From owner-srs@net.bio.net Wed Oct 01 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!news-peer.sprintlink.net!news.sprintlink.net!Sprint!uunet!in5.uu.net!netnews.sbphrd.com!not-for-mail From: Filip Fuma Newsgroups: bionet.software.srs Subject: Query Form Page "Use view" selection Date: Thu, 02 Oct 1997 17:12:43 -0400 Organization: SmithKline Beecham Pharmaceuticals Research & Development Lines: 11 Message-ID: <34340E4B.2FEE@phu815.um.us.sbphrd.com> NNTP-Posting-Host: phu823.sbphrd.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5.1 sun4u) CC: filip_fuma-1@sbphrd.com In the Query Form page, the default predefined view is "* Names only *". Given a databank, is there any way to change the default view from "* Names only *" to another view which is applicable to that databank? Filip Fuma Senior Software Engineer Advanced Information Technology SmithKline Beecham Pharmaceuticals R&D From owner-srs@net.bio.net Thu Oct 02 23:00:00 1997 Path: biosci!daresbury!uninett.no!news.algonet.se!news.maxwell.syr.edu!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!204.238.120.130!jump.net!grunt.dejanews.com!not-for-mail Date: Fri, 03 Oct 1997 12:52:02 -0600 From: Reinhard.doelz@pharma.novartis.com Subject: fasta indexing in SRS Newsgroups: bionet.software.srs Message-ID: <875898768.8282@dejanews.com> Reply-To: reinhard.doelz@pharma.novartis.com Organization: Deja News Posting Service To: reinhard.doelz@pharma.novartis.com X-Article-Creation-Date: Fri Oct 03 17:12:50 1997 GMT X-Originating-IP-Addr: 194.151.3.11 (gatekeeper.sandoz.att.nl) X-Http-User-Agent: Mozilla/3.01SC-SGI (X11; I; IRIX 5.3 IP19) X-Authenticated-Sender: Reinhard.doelz@pharma.novartis.com Lines: 12 I'd like to get information on two issues: 1) Has someone created an icarus file for fasta files or fasta- formatted GCG databases? 2) Has someone successfully used srs5.05 for genbank/gcg binary indexed in gcg (9)? Thanks for any pointer, hint, code and suggestions. Regards Reinhard -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-srs@net.bio.net Thu Oct 02 23:00:00 1997 Path: biosci!britbio.co.uk!dudgeon From: dudgeon@britbio.co.uk (Tim Dudgeon) Newsgroups: bionet.software.srs Subject: parsing confusion: for icarus gurus only Date: 3 Oct 1997 08:24:34 -0700 Organization: British Biotech Lines: 64 Sender: daemon@net.bio.net Distribution: world Message-ID: <34350E9E.167E@britbio.co.uk> NNTP-Posting-Host: net.bio.net Hi, Could someone explain to me why this works #!/bin/env icarus $rules={ entry: ~ {$In:[file:text] $Out pre{$Skip:0}} ('>' {$Not} ln)* '>' {$entryFip=$Fip $Wrt} ('>' {$Not} ln {$App})* ~ ln: ~ /[^\n]*\n/ ~ } if:$TestMode { $job = $JobNew:[prod:$rules skip:" " fileName:'/fasta/format/file'] while:$JobHasInput:$job { $JobTokens:[$job name:entry print:1] $JobNext:$job } } but this doesn't, because it only gets the first entry in the file #!/bin/env icarus $rules={ data: ~ {$In:[file:text] $Out pre{$Skip:0}} ln {$Wrt} (ln {$App})* ~ entry: ~ {$In:data $Out} ('>' {$Not} ln)* '>' {$entryFip=$Fip $Wrt} ('>' {$Not} ln {$App})* ~ ln: ~ /[^\n]*\n/ ~ } if:$TestMode { $job = $JobNew:[prod:$rules skip:" " fileName:'/fasta/format/file'] while:$JobHasInput:$job { $JobTokens:[$job name:entry print:1] $JobNext:$job } } The example is a bit contrived, but I need to break up a file into bits before parsing because the data for each entry is non-contiguous, and I can't get it to work. Many thanks for suggestions Tim -- Dr. Tim Dudgeon Phone: 01865 748747 British Biotech Pharmaceuticals Ltd. FAX: 01865 717598 Watlington Road, Oxford, OX4 5LY, UK email: dudgeon@britbio.co.uk From owner-srs@net.bio.net Fri Oct 03 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!192.220.251.22!netnews.nwnet.net!news-hub.interserv.net!news.interserv.com!bestprice16.com From: "BUYNOW" software@bestprice16.com Newsgroups: bionet.software.srs Subject: ||||||||||||||||||||||||| M S O F F I C E P R O 97 $1 4 5 ||||||||||||||||||||||||| Date: Sat, 04 Oct 1997 00:12:58 -0700 Organization: KLM9 Lines: 98 Message-ID: <041097001258@bestprice16.com> NNTP-Posting-Host: hdn102-014.hil.compuserve.com /_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ M S O F F I C E P R O 97 (CD Only) > > > $ 1 4 5 < < < ++++++++++++++++ http://cyberswap.com ++++++++++++++++ <<>=>>>>===<==>>>=<= From owner-srs@net.bio.net Sun Oct 05 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!thetimes.pixel.kodak.com!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.4!news-pen-4.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-dc-26.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!howland.erols.net!surfnet.nl!barba.uci.kun.nl!sci.kun.nl!not-for-mail From: Ewoud Smit Newsgroups: bionet.software.srs Subject: Re: parsing confusion: for icarus gurus only Date: Mon, 06 Oct 1997 12:04:48 +0200 Organization: CAOS/CAMM: National Center for Computer-Aided Chemistry and Bioinformatics Lines: 19 Message-ID: <3438B7C0.41C6@sci.kun.nl> References: <34350E9E.167E@britbio.co.uk> NNTP-Posting-Host: cammsg1.caos.kun.nl 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 IP19) Hi Tim, One posible fault I could detect is that you try to set a file-pointer when your input is not a file but a token-table. Thus no file pointers are set and only the first entry is found (Fip=0 -> begin of file) Regards, Ewoud --------------------------------------------------------------------- Ewoud Smit Email: esmit@caos.kun.nl CAOS/CAMM Center Phone: +31 24 3653358 University of Nijmegen Fax: +31 24 3652977 Toernooiveld 1 6525 ED Nijmegen The Netherlands URL: http://www.caos.kun.nl/ --------------------------------------------------------------------- From owner-srs@net.bio.net Mon Oct 06 23:00:00 1997 Date: Tue, 07 Oct 1997 05:01:26 -0600 From: Tim Dudgeon Subject: Re: srscheck: indexing emblnew w/o embl Newsgroups: bionet.software.srs Message-ID: <876217263.14874@dejanews.com> Organization: Deja News Posting Service References: <342FB710.41C6@britbio.co.uk> X-Article-Creation-Date: Tue Oct 07 09:41:03 1997 GMT X-Originating-IP-Addr: 193.130.179.2 (gateway.britbio.co.uk) X-Http-User-Agent: Mozilla/3.01SC-SGI (X11; I; IRIX 6.2 IP22) via proxy gateway CERN-HTTPD/3.0 libwww/2.17 X-Authenticated-Sender: Tim Dudgeon Lines: 25 Path: biosci!news.ic.sunysb.edu!news-pen-15.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.4!news-pen-4.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-dc-26.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!europa.clark.net!208.134.241.18!newsfeed.internetmci.com!204.238.120.130!jump.net!grunt.dejanews.com!not-for-mail OK, I fixed it now. the problem was not with SRS, but with the GCG script that built the embl updates, which did a chmod +w `name -f EMBLDir`/*.* This had the effect of tricking srscheck into thinking all of embl had been updated, even though the date stamps on the embl files were not changed. The answer: either put embl updates in a different directory to the embl release or change the offending line to chmod +w `name -f EMBLDir`/em_new.* Cheers Tim =============================================================== Dr. Tim Dudgeon Phone: 01865 748747 British Biotech Pharmaceuticals Ltd. FAX: 01865 717598 Watlington Road, Oxford, OX4 5LY, UK email: dudgeon@britbio.co.uk -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-srs@net.bio.net Tue Oct 07 23:00:00 1997 From: alexander_tress@student.uni-ulm.de (Alexander Tress) Newsgroups: bionet.software.srs Subject: Re: srsbuild: 7864 Memory fault Date: Wed, 08 Oct 1997 18:01:04 GMT References: <343236EB.41C6@britbio.co.uk> X-Newsreader: Forte Free Agent 1.0.82 NNTP-Posting-Host: port16-highway.extern.uni-ulm.de Message-ID: <343b4bf5.0@news.uni-ulm.de> Lines: 47 Path: biosci!news.ic.sunysb.edu!news-pen-15.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.4!news-pen-4.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-dc-26.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news-peer.gsl.net!news.gsl.net!gip.net!fu-berlin.de!news.belwue.de!news.uni-ulm.de!port16-highway.extern.uni-ulm.de dudgeon@britbio.co.uk (Tim Dudgeon) wrote: Hello ! >I've started getting core dumps during building indexes for emblnew: >...no. 323100, SAZ83159 >...no. 323400, SCL8083 >...no. 323700, SCYBR031W >...no. 324000, SCYDL065C >...no. 324300, SCYGL118C >/usr/local/srs5_05/srs/etc/srsupdate: 7864 Memory fault - core dumped >Has anyone seen this and know the answer? The 'srsupdate' is only a script with several calls from the executable 'srsbuild'. I got the same error while compressing the previously build index which is issued later in the 'srsupdate'-script. Make the following steps ( one of this will solve the problem ) 1. Check the memory-utilization, perhaps you have to increase the swapsize ( unfortunately the perfomance will decrease dramatically while swaping ) 2. If there is enough virtual memory check your user-limits ( ulimit -a ). Set the values to ulimited if possible or to the highest possible value. Point 2 solved the problem I had with srsupdate on a DEC-Station with 512MB RAM and 1GB Swapsize ( indexed file : 350MB, 250000 records ). Regards, Alex Alexander Tress Tel/Fax : +49 731 58489 Tel : +49 7384 498 Uni Ulm E-Mail : Alexander.Tress@student.uni-ulm.de Pin Germany alex@pin.de From owner-srs@net.bio.net Wed Oct 08 23:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.nacamar.de!news-hh.maz.net!news-zh.switch.ch!news.belnet.be!news.vub.ac.be!usenet From: Robert Herzog Newsgroups: bionet.software.srs Subject: SRS 5 and "include in list option" Date: Thu, 09 Oct 1997 11:13:17 +0100 Organization: ULB Bio Informatique Lines: 58 Message-ID: <343CAE3D.6B1A@ulb.ac.be> NNTP-Posting-Host: dbmben1.ulb.ac.be Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (Win95; I) CC: tech@embnet.org, techmgr@embnet.org, thure.etzold@ebi.ac.uk Hello, I am puzzled by the curious behaviour of SRS5 when it is asked to produce results including some fields, by using the "Include in list" check boxes. I am not aware of a discussion about this on this list. (there is too much noise from the sex fans...) I get a proper answer from the searches in PIR and Swissprot on our server, but for the first entry, the bank ID is shown in capitals, and for all the next, in small lettres. like this : (copy-pasted from netscape) SWISSPROT:A1AF_CAVPO ID A1AF_CAVPO STANDARD; PRT; 403 AA. DE ALPHA-1-ANTIPROTEINASE F PRECURSOR (ALPHA-1-ANTITRYPSIN) (ALPHA-1- DE PROTEINASE INHIBITOR) (APF) (FRAGMENT). OS CAVIA PORCELLUS (GUINEA PIG). swissprot:A1AS_CAVPO ID A1AS_CAVPO STANDARD; PRT; 405 AA. DE ALPHA-1-ANTIPROTEINASE S PRECURSOR (ALPHA-1-ANTITRYPSIN) (ALPHA-1- DE PROTEINASE INHIBITOR) (APS). OS CAVIA PORCELLUS (GUINEA PIG). swissprot:A1AT_SHEEP ID A1AT_SHEEP STANDARD; PRT; 416 AA. DE ALPHA-1-ANTIPROTEINASE PRECURSOR (ALPHA-1-ANTITRYPSIN) (ALPHA-1- DE PROTEINASE INHIBITOR). OS OVIS ARIES (SHEEP). When I try a search with "Include from list" on our EMBL databank, I get only the first entry, completetly, and the ID of the second entry. Thereafter, all is blank. Like this (copy/pasted) EMBL:ASPPRCA ID ASPPRCA standard; DNA; PRO; 1952 BP. DE Anabaena sp.PCC7120 prcA gene embl:EC82K The same search without asking for "Include..." is complete. We index the GCG files SRS. The problem exists on several other servers (Pasteur Paris, SEQNET, Oxford,...) but others (EBI, Infobiogen, Heidelberg, ...) behave normally. We have 5.05 running. Comments ? I send copy of this to the EMBnet tech manager and to Thure himself... Robert Herzog From owner-srs@net.bio.net Wed Oct 08 23:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.nacamar.de!eerie.fr!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: SRS 5 and "include in list option" Date: Thu, 09 Oct 1997 11:33:28 +0100 Organization: EMBL-EBI Lines: 40 Message-ID: <343CB2F8.E423CDC7@ebi.ac.uk> References: <343CAE3D.6B1A@ulb.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: Robert Herzog X-Priority: 3 (Normal) Robert Herzog wrote: > > Hello, > I am puzzled by the curious behaviour of SRS5 when it is asked to > produce results including some fields, by using the "Include in list" > check boxes. > I am not aware of a discussion about this on this list. (there is too > much noise from the sex fans...) > I get a proper answer from the searches in PIR and Swissprot on our > server, but for the first entry, the bank ID is shown in capitals, and > for all the next, in small lettres. that behaviour is caused by a bug which is already fixed for version 5.1 > When I try a search with "Include from list" on our EMBL databank, I get > only the first entry, completetly, and the ID of the second entry. > Thereafter, all is blank. Like this (copy/pasted) > > EMBL:ASPPRCA > > ID ASPPRCA standard; DNA; PRO; 1952 BP. > DE Anabaena sp.PCC7120 prcA gene > > embl:EC82K > > The same search without asking for "Include..." is complete. > don't know about that one myself. Most often i go into the view manager and create a view rather than checking the fields in the query form - there is another problem that the field selection seems to disappear after seeing several chunks. This is also what changed in 5.1: whenever you do a field selection in the queyr form a view is defined from that which stays for the rest of the session regards thure From owner-srs@net.bio.net Wed Oct 08 23:00:00 1997 Path: biosci!agate!newsgate.duke.edu!solaris.cc.vt.edu!newsrelay.netins.net!uunet!in5.uu.net!netnews.sbphrd.com!not-for-mail From: Ray Wang Newsgroups: bionet.software.srs Subject: The problems in SRS Date: Thu, 09 Oct 1997 16:10:06 -0400 Organization: SmithKline Beecham Pharmaceuticals Research & Development Lines: 43 Message-ID: <343D3A1E.3290@mh.us.sbphrd.com> NNTP-Posting-Host: phu824.sbphrd.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5.1 sun4u) CC: W_David_Benton@sbphrd.com Hello, We meet the following problems in SRS. When we search some of the databanks using several fields to display the query results, for example, searching OWL, one of the results like this (using ID, DESCRIPTION, DATE): OWL ID Description Date OWL:FAAA_HUMAN FAAA_HUMAN FUMARYLACETOACETASE EC A HREF wgetz id auO117aVgL e enzyme 3 7 1 2 FUMARYLACETOACETATE HYDROLASE BETA DIKETONASE FAA HOMO SAPIENS HUMAN The EC number should be hyperlinked instead. Some of other sites Oxford, Hinxton... behave the same. The SRS 5.05 version is running. Any suggestions on this? Ray Wang Software Engineer Adanced Information Technology SmithKline Beecham R&D From owner-srs@net.bio.net Thu Oct 09 23:00:00 1997 Path: biosci!HRBMU.HRBMU.EDU.CN!jinbguo From: jinbguo@HRBMU.HRBMU.EDU.CN (jinbguo) Newsgroups: bionet.software.srs Subject: How to retrieve the CONTIG on the internet? Date: 10 Oct 1997 04:32:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 5 Sender: daemon@net.bio.net Distribution: world Message-ID: <343EE467.1601@hrbmu.hrbmu.edu.cn> NNTP-Posting-Host: net.bio.net I am very happy to receive any help about the CONTIG retrieving message. ANY HELP WILL BE APPRECIATED. Pleased send email to jinbguo@hrbmu.hrbmu.edu.cn From owner-srs@net.bio.net Fri Oct 10 23:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!news.misty.com!www.nntp.primenet.com!globalcenter0!news.primenet.com!nntp.primenet.com!newsfeed.internetmci.com!206.229.87.25!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!198.69.104.3!ddi2.digital.net!not-for-mail From: INSTANT SEX APPEAL Newsgroups: bionet.software.srs Subject: HOW TO ATTRACT GIRLS INSTANTLY....Secrets to instant sex appeal Date: 11 Oct 1997 01:24:37 GMT Organization: INSTANT SEX APPEAL Lines: 137 Message-ID: <61mkgl$p8u$6401@ddi2.digital.net> NNTP-Posting-Host: max-orl1-15.digital.net HOW TO ATTRACT GIRLS INSTANTLY....Secrets to instant sex appeal PURE INSTINCT PHEROMONE ATTRACTANT FOR MEN WILL GIVE YOU AN UNFAIR ADVANTAGE WITH WOMEN GUARANTEED (or your money back)! Everyone knows that some men (a tiny minority) are able to instantly attract women. It used to be known as "animal magnetism". Scientists now say this natural attraction is due to pheromones - body smells that are not consciously detected, but that effect the behavior of others towards the person giving off these chemical signals. It's natures way of attracting the opposite sex. Scientists have now isolated and synthesized two natural Attractants- androstenol and androstenone pheromone. Carefully controlled experiments show they work and have been widely reported on television and in both the British and international press. Androstenone pheromone has been successfully tested on BBC TV's "TOMORROWS WORLD" and by Desmond Morris (Author of "The Naked Ape" and "Manwatching" and renowned human behaviorist) on BBC TV's "Friday Night... Saturday Morning." New improved formula PURE INSTINCT from ICT Research Technology contains both ANDROSTENOL and ANDROSTENONE pheromone and produces and undetectable scent that subconsciously attracts women to the wearer. PURE INSTINCT is the world's number one selling and the most concentrated (5 - 7 x normal active strength) pheromone spray for men - don't be misled by cheaper (or more expensive) imitations. WHAT THE PRESS SAY: * Lowell Ponte, a former consultant on exotic weapons and a Readers Digest science writer, said in an interview that "use of the recently discovered chemical Androstenone should be banned. Congress should pass a law making it a crime to use this chemical to influence voters by making politicians appear more lovable. - The San Francisco Chronicle - * "The stuff attracts women like you wouldn't believe" - Colorado Telegraph * "And now this pheromone has been marketed, we've tested it - and good grief it works" - Koave * "pheromones influence human behavior in a subtle way. Women are attracted to the smell" - The Daily Telegraph * "Pure Instinct is likely to produce a state of sexual excitement or arousal" - Men Only (Vol. #44 No. 4) Much of our sales of PURE INSTINCT are reorders from existing users, reports confirm success. "PURE INSTINCT really does seem to work! The most dramatic instances have occurred when wearing it at discos. Girls just drift towards me and start flirting." -DT Cardiff "I Knew PURE INSTINCT wasn't a gimmick when one of the girls at work, quite out of character, started to seduce me when we were alone in the office." -SD Nottingham PURE INSTINCT comes in a discreet 15ml pocket roll on container with full instructions, Ideal for any man who wants to join that lucky few who have more than their fair share of sex appeal. 30 DAY MONEY BACK GUARANTEE If you are not 100% delighted with the results from using PURE INSTINCT simply return remainder within 30 days for a full refund- No questions asked! C O N F I D E N T I A L I T Y Note: We do not sell our database to any other company, all of our order processing is done by our company alone, and orders are sent in plain, nondescript packaging. The confidentiality of our customers is maintained above all. To order the " Pure Instinct Pheromone Sex Attractant" please fill out the following form and mail it to the address below. (Feel free to write out the order form by hand, All funds must equal US dollars. OVERSEAS ORDERS WELCOME BUT MUST PAY WITH US CASH INTERNATIONAL MONEY ORDER OR TRAVELLERS CHECK _________________________________________ Yes! I want to attract more women please send me _______ bottles of PURE INSTINCT Price $29.95(U.S.) + $4.00 S/H U.S. OVERSEAS $8.00 S/H. Please allow 1-2 WEEKS FOR DELIVERY. I understand that if I'm not 100% delighted, simply return remainder within 30 days for a full refund. I have enclosed check, cash or money-order for ___________ (U.S.) Name (Please use block letters) _______________________________________________ Address: _________________________________ City, St.: _________________________________ Zip: __________________ E-Mail : ______________________ Please Mail to: SMG Enterprises 1970 E. Osceola Pkwy Suite 242 Kissimmee Fl.34743 From owner-srs@net.bio.net Sat Oct 11 23:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!192.220.251.22!netnews.nwnet.net!news-hub.interserv.net!news.interserv.com!bestprice16.com From: "JUSTDOIT" 4less@bestprice16.com Newsgroups: bionet.software.srs Subject: +++++++++++ M S O F F I C E P R O 97 $1 4 5 ++++++++++++ Date: Thu, 09 Oct 1997 19:43:46 -0700 Organization: DEF1 Lines: 17 Message-ID: <091097194346@bestprice16.com> NNTP-Posting-Host: hdn112-174.hil.compuserve.com /_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ M S O F F I C E P R O 97 (CD Only) > > > $ 1 4 5 < < < ++++++++++++++++++++++++++ http://www.iaoauction.com/auction/ ++++++++++++++++++++++++++ ><=><>=<==<=<>><><>< From owner-srs@net.bio.net Sun Oct 12 23:00:00 1997 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!EU.net!sun4nl!193.78.240.11.MISMATCH!sun4nl!star.cs.vu.nl!newshost.vu.nl!not-for-mail From: Jeroen Bos Newsgroups: bionet.software.srs Subject: Search for a transcription activator. Date: Mon, 13 Oct 1997 14:52:09 +0200 Organization: Vrije Universiteit Amsterdam Lines: 8 Message-ID: <34421977.6F60@chem.vu.nl> Reply-To: jbos@chem.vu.nl NNTP-Posting-Host: rubidium.chem.vu.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.03 (Macintosh; I; PPC) Hello, I have a sequence that is a possible binding domain for a transcriptional activator. I wanna know if this domain already has been identified by someone. Could anyone tell me if it is possible to do this by the SRS and if it is possible how I should do this. Jeroen Bos From owner-srs@net.bio.net Tue Oct 14 23:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!news.misty.com!www.nntp.primenet.com!globalcenter0!news.primenet.com!nntp.primenet.com!howland.erols.net!newsxfer3.itd.umich.edu!news.join.ad.jp!wnoc-tyo-news!aist-nara!odins-suita!chiba-ns!villon.nig.ac.jp!mkikuchi From: mkikuchi@genes.nig.ac.jp (Masayuki Kikuchi) Newsgroups: bionet.software.srs Subject: srsbuild: can not merge ID field of embl Date: 14 Oct 1997 10:11:17 GMT Organization: National Institute of Genetics, Japan. Lines: 21 Message-ID: <61vgg5$c2p$1@villon.nig.ac.jp> NNTP-Posting-Host: watson.genes.nig.ac.jp X-Newsreader: mnews [version 1.20] 1996-12/08(Sun) I'm running SRS5.05 and would like to index embl. When I merge index partitions of "ID" to a single index, SRSBUILD won't index and the message: % srsbuild embl -f "id" -m "/SRS/srs5.05/etc/message.dat" could not be opened % % ls /SRS/srs5.05/etc/message.dat /SRS/srs5.05/etc/message.dat % I can merge index partitions of other field. Would anyone have any hint? Thank you! -- Masayuki Kikuchi (mkikuchi@genes.nig.ac.jp) From owner-srs@net.bio.net Thu Oct 16 23:00:00 1997 Path: biosci!mserv1.dl.ac.uk!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: guiType:multi Date: Fri, 17 Oct 1997 17:07:45 +0100 Organization: SEQNET Lines: 45 Distribution: bionet Message-ID: <34478D51.167E@dl.ac.uk> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) Hi Guys, Does anybody know how to use the "guiType:multi" in srs applications ? It apparently should allow you to select multiple items from an options list, but sofar I have not been able to transfer the multple selected items to the command line. In appl.i, there is an example of this $AppOpt:[consistency group:@OTHER_OPTS type:bool guiType:multi prompt:'' values:{ $OptVal:[consistency valInt:1 prompt:consistency] $OptVal:[span2 prompt:span2] $OptVal:[span1 prompt:span1] $OptVal:[span prompt:span] } ] which is then put on the command line for blast with: |($Alt:[$opt.span1 t:' -span1'])\ |($Alt:[$opt.span2 t:' -span2'])\ |($Alt:[$opt.span t:' -span'])\ |($Alt:[$opt.consistency t:' -consistency'])\ This allows you to select any of these options - but in practice, if you select any of these options, the -consistency parameter is put on the command line... 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 Thu Oct 16 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!feed1.news.luth.se!luth.se!news-ge.switch.ch!serra.unipi.it!sirio.cineca.it!gopher From: server srswww Newsgroups: bionet.software.srs Subject: troubles in indexing EMBL 51 (ORIG FORMAT) Date: Fri, 17 Oct 1997 18:39:46 +0200 Organization: Cineca Lines: 84 Message-ID: <344794D1.20914C41@eos.bio.unipd.it> NNTP-Posting-Host: eos.bio.unipd.it Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------DE54E31CE28885A6795F0BD9" X-Mailer: Mozilla 4.03 [en] (X11; I; SunOS 5.5 sun4m) --------------DE54E31CE28885A6795F0BD9 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit We are trying to index EMBL 51 in SRS5 I selected (commenting and outcommenting lines) ORIG FORMAT in embl.i and embl.is. I inserted est8, est9, est10 and est11 in embl.is but we had troubles: est8.dat:6565666: error: syntax error, production `authors' : |vage A.R., Fields C. and Venter J.C. | .....................................^ no match with |^[,;]| (a lot of time!) and later we had: error: file could not be opened, "/export/home/srswww/srs/index/embl_id_8.inx" for all indexes Can someone help us? Where's the problem? Thank you very much for your collaboration Nicola Cannata CRIBI, University of Padova, Italy --------------DE54E31CE28885A6795F0BD9 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit We are trying to index EMBL 51 in SRS5

I selected (commenting and outcommenting lines) ORIG FORMAT in embl.i and
embl.is. I inserted est8, est9, est10 and est11 in embl.is

but we had troubles:

est8.dat:6565666: error: syntax error, production
`authors' :

|vage A.R., Fields C. and Venter J.C. |

.....................................^

  no match with |^[,;]|

(a lot of time!)

and later we had:

error: file could not be opened,
"/export/home/srswww/srs/index/embl_id_8.inx"

for all indexes
 

Can someone help us? Where's the problem?

Thank you very much for your collaboration
 

Nicola Cannata
CRIBI, University of Padova, Italy
  --------------DE54E31CE28885A6795F0BD9-- From owner-srs@net.bio.net Sat Oct 18 23:00:00 1997 Path: biosci!agate!howland.erols.net!newsxfer3.itd.umich.edu!oleane!jussieu.fr!infobiogen.fr!lovelace.infobiogen.fr!dessen From: dessen@lovelace.infobiogen.fr (Philippe Dessen) Newsgroups: bionet.software.srs Subject: SRS 5 getz Date: 19 Oct 1997 13:28:24 GMT Organization: GIS INFOBIOGEN, 7 rue Guy Moquet BP8, 94801 VILLEJUIF, France Lines: 19 Message-ID: <62d1to$n3n@caroll.infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: TIN [version 1.2 PL2] In the SRS4 version there is an option to read a file containing a listt of queries -qf [""] name of file containing a list of queries We have not found the similar option in the SRS5 version ?? Is it nevertheless a similar option ? That is faster to use it than to have a loop script. Philippe Dessen -- ------------------------------------------------------- Philippe Dessen GIS INFOBIOGEN 7 rue Guy Moquet BP8, 94801 VILLEJUIF Cedex, France tel : +33 1 45 59 52 41 fax : +33 1 45 59 52 50 e-mail : dessen@infobiogen.fr http://www.infobiogen.fr ------------------------------------------------------- From owner-srs@net.bio.net Sat Oct 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 Oct 1997 02:00:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199710190900.CAA26106@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 Oct 19 23:00:00 1997 Path: biosci!daresbury!uninett.no!newsfeed.nacamar.de!newscore.univie.ac.at!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: guiType:multi Date: Mon, 20 Oct 1997 17:40:38 +0100 Organization: EMBL-EBI Lines: 12 Message-ID: <344B8986.80E2A42@ebi.ac.uk> References: <34478D51.167E@dl.ac.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: Martin Hilbers X-Priority: 3 (Normal) Martin Hilbers wrote: > > ... > This allows you to select any of these options - but in practice, > if you select any of these options, the -consistency parameter is > put on the command line... yes you are right - this is a 'glitch' that escaped me completely - there is fortunately a way out - will fix it thure From owner-srs@net.bio.net Sun Oct 19 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!thetimes.pixel.kodak.com!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.131!news-pen-1.sprintlink.net!news-east.sprintlink.net!news-dc-26.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!eerie.fr!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: SRS 5 getz Date: Mon, 20 Oct 1997 17:30:01 +0100 Organization: EMBL-EBI Lines: 26 Message-ID: <344B8709.D2746C83@ebi.ac.uk> References: <62d1to$n3n@caroll.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: Philippe Dessen X-Priority: 3 (Normal) Philippe Dessen wrote: > > In the SRS4 version there is an option to read a file containing > a listt of queries > > -qf [""] name of file containing a list of queries i was not awaer that anybody was using that option - am working on getz at the moment and resinstantiate old options and add new ones the changes to getz are -d and -t will be back in 5.1 -qf will be easy to put back as well -ll (list length) and -lb (list begin) to get only chunks back from getz (this is analogous to wgetz options) -i (indextokens) lets you display the tokens generated for parsing - it is analogous to srsbuild -d, the advantage here is that ne can do any getz query and then have the index tokens displayed. This should be useful for improving parsers that go wrong for particular entries only ...now is the time for asking for more options! regards Thure From owner-srs@net.bio.net Sun Oct 19 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!howland.erols.net!EU.net!sun4nl!sun4nl!sci.kun.nl!not-for-mail From: Ewoud Smit Newsgroups: bionet.software.srs Subject: Re: troubles in indexing EMBL 51 (ORIG FORMAT) Date: Mon, 20 Oct 1997 10:21:31 +0200 Organization: CAOS/CAMM: National Center for Computer-Aided Chemistry and Bioinformatics Lines: 140 Message-ID: <344B148B.7FBD40A4@sci.kun.nl> References: <344794D1.20914C41@eos.bio.unipd.it> NNTP-Posting-Host: cammsg1.caos.kun.nl Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------9749CEACAB560D9C7EC0116E" X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX 5.3 IP19) --------------9749CEACAB560D9C7EC0116E Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit server srswww wrote: > We are trying to index EMBL 51 in SRS5 > > I selected (commenting and outcommenting lines) ORIG FORMAT in embl.i > and > embl.is. I inserted est8, est9, est10 and est11 in embl.is > > but we had troubles: > > est8.dat:6565666: error: syntax error, production > `authors' : > > |vage A.R., Fields C. and Venter J.C. | > > .....................................^ > That "and" is not supported in the embl syntax author fields should end with ';'and authors should be separated by ',' so it looks like your est8.dat file has the wrong syntax. > no match with |^[,;]| > > (a lot of time!) > > and later we had: > > error: file could not be opened, > "/export/home/srswww/srs/index/embl_id_8.inx" > This is probably a propagated error caused by the one above, should not be herewhen above problem is solved, if it remains it's most likely due to unix file modes being set to read-only. > for all indexes > > > Can someone help us? Where's the problem? > > Thank you very much for your collaboration > > > Nicola Cannata > CRIBI, University of Padova, Italy > Regards, Ewoud Smit -- --------------------------------------------------------------------- Ewoud Smit Email: esmit@caos.kun.nl CAOS/CAMM Center Phone: +31 24 3653358 University of Nijmegen Fax: +31 24 3652977 Toernooiveld 1 6525 ED Nijmegen The Netherlands URL: http://www.caos.kun.nl/ --------------------------------------------------------------------- The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but 'That's funny...' -Isaac Asimov --------------9749CEACAB560D9C7EC0116E Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit server srswww wrote:

 We are trying to index EMBL 51 in SRS5

I selected (commenting and outcommenting lines) ORIG FORMAT in embl.i and
embl.is. I inserted est8, est9, est10 and est11 in embl.is

but we had troubles:

est8.dat:6565666: error: syntax error, production
`authors' :

|vage A.R., Fields C. and Venter J.C. |

.....................................^
 

That "and" is not supported in the embl syntax author fields should end with ';'and authors should be separated by ',' so it looks like your est8.dat file has the
wrong syntax.

  no match with |^[,;]|

(a lot of time!)

and later we had:

error: file could not be opened,
"/export/home/srswww/srs/index/embl_id_8.inx"
 

This is probably a propagated error caused by the one above, should not be herewhen above problem is solved, if it remains it's most likely due to unix file modes
being set to read-only.

for all indexes
 

Can someone help us? Where's the problem?

Thank you very much for your collaboration
 

Nicola Cannata
CRIBI, University of Padova, Italy
 

 Regards, Ewoud Smit 
-- 
---------------------------------------------------------------------
Ewoud Smit                      Email: esmit@caos.kun.nl
CAOS/CAMM Center                Phone: +31 24 3653358
University of Nijmegen          Fax:   +31 24 3652977
Toernooiveld 1
6525 ED Nijmegen
The Netherlands                 URL: http://www.caos.kun.nl/
---------------------------------------------------------------------
The most exciting phrase to hear in science, the one that heralds new 
discoveries, is not 'Eureka!' but 'That's funny...' -Isaac Asimov
  --------------9749CEACAB560D9C7EC0116E-- From owner-srs@net.bio.net Sun Oct 19 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: troubles in indexing EMBL 51 (ORIG FORMAT) Date: Mon, 20 Oct 1997 17:43:41 +0100 Organization: EMBL-EBI Lines: 21 Message-ID: <344B8A3D.E88C0792@ebi.ac.uk> References: <344794D1.20914C41@eos.bio.unipd.it> 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: server srswww X-Priority: 3 (Normal) server srswww wrote: > and later we had: > > error: file could not be opened, > "/export/home/srswww/srs/index/embl_id_8.inx" > > for all indexes the syntax warnings are normal since the author lines in EMBL contain many errors. the file open error is serious. It comes most likely from a limitation of the max number of open files per process. to get rid of that do % unlimit before the indexing regards thure From owner-srs@net.bio.net Tue Oct 21 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!thetimes.pixel.kodak.com!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.131!news-pen-1.sprintlink.net!news-east.sprintlink.net!news-dc-26.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!uninett.no!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: Re: SRS 5 getz Date: 22 Oct 1997 14:32:59 GMT Organization: EMBL, Heidelberg, Germany Lines: 27 Distribution: world Message-ID: <62l2qr$650@lion.embl-heidelberg.de> References: <62d1to$n3n@caroll.infobiogen.fr> <344B8709.D2746C83@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:344B8709.D2746C83@ebi.ac.uk Hello Thure > ...now is the time for asking for more options! okey, that's nice! 1. Can we have alias names to databases (single database or group of databases). This would solve some problem when we suddenly change database name (emnew --> emblnew for example) and the external links from other sources to this database works. 2. somebody should continue asking from here... 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 Wed Oct 22 23:00:00 1997 From: "Stephen" Newsgroups: 3b,3b.tech,5col.forsale,alt.angst.xibo.sex,alt.binaries.w-software,alt.community.local-money,alt.comp.software.tools,at.tuwien.software,bionet.software.acedb,bionet.software.gcg,bionet.software.pc,bionet.software.srs,bionet.software.staden,bi Subject: 20M of internet linked accounting software for $5M! Date: Wed, 22 Oct 1997 19:59:12 -0400 Lines: 30 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 207.243.133.154 Message-ID: <344e9394.0@news.bravo.net> Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!207.48.46.15!news.bravo.net!207.243.133.154 Xref: biosci bionet.software.acedb:1484 bionet.software.gcg:2854 bionet.software.srs:825 bionet.software.staden:558 Here's HOW. I have WON a legal copy of Data Pro EZ NOW! accounting software with all you need to link this software directly to the internet. It will update your inventory immediately directly to the internet. Show pictures of every product and change it in seconds if you need to. You can set up for your customers to purchase DIRECTLY ON LINE! Link it with other modules and have your customers check the status of an order, make payments directly towards their account. See their account balances....and MUCH MUCH MORE! Because I have WON it directly from Data Pro I am entitled to sell this software NO STRINGS ATTACHED for what ever I want. If we had not already had an on line system we would be using it right now. So now instead of buying it from them for $20M I'm willing to sell my copy for $5M Data Pro sells it right now for $20,000.00 go and see! I can sell 1 copy ONLY for just $5,000.00 First check out http://www.dpro.com and take a tour of a sample store. Then check out their price for the internet linking software EZ NOW!. You'll see it's $20M or more. Then visit http://www.computer-supplies.com Do a search under our "SEARCH" engine for "Data Pro" and check out our price. Remember I only have 1 copy This can never be repeated again! Better check it out NOW!!! From owner-srs@net.bio.net Wed Oct 22 23:00:00 1997 From: "Stephen" Newsgroups: 3b,3b.tech,5col.forsale,alt.angst.xibo.sex,alt.binaries.w-software,alt.community.local-money,alt.comp.software.tools,at.tuwien.software,bionet.software.acedb,bionet.software.gcg,bionet.software.pc,bionet.software.srs,bionet.software.staden,bi Subject: 20M of internet acctg software for $5M! Date: Wed, 22 Oct 1997 20:04:28 -0400 Lines: 27 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 207.243.133.154 Message-ID: <344e94d0.0@news.bravo.net> Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!207.48.46.15!news.bravo.net!207.243.133.154 Xref: biosci bionet.software.acedb:1485 bionet.software.gcg:2855 bionet.software.srs:826 bionet.software.staden:559 Here's HOW. I have WON a legal copy of Data Pro EZ NOW! accounting software with all you need to link this software directly to the internet. It will update your inventory immediately directly to the internet. Show pictures of every product and change it in seconds if you need to. You can set up for your customers to purchase DIRECTLY ON LINE! Link it with other modules and have your customers check the status of an order, make payments directly towards their account. See their account balances....and MUCH MUCH MORE! Because I have WON it directly from Data Pro I am entitled to sell this software NO STRINGS ATTACHED for what ever I want. If we had not already had an on line system we would be using it right now. So now instead of buying it from them for $20M I'm willing to sell my copy for $5M Data Pro sells it right now for $20,000.00 go and see! I can sell 1 copy ONLY for just $5,000.00 First check out http://www.dpro.com and take a tour of a sample store. Then check out their price for the internet linking software EZ NOW!. You'll see it's $20M or more. Then visit http://www.computer-supplies.com Do a search under our "SEARCH" engine for "Data Pro" and check out our price. Remember I only have 1 copy This can never be repeated again! Better check it out NOW!!! From owner-srs@net.bio.net Wed Oct 22 23:00:00 1997 Path: biosci!daresbury!server5.netnews.ja.net!server6.netnews.ja.net!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: SRS 5 getz Date: Thu, 23 Oct 1997 11:47:14 +0100 Organization: EMBL-EBI Lines: 29 Message-ID: <344F2B32.456DC61@ebi.ac.uk> References: <62d1to$n3n@caroll.infobiogen.fr> <344B8709.D2746C83@ebi.ac.uk> <62l2qr$650@lion.embl-heidelberg.de> 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: Ramu Chenna X-Priority: 3 (Normal) Ramu Chenna wrote: > 1. Can we have alias names to databases (single database or group > of databases). > This would solve some problem when we suddenly change database name > (emnew --> emblnew for example) and the external links from other > sources to this database works. have been thinking about this for some time. The problem is that a more general approach is needed since often not only the databank name may vary but also the identifier for the entry which can be either an accession number or entry name - thinking of the information you find in blast files. Would like to have a system where all of the following are understood: sw|P00123 sw:P00123 swissprot:P00123 SWISS|ACHA_HUMAN to make it even more complicated, we have here at ebi 'virtual databanks' like 'swall' which i think contains: swissprot, sptrembl, swissnew and sptremblnew ... so definetely for after 5.1 ...any further comments on that? regards thure From owner-srs@net.bio.net Wed Oct 22 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!eecs-usenet-02.mit.edu!nntprelay.mathworks.com!newsfeed.ecrc.net!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: 3b,3b.tech,5col.forsale,alt.angst.xibo.sex,alt.binaries.w-software,alt.community.local-money,alt.comp.software.tools,at.tuwien.software,bionet.software.acedb,bionet.software.gcg,bionet.software.pc,bionet.software.srs,bionet.software.staden,bi Subject: Re: 20M of internet linked accounting software for $5M! Date: 23 Oct 1997 10:00:35 GMT Organization: EMBL, Heidelberg, Germany Lines: 12 Distribution: world Message-ID: <62n783$ndb@lion.embl-heidelberg.de> References: <344e9394.0@news.bravo.net> 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:344e9394.0@news.bravo.net Xref: biosci bionet.software.acedb:1488 bionet.software.gcg:2858 bionet.software.srs:827 bionet.software.staden:560 "Stephen" wrote: count balances....and MUCH MUCH MORE! > > >Data Pro sells it right now for >$20,000.00 go and see! I can sell 1 copy ONLY for do not you live with neighbours ? if you can sell only 1 copy you can sell it to them, why to put it on internet ? Foolish! ramu From owner-srs@net.bio.net Wed Oct 22 23:00:00 1997 Path: biosci!base4.com!joew From: joew@base4.com (Joe Wang) Newsgroups: bionet.software.srs Subject: Link problem for getz (srs5.05) Date: 23 Oct 1997 13:34:02 -0700 Organization: Base4 Bioinformatics Lines: 19 Sender: daemon@net.bio.net Distribution: world Message-ID: <344FB3C0.FE22DD3F@base4.com> Reply-To: joew@base4.com NNTP-Posting-Host: net.bio.net According to the SRS menu, if I want to get all human CDSs from GenBank, I should do: getz '[genbank-org:homo] \> [genbank-ftk:cds]' -f seq Instead of the CDSs, I get the entire sequence tries. When I do: getz '[genbank-ftk:cds] \< [genbank-org:homo] ' -f seq I get all the CDSs from GenBank (not only the human ones). If I don't use the escape "\", I get nothing. It looks like that the linking function ">" or "<" is not working. Any suggestions? Joe From owner-srs@net.bio.net Wed Oct 22 23:00:00 1997 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: genbank 103 with SRS5 Date: Thu, 23 Oct 1997 15:16:08 +0100 Organization: SEQNET Lines: 34 Distribution: bionet Message-ID: <344F5C28.41C6@dl.ac.uk> References: <344F5222.7A38@infobiogen.fr> 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: Jean-Marc Plaza Jean-Marc Plaza wrote: > > Hello, > we have some troubles with genbank 103 about indexing > FeatureQualifier (ftq) with SRS5.05 > The two first indexing steps are ok: > srsbuild GENBANK -f ' ftq' -xdir 'SRSINX:' -odir 'SRSINX:' -s 'unix' > srsbuild GENBANK -c -f ' ftq' -xdir 'SRSINX:' -odir 'SRSINX:' -s 'unix' > > but the step of murging index partitions to a single index make > a core dumped > srsbuild GENBANK -m -f ' ftq' -xdir 'SRSINX:' -odir 'SRSINX:' -s 'unix' > > need help > > Regards, > > Jean-marc No solution - just confirmation that we had the same problem at SEQNET. (genbank in gcg format) Martin -- ------------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/Person.asp?m.p.hilbers | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.seqnet.dl.ac.uk/ | ------------------------------------------------------------------- From owner-srs@net.bio.net Wed Oct 22 23:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!oleane!jussieu.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: genbank 103 with SRS5 Date: Thu, 23 Oct 1997 15:33:22 +0200 Organization: INFOBIOGEN Lines: 26 Message-ID: <344F5222.7A38@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, we have some troubles with genbank 103 about indexing FeatureQualifier (ftq) with SRS5.05 The two first indexing steps are ok: srsbuild GENBANK -f ' ftq' -xdir 'SRSINX:' -odir 'SRSINX:' -s 'unix' srsbuild GENBANK -c -f ' ftq' -xdir 'SRSINX:' -odir 'SRSINX:' -s 'unix' but the step of murging index partitions to a single index make a core dumped srsbuild GENBANK -m -f ' ftq' -xdir 'SRSINX:' -odir 'SRSINX:' -s 'unix' need help Regards, 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 Oct 23 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: Link problem for getz (srs5.05) Date: 24 Oct 1997 10:02:05 +0100 Organization: The Sanger Centre Lines: 73 Sender: pmr@unst Message-ID: References: <344FB3C0.FE22DD3F@base4.com> NNTP-Posting-Host: unst.sanger.ac.uk X-Newsreader: Gnus v5.3/Emacs 19.34 joew@base4.com (Joe Wang) writes: > > According to the SRS menu, if I want to get all human > CDSs from GenBank, I should do: > getz '[genbank-org:homo] \> [genbank-ftk:cds]' -f seq > > Instead of the CDSs, I get the entire sequence tries. > > When I do: > getz '[genbank-ftk:cds] \< [genbank-org:homo] ' -f seq > > I get all the CDSs from GenBank (not only the human ones). > > If I don't use the escape "\", I get nothing. > > It looks like that the linking function ">" or "<" is not working. > > Any suggestions? The "\>" is wrong - you should just use ">" or "<". I suspect your GenBank release does no have "Homo" explicitly in the taxonomy. Maybe the human entries are indexed only as "homo sapiens". If so, the [genbank-org:homo] part of the query will not work. You can quickly check this with: (srs5) getz -lv '[genbank-org:homo*]' (srs4) getz -rep '[genbank-org:homo*]' Yikes - just tried that here with EMBL 51, and found a really weird one: % getz -lv '[embl-org:homo*]' //////////////////////////////////////////////////////////////////////////// Values in "EMBL" homo 829492 homo sapiens 829491 //////////////////////////////////////////////////////////////////////////// report of query "[embl-org:homo*]" .. and the reason is, two sets of OS and OC lines: % getz "[embl-org:homo\!homo sapiens]" -e|more ID H17BHYD standard; DNA; HUM; 21764 BP. XX AC M84472; XX NI g806392 XX DT 25-DEC-1992 (Rel. 34, Created) DT 13-OCT-1996 (Rel. 49, Last updated, Version 11) XX DE Human 17-beta-hydroxysteroid dehydrogenase (EDH17B1 and EDH17B2) DE genes, complete coding regions and flanks. XX KW 17-beta-dehydrogenase; 17-beta-hydroxysteroid dehydrogenase; KW Alu repeat; estradiol. XX OS Homo OC Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata; OC Vertebrata; Eutheria; Primates; Catarrhini; Hominidae. XX OS Homo sapiens (human) OC Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata; OC Vertebrata; Eutheria; Primates; Catarrhini; Hominidae; Homo. XX From owner-srs@net.bio.net Thu Oct 23 23:00:00 1997 Path: biosci!agate!howland.erols.net!ais.net!logbridge.uoregon.edu!su-news-hub1.bbnplanet.com!su-news-feed1.bbnplanet.com!news.bbnplanet.com!newsgate.tandem.com!uunet!in3.uu.net!netnews.sbphrd.com!not-for-mail From: Ray Wang Newsgroups: bionet.software.srs Subject: View Manager Date: Fri, 24 Oct 1997 16:30:44 -0400 Organization: SmithKline Beecham Pharmaceuticals Research & Development Lines: 10 Message-ID: <34510574.F6C@mh.us.sbphrd.com> NNTP-Posting-Host: phu824.sbphrd.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5.1 sun4u) Hello, Find a problem when getting into View Manager page: no table displayed under the three selection buttons. Doubt about the part in SRSWWW.i file, but haven't figured out where the really error comes from. Would anyone give an advice? Thanks a lot. Ray From owner-srs@net.bio.net Thu Oct 23 23:00:00 1997 Path: biosci!agate!howland.erols.net!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Rodrigo Lopez Newsgroups: bionet.software.srs Subject: Re: Link problem for getz (srs5.05) Date: Fri, 24 Oct 1997 18:17:59 +0100 Organization: EMBL-EBI Lines: 35 Message-ID: <3450D847.7D6F5AF6@ebi.ac.uk> References: <344FB3C0.FE22DD3F@base4.com> Reply-To: rls@ebi.ac.uk NNTP-Posting-Host: snowy.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (Win95; I) Peter Rice wrote: .. and the reason is, two sets of OS and OC lines: % getz "[embl-org:homo\!homo sapiens]" -e|more ID H17BHYD standard; DNA; HUM; 21764 BP. XX AC M84472; XX NI g806392 XX DT 25-DEC-1992 (Rel. 34, Created) DT 13-OCT-1996 (Rel. 49, Last updated, Version 11) XX DE Human 17-beta-hydroxysteroid dehydrogenase (EDH17B1 and EDH17B2) DE genes, complete coding regions and flanks. XX KW 17-beta-dehydrogenase; 17-beta-hydroxysteroid dehydrogenase; KW Alu repeat; estradiol. XX OS Homo OC Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata; OC Vertebrata; Eutheria; Primates; Catarrhini; Hominidae. XX OS Homo sapiens (human) OC Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata; OC Vertebrata; Eutheria; Primates; Catarrhini; Hominidae; Homo. XX But this is clearly only happening on your SRS server. The EBI's server reports the above entry as the only one with that mistake for which EBI appologice (its a Genbank entry anyway!). R:) From owner-srs@net.bio.net Thu Oct 23 23:00:00 1997 Newsgroups: bionet.software.srs Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!news-peer.gsl.net!news.gsl.net!gip.net!news.idt.net!nntp2.cerf.net!nntp3.cerf.net!news.msi.com!uucp From: Maurice Manning Subject: nr database X-Nntp-Posting-Host: iris45 Content-Type: text/plain; charset=us-ascii Message-ID: <3450C680.71867EB8@msi.com> Sender: uucp@msi.com Content-Transfer-Encoding: 7bit Organization: Molecular Simulations Inc. Mime-Version: 1.0 Date: Fri, 24 Oct 1997 16:02:08 GMT X-Mailer: Mozilla 4.02 [en] (X11; I; IRIX 6.3 IP32) X-Disclaimer: _ Unless stated otherwise, everything in this message is personal opinion and nothing in it is an official statement of Molecular Simulations Inc. Lines: 19 Am trying to hook the nr ( and nt) blast databases into my SRS system. cannot find the correct config file (*.i) although this is one of the options on the WWW SRS server. any info appreciated Maurice -- Maurice Manning Molecular Simulations, Inc. mmanning@msi.com 9685 Scranton Road (619) 546 - 5316 San Diego, Ca 92121-3752 Web: http://www.msi.com -disclaimer- unless stated otherwise, everything in the above message is personal opinion and nothing in it is an official statement of molecular simulations inc. From owner-srs@net.bio.net Fri Oct 24 23:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!news.misty.com!news-xfer.netaxs.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!sunqbc.risq.qc.ca!news.uow.edu.au!news.cs.su.oz.au!metro!metro!unsw.edu.au!not-for-mail From: "NewbizCracker" Newsgroups: alt.binaries.warez.win95-apps,alt.binaries.warez.win95-fonts,alt.binaries.warez.win95-internet,alt.binaries.warez.win95-3d,alt.2600.crackz,aus.tv.x-files,alt.hackintosh,alt.2600.hackerz,alt.hacker,comp.lang.java.softwaretools,uk.media.tv.sf.x-files,alt.hackers.malicious,alt.hackers.groups,alt.2600.cardz,bionet.software.srs,bionet.software.x-plor,news.software.misc,alt.binaries.cracks,alt.videogames.hacking,alt.dss.hack,alt.killfile,alt.binaries.x-files.ga Subject: Serial no for all Latest Applications, thousand of serial no!!!!!!!!!!!! Date: Fri, 24 Oct 97 07:51:54 GMT Organization: University of New South Wales Lines: 32 Message-ID: <62pk28$bgd$4@mirv.unsw.edu.au> Reply-To: kevinlee@geocities.com NNTP-Posting-Host: la09.arch.unsw.edu.au Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="----------------Rover042856" X-Newsreader: NewsRover (www.NewsRover.com) Xref: biosci bionet.software.srs:837 bionet.software.x-plor:1546 ***************************************************************** WAREZ WAREZ WAREZ WAREZ WAREZ WAREZ WAREZ WAREZ WAREZ WAREZ WAREZ XXX PASSWORD XXX PASSWORD XXX PASSWORD XXX PASSWORD XXX PASSWORD FREEZ FREEZ FREEZ FREEZ FREEZ FREEZ FREEZ FREEZ FREEZ FREEZ FREEZ FILEZ FILEZ FILEZ FILEZ FILEZ FILEZ FILEZ FILEZ FILEZ FILEZ FILEZ GAMEZ GAMEZ GAMEZ GAMEZ GAMEZ GAMEZ GAMEZ GAMEZ GAMEZ GAMEZ GAMEZ ***************************************************************** Most complete latest listing of Warez sites on NET, Tons of APPz, Crackz, Gamez, XXX, Mp3z, Filez Ftpz, Direct download, Free Stuff. located at: 1 http://www.geocities.com/SiliconValley/Horizon/3759/ 2 http://members.tripod.com/~KevinLee/ 3 http://www.freetown.com/Suburbs/GardenAcres/1035/ 4 http://homepage.usr.com/k/kevinlee/ enjoy!!! Kevin ***************************************************************** APPZ APPZ APPZ APPZ APPZ APPZ APPZ APPZ APPZ APPZ APPZ APPZ APPZ FTPZ FTPZ FTPZ FTPZ FTPZ FTPZ FTPZ FTPZ FTPZ FTPZ FTPZ FTPZ FTPZ CRACKZ CRACKZ CRACKZ CRACKZ CRACKZ CRACKZ CRACKZ CRACKZ CRACKZ CRACKZ MP3Z MP3Z MP3Z MP3Z MP3Z MP3Z MP3Z MP3Z MP3Z MP3Z MP3Z MP3Z MP3Z FREEZ ***************************************************************** From owner-srs@net.bio.net Sun Oct 26 22:00:00 1997 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: genbank 103 with SRS5 Date: Mon, 27 Oct 1997 10:16:47 +0000 Organization: SEQNET Lines: 49 Distribution: bionet Message-ID: <34546A0F.41C6@dl.ac.uk> References: <344F5222.7A38@infobiogen.fr> 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: Jean-Marc Plaza CC: etzold@ebi.ac.uk Jean-Marc Plaza wrote: > > Hello, > we have some troubles with genbank 103 about indexing > FeatureQualifier (ftq) with SRS5.05 > The two first indexing steps are ok: > srsbuild GENBANK -f ' ftq' -xdir 'SRSINX:' -odir 'SRSINX:' -s 'unix' > srsbuild GENBANK -c -f ' ftq' -xdir 'SRSINX:' -odir 'SRSINX:' -s 'unix' > > but the step of murging index partitions to a single index make > a core dumped > srsbuild GENBANK -m -f ' ftq' -xdir 'SRSINX:' -odir 'SRSINX:' -s 'unix' > > need help > > Regards, > > 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 > --------------------------------------------------- Might this be caused by a constant determining the maximum number of entries associated with a key? The ftq key "dbx_ref" appears to be related to 2254812 entries. A grep for 2000000 in the source code did show a few constants set to that value, but none seemed to be related to this (quickly judged from there names/files) - but maybe the SRS-team can tell us more. Cheers, Martin -- ------------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/Person.asp?m.p.hilbers | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.seqnet.dl.ac.uk/ | ------------------------------------------------------------------- From owner-srs@net.bio.net Tue Oct 28 22:00:00 1997 Path: biosci!britbio.co.uk!dudgeon From: dudgeon@britbio.co.uk (Tim Dudgeon) Newsgroups: bionet.software.srs Subject: Applications as sequences Date: 29 Oct 1997 01:46:43 -0800 Organization: British Biotech Pharmaceuticals Plc Lines: 54 Sender: daemon@net.bio.net Distribution: world Message-ID: <345704CD.505E4D84@britbio.co.uk> NNTP-Posting-Host: net.bio.net This is a multi-part message in MIME format. --------------CFA352F88D59FA4ED3C5AED9 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi SRS developers, could you clarify something in SRS5.05 for me. I have some applications that generate sequences (e.g contig assembbly). However, as applications they have to be in $library.group @APPLICATION_LIBS, not @SEQUENCE_LIBS. Is there any way to be able to treat the database generated from the application as a sequence dastabase, and hence be able to run further applications on them. I note there is a $library.datatype parameter that can be set to noseq, dna or protein, but setting this appears to have no effect (and this parameter is not used in any .i files). The only solution to me appears to be to call getz once the application database has been created, to generate all the sequences in the application database as a seperate file that can then be indexed as a sequence database, and then link from the application database to the sequence database to get a the sequences. Not a very elegant solution! Suggestions welcome. Tim -- Dr. Tim Dudgeon Phone: 01865 748747 British Biotech Pharmaceuticals Plc. FAX: 01865 717598 Watlington Road, Oxford, OX4 5LY, UK email: dudgeon@britbio.co.uk --------------CFA352F88D59FA4ED3C5AED9 Content-Type: text/x-vcard; charset=us-ascii; name="vcard.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Tim Dudgeon Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Tim Dudgeon n: Dudgeon;Tim org: British Biotech Pharmaceuticals plc adr: Watlington Road;;;Oxford;Oxon;OX4 5LY;UK email;internet: dudgeon@britbio.co.uk title: Dr. tel;work: (44) 1865 748747 tel;fax: (44) 1865 717598 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------CFA352F88D59FA4ED3C5AED9-- From owner-srs@net.bio.net Tue Oct 28 22:00:00 1997 Path: biosci!britbio.co.uk!dudgeon From: dudgeon@britbio.co.uk (Tim Dudgeon) Newsgroups: bionet.software.srs Subject: Re: Applications as sequences Date: 29 Oct 1997 09:22:36 -0800 Organization: British Biotech Pharmaceuticals Plc Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <34576FAC.EC5FF06D@britbio.co.uk> NNTP-Posting-Host: net.bio.net Ok, so I tracked that problem down eventually. Answer is quite simple. Make sure $libformat.contains is set to @PROTSEQ_DATA or @DNASEQ_DATA as appropriate. That allows the entries to be recognised as sequences and allows applications to be run on them. Well, it should do, but then I came across a further problem. The application has to be set up to be of $library.type set to user, with the files being located in the directory corresponding to the current session id. However SRS appears unable to launch applications from these types of database as it is unable to find the file containing the sequences (the file that was indexed). If you switch the directory containing the files ($libloc.dir) to be a hard coded directory rather than the current session directory then it works fine, but then multiple users would trash each others files. Has anyone encountered something like this? Suggestions are welcome. Tim -- Dr. Tim Dudgeon Phone: 01865 748747 British Biotech Pharmaceuticals Plc. FAX: 01865 717598 Watlington Road, Oxford, OX4 5LY, UK email: dudgeon@britbio.co.uk From owner-srs@net.bio.net Wed Oct 29 22:00:00 1997 Message-ID: <34585F96.237C@lion-ag.de> Date: Thu, 30 Oct 1997 11:21:10 +0100 From: Antoine de Daruvar X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 Newsgroups: bionet.software.srs CC: Antoine de Daruvar Subject: Re: genbank 103 with SRS5 References: <344F5222.7A38@infobiogen.fr> <34546A0F.41C6@dl.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: gate.lion-ag.de Lines: 33 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-fra.maz.net!news.farside.net!gate.lion-ag.de > > we have some troubles with genbank 103 about indexing > > FeatureQualifier (ftq) with SRS5.05 > > The two first indexing steps are ok: > > srsbuild GENBANK -f ' ftq' -xdir 'SRSINX:' -odir 'SRSINX:' -s 'unix' > > srsbuild GENBANK -c -f ' ftq' -xdir 'SRSINX:' -odir 'SRSINX:' -s 'unix' > > > > but the step of murging index partitions to a single index make > > a core dumped > > srsbuild GENBANK -m -f ' ftq' -xdir 'SRSINX:' -odir 'SRSINX:' -s 'unix' > > --------------------------------------------------- > > Might this be caused by a constant determining the maximum number > of entries associated with a key? The ftq key "dbx_ref" appears > to be related to 2254812 entries. A grep for 2000000 in the > source code did show a few constants set to that value, but > none seemed to be related to this (quickly judged from there > names/files) - but maybe the SRS-team can tell us more. > I am having also this problem with other databases and keys (with less then 2000000 ref). What makes it tricky is that the dump is not systematic.... I am using srs 5.05 on SGI origin 2000 Antoine -- Antoine de Daruvar LION bioscience AG Im Neuenheimer Feld 517 D-69120 Heidelberg eMail daruvar@lion-ag.de WWW http://www.lion-ag.de From owner-srs@net.bio.net Wed Oct 29 22:00:00 1997 Path: biosci!daresbury!uninett.no!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: FASTA style database in SRS (one solution!) Date: 30 Oct 1997 16:39:17 GMT Organization: EMBL, Heidelberg, Germany Lines: 46 Distribution: world Message-ID: <63ad7l$ak9@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: quoted-printable 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 the impatient' Many people asked about using the following fasta (???) format database with SRS. One of the solution is to convert it to swiss format and use it. (Many other applications can also use this db, eg., gcg programs) >/:swissnew|P80385|AAKG_RAT 5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-1 SUBUNIT (AMPK GAMMA CHAIN).//:trembl|X95578|RNAMPKGAM_1 product= : "AMP-activated protein kinase gamma"; R.norvegicus mRNA for gamma subunit of AMP-activated protein kinase //:gp|X95578|1185271 AM= P-activated protein kinase gamma [Rattus norvegicus] MESVAAESAPAPENEHSQETPESNSSVYTTFMKSHRCYDLIPTSSKLVVFDTSLQVKKAF FALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVY pickup the conversion program from http://www.embl-heidelberg.de/~chenna/funnyFasta2swiss.is and then you can copy the syntax and structure files for this from embl srs server to use with SRS. They are nrdb.i and nrdb.is (you know how to get them, don't you?) if you are converting a nuc database then change $SeqPrint:[format:swiss] to $SeqPrint:[format:embl] in the funnyFasta2swiss.is file. I wrote funnyFasta2swiss.is long time back and took time to locate it. enjoy and thank me ! Ramu _______________________________________________________________ Chenna Ramu; EMBL; Postfach 10.2209; 69012 Heidelberg; Germany. Email: chenna@embl-heidelberg.de Url: http://www.embl-heidelberg.de/~chenna/ Tel: (49) 6221 387530 (Off) ; Fax: (49) 6221 387517 ______ From owner-srs@net.bio.net Thu Oct 30 22:00:00 1997 Path: biosci!agate!howland.erols.net!ais.net!news.stealth.net!solace!mn6.swip.net!seunet!news2.swip.net!inet-1.pnu.com!not-for-mail From: Staffan Bergh Newsgroups: bionet.software.srs Subject: Re: FASTA style database in SRS (one solution!) Date: 31 Oct 1997 08:34:45 +0100 Organization: Pharmacia & Upjohn Lines: 129 Message-ID: References: <63ad7l$ak9@lion.embl-heidelberg.de> NNTP-Posting-Host: sgibest.sto.se.pnu.com X-Newsreader: Gnus v5.3/Emacs 19.34 Here's another solution. Enjoy. /staffan Staffan Bergh Pharmacia & Upjohn, P14:5, SE-112 87 Stockholm, Sweden email: Staffan.Bergh@eu.pnu.com + Don't let that horse eat that violin phone: (int+46) 08 695 9884 + cried Chagall's mother fax: (int+46) 08 695 4084 + but he kept right on painting mobile: (int+46) 070 898 8829 + -- Lawrence Ferlinghetti ### fastafile.is ### #!/bin/env icarus #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # $Id: fastafile.is,v 1.2 1997/10/13 13:08:55 staffan Exp $ # $Log: fastafile.is,v $ # Revision 1.2 1997/10/13 13:08:55 staffan # Check in of file from test directory # # Revision 1.2 1997/10/13 13:05:57 staffan # Fixed a lot of things. Now works! # # Revision 1.1 1997/10/06 16:03:11 staffan # Initial revision # # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ $rules={ entry: ~ {$In:[file:text] $Out pre{$Skip:0}} ('>' {$Not} ln)* ('>' {$entryFip=$Fip} name {$Wrt $entryName=$1} appLn)? ~ # data fields fields: ~ {$In:entry $Out $Skip:1} (name {$Wrt:[id]} / *([^\n]*)/ {$Wrt:[des]}) ~ sequence: ~ {$In:[file:seq share:text] $Out pre {$s=$SeqNew:$entryName $seqFip=$Fip} $Wrt:[s:$entryName] $SeqMake:$s} (idline ln (/^([^>]+)/ {$SeqApp:[$s s:$Ct]})*) ~ # indexing id: ~ {$In:[fields c:id] $Out} /.+/ {$Wrt} ~ des: ~ {$In:[fields c:des] $Out} (/[0-9]+\.[0-9]+/ {$Uniq} | # catch floats before we see a fullstop stopwords | # skip stopwords /[\.\;] +/ | # a trailing punct. mark with spaces after is a separator /[^-A-Za-z0-9\_]+/ | # as is anything that doesn't match a alphanum etc (/[-A-Za-z0-9\:\_]+/ # everything else is a word { $split = $Trim:[$Ct skip:":"] # trim off a trailing ':' $Uniq:[s:$split] } ) )* ~ # other lead: ~ '>' ~ name: ~ /[-a-zA-Z0-9_\.]+/ ~ title: ~ / *[^\n]*/ ~ idline: ~ /^>/ name ~ appLn: ~ /[^\n]*\n/ {$App} ~ ln: ~ /[^\n]*\n/ ~ word: ~ /[-A-Za-z0-9_]+/ ~ sep: ~ /[^-A-Za-z0-9_]+/ ~ seqline: ~ /^[A-Za-z]+\n/ ~ lnbreak: ~ /\n$/ ~ stopwords: ~ ('in' | 'for' | 'to' | 'by' | 'of') ~ } if:$TestMode { $job = $JobNew:[prod:$rules skip:" " fileName:'/net/honken/disk2/databases/genomes/fasta/seq/h_influenzae.seq'] while:$JobHasInput:$job { $JobTokens:[$job name:entry print:1] $JobTokens:[$job name:sequence print:1] # $JobTokens:[$job name:fields print:1] # $JobTokens:[$job name:'fields|id' print:1] # $JobTokens:[$job name:'id' print:1] # $JobTokens:[$job name:'des' print:1] $JobNext:$job # $print:"----------------------------------------------\n" } } ### fastafile.i ### #!/bin/env icarus #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # $Id: fastafile.i,v 1.1 1997/10/13 15:58:52 staffan Exp $ # $Log: fastafile.i,v $ # Revision 1.1 1997/10/13 15:58:52 staffan # Initial revision # #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # You need to select one of these FORMATs in your .i file FASTASEQS_FORMAT:$libformat:[syntax:@FASTADB_SYNTAX contains:@DNASEQ_DATA tableFormat:left fileType:{@FASTADB_FILE @FASTADB_SEQ} fields:{ $field:[@DF_ID code:id index:id indexToken:id] $field:[@DF_Description code:des index:str indexToken:des tableToken:des] FASTASeq:$field:[@DF_DNASequence token:sequence format:fasta] } ] FASTAPEPS_FORMAT:$libformat:[syntax:@FASTADB_SYNTAX contains:@PROTSEQ_DATA tableFormat:left fileType:{@FASTADB_FILE @FASTADB_SEQ} fields:{ $field:[@DF_ID code:id index:id indexToken:id] $field:[@DF_Description code:des index:str indexToken:des tableToken:des] FASTAPep:$field:[@DF_ProtSequence token:sequence format:fasta] } ] FASTADB_SYNTAX:$syntax:[file:"SRSDB:fastafile.is" ignore:" \t"] FASTADB_FILE:$filetype:[text maxline:10000] FASTADB_SEQ:$filetype:[seq shareWith:@FASTADB_FILE fieldTokens:sequence fipVar:seqFip] From owner-srs@net.bio.net Thu Oct 30 22:00:00 1997 From: chenna@embl-heidelberg.de Subject: : FASTA style database in SRS (one solution!) Date: Fri, 31 Oct 1997 07:52:28 -0600 Message-ID: <878305191.10676@dejanews.com> Newsgroups: bionet.software.srs Organization: Deja News Posting Service Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!204.238.120.130!jump.net!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Fri Oct 31 13:39:51 1997 GMT X-Authenticated-Sender: chenna@embl-heidelberg.de X-Http-User-Agent: Mozilla/3.01 (X11; I; IRIX 5.3 IP22) X-Originating-IP-Addr: 192.54.41.195 (shag.EMBL-Heidelberg.DE) Lines: 69 Hello 'All the impatient' (Looks like posting from embl does not reach propery, again posting from dejanews!) Many people asked about using the following fasta (???) format database with SRS. One of the solution is to convert it to swiss format and use it. (Many other applications can also use this db, eg., gcg programs) funnyFasta entries looks like this! >/:swissnew|P80385|AAKG_RAT 5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-1 SUBUNIT (AMPK GAMMA CHAIN).//:trembl|X95578|RNAMPKGAM_1 product : "AMP-activated protein kinase gamma"; R.norvegicus mRNA for gamma subunit of AMP-activated protein kinase //:gp|X95578|1185271 AM P-activated protein kinase gamma [Rattus norvegicus] MESVAAESAPAPENEHSQETPESNSSVYTTFMKSHRCYDLIPTSSKLVVFDTSLQVKKAF FALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVY pickup the conversion program from http://www.embl-heidelberg.de/~chenna/funnyFasta2swiss.is and then you can copy the syntax and structure files for this from embl srs server to use with SRS. They are nrdb.i and nrdb.is (you know how to get them, don't you?) if you are converting a nuc database then change $SeqPrint:[format:swiss] to $SeqPrint:[format:embl] in the funnyFasta2swiss.is file. I wrote funnyFasta2swiss.is long time back and took time to locate it. enjoy ! 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 ______ -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet