From owner-srs@net.bio.net Thu Mar 07 22:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: yet another bug in SRS Date: 8 Mar 1996 17:09:28 GMT Organization: Belgian EMBnet Node Lines: 11 Message-ID: <4hppk8$bhn@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] When I search in TFSITE for Y$ENO2_03 in the ID field with the Makewild option turned of, I find the entry. However, when I search for Y$EN or Y$ENO2_03 with the Makewild option turned on, I find nothing. In fact the interface passes to the program an instruction to search for " [TFSITE-ID:y$eno2_03]" instead of " [TFSITE-ID:y$eno2_03*]". Similar things happen with some other databanks too, although not with all. Has someone already noticed this earlier ? I am curious, Dr. Guy Bottu From owner-srs@net.bio.net Wed Mar 13 22:00:00 1996 Newsgroups: bionet.software.srs Path: biosci!agate!howland.reston.ans.net!surfnet.nl!sun4nl!sci.kun.nl!caos.kun.nl!schaft From: schaft@caos.kun.nl (Gijs Schaftenaar) Subject: Re: yet another bug in SRS Message-ID: <1996Mar13.142021.16275@caos.kun.nl> Sender: root@caos.kun.nl (System PRIVILEGED Account) Nntp-Posting-Host: cammsg1.caos.kun.nl Organization: CAOS/CAMM References: <4hppk8$bhn@rc1.vub.ac.be> Date: Wed, 13 Mar 1996 14:20:21 GMT Lines: 28 gbottu@ben.vub.ac.be (Guy Bottu) writes: >When I search in TFSITE for Y$ENO2_03 in the ID field with the Makewild >option turned of, I find the entry. However, when I search for Y$EN or >Y$ENO2_03 with the Makewild option turned on, I find nothing. In fact >the interface passes to the program an instruction to search for >" [TFSITE-ID:y$eno2_03]" instead of " [TFSITE-ID:y$eno2_03*]". >Similar things happen with some other databanks too, although not with all. >Has someone already noticed this earlier ? > I am curious, > Dr. Guy Bottu Which interface are you referring to this time ?. Since the "yet" in your Subject I assume you mean the srscurs/srstk interfaces. Well let me inform you that the WWW interface doesnt find it with a wildcard and neither does getz. This is YET again a unfounded criticism of the srscurs/srstk interfaces from your side, it is beginning to sound like you have a grudge against me. Since I have never met you in person, do you dislike dutch people in general? G. Schaftenaar From owner-srs@net.bio.net Wed Mar 13 22:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!fu-berlin.de!zrz.TU-Berlin.DE!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: yet another bug in SRS Date: Thu, 14 Mar 1996 21:14:43 +0100 Organization: EMBL Lines: 20 Distribution: world Message-ID: <31487E33.41C6@embl-heidelberg.de> References: <4hppk8$bhn@rc1.vub.ac.be> <1996Mar13.142021.16275@caos.kun.nl> NNTP-Posting-Host: kappa.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; OSF1 V2.0 alpha) gbottu@ben.vub.ac.be (Guy Bottu) writes: >When I search in TFSITE for Y$ENO2_03 in the ID field with the Makewild >option turned of, I find the entry. However, when I search for Y$EN or >Y$ENO2_03 with the Makewild option turned on, I find nothing. In fact >the interface passes to the program an instruction to search for >" [TFSITE-ID:y$eno2_03]" instead of " [TFSITE-ID:y$eno2_03*]". i haven't noticed that before ...but it must have been there all the time and i could reproduce it ....there is now obvious reason so i need do some debugging - will post a fix soon thure =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-srs@net.bio.net Wed Mar 13 22:00:00 1996 Newsgroups: bionet.software.srs Path: biosci!agate!howland.reston.ans.net!surfnet.nl!sun4nl!sci.kun.nl!caos.kun.nl!schaft From: schaft@caos.kun.nl (Gijs Schaftenaar) Subject: Re: yet another bug in SRS Message-ID: <1996Mar13.141203.16135@caos.kun.nl> Sender: root@caos.kun.nl (System PRIVILEGED Account) Nntp-Posting-Host: cammsg1.caos.kun.nl Organization: CAOS/CAMM References: <4hppk8$bhn@rc1.vub.ac.be> Date: Wed, 13 Mar 1996 14:12:03 GMT Lines: 32 gbottu@ben.vub.ac.be (Guy Bottu) writes: >When I search in TFSITE for Y$ENO2_03 in the ID field with the Makewild >option turned of, I find the entry. However, when I search for Y$EN or >Y$ENO2_03 with the Makewild option turned on, I find nothing. In fact >the interface passes to the program an instruction to search for >" [TFSITE-ID:y$eno2_03]" instead of " [TFSITE-ID:y$eno2_03*]". >Similar things happen with some other databanks too, although not with all. >Has someone already noticed this earlier ? > I am curious, > Dr. Guy Bottu Which interface are you referring to this time ?. Since the "yet" in your Subject I assume you mean the srscurs/srstk interfaces. Well let me inform you that the WWW interface doesnt find it with a wildcard and neither does getz. This is YET again a unfounded criticism of the srscurs/srstk interfaces from your side, it is beginning to sound like you have a grudge against me. Since I have never met you in person, do you dislike dutch people in general? G. Schaftenaar -- +----------------------------+-----------------------------------+ Gijs Schaftenaar, Drs. | CAOS/CAMM Center Email: schaft@caos.kun.nl | University of Nijmegen URL : http://www.caos.kun.nl/staff/schaft.html From owner-srs@net.bio.net Thu Mar 14 22:00:00 1996 Path: biosci!daresbury!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: yet another bug in SRS Date: 15 Mar 1996 09:38:23 GMT Organization: The Sanger Centre Lines: 28 Distribution: world Message-ID: References: <4hppk8$bhn@rc1.vub.ac.be> <1996Mar13.142021.16275@caos.kun.nl> <31487E33.41C6@embl-heidelberg.de> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: Thure Etzold's message of Thu, 14 Mar 1996 21:14:43 +0100 In article <31487E33.41C6@embl-heidelberg.de> Thure Etzold writes: > gbottu@ben.vub.ac.be (Guy Bottu) writes: > >When I search in TFSITE for Y$ENO2_03 in the ID field with the Makewild > >option turned of, I find the entry. However, when I search for Y$EN or > >Y$ENO2_03 with the Makewild option turned on, I find nothing. In fact > >the interface passes to the program an instruction to search for > >" [TFSITE-ID:y$eno2_03]" instead of " [TFSITE-ID:y$eno2_03*]". > > i haven't noticed that before ...but it must have been there all the > time and i could reproduce it ....there is now obvious reason so > i need do some debugging - will post a fix soon Bet it has something to do with the dollar sign. If so, it's lucky that SwissProt dropped them. Looking for "*$*" in other databases seems to find every entry, regardless of whether there is a dollar in the name. All Fred Blattner's E.coli sequence in EMBL has entry names beginning with "ECU" and SRS finds them perfectly. Ah, I forgot. It's called the "EURO" now so it doesn't count as an example. Well, it finds entries with "NEURO" in the name so it's still OK :-) -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr/ | England From owner-srs@net.bio.net Thu Mar 14 22:00:00 1996 Newsgroups: bionet.software,bionet.molbio.evolution,bionet.software.srs,bionet.info-theory,bionet.software.staden Path: biosci!agate!howland.reston.ans.net!nntp.coast.net!fu-berlin.de!zrz.TU-Berlin.DE!news.dfn.de!news.uni-bielefeld.de!techfak.uni-bielefeld.de!fuellen From: fuellen@techfak.uni-bielefeld.de (Georg Fuellen) Subject: Consulting students for 2nd Edition of Biocomputing Course wanted ! Message-ID: Sender: fuellen@TechFak.Uni-Bielefeld.DE (Georg Fuellen) Date: Fri, 15 Mar 1996 12:24:17 GMT Reply-To: vsns-bcd-admcoord@techfak.uni-bielefeld.de (Georg Fuellen) Nntp-Posting-Host: salbei.techfak.uni-bielefeld.de Organization: Universitaet Bielefeld, Technische Fakultaet. X-Newsreader: xrn 8.01 Followup-To: bionet.software Lines: 86 Xref: biosci bionet.software:14981 bionet.molbio.evolution:4334 bionet.software.srs:240 bionet.info-theory:4054 bionet.software.staden:182 The full version of the following announcement has just been sent to the bionet.announce moderator, etc. If you're not reading bionet.announce, or you don't want to wait until the message is approved & redistributed, please read it at http://www.techfak.uni-bielefeld.de/bcd/Adm/recruit.html ================== After the successful completion of the 1995 GNA-VSNS Biocomputing Course (see our homepage at http://www.techfak.uni-bielefeld.de/bcd/welcome.html, OR http://merlin.mbcr.bcm.tmc.edu:8001/bcd/welcome.html, OR http://info.mcc.ac.uk/hpctec/courses/Biocomputing/vsns/bcd/welcome.html ) we are now preparing for the second edition, starting approx. April 29, and lasting for approx. 11 weeks. The entire course material will be delivered through the Internet, and instruction will take place via the electronic conferencing system BioMOO at Weizmann Institute, Israel. We are once again looking for "Consulting Students", i.e. students who are guaranteed admission in return for helping us in technical and administrative matters. If you're seriously interested in any of these "jobs", please contact the course coordinator, vsns-bcd-admcoord@techfak.uni-bielefeld.de (Georg Fuellen) as soon as possible ! Enrollment into the Summer 1996 course may be limited to approx. 30 students (depending on the availability of instructors), so this is your excellent chance for getting a free ticket to an exciting, cutting-edge learning experience in biocomputing ! If you are _not_ interested in any of these "jobs", the one and only thing you can do right now is to subscribe to our vsns-bcd-prospective mailing list, by sending email to majordomo@hrz.uni-bielefeld.de, with no subject, and the following body: subscribe vsns-bcd-prospective and wait for the announcement of more 1996 consulting student jobs, etc ! [ List of "Consulting student jobs" and the disclaimer can be found at http://www.techfak.uni-bielefeld.de/bcd/Adm/recruit.html ] Global Network Academy (GNA) course catalog entry: Title: Biocomputing I: Sequence Analysis Main Coordinator: Georg Fuellen, M.Sc. (MIT, 1994), Diplom-Inform. (Saarbruecken, 1992). For up-to-date information, and to obtain a list of all collaborators, please use a www/hypertext browser (e.g. Netscape, Mosaic, Lynx) to visit http://www.techfak.uni-bielefeld.de/bcd/welcome.html Description: Graduate students and students close to the completion of their undergraduate studies shall be given a profound introduction into biosequence analysis and comparison. Instructors shall guide them through a peer-reviewed hypertext book, by means of weekly online discussion sessions, supplemented by homework, personal advice, mailing list discussions, and project work. The core units shall cover Pairwise Alignment, Networking, Multiple Alignment, Mathematical Analysis of Sequence Data, and Genetic Algorithms and Protein Folding (Teaser Chapter). Sponsors: VSNS, Association for the Promotion of Science and Humanities in Germany, Research Group in Practical Computer Science (Univ. of Bielefeld) Instructor's email address: (PLEASE VISIT OUR HOMEPAGE FIRST !) vsns-bcd-admcoord@techfak.uni-bielefeld.de Schedule: Regular intervals throughout the week (to be announced) ~11 weeks, expected to start around April 29, 1996 Location: BioMOO (telnet bioinformatics.weizmann.ac.il 8888) Level: late undergraduate (senior) or early graduate Credits: None. Language of Instruction: English Status: under construction (registration is scheduled for early April 1996.) Requirements: Technical: telnet, www/hypertext browser supporting black&white graphics, and forms. Academic: undergraduate level maths experience, computer science and/or molecular biology. -- best wishes, georg fuellen@dali.Mathematik.Uni-Bielefeld.DE, fuellen@MIT.EDU http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/georgF.html From owner-srs@net.bio.net Thu Mar 14 22:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Re: yet another bug in SRS Date: 15 Mar 1996 15:24:11 GMT Organization: Brussels Free Universities (VUB/ULB), Belgium Lines: 15 Message-ID: <4ic22r$l74@rc1.vub.ac.be> References: <4hppk8$bhn@rc1.vub.ac.be> <1996Mar13.141203.16135@caos.kun.nl> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] Gijs Schaftenaar (schaft@caos.kun.nl) wrote: : Which interface are you referring to this time ?. Since the "yet" in your : Subject I assume you mean the srscurs/srstk interfaces. Well let me inform : you that the WWW interface doesnt find it with a wildcard and neither does : getz. : This is YET again a unfounded criticism of the srscurs/srstk interfaces from : your side, it is beginning to sound like you have a grudge against me. : Since I have never met you in person, do you dislike dutch people in general? Not at all, not at all... The bug occurs also with the WWW interface and also at other sites. Guy Bottu From owner-srs@net.bio.net Thu Mar 14 22:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!infobiogen.fr!jussieu.fr!oleane!tank.news.pipex.net!pipex!swrinde!newsfeed.internetmci.com!EU.net!sun4nl!surfnet.nl!swsbe6.switch.ch!scsing.switch.ch!news.rediris.es!news.belnet.be!news.sri.ucl.ac.be!usenet From: Dufrene Marc Newsgroups: bionet.software.srs Subject: WG-Biodiv meeting - Change of meeting place Date: Fri, 15 Mar 1996 16:55:20 +0000 Organization: ECOL/UCL Lines: 10 Distribution: world Message-ID: <3149A0F8.15B4@ecol.ucl.ac.be> NNTP-Posting-Host: 130.104.7.104 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; I; PPC) Dear All, As the "Universite libre de bruxelles" would be on strike on the 21th of March, the User Committee meeting will be held in another place (maybe VUB or Belnet rooms). Monday, you will receive the definitive place of the meeting. Thanks. M. Dufrene From owner-srs@net.bio.net Mon Mar 18 22:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 19 Mar 1996 02:00:35 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 149 Sender: daemon@net.bio.net Distribution: world Message-ID: <199603191000.CAA14051@net.bio.net> NNTP-Posting-Host: net.bio.net I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We have three sponsors to date with a couple more pending. The process is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we hope to have new and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. 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. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Statistics are for the four week period from 22 Jan. - 18 Feb. 1996 and usage continues to grow. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5000 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 600 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. ---------------------------------------------------------------------- From owner-srs@net.bio.net Wed Mar 20 22:00:00 1996 Path: biosci!agate!howland.reston.ans.net!tank.news.pipex.net!pipex!oleane!jussieu.fr!infobiogen.fr!news From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: Help for excceed size Date: 21 Mar 1996 13:46:02 GMT Organization: INFOBIOGEN Lines: 16 Message-ID: <4irmiq$sd4@lovelace.infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 5.4 sun4d) X-URL: news:bionet.software.srs Help ! Does anyone can tell what can i do with an error message such as e__exceedsize, attempt to write beyond end of block name of block:array addr, size: 20000 It occurs when i run srssection for a new bank. Thanks for your help in advance. --------------------------------------------------- Jean-Marc PLAZA INFOBIOGEN - CNRS 7, rue Guy Moquet BP8 94801 VILLEJUIF Cedex, France tel: +33 45 59 52 39 fax: +33 45 59 52 50 e-mail: plaza@infobiogen.fr --------------------------------------------------- From owner-srs@net.bio.net Wed Mar 20 22:00:00 1996 Path: biosci!daresbury!bioftp.unibas.ch!news.vub.ac.be!news.belnet.be!news.rediris.es!news.uoregon.edu!tank.news.pipex.net!pipex!oleane!jussieu.fr!infobiogen.fr!news From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: Re: Help for excceed size Date: 21 Mar 1996 16:37:36 GMT Organization: INFOBIOGEN Lines: 13 Message-ID: <4is0kg$sd4@lovelace.infobiogen.fr> References: <4irmiq$sd4@lovelace.infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 5.4 sun4d) To: plaza@infobiogen.fr X-URL: news:4irmiq$sd4@lovelace.infobiogen.fr Ok , i find it by myself I increase the max length of string assignement (SDLxXADDR) in sdl.h Bye, bye --------------------------------------------------- Jean-Marc PLAZA INFOBIOGEN - CNRS 7, rue Guy Moquet BP8 94801 VILLEJUIF Cedex, France tel: +33 45 59 52 39 fax: +33 45 59 52 50 e-mail: plaza@infobiogen.fr --------------------------------------------------- From owner-srs@net.bio.net Mon Mar 25 22:00:00 1996 Path: biosci!agate!howland.reston.ans.net!nntp.coast.net!fu-berlin.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: indices for TREMBL, EMBL Date: Tue, 26 Mar 1996 09:48:07 +0100 Organization: EMBL Lines: 56 Distribution: world Message-ID: <3157AF47.41C6@embl-heidelberg.de> NNTP-Posting-Host: kappa.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; OSF1 V2.0 alpha) dear all, we have built the new TREMBL. You can get it from felix.embl-heidelberg.de get the file pub/databases/trembl/trembl.dat about indexing embl: I noticed that the feature index got very large since the parser entered the /translation= ...into the index to prevent this edit embl.sdl and change the production 'qualifier' so that it includes 'translate' and then add the production 'translate' qualifier = ecnumber | citation | translate | qual; translate = '/TRANSLATION=' '\"' { ~\"~ } '\"'; here is also a better production 'comment' comment = { (~A-Za-z0-9~ ) | (~A-Za-z0-9~ ) }; that will also reduce the size of the index you can find out what enters the index by srsbuild -f features embl -d ...of course that is not that useful since EMBL starts with all these ests once you have the index you can do getz '[embl-features:*]' -rep ...this prints all the words that match '*' one last thing about srs5: I will probably start distributing beta-version in around mid-april to end of april. The main improvement will be with parsing so that problems as those above are much easier to find and to fix. We are aware of the problems indexing large databank as EMBL and Genbank. There is a way out by indexing the individual indices individually and merging the indices later - I will try to implement that as soon as possible. regards Thure -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany