From owner-srs@net.bio.net Mon Jan 05 22:00:00 1998 From: luca.toldo@merck.de To: etzold@ebi.ac.uk,verde@ebi.ac.uk Subject: Re: SRS version 5.1.0 Date: Tue, 06 Jan 1998 07:21:20 -0600 Message-ID: <884091913.96403466@dejanews.com> Newsgroups: bionet.software.srs Organization: Deja News Posting Service Path: biosci!agate!logbridge.uoregon.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail References: <349F1559.F7B77CE2@ebi.ac.uk> X-Article-Creation-Date: Tue Jan 06 13:05:14 1998 GMT X-Authenticated-Sender: luca.toldo@merck.de X-Http-User-Agent: Mozilla/4.04 [en] (WinNT; I) via proxy gateway CERN-HTTPD/3.0 libwww/2.17 X-Originating-IP-Addr: 155.250.128.1 (wingate.merck.de) Lines: 23 In article <349F1559.F7B77CE2@ebi.ac.uk>, Thure Etzold wrote: > > Dear all, > > happy Christmas and lots of new features. Have fun! The best wishes of happy Christmas and happy new year 1998 to Thure, Giorgio and the entire SRS team at EBI, which is providing the Scientific Community with such a powerfull tool as SRS ! Best wishes to SRS5.1 to keep up with its preceding versions, and wishes for its outcomes ! Compliments again Dr. Luca Ida Giovanni TOLDO (Ph.D.) MERCK KGaA Darmstadt Germany -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-srs@net.bio.net Tue Jan 06 22:00:00 1998 From: luca.toldo@merck.de To: etzold@ebi.ac.uk Subject: Q&A: How to install SRS5.1.0 on a Netscape server Date: Wed, 07 Jan 1998 02:51:11 -0600 Message-ID: <884162458.1130168322@dejanews.com> Newsgroups: bionet.software.srs Organization: Deja News Posting Service Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Wed Jan 07 08:40:58 1998 GMT X-Authenticated-Sender: luca.toldo@merck.de X-Http-User-Agent: Mozilla/4.04 [en] (WinNT; I) via proxy gateway CERN-HTTPD/3.0 libwww/2.17 X-Originating-IP-Addr: 155.250.128.1 (wingate.merck.de) Lines: 70 It happens that not everybody is running the same version of the httpd, and it happens as well that Netscape Enterprise Server is a rather common httpd. What follows is a "how-to-install-srs-on-netscape-enterprise-server" that I communicated on the 23.04.97 to the SRS developers but that never made it into the official distribution since for what I understand they do not use the Netscape httpd server and therefore could not easily test it on their side. Please, notice that the following information is provided on an AS-IS basis, and you agree in using this information at your own risk (:->). 1) in obj.conf a) include the following object: (example below done assuming the full path to the home page be /usr/local/htdocs) ObjectType fn="force-type" type="magnus-internal-cgi" Service fn="send-cgi" b) include in the _default_ Object: (example below done assuming the full path to the srs install be /home/srs) NameTrans from="/srs5/" fn="pfx2dir" dir="/home/srs/srs/www" 2) place in /usr/local/htdocs the link to the /home/srs/srs/www and call it srs5: %ln -s /home/srs/srs/www /usr/local/htdocs/srs5 3) for matter of practice I then did the following but perhaps could be done also in a "cleaner" way: a) mkdir /usr/local/htdocs/srs5bin/cgi-bin b) cp /home/srs/srs/www/bin/wgetz /usr/local/htdocs/srs5bin/cgi-bin/wgetz Once those modifications to the obj.conf are manually done (unfortunately this process cannot be performed through the web interface to the Netscape server), then send a hangup to the server and restart it (can as well use the web interface, reload the config files stop and start the server). Considerations -------------- Using the above mechanism, I maintain several versions of the SRS system running on the same machine and simply have each of them in a different directory e.g. /home/srs/srs5.0.4 /home/srs/srs5.0.5 /home/srs/srs5.1.0 etc.. and the entire setup is pretty simple to manage ... Perhaps this information could be included in the SRS FAQ and/or in the message returned upon completion of %srsinstall www I do not consider this contribution as specially crucial but still, could save some time specially to new srs maintainers ... Regards, Compliments, and happy new year Dr. Luca I.G. TOLDO -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-srs@net.bio.net Tue Jan 06 22:00:00 1998 From: luca.toldo@merck.de To: etzold@ebi.ac.uk Subject: Q: Performance of SRS5.1.0 Date: Wed, 07 Jan 1998 04:01:11 -0600 Message-ID: <884166646.1201471495@dejanews.com> Newsgroups: bionet.software.srs Organization: Deja News Posting Service Path: biosci!daresbury!server5.netnews.ja.net!nntp.news.xara.net!xara.net!news.maxwell.syr.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Wed Jan 07 09:50:46 1998 GMT X-Authenticated-Sender: luca.toldo@merck.de X-Http-User-Agent: Mozilla/4.04 [en] (WinNT; I) via proxy gateway CERN-HTTPD/3.0 libwww/2.17 X-Originating-IP-Addr: 155.250.128.1 (wingate.merck.de) Lines: 62 Dear Colleagues, I was just wondering if benchmarks on the performance of the srsbuild process were available or were foreseen to be exploited. I agree that since the srsbuild is relying on the icarus scripts which can be changed at any site appropriately, at least theoretically it could be troublesome to compare indexing performance. Moreover, since the indexing time is certainly dependent upon the size and the format of the database used there are various parameters to be taken into consideration. Certainly wether the data and index disks are local or remotely mounted that as well can make a difference .. as well as the machine load etc... Finally, since the index generation process is composed of several steps, the choice of which of the srsbuild atomic operations is also a variable. However, I think that is useful know quantitatively about the performance of the srsbuild step and its monitoring on wide range of platforms. Hereafter I provide an example of a record which one may consider as prototype for this kind of data-collection ... restricting to the very first srsbuild command launched, the one which is launched with the parameters: srsbuild XXXXX -xdir XXX: -odir XXX: -s unix -nn --------------------------- A) Hardware parameters Processor type: CPU speed: data location: index location: B) Operating System information Operating System Name: Operating System Version: C) Database specific information Database: Format: DBRelease: SRSRelease: D) Performance real cpu time: user cpu time: sys cpu time: ------------------------ Since certain Organizations could feel that this data contain proprietary information, the report could be then "anonymized" by the SRS maintainers, which each of us trust fully. This is just a suggestion, which hope will stimulate discussion and actions on this important aspect, which fits into the general area of performance in biocomputing... regards and compliments Dr. Luca I.G. TOLDO -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-srs@net.bio.net Thu Jan 08 22:00:00 1998 From: luca.toldo@merck.de To: etzold@ebi.ac.uk Subject: BUG+ Q.&A.: How to build offline indexes with SRS 5.1.0 Date: Fri, 09 Jan 1998 09:01:17 -0600 Message-ID: <884357601.1744961551@dejanews.com> Newsgroups: bionet.software.srs Organization: Deja News Posting Service Path: biosci!daresbury!uninett.no!news.algonet.se!newsfeed.direct.ca!logbridge.uoregon.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Fri Jan 09 14:53:21 1998 GMT X-Authenticated-Sender: luca.toldo@merck.de X-Http-User-Agent: Mozilla/4.04 [en] (WinNT; I) via proxy gateway CERN-HTTPD/3.0 libwww/2.17 X-Originating-IP-Addr: 155.250.128.1 (wingate.merck.de) Lines: 53 Dear SRS bionet-ters, I hope each of you had already time to investigate on the great contents of the latest version of SRS 5.1.0 ! Really a nice piece of work what the brilliant Team coordinated by Thure Etzold did recently. We should all be grateful to them for their really useful tool ! Hereafter I would like to inform you of a really minor inconvenient which I just encountered right now while exploring for the first time the -off flag in srscheck and srsupdate . You are perfectly aware that with the version 5.1.0 is possible to have offline index generation so that one could build indexes for different versions of the flat files and then move the flat file and the indexes at the same time to the new location. This is a really GREAT possibility that the SRS team did since infact it was a current problem when large database updates where happening ... Now, the problem is that after one has generated the appropriate srsupdate with the command %srscheck -off then launching the srsupdate will result in a SRSICA error "error: file could not be opened, "SRSOFFINX:..." followed by a bunch of srsupdate core dumps (exactely one for each invokation of srsbuild in the srsupdate script minus 1). The reason for that is that there is an inconsistency between the content of the environment variable SRSOFFINX and what is distributed in the srs5.1.0 tar file. SRSOFFINX points to $SRSROOT/offindex but the tar archive instead upon untarring will generate the indexOff directory instead. The problem is very easily solved, therefore, by simply this command: mv $SRSROOT/indexOff $SRSROOT/offindex Infact, I have the feeling that the SRS developers _do_ want the directory be called offindex since it appears specifically both in each of the scripts: $SRSROOT/etc/templ-prep_srs $SRSROOT/etc/templ-prep_srs.sh $SRSROOT/etc/prep_srs $SRSROOT/etc/prep_srs.sh Perhaps in the next release of the SRS5.1.0 tar the SRS developers will include this change by default... Regards and good SRS-sing ! Dr. Luca Ida Giovanni TOLDO (Ph.D.) -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-srs@net.bio.net Thu Jan 08 22:00:00 1998 From: luca.toldo@merck.de To: etzold@ebi.ac.uk Subject: Q.&A.:How To load proteinChart from the local Server Date: Fri, 09 Jan 1998 09:52:12 -0600 Message-ID: <884361014.1943797762@dejanews.com> Newsgroups: bionet.software.srs Organization: Deja News Posting Service Path: biosci!agate!arclight.uoregon.edu!logbridge.uoregon.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Fri Jan 09 15:50:14 1998 GMT X-Authenticated-Sender: luca.toldo@merck.de X-Http-User-Agent: Mozilla/4.04 [en] (WinNT; I) via proxy gateway CERN-HTTPD/3.0 libwww/2.17 X-Originating-IP-Addr: 155.250.128.1 (wingate.merck.de) Lines: 25 Dear Colleagues, A small tip when installing SRS5.1.0 and want to provide your users with the fastest feed with the marvellous proteinChart applet: 1.modify srsgen.i : in the codebase replace the call to ebi with your own machine and path ... 2. srssection In that way, when the applet is requested its classes (perhaps in the future a single jar ?) are downloaded from your server and not "across the world" and this could /should provide your users with a faster feedback (specially if your connection to internet is not very high). I would like to stress the point that the applet integration how had been reimplemented in version 5.1.0 is really GREAT since does not require any longer modifying the C source code and allows a much greater possibility to add applet viewers to the results of queries. My compliments for the excellent work done in Dr. Etzold's group ! regards Dr. Luca Ida Giovanni TOLDO (Ph.D.) -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-srs@net.bio.net Thu Jan 08 22:00:00 1998 From: luca.toldo@merck.de To: etzold@ebi.ac.uk Subject: BUG? srsupd.pl in version 5.1.0 Date: Fri, 09 Jan 1998 10:11:43 -0600 Message-ID: <884361966.1958346761@dejanews.com> Newsgroups: bionet.software.srs Organization: Deja News Posting Service Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!news.maxwell.syr.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Fri Jan 09 16:06:06 1998 GMT X-Authenticated-Sender: luca.toldo@merck.de X-Http-User-Agent: Mozilla/4.04 [en] (WinNT; I) via proxy gateway CERN-HTTPD/3.0 libwww/2.17 X-Originating-IP-Addr: 155.250.128.1 (wingate.merck.de) Lines: 17 Dear SRS managers, I have just noticed that etc/srsupd.pl distributed with srs5.1.0 contains also the following lines in addition to the ones in previous version srs5.0.5: $com = "srscheck -L pdbreport -o $srsupd; " . "$srsupd"; system ($com"); I was just wondering and I think that perhaps are a left-over from a local version of those scripts by the SRS developers ? Regards Dr. Luca Ida Giovanni TOLDO (Ph.D.) -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-srs@net.bio.net Thu Jan 08 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!news.maxwell.syr.edu!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Thure Etzold Newsgroups: bionet.software.srs Subject: revised srs5.1.0 Date: Fri, 09 Jan 1998 16:49:25 +0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 30 Message-ID: <34B65514.CC8FC09A@ebi.ac.uk> NNTP-Posting-Host: o2-3.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX 6.3 IP32) dear all, a few problems have been reported with version 5.1 that i have now fixed. I replaced the srs5.1.0.tar.gz with the new version file rather than making yet another release. The following problems have been solved: o The directory indexOff was renamed to offindex. o The tar file includes all documentation. o On some platforms the offline index directory was used as default. o OSF has a very low limit for the stack size, Solaris a low limit. on file descriptors which both affect indexing of large databanks. I included an unlimit command for stacksize and descriptors in the script generated by srscheck. o Merging very large indices crashed because of an allocation limit o Very large sequences could not be submitted because of an allocation limit. o TRANSFAC *.i files have been updated to the version at GBF/Braunschweig. o ...and some more mysterious bugs. many thanks for all who sent me error reports! regards Thure From owner-srs@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!agate!newsfeed.kornet.nm.kr!nntp.kreonet.re.kr!news.maxwell.syr.edu!Supernews60!supernews.com!Supernews69!not-for-mail From: "joedapro" Newsgroups: bionet.software.srs Subject: [[[ ADVERTISE YOUR BUSINESS AND MAKE MONEY $$$ ]]] Date: Sat, 10 Jan 1998 21:40:15 -0800 Organization: All USENET -- http://www.Supernews.com Lines: 34 Message-ID: <699l7g$gap$1@usenet87.supernews.com> NNTP-Posting-Host: 16729@207.211.62.211 X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 The PC-SUPER-ADVERTISER system is the most simple, powerful and affordable Money Making program in the world! $$$$$ It costs only $ 6 USD one time! $$$$$ ------------------------------- But wait ... before you pay, check out these features: - Advertising Space is our PRODUCT. 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Please contact Joe at: joedapro@hotmail.com Subject: PSA From owner-srs@net.bio.net Sat Jan 10 22:00:00 1998 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!128.230.129.106!news.maxwell.syr.edu!Supernews60!supernews.com!Supernews69!not-for-mail From: "joedapro" Newsgroups: bionet.software.srs Subject: [[[ Become a Software Distributor ! ]]] Date: Sat, 10 Jan 1998 21:42:11 -0800 Organization: All USENET -- http://www.Supernews.com Lines: 17 Message-ID: <699l98$dov$1@usenet76.supernews.com> NNTP-Posting-Host: 14111@207.211.62.211 X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Work from home with your PC distributing software and information all over the world via E-mail and the Internet. Our exclusive software PC-SUPER-MLM will give you all the information and tools you need to start your own Computer Based Business as a Software Distributor. 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Please contact Joe at: joedapro@hotmail.com Subject: PSM From owner-srs@net.bio.net Sun Jan 11 22:00:00 1998 From: luca.toldo@merck.de To: etzold@ebi.ac.uk,verde@ebi.ac.uk Subject: Re: Q.&A.:How To load proteinChart from the local Server Date: Mon, 12 Jan 1998 07:32:24 -0600 Message-ID: <884611493.1115553796@dejanews.com> Newsgroups: bionet.software.srs Organization: Deja News Posting Service Path: biosci!daresbury!uninett.no!newscore.univie.ac.at!news-raspail.gip.net!news-peer.gip.net!news.gsl.net!gip.net!news.maxwell.syr.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail References: <884361014.1943797762@dejanews.com> X-Article-Creation-Date: Mon Jan 12 13:24:54 1998 GMT X-Authenticated-Sender: luca.toldo@merck.de X-Http-User-Agent: Mozilla/4.04 [en] (WinNT; I) via proxy gateway CERN-HTTPD/3.0 libwww/2.17 X-Originating-IP-Addr: 155.250.128.1 (wingate.merck.de) Lines: 53 Dear Colleagues, in the new revision of srs5.1.0 that Dr. Etzold deposited, there is PLENTY of applet viewers ! That is really a great added value that Dr. Etzold and Giorgio Verde did recently and not very much appreciated yet by the SRS users ! We must be very grateful for the excellent work that Team is exploiting in EBI ! Here I would like just to suggest you a trick I find great: instead of placing all those single .class's that then soon or later will clash between different codes, pack up in a JAR all the classes needed and then use the archive command in the applet call. The speedup also in downloading is NOTICEABLE and the maintenance of your www server much improved ! Here is what I did, building the JAR using JDK1.1.5 on a Sun, and testing the applet successfully using as browser Netscape 4.0.4 on Windows NT: 1) Pack all the classes of an applet in a single compressed archive (in this example I built the jar for all the classes needed by AlignChartApplet) jar -cfM AlignChartApplet.jar *.class 2) Move the jar in the location where one wants to be fetched from, in this case I just place it in the $SRSWWW/java directory for sake of simplicity 3) Modify the icarus code so that it looks like this: | | archive="AlignChartApplet.jar" | | please notice that the "fullpath" should be replaced by the fullpath you have set for the srs server... obviously ! 4) srssection N.B. JAR are a feature of JDK1.1 and thus as long as a browser is JDK1.1 compliant then this feature as well should be supported. Hope this help, and perhaps could be included in the next SRS 5.1.X distrib ? Dr. Luca Ida Giovanni TOLDO (Ph.D.) -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-srs@net.bio.net Mon Jan 12 22:00:00 1998 From: luca.toldo@merck.de To: etzold@ebi.ac.uk,verde@ebi.ac.uk Subject: SRS5.1.0BUG? Q: Core dump when getz -vf ? Date: Tue, 13 Jan 1998 04:11:41 -0600 Message-ID: <884685990.1818165255@dejanews.com> Newsgroups: bionet.software.srs Organization: Deja News Posting Service Path: biosci!agate!arclight.uoregon.edu!news-xfer.netaxs.com!news.maxwell.syr.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Tue Jan 13 10:06:30 1998 GMT X-Authenticated-Sender: luca.toldo@merck.de X-Http-User-Agent: Mozilla/4.04 [en] (WinNT; I) via proxy gateway CERN-HTTPD/3.0 libwww/2.17 X-Originating-IP-Addr: 155.250.128.1 (wingate.merck.de) Lines: 18 Dear Bionet SRS mainainters, I was just wondering if you also are observing on IRIX 6.4 that SRS 5.1.0 getz produces a core dump when invoked with the following statement: getz '[swissprot-id:100k_RAT]' -vf cit The same command is not failing when operating on version 5.0.5 The swissprot indexes are fully working and operational otherwhise as could be checked by the wgetz properly working ... any feedback is welcome ! regards Dr. Luca Ida Giovanni TOLDO (Ph.D.) -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-srs@net.bio.net Tue Jan 13 22:00:00 1998 From: Tim Dudgeon Subject: Re: blast on srs5.1 Date: Wed, 14 Jan 1998 11:33:29 -0600 Message-ID: <884798805.425590801@dejanews.com> Newsgroups: bionet.software.srs Organization: British Biotech Path: biosci!agate!arclight.uoregon.edu!logbridge.uoregon.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Wed Jan 14 17:26:45 1998 GMT X-Authenticated-Sender: Tim Dudgeon X-Http-User-Agent: Mozilla/4.04 [en] (Win95; I) via proxy gateway CERN-HTTPD/3.0 libwww/2.17 X-Originating-IP-Addr: 193.130.179.2 (gateway.britbio.co.uk) Lines: 32 I've come across the solution to a previously posted message about blast output not being correctly parsed. I think the reason is that in SRS5.1 the blast output is now expected to be in the format that is derived from GCG's TOBLAST program rather than NCBI's *2fasta and setdb programs. The NCBI programs produce alignment headers that look like >SW|acc|id des whilst toblast generated headers like this >SW:id acc des where acc is the accession number, id is the entry id and des is the description line. So you either need to switch to using the GCG program to generate the blast databases, or to modify blast.is to read the NCBI generated data. Hope this helps. Tim -- Dr. Tim Dudgeon Phone: 01865 748747 British Biotech Pharmaceuticals Plc. FAX: 01865 717598 Watlington Road, Oxford, OX4 5LY, UK email: dudgeon@britbio.co.uk -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-srs@net.bio.net Tue Jan 13 22:00:00 1998 From: Tim Dudgeon Subject: Q&A: SRS5.1 and applications Date: Wed, 14 Jan 1998 11:12:33 -0600 Message-ID: <884797523.420872193@dejanews.com> Newsgroups: bionet.software.srs Organization: British Biotech Path: biosci!agate!arclight.uoregon.edu!logbridge.uoregon.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Wed Jan 14 17:05:24 1998 GMT X-Authenticated-Sender: Tim Dudgeon X-Http-User-Agent: Mozilla/4.04 [en] (Win95; I) via proxy gateway CERN-HTTPD/3.0 libwww/2.17 X-Originating-IP-Addr: 193.130.179.2 (gateway.britbio.co.uk) Lines: 41 In the light of previous postings to this newsgroup here is another minor fix to SRS5.1 that people might find useful. I've encountered a problem with configuring applications in SRS5.1 whereby you do not get all the applications that are configured in DNASEQ_DATA:$datatype.applications or PROTSEQ_DATA:$datatype.applications (defined in srsgen.i). For instance, if you include BLAST_APP and CLUSTALW_APP as your only applications you only get BLAST accessible in SRSWWW when you have the results of a protein database query. The reason is that PROTSEQ_DATA contains the following: PROTSEQ_DATA:$DataType:[ProteinSequence applications:{@?BLAST_APP @?SW_APP @?FASTA_APP @?CLUSTALW_APP @?PPSEARCH_APP } ] and as SW_APP is not defined ($libloc:[@SW_DB dir:"" indexDir:""] is commented out in srsdb.i) you only get BLAST, as any misssing application appears to prevent SRS 'reading on' to get the full list. To solve the problem remove any unused applications, i.e. PROTSEQ_DATA:$DataType:[ProteinSequence applications:{@?BLAST_APP @?CLUSTALW_APP } ] Hope this helps. Tim -- Dr. Tim Dudgeon Phone: 01865 748747 British Biotech Pharmaceuticals Plc. FAX: 01865 717598 Watlington Road, Oxford, OX4 5LY, UK email: dudgeon@britbio.co.uk -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-srs@net.bio.net Tue Jan 13 22:00:00 1998 Path: biosci!AMC.UVA.NL!a.h.vankampen From: a.h.vankampen@AMC.UVA.NL ("A.H. van kampen ", automat) Newsgroups: bionet.software.srs Subject: problem with srsbuild Date: 14 Jan 1998 04:53:00 -0800 Organization: Academic Medical Centre Amsterdam Lines: 31 Sender: daemon@net.bio.net Distribution: world Message-ID: <34BCB4F5.EAB66B14@amc.uva.nl> NNTP-Posting-Host: net.bio.net Dear, After building the database index of EMBL and PIR, the next command results in a 'segmentation fault': time srsbuild -i EMBL PIR -xdir 'SRSINX:' -odir 'SRSINX:' -s 'unix' Is this a known problem, or may this error bedue to a local (mis)configuration problem. Building the other links between databases does not give any problems. Regards, Antoine -- --------------------------------------- | Dr. Antoine H.C. van Kampen | | Academic Medical Center Amsterdam | | Cluster Research Support (ADIV-D01) | | Meibergdreef 9 | | 1105 AZ Amsterdam, the Netherlands | -------------------------------------------------| | Phone: ++31-20-5667096 | | Fax: ++31-20-5669020 | | Email: a.h.vankampen@amc.uva.nl | | www: http://www.amc.uva.nl/ | ------------------------------------- From owner-srs@net.bio.net Wed Jan 14 22:00:00 1998 Path: biosci!daresbury!uninett.no!news-feed.ifi.uio.no!recycled.news.erols.com!howland.erols.net!fastnet!uunet!in2.uu.net!munnari.OZ.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: Indexing with SRS5.1.0 Date: 15 Jan 98 15:57:04 +1000 Organization: Walter & Eliza Hall Institute Lines: 19 Message-ID: <1998Jan15.155704@wehi> NNTP-Posting-Host: wehiu.wehi.edu.au X-Trace: wehid.wehi.EDU.AU 884840374 12290 (None) 128.250.252.27 X-Complaints-To: newsmaster@wehi.edu.au Dear SRS Managers To upgrade to SRS5.1.0 is it necessary to reindex all your files? I have been testing some of my databases, when I try to getz entries from the old indices I have a core dump. Thanking you in anticipation Cheers, 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 14 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!feed1.news.luth.se!luth.se!Cabal.CESspool!bofh.vszbr.cz!news.maxwell.syr.edu!newsfeed.nacamar.de!univ-lyon1.fr!news.ujf-grenoble.fr!ciril.fr!u-strasbg.fr!news From: pingouin@chouchen.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software.srs Subject: Re: blast on srs5.1 Date: 15 Jan 1998 14:34:07 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 32 Message-ID: <69l6ov$h@news.u-strasbg.fr> References: <884798805.425590801@dejanews.com> <69keet$nrt@news.u-strasbg.fr> <34BE13D4.22C685A0@ebi.ac.uk> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: chouchen.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.8 In article <34BE13D4.22C685A0@ebi.ac.uk>, Thure Etzold writes: > The BLAST parser in the SRS distribution is for an older version of BLAST. I > would be really grateful for suggestions on a syntax that is suitable for > different > versions. I hope Fred will be able to. Just wait (if you can't, just hack DBWatcher C code from the current distribution : ftp://ftp-igbmc.u-strasbg.fr/pub ). In fact, I can't remember, if it works for all the Blast versions or only for the new ones. Can't check now. It would take less time waiting for Fred. > We use here at EBI indeed the GCG tools to generate the databanks > in > FASTA format. The parser that reads the title line of each BLAST entry should > be able to read a variety of formats but there is no way of telling whether > entry > name or accession number comes first. If you check the format of what you are currently reading? I think you can use, from both names, the one that share the format you expect, no? Just an idea... François. -- François Jeanmougin | groupe de bioinformatique / bioinformatics groupe tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France From owner-srs@net.bio.net Wed Jan 14 22:00:00 1998 Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: blast on srs5.1 Date: Thu, 15 Jan 1998 13:49:09 +0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 26 Message-ID: <34BE13D4.22C685A0@ebi.ac.uk> References: <884798805.425590801@dejanews.com> <69keet$nrt@news.u-strasbg.fr> NNTP-Posting-Host: o2-3.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX 6.3 IP32) Francois Jeanmougin wrote: > In article <884798805.425590801@dejanews.com>, > Tim Dudgeon writes: > > I've come across the solution to a previously posted message about blast > > output not being correctly parsed. > > I think it's not only an expected GCG ouput, it is also because > different version of blast gives different output. We experienced such > problems with DBWatcher... > If I remember correctly, Fred found a way to parse easily > both outputs, but, Fred is out this week, so he will confirm next > week if I'm right. The BLAST parser in the SRS distribution is for an older version of BLAST. I would be really grateful for suggestions on a syntax that is suitable for different versions. We use here at EBI indeed the GCG tools to generate the databanks in FASTA format. The parser that reads the title line of each BLAST entry should be able to read a variety of formats but there is no way of telling whether entry name or accession number comes first. Thure From owner-srs@net.bio.net Wed Jan 14 22:00:00 1998 From: Tim Dudgeon Subject: Re: Indexing with SRS5.1.0 Date: Thu, 15 Jan 1998 05:01:56 -0600 Message-ID: <884861929.1079246858@dejanews.com> Newsgroups: bionet.software.srs Organization: British Biotech Path: biosci!daresbury!uninett.no!news.algonet.se!newsfeed.direct.ca!news-peer.sprintlink.net!news.sprintlink.net!Sprint!news.maxwell.syr.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail References: <1998Jan15.155704@wehi> X-Article-Creation-Date: Thu Jan 15 10:58:49 1998 GMT X-Authenticated-Sender: Tim Dudgeon X-Http-User-Agent: Mozilla/4.04 [en] (Win95; I) via proxy gateway CERN-HTTPD/3.0 libwww/2.17 X-Originating-IP-Addr: 193.130.179.2 (gateway.britbio.co.uk) Lines: 22 In article <1998Jan15.155704@wehi>, janice@wehi.edu.au (Janice Coventry, Walter and Eliza Hall Institute) wrote: > To upgrade to SRS5.1.0 is it necessary to reindex all your files? > I have been testing some of my databases, when I try > to getz entries from the old indices I have a core dump. Do you need to reindex? Almost certainly yes. Quite a bit has changed under the skin in 5.1 (especially subentries), and all the *.i and *.is files have been changed to account for these changes. I would therefore be very suprised if old indexes were still compatible. Tim -- Dr. Tim Dudgeon Phone: 01865 748747 British Biotech Pharmaceuticals Plc. FAX: 01865 717598 Watlington Road, Oxford, OX4 5LY, UK email: dudgeon@britbio.co.uk -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-srs@net.bio.net Wed Jan 14 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!eru.mt.luth.se!feed1.news.luth.se!luth.se!news-ge.switch.ch!news-zh.switch.ch!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!eerie.fr!cnusc.fr!ciril.fr!u-strasbg.fr!news From: pingouin@chouchen.u-strasbg.fr (Francois Jeanmougin) Newsgroups: bionet.software.srs Subject: Re: blast on srs5.1 Date: 15 Jan 1998 07:39:09 GMT Organization: CRC - Universite Louis Pasteur - Strasbourg France Lines: 16 Message-ID: <69keet$nrt@news.u-strasbg.fr> References: <884798805.425590801@dejanews.com> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: chouchen.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: knews 0.9.8 In article <884798805.425590801@dejanews.com>, Tim Dudgeon writes: > I've come across the solution to a previously posted message about blast > output not being correctly parsed. I think it's not only an expected GCG ouput, it is also because different version of blast gives different output. We experienced such problems with DBWatcher... If I remember correctly, Fred found a way to parse easily both outputs, but, Fred is out this week, so he will confirm next week if I'm right. François. -- François Jeanmougin | groupe de bioinformatique / bioinformatics groupe tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France From owner-srs@net.bio.net Wed Jan 14 22:00:00 1998 Path: biosci!AMC.UVA.NL!a.h.vankampen From: a.h.vankampen@AMC.UVA.NL ("A.H. van kampen ", automat) Newsgroups: bionet.software.srs Subject: A few questions Date: 15 Jan 1998 08:19:10 -0800 Organization: Academic Medical Centre Amsterdam Lines: 38 Sender: daemon@net.bio.net Distribution: world Message-ID: <34BE36C4.A79D13E6@amc.uva.nl> NNTP-Posting-Host: net.bio.net Hello, I have a few (basic) questions about setting up a local SRS site. 1) What are the main advantages for having a local copy of databases like embl, swissprot, etc. It seems that the response time for searching in a remote database is still acceptable. 2) What is the best strategy for maintaining a local set of databases? e.g., is everyone updating their databases with ftp each day. 3) Is everyone using identical configuration files (i.e. *.i and *.is) files for the databases. Since I'm new to the field, i'm trying to get some idea of maintaining local databases is worth the effort. Regards, Antoine van Kampen -- --------------------------------------- | Dr. Antoine H.C. van Kampen | | Academic Medical Center Amsterdam | | Cluster Research Support (ADIV-D01) | | Meibergdreef 9 | | 1105 AZ Amsterdam, the Netherlands | -------------------------------------------------| | Phone: ++31-20-5667096 | | Fax: ++31-20-5669020 | | Email: a.h.vankampen@amc.uva.nl | | www: http://www.amc.uva.nl/ | ------------------------------------- From owner-srs@net.bio.net Thu Jan 15 22:00:00 1998 Newsgroups: bionet.software.srs Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!newsfeed.internetmci.com!192.87.106.104!surfnet.nl!barba.uci.kun.nl!sci.kun.nl!caos.kun.nl!root From: "K. Cuelenaere" Subject: Re: Indexing with SRS5.1.0 Content-Type: text/plain; charset=us-ascii Message-ID: <34BF6543.2781@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: <1998Jan15.155704@wehi> Mime-Version: 1.0 Date: Fri, 16 Jan 1998 13:48:51 GMT X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 6.2 IP22) Lines: 29 Janice Coventry, Walter and Eliza Hall Institute wrote: > > Dear SRS Managers > > To upgrade to SRS5.1.0 is it necessary to reindex all your files? > I have been testing some of my databases, when I try > to getz entries from the old indices I have a core dump. > > Thanking you in anticipation Retrieving non-sequence entries (like prosite and pdb) seems to work with us (haven't tested them all though). It looks to me all the sequence databases have to be re-indexed because sequences are now treated as objects. So when you try to use the old indices with the new .i and .is files, you'll get an error saying that the sequence is not of the "object" type. Using the old .i and .is files with 5.1 still seems possible... Regards, 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 Jan 15 22:00:00 1998 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: A few questions Date: 16 Jan 1998 17:03:47 +0000 Organization: The Sanger Centre Lines: 41 Sender: pmr@unst.sanger.ac.uk Message-ID: References: <34BE36C4.A79D13E6@amc.uva.nl> NNTP-Posting-Host: unst.sanger.ac.uk X-Newsreader: Gnus v5.5/Emacs 20.2 a.h.vankampen@AMC.UVA.NL ("A.H. van kampen ", automat) writes: > I have a few (basic) questions about setting up a local SRS site. > > 1) What are the main advantages for having a local copy of > databases like embl, swissprot, etc. It seems that the response > time > for searching in a remote database is still acceptable. That applies to searching for a few entries through the Web interface. But you can do a lot through the command line interface, especially with links and subsets of the databases very quickly and efficiently, and this is not available through the Web interface (and therefore must be done locally). > 2) What is the best strategy for maintaining a local set of databases? > e.g., is everyone updating their databases with ftp each day. Sites have their own strategies. "best" depends on your own needs. There is a databank of databanks that shows you when other sites have updated, so you can follow their strategies. It often depends on how much you need the very latest entries, and how long indexing takes. > 3) Is everyone using identical configuration files (i.e. *.i and *.is) > files > for the databases. From SRS 5.1 I hope to use the standard .i and .is files (and .it for the database information). Where I diverge I will pass on the changes through Thure (who is only a few metres away :-) SRS 5.1 makes this much easier to do than with, for example, SRS 4.0.8. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Sun Jan 18 22:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 Jan 1998 02:00:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199801191000.CAA15831@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 Mon Jan 19 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!Cabal.CESspool!bofh.vszbr.cz!newsfeed.eerie.fr!jussieu.fr!univ-lyon1.fr!cnusc.fr!ciril.fr!u-strasbg.fr!news From: Frederic PLEWNIAK Newsgroups: bionet.software.srs Subject: Re: blast on srs5.1 Date: Tue, 20 Jan 1998 11:15:25 +0100 Organization: IGBMC Lines: 15 Message-ID: <34C4793D.919@igbmc.u-strasbg.fr> References: <884798805.425590801@dejanews.com> <69keet$nrt@news.u-strasbg.fr> NNTP-Posting-Host: didon.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5 sun4m) > I think it's not only an expected GCG ouput, it is also because > different version of blast gives different output. We experienced such > problems with DBWatcher... > If I remember correctly, Fred found a way to parse easily > both outputs, but, Fred is out this week, so he will confirm next > week if I'm right. > François. > Oh! my... Just comin' back from a sweet quiet week off lab and now... François, you're too fast to jump onto your keyboard ;o)... Sorry to let you down but DBWatcher doesn't really parse title lines in BLAST output. Not the way SRS does anyway! And it is certainly not able to tell the accession number from the ID... Sorry... Fred From owner-srs@net.bio.net Mon Jan 19 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!newsfeed.eerie.fr!jussieu.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: links in srs5.0.1 Date: Tue, 20 Jan 1998 16:35:32 +0100 Organization: INFOBIOGEN Lines: 70 Message-ID: <34C4C443.4CB5E5B@infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------FAD1AFB6B4D91FEF8AF019A0" X-Mailer: Mozilla 4.04 [en] (X11; I; SunOS 5.5.1 sun4u) --------------FAD1AFB6B4D91FEF8AF019A0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, we succeed in installing the new versions of srs5.01 but we find one problem when you want to valid the selection of databank in the link window or in the query manager(link): there is an internal server error message. (the error_log gives this message: [Tue Jan 20 15:30:56 1998] access to /env/infobiogen/pack/srs5/www/bin/wgetz failed for lovelace.infobiogen.fr, reason: Premature end of script headers The same query link with getz work well. Thanks in advance for your help, 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 --------------------------------------------------- --------------FAD1AFB6B4D91FEF8AF019A0 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all,
 

we succeed in installing the new versions of srs5.01 but
we find one problem when you want to valid the selection of databank in
the link window or in the query manager(link): there is an internal server error message.
(the error_log gives this message:
[Tue Jan 20 15:30:56 1998] access to /env/infobiogen/pack/srs5/www/bin/wgetz
failed for lovelace.infobiogen.fr, reason: Premature end of script headers

The same query link  with getz work well.

Thanks in advance for your help,

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
---------------------------------------------------
  --------------FAD1AFB6B4D91FEF8AF019A0-- From owner-srs@net.bio.net Mon Jan 19 22:00:00 1998 Path: biosci!agate!howland.erols.net!nntp.abs.net!newspeer.monmouth.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: "Thure Etzold" Newsgroups: bionet.software.srs Subject: Re: blast on srs5.1 Date: Wed, 21 Jan 1998 00:12:28 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 31 Message-ID: <6a24g9$9rp$1@niobium.hgmp.mrc.ac.uk> References: <884798805.425590801@dejanews.com> <69keet$nrt@news.u-strasbg.fr> <34C4793D.919@igbmc.u-strasbg.fr> NNTP-Posting-Host: idefix.ebi.ac.uk X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Frederic PLEWNIAK wrote in message <34C4793D.919@igbmc.u-strasbg.fr>... >> I think it's not only an expected GCG ouput, it is also because >> different version of blast gives different output. We experienced such >> problems with DBWatcher... >> If I remember correctly, Fred found a way to parse easily >> both outputs, but, Fred is out this week, so he will confirm next >> week if I'm right. >> François. >> >Oh! my... Just comin' back from a sweet quiet week off lab and now... >François, you're too fast to jump onto your keyboard ;o)... Sorry to >let you down but DBWatcher doesn't really parse title lines in BLAST >output. Not the way SRS does anyway! And it is certainly not able >to tell the accession number from the ID... Sorry... well, too bad! I think the only way to get around this is to create separate versions of .i and .is for different versions of blast. This would be reasonable since not only the format of the output but also the program options change parsing the title line for entry names and accession numbers is another problem and could be alleviated by including productions for both in the syntax where only one is active at a time. I used a similar solution for switching between gcg and native format for most sequence database . regards thure From owner-srs@net.bio.net Tue Jan 20 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!4.1.16.34!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!uunet!in2.uu.net!nntp.earthlink.net!usenet From: sales@inforia.com Newsgroups: bionet.software.srs Subject: ZDNet Hotfile & Editor's Pick!! Date: Wed, 21 Jan 1998 19:02:33 GMT Organization: EarthLink Network, Inc. Lines: 29 Message-ID: <34c64644.7090536@news.earthlink.net> NNTP-Posting-Host: 207.217.234.33 X-Newsreader: Forte Agent .99e/32.227 ******************************************************** Inforia Quest won ZDNet Hotfile Editor's Pick!! ******************************************************** How Preston Gralla talks about Inforia Quest: It lets you look through dozens of search engines and sites simultaneously, and customize your search to use only those sites and engines you want. You can confine your search to news sites, entertainment sites, Usenet newsgroups, or technology sites. And you can create customized searches of your own. The program reports not just the links it finds, but also the relevance to your search, the date the page was updated, and the page size. Most useful is the summary it provides for each page. And it even checks the links it finds to see whether they're still live. I use this program several times every day. It's a keeper. (From: http://www.hotfiles.com/prespick/pres0198.html) So why hesitate? Download IQ now for a free trial and enjoy the 5-star award program. For further product info, go to http://www.inforia.com/quest. Wish you had a happy Internet surfing! From owner-srs@net.bio.net Wed Jan 21 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Weare@EuropeMail.com (Johnathon Weare) Newsgroups: bionet.software.srs Subject: javascript required message Date: 22 Jan 1998 16:46:55 +0100 Organization: Biocomputing, EMBL Heidelberg, Germany Lines: 13 Sender: weare@fifi.embl-heidelberg.de Distribution: world Message-ID: NNTP-Posting-Host: fifi.embl-heidelberg.de To: etzold@ebi.ac.uk Cc: chenna Encryption-by: McWurst McWurst-Schluessel: O*Uef!$p&^afC1fe@0n--9`#gA||~[gf)*fcq26 X-Newsreader: Gnus v5.3/Emacs 19.34 By my calculations at least 10% of users cannot use SRS 5.10 at all - they just get a blank page. When users have old browsers or javascript is turned off, they click on start and get a blank page. I suggest a short message for these non javascript browsers. Johnny -- Johnathon Weare -- EMBL -- Weare@EuropeMail.com --- http://www.gpcr.org/johnny/ From owner-srs@net.bio.net Wed Jan 21 22:00:00 1998 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: "Thure Etzold" Newsgroups: bionet.software.srs Subject: Re: javascript required message Date: Fri, 23 Jan 1998 07:17:15 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 23 Message-ID: <6a864s$cu7$1@niobium.hgmp.mrc.ac.uk> References: NNTP-Posting-Host: idefix.ebi.ac.uk X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Johnathon Weare wrote in message ... > > >By my calculations at least 10% of users cannot use SRS 5.10 at all - they >just get a blank page. > >When users have old browsers or javascript is turned off, they click on >start and get a blank page. I suggest a short message for these non >javascript browsers. point taken! problem should be only if javascript is turned off. there are two versions of the top page with and without javascript. The one with javascript is chosen only if the client has something like "Mozilla4" in the HTTP_USER_AGENT ...this selects all netscape4, communicator and most ie4 browsers regards Thure From owner-srs@net.bio.net Thu Jan 22 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Weare@EuropeMail.com (Johnathon Weare) Newsgroups: bionet.software.srs Subject: Re: javascript required message Date: 23 Jan 1998 14:20:08 +0100 Organization: Biocomputing, EMBL Heidelberg, Germany Lines: 27 Sender: weare@fifi.embl-heidelberg.de Distribution: world Message-ID: References: <6a864s$cu7$1@niobium.hgmp.mrc.ac.uk> NNTP-Posting-Host: fifi.embl-heidelberg.de To: etzold@ebi.ac.uk Encryption-by: McWurst McWurst-Schluessel: O*Uef!$p&^afC1fe@0n--9`#gA||~[gf)*fcq26 X-Newsreader: Gnus v5.3/Emacs 19.34 >>>>> "TE" == Thure Etzold writes: TE> Johnathon Weare wrote in message ... >> By my calculations at least 10% of users cannot use SRS 5.10 at all >> - they just get a blank page. TE> point taken! problem should be only if javascript is turned TE> off. there are two versions of the top page with and without TE> javascript. The one with javascript is chosen only if the client TE> has something like "Mozilla4" in the HTTP_USER_AGENT ...this TE> selects all netscape4, communicator and most ie4 browsers OK - so take 10% off my estimate and add one person! Any chance of a non javascript link to the alternate start page? Could be hidden by a javascript part for elegance. Must say I like the interface changes Thure, cheers, Johnny -- Johnathon Weare -- EMBL -- Weare@EuropeMail.com --- http://www.gpcr.org/johnny/ From owner-srs@net.bio.net Mon Jan 26 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!news-peer.sprintlink.net!news-backup-east.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!129.174.1.8!portal.gmu.edu!news From: Joseph Nepomuceno Newsgroups: bionet.software.srs Subject: -----Free Software Download------ Date: 27 Jan 1998 04:09:26 GMT Organization: George Mason University, Fairfax, Virginia, USA Lines: 31 Message-ID: <6ajmlm$5fa@portal.gmu.edu> NNTP-Posting-Host: osf1.gmu.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) > ____________________________________________________________ > ******* Announcing the Mortgage Manager(TM) Software ******* > ------------------------------------------------------------ > Would you like to try our mortgage analysis software? > It's FREE and all you have to do is download it from our site > at > > > The software will analyze your home mortgage and provide > you with a FREE service that will allow you to... > > > * Save thousands of dollars without refinancing. > * Cut years off your mortgage without increasing your payment. > * Build equity in your home 300% faster > * Audit your loan automatically to find lender mistakes > which occur about 50% of the time according to the F.D.I.C. > > > > For more information please go to: > http://www.angelfire.com/biz/freesoftware95 > > > To download now please go to: > http://www.angelfire.com/biz/freesoftware95/download.html > > *When running the software remember to use CODE: 22701... > this will unlock the software. From owner-srs@net.bio.net Tue Jan 27 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!europa.clark.net!208.134.241.18!newsfeed.internetmci.com!199.117.161.1!csn!nntp-xfer-1.csn.net!news.acsu.buffalo.edu!srv1.drenet.dnd.ca!crc-news.doc.ca!nott!utnut!bioinfo.med.utoronto.ca!resunix.sickkids.on.ca!manuel_buchwald From: ali@genet.sickkids.on.ca (Alex Dong Li) Newsgroups: bionet.software.srs Subject: Webblast--a program to do gapped blast from unix command line Date: Thu, 29 Jan 1998 01:18:39 GMT Organization: The Hospital For Sick Children Lines: 33 Message-ID: <6aoann$2a5$13@resunix.sickkids.on.ca> NNTP-Posting-Host: 142.20.38.249 X-Newsreader: News Xpress 2.01 Webblast--a program to do gapped blast from unix command line webblast, written in perl, does NCBI gapped blast search (version 2) by mimicing a www client (such as Netscape &IE) from the unix command line, and saves the results as local files. Most options are similar to those available from NCBI blast page. Currently the graphical overview is not available. Some examples are: webblast -format=fasta sample1.seq webblast -prog=blastn -datab=nr -align=25 -notask webblast -prog=blastp -datab=swissprot -email=smith@dept.univ.edu Input sequence file(s) can be in GCG, fasta or plain text format . (you need to specify by "-format=fasta" or "-format=text" if files are in last two formats). If no filename is specified, all files in current directory will be blasted. It is available at http://www.genet.sickkids.on.ca/bioinfo_resources/software.html To install the program on your own machine, 0) install perl for unix (For most networked unix machines, perl should have been installed. If not, contact your system admin), 1) copy webblast and postclient.pl to your system, 2) change the file permissions so that you can run them, 3) modify the two files according to the instruction in the headers If you have any suggestions/comments, please let me know. Regards, Alex Dong Li