding for wgetz. So your query should be > >http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?[libs={embl_SP_emblnew}-AccNumber:L32145*]+-e -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Tue Jul 15 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: Re: Linking to queries Date: 16 Jul 1997 08:12:40 GMT Organization: EMBL Heidelberg Lines: 28 Distribution: world Message-ID: <5qhvpo$4j3@lion.embl-heidelberg.de> References: <33CA2C68.31D2@icrf.icnet.uk> <33CA441B.818B4354@ebi.ac.uk> <5qgnar$f57$1@dismay.ucs.indiana.edu> NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) X-URL: news:5qgnar$f57$1@dismay.ucs.indiana.edu gilbertd@bio.indiana.edu (Don Gilbert) wrote: >I vote for adding comma ',' to the list of legal library separartors. > Yes Good idea, we can still make it an optional. For immediate implimentation you can edit srsquery.i and modify the production 'searchLibs' by adding ','? (I underlined with '^' letter here). searchLibs: ~ ( /([a-zA-Z0-9_]+) *=/ {$g=$DbGroup:[init:$1]} | x{$g=$DbGroup:[init:default]}) ('{' (name {$DbGroup:[$g db:$ct]} ','? )* '}' | ^^^^ ^^^^ name {$g=$DbGroup:[$g db:$ct]} ) ~ Ramu ________________________________________________________________________________ Chenna Ramu; EMBL; Postfach 10.2209; 69012 Heidelberg; Germany. _/_/_/ _/_/_/ Email: chenna@embl-heidelberg.de _/ _/ _/ Url: http://www.embl-heidelberg.de/~chenna/ _/ . _/_/_/ Tel: (49) 6221 387530 (Off) ; Fax: (49) 6221 387517 _/ _/ _/ _/_/_/ _/ _/ From owner-srs@net.bio.net Tue Jul 15 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!news.icnet!not-for-mail From: Aengus Stewart Newsgroups: bionet.software.srs Subject: Re: Linking to queries Date: Wed, 16 Jul 1997 10:45:09 +0100 Organization: Imperial Cancer Research Fund Lines: 46 Message-ID: <33CC9825.2F1C@icrf.icnet.uk> References: <33CA2C68.31D2@icrf.icnet.uk> <33CA441B.818B4354@ebi.ac.uk> <5qhuf6$4j3@lion.embl-heidelberg.de> NNTP-Posting-Host: fingermouse.lif.icnet.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; OSF1 V4.0 alpha) Ramu Chenna wrote: > > etzold wrote: > >> > >> Query "[libs={embl emblnew}-AccNumber: L32145*] " found 1 entries > >> > >> http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?[libs={embl > >> emblnew}-AccNumber: L32145*]+-e > >> > >> However this returns arguments missing. > >> I have tried variations on this to no avail. > >> > >> Is it possible? > > > > > >you can search as many databanks as you want by including them in > >a list within { and }. But the databank names must be > >separated by a space which is interpreted as the end of arguments to > >the cgi command. > >A '+' instead of the ' ' doesn't solve the problem > >either since it occurs within the srs query, which is a single > >argument which is split into two arguments by the space that replaces > >the > >'+'. > > > >But there is a solution! use a '_SP_' instead of the ' '. This is > >the internal encoding for wgetz. So your query should be > > > >http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?[libs={embl_SP_emblnew}-AccNumber:L32145*]+-e > > mmm... Thure still it does not work because of 'libs=' , better to omit that. > > http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?[{embl_SP_emblnew}-AccNumer:L32145*]+-e > > should work! Yup I caught that as soon as Thure sent it to me. Aengus ---------------------------------------------------------------------- Aengus Stewart aengus.stewart@icrf.icnet.uk Bioinformatics Support Tel: +44 (0)171 269 3679 Imperial Cancer Research Fund Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK ---------------------------------------------------------------------- From owner-srs@net.bio.net Tue Jul 15 23:00:00 1997 Path: biosci!daresbury!uninett.no!news-feed.inet.tele.dk!news.maxwell.syr.edu!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: Re: Linking to queries Date: 16 Jul 1997 07:49:58 GMT Organization: EMBL Heidelberg Lines: 46 Distribution: world Message-ID: <5qhuf6$4j3@lion.embl-heidelberg.de> References: <33CA2C68.31D2@icrf.icnet.uk> <33CA441B.818B4354@ebi.ac.uk> NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) X-URL: news:33CA441B.818B4354@ebi.ac.uk etzold wrote: >> >> Query "[libs={embl emblnew}-AccNumber: L32145*] " found 1 entries >> >> http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?[libs={embl >> emblnew}-AccNumber: L32145*]+-e >> >> However this returns arguments missing. >> I have tried variations on this to no avail. >> >> Is it possible? > > >you can search as many databanks as you want by including them in >a list within { and }. But the databank names must be >separated by a space which is interpreted as the end of arguments to >the cgi command. >A '+' instead of the ' ' doesn't solve the problem >either since it occurs within the srs query, which is a single >argument which is split into two arguments by the space that replaces >the >'+'. > >But there is a solution! use a '_SP_' instead of the ' '. This is >the internal encoding for wgetz. So your query should be > >http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?[libs={embl_SP_emblnew}-AccNumber:L32145*]+-e mmm... Thure still it does not work because of 'libs=' , better to omit that. http://srs.ebi.ac.uk:5000/srs5bin/cgi-bin/wgetz?[{embl_SP_emblnew}-AccNumer:L32145*]+-e should work! Ramu -- ________________________________________________________________________________ Chenna Ramu; EMBL; Postfach 10.2209; 69012 Heidelberg; Germany. _/_/_/ _/_/_/ Email: chenna@embl-heidelberg.de _/ _/ _/ Url: http://www.embl-heidelberg.de/~chenna/ _/ . _/_/_/ Tel: (49) 6221 387530 (Off) ; Fax: (49) 6221 387517 _/ _/ _/ _/_/_/ _/ _/ From owner-srs@net.bio.net Thu Jul 17 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.apfel.de!univ-lyon1.fr!pasteur.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: getting default fasta format in SRS5 Date: Fri, 18 Jul 1997 11:53:08 +0200 Organization: INFOBIOGEN Lines: 23 Message-ID: <33CF3D04.622F@infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; SunOS 5.5.1 sun4u) Hello ! Just a two questions for SRS5: 1)Is there a simply way to get fasta format by default? Do i only need to change in all *.i the line: EMBLSeq:$field:[@DF_DNASequence token:sequence format:embl] into ^^^^ EMBLSeq:$field:[@DF_DNASequence token:sequence format:fasta] ^^^^^ 2)In the same way , How could i do for ClustalW, fasta, blast, to display the selected sequence(s) in a fasta format by default Thanks in advance for helping me Jean-Marc -- --------------------------------------------------- Jean-Marc PLAZA INFOBIOGEN - CNRS 7, rue Guy Moquet BP8 94801 VILLEJUIF Cedex, France tel: +33 45 59 52 39 fax: +33 45 59 52 50 e-mail: plaza@infobiogen.fr --------------------------------------------------- From owner-srs@net.bio.net Thu Jul 17 23:00:00 1997 Path: biosci!rutgers!news.sgi.com!news.maxwell.syr.edu!news-peer.sprintlink.net!news-sea-19.sprintlink.net!news-in-west.sprintlink.net!news.sprintlink.net!Sprint!131.103.1.114!chi-news.cic.net!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: genbank features parsing for v5? Date: 18 Jul 1997 13:23:06 GMT Organization: Biology, Indiana University - Bloomington Lines: 12 Message-ID: <5qnqnq$1kj$1@dismay.ucs.indiana.edu> NNTP-Posting-Host: chipmunk.bio.indiana.edu IUBio archive serves out genbank now using srs v.5. I had to revise the distrubition icarus files for genbank to get them working, and didn't get to correct the features table parsing yet. I'm full up with other tasks just now, and some users of this service need the genbank features to work properly. Does anyone else have icarus files for genbank that do this? Thanks, DOn -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Fri Jul 18 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 Jul 1997 02:00:07 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199707190900.CAA14678@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-srs@net.bio.net Sun Jul 20 23:00:00 1997 Path: biosci!agate!usenet.INS.CWRU.Edu!news.apk.net!uunet!in3.uu.net!204.27.65.11!news-out.communique.net!communique!hunter.premier.net!feed1.news.erols.com!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: (no subject) Date: 21 Jul 1997 12:26:42 GMT Organization: EMBL Heidelberg Lines: 20 Distribution: world Message-ID: <5qvki2$q92@lion.embl-heidelberg.de> NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) X-URL: news:bionet.software.srs?ALL Hi All! I thought it is better to keep a 'SRS TIPS' since many people started asking, mailing me about some trivial things! If you have something to add please send it to me, I will add them. http://www.embl-heidelberg.de/~chenna/srstips.html Ramu _______________________________________________________________ Chenna Ramu; EMBL; Postfach 10.2209; 69012 Heidelberg; Germany. Email: chenna@embl-heidelberg.de Url: http://www.embl-heidelberg.de/~chenna/ Tel: (49) 6221 387530 (Off) ; Fax: (49) 6221 387517 ______ From owner-srs@net.bio.net Sun Jul 20 23:00:00 1997 Path: biosci!rutgers!uwm.edu!news.he.net!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: SRS TIPS Date: 21 Jul 1997 12:34:14 GMT Organization: EMBL Heidelberg Lines: 22 Distribution: world Message-ID: <5qvl06$q92@lion.embl-heidelberg.de> NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) X-URL: news:bionet.software.srs?ALL Hi All! I thought it is better to keep a 'SRS TIPS' since many people started asking, mailing me about some trivial things! If you have something to add please send it to me, I will add them. http://www.embl-heidelberg.de/~chenna/srstips.html Ramu -- _______________________________________________________________ Chenna Ramu; EMBL; Postfach 10.2209; 69012 Heidelberg; Germany. Email: chenna@embl-heidelberg.de Url: http://www.embl-heidelberg.de/~chenna/ Tel: (49) 6221 387530 (Off) ; Fax: (49) 6221 387517 ______ From owner-srs@net.bio.net Sun Jul 20 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!newsfeed.direct.ca!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Weare@EuropeMail.com (Johnathon Weare) Newsgroups: bionet.software.srs Subject: Re: SRS TIPS Date: 21 Jul 1997 16:57:24 +0200 Organization: Biocomputing, EMBL Heidelberg, Germany Lines: 23 Sender: weare@fifi.embl-heidelberg.de Distribution: world Message-ID: References: <5qvl06$q92@lion.embl-heidelberg.de> NNTP-Posting-Host: fifi.embl-heidelberg.de Encryption-by: McWurst McWurst-Schluessel: O*Uef!$p&^afC1fe@0n--9`#gA||~[gf)*fcq26 X-Newsreader: Gnus v5.3/Emacs 19.34 >>>>> "R" == Ramu Chenna writes: R> Hi All! I thought it is better to keep a 'SRS TIPS' since many R> people started asking, mailing me about some trivial things! If you R> have something to add please send it to me, I will add them. R> http://www.embl-heidelberg.de/~chenna/srstips.html The most trivial question I still get is combining multiple words in the query form, despite it now including some help. I have an srs printable handout page for beginners to get started - SRS5 in 10 minutes http://www.sander.embl-heidelberg.de/johnny/srs.html ...which now has a link to your tip page. thanks, Johnny -- Johnathon Weare http://www.gpcr.org/johnny/ EMBL, Meyerhofstr 1, Heidelberg, Germany http://swift.embl-heidelberg.de/ Tel +49 (0)6221 387456, Fax +49 (0)6221 387517 Weare@EuropeMail.com From owner-srs@net.bio.net Sun Jul 20 23:00:00 1997 Message-ID: <33D3E52E.BB134F22@aachen.netsurf.de> Date: Tue, 22 Jul 1997 00:39:42 +0200 From: Richard Bach X-Mailer: Mozilla 4.0 [en] (Win95; I) MIME-Version: 1.0 Newsgroups: bionet.software.srs Subject: blood flow simulation model X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: a08.aachen.netsurf.de Organization: IVM GmbH - Server (Feeder) Ahrweiler Lines: 11 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!newsfeed.nacamar.de!blackbush.xlink.net!news.ivm.net!a08.aachen.netsurf.de hi im a medical student searching for a cardiovascular simulation model on pc. i intend to simulate possible cardiovascular changes, especially brain perfusion changes, during hemodialysis treatment. any help or suggestion welcome. thanx in advance... cand. med Richard Bach Innere Medizin II, Klinikum Aachen From owner-srs@net.bio.net Wed Jul 23 23:00:00 1997 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: lookup and SRS5, it can be done ! Date: 24 Jul 1997 13:51:06 GMT Organization: Belgian EMBnet Node Lines: 38 Message-ID: <5r7mka$poa@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] It is possible to make lookup work with the indexes of SRS5. I am of course talking about the lookup modified according to R. Doelz, ex-manager of the Swiss EMBnet Node. First, in the directory .../srs5_05/etc/osf put links : srswin.ptr -> .../srs4_08/etc/osf/srswin.ptr srswin.sec -> .../srs4_08/etc/osf/srswin.sec and in the file .../gcg8_1/gcgstartup add a line : source .../srs5_05/etc/prep_srs So, the modified lookup will use the search engine of SRS4 to search in the indexes made by SRS5. Second, you must make sure that the definitions of libraries and fields in the lookup source code, the odd files of SRS4 and the icarus files of SRS5 are in harmony. for each library/databank you need the same name and number, e.g. in SRS4 *.sdl : #libid /n=15 #library /name=EMBL in SRS5 *.i : $libid:[15] $library:[EMBL] for each field/index you need the same shortname, e.g. in lookup.c : {Definition, Text, "DEFInition", "DES", in SRS4 *.sdl : #srsfield /shortname=DES in SRS5 *.i : $srsfield:[short:DES] the index types must also have the same names in SRS4 srsgeneral.sdl : #idtype /id=%%SRSxSFTID /name="SubEntry-ID" in SRS5 srsgen.i : SUBENTRY_ID:$idtype:['SubEntry-ID'] With this, we can at the BEN site abandon the SRS4 indexes. Just in time, because we were looking out with fear for EMBL release 52 ! A final problem is that changing names of fields in lookup is trivial, adding new fields is tricky. I suspect a bug in the GCG 8 lookup source code. I will wait till we have the GCG 9 source code to proceed. Guy Bottu this message has also been posted to : bionet.software.gcg From owner-srs@net.bio.net Fri Jul 25 23:00:00 1997 Path: biosci!agate!howland.erols.net!europa.clark.net!169.207.30.81!newsfeeds.sol.net!newsspool.sol.net!newspump.wustl.edu!fas-news.harvard.edu!oitnews.harvard.edu!purdue!mozo.cc.purdue.edu!news.iupui.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: improvement suggestions Date: 26 Jul 1997 18:23:59 GMT Organization: Biology, Indiana University - Bloomington Lines: 74 Message-ID: <5rdfbv$n8f$1@dismay.ucs.indiana.edu> NNTP-Posting-Host: chipmunk.bio.indiana.edu Suggestions for future versions of SRS I think SRS is great software for many genome informatics needs. We are now using it as the main search engine in the FlyBase project (http://flybase.bio.indiana.edu/, see e.g., the Genes section searches). Based on using SRS for Genbank and related sequence data at IUBio and for the Drosophila data of quite a variety, I have several suggestions These are in rough order of importance to me, and possibly to others. Maybe some of these are possible now and I haven't looked hard enough. If not, I will try to add some of them and pass code on to Thure and colleagues. -- Sequence output format -- default should always be the native format, untouched by SRS (current return of genbank data is a bogus format that can't be interpreted well, it is missing the ORIGIN line, the sequence data is in EMBL not GENBANK style; maybe part of this is icarus indexing mistakes). -- offer GENBANK and PIR/CODATA output formats as primary standard sequence formats -- Query symbol neutrality The symbols that SRS now requires in queries for operations and parsing clash with symbols used above (in unix and http command strings) and below (in biological data). Especially because of the latter, it is difficult to use escape characters to do the kinds of queries needed. There should be query-time switches for getz, wgetz and such that let the caller set symbols used for query parsing, including &|![]={}-. At the least offer query-time symbol swapping, so that any single parsing symbol can be changed to another in meaning. The high ascii set would make a good option. But it would also be nice to allow strings, such as _AND_ for &, _OR_ for |, _OPEN_PHRASE_ for [, _CLOSE_PHRASE_ for ], etc. in queries. -- Case sensitive searches This should be available as a query-time, user choice for any field. Perhaps there should be an index-time switch that will say if a field has case sensitive potential, if it is compute expensive at query-time. -- Index numeric ranges For example, a map range such as "123-456" should be indexed so it can be queried as a numeric range. Query such as 124, 234, 345 should all match such a range. Several ranges per field must be possible. In WAIS, we just stored the text string of such a field, and did a numeric range test at query time. -- Cache query results and use that for quick lookups of next page data. wgetz, and other srs query drivers, offer a page of results for a given query, plus additional page links. These additional page links redo the same query at a sometimes large cpu cost. It would be nice to have the full match set for each query cached (for maybe an hour, in SRSTMP:) and used to serve multipage requests of same query. -- Relevance ranking Allow fields to store word counts per record in indexes, and use these counts for one form of relevance calculation. Relevance ranking can markedly improve the usability of query results, where those with the most query words (or however defined as most relevant) are sorted to the top of the results list. Relevance ranking has been standard in WAIS and related text indexing. -- Lists of words to ignore in indexing Use lists/files of common words to ignore at indexing (a, and, the, ...). Let the icarus parsing script read such a list from common file/data and apply to storing indices from any particular fields. Maybe we can do this now in the rich icarus; if so an example would be nice. -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Sat Jul 26 23:00:00 1997 Path: biosci!agate!usenet.INS.CWRU.Edu!news.apk.net!uunet!in3.uu.net!204.27.65.11!news-out.communique.net!communique!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!ix.netcom.com!news From: "Jimmy(Hyo Jun) Kim" Newsgroups: bionet.software.srs Subject: software for sale Date: 27 Jul 1997 04:33:08 GMT Organization: Gen-X Lines: 7 Message-ID: <01bc9a5f$d2552fa0$c3a220cc@mainfraim> NNTP-Posting-Host: jcx-nj10-03.ix.netcom.com X-NETCOM-Date: Sat Jul 26 11:33:08 PM CDT 1997 X-Newsreader: Microsoft Internet News 4.70.1161 Adobe Photoshop 3.0 full verson $75 Corel Draw 6.0 Full Version $75 Visual FoxPro 5.0 Full Version $150 Visual Basic Pro. 4.0 Full Version $100 Windows 95 OEM Full Version (with startup disk) $75 USRobotics Sportster 33.6 ext. Modem w/ voice $100 From owner-srs@net.bio.net Sun Jul 27 23:00:00 1997 From: etzold Newsgroups: bionet.software.srs Subject: Re: improvement suggestions Date: Mon, 28 Jul 1997 14:49:28 +0100 Organization: EMBL-EBI Lines: 129 Message-ID: <33DCA367.22B63DB6@ebi.ac.uk> References: <5rdfbv$n8f$1@dismay.ucs.indiana.edu> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: Don Gilbert X-Priority: 3 (Normal) Path: biosci!agate!howland.erols.net!newsfeed.nacamar.de!easynet-uk!news.mite.net!uknet!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail Don Gilbert wrote: > Based on using SRS for Genbank and related sequence data at IUBio and for > the Drosophila data of quite a variety, I have several suggestions > > -- Sequence output format > -- default should always be the native format, untouched by SRS (current > return of genbank data is a bogus format that can't be interpreted well, > it is missing the ORIGIN line, the sequence data is in EMBL not GENBANK > style; maybe part of this is icarus indexing mistakes). > -- offer GENBANK and PIR/CODATA output formats as primary standard > sequence formats we are working on that at the moment - currently it is not possible to get the native format - the sequence is always first converted into internal structure and then converted back > > -- Query symbol neutrality > The symbols that SRS now requires in queries for operations and parsing > clash with symbols used above (in unix and http command strings) and below > (in biological data). Especially because of the latter, it is difficult > to use escape characters to do the kinds of queries needed. that can be hard in some cases but i think most problematic are the logical and link operators ....see below > > There should be query-time switches for getz, wgetz and such that let the > caller set symbols used for query parsing, including &|![]={}-. > At the least offer query-time symbol swapping, so that any single parsing > symbol can be changed to another in meaning. The high ascii set would > make a good option. But it would also be nice to allow strings, such > as _AND_ for &, _OR_ for |, _OPEN_PHRASE_ for [, _CLOSE_PHRASE_ for ], > etc. in queries. that is quite possible, i even thought of using AND OR BUTNOT and LINKL and LINKR for & | ! < > respectively, changing that is quite easy since the query language is parsed by icarus - have a look at "SRSICA/srsquery.i". I will try to include the operators for the next release > > -- Case sensitive searches > This should be available as a query-time, user choice for any field. > Perhaps there should be an index-time switch that will say if a field > has case sensitive potential, if it is compute expensive at query-time. ok, that should be useful in some cases and is definetely possible to implement > > -- Index numeric ranges > For example, a map range such as "123-456" should be indexed so it > can be queried as a numeric range. Query such as 124, 234, 345 should > all match such a range. Several ranges per field must be possible. > In WAIS, we just stored the text string of such a field, and did a numeric > range test at query time. you can do that even now ...but it may look a little strange. index ('range' index) for each entry exactly two numbers ...or none which are highbound and lowbound eg 50 and 200. to find all the ranges that include 124 do '[db-range#:124] & [db-range#124:]' the assumption is that to get a match you need a hit in anything lesser the queyr and anything greater - the inersection with & makes sure you have both - if one of the boundaries is exactly 124 then this is ok if it is high or low bound > > -- Cache query results and use that for quick lookups of next page data. > wgetz, and other srs query drivers, offer a page of results for a given > query, plus additional page links. These additional page links redo > the same query at a sometimes large cpu cost. It would be nice to have > the full match set for each query cached (for maybe an hour, in SRSTMP:) > and used to serve multipage requests of same query. ok, feasible - could make this conditionally up to a certain set size > > -- Relevance ranking > Allow fields to store word counts per record in indexes, > and use these counts for one form of relevance calculation. Relevance > ranking can markedly improve the usability of query results, where those > with the most query words (or however defined as most relevant) are sorted > to the top of the results list. Relevance ranking has been standard in > WAIS and related text indexing. relevance ranking could be done by storing a word count in the index whih is fine with simple queries searching a single word, however the problem is with complex queries - each query part contributes a score, how do you compute the overall score, how do deal with 'but not' queries? > > -- Lists of words to ignore in indexing > Use lists/files of common words to ignore at indexing (a, and, the, ...). > Let the icarus parsing script read such a list from common file/data and > apply to storing indices from any particular fields. Maybe we > can do this now in the rich icarus; if so an example would be nice. if you don't have too many you could include them into the .is file $stoplist={a:1 and:1 the:1 ...} #the 'ones' are arbitrary ...there has to be a value after the name indexword: .... {if:$stoplist.$Ct==0 $Wrt} # $stoplist.$Ct is by default 0 if not defined thanks for your suggestions. I think most of them will be implemented at some stage. The only problematic one is the ranking regards thure From owner-srs@net.bio.net Tue Jul 29 23:00:00 1997 Path: biosci!agate!usenet.INS.CWRU.Edu!vncnews!HSNX!news.theriver.com!news-feed.inet.tele.dk!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gsl.net!news.gsl.net!uwm.edu!msunews!harbinger.cc.monash.edu.au!news.rmit.EDU.AU!news.unimelb.edu.au!wehi.edu.au!wehi!janice From: janice@wehi.edu.au (Janice Coventry, Walter and Eliza Hall Institute) Newsgroups: bionet.software.srs Subject: indexing large databases Date: 30 Jul 97 11:52:55 +1000 Organization: Walter & Eliza Hall Institute Lines: 18 Message-ID: <1997Jul30.115255@wehi> NNTP-Posting-Host: wehiu.wehi.edu.au Dear All I am wondering if there is any way to index files in background while keeping the old files intact. This would be handy with the large databases like Genbank which can take a few days to index and so are effectively out of action for those days. Thank you in anticipation Janice ================================================================================ Janice Coventry The Walter and Eliza Hall Institute of Medical Research, P.O. Royal Melbourne Hospital, Victoria, 3050, Australia. Phone: International +61-3-9345-2586 FAX: International +61-3-9347-0852 National 03-9345-2586 National 03-9347-0852 Email: janice@wehi.edu.au =============================================================================== From owner-srs@net.bio.net Tue Jul 29 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!oleane!pasteur.fr!jussieu.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: maybe a bug in srs5 Date: Wed, 30 Jul 1997 15:48:07 +0200 Organization: INFOBIOGEN Lines: 20 Message-ID: <33DF4617.3143@infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; SunOS 5.5.1 sun4u) Hi, I find a problem is SRS5.05 with the description and the number of links you want to display if you click on links in Swissprot for instance. This error occured in severals others SRS5 server but the error message are different. Regards, -- --------------------------------------------------- Jean-Marc PLAZA INFOBIOGEN - CNRS 7, rue Guy Moquet BP8 94801 VILLEJUIF Cedex, France tel: +33 45 59 52 39 fax: +33 45 59 52 50 e-mail: plaza@infobiogen.fr --------------------------------------------------- From owner-srs@net.bio.net Wed Jul 30 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: etzold Newsgroups: bionet.software.srs Subject: Re: maybe a bug in srs5 Date: Thu, 31 Jul 1997 10:37:52 +0100 Organization: EMBL-EBI Lines: 22 Message-ID: <33E05CF0.BBD503F5@ebi.ac.uk> References: <33DF4617.3143@infobiogen.fr> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: Jean-Marc Plaza X-Priority: 3 (Normal) Jean-Marc Plaza wrote: > > Hi, > I find a problem is SRS5.05 with the description > and the number of links you want to display if you > click on links in Swissprot for instance. > This error occured in severals others SRS5 server > but the error message are different. the proper way to find out about the links from and to swissprot in the information page is to go to the "links to" and "links from" section and click on, eg, "EMBL" etc. In the table of indices/fields is also the "link" field represented. if you click it, you get the field description with the "browse index" option. That shouldn't be there since the contents of the "link" data-field are not indexed at all. It used to be like that in SRS4. I will make sure this doesn't appear in non indexed data-fields regards thure