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Please reply to: cdzcd@usa.net Fax: +441716917580 From owner-srs@net.bio.net Tue May 04 10:22:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!newsfeed.nacamar.de!fu-berlin.de!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Dr Thon de Boer Newsgroups: bionet.software.srs Subject: Inconsistent number of entries error in SRS5.1 Date: Tue, 04 May 1999 12:15:23 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 23 Message-ID: <372ED6CB.6DA87F11@hgmp.mrc.ac.uk> NNTP-Posting-Host: lutetium.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 925816618 27420 193.62.192.71 (4 May 1999 11:16:58 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 4 May 1999 11:16:58 GMT X-Mailer: Mozilla 4.51 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en Hi, I'm trying to index the FSSP database and i get a strange 'error' message when I do a SRSCHECK -l FSSP : library "FSSP" had previously 1531, now 1627 entries ======> must build indices for library "FSSP" When I then do a SRSUPDATE and check the database again, I get the same error. I've even tried deleting the indices all together and the error still comes up (after the second SRSCHECK that is). Does anyone know what is going on here ? I think the numbers come from a descrepancy between the number of keys indexed and the number of entry references, since the two numer (1531 and 1627) come up in the info bit on the FSSP page. Thanks, Thon de Boer HGMP-RC, Hinxton From owner-srs@net.bio.net Tue May 04 13:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!dispose.news.demon.net!demon!news-lond.gip.net!news.gsl.net!gip.net!bignews.mediaways.net!fu-berlin.de!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: Inconsistent number of entries error in SRS5.1 Date: 04 May 1999 14:59:06 +0100 Organization: The Sanger Centre Message-ID: References: <372ED6CB.6DA87F11@hgmp.mrc.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk X-Trace: niobium.hgmp.mrc.ac.uk 925826065 29346 193.60.84.160 (4 May 1999 13:54:25 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 4 May 1999 13:54:25 GMT X-Newsreader: Gnus v5.5/Emacs 20.2 Lines: 32 Dr Thon de Boer writes: > I'm trying to index the FSSP database and i get a strange 'error' > message when I do a SRSCHECK -l FSSP : > > library "FSSP" had previously 1531, now 1627 entries > ======> must build indices for library "FSSP" > > When I then do a SRSUPDATE and check the database again, I get the same > error. > I've even tried deleting the indices all together and the error still > comes up (after the second SRSCHECK that is). > > Does anyone know what is going on here ? > > I think the numbers come from a descrepancy between the number of keys > indexed and the number of entry references, since the two numer (1531 > and 1627) come up in the info bit on the FSSP page. Something to do with 96 entries failing to parse correctly. I have a fix in our fssp.is file that should work (but we have not updated FSSP recently). DSSP sometimes suffers from the same problems. Or it could be a file naming problem. Check fssp.i to see what file name wildcard you are using and check what that finds in the FSSP data directory. -- ---------------------------------------------------------------------- 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 Tue May 04 15:22:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!colt.net!newspeer.clara.net!news.clara.net!uknet!nntp.news.uk.psi.net!goya.lionbio.co.uk!not-for-mail From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: Inconsistent number of entries error in SRS5.1 Date: Tue, 04 May 1999 16:55:18 +0100 Organization: Lion Bioscience Message-ID: <372F1866.753C73C8@lionbio.co.uk> References: <372ED6CB.6DA87F11@hgmp.mrc.ac.uk> NNTP-Posting-Host: dix.lionbio.co.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en Lines: 49 Dr Thon de Boer wrote: > > Hi, > > I'm trying to index the FSSP database and i get a strange 'error' > message when I do a SRSCHECK -l FSSP : > > library "FSSP" had previously 1531, now 1627 entries > ======> must build indices for library "FSSP" > > When I then do a SRSUPDATE and check the database again, I get the same > error. > I've even tried deleting the indices all together and the error still > comes up (after the second SRSCHECK that is). > > Does anyone know what is going on here ? > > I think the numbers come from a descrepancy between the number of keys > indexed and the number of entry references, since the two numer (1531 > and 1627) come up in the info bit on the FSSP page. > > Thanks, Thon de Boer > HGMP-RC, Hinxton That is probably due to some fssp entries which are not conforming to the correct format, and srs fails to pick up the id. Try: id: ~ {$In:[fields c:pdbid] $Out pre $Skip:1} x {$Wrt:[c:id s:$JobFile.name:name]} ~ as production for your id fields - so at least you will get an id for those files. (Not that also all kinds of other indexing errors may occur with those files - but at least srscheck will no longer complain) Cheers, Martin -- ----------------------------------------------------- Martin Hilbers Customer Support Specialist LION Bioscience Main: +44 (0) 1223 224 700 Sheraton House Phone: +44 (0) 1223 224 711 Castle Park Fax: +44 (0) 1223 224 701 Cambridge CB3 0AX UNITED KINGDOM Email:hilbers@lionbio.co.uk ----------------------------------------------------- From owner-srs@net.bio.net Wed May 05 05:00:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!intgwpad.nntp.telstra.net!news1.optus.net.au!optus!vrn.edu.au!news.swin.edu.au!news.unimelb.edu.au!wehi.edu.au!wehi!janice From: janice@wehi.edu.au (Janice Coventry, Walter and Eliza Hall Institute) Newsgroups: bionet.software.srs Subject: Re: Inconsistent number of entries error in SRS5.1 Date: 5 May 99 15:54:02 +1000 Organization: Walter & Eliza Hall Institute Lines: 33 Message-ID: <1999May5.155402@wehi> References: <372ED6CB.6DA87F11@hgmp.mrc.ac.uk> NNTP-Posting-Host: wehiu.wehi.edu.au X-Trace: wehid.wehi.EDU.AU 925883672 16117 (None) 128.250.252.27 X-Complaints-To: newsmaster@wehi.edu.au In article <372ED6CB.6DA87F11@hgmp.mrc.ac.uk>, Dr Thon de Boer writes: > Hi, > > I'm trying to index the FSSP database and i get a strange 'error' > message when I do a SRSCHECK -l FSSP : > > library "FSSP" had previously 1531, now 1627 entries > ======> must build indices for library "FSSP" > > When I then do a SRSUPDATE and check the database again, I get the same > error. > I've even tried deleting the indices all together and the error still > comes up (after the second SRSCHECK that is). > > Does anyone know what is going on here ? > > I think the numbers come from a descrepancy between the number of keys > indexed and the number of entry references, since the two numer (1531 > and 1627) come up in the info bit on the FSSP page. > > Thanks, Thon de Boer > HGMP-RC, Hinxton > > I have experienced a similar problem with FSSP though the difference between the numbers if much less (only nine), I have tracked my problem down to some fssp files which do not have anything in the pdbid field, for example, 1bgh.fssp. I think perhaps your problem may be different as the discrepancy I experience is much smaller. Janice which do not From owner-srs@net.bio.net Wed May 05 11:54:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!newsfeed.icl.net!newsfeed.nacamar.de!fu-berlin.de!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Dr Thon de Boer Newsgroups: bionet.software.srs Subject: Re: Inconsistent number of entries error in SRS5.1 Date: Wed, 05 May 1999 13:47:47 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Message-ID: <37303DF3.60DB6B83@hgmp.mrc.ac.uk> References: <372ED6CB.6DA87F11@hgmp.mrc.ac.uk> <372F1866.753C73C8@lionbio.co.uk> NNTP-Posting-Host: lutetium.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 925908563 24457 193.62.192.71 (5 May 1999 12:49:23 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 5 May 1999 12:49:23 GMT X-Mailer: Mozilla 4.51 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en Lines: 29 Martin Hilbers wrote: > Dr Thon de Boer wrote: > > > > Hi, > > > > I'm trying to index the FSSP database and i get a strange 'error' > > message when I do a SRSCHECK -l FSSP : > > > > library "FSSP" had previously 1531, now 1627 entries > > ======> must build indices for library "FSSP" > > That is probably due to some fssp entries which are not conforming to > the > correct format, and srs fails to pick up the id. Try: > > id: ~ {$In:[fields c:pdbid] $Out pre $Skip:1} > x {$Wrt:[c:id s:$JobFile.name:name]} ~ > > as production for your id fields - so at least you will get an id for > those files. (Not that also all kinds of other indexing errors may occur > with those files - but at least srscheck will no longer complain) > Thanks very much martin, It worked...srscheck is silent now ;-) Thon From owner-srs@net.bio.net Wed May 12 10:57:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!unlisys!news.snafu.de!fu-berlin.de!server1.netnews.ja.net!hgmp.mrc.ac.uk!pegasus.csx.cam.ac.uk!not-for-mail From: timc@chiark.greenend.org.uk (Tim Cutts) Newsgroups: bionet.software.srs Subject: LocusLink Date: 12 May 1999 12:48:34 +0100 (BST) Organization: Linux Unlimited Lines: 9 Message-ID: NNTP-Posting-Host: rrw1000.sel.cam.ac.uk Originator: timc@news.chiark.greenend.org.uk ([127.0.0.1]) Has anyone written a parser for the LocusLink files? (http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html) The tabe delimited file LL.out looks easy, but the other file, which contains the most information, looks a lot harder. Has anyone already done this? Tim. From owner-srs@net.bio.net Fri May 14 10:24:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!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: LocusLink Date: Fri, 14 May 1999 12:18:53 +0100 Organization: EMBL - EBI Message-ID: <373C069D.3E57D698@ebi.ac.uk> References: 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 926680733 15053 193.62.196.199 (14 May 1999 11:18:53 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 14 May 1999 11:18:53 GMT To: Tim Cutts X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en Lines: 24 Tim Cutts wrote: > > Has anyone written a parser for the LocusLink files? > (http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html) > > The tabe delimited file LL.out looks easy, but the other file, which > contains the most information, looks a lot harder. Has anyone already > done this? > > Tim. No. Not yet. but I'll have a go soon. -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 Fri May 14 17:35:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!news-feed.inet.tele.dk!bofh.vszbr.cz!newsfeed.tli.de!newsfeed.nacamar.de!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.gwdg.de!not-for-mail From: Steffen Schmidt Newsgroups: bionet.software.srs Subject: BRENDA Date: Fri, 14 May 1999 19:27:58 +0200 Organization: GWDG, Goettingen Lines: 33 Message-ID: <373C5D1E.BFDF98F7@Uni-MolGen.gwdg.de> NNTP-Posting-Host: 134.76.70.65 Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------7D7B9D8594A17839E6F93965" X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en This is a multi-part message in MIME format. --------------7D7B9D8594A17839E6F93965 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, does anybody know why the entries of the enzymatic activity in BRENDA with negativ (always -999) values? --------------7D7B9D8594A17839E6F93965 Content-Type: text/x-vcard; charset=us-ascii; name="sschmid2.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Steffen Schmidt Content-Disposition: attachment; filename="sschmid2.vcf" begin:vcard n:Schmidt;Steffen tel;work:Arbeitsgruppe PD Dr. R. Sterner x-mozilla-html:FALSE url:http://www.gwdg.de/~sschmid3 org:Institut für Mikrobiologie und Genetik;Abteilung für molekulare Genetik und präparative Molekularbiologie adr:;;Grisebachstr. 8;37077 Göttingen;;; version:2.1 email;internet:sschmid2@Uni-MolGen.gwdg.de title:Georg-August Universität Göttingen fn:Steffen Schmidt end:vcard --------------7D7B9D8594A17839E6F93965-- From owner-srs@net.bio.net Tue May 18 07:33:00 1999 Path: biosci!COMPUSERVE.COM!23367.702 From: 23367.702@COMPUSERVE.COM Newsgroups: bionet.software.srs Subject: THE RULES HAVE CHANGED! Date: 18 May 1999 01:33:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: <199905180833.BAA00743@net.bio.net> NNTP-Posting-Host: net.bio.net NET-DETECTIVE-4.0 "EASY WAY TO FIND OUT ANYTHING ABOUT ANYONE" http://3465215261/3568952145232/ NET DETECTIVE 4.0 TAKES YOU BEYOND WHAT SEARCH ENGINES CAN DO! 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CLICK HERE: http://3465215261/3568952145232/ Thanks, Gayle McNeil McNeil Software Security Software Developers Since 1995 REMOVES jason9091@excite.com From owner-srs@net.bio.net Wed May 19 07:41:00 1999 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!dispose.news.demon.net!demon!newspeer.clara.net!news.clara.net!newsfeed.nacamar.de!fu-berlin.de!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Heikki Lehvaslaiho Newsgroups: bionet.software.srs Subject: Re: LocusLink Date: Wed, 19 May 1999 09:36:08 +0100 Organization: EMBL - EBI Message-ID: <374277F8.6486D250@ebi.ac.uk> References: <373C069D.3E57D698@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 927102968 21148 193.62.196.199 (19 May 1999 08:36:08 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 19 May 1999 08:36:08 GMT To: Tim Cutts X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX64 6.2 IP28) X-Accept-Language: en Lines: 66 Heikki Lehvaslaiho wrote: > > Tim Cutts wrote: > > > > Has anyone written a parser for the LocusLink files? > > (http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html) > > > > The tabe delimited file LL.out looks easy, but the other file, which > > contains the most information, looks a lot harder. Has anyone already > > done this? > > > > Tim. > > No. Not yet. but I'll have a go soon. It's done. have a look at: http://srs.ebi.ac.uk/srs5bin/cgi-bin/wgetz?-fun+PageQueryForm+-l+LOCUSLINK I had to modify the field structure quite a bit to have a nice listing, but that is done at runtime so does not matter. The following is relevant only if you want ot copy the parsers into your own server: In addition to creating the normal .i, .is and .it files, I put two of $hrefs into srsgen.i: # general entrez link #db= m for medline, n for nucleotide, p for protein # t for structure, c gor genome #good defaults: form=6 & Dopt=g $href:[entrezR link: |%s\ ] $href:[unigeneR link:|%s ] Also, to get a default view that somewhat duplicates NCBI's listing, I added the following definition into views.i: LocusLink_View:$View:[LocusLink root:$Vlib:@LOCUSLINK_DB rootFields:{ $VField:@DF_GeneName $VField:@DF_Description $VField:@DF_ChrLocation $VField:@DF_LINK } ] Let me know if there is something I missed, -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 May 19 08:00:00 1999 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 May 1999 02:00:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199905190900.CAA07969@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 Thu May 20 08:05:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!arclight.uoregon.edu!wn4feed!worldnet.att.net!128.230.129.106!news.maxwell.syr.edu!news.belnet.be!news.rediris.es!news.uam.es!not-for-mail From: jr@cnb.uam.es (José R. Valverde) Newsgroups: bionet.software.srs Subject: EMBnet course Date: 20 May 1999 08:55:45 GMT Organization: EMBnet/CNB Lines: 54 Message-ID: <7i0imh$9lr$3@acebo.sdi.uam.es> NNTP-Posting-Host: foxtrot.cnb.uam.es Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: acebo.sdi.uam.es 927190545 9915 150.244.23.5 (20 May 1999 08:55:45 GMT) X-Complaints-To: abuse@uam.es NNTP-Posting-Date: 20 May 1999 08:55:45 GMT X-Newsreader: knews 1.0b.1 EMBnet/CNB, the Spanish National EMBnet node is pleased to announce the EMBnet International course on Bioinformatics for System Managers EMBnet/CNB 05-09 October 1999 Location: The course will be held at the Spanish EMBnet node in CNB-CSIC and at AdI of the U. Autónoma de Madrid, Cantoblanco, Madrid, SPAIN. Contents: An introduction to Bioinformatics for computer scientists describing the basics of Bioinformatics, setup and maintenance of a Bioinformatics facility, commonly used tools and databases, and including both theoretical and practical lectures. Speakers: * Martin Bishop (HGMP-RC, UK) * Marc Colet (BEN - Belgian EMBnet node) * Peter Rice (HGMP-RC, UK) * José R. Valverde (EMBnet/CNB) Assistance: A limited number students will be accepted. Selection will be based on curriculum, student motivation and utility of the course for the applicants. Cost: * 601 Euro (100000 ESP) for academic students * 1202 Euro (200000 ESP) for commercial students Application: Send a sort curriculum, a short description of your interests and motivation for attending the course to the contact address below before 30-June-1999. Contact address: For details on the course, submitting applications, or any other queries, please use any of these addresses: * Mail: EMBnet/CNB. Campus UAM. Cantoblanco, 28049. Madrid - SPAIN * e-mail: training@es.embnet.org * Fax: +34 915854505 (addressed to EMBnet/CNB) * WWW: http://www.es.embnet.org/Services/training/smc99/ Details: are available on our WWW server and upon request. This course is the result of cooperation between: [EMBnet/CNB] [CNB] [CSIC] [ADI - UAM] [HGMR-RC (UK)] [BEN (BE)] From owner-srs@net.bio.net Fri May 21 13:03:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server6.netnews.ja.net!server4.netnews.ja.net!server2.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: bvaughan@hgmp.dot.mrc.dot.ac.dot.uk (Bren Vaughan) Newsgroups: bionet.software.srs Subject: SRS and Linux.... Date: 21 May 1999 13:57:44 GMT Organization: HGMP Resource Center Lines: 24 Message-ID: <7i3ooo$gmc$3@niobium.hgmp.mrc.ac.uk> Reply-To: bvaughan@hgmp.dot.mrc.dot.ac.dot.uk NNTP-Posting-Host: thorium.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Trace: niobium.hgmp.mrc.ac.uk 927295064 17100 193.62.192.90 (21 May 1999 13:57:44 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 21 May 1999 13:57:44 GMT X-Newsreader: knews 1.0b.1 Hi, I am experiencing some strange behaviour with SRS on Linux. Basically, I have recently installed SRS on Red Hat Linux 5.2 and all seemed OK. However, I have a simplified HTML search interface which calls wgetz and this works fine on Solaris but when I use the same HTML on Linux it performs the search and displays the results as per normal, but when I click on an actual entry, it gives me an error saying e.g. file could not be opened "ZGe1BW9BV" Now when I use the full SRS interface on Linux there is no problem. I had a look and what is happening is that the simple search does create the temporary directory ZGe1BW9BV, but does not seem to create a user.par file there. If I do a full search and copy across the user.par file it fixes the problem but obviously this is not a solution. Is there any obvious reason why this should work on Solaris and not on Linux? thanks, Bren Vaughan From owner-srs@net.bio.net Tue May 25 16:35:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: momanning@my-dejanews.com Newsgroups: bionet.software.srs Subject: SequenceSimple for PDB Date: Tue, 25 May 1999 17:20:23 GMT Organization: Deja.com - Share what you know. Learn what you don't. Lines: 12 Message-ID: <7iem4j$52d$1@nnrp1.deja.com> NNTP-Posting-Host: 146.202.25.29 X-Article-Creation-Date: Tue May 25 16:53:17 1999 GMT X-Http-User-Agent: Mozilla/4.0 (compatible; MSIE 4.01; Windows NT) X-Http-Proxy: 1.0 x25.deja.com:80 (Squid/1.1.22) for client 146.202.25.29 would like to have a view that will give me a short description line for PDB in the same way that " -view SequenceSimple" does for genbank and swissprot. has anyone written or know of such a view? thanks, Maurice --== Sent via Deja.com http://www.deja.com/ ==-- ---Share what you know. Learn what you don't.--- From owner-srs@net.bio.net Tue May 25 19:48:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!news-stock.gip.net!news.gsl.net!gip.net!newssvt07.tk!nspixp2!wnoc-tyo-news!news.join.ad.jp!news-sv.sinet!villon.nig.ac.jp!mkikuchi From: mkikuchi@genes.nig.ac.jp (Masayuki Kikuchi) Newsgroups: bionet.software.srs Subject: How to get NICEDOM database Date: 24 May 1999 08:28:17 GMT Organization: National Institute of Genetics, Japan. Lines: 10 Message-ID: <7ib2j1$mgq$1@villon.nig.ac.jp> NNTP-Posting-Host: wolf.genes.nig.ac.jp X-Newsreader: mnews [version 1.21PL5] 1999-04/04(Sun) Dear SRS managers, I would like to know how to get(make) NICEDOM database for SRS. I searched the EBI ftp server(ftp://ftp.ebi.ac.uk/pub/databases/prodom/), but could not find it. Sincerely yours, -- DNA Data Bank of Japan Masayuki Kikuchi (mkikuchi@genes.nig.ac.jp) From owner-srs@net.bio.net Tue May 25 21:55:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!logbridge.uoregon.edu!newspeer1.nac.net!news.maxwell.syr.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail From: momanning@my-dejanews.com Newsgroups: bionet.software.srs Subject: new genbank parser Date: Tue, 25 May 1999 22:37:21 GMT Organization: Deja.com - Share what you know. Learn what you don't. Lines: 6 Message-ID: <7if8n1$k0b$1@nnrp1.deja.com> NNTP-Posting-Host: 146.202.25.29 X-Article-Creation-Date: Tue May 25 22:37:21 1999 GMT X-Http-User-Agent: Mozilla/4.05 [en] (WinNT; I) X-Http-Proxy: 1.0 x29.deja.com:80 (Squid/1.1.22) for client 146.202.25.29 there is now a VERSION line in genbank. is there an updated parser for this mod? (orig format) --== Sent via Deja.com http://www.deja.com/ ==-- ---Share what you know. Learn what you don't.--- From owner-srs@net.bio.net Thu May 27 06:43:00 1999 Path: biosci!rutgers!nntp.upenn.edu!newsserver.jvnc.net!198.138.0.5!newshub.northeast.verio.net!newspeer.monmouth.com!newsswitch.lcs.mit.edu!newsfeed.cwix.com!202.54.1.25!news.vsnl.net.in!not-for-mail From: "Anisha" Newsgroups: bionet.software.srs Subject: YOUNG BEAUTIFUL MODEL AVAILABLE Date: Thu, 27 May 1999 13:05:46 +0530 Organization: VSNL Lines: 175 Message-ID: <7ik0k4$jem$1@news.vsnl.net.in> NNTP-Posting-Host: ppp-185-238.bng.vsnl.net.in Mime-Version: 1.0 Content-Type: multipart/related; boundary="----=_NextPart_000_026C_01BEA841.A2A956E0"; type="multipart/alternative" X-Trace: news.vsnl.net.in 927827396 19926 203.197.185.238 (27 May 1999 17:49:56 GMT) X-Complaints-To: postmaster@news.vsnl.net.in NNTP-Posting-Date: 27 May 1999 17:49:56 GMT X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 This is a multi-part message in MIME format. ------=_NextPart_000_026C_01BEA841.A2A956E0 Content-Type: multipart/alternative; boundary="----=_NextPart_001_026D_01BEA841.A2A956E0" ------=_NextPart_001_026D_01BEA841.A2A956E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi!=20 My name is Anisha.=20 I am 24 yrs old beautiful model from Paris, I would like to accompany you (discerning gentlemen) for dining, entertainment and pleasure in Europe.=20 I've long black hair and dark eyes,a slim good figure with beautiful = face=20 I am well educated, sociable, polite and fun to be with.=20 If you'd like to arrange a liaison, you can contact me at : =20 ------=_NextPart_001_026D_01BEA841.A2A956E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 

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AFFFFABRRRQB/9k= ------=_NextPart_000_026C_01BEA841.A2A956E0-- From owner-srs@net.bio.net Thu May 27 09:38:00 1999 Path: biosci!news.stanford.edu!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!newsfeed.nacamar.de!newsfeed.nacamar.de!fu-berlin.de!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Dr Thon de Boer Newsgroups: bionet.software.srs Subject: Is there a maximum string length for patternmatching ? Date: Thu, 27 May 1999 11:30:02 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Message-ID: <374D1EA9.71036973@hgmp.mrc.ac.uk> NNTP-Posting-Host: lutetium.hgmp.mrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 927801130 21024 193.62.192.71 (27 May 1999 10:32:10 GMT) X-Complaints-To: news@hgmp.mrc.ac.uk NNTP-Posting-Date: 27 May 1999 10:32:10 GMT X-Mailer: Mozilla 4.6 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en Lines: 18 Hi, I am trying to write a parser in SRS5.1 for a FASTA formatted file and did succeed to a certain extent, but I seem to be running into some limits. The parser trips over a line with a length of 2943 characters.....It goes into a infinite loop and doesnlt parse anything anymore.... I have instructed the maxline parameter in the filetype definition in SRSGEN.I to be 10000 so this can't be the problem. Is there a maximum length of the string that can be parsed by patternmatching ? Is this a hardcoded setting or is there some parameter I can set ? Thanks, Thon de Boer HGMP-RC, Hinxtion From owner-srs@net.bio.net Fri May 28 15:14:00 1999 Path: biosci!pravda.ucr.edu!ihnp4.ucsd.edu!newsfeed.berkeley.edu!news-peer.gip.net!news-penn.gip.net!news.gsl.net!gip.net!iafrica.com!nnrp01.iafrica.com!nnrp01.iafrica.com!not-for-mail From: Springbok@Eudoramail.com Newsgroups: bionet.software.srs Subject: IAMSTUCK.COM - Solve your software problems Date: Fri, 28 May 1999 16:08:16 GMT Organization: UUNET Internet Africa Lines: 3 Message-ID: <374eb206.173960554@ct-news.iafrica.com> NNTP-Posting-Host: cpt-ts531-204.mweb.co.za X-Trace: nnrp01.ops.uunet.co.za 927907692 54503 196.2.56.204 (28 May 1999 16:08:12 GMT) X-Complaints-To: abuse@iafrica.com NNTP-Posting-Date: 28 May 1999 16:08:12 GMT X-Newsreader: Forte Free Agent 1.11/32.235 This site - IAMSTUCK.COM was great for solving my software problems. From owner-srs@net.bio.net Sat May 29 08:07:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!dispose.news.demon.net!demon!ayres.ftech.net!news.ftech.net!peer.news.nildram.co.uk!newsfeed.wirehub.nl!news.algonet.se!algonet!masternews.telia.net!newsfeed.bcn.ttd.net!news.mad.ttd.net!not-for-mail From: tarifa@justa.ya (ThunderBoy. ) Newsgroups: bionet.software.srs Subject: Looking for cosmos 1.61 Date: Sat, 29 May 1999 09:00:33 GMT Organization: PEPSI MAX. Message-ID: <374ec186.2752285@news.interferr.com> Reply-To: capi@interferr.com NNTP-Posting-Host: 192.240.77.195.in-addr.arpa X-Newsreader: Forte Free Agent 1.11/32.235 Cache-Post-Path: cache0!unknown@195-57-245-19.usr.ans.es X-Cache: nntpcache 2.3.2 (see http://www.nntpcache.org/) Lines: 13 I´m trying to find Cosmos 1.61 or crack for this. Please send me some information. capi@interferr.com From owner-srs@net.bio.net Sun May 30 18:37:00 1999 Path: biosci!DELTA.BC1.CA!puibua93 From: puibua93@DELTA.BC1.CA (buiuipe) Newsgroups: bionet.software.srs Subject: Millions want SP now... Date: 30 May 1999 12:37:33 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 47 Sender: daemon@net.bio.net Distribution: world Message-ID: <199905303284QAA23645@guiyopl.studiotech.hu> NNTP-Posting-Host: net.bio.net (SP) COULD MAKE YOU A LOT OF MONEY! =================================== **Make Money Selling the next blockbuster software (SP)! **As far as we know, (SP) has no competition! **42 Million potential buyers on the Net! **SP's potential market is $8.4 BILLION! 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