From owner-srs@net.bio.net Sun May 03 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!europa.clark.net!194.162.162.196!newsfeed.nacamar.de!univ-lyon1.fr!not-for-mail From: "GB" Newsgroups: bionet.software.srs Subject: looking for some softwares.. Date: 4 May 1998 12:45:43 GMT Organization: C.I.S.M. Universite Claude Bernard Lyon 1 / INSA de Lyon Lines: 7 Message-ID: <01bd775a$75334c20$78a539c2@pcbricca.lyon151.inserm.fr> NNTP-Posting-Host: pcbricca.lyon151.inserm.fr X-Newsreader: Microsoft Internet News 4.70.1155 Hello, I start being interested in nucleic acid sequences and manipulations and I wopuld appreciate to have an easy to use program for primer or oligonucleotide design running on a PC. Do anybody knows from I could download such a thing ? Thank you in advance Giampiero Bricca From owner-srs@net.bio.net Tue May 05 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newshub.northeast.verio.net!news-peer.gip.net!news-dc.gip.net!news.gsl.net!gip.net!news.belnet.be!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Re: SRS through GCG? Date: 6 May 1998 18:45:43 GMT Organization: Belgian EMBnet Node Lines: 26 Message-ID: <6iqb4n$197$1@mach.vub.ac.be> References: <6idftb$6t2$1@franklin.ljcrf.edu> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] It is possible to use the same indexes for lookup and the native SRS, since GCG 8 lookup, GCG 9 lookup, SRS 4 and SRS 5 use the same format for indexes. There are however two problems : - the lookup of GCG uses the sdl files of SRS 4, while SRS 5 uses a new kind of files (i and is Icarus files). Although you need only one version of the indexes, you would have to keep SRS 4 and SRS 5 in parallel or decide to use only the older SRS 4. If you decide to install SRS 5, you will need to do a lot of hacking to make sure that library names, library numbers and srsfield shortnames are consistently the same in the sdl and Icarus files. - Reinhard Doelz found a way to hack the code of GCG 8 lookup to make it work with indexes generated by SRS 4 and recently I made GCG 9 lookup work with the indexes generated by SRS 5. One thing to do was to make sure that lookup reads only indexes for Sequence databanks and not others. Unfortunately, GCG has become touchy about its source code and we are not allowed to make the modified code public. I have no experience with the opposite operation, to make the native SRS work with indexes generated by GCG, but it should be possible. Note that you would have an SRS without sequencerelated databanks and without links. Note also that there is a good reason for using SRS 5 rather than SRS 4/GCG : it indexes a lot faster ! So, forget about it or take your start on a road full of obstacles... Guy Bottu From owner-srs@net.bio.net Thu May 07 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!feed2.news.erols.com!erols!news.maxwell.syr.edu!newsfeed1.swip.net!seunet!news2.swip.net!inet-1.pnu.com!not-for-mail From: Staffan Bergh Newsgroups: bionet.software.srs Subject: Re: SRS through GCG? Date: 08 May 1998 17:06:53 +0200 Organization: Pharmacia & Upjohn Lines: 56 Message-ID: References: <6idftb$6t2$1@franklin.ljcrf.edu> <6iqb4n$197$1@mach.vub.ac.be> NNTP-Posting-Host: sgibest.sto.se.pnu.com X-Newsreader: Gnus v5.3/Emacs 19.34 gbottu@ben.vub.ac.be (Guy Bottu) writes: One solution to the problem would be to simply replace lookup with something that uses getz directly, e.g. a perl script. Even neater would be if there was a daemonized version of getz that could take it's input from a socket, so that you could use the srs indices on a remote machine. Has anyone done something along these lines? I've started on the lookup replacement and was thinking that I would write a perl wrapper for getz that I could then run as a daemon on the SRS server (since we have GCG and SRS on different machines), but if it already exists it would be a bit stupid to reinvent it ... Cheers /staffan ----------------------------------------------------------------------- Staffan Bergh Pharmacia & Upjohn, P14:5, SE-112 87 Stockholm, Sweden email: Staffan.Bergh@eu.pnu.com + Don't let that horse eat that violin phone: (int+46) 08 695 9884 + cried Chagall's mother fax: (int+46) 08 695 4084 + but he kept right on painting mobile: (int+46) 070 898 8829 + -- Lawrence Ferlinghetti > Guy Bottu said: > It is possible to use the same indexes for lookup and the native SRS, > since GCG 8 lookup, GCG 9 lookup, SRS 4 and SRS 5 use the same format > for indexes. > There are however two problems : > - the lookup of GCG uses the sdl files of SRS 4, while SRS 5 uses a new > kind of files (i and is Icarus files). Although you need only one > version of the indexes, you would have to keep SRS 4 and SRS 5 in > parallel or decide to use only the older SRS 4. If you decide to install > SRS 5, you will need to do a lot of hacking to make sure that library > names, library numbers and srsfield shortnames are consistently the > same in the sdl and Icarus files. > - Reinhard Doelz found a way to hack the code of GCG 8 lookup to make it > work with indexes generated by SRS 4 and recently I made GCG 9 lookup > work with the indexes generated by SRS 5. One thing to do was to make > sure that lookup reads only indexes for Sequence databanks and not > others. Unfortunately, GCG has become touchy about its source code and > we are not allowed to make the modified code public. I have no > experience with the opposite operation, to make the native SRS work with > indexes generated by GCG, but it should be possible. Note that you would > have an SRS without sequencerelated databanks and without links. Note > also that there is a good reason for using SRS 5 rather than SRS 4/GCG : > it indexes a lot faster ! > > So, forget about it or take your start on a road full of obstacles... > > Guy Bottu From owner-srs@net.bio.net Thu May 07 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gip.net!news.gsl.net!gip.net!newsfeed.nacamar.de!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Ewan Birney Newsgroups: bionet.software.srs Subject: Re: SRS through GCG? Date: Fri, 08 May 1998 17:07:08 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 32 Message-ID: <35532DAC.845@sanger.ac.uk> References: <6idftb$6t2$1@franklin.ljcrf.edu> <6iqb4n$197$1@mach.vub.ac.be> NNTP-Posting-Host: ics-sparc1.sanger.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5 sun4u) To: Staffan Bergh Staffan Bergh wrote: > > gbottu@ben.vub.ac.be (Guy Bottu) writes: > > One solution to the problem would be to simply replace lookup with > something that uses getz directly, e.g. a perl script. > > Even neater would be if there was a daemonized version of getz that > could take it's input from a socket, so that you could use the srs > indices on a remote machine. > > Has anyone done something along these lines? I've started on the > lookup replacement and was thinking that I would write a perl wrapper > for getz that I could then run as a daemon on the SRS server (since we > have GCG and SRS on different machines), but if it already exists it > would be a bit stupid to reinvent it ... > > Cheers /staffan Staffan - this would be good. I actually have always been wanting to get a cleaner Perl/XS type interface into the SRS internals but haven't got around getting over the energy barrier of understanding's SRS's API... (go on srsdev people, why not have a perl/XS interface?) Ewan Birney http://www.sanger.ac.uk/Users/birney/ From owner-srs@net.bio.net Tue May 12 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!news-peer-west.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!news-peer.gip.net!news.gsl.net!gip.net!newshub.northeast.verio.net!news-feed.inet.tele.dk!bofh.vszbr.cz!news.algonet.se!rill.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: [Q] Installing SRS5 Date: Wed, 13 May 1998 16:07:13 +0100 Organization: SEQNET Lines: 59 Distribution: bionet Message-ID: <3559B721.9CE38F7C@dl.ac.uk> References: <3559B3FA.FF6@genetique.uvsq.fr> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP12) Jean-Loup Risler wrote: > > Dear Gurus, > > I am trying to install SRS5.0.1 on my Dec AlphaServer 2100 running > DU4.0B. > > I have done what I should (I think) in the srsdb.i, embl.i, etc ... > files. > > Running srscheck and then srsupdate, I have consistently some > problems with the "new" databanks: emblnew, swissprotnew, sptremblnew. > > The building of the indices and/or the links for these banks fail > with a "segmentation fault" and a core dump. I can see no problem > with the "main" banks (embl, swissprot, sptrembl). > > Curiously, the "new" databanks are processed OK if I re-run srscheck > and srsupdate after having indexed the main banks. > srs still has a problem with databases sharing the same format - if you try updating a number of such databases (eq embl and emnew) in one go, it will only do the srsbuild for the first one, for the second it will try the "srsbuild -c" and "srsbuild -m", and try to build the links, but without the results of "srsbuild" these obviously fail. A workaround for this is to define separate formats for emblnew (EMNEW_FORMAT and EmNewFeatures_Format - or something like that) These formats are identical to the original ones. (At least this is what I did on our server) > Could it come from a bad parameter tuning of my machine? > > Finally, after having repeated some times the "srscheck-srsupdate" > cycle, everything seems to have been indexed OK. > > But now Netscape refuses to start a new SRS session with the > message "file could not be opened: /srs/tmp/1TZMo193nkD". > Apart from a trivial permission thing - I once spend half a day trying to find why I got this type of error and it turned out to be caused by a srs core-dump which had filled the disk.... (srs core dumps tend to be very large - or our disks very small..-) Cheers, martin -- ------------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/Person.asp?m.p.hilbers | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.seqnet.dl.ac.uk/ | ------------------------------------------------------------------- From owner-srs@net.bio.net Tue May 12 23:00:00 1998 Path: biosci!agate!arclight.uoregon.edu!news-out.internetmci.com!newsfeed.internetmci.com!209.95.128.196!news-nyc.telia.net!masternews.telia.net!fu-berlin.de!jussieu.fr!uvsq.fr!not-for-mail From: Jean-Loup Risler Newsgroups: bionet.software.srs Subject: [Q] Installing SRS5 Date: Wed, 13 May 1998 16:53:46 +0200 Organization: Universite de Versailles/St Quentin en Yvelines - France Lines: 39 Message-ID: <3559B3FA.FF6@genetique.uvsq.fr> NNTP-Posting-Host: genome.genetique.uvsq.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; OSF1 V4.0 alpha) Dear Gurus, I am trying to install SRS5.0.1 on my Dec AlphaServer 2100 running DU4.0B. I have done what I should (I think) in the srsdb.i, embl.i, etc ... files. Running srscheck and then srsupdate, I have consistently some problems with the "new" databanks: emblnew, swissprotnew, sptremblnew. The building of the indices and/or the links for these banks fail with a "segmentation fault" and a core dump. I can see no problem with the "main" banks (embl, swissprot, sptrembl). Curiously, the "new" databanks are processed OK if I re-run srscheck and srsupdate after having indexed the main banks. Could it come from a bad parameter tuning of my machine? Finally, after having repeated some times the "srscheck-srsupdate" cycle, everything seems to have been indexed OK. But now Netscape refuses to start a new SRS session with the message "file could not be opened: /srs/tmp/1TZMo193nkD". Can you help me? Jean-loup -- --------------------------------------------------------------------- | Jean-Loup Risler | | | Universite de Versailles | Tel: 33 (0)1 39 25 45 54 | | Lab. Genome et Informatique | Fax: 33 (0)1 39 25 45 69 | | Batiment Buffon | | | 45 Avenue des Etats-Unis | email: risler@genetique.uvsq.fr | | 78035 Versailles Cedex France | | --------------------------------------------------------------------- Les cerveaux sont malencontreusement pourvus d'estomac (J. Perrin) From owner-srs@net.bio.net Thu May 14 23:00:00 1998 Newsgroups: bionet.software.srs Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!surfnet.nl!barba.uci.kun.nl!sci.kun.nl!caos.kun.nl!root From: "K. Cuelenaere" Subject: Re: [Q] Installing SRS5 Content-Type: text/plain; charset=us-ascii Message-ID: <355C48CB.31DF@caos.kun.nl> Sender: root@caos.kun.nl (System PRIVILEGED Account) NNTP-Posting-Host: cammsg11.caos.kun.nl Content-Transfer-Encoding: 7bit Cc: koenc@caos.kun.nl Organization: CAOS/CAMM Center References: <3559B3FA.FF6@genetique.uvsq.fr> <3559B721.9CE38F7C@dl.ac.uk> Mime-Version: 1.0 Date: Fri, 15 May 1998 13:53:15 GMT X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 6.2 IP22) Lines: 40 Martin Hilbers wrote: > srs still has a problem with databases sharing the same format - if you > try updating a number of such databases (eq embl and emnew) in one > go, it will only do the srsbuild for the first one, for the second > it will try the "srsbuild -c" and "srsbuild -m", and try to build > the links, but without the results of "srsbuild" these obviously fail. > A workaround for this is to define separate formats for emblnew > (EMNEW_FORMAT and EmNewFeatures_Format - or something like that) > These formats are identical to the original ones. > > (At least this is what I did on our server) That's a good workaround Martin. Do you perhaps also know if something like this can be done: EMNEW_FORMAT:@EMBL_FORMAT so using the EMBL_FORMAT (libformat) object for the creation of the EMNEW_FORMAT object... it doesn't work this way. Also, I've been trying things like $ParObj:[name:EMNEW_FORMAT set:($ParObj:[name:EMBL_FORMAT])] but that didn't work... so for the moment we've got 4 identical formats defined (EMBL_FORMAT, EMBL_EST_FORMAT, EMBLNEW_FORMAT, and EMBLNEW_EST_FORMAT) in embl.i ... but we can live with that. Groetjes, Koen. -------------------------------------------------------------- Koen Cuelenaere Email: koenc@caos.kun.nl CAOS/CAMM Center Phone: +31 24 3653383 University of Nijmegen Fax: +31 24 3652977 Toernooiveld 6525 ED Nijmegen The Netherlands URL: http://www.caos.kun.nl/ -------------------------------------------------------------- From owner-srs@net.bio.net Thu May 14 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!la-news-feed1.bbnplanet.com!news.bbnplanet.com!newsfeed1.earthlink.net!news-out.internetmci.com!newsfeed.internetmci.com!209.95.128.196!news-nyc.telia.net!masternews.telia.net!feed1.news.luth.se!luth.se!news-ge.switch.ch!news-fra1.dfn.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.tu-bs.de!rzlimes.gbf-braunschweig.de!not-for-mail From: "Thomas Heinemeyer" Newsgroups: bionet.software.srs Subject: TRANSFAC 3.4 Date: 15 May 1998 13:00:12 GMT Organization: Gesellschaft fuer Biotechnologische Forschung mbH Lines: 52 Message-ID: <01bd8000$c57ed1a0$db030101@cyber_tom> NNTP-Posting-Host: gen219.gbf-braunschweig.de X-Newsreader: Microsoft Internet News 4.70.1161 The TRANSFAC server now has made accessible the new release 3.4 of the TRANSFAC database (Heinemeyer et al., 1998, Nucleic Acids Res. 26:364-370): http://transfac.gbf.de/ TRANSFAC is a database on eukaryotic transcription factors and their binding sites. As new features, it visualizes the items of the feature list (FACTOR table) as well as element positions within regulatory regions (GENE table). Moreover, the data volume has increased comprising now 2376 FACTOR and 4945 SITE entries. The SRS 5.1.0 version on the TRANSFAC server also offers access to the databases TRRD (Transcription Regulatory Region Database, Institute of Cytology and Genetics [ICG], Novosibirsk, Russia; N. A. Kolchanov/A. Kel et al.) and to COMPEL, a database on composite elements (joint effort by ICG and GBF). Available at: http://transfac.gbf.de/srs5/ As many users know, the sequence information contained in the SITE table is used by PatSearch 1.1 to interactively scan DNA sequences for potential TF binding sites. This program is accessible at: http://transfac.gbf.de/cgi-bin/patSearch/patsearch.pl An updated library of matrices for transcription factor binding sites is provided which can be used for sequence analysis with MatInspector release 2.2 (Quandt et al., 1995, Nucleic Acids Res. 23:4878-4884). This tool is available at http://transfac.gbf.de/cgi-bin/matSearch/matsearch.pl or at http://www.gsf.de/BIODV/matinspector.html (Thomas Werner and coworkers). Please, forward this mail to your colleagues which may be interested in using these tools. On behalf of the TRANSFAC team: Edgar Wingender Thomas Heinemeyer GBF - Braunschweig, May 15, 1998 ------------------------------------------------------------ TRANSFAC-Team Tel.: +49(0)531 6181 427 Ges. f. Biotechn. Forsch. mbH Fax: +49(0)531 6181 266 Abt. Genomanalyse E-Mail: transfac@gbf.de Mascheroder Weg 1 http://transfac.gbf.de/ D-38124 Braunschweig From owner-srs@net.bio.net Thu May 14 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!158.43.192.17!rill.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: [Q] Installing SRS5 Date: Fri, 15 May 1998 16:13:11 +0100 Organization: SEQNET Lines: 56 Distribution: bionet Message-ID: <355C5B87.18D0DB80@dl.ac.uk> References: <3559B3FA.FF6@genetique.uvsq.fr> <3559B721.9CE38F7C@dl.ac.uk> <355C48CB.31DF@caos.kun.nl> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP12) K. Cuelenaere wrote: > > Martin Hilbers wrote: > > > srs still has a problem with databases sharing the same format - if you > > try updating a number of such databases (eq embl and emnew) in one > > go, it will only do the srsbuild for the first one, for the second > > it will try the "srsbuild -c" and "srsbuild -m", and try to build > > the links, but without the results of "srsbuild" these obviously fail. > > A workaround for this is to define separate formats for emblnew > > (EMNEW_FORMAT and EmNewFeatures_Format - or something like that) > > These formats are identical to the original ones. > > > > (At least this is what I did on our server) > > That's a good workaround Martin. Do you perhaps also know > if something like this can be done: > > EMNEW_FORMAT:@EMBL_FORMAT > > so using the EMBL_FORMAT (libformat) object for the > creation of the EMNEW_FORMAT object... it doesn't work > this way. Also, I've been trying things like > > $ParObj:[name:EMNEW_FORMAT set:($ParObj:[name:EMBL_FORMAT])] > > but that didn't work... > I have not tried that sort of things. I had a brief look at why srscheck goes wrong with this, but could not find anything obvious and just went for this brute force approach. > so for the moment we've got 4 identical formats defined > (EMBL_FORMAT, EMBL_EST_FORMAT, EMBLNEW_FORMAT, and EMBLNEW_EST_FORMAT) > in embl.i ... but we can live with that. > Don't forget - you need to do the same for the subentries (EmblFeatures_Format etc). And (completely unimportant detail) I did not put it all in embl.i, but gave each database its own .i file in which the format is declared - that has the advantage that there is a .i file to be retrieved from the database description page. Cheers, Martin -- ------------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/Person.asp?m.p.hilbers | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.seqnet.dl.ac.uk/ | ------------------------------------------------------------------- From owner-srs@net.bio.net Mon May 18 23:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 May 1998 02:00:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199805190900.CAA18079@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 May 26 23:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: EPD 54 new format Date: 27 May 1998 16:31:28 +0100 Organization: The Sanger Centre Lines: 21 Sender: pmr@unst.sanger.ac.uk Message-ID: NNTP-Posting-Host: unst.sanger.ac.uk X-Newsreader: Gnus v5.5/Emacs 20.2 There appears to be a new EPD format for release 54. I picked it up from ftp://ftp.epd.unil.ch/pub/databases/epd/ and updated the epd.i, epd.is and epd.it files. It is a much nicer format, though something strange is happening to the accession numbers. For example, the first entry can be E17001, EP17001 or EP017001 but there is nothing identical in the epd.dat and epd.blk files. Never mind, I faked it thanks to Icarus :-) I also indexed the .blk file as "EPDSEQ". The epd Icarus files are available from our SRS5 server as usual: http://www.sanger.ac.uk/srs5/ -- ---------------------------------------------------------------------- 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 26 23:00:00 1998 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!woodstock.news.demon.net!demon!dispose.news.demon.net!demon!nntp.news.xara.net!xara.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: David Kreil Newsgroups: bionet.software.srs Subject: Re: SRS through Perl or a 'demon'? Date: Wed, 27 May 1998 18:44:36 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Message-ID: <356C5103.F19DB964@my.browser> References: <6idftb$6t2$1@franklin.ljcrf.edu> <6iqb4n$197$1@mach.vub.ac.be> <35532DAC.845@sanger.ac.uk> NNTP-Posting-Host: circinus.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX64 6.2 IP25) To: Ewan Birney Lines: 58 Ewan Birney wrote: > Staffan Bergh wrote: > > > > gbottu@ben.vub.ac.be (Guy Bottu) writes: > > > > One solution to the problem would be to simply replace lookup with > > something that uses getz directly, e.g. a perl script. > > > > Even neater would be if there was a daemonized version of getz that > > could take it's input from a socket, so that you could use the srs > > indices on a remote machine. > > Staffan - this would be good. I actually have always been wanting to get > a cleaner > Perl/XS type interface into the SRS internals but haven't got around > getting over > the energy barrier of understanding's SRS's API... (go on srsdev people, > why not > have a perl/XS interface?) > > Ewan Birney > > http://www.sanger.ac.uk/Users/birney/ Re demon: Thierry Coupaye (coupaye@ebi.ac.uk) has been developing a CORBA object server for SRS. Other object servers would be as feasible and might (through the SRS object manager streams) even support server-side object assembly to client specifications Re perl: I have had a look at exporting the SRS C/Icarus API via Perl XS. Understanding the SRS C API is quite easy and everybody is welcome :-) There have been some nasty problems caused by Perl/SRS type conflicts (need to include headers from both). I got a `prototype' version running, all else is just plain straightforward work (but quite a bit of it). So if someone wants to go ahead, I'll be happy to assist, but don't expect me to do a complete Perl interface on my own in the near future. How much work this is exactly depends a lot at how tight an integration into the `Perl feel' you want. As far as I understood it, Thure would prefer an export of SRS objects into Perl name space with attribute access mapping to SRS Object attribute access, which means tied variables and/or hashes, which I am not into yet... Cheers, David. -- --------------------------------------------------------------------------- David Philip Kreil at the EMBL ("`-''-/").___..--''"`-._ European Bioinformatics Institute `6_ 6 ) `-. ( ).`-.__.`) Wellcome Trust Genome Campus (_Y_.)' ._ ) `._ `. ``-..-' Cambridge. Kreil@EBI.ac.UK _..`--'_..-_/ /--'_.' ,' ++44 1223 49-4663, fax -4468 (il),-'' (li),' ((!.-'