From owner-srs@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news-res.gsl.net!news.gsl.net!usenet.eel.ufl.edu!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-angers.fr!ciril.fr!u-strasbg.fr!news From: Frederic PLEWNIAK Newsgroups: bionet.software.srs Subject: SRS with compressed EMBL files??? Date: Tue, 02 Jul 1996 11:51:29 +0200 Organization: IGBMC Lines: 21 Message-ID: <31D8F121.39C5@igbmc.u-strasbg.fr> Reply-To: plewniak@igbmc.u-strasbg.fr NNTP-Posting-Host: didon.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.5 sun4m) Hello, I was wondering if anyone has successfully built SRS indices from compressed EMBL files (*.dat.Z). I have tried this in embl.sdl but it does not seem to work : #filetype /ID=%EMBLREF_FILE /single_entries=no /typename="dat.Z" /maxline=90 /exitstr=" " /pipe="zcat %s" #filetype /ID=%EMBLSEQ_FILE /begstr="SQ " /advance=1 /single_entries=no /typename="dat.Z" /maxline=90 /exitstr="//" /pipe="zcat %s" Any suggestion? All the best, Fred From owner-srs@net.bio.net Mon Jul 01 23:00:00 1996 Path: biosci!rutgers!gatech!newsfeed.internetmci.com!howland.reston.ans.net!surfnet.nl!netkid.att.nl!gatekeeper.sandoz.att.nl!root From: Reinhard Doelz Newsgroups: bionet.software.srs Subject: Re: SRS with compressed EMBL files??? Date: Tue, 02 Jul 1996 12:34:51 +0200 Organization: a Digital Internet AlphaServer Site Lines: 16 Message-ID: <31D8FB4B.41C6@GWA.SANDOZ.COM> References: <31D8F121.39C5@igbmc.u-strasbg.fr> NNTP-Posting-Host: bigone.chbs.sandoz.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP19) Frederic PLEWNIAK wrote: > I was wondering if anyone has successfully built SRS indices from > compressed EMBL files (*.dat.Z). I have tried this in embl.sdl but > it does not seem to work : > > #filetype /ID=%EMBLREF_FILE > /single_entries=no > /typename="dat.Z" /maxline=90 /exitstr=" " > /pipe="zcat %s" I would expect that the substitutional compression, even if the pipe concept works, would inhibit a smooth operation. The Entrez data on CD ROM were lzhuffed. Maybe this could work with gzip? Regards Reinhard From owner-srs@net.bio.net Tue Jul 02 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news-res.gsl.net!news.gsl.net!usenet.eel.ufl.edu!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-angers.fr!ciril.fr!u-strasbg.fr!news From: Frederic PLEWNIAK Newsgroups: bionet.software.srs Subject: Re: SRS with compressed EMBL files??? Date: Wed, 03 Jul 1996 11:02:28 +0200 Organization: IGBMC Lines: 8 Message-ID: <31DA3724.2373@igbmc.u-strasbg.fr> References: <31D8F121.39C5@igbmc.u-strasbg.fr> <31D8FB4B.41C6@GWA.SANDOZ.COM> NNTP-Posting-Host: didon.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.5 sun4m) Reinhard Doelz wrote: > (...) Maybe this could work with gzip? > I've tried as well and got nothing... Furthermore if it could work reasonably well with the *.dat.Z files as distributed by EBI it would save the trouble of uncompressing them and quite a good deal of disk space... Fred From owner-srs@net.bio.net Sun Jul 07 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!harbinger.cc.monash.edu.au!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: SRS with compressed EMBL files??? Date: Mon, 08 Jul 1996 13:33:42 +0200 Organization: EMBL Lines: 33 Distribution: world Message-ID: <31E0F216.41C6@embl-heidelberg.de> References: <31D8F121.39C5@igbmc.u-strasbg.fr> NNTP-Posting-Host: rook.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b5aGold (X11; I; IRIX 5.3 IP12) To: plewniak@igbmc.u-strasbg.fr Frederic PLEWNIAK wrote: > > Hello, > I was wondering if anyone has successfully built SRS indices from > compressed EMBL files (*.dat.Z). I have tried this in embl.sdl but > it does not seem to work : > unfortunately this is not possible since gzip or gunzip can compress only entire files, in the case of EMBL a file such as bac.dat. How can you get a single entry without uncompressing the entire file? The data on the Entrez CD-rom is compressed on an entry basis which is different. I put in the option to access compressed file for databanks like PDB where each entry is contained in a single file. For the EMBL databank such a structure, even if the single files were compressed, would probably require even more diskspace. I would be interested in a 'public' program or function that compresses and uncompresses single strings so that it can be used if srs (SRSWWW or getz) are the only direct accessors of a databank. 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 From owner-srs@net.bio.net Thu Jul 18 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 19 Jul 1996 02:00:09 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 154 Sender: daemon@net.bio.net Distribution: world Message-ID: <199607190900.CAA25081@net.bio.net> NNTP-Posting-Host: net.bio.net BIOSCI is about halfway to its funding goal!! 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 are only about halfway to our funding goal and need to raise further funds to avoid having to curtail services at net.bio.net. Fundraising 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 will be getting newer 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. Please contact us for further details. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5500 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 800 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. Ads can also be displayed on various combinations of other BIOSCI/bionet newsgroups. Please contact us at biosci-help@net.bio.net for details. ---------------------------------------------------------------------- From owner-srs@net.bio.net Sun Jul 21 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!news-res.gsl.net!news.gsl.net!hunter.premier.net!news.cais.net!mr.net!news.ios.com!usenet From: shahvika@pilot.msu.edu (Vikas Shah) Newsgroups: bionet.software.srs Subject: Molecular Modelling Date: Mon, 22 Jul 1996 16:17:57 GMT Organization: Michigan State University Lines: 14 Sender: Vikas Shah Message-ID: <31f3a9ad.2804866@news.ios.com> Reply-To: shahvika@pilot.msu.edu NNTP-Posting-Host: ppp-21.ts-1.hck.idt.net X-Newsreader: Forte Agent .99e/32.227 I am an undergraduate student at Michigan State University, entering my junior year this fall. I am investigating molecular modelling packages for research I plan on doing next summer, and am writing to ask for help and recommendations regarding the wide variety of packages out there. I need to be able to do energy minimizations as well as geometry optimizations, predict electron densities, zoom in and out among structures, and - if possible - view and record particle-particle interactions. Here's the catch -- I am running an IBM 486DX2 66 Mhz with 20 MB of RAM and 1 MB vRAM with Win95. I am planning on upgrading if possible, but that will depend on funding. Forget system speed for now, I just need to know the best packages out there. Please mail shahvika@pilot.msu.edu. Thank you. Vikas Shah From owner-srs@net.bio.net Thu Jul 25 23:00:00 1996 Path: biosci!agate!newsgate.duke.edu!newshost.convex.com!cnn.exu.ericsson.se!eua.ericsson.se!news.algonet.se!news.hebel.net!news.sics.se!news.csc.fi!usenet From: Heikki Lehväslaiho Newsgroups: bionet.software.srs Subject: Long sequence accession numbers! Date: Fri, 26 Jul 1996 10:00:50 +0300 Organization: CSC Scientific Computing Lines: 27 Message-ID: <31F86D22.477E@csc.fi> Reply-To: Heikki.Lehvaslaiho@csc.fi NNTP-Posting-Host: siru.csc.fi Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 2.02 (Macintosh; I; PPC) Fellow SRS managers, This happened to me and it seems it's happening to others too: When new EMBL entries with long accession numbers started coming in a few days ago, I fixed GCG but forgot SRS. Make sure that in the file embl.odd the line accnr = ^A-Z^ ~0-9~; has been changed to (for example) accnr = ~A-Z~ ~0-9~; And while you are at it, do the same change to genbank.odd, too. Cheers, -Heikki _____ _/ _/________________________________________________ _/ _/ _/ _/ _/ Heikki Lehväslaiho _/_/_/_/_/ CSC Scientific Computing _/ _/ _/ Tietotie 6, P.O. Box 405, FIN-02101 Espoo FINLAND _/ _/ _/ Phone: +358 0 457 2076 FAX: +358 0 457 2302 _/ The Finnish EMBnet node __ _/_/_/_/_/___________________________________________________