From owner-srs@net.bio.net Tue Nov 03 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.idt.net!feed2.nntp.acc.ca!feed.nntp.acc.ca!peerfeed.ncal.verio.net!news1.best.com!news3.best.com!nntp1.ba.best.com!not-for-mail From: "Genome Jobs" Newsgroups: bionet.software.srs Subject: Jobs in bioinformatics at www.genomejobs.com Date: Wed, 4 Nov 1998 02:13:43 -0800 X-Newsreader: Microsoft Outlook Express 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Lines: 18 Message-ID: <36402898$0$29744@nntp1.ba.best.com> NNTP-Posting-Host: dynamic10.pm05.sf3d.best.com X-Trace: nntp1.ba.best.com 910174360 29744 209.24.235.10 Jobs in bioinformatics at www.genomejobs.com We have listings of jobs and companies in bioinformatics, genomics, software engineering, biotechnology, pharmaceutical, and scientific jobs where biology meets computers Free to job seekers Great opportunites at Great Companies www.genomejobs.com Jobs in bioinformatics, genomics, biotechnology, computers, databases, chips, microarrays, various engineers, proteomics, scientists, research associates, database administrators, database architects, database engineers, software engineers, analyst programmers, scientific programmer, software developer, molecular biologist, microbiologist, cheminformatics, pharmatics, biostatistics, SAS programmers, medicinal chemistry, drug discovery, mathematicians, algorithm specialists, web developers, and more. From owner-srs@net.bio.net Tue Nov 03 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!newsfeed.wirehub.nl!news.belnet.be!news.vub.ac.be!bigben!gbottu From: gbottu@bigben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: taxonomy database ? Date: 4 Nov 1998 15:02:10 GMT Organization: Brussels Free Universities VUB/ULB Lines: 6 Message-ID: <71pq9i$34m$1@mach.vub.ac.be> NNTP-Posting-Host: bigben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] Just a simple question : does someone know an anonymous ftp site with an up-to-date version of the "taxonomy" database, for which there are icarus files in the release of SRS5 ? Thanks in advance, Dr. Guy Bottu From owner-srs@net.bio.net Wed Nov 04 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!news-lond.gip.net!news.gsl.net!gip.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: Thu, 05 Nov 1998 09:42:40 +0000 Organization: EMBL - EBI Lines: 31 Message-ID: <36417310.D2ABC137@ebi.ac.uk> References: <71pq9i$34m$1@mach.vub.ac.be> NNTP-Posting-Host: cetus.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 910258961 6212 193.62.196.199 (5 Nov 1998 09:42:41 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 5 Nov 1998 09:42:41 GMT X-Mailer: Mozilla 4.5b2 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en Guy, The taxonomy database in question is the NCBI taxonomy database which we here at EBI have based on sequence databank collaboration. The data are in table dumps read in relational system. I've been experimenting with EMBL programmers to get a reasonable flat file out of it. Things have been quite stable for some time now. I'll find out if we can put the file in our public FTP server. -Heikki Guy Bottu wrote: > > Just a simple question : does someone know an anonymous ftp site with an > up-to-date version of the "taxonomy" database, for which there are > icarus files in the release of SRS5 ? > > Thanks in advance, > Dr. Guy Bottu -- ______ _/ _/_____________________________________________________ _/ _/ http://www2.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From owner-srs@net.bio.net Wed Nov 04 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!gin.ebi.ac.uk!redaschi From: Nicole Redaschi Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: Thu, 5 Nov 1998 11:18:06 +0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 52 Message-ID: References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> Reply-To: Nicole Redaschi NNTP-Posting-Host: gin.ebi.ac.uk Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 910264688 20801 193.62.196.129 (5 Nov 1998 11:18:08 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 5 Nov 1998 11:18:08 GMT In-Reply-To: <36417310.D2ABC137@ebi.ac.uk> Guy & Heikki, we also had requests from other people to make the taxonomy flatfile we produce for in-house use publically available. You can find it on our ftp site ftp://ftp.ebi.ac.uk/pub/databases/taxonomy. -nicole On Thu, 5 Nov 1998, Heikki Lehvaslaiho wrote: > Guy, > > The taxonomy database in question is the NCBI taxonomy database which we > here at EBI have based on sequence databank collaboration. The data are > in table dumps read in relational system. I've been experimenting with > EMBL programmers to get a reasonable flat file out of it. Things have > been quite stable for some time now. > > I'll find out if we can put the file in our public FTP server. > > -Heikki > > > Guy Bottu wrote: > > > > Just a simple question : does someone know an anonymous ftp site with an > > up-to-date version of the "taxonomy" database, for which there are > > icarus files in the release of SRS5 ? > > > > Thanks in advance, > > Dr. Guy Bottu > > -- > ______ _/ _/_____________________________________________________ > _/ _/ http://www2.ebi.ac.uk/mutations/ > _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk > _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute > _/ _/ _/ Wellcome Trust Genome Campus, Hinxton > _/ _/ _/ Cambs. CB10 1SD, United Kingdom > _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 > ___ _/_/_/_/_/________________________________________________________ > > ------------------------------------------------------------------- Nicole Redaschi Email: redaschi@ebi.ac.uk EMBL Outstation - Hinxton Tel: +44 (0)1223 494640 European Bioinformatics Institute Fax: +44 (0)1223 494468 Wellcome Trust Genome Campus Hinxton, Cambs. CB10 1SD, UK URL: http://www.ebi.ac.uk ------------------------------------------------------------------- From owner-srs@net.bio.net Wed Nov 04 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: 05 Nov 1998 14:02:37 +0000 Organization: The Sanger Centre Lines: 42 Message-ID: References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 910274469 10412 193.60.84.160 (5 Nov 1998 14:01:09 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 5 Nov 1998 14:01:09 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 Nicole Redaschi writes: > we also had requests from other people to make the taxonomy flatfile we > produce for in-house use publically available. You can find it on our ftp > site ftp://ftp.ebi.ac.uk/pub/databases/taxonomy. OK, I have the data and I am using the icarus files from the EBI to replace the old ones in the SRS 5.1 distribution. The -e and -f output options do not seem to work very well - they give the bare values and not the line from the entry. Seems to be because of the funny way the fields are saved in taxonomy.is which throws away the line code: > fields: ~ {$In:entry $Out $Skip:1} > ('//' | > /([A-Z][^:]+): ([^\n]*)\n/ > {$s=$2 $Wrt:[$fn.$Trim:$1 s:$Trim:$s]} | > ln {$App} > )+ x{$Wrt:[children s:' ']} > ~ The links to TAX_UP and TAX_DOWN are fun in their way - but can I get *all* ancestors or descendants directly rather than one at a time? getz -e '[taxonomy-taxon:caenorhabditis elegans] > tax_up > tax_up \ > tax_up > tax_up > tax_up > tax_up > tax_up > tax_up > tax_up \ > tax_up > tax_up > tax_up > tax_up > tax_up > tax_up > tax_up \ > tax_up' 1 0 no rank 1 root -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Wed Nov 04 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!news-ge.switch.ch!serra.unipi.it!sun01.iigb.na.cnr.it!ue3000.iigb.na.cnr.it!rallo@iigbna.iigb.na.cnr.it From: Claudia Rallo Newsgroups: bionet.software.srs Subject: swissprot update Date: Thu, 05 Nov 1998 16:57:13 +0000 Organization: IIGB Lines: 27 Message-ID: <3641D8DB.4347E7D1@iigbna.iigb.na.cnr.it> Reply-To: claudia@iigbna.iigb.na.cnr.it NNTP-Posting-Host: claudia.iigb.na.cnr.it Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 (Macintosh; I; PPC) I have the SRS 5.1 distribution. I tryto update a Swissprot db with this procedure: # # srscheck ++++++> must rebuild index "FtKey" for SWISSPROT, is not up to date ++++++> must rebuild index "FtLength" for SWISSPROT, is not up to date ++++++> must rebuild index "FtDescription" for SWISSPROT, is not up to date # # srsbuild SWISSPROT -f "ftk ftl ftd" -xdir SRSINX: -odir SRSINX: -s unix -nn ...processing SWISSPROT ...processing /usr/users/dbdata/swissprot/swissprot.ref ...processing /usr/users/dbdata/swissprot/swissprot.seq Segmentation fault (core dumped) # I have try with srsupdate but I have the same results. Can you help me?? I have a alpha server with "OSF1 V4.0" and 256 MB RAM Claudia Rallo From owner-srs@net.bio.net Thu Nov 05 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!netnews.com!newsin.iconnet.net!world6.bellatlantic.net!world4.bellatlantic.net!news From: jaugust@bellatlantic.net (John Augustine) Newsgroups: bionet.software.srs Subject: RE:LONG FILENAME ALTERNATIVE Date: Fri, 06 Nov 1998 15:04:07 GMT Organization: Bell Atlantic Internet Solutions Lines: 12 Message-ID: <36430ba3.2125652@news4.bellatlantic.net> NNTP-Posting-Host: client-151-197-124-2.bellatlantic.net X-Newsreader: Forte Free Agent 1.1/16.230 Someone, not long ago, was asking for an alternative to the "Long Filename" system (Windows 95/98), to have comments about files which can easily be edited. This person accumulated many files (.ZIP) downloaded from various FTP sites, and could not remember, by looking at the filenames in the directory, what many of the files are for. There is a program called "Directory Comments" for MS-Dos available at HOTFILES.COM (ZD Net) which allows you to easily add or change comments about your files. The comments are NOT stored in the directory or attached to the file/s, but in a separate log file (in ascii text). From owner-srs@net.bio.net Sun Nov 08 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!howland.erols.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: "Thure Etzold" Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: Mon, 9 Nov 1998 08:56:41 -0800 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 51 Message-ID: <726bqo$9fb$1@niobium.hgmp.mrc.ac.uk> References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> NNTP-Posting-Host: idefix.ebi.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 910602904 9707 193.62.196.98 (9 Nov 1998 09:15:04 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 9 Nov 1998 09:15:04 GMT X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 > > >The links to TAX_UP and TAX_DOWN are fun in their way - but can I get >*all* ancestors or descendants directly rather than one at a time? > >getz -e '[taxonomy-taxon:caenorhabditis elegans] > tax_up > tax_up \ > > tax_up > tax_up > tax_up > tax_up > tax_up > tax_up > tax_up \ > > tax_up > tax_up > tax_up > tax_up > tax_up > tax_up > tax_up \ > > tax_up' yes you can - the solution is getz -e '[taxonomy-taxon:caenorhabditis elegans] >^ tax_up' the >^ is a new operator and performs the link to tax_up recursively until there are no more links available. This also works the other way round getz -e '[taxonomy-taxon:nematoda]>^tax_dn' gives you the entire subtree, including 'nematoda' (the ^ after the link should be reminiscent of a (sub) tree) it is also possible to get only the leaves in a subtree defined by a query getz -e '[taxonomy-taxon:nematoda]>_ tax_dn Btw, these two link operators are even documented in the chapter about the SRS query language regards thure >1 >0 >no rank >1 >root > >-- >---------------------------------------------------------------------- >Peter Rice | Informatics Division, The Sanger Centre, >E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, >Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England >Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Sun Nov 08 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!dispose.news.demon.net!demon!newsfeed.nacamar.de!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: "Thure Etzold" Newsgroups: bionet.software.srs Subject: Re: swissprot update Date: Mon, 9 Nov 1998 09:00:30 -0800 Organization: MRC Human Genome Mapping Project Resource Centre Message-ID: <726c1t$b0b$1@niobium.hgmp.mrc.ac.uk> References: <3641D8DB.4347E7D1@iigbna.iigb.na.cnr.it> NNTP-Posting-Host: idefix.ebi.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 910603133 11275 193.62.196.98 (9 Nov 1998 09:18:53 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 9 Nov 1998 09:18:53 GMT X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Lines: 27 Claudia Rallo wrote in message <3641D8DB.4347E7D1@iigbna.iigb.na.cnr.it>... >I have the SRS 5.1 distribution. >I tryto update a Swissprot db with this procedure: ># ># srscheck >++++++> must rebuild index "FtKey" for SWISSPROT, is not up to date >++++++> must rebuild index "FtLength" for SWISSPROT, is not up to date >++++++> must rebuild index "FtDescription" for SWISSPROT, is not up to >date ># This problem is caused by a bug in SRSSOU:srscheck.c. You can edit the file and replace all occurrances of "LibNextField" by "LibNextAllField" the rebuild srscheck with srsmake srscheck Also apply bug fix posted on 28.10. regards thure From owner-srs@net.bio.net Mon Nov 09 22:00:00 1998 Path: biosci!ihnp4.ucsd.edu!sdd.hp.com!usc!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.gtei.net!portc02.blue.aol.com!audrey01.news.aol.com!not-for-mail From: mattfry80@aol.com (MattFry80) Newsgroups: bionet.software.srs Subject: SHAREWARE/FREEWARE SITE! cHECK IT OUT! Lines: 22 NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Date: 10 Nov 1998 01:35:33 GMT Organization: AOL http://www.aol.com Message-ID: <19981109203533.00770.00001825@ng30.aol.com> IF YOU LIKE FREE STUFF CHECK OUT THIS KICK @SS RESOURCE! Freeware, Shareware, Freebies, Samples, Resources, and a little Comedy Too! http://members.aol.com/MattFry80/soft.html Click Here For Freeware/Shareware! http://members.aol.com/MattFry80/survey.html Click Here To Get Money For Filling Out Surveys! http://members.aol.com/MattFry80/thefreezone.html Click Here To Get Free Stuff and Samples From All Over The Internet! OR CHECK OUT THE MAIN PAGE! http://members.aol.com/MattFry80/myworld.html cLIcK hERE! GREAT RESOURCE FOR FREE STUFF ALL OVER THE NET! ENJOY! From owner-srs@net.bio.net Tue Nov 10 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!nntp.news.xara.net!xara.net!server6.netnews.ja.net!newsfeed.ed.ac.uk!not-for-mail From: Colin Semple Newsgroups: bionet.software.srs Subject: scripting for getz Date: Wed, 11 Nov 1998 12:28:42 +0000 Organization: MRC Human Genetics Unit Lines: 45 Message-ID: <364982FA.2AF0@hgu.mrc.ac.uk> NNTP-Posting-Host: milburn.hgu.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: scotsman.ed.ac.uk 910787267 17685 193.63.65.73 (11 Nov 1998 12:27:47 GMT) X-Complaints-To: usenet@scotsman.ed.ac.uk NNTP-Posting-Date: 11 Nov 1998 12:27:47 GMT X-Mailer: Mozilla 3.04Gold (X11; I; SunOS 5.6 sun4u) Dear all, I'm rather new to getz and for some reason can't get scripts incorporating getz queries to behave properly on the hgmp server. The script below looks like it should work but generates the error message: SRSICA:icarus.i:0: error: invalid character, character "'" is not allowed within parameter "fieldList" Any help/advice you can give me would be much appreciated, here's the script: #!/bin/tcsh -f #script to make getz queries set noglob set name = N22117 set query = "'[libs={embl emblnew}-AllText: $name*]'" echo query = $query set bit = "-f 'AccNumber seq' -sf 'fasta'" echo getz $query $bit getz $query $bit > jim #this works from command line: #getz '[libs={embl emblnew}-AllText: N22117*]' -f 'AccNumber seq' -sf 'fasta' > jim -- Colin Semple MRC Human Genetics Unit Western General Hospital Edinburgh EH4 2XU Tel: + 44 - (0) 131-332-2471 x4001 Fax: + 44 - (0) 131-343-2620 Email: C.Semple@hgu.mrc.ac.uk Web: http://www.hgu.mrc.ac.uk/Users/colins From owner-srs@net.bio.net Wed Nov 11 22:00:00 1998 Path: biosci!IEC-NICHIBEI.OR.JP!ticaegi14 From: ticaegi14@IEC-NICHIBEI.OR.JP (Photo Transfer Specialties) Newsgroups: bionet.software.srs Subject: Photo Mousepads...........Great Gift Idea! Date: 11 Nov 1998 23:48:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 160 Sender: daemon@net.bio.net Distribution: world Message-ID: <199811111464IAA48149@ChristmasGift.on.ca> NNTP-Posting-Host: net.bio.net GREAT CHRISTMAS GIFT IDEA! PHOTO TRANSFER SPECIALTIES! MOUSEPADS WITH YOUR FAVORITE PHOTOS! Now you can have your favorite photos printed onto mousepads! Photo mousepads are our most popular gift year after year! In the past we have provided our HIGH QUALITY mousepads to thousands of customers. Most are so pleased they reorder each year! Photo mousepads make a PERFECT GIFT for ANYONE! Replace boring, dirty, frayed mousepads! Instead of plain, generic, boring corporate logos you can have PERSONALIZED photo mousepads brighten your desktop! PHOTO Mousepads are DAILY REMINDERS of your favorite: CHILDREN, PETS, EVENTS....... WEDDING PHOTOS, FAMILY, GRADUATION..... LOVED ONES,HOLIDAY PHOTOS,GRANDCHILDREN..... Anything you choose! Use your imagination! These HIGH QUALITY,LONG LASTING mousepads are non-skid 1/4" rubber bottoms with comfortable, washable cloth tops. PHOTO TRANSFER SPECIALTIES uses the latest technology available to transfer your favorite 3x5,4x6,5x7,and 8x10 photos onto mousepads. Your photos will be safely RETURNED with your order! This year we are offering a great new LOW PRICE and we are accepting CONVENIENT credit card payment as well as checks and money orders! ORDERS filled FAST and at a great new LOW PRICE! EASY ORDER FORM Please complete and PRINT this form. Mail your photograph(s), payment, and completed order form to the address below along with: ______Check or _____ Money Order Payable to: PHOTO TRANSFER SPECIALTIES Or pay by VISA or MASTERCARD by filling out this CONVENIENT order form! ____ VISA ____ MASTERCARD Card number: __________________________________ (16 Digits) Expiration Date: ______________________________ Name on card: _________________________________ Billing Address:________________________________ ________________________________ Indicate amount: _______________________________ Signature :___________________________________ Date: __________________________________________ Email address(optional):________________________ CREDIT CARDS : All information must be accurate and complete for proper verification. Incomplete orders cannot be processed and will be returned. Charges on your statement will appear as Pacific Coast Mail Order. $ 10.99 EACH Photo Mousepads $ 9.99 EACH Additional Pads $ 2.50 EACH Shipping and Handling $ 1.05 EACH California residents (sales tax) * International $5.00 each shipping. Address Mousepads to be shipped to: Name: ____________________________________ Address: ____________________________________ Phone # ____________________________________ City,State,Zip_________________________________ Mail Payment, Photographs, and completed order form to: PHOTO TRANSFER SPECIALTIES P.O. BOX #782 ROSS, CA 94957 * Please allow 2 weeks for delivery. * All orders postmarked by December 10th are guaranteed Christmas delivery! * Please feel free to copy and distribute this order form as you like. Combine your order with friends and coworkers and save $1.00 on each additional mousepad. This is a one time only mailing! You have already been placed on our remove list and will not receive another offer from us! Thank You! From owner-srs@net.bio.net Wed Nov 11 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.cwix.com!158.43.192.17!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: and geneticcode database ? Date: 12 Nov 1998 16:51:32 +0000 Organization: The Sanger Centre Lines: 54 Message-ID: References: <72etd9$7c9$1@mach.vub.ac.be> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 910889569 6739 193.60.84.160 (12 Nov 1998 16:52:49 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 12 Nov 1998 16:52:49 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 gbottu@bigben.vub.ac.be (Guy Bottu) writes: > I have just retrieved the taxonomy database from the EBI anonymous ftp server > (thanks, Nicole Redaschi !), but I have a new problem : taxonomy contains > links to geneticcode. Where can we find a suitable version of geneticcode ? > The file http://www.ncbi.nlm.nih.gov:6224/DIRSUB/gc.prt seems not to be > available anymore and is maybe not in the right format. The file is at: ftp://ncbi.nlm.nih.gov/entrez/misc/data/gc.prt geneticcode.is needs minor editing because the file uses tabs: Change all 3 cases of ' {' to '\t{' P.S. Thanks to NCBI for the acknowledgement :-) Now, when I build the links from taxonomy to geneticcode, how come I get only 6/12 genetic codes linked? The missing ones are listed below. They include "Eubacterial" - i.e. all the bacteria (which have alternate start codons GTG, CTG and TTG). getz 'geneticcode ! (geneticcode < taxonomy)' -f name -f id "Ciliate Macronuclear and Daycladacean" "SGC5" 6 "Protozoan Mitochondrial (and Kinetoplast)" "SGC6" 7 "[OBSOLETE, posttranscriptional editing only] Plant Mitochondrial/Chloroplast" "SGC7" 8 "Euplotid Macronuclear" "SGC9" 10 "Eubacterial" 11 "Group II yeasts (Nuc Acids Res 1993, 21:4039)" 12 -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Wed Nov 11 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!btnet-peer!btnet!news-lond.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!news.belnet.be!news.vub.ac.be!bigben!gbottu From: gbottu@bigben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: and geneticcode database ? Date: 12 Nov 1998 15:04:09 GMT Organization: Brussels Free Universities VUB/ULB Lines: 7 Message-ID: <72etd9$7c9$1@mach.vub.ac.be> NNTP-Posting-Host: bigben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] I have just retrieved the taxonomy database from the EBI anonymous ftp server (thanks, Nicole Redaschi !), but I have a new problem : taxonomy contains links to geneticcode. Where can we find a suitable version of geneticcode ? The file http://www.ncbi.nlm.nih.gov:6224/DIRSUB/gc.prt seems not to be available anymore and is maybe not in the right format. Guy Bottu From owner-srs@net.bio.net Thu Nov 12 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed1.swip.net!swipnet!news.tele2.nl!newsfeed.wirehub.nl!news.belnet.be!news.vub.ac.be!bigben!gbottu From: gbottu@bigben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Re: and geneticcode database ? Date: 13 Nov 1998 14:23:06 GMT Organization: Brussels Free Universities VUB/ULB Lines: 22 Message-ID: <72hfca$knn$1@mach.vub.ac.be> References: <72etd9$7c9$1@mach.vub.ac.be> NNTP-Posting-Host: bigben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] I have installed the file from ftp://ncbi.nlm.nih.gov/entrez/misc/data/gc.prt but there remain problems. 1. The Icarus files from the EBI contain some error : $link:[@TAXONOMY_DB to:@?GENETICCODE_DB token:'name|gc' toField:@DF_ID] $link:[@TAXONOMY_DB to:@?GENETICCODE_DB token:'name|mgc' toField:@DF_ID] makes that the linktable for the mitochondrial code overwrites the linktable for the code. One solution would be to give both linktables a different name. Another solution, which I chose, is to merge the two genetic code fields. You can retrieve the Icarus files from our SRS server at http://www.be.embnet.org/srs It turns out that only genetic codes 7 and 8 are not referenced in taxonomy. 2. Alas ! taxonomy does reference genetic codes 13, 14 and 15 and these are not found in the gc.prt file Anyone an idea about where to find them ? Guy Bottu From owner-srs@net.bio.net Thu Nov 12 22:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: and geneticcode database ? Date: 13 Nov 1998 16:11:01 +0000 Organization: The Sanger Centre Lines: 47 Message-ID: References: <72etd9$7c9$1@mach.vub.ac.be> <72hfca$knn$1@mach.vub.ac.be> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 910973363 26595 193.60.84.160 (13 Nov 1998 16:09:23 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 13 Nov 1998 16:09:23 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 gbottu@bigben.vub.ac.be (Guy Bottu) writes: > It turns out that only genetic codes 7 and 8 are not referenced in > taxonomy. I still only get 6 codes linked. I used the taxonomy file ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat > 2. Alas ! taxonomy does reference genetic codes 13, 14 and 15 and these > are not found in the gc.prt file > Anyone an idea about where to find them ? They were in the EGCG 8.1 local data files as trans12.txt ... trans14.txt. The filename numbers are 1 less than the NCBI numbers but match the NCBI SGC codes :-) 13 is Ascidian Mitochondrial Ascidian Mitochondrial Standard W Trp TGA * End TGA M Met ATA I Ile ATA G Gly AGA R Arg AGA G Gly AGG R Arg AGG 14 is Flatworm Mitochondrial Flatworm Mitochondrial Standard Y Tyr TAA * End TAA W Trp TGA * End TGA S Ser AGA R Arg AGA S Ser AGG R Arg AGG 15 is Blepharisma Macronuclear Blepharisma Macronuclear Standard Q Gln TAG * End TAG -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Sun Nov 15 22:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!chicago-news-feed1.bbnplanet.com!news.gtei.net!cyclone.i1.net!uunet!in1.uu.net!news1-gui.server.ntli.net!news-feed.ntli.net!news5-gui.server.ntli.net!news-feed.ntli.net!server4.netnews.ja.net!server2.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: Mon, 16 Nov 1998 17:46:44 +0000 Organization: EMBL - EBI Lines: 37 Message-ID: <36506504.AAFD8718@ebi.ac.uk> References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> NNTP-Posting-Host: cetus.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 911238404 9488 193.62.196.199 (16 Nov 1998 17:46:44 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 16 Nov 1998 17:46:44 GMT X-Mailer: Mozilla 4.5b2 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en Peter Rice wrote: > > The -e and -f output options do not seem to work very well - they give > the bare values and not the line from the entry. Seems to be because of > the funny way the fields are saved in taxonomy.is which throws away > the line code: Peter, Thure and I had a go on the taxonomy files. Take a look at http://srs.ebi.ac.uk/srs5bin/cgi-bin/wgetz?-fun+PageQueryForm+-l+TAXONOMY The line codes are now there for command line access and a new view has been created for viewing and navigating the hierarchy. It's not perfect, yet, but maybe after the next SRS version... All Thure's examples from the previous message on this thread work now. tax_dn needs to be writen tax_down: getz -e '[taxonomy-taxon:caenorhabditis elegans] >^ tax_up' getz -e '[taxonomy-taxon:nematoda]>^tax_down' getz -e '[taxonomy-taxon:nematoda]>_tax_down' The queries inside '' characters above can be written into the expression field of the query manager, too. -Heikki ______ _/ _/_____________________________________________________ _/ _/ http://www2.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From owner-srs@net.bio.net Wed Nov 18 22:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in4.uu.net!newsfeed.xcom.net!newsfeed.cwix.com!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.gtei.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: Tue, 17 Nov 1998 15:37:16 +0000 Organization: EMBL - EBI Lines: 28 Message-ID: <3651982C.83BECC25@ebi.ac.uk> References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> <36506504.AAFD8718@ebi.ac.uk> <3651756A.388398DD@ebi.ac.uk> <36517A7C.208D252@ebi.ac.uk> <36518EEE.EA261FDC@ebi.ac.uk> NNTP-Posting-Host: cetus.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 911317037 15537 193.62.196.199 (17 Nov 1998 15:37:17 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 17 Nov 1998 15:37:17 GMT To: Peter Rice X-Mailer: Mozilla 4.5b2 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en Peter Rice wrote: > > Heikki Lehvaslaiho writes: > > Peter Rice wrote: > > > The common name(s) do not seem to be indexed. Can they be added? > > > > They are indexed but since there are 10 different fields that contain > > other than the accepted scientific name, there are no specific search > > fields for all of them. You can search them using AllText field. > > So, for example, how do I search TAXONOMY for "human" ? > > % getz '[taxonomy-all:human]' -e Works for me. There must still be some minor discrepancy between Sanger and EBI files. -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ http://www2.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From owner-srs@net.bio.net Wed Nov 18 22:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in1.uu.net!cpk-news-hub1.bbnplanet.com!news.gtei.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: Tue, 17 Nov 1998 14:57:50 +0000 Organization: EMBL - EBI Lines: 49 Message-ID: <36518EEE.EA261FDC@ebi.ac.uk> References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> <36506504.AAFD8718@ebi.ac.uk> <3651756A.388398DD@ebi.ac.uk> <36517A7C.208D252@ebi.ac.uk> NNTP-Posting-Host: cetus.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 911314670 14886 193.62.196.199 (17 Nov 1998 14:57:50 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 17 Nov 1998 14:57:50 GMT To: Peter Rice X-Mailer: Mozilla 4.5b2 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en Peter Rice wrote: > > Heikki Lehvaslaiho writes: > > Peter Rice wrote: > > > > > But how do I download the EBI's views.i ? > > > > I suppose you can not. Sorry. A link will be added into SRS web > > interface in due time. > > > > Put this into your views.i and then srssection: > > OK, now I get the view (except I do not see taxonomy as the default view > for the database). taxonomy.i: TAXONOMY_DB: add "defaultView:@Tax_View" > When I look at the up link (red arrow) it looks fine up to "Eukaryota" > but then I see 12 other Taxons including "lobe-finned fish and > tetrapod clade" and "Fungi/Metazoa group" (on my server and the EBI > server). Strange because "Eukaryota" has a parent-id of 1 which should > be straight up to "root". I was afraid you'd eventually ask that. 8-). At the moment we have to show the entries in the order they apper in the (flat file) database and the (relational) database does not have an easy handle to sort them easily and fast other than by rank. The ones that are clustered on the top of the list below root all have rank: 'no rank'. We really have to wait for the next SRS & Icarus version to do better. > The common name(s) do not seem to be indexed. Can they be added? They are indexed but since there are 10 different fields that contain other than the accepted scientific name, there are no specific search fields for all of them. You can search them using AllText field. -Heikki ______ _/ _/_____________________________________________________ _/ _/ http://www2.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From owner-srs@net.bio.net Wed Nov 18 22:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in5.uu.net!news-feeds.jump.net!newshub.northeast.verio.net!woodstock.news.demon.net!demon!dispose.news.demon.net!demon!news-lond.gip.net!news.gsl.net!gip.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: 17 Nov 1998 13:51:11 +0000 Organization: The Sanger Centre Message-ID: References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> <36506504.AAFD8718@ebi.ac.uk> <3651756A.388398DD@ebi.ac.uk> <36517A7C.208D252@ebi.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 911310568 13780 193.60.84.160 (17 Nov 1998 13:49:28 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 17 Nov 1998 13:49:28 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 Lines: 28 Heikki Lehvaslaiho writes: > Peter Rice wrote: > > > But how do I download the EBI's views.i ? > > I suppose you can not. Sorry. A link will be added into SRS web > interface in due time. > > Put this into your views.i and then srssection: OK, now I get the view (except I do not see taxonomy as the default view for the database). When I look at the up link (red arrow) it looks fine up to "Eukaryota" but then I see 12 other Taxons including "lobe-finned fish and tetrapod clade" and "Fungi/Metazoa group" (on my server and the EBI server). Strange because "Eukaryota" has a parent-id of 1 which should be straight up to "root". The common name(s) do not seem to be indexed. Can they be added? -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Wed Nov 18 22:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in5.uu.net!newsfeed.cwix.com!158.43.192.17!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: Tue, 17 Nov 1998 13:30:36 +0000 Organization: EMBL - EBI Lines: 28 Message-ID: <36517A7C.208D252@ebi.ac.uk> References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> <36506504.AAFD8718@ebi.ac.uk> <3651756A.388398DD@ebi.ac.uk> NNTP-Posting-Host: cetus.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 911309436 13476 193.62.196.199 (17 Nov 1998 13:30:36 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 17 Nov 1998 13:30:36 GMT To: Peter Rice X-Mailer: Mozilla 4.5b2 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en Peter Rice wrote: > But how do I download the EBI's views.i ? I suppose you can not. Sorry. A link will be added into SRS web interface in due time. Put this into your views.i and then srssection: Tax_View:$View:[Taxonomy root:$Vlib:@TAXONOMY_DB rootFields:{ $VField:@DF_Navigate $VField:@DF_Taxon $VField:@DF_Rank } ] -Heikki ______ _/ _/_____________________________________________________ _/ _/ http://www2.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From owner-srs@net.bio.net Wed Nov 18 22:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in5.uu.net!newsfeed.cwix.com!158.43.192.17!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: 17 Nov 1998 13:24:01 +0000 Organization: The Sanger Centre Lines: 18 Message-ID: References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> <36506504.AAFD8718@ebi.ac.uk> <3651756A.388398DD@ebi.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 911308939 13151 193.60.84.160 (17 Nov 1998 13:22:19 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 17 Nov 1998 13:22:19 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 Heikki Lehvaslaiho writes: > You also need to check the changes in view.i (+Tax_View) and srsdb.is > (+taxupR, +taxdnR). You also need to copy the up and down icons into > www/images directory. I found the changes in srsdb.is (not srsdb.i) I found the images (red and blue arrows) in /srs5/images/up.gif and down.gif But how do I download the EBI's views.i ? -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Wed Nov 18 22:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in3.uu.net!falcon.america.net!newsfeed.atl!news.maxwell.syr.edu!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: Tue, 17 Nov 1998 13:08:58 +0000 Organization: EMBL - EBI Lines: 32 Message-ID: <3651756A.388398DD@ebi.ac.uk> References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> <36506504.AAFD8718@ebi.ac.uk> NNTP-Posting-Host: cetus.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 911308138 13146 193.62.196.199 (17 Nov 1998 13:08:58 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 17 Nov 1998 13:08:58 GMT To: Peter Rice X-Mailer: Mozilla 4.5b2 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en Peter Rice wrote: > > Heikki Lehvaslaiho writes: > > Thure and I had a go on the taxonomy files. Take a look at > > > > http://srs.ebi.ac.uk/srs5bin/cgi-bin/wgetz?-fun+PageQueryForm+-l+TAXONOMY > > Seems to also need changes to swissprot.i and embl.i to remove the > alternative links to taxonomy... Yes, the links are better placed in taxonomy.i file. > Any other connected changes needed? You also need to check the changes in view.i (+Tax_View) and srsdb.is (+taxupR, +taxdnR). You also need to copy the up and down icons into www/images directory. I updated the files this morning to make taxview the default view. -Heikki P.S. I'll see what I can do to geneticcode database. ______ _/ _/_____________________________________________________ _/ _/ http://www2.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From owner-srs@net.bio.net Wed Nov 18 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software.srs Subject: Re: and geneticcode database ? Date: Tue, 17 Nov 1998 14:42:55 +0000 Organization: EMBL - EBI Lines: 51 Message-ID: <36518B6F.B5D1FA68@ebi.ac.uk> References: <72etd9$7c9$1@mach.vub.ac.be> <72hfca$knn$1@mach.vub.ac.be> <72rop6$ord$1@mach.vub.ac.be> NNTP-Posting-Host: cetus.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 911313775 14570 193.62.196.199 (17 Nov 1998 14:42:55 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 17 Nov 1998 14:42:55 GMT To: Guy Bottu X-Mailer: Mozilla 4.5b2 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en Guy Bottu wrote: > > : I still only get 6 codes linked. I used the taxonomy file > : ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat > > That is because the taxonomy.i file at the EBI contains some error. To > convince yourself of this, search in taxonomy the taxon "homo sapiens" > and link to geneticcode, you will see that you find only "Vertebratrate > Mitochondrial" and not "Standard". The cause of the problem is that the > link from taxonomy to geneticcode is defined twice. > > Guy Bottu I've corrected a number of errors. The link is now performed only once and link keys are read from a new token table created by production called l_gencode. Since links are created from taxonomy to geneticcode, the taxonomy files change again. Sorry, Peter! The previous version of gc.prt file contained the IDs 13-15 so I copied them from there into a new file and put it into EBI FTP site: ftp://ftp.ebi.ac.uk/pub/databases/geneticcode/ I've informed NCBI about the problem. After this the only codes that are not referenced by taxonomy database are: Query "geneticcode! (taxonomy>geneticcode) " found 2 entries id 7 Protozoan Mitochondrial (and Kinetoplast) id 8 [OBSOLETE, posttranscriptional editing only] Plant Mitochondrial/Chloroplast It's all yours to play with now. Have fun, -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ http://www2.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From owner-srs@net.bio.net Wed Nov 18 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!news.belnet.be!news.vub.ac.be!bigben!gbottu From: gbottu@bigben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Re: and geneticcode database ? Date: 17 Nov 1998 12:04:54 GMT Organization: Brussels Free Universities VUB/ULB Lines: 11 Message-ID: <72rop6$ord$1@mach.vub.ac.be> References: <72etd9$7c9$1@mach.vub.ac.be> <72hfca$knn$1@mach.vub.ac.be> NNTP-Posting-Host: bigben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] : I still only get 6 codes linked. I used the taxonomy file : ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat That is because the taxonomy.i file at the EBI contains some error. To convince yourself of this, search in taxonomy the taxon "homo sapiens" and link to geneticcode, you will see that you find only "Vertebratrate Mitochondrial" and not "Standard". The cause of the problem is that the link from taxonomy to geneticcode is defined twice. Guy Bottu From owner-srs@net.bio.net Wed Nov 18 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!howland.erols.net!news-stl.cp.verio.net!typhoon.stlnet.com!uunet!in3.uu.net!news1-gui.server.ntli.net!news-feed.ntli.net!news5-gui.server.ntli.net!news-feed.ntli.net!server4.netnews.ja.net!server2.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: 17 Nov 1998 09:48:48 +0000 Organization: The Sanger Centre Lines: 16 Message-ID: References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> <36506504.AAFD8718@ebi.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 911296026 9852 193.60.84.160 (17 Nov 1998 09:47:06 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 17 Nov 1998 09:47:06 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 Heikki Lehvaslaiho writes: > Thure and I had a go on the taxonomy files. Take a look at > > http://srs.ebi.ac.uk/srs5bin/cgi-bin/wgetz?-fun+PageQueryForm+-l+TAXONOMY Seems to also need changes to swissprot.i and embl.i to remove the alternative links to taxonomy... Any other connected changes needed? -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Wed Nov 18 22:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-dc-2.sprintlink.net!news-east1.sprintlink.net!news-peer1.sprintlink.net!news.sprintlink.net!newsfeed.direct.ca!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: 17 Nov 1998 16:19:34 +0000 Organization: The Sanger Centre Lines: 30 Message-ID: References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> <36506504.AAFD8718@ebi.ac.uk> <3651756A.388398DD@ebi.ac.uk> <36517A7C.208D252@ebi.ac.uk> <36518EEE.EA261FDC@ebi.ac.uk> <3651982C.83BECC25@ebi.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 911319471 16206 193.60.84.160 (17 Nov 1998 16:17:51 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 17 Nov 1998 16:17:51 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 Heikki Lehvaslaiho writes: > Peter Rice wrote: > > So, for example, how do I search TAXONOMY for "human" ? > > > > % getz '[taxonomy-all:human]' -e > > Works for me. There must still be some minor discrepancy between Sanger > and EBI files. taxonomy.i and taxonomy.is are identical. Our taxonomy.dat is the one on the EBI ftp server (dated 5-Nov) What else could be different in the way "alltext" can be defined? Aha - srsgen.i has lots of places with "group:@DF_ALL" added. Still not enough though - Hmmm. EBI has more keys under "taxon" indexed on 9-Nov. Searching taxon at EBI lets me find "human" but at Sanger it does not. Does it still work if you srssection and reindex at EBI with the current taxonomy icarus files? - ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Wed Nov 18 22:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!news.idt.net!newspeer.monmouth.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: 17 Nov 1998 15:24:19 +0000 Organization: The Sanger Centre Lines: 40 Message-ID: References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> <36506504.AAFD8718@ebi.ac.uk> <3651756A.388398DD@ebi.ac.uk> <36517A7C.208D252@ebi.ac.uk> <36518EEE.EA261FDC@ebi.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 911316157 15223 193.60.84.160 (17 Nov 1998 15:22:37 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 17 Nov 1998 15:22:37 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 Heikki Lehvaslaiho writes: > Peter Rice wrote: > > The common name(s) do not seem to be indexed. Can they be added? > > They are indexed but since there are 10 different fields that contain > other than the accepted scientific name, there are no specific search > fields for all of them. You can search them using AllText field. So, for example, how do I search TAXONOMY for "human" ? % getz '[taxonomy-all:human]' -e ... returns nothing ... Looks to me like "alltext" is not indexed. Nor does it show the common names. % getz '[taxonomy-spc:homo sapiens]' -e ID : 9606 PARENT ID : 9605 RANK : species GC ID : 1 MGC ID : 2 SCIENTIFIC NAME : Homo sapiens PREFERRED COMMON NAME : human COMMON NAME : man // % getz '[taxonomy-spc:homo sapiens]' -t RANK : species GC ID : 1 MGC ID : 2 SCIENTIFIC NAME : Homo sapiens -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Wed Nov 18 22:00:00 1998 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!uunet!in5.uu.net!news1-gui.server.ntli.net!news-feed.ntli.net!news5-gui.server.ntli.net!news-feed.ntli.net!server4.netnews.ja.net!server2.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: Wed, 18 Nov 1998 10:26:51 +0000 Organization: EMBL - EBI Lines: 40 Message-ID: <3652A0EB.DFECD45D@ebi.ac.uk> References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> <36506504.AAFD8718@ebi.ac.uk> <3651756A.388398DD@ebi.ac.uk> <36517A7C.208D252@ebi.ac.uk> <36518EEE.EA261FDC@ebi.ac.uk> <3651982C.83BECC25@ebi.ac.uk> NNTP-Posting-Host: cetus.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 911384811 10346 193.62.196.199 (18 Nov 1998 10:26:51 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 18 Nov 1998 10:26:51 GMT To: Peter Rice X-Mailer: Mozilla 4.5b2 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en Peter Rice wrote: > < $field:[@DF_Taxon code:sciname index:str indexToken:'name|sciname'] > --- > > $field:[@DF_Taxon code:sciname index:str indexToken:name] > > name is all the "name" fields. "name|sciname" is the scientific name only. > > That fixes it. Time to revert one of your changes ? You are right. One old taxonomy index has not been purged during these frantic changes to the code. The organization, however needs some rethinking. 1. I removed genetic codes from name production and put them into a new one. That allows deletion of special production for linking (l_gencode). 2. Same goes for species. l-species production can be removed if species production contains only scientific name. Species production's main use is to link other databases, anyway. 3. The we need one field that contains all the possible names, so that AllText, which is what most people use anyway, can access names like 'man' and 'human'. Taxon is, really, a good production for that. Also, the taxonomy view lists all available names. Corresponding changes in .i file, srssection, srsbuild, srsbuild links, and everyone is happy. At least for a while. Hopes, -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ http://www2.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From owner-srs@net.bio.net Wed Nov 18 22:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-in-east1.sprintlink.net!news.sprintlink.net!newshub.northeast.verio.net!newsfeed1.swip.net!swipnet!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: 17 Nov 1998 16:34:42 +0000 Organization: The Sanger Centre Lines: 21 Message-ID: References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> <36506504.AAFD8718@ebi.ac.uk> <3651756A.388398DD@ebi.ac.uk> <36517A7C.208D252@ebi.ac.uk> <36518EEE.EA261FDC@ebi.ac.uk> <3651982C.83BECC25@ebi.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 911320379 16206 193.60.84.160 (17 Nov 1998 16:32:59 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 17 Nov 1998 16:32:59 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 Peter Rice writes: > Still not enough though - Hmmm. EBI has more keys under "taxon" > indexed on 9-Nov. Searching taxon at EBI lets me find "human" but at > Sanger it does not. Something like this difference in an older version of taxonomy.i: < $field:[@DF_Taxon code:sciname index:str indexToken:'name|sciname'] --- > $field:[@DF_Taxon code:sciname index:str indexToken:name] name is all the "name" fields. "name|sciname" is the scientific name only. That fixes it. Time to revert one of your changes ? -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Thu Nov 19 22:00:00 1998 Path: biosci!CS.Arizona.EDU!math.arizona.edu!noao!ncar!newsxfer.itd.umich.edu!nntp-out.monmouth.com!newspeer.monmouth.com!news.maxwell.syr.edu!newsfeed.slurp.net!not-for-mail Message-ID: <3653852C.7C4F@hadenough.com> From: Maurice X-Mailer: Mozilla 3.04Gold (Win95; I) MIME-Version: 1.0 Newsgroups: comp.software.year-2000,at.tuwien.software,bionet.software,bionet.software.acedb,bionet.software.gcg,bionet.software.srs,bionet.software.staden Subject: Re: I found the Y2K software References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 11 Date: Wed, 18 Nov 1998 20:40:44 -0600 NNTP-Posting-Host: 209.144.5.99 X-Trace: newsfeed.slurp.net 911442045 209.144.5.99 (Wed, 18 Nov 1998 20:20:45 CDT) NNTP-Posting-Date: Wed, 18 Nov 1998 20:20:45 CDT Xref: biosci bionet.software:22301 bionet.software.acedb:2046 bionet.software.gcg:3312 bionet.software.srs:1271 bionet.software.staden:784 Internet wrote: > > If your worried like we were about losing all our data on your computer > from The Year 2K bug? > As the millennium nears YOU are at risk. > Click this link for the software to save your financial,personal, and > buisness data! > http://www.y2kmarket.com I dont know exactly what the software will do, but the problem of the embedded chips that only go up to 1999 will STILL be a problem. Good luck to us all I guess. From owner-srs@net.bio.net Thu Nov 19 22:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in5.uu.net!newsfeed.cwix.com!158.43.192.17!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: SRS man pages - missing figure Date: 18 Nov 1998 14:13:40 +0000 Organization: The Sanger Centre Lines: 10 Message-ID: NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 911398315 13790 193.60.84.160 (18 Nov 1998 14:11:55 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 18 Nov 1998 14:11:55 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 The SRSWWW manual at the EBI seems to be missing the first figure. This is file mi_srswww.html, missing "srswww.gif" -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Thu Nov 19 22:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in5.uu.net!nntp.abs.net!news.maxwell.syr.edu!firehose.mindspring.net!firehose.mindspring.com!not-for-mail From: swamerica@swamerica.com Newsgroups: bionet.software.srs Subject: Free Down Load, Great! Software prices 2568 Date: 19 Nov 1998 13:28:04 GMT Organization: MindSpring Enterprises Lines: 3 Message-ID: <7316d4$qs5$11@camel18.mindspring.com> NNTP-Posting-Host: cf.45.de.32 Check out this new site, free down load,great software price. http://www.swamerica.com huusdxbrplodnjgdwlope From owner-srs@net.bio.net Thu Nov 19 22:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in2.uu.net!xmission!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.gtei.net!firehose.mindspring.com!not-for-mail From: swamerica@swamerica.com Newsgroups: bionet.software.srs Subject: Great Software site 8372 Date: 19 Nov 1998 13:39:59 GMT Organization: MindSpring Enterprises Lines: 3 Message-ID: <73173f$gst$11@camel19.mindspring.com> NNTP-Posting-Host: cf.45.de.32 checkout @Software America http://www.swamerica.com unmtbvpgllsjlgzsbscdisoprpltund From owner-srs@net.bio.net Thu Nov 19 22:00:00 1998 Path: biosci!CS.Arizona.EDU!noao!math.arizona.edu!news.Arizona.EDU!uunet!in5.uu.net!typhoon.stlnet.com!cyclone.i1.net!newsfeed.enteract.com!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.gtei.net!firehose.mindspring.com!not-for-mail From: swamerica@swamerica.com Newsgroups: bionet.software.srs Subject: swamerica 218 Date: 19 Nov 1998 14:59:12 GMT Organization: MindSpring Enterprises Lines: 3 Message-ID: <731bo0$cst$11@camel29.mindspring.com> NNTP-Posting-Host: cf.45.9a.bd check out http://www.swamerica.com great software prices tmcxrewctkblichhnngvsipletgtqfqsqwqcuxivgqinocfsvrddeixrtrfwkrwizfsxfemruvciugxvgz From owner-srs@net.bio.net Sat Nov 21 22:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!news.maxwell.syr.edu!newsfeed.cwix.com!24.130.1.14!lsnws01.we.mediaone.net!24.130.4.9!clnws01.we.mediaone.net.POSTED!not-for-mail Message-ID: <3657BBDB.3E3D26A@hotmail.com> From: Betty McMannis Reply-To: bettym@hotmail.com X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software.srs Subject: www.softwareforless.net I just came across a terrific site with low-priced new software. They have everything -- Win, Mac and DOS. Prices are up to 75 percent off retail.....and they have major titles too. Definitely worth looking into. BettyM http://www Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Lines: 14 Date: Sat, 21 Nov 1998 23:23:07 -0800 NNTP-Posting-Host: 24.130.41.18 X-Trace: clnws01.we.mediaone.net 911719247 24.130.41.18 (Sat, 21 Nov 1998 23:20:47 PDT) NNTP-Posting-Date: Sat, 21 Nov 1998 23:20:47 PDT Organization: MediaOne Express, Western Region www.softwareforless.net I just came across a terrific site with low-priced new software. They have everything -- Win, Mac and DOS. Prices are up to 75 percent off retail.....and they have major titles too. Definitely worth looking into. BettyM http://www.softwareforless.net From owner-srs@net.bio.net Sun Nov 22 22:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!news-nyc.telia.net!newsfeed-zh.ip-plus.net!news-zh.switch.ch!news.belnet.be!news.vub.ac.be!bigben!gbottu From: gbottu@bigben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Re: taxonomy database ? Date: 23 Nov 1998 07:46:15 GMT Organization: Brussels Free Universities VUB/ULB Lines: 19 Message-ID: <73b3s7$7o3$1@mach.vub.ac.be> References: <71pq9i$34m$1@mach.vub.ac.be> <36417310.D2ABC137@ebi.ac.uk> <36506504.AAFD8718@ebi.ac.uk> <3651756A.388398DD@ebi.ac.uk> <36517A7C.208D252@ebi.ac.uk> <36518EEE.EA261FDC@ebi.ac.uk> NNTP-Posting-Host: bigben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] : > When I look at the up link (red arrow) it looks fine up to "Eukaryota" : > but then I see 12 other Taxons including "lobe-finned fish and : > tetrapod clade" and "Fungi/Metazoa group" (on my server and the EBI : > server). Strange because "Eukaryota" has a parent-id of 1 which should : > be straight up to "root". : I was afraid you'd eventually ask that. 8-). At the moment we have to : show the entries in the order they apper in the (flat file) database and : the (relational) database does not have an easy handle to sort them : easily and fast other than by rank. The ones that are clustered on the : top of the list below root all have rank: 'no rank'. We really have to : wait for the next SRS & Icarus version to do better. Just a suggestion : is it not better to let the red arrow move you up just one level in the hierarchy rather then give all the higher taxa. This would give a less confusing output. Guy Bottu From owner-srs@net.bio.net Sun Nov 22 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed1.swip.net!swipnet!newsfeed1.uni2.dk!fox.novo.dk!not-for-mail From: Morten Stig Andersen Newsgroups: bionet.software.srs Subject: Error in HSSP links Date: 23 Nov 1998 15:00:34 +0100 Organization: Novo Nordisk A/S Lines: 18 Message-ID: <39iug6y0e5.fsf@monk.novo.dk> NNTP-Posting-Host: monk.novo.dk X-Trace: fox.novo.dk 911829638 13366 152.73.51.67 (23 Nov 1998 14:00:38 GMT) X-Complaints-To: usenet@fox.novo.dk NNTP-Posting-Date: 23 Nov 1998 14:00:38 GMT X-Newsreader: Gnus v5.5/XEmacs 20.4 - "Emerald" I get this error when I try to link to the HSSP database (i.e. "getz '[swissprot-id:ppat_human] > hssp'"): SRSICA:srsquery.i:24: error: limitexceeded, Maximum number of "links in buffer" is 450000 Has anyone got a fix? Thanks, -- =-=-=-=-=-=-=-=-=-=-=-= \,`/ / -=-=-=-=-=-=-=-=-=-=-=-=-= Morten Stig Andersen _).. `_ 9M1.83 ( __ -\ Scientific Computing Tel: +45 444 26959 '`. Novo Nordisk A/S Fax: +45 444 26003 ( \>_-_, DK-2880 Bagsvaerd MoSA@novo.dk _||_ ~-/ Denmark From owner-srs@net.bio.net Mon Nov 23 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed1.swip.net!swipnet!masternews.telia.net!news-feed.inet.tele.dk!bofh.vszbr.cz!news-lond.gip.net!news.gsl.net!gip.net!dispose.news.demon.net!demon!diablo.dera.gov.uk!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: OMIM DnaMutType fails Date: 24 Nov 1998 13:04:28 +0000 Organization: The Sanger Centre Message-ID: NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 911912567 4579 193.60.84.160 (24 Nov 1998 13:02:47 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 24 Nov 1998 13:02:47 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 Lines: 21 Queries on OMIM "DnaMutType" fail on our server and at EBI: Queries on the Web server give an error. getz gives: getz '[omim-dnamuttype:point]' SRSICA:icarus.i:16: error: library ID does not exist, no library with ID "0" is defined Segmentation fault Seems to be something strange about the was this index is defined in omim.i - It is indexed OK (4 different values) but queries on it always fail. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Mon Nov 23 22:00:00 1998 Path: biosci!IGS.CNRS-MRS.FR!poirot From: poirot@IGS.CNRS-MRS.FR (Olivier POIROT) Newsgroups: bionet.software.srs Subject: List of queries with getz Date: 24 Nov 1998 03:09:33 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <365A92E2.C1144E31@igs.cnrs-mrs.fr> NNTP-Posting-Host: net.bio.net Is it possible to use a file containing a list of Ids with getz (SRS version 5.1)? Olivier Poirot -- Olivier Poirot, poirot@igs.cnrs-mrs.fr Information Genetique et Structurale 31 ch. Joseph Aiguier 13402 MARSEILLE Cedex 20 From owner-srs@net.bio.net Mon Nov 23 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: "Thure Etzold" Newsgroups: bionet.software.srs Subject: Re: Error in HSSP links Date: Tue, 24 Nov 1998 12:26:46 -0800 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 24 Message-ID: <73e9vo$49v$1@niobium.hgmp.mrc.ac.uk> References: <39iug6y0e5.fsf@monk.novo.dk> NNTP-Posting-Host: dhcp14.ebi.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 911911736 4415 193.62.196.23 (24 Nov 1998 12:48:56 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 24 Nov 1998 12:48:56 GMT X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Morten Stig Andersen wrote in message <39iug6y0e5.fsf@monk.novo.dk>... >I get this error when I try to link to the HSSP database > >(i.e. "getz '[swissprot-id:ppat_human] > hssp'"): > >SRSICA:srsquery.i:24: error: limitexceeded, Maximum number of "links in buffer" is 450000 > Currently there is no size limit building a link, but there is one for using them. You can increase that by editing "SRSSOU:link.c". Increase the value for constant LNKxBUFFSIZ after that recompile getz and wgetz. This problem has been removed for the next version where links can have any size regards thure From owner-srs@net.bio.net Mon Nov 23 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!woodstock.news.demon.net!demon!dispose.news.demon.net!demon!diablo.dera.gov.uk!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software.srs Subject: Re: List of queries with getz Date: Tue, 24 Nov 1998 13:04:31 +0000 Organization: EMBL - EBI Message-ID: <365AAEDF.B5907AFA@ebi.ac.uk> References: <365A92E2.C1144E31@igs.cnrs-mrs.fr> NNTP-Posting-Host: cetus.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 911912671 4727 193.62.196.199 (24 Nov 1998 13:04:31 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 24 Nov 1998 13:04:31 GMT X-Mailer: Mozilla 4.5b2 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en Lines: 73 Olivier POIROT wrote: > > Is it possible to use a file containing a list of Ids with getz (SRS > version 5.1)? Dear Olivier, I suppose you mean lists like these: % more my.list EMBL:AB015259 EMBL:AB015260 EMBL:AB015261 EMBL:AB015262 % getz needs its input formatted in a slightly different way. Let's write a script, in icarus of course, that does what you want and can be extended as needed. Create a file named 'list.i', put the follwing lines into it and give it execute permissions: -------------------------cut---------------------------------- #!/bin/env icarus if:($ArgN<2) { $Print:|Usage: list.i srs_entry_name_list [>entries] $Exit } $infile = $Arg:2 $rules={ entry: ~ {$In:[file:text] $Out} ln? {$Wrt} ~ printout: ~ {$In:entry $Out} /([^:]+):([^\n]+)/ {$System:["getz '[$1-id:$2]' -e" out:stdout]} ~ #other ln: ~ /[^\n]*\n/ ~ } if:$TestMode { $job = $JobNew:[prod:$rules fileName:$infile] while:$JobHasInput:$job { $JobTokens:[$job name:printout print:0] $JobNext:$job } } -------------------------cut---------------------------------- Command % list.i my.list > my.seqs will then put those entries into a file 'my.seqs' Have fun, -Heikki ______ _/ _/_____________________________________________________ _/ _/ http://www2.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From owner-srs@net.bio.net Mon Nov 23 22:00:00 1998 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.wli.net!howland.erols.net!newspeer.monmouth.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: List of queries with getz Date: 24 Nov 1998 13:52:02 +0000 Organization: The Sanger Centre Lines: 38 Message-ID: References: <365A92E2.C1144E31@igs.cnrs-mrs.fr> <365AAEDF.B5907AFA@ebi.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 911915413 5527 193.60.84.160 (24 Nov 1998 13:50:13 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 24 Nov 1998 13:50:13 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 Heikki Lehvaslaiho writes: > Olivier POIROT wrote: > > Is it possible to use a file containing a list of Ids with getz (SRS > > version 5.1)? > Dear Olivier, > I suppose you mean lists like these: > % more my.list > EMBL:AB015259 > EMBL:AB015260 > EMBL:AB015261 > EMBL:AB015262 > % > getz needs its input formatted in a slightly different way. Let's > write a script, in icarus of course, that does what you want and can > be extended as needed. Not really what is needed. That Icarus script just runs getz for each sequence and writes the results to stdout. I have asked Thure several times for the SRS 4 capability to use a list of entries as a query. Then you can do things like: getz '@my.list > swissprot' getz '@my.list' -f 'id acc des' getz '@my.list ! (embl < emblnew)' So far no sign of this appearing, though Thure promised it was not difficult. I really miss this capability. The lists can be created by getz (they are the default output) but cannot be used since SRS 4 went away. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Mon Nov 23 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed1.swip.net!swipnet!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software.srs Subject: Analysing SRS database usage Date: Tue, 24 Nov 1998 14:10:38 +0000 Organization: EMBL - EBI Lines: 94 Message-ID: <365ABE5E.D4412BEF@ebi.ac.uk> NNTP-Posting-Host: cetus.ebi.ac.uk Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------C5CA10782BDAFB1E2871F0C0" X-Trace: niobium.hgmp.mrc.ac.uk 911916639 5846 193.62.196.199 (24 Nov 1998 14:10:39 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 24 Nov 1998 14:10:39 GMT X-Mailer: Mozilla 4.5b2 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en This is a multi-part message in MIME format. --------------C5CA10782BDAFB1E2871F0C0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit SRS managers, You might have noticed that standard httpd log analysing programs are of no use if you want to analyse SRS usage. The relevant requests call wgetz with a long list of options and, to make situation even worse, session IDs are there and make almost every request unique. The attached icarus script modifies those requests that have a database name among wgetz options by stripping out everything else. cetus.ebi.ac.uk - - [24/Nov/1998:12:32:48 +0000] "GET /srs5bin/cgi-bin/wgetz?-id+4ktgJ1ALlWR+-e+[EMBL-ID:'AB015367'] HTTP/1.0" 200 3140 becomes : cetus.ebi.ac.uk - - [24/Nov/1998:12:32:48 +0000] "GET EMBL" 200 3140 This is something that any log analyser program can sort properly. Yours, -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ http://www2.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ --------------C5CA10782BDAFB1E2871F0C0 Content-Type: text/plain; charset=us-ascii; name="logmod.i" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="logmod.i" #!/bin/env icarus # # logmod.i # Cleans SRS HTTPD log file entries of wgetz options and session ids # so that the use of databases can be summed up. # # Heikki Lehvaslaiho, EMBL-EBI # heikki@ebi.ac.uk # # v.1.1 Nov 23 1998 # if:($ArgN<2) { $Print:|Usage: logmod.i http_log_file [> modified_http_log_file] $Exit } $logfile = $Arg:2 $rules={ hit: ~ {$In:[file:text] $Out pre $Skip:0} ln? {$Wrt} ~ dbhit: ~ {$In:hit $Out} /.*GET / #note: ignores queries for number of links between databases ( /[-\+](info|e|lib|l)[\+=]\\[?([^-\+ ]+)/ {$Wrt:[s:$2] $name=$2} | /./ )+ ~ write: ~ {$In:hit $Out pre $Request:dbhit } /(.*GET )\/srs5bin\/cgi-bin\/wgetz/ {$Print:$1} /[^"]+(.*)/ {if:$name!='' $Print:"$name$1" else $Print:$Ct} | /.*/ {$Print:$Ct} ~ #other ln: ~ /[^\n]*\n/ ~ } if:$TestMode { $job = $JobNew:[prod:$rules skip:" \r\n" fileName:$logfile] while:$JobHasInput:$job { $JobTokens:[$job name:write print:0] $JobNext:$job } } --------------C5CA10782BDAFB1E2871F0C0-- From owner-srs@net.bio.net Sat Nov 28 22:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-dc-2.sprintlink.net!news-east1.sprintlink.net!news-peer1.sprintlink.net!news.sprintlink.net!newsfeed.berkeley.edu!newsfeed.cwix.com!209.44.33.119!hub1.ispnews.com!news14.ispnews.com.POSTED!not-for-mail From: wnwnis@YAHOO.COM Newsgroups: bionet.software.srs Subject: LOWEST PRICES ON MAGAZINES 2691 Lines: 63 Message-ID: NNTP-Posting-Host: 207.240.233.44 X-Trace: news14.ispnews.com 912375011 207.240.233.44 (Sun, 29 Nov 1998 16:30:11 EDT) NNTP-Posting-Date: Sun, 29 Nov 1998 16:30:11 EDT Organization: ISPNews http://ispnews.com Date: Sun, 29 Nov 1998 21:30:11 GMT For a complete magazine discount list (175 magazines) click on http://ourworld.compuserve.com/homepages/magazine_man COMPUTER MAGAZINES AT HUGE DISCOUNTS //////////////////////////////////// Magazine Reg. Price. One Year Three Years Byte $35 sale $10.00 sale $15.00 (2 yr.) Computer Shopper $40 sale $15.00 sale $35.00 Family PC $25 sale $10.00 sale $25.00 Home Office Computing $20 sale $8.50 sale $20.00 PC Computing $25 sale $10.00 sale $25.00 PC World $30 sale $10.00 sale $25.00 Windows $25 sale $8.50 sale $15.00 (2 yr.) SPECIAL - US Magazine - 1 year regularly $42 only $7.50 $20 three years Playboy - 1 year regularly $42 only $20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Save Big Bucks On All Your Magazine Subscriptions including Renewals and Gifts with the security of an 800 number and the safety and confidence of a credit card transaction ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CALL 800-958-2650 ext. 300 to order with your credit card ------ ORDER ALL YOUR MAGAZINE SUBSCRIPTIONS AT HUGE DISCOUNTS ------ *** RENEW OR ADVANCE RENEW YOUR CURRENT SUBSCRIPTIONS AT VERY LOW PRICES *** BUY NEW SCRIPTIONS AT HUGE DISCOUNTS *** GIVE GIFTS (PERFECT FOR CHRISTMAS) AT HUGE SAVINGS (GIFT CARD INCLUDED) You can't beat these prices (good for only 30 days) ORDER TODAY! There is a $2.00 per order processing fee. CALL 800-958-2650 ext. 300 to order with your credit card For a complete magazine discount list (175 magazines) click on http://ourworld.compuserve.com/homepages/magazine_man Best Deal Magazines 217 E. 86th Street New York, NY 10028 voice or fax 212-426-7492 *** These prices are good for 30 days only. Order today. For my complete list of more than 175 magazines at huge discounts see above. wglghtscypcvtiuhxodnsunykrhskhgysszrtefwfwzrgrdxyntuelwefpzjfuter From owner-srs@net.bio.net Mon Nov 30 22:00:00 1998 Path: biosci!aerotek.com!bmckee From: bmckee@aerotek.com Newsgroups: bionet.software.srs Subject: Searching for a Risk Assessor/Toxicologist Date: 1 Dec 1998 11:39:58 -0800 Organization: Aerotek Lines: 57 Sender: daemon@net.bio.net Distribution: world Message-ID: <36644502.69B74510@aerotek.com> Reply-To: bmckee@aerotek.com NNTP-Posting-Host: net.bio.net This is a multi-part message in MIME format. --------------BDB635A777075FFEF4F25489 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Environmental and infrastructure engineering company is seeking a senior toxicologist/risk assessor. The positions requires a minimum of 10 years of experience in consulting and advanced degrees (Ph D.) are preferred. The positions will involve growing and managing our risk services for the geographic area and include both technical and business development goals. Responsibilities will include marketing, strategy development, proposal and report writing, project management, and client and agency negotiations. Candidates must have expertise in human health risk assessment as applied to RCRA, CERCLA, and various state regulatory programs. Litigation support and expert testimony experience is a plus. Experience in ecological risk assessment is also desirable. Successful candidates will be recognized technical experts with proven business development skills and be able to work well within a team. We are looking for a person who is interested in a permanent position, and the office is located in Baton Rouge, Louisiana. There will be some travel in the area to help to develop business/accounts. PLEASE CALL IMMEDIATELY IF YOU ARE INTERESTED! 800-669-3960 and speak to Paul Hyde or BJ McKee, of FAX you resume to 504/733-6813. Thanks! --------------BDB635A777075FFEF4F25489 Content-Type: text/x-vcard; charset=us-ascii; name="vcard.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for BJ McKee Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: BJ McKee n: McKee;BJ org: AEROTEK Contract Engineering adr;dom: 800 Commerce Road East;;Suite 300;New Orleans;Louisiana;70123; email;internet: bmckee@aerotek.com title: Senior Technical Recruiter tel;work: 800/669-3690 x4042 tel;fax: 504/733-6813 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------BDB635A777075FFEF4F25489--