From owner-srs@net.bio.net Fri Jan 01 22:00:00 1999 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!news.maxwell.syr.edu!diablo.theplanet.net!join.news.pipex.net!pipex!duke.telepac.pt!news.telepac.pt!not-for-mail From: "Henrique d'Aguiar" Newsgroups: bionet.software.srs Subject: Can anybody give/sell me HIP HOP EJAY FULL VERSION? Date: Sat, 2 Jan 1999 15:57:02 -0100 Lines: 4 Message-ID: <76lj2u$4vt$1@duke.telepac.pt> NNTP-Posting-Host: 194.65.220.249 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Can anybody give/sell me HIP HOP EJAY FULL VERSION? Please reply to flammabledance@yahoo.com From owner-srs@net.bio.net Sat Jan 02 22:00:00 1999 Path: biosci!bcm.tmc.edu!news.tamu.edu!cs.utexas.edu!howland.erols.net!newsfeed.concentric.net!207.155.183.80.MISMATCH!global-news-master From: sjtlup@k.com Newsgroups: han.sci.misc,han.sys.cray,han.comp.internet,han.sci.astro,han.test,han.sys.linux,han.sys.sun,han.sys.hp,han.comp.security,han.net.kornet,han.net.kreonet,han.net.services,han.rec.humor,han.rec.misc,han.sys.ibmpc,han.sys.mac,belnet.wg-lib,stl.forsale,bionet.software.srs,pg.internet.pg-online Subject: PURE XXX QUALITY PICS 6538 Date: 03 Jan 1999 02:58:12 PST Organization: Concentric Internet Services Lines: 3 Message-ID: <368e622a.0@earth.GAIANET.NET> NNTP-Posting-Host: earth.gaianet.net www.chickpages.com/musicmania/placezz ilsptbkjfvtjkrbegcpnmpnodkdxqdkesuwmblkqmlqinmnjvlwoiztsxzhsmjoxwefcjykekhgmgpdjjkqop From owner-srs@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!oleane!jussieu.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: need help Date: Tue, 05 Jan 1999 09:54:57 +0100 Organization: INFOBIOGEN Lines: 78 Message-ID: <3691D361.6B5E14F7@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 4.5 [en] (X11; I; SunOS 5.6 sun4u) X-Accept-Language: en hello, I find a problem when indexing embl 57 in srs for the feature PID only(ftpid). The srsbuild crashes with the -m option which Merge index partitions to a single index: .... + time srsbuild EMBL -c -f pid -xdir SRSINX: -odir SRSINX: ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_1.ids" size: 1 kbytes, IDs: 0 ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_2.ids" size: 1 kbytes, IDs: 0 ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_3.ids" size: 1 kbytes, IDs: 0 ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_4.ids" size: 5 kbytes, IDs: 662 ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_5.ids" size: 1 kbytes, IDs: 1 ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_6.ids" size: 1 kbytes, IDs: 0 ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_7.ids" size: 1 kbytes, IDs: 1 ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_8.ids" size: 4 kbytes, IDs: 557 ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_9.ids" size: 129 kbytes, IDs: 21459 ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_10.ids" size: 61 kbytes, IDs: 10043 ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_11.ids" size: 598 kbytes, IDs: 99591 ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_12.ids" size: 1144 kbytes, IDs: 190535 ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_13.ids" size: 253 kbytes, IDs: 42043 ...program "srsbuild" completed successfully. real 4.6 user 0.9 sys 1.0 + time srsbuild EMBL -m -f pid -xdir SRSINX: -odir SRSINX: time: command terminated abnormally. Could someone give me a clue? Thanks for your help in advance 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 Wed Jan 06 22:00:00 1999 Path: biosci!CS.Arizona.EDU!news.Arizona.EDU!uunet!in5.uu.net!newsm2.ibm.net!ibm.net!news-peer.gip.net!news.gsl.net!gip.net!sunqbc.risq.qc.ca!news.imp.ch!imp.ch!news.core.genedata.com!ischia.ch.genedata.com From: Tim Eyres Newsgroups: bionet.software.srs Subject: Re: need help Date: Tue, 05 Jan 1999 10:33:02 +0100 Organization: GeneData AG Lines: 13 Message-ID: <3691DC4E.FB2EF604@genedata.com> References: <3691D361.6B5E14F7@infobiogen.fr> NNTP-Posting-Host: mentolat-e0.core.genedata.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; I) > The srsbuild crashes with the -m option which Merge index partitions > to a single index: > > + time srsbuild EMBL -m -f pid -xdir SRSINX: -odir SRSINX: > time: command terminated abnormally. > Looks like to me like srsbuild completes succesfully and time sends to stdout the amount of time taken to complete, then time terminates abnormally. So perhaps it's time that crashes and not srsbuild? Looking at your output the indicies should be built correctly. Tim From owner-srs@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.concentric.net!newspeer1.nac.net!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: sabino@area.ba.cnr.it Newsgroups: bionet.software.srs Subject: Can any help me Date: 4 Jan 1999 13:06:16 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 31 Message-ID: <76qec8$65u$1@mserv2.dl.ac.uk> NNTP-Posting-Host: mserv2.dl.ac.uk Original-To: bio-srs@dl.ac.uk content-length: 1137 Return-Path: Data: Mon, 04 Jan 1999 14:05:13 +0100 X-Sender: sabino@area.ba.cnr.it Hi Thure, I have a problem with the comand srssection. I have installed new embl release (57), and I have modified the embl.i file, because there are new division (em_gss5 and em_est20). When I execute the script srssection I have this error: 15249 Memory fault - core dumped If I delete in the embl.i the definition of the new division (em_gss5, em_est20) I have not received any error. Any help, Thanks in advance Sabino Liuni ================================================ Dr. Sabino LIUNI Area di Ricerca CNR Administrator for the Via Amendola 166/5 Italian EMBnet Node 70126 Bari (Italy) tel. +39-80-5482176/5482130 Fax. +39-80-5484467 E_mail:sabino@area.ba.cnr.it ----------------------------------------------- OPEN YOUR EYES TO THE WORLD OF BIOCOMPUTING ----------------------------------------------- From owner-srs@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!news.stanford.edu!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: Peter Rice Newsgroups: bionet.software.srs Subject: Re: need help Date: 05 Jan 1999 09:35:28 +0000 Organization: The Sanger Centre Lines: 44 Message-ID: References: <3691D361.6B5E14F7@infobiogen.fr> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 915528779 18639 193.60.84.160 (5 Jan 1999 09:32:59 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 5 Jan 1999 09:32:59 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 Jean-Marc Plaza writes: > hello, > I find a problem when indexing embl 57 in srs > for the feature PID only(ftpid). > The srsbuild crashes with the -m option which Merge index partitions > to a single index: > > .... > + time srsbuild EMBL -c -f pid -xdir SRSINX: -odir SRSINX: > ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_1.ids" > size: 1 kbytes, IDs: 0 > > + time srsbuild EMBL -m -f pid -xdir SRSINX: -odir SRSINX: > time: command terminated abnormally. > > Could someone give me a clue? The "IDs: 0" is the clue. SRS has big problems when the first section of the index has no data. The empty file breaks the merge. Thure knows about it. I guess there will be a fix in SRS 6 :-) You can get "Ids: 0" for the PID index if you start with ESTs because there are no CDS features in the EST entries. Change the order of the EMBL files to have something else first. I currently use "pro" (flatfile). EBI uses "em_ba" (GCG). Sorry, but if you change the order of the files you have to rebuild *all* the indices. There are SRS index files at the EBI FTP server - but the filenames are only for GCG format. I have a version at Sanger that worked with the FTP index files for flat files (I had to add the filenames in the right order) and also has NID indexed. -- ---------------------------------------------------------------------- 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 Jan 06 22:00:00 1999 Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!newsgate.netvigator.com!news.netvigator.com!usenet From: cathy168@yahoo.com Newsgroups: bionet.plants.education,bionet.software,bionet.software.acedb,bionet.software.srs,bionet.software.x-plor Subject: Successful business!Earn more $$$$$ Date: Thu, 07 Jan 1999 21:53:31 +0800 Organization: Netvigator Lines: 41 Message-ID: <3694BC5B.485445A@yahoo.com> NNTP-Posting-Host: hhtck002175.netvigator.com Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------487F57E49C6C6B962207EE37" X-Mailer: Mozilla 4.06 [en] (Win95; I) Xref: biosci bionet.plants.education:4496 bionet.software:22584 bionet.software.acedb:2100 bionet.software.srs:1323 bionet.software.x-plor:2229 This is a multi-part message in MIME format. --------------487F57E49C6C6B962207EE37 Content-Type: multipart/alternative; boundary="------------8E11FD86060A6ACA7CB72013" --------------8E11FD86060A6ACA7CB72013 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit --------------8E11FD86060A6ACA7CB72013 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit   --------------8E11FD86060A6ACA7CB72013-- --------------487F57E49C6C6B962207EE37 Content-Type: text/plain; charset=us-ascii; name="international business opportunity-1.txt" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="international business opportunity-1.txt" International Business Opportunity We have an exceptional independent, international business opportunity supported by a fast track training system. 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Call now for details: (852) 82010112 Partick Kwok or e-mail to: cathy168@yahoo.com --------------487F57E49C6C6B962207EE37-- From owner-srs@net.bio.net Wed Jan 06 22:00:00 1999 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.gsl.net!gip.net!news.maxwell.syr.edu!news.mel.connect.com.au!news.unimelb.edu.au!wehi.edu.au!wehi!janice From: janice@wehi.edu.au (Janice Coventry, Walter and Eliza Hall Institute) Newsgroups: bionet.software.srs Subject: Index files Date: 7 Jan 99 12:57:17 +1000 Organization: Walter & Eliza Hall Institute Lines: 13 Message-ID: <1999Jan7.125717@wehi> NNTP-Posting-Host: wehiu.wehi.edu.au X-Trace: wehid.wehi.EDU.AU 915674309 5756 (None) 128.250.252.27 X-Complaints-To: newsmaster@wehi.edu.au Hello Is it possible to have the index files spread over two different directories as our current disk is filling up. Thanks in advance Janice ================================================================================ Janice Coventry The Walter and Eliza Hall Institute of Medical Research, P.O. Royal Melbourne Hospital, Victoria, 3050, Australia. Phone: International +61-3-9345-2564 FAX: International +61-3-9347-0852 National 03-9345-2564 National 03-9347-0852 Email: janice@wehi.edu.au =============================================================================== From owner-srs@net.bio.net Wed Jan 06 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!netnews.com!newspeer.monmouth.com!news.imp.ch!imp.ch!news.core.genedata.com!ischia.ch.genedata.com From: Tim Eyres Newsgroups: bionet.software.srs Subject: Re: need help Date: Tue, 05 Jan 1999 10:49:24 +0100 Organization: GeneData AG Lines: 10 Message-ID: <3691E024.25BB6F32@genedata.com> References: <3691D361.6B5E14F7@infobiogen.fr> <3691DC4E.FB2EF604@genedata.com> NNTP-Posting-Host: mentolat-e0.core.genedata.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (WinNT; I) > + time srsbuild EMBL -c -f pid -xdir SRSINX: -odir SRSINX: > ...wrote IDs file "/env/lovelace/env_ibg/pack/srs5/index/embl_pid_1.ids" > size: 1 kbytes, IDs: 0 > > + time srsbuild EMBL -m -f pid -xdir SRSINX: -odir SRSINX: > time: command terminated abnormally. Oops looks like I should read news more closely... Tim From owner-srs@net.bio.net Fri Jan 08 22:00:00 1999 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-europe.sprintlink.net!news.sprintlink.net!Sprint!feed1.news.luth.se!luth.se!news-ge.switch.ch!news.unige.ch!news From: Alain GATEAU Newsgroups: bionet.software.srs Subject: Re: Index files Date: Fri, 08 Jan 1999 15:52:17 +0100 Organization: University of Geneva Lines: 16 Message-ID: <36961BA1.E43@cmu.unige.ch> References: <1999Jan7.125717@wehi> NNTP-Posting-Host: cmusun18.unige.ch Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.6 sun4m) Janice Coventry, Walter and Eliza Hall Institute wrote: > > Hello > Is it possible to have the index files spread over two different > directories as our current disk is filling up. > Thanks in advance > Janice > it should be possible but you'll have to edit srsdb.i and for each active library put the appropriate index path: $libloc:[@SWISSPROT_DB dir:"$dataRoot/" indexDir:"indexpath1"] $libloc:[@EMBL_DB dir:"$dataRoot/ "indexDir:"indexpath2"] ... alain From owner-srs@net.bio.net Sat Jan 09 22:00:00 1999 Message-ID: <36989A80.8E6BA25C@doelz.com> Date: Sun, 10 Jan 1999 13:18:08 +0100 From: Reinhard Doelz Organization: Verlag Ute DOelz X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 Subject: Re: Index files References: <1999Jan7.125717@wehi> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Newsgroups: bionet.software.srs Path: biosci!agate!newsfeed.berkeley.edu!netnews.com!newspeer1.nac.net!WCG!arl-news-svc-3.compuserve.com!news-master.compuserve.com!nntp-nih2naaa.compuserve.com Lines: 23 Regarding the changes in srsdb.i proposed earlier, another possibility is to initiate a "logical volume" - this depends on the vendor of your operating system. It basically pretends to have a larger disk and "stripes" across different file systems. I've done it on VMS, IRIX and Solaris. Regards Reinhard "Janice Coventry, Walter and Eliza Hall Institute" wrote: > Hello > Is it possible to have the index files spread over two different > directories as our current disk is filling up. > Thanks in advance > Janice > ================================================================================ > Janice Coventry > The Walter and Eliza Hall Institute of Medical Research, > P.O. Royal Melbourne Hospital, Victoria, 3050, Australia. > Phone: International +61-3-9345-2564 FAX: International +61-3-9347-0852 > National 03-9345-2564 National 03-9347-0852 > Email: janice@wehi.edu.au > =============================================================================== From owner-srs@net.bio.net Sun Jan 10 22:00:00 1999 Path: biosci!SENTURY.COM!Directmarketing From: Directmarketing@SENTURY.COM Newsgroups: bionet.software.srs Subject: FREE! Download! URL Submission Software! Over 700+ Search Engines & Links (Growing Monthly!) Date: 11 Jan 1999 04:44:35 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 68 Sender: daemon@net.bio.net Distribution: world Message-ID: <199901111244.EAA02632@net.bio.net> Reply-To: Sentury@marketing.com NNTP-Posting-Host: net.bio.net Dear bio-srs * * * ADVERTISE! * * * YOUR BUSINESS OR RESUME ALL OVER THE WORLD! 700+ Search Engines & Links and Growing Monthly! This is a great opportunity for Students, Businesses and Employment Seekers!, Promote your Resume, Business or Personal Website for world wide exposure! Make it easier for yourself and get the advantage? Do you have a Website? Why not submit to as many search engines as possible? Get the word out! Get your Website or Resume recognized! Increase your response and or Sales! FREE! Download and Working Demo! http://www.pathcom.com/~tlrglobe/submission.html A GREAT! Way to Promote Your Business! or Yourself! Advertise Worldwide! Write a Webpage and Advertise! It's Easy! and it Works! Submission Categories Include: Travel, Real Estate, Business, Import & Export, Banking, Business, Communications, Computers, Computer Software,Computer Services,Consultants,Finance, Lifestyle, Health, Fashion, Retail, Many others to choose from. Choose your own Key Search Words, Your own Product, Service or Resume Description. You will get an email from search engines indicating your Website submissions. Also an HTML version of your uploads. Thank you in advance for your time and consideration. __________________________________ From owner-srs@net.bio.net Tue Jan 12 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!remarQ73!supernews.com!news.he.net!sws1.ctd.ornl.gov!not-for-mail From: "Denise D. Schmoyer" Newsgroups: bionet.software.srs Subject: Re: need help Date: Wed, 13 Jan 1999 07:45:12 -0500 Organization: Oak Ridge National Lab, Oak Ridge, TN Lines: 33 Message-ID: <369C9558.C6670A0F@ornl.gov> References: <3691D361.6B5E14F7@infobiogen.fr> NNTP-Posting-Host: dcssun.lsd.ornl.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (X11; U; SunOS 5.6 sun4u) X-Accept-Language: en Peter Rice wrote: > Jean-Marc Plaza writes: > > > hello, > > I find a problem when indexing embl 57 in srs > > for the feature PID only(ftpid). > > The srsbuild crashes with the -m option which Merge index partitions > > to a single index: > > > SRS has big problems when the first section of the index has no data. > The empty file breaks the merge. Thure knows about it. I guess there > will be a fix in SRS 6 :-) > > ---------------------------------------------------------------------- > Peter Rice | Informatics Division, The Sanger Centre, I experienced this same problem with an index I was building for Genbank. I was able to work around the problem by increasing the number of entries that are to be indexed separately for later merging. This is done in the databank .i file with the partsize argument for the $library class. I increased the partsize from 100000 to 500000, my first section of the index then had some IDs so the merge worked. ---------------------------------------------------------- Denise Schmoyer Oak Ridge National Laboratory E-mail: dcs@ornl.gov Phone: (423) 574-5707 From owner-srs@net.bio.net Sat Jan 16 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!206.172.150.11!news1.bellglobal.com!news20.bellglobal.com.POSTED!not-for-mail From: neofwe@broadcast.net Newsgroups: bionet.software.srs,uw.mfcf.software.mac Subject: $300 of software for only $29.99 7381 Lines: 7 Message-ID: Date: Sun, 17 Jan 1999 22:47:59 GMT NNTP-Posting-Host: 142.217.240.79 X-Trace: news20.bellglobal.com 916613279 142.217.240.79 (Sun, 17 Jan 1999 17:47:59 EDT) NNTP-Posting-Date: Sun, 17 Jan 1999 17:47:59 EDT Organization: Bell Solutions to sell: stealth 3.2 mass mailer,send 250,000 e-mail per hour, dynamic submission 2000, submit your website over 630 search engines,post agent 3.5, post your message over 25000 newgroups.all of my software are fully registered.ask only $29.99 for all the package,can send cod.contact mathew@broadcast.net slp From owner-srs@net.bio.net Mon Jan 18 22:00:00 1999 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 Jan 1999 02:00:15 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199901191000.CAA16811@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 Tue Jan 19 22:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!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: CUTG index files Date: 20 Jan 1999 10:32:41 +0000 Organization: The Sanger Centre Lines: 18 Message-ID: NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 916828190 4405 193.60.84.160 (20 Jan 1999 10:29:50 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 20 Jan 1999 10:29:50 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 I have updated the Icarus parser (cutg.is) for the CUTG codon usage database so that the 'Organism' index includes species names in the same format as the other databases. This allows CUTG to be linked to TAXONOMY (or any database with an Organism index) so you can go directly from any sequence to the codon usage table. CUTG seems to be currently only updated on the ftp.dna.affrc.go.jp server and not on the mirrors. Most other SRSWWW servers (except DKFZ) have an older release (104) than the one I picked up yesterday (108). -- ---------------------------------------------------------------------- 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 Jan 21 22:00:00 1999 From: "Andrew Bratcher" Newsgroups: bionet.software.srs Subject: GOT BILLS Date: Fri, 22 Jan 1999 13:32:26 -0600 Lines: 3 X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 NNTP-Posting-Host: 207.150.25.176 Message-ID: <36a8dcb6.0@206.52.66.203> Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.corridex.com!newshub.northeast.verio.net!news-stl.cp.verio.net!206.52.66.203!207.150.25.176 From owner-srs@net.bio.net Tue Jan 26 22:00:00 1999 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!not-for-mail From: timc@chiark.greenend.org.uk (Tim Cutts) Newsgroups: bionet.software.srs Subject: Very poor srsbuild performance Date: 27 Jan 1999 11:37:02 +0000 (GMT) Organization: Linux Unlimited Lines: 29 Message-ID: <64q*x67Qn@news.chiark.greenend.org.uk> NNTP-Posting-Host: rrw1000.sel.cam.ac.uk Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1]) We are having problems with extremely poor performance building indexes on our main server machine: Hardware: Sun Enterprise 3000, 2 CPUs, 1.25 GB RAM Software: Solaris 2.5.1 I compiled SRS using gcc 2.8.1 Building Genbank indexes, I discovered to my horror that it is only managing to process about 25 entries a second, even when the machine is otherwise completely unloaded. At that rate, of course, the index build will take about a day and a half. However, when it gets to merge the temporary index files it crashes anyway. I tried an index build on my home PC (a 350 MHz PII with 128 MB RAM) and found it manages well over 100 records a second! How can a PC that cost less than a thousand pounds be that much faster than a dedicated Sun server that cost well over ten times as much? I used to work with SGI Origin machines, and found these to be very quick, but this Enterprise 3000 is a real dog. Does anyone have any suggestions what we can do to improve the performance? Thanks in advance... Tim. From owner-srs@net.bio.net Tue Jan 26 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!isdnet!oleane!jussieu.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: PIR sequences in SRS Date: Wed, 27 Jan 1999 10:01:23 +0100 Organization: INFOBIOGEN Lines: 32 Message-ID: <36AED5E3.3B2D266B@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 4.5 [en] (X11; I; SunOS 5.6 sun4u) X-Accept-Language: en Hello, there is a parsing problem for PIR sequences (pirref-pirseq) where the composition is not respected. In pir1.seq data we have: >P1;CCDG cytochrome c - dog GDVEKGKKIFVQK(C.A.Q.C.H.T.V.E)KGGKHKTGPNLHGLFGRKTGQAPGFSYTDANKNKGITWGEETLMEYLENP KKYIPGTKMIFAGIKKTGERADLIAYLKKATKE* but in SRS parentheses are removed: >P1;CCDG GDVEKGKKIF VQKC.A.Q.C .H.T.V.EKG GKHKTGPNLH GLFGRKTGQA PGFSYTDANK NKGITWGEET LMEYLENPKK YIPGTKMIFA GIKKTGERAD LIAYLKKATK E* Thanks for your help in advance -- --------------------------------------------------- Jean-Marc PLAZA INFOBIOGEN - CNRS 7, rue Guy Moquet BP8 94801 VILLEJUIF Cedex, France tel: +33 45 59 52 39 fax: +33 45 59 52 50 e-mail: plaza@infobiogen.fr --------------------------------------------------- From owner-srs@net.bio.net Wed Jan 27 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!newsxfer3.itd.umich.edu!newsxfer.itd.umich.edu!news.join.ad.jp!news-sv.sinet!villon.nig.ac.jp!mkikuchi From: mkikuchi@genes.nig.ac.jp (Masayuki Kikuchi) Newsgroups: bionet.software.srs Subject: AllText field Date: 28 Jan 1999 07:02:17 GMT Organization: National Institute of Genetics, Japan. Lines: 20 Message-ID: <78p21p$cvb$1@villon.nig.ac.jp> NNTP-Posting-Host: wolf.genes.nig.ac.jp X-Newsreader: mnews [version 1.21] 1997-12/23(Tue) I use SRS Ver.5.1.0 on Solaris 2.6. Now AllText field isn't include Feture fields in EMBL, SWISSPROT and so on. I hope that AllText field include Feture fields. So, I modified the srsgen.i file next, and tried reindexing. 98,99c98,99 < DF_FtSource:$SrsField:[FtSource short:fts] < DF_FtDescription:$SrsField:[FtDescription short:ftd] --- > DF_FtSource:$SrsField:[FtSource short:fts group:@DF_ALL] > DF_FtDescription:$SrsField:[FtDescription short:ftd group:@DF_ALL] But these field didn't append one of AllText field. Please send me some information to resolve this problem. Regards -- DNA Data Bank of Japan Masayuki Kikuchi (mkikuchi@genes.nig.ac.jp) From owner-srs@net.bio.net Fri Jan 29 22:00:00 1999 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.cwix.com!152.163.199.19!portc03.blue.aol.com!audrey03.news.aol.com!not-for-mail From: rvan1115@aol.com (RVan1115) Newsgroups: bionet.software.srs Subject: read about computers Lines: 2 NNTP-Posting-Host: ladder03.news.aol.com X-Admin: news@aol.com Date: 30 Jan 1999 04:55:48 GMT Organization: AOL http://www.aol.com Message-ID: <19990129235548.28852.00001338@ng101.aol.com> computer magazines and magazines for the whole ffamily go to http://www.myfreeoffice/magazines/index.html From owner-srs@net.bio.net Sun Jan 31 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!btnet-peer!btnet!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software.srs Subject: Re: AllText field Date: Mon, 01 Feb 1999 09:55:44 +0000 Organization: EMBL - EBI Lines: 32 Message-ID: <36B57A20.24A36CDB@ebi.ac.uk> References: <78p21p$cvb$1@villon.nig.ac.jp> NNTP-Posting-Host: cetus.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 917862944 17428 193.62.196.199 (1 Feb 1999 09:55:44 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 1 Feb 1999 09:55:44 GMT To: Masayuki Kikuchi X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en Masayuki Kikuchi wrote: > > I use SRS Ver.5.1.0 on Solaris 2.6. > > Now AllText field isn't include Feture fields in EMBL, SWISSPROT and so on. > I hope that AllText field include Feture fields. > So, I modified the srsgen.i file next, and tried reindexing. > > 98,99c98,99 > < DF_FtSource:$SrsField:[FtSource short:fts] > < DF_FtDescription:$SrsField:[FtDescription short:ftd] > --- > > DF_FtSource:$SrsField:[FtSource short:fts group:@DF_ALL] > > DF_FtDescription:$SrsField:[FtDescription short:ftd group:@DF_ALL] > > But these field didn't append one of AllText field. > Please send me some information to resolve this problem. It should work. Are you sure you recompiled by command 'srssection' before reindexing? -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 ___ _/_/_/_/_/________________________________________________________