From owner-acedb@hgmp.mrc.ac.uk Wed Apr 5 09:37:55 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 19B7317A75; Wed, 5 Apr 2000 09:37:55 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 8C18117A73; Wed, 5 Apr 2000 09:37:53 +0100 (BST) Received: from isgate.is (isgate.is [193.4.58.51]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA19227 for ; Tue, 4 Apr 2000 17:43:40 +0100 (BST) Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by isgate.is (8.9.3r/8.9.0Imo) with ESMTP id QAA15445 for ; Tue, 4 Apr 2000 16:43:34 GMT Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.13 #2) id 12cWPO-0007TF-00 for bionet-software-acedb@moderators.isc.org; Tue, 04 Apr 2000 17:42:30 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 12cWQL-0002ue-00; Tue, 4 Apr 2000 17:43:29 +0100 To: bionet-software-acedb@moderators.isc.org From: Jamie Kincaid Newsgroups: bionet.software.acedb Subject: Viewing DNA alignments in webace Organization: ACS, The University of Nottingham Message-ID: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 954866609 11198 128.243.116.150 (4 Apr 2000 16:43:29 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 4 Apr 2000 16:43:29 GMT X-Sender: jamie@thale Date: Wed, 5 Apr 2000 09:37:53 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello, In webace when you are viewing a sequence with homologies there is a very nice feature 'Show homology table / DNA alignments' which shows sequence matches by base pair whereby orange indicates match, and blue mismatch. However I notice it doesn't do gapped alignments. Is there a software fix or an option for doing this? Alternatively is there another way (perhaps using AceBrowser) where you can view alignments at the base pair level and include gaps. Regards, Jamie _______________________________________________________________________________ Jamie Kincaid Nottingham Arabidopsis Stock Centre (NASC) School of Biological Sciences University of Nottingham, Nottingham, NG7 2RD Phone: 0115 951 3091 Fax: 0115 951 3297 NASC website: nasc.nott.ac.uk From owner-acedb@hgmp.mrc.ac.uk Mon Apr 10 15:01:00 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id F25B717A90; Mon, 10 Apr 2000 15:00:59 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C38CF17A7A; Mon, 10 Apr 2000 15:00:52 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA18894 for ; Mon, 10 Apr 2000 11:05:59 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA27331 for bionet-software-acedb@net.bio.net; Mon, 10 Apr 2000 11:05:58 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: acedb newsletter... Organization: Sanger Centre Message-ID: <38F1A785.299AB51D@sanger.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 955361158 27329 193.60.84.177 (10 Apr 2000 10:05:58 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 10 Apr 2000 10:05:58 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Mon, 10 Apr 2000 15:00:52 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Here at the Sanger Centre I have started a monthly newsletter in an attempt to better communicate what's happening to acedb month by month. The basic idea is to say "this month we added blah, blah to fmap, XXXX to the windows version" and so on. Although the newsletter is slightly biased towards Sanger users I thought that people here might like to see it. You can either view them at: http://www.acedb.org/winfo/Newsletters/ or I can add you to my mailing list to receive a plain text version of the newsletters. cheers Ed ------------------------------------------------------------------------------ | Ed Griffiths, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 (switch +44 1223 834244) Fax: +44 1223 494919 | ------------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Mon Apr 10 15:30:32 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C33CB17A67; Mon, 10 Apr 2000 15:30:29 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 78C4517A5B; Mon, 10 Apr 2000 15:30:27 +0100 (BST) Received: (from daemon@localhost) by hgmp.mrc.ac.uk (8.9.3/8.9.3) id PAA12977 for bionet-software-acedb@net.bio.net; Mon, 10 Apr 2000 15:19:25 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: dsmith@ucsd.edu (Doug Smith) Newsgroups: bionet.software.acedb Subject: xace 4.7 Protein Display Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Received: from biomail.ucsd.edu (biomail.ucsd.edu [132.239.58.91]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA12964 for ; Mon, 10 Apr 2000 15:19:15 +0100 (BST) X-Received: from [24.30.148.200] (dt046nc8.san.rr.com [24.30.148.200]) by biomail.ucsd.edu (8.9.3/8.9.3-IH) with ESMTP id HAA07173 for ; Mon, 10 Apr 2000 07:19:12 -0700 (PDT) X-Sender: dsmith@biomail.ucsd.edu X-To: acedb@hgmp.mrc.ac.uk Date: Mon, 10 Apr 2000 15:30:27 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I note that the xace 4.7 Protein Display has a seqFeature type of column. I presume this can be used for coordinate info on motifs and the like. We are interested in such annotation for protein displays in DictyDB. Is anyone doing this sort of thing in their ACEDB databases? If so, could someone point to a few specific protein objects in an ACEDB database that they have whereby they do this? Even better, could you send me as an email attachment a couple of .ace pieces of data for such Protein objects and for the View object for the Protein class? Thanks so much -Doug ----------------------------------------------------------------- Douglas W. Smith Professor of Biology UCSD Phone: 858-534-2620 Department of Biology, 0116 UCSD FAX: 858-534-7108 UCSD Home FAX: 858-4573686 La Jolla, CA 92093-0116 email: dsmith@ucsd.edu Home Page: http://www.biology.ucsd.edu/others/dsmith/dnasys.html --- From owner-acedb@hgmp.mrc.ac.uk Thu Apr 13 09:39:36 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E864417ACB; Thu, 13 Apr 2000 09:39:35 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 47D6417A60; Thu, 13 Apr 2000 09:39:34 +0100 (BST) Received: (from daemon@localhost) by hgmp.mrc.ac.uk (8.9.3/8.9.3) id RAA06207 for bionet-software-acedb@net.bio.net; Tue, 11 Apr 2000 17:33:02 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: matthews@greengenes.cit.cornell.edu (Dave Matthews) Newsgroups: bionet.software.acedb Subject: case-sensitivity of Keywords Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200004111632.MAA26399@greengenes.cit.cornell.edu> X-Received: from greengenes.cit.cornell.edu (GREENGENES.CIT.CORNELL.EDU [128.253.246.43]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA06185 for ; Tue, 11 Apr 2000 17:32:54 +0100 (BST) X-Received: (from matthews@localhost) by greengenes.cit.cornell.edu (8.9.3/8.9.3) id MAA26399 for ACEDB newsgroup ; Tue, 11 Apr 2000 12:32:53 -0400 (EDT) X-To: ACEDB newsgroup Date: Thu, 13 Apr 2000 09:39:34 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Is it possible to make the ?Keyword class non-Case-Sensitive? It appears to be a System class and not controlled by wspec/options.wrm. I don't see any way to turn the case-sensitivity off. (in ace4_7m or 4_8c) - Dave --- From owner-acedb@hgmp.mrc.ac.uk Thu Apr 13 09:41:00 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1BD7217B3B; Thu, 13 Apr 2000 09:41:00 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 50EC817ACB; Thu, 13 Apr 2000 09:40:58 +0100 (BST) Received: from beaver.cs.washington.edu (beaver.cs.washington.edu [128.95.1.1]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id BAA22453 for ; Wed, 12 Apr 2000 01:26:55 +0100 (BST) Received: from nntp4.u.washington.edu (root@nntp4.u.washington.edu [140.142.17.38]) by beaver.cs.washington.edu (8.9.3/8.9.3/0.3) with ESMTP id RAA21721 for ; Tue, 11 Apr 2000 17:26:50 -0700 (PDT) (envelope-from root@nntp4.u.washington.edu) Received: (from root@localhost) by nntp4.u.washington.edu (8.9.3+UW99.09/8.9.3+UW00.01) id RAA42160 for bionet-software-acedb@beaver.cs.washington.edu; Tue, 11 Apr 2000 17:26:49 -0700 To: bionet-software-acedb@cs.washington.edu From: Carson Thoreen Newsgroups: bionet.software.acedb Subject: compiling ace for Mac OSX Organization: Dept. of Molecular Biotechnology Message-ID: <38F3C368.AAB7F985@brown.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Trace: nntp4.u.washington.edu 955499208 20654 (None) 140.142.17.39 X-Complaints-To: help@cac.washington.edu X-Mailer: Mozilla 4.72 (Macintosh; I; PPC) X-Accept-Language: en,pdf Date: Thu, 13 Apr 2000 09:40:58 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello -- Has anyone had any luck compiling aceserver for Mac OS X (~Nextstep)? There aren't any Xlibs, but I don't think that aceserver needs them. Anyone with ideas, please send them my way! Carson Thoreen Carson_Thoreen@brown.edu From owner-acedb@hgmp.mrc.ac.uk Thu Apr 13 13:33:29 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2EEB917AFC; Thu, 13 Apr 2000 13:33:29 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id F1EF017A56; Thu, 13 Apr 2000 13:33:23 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA03978 for ; Thu, 13 Apr 2000 09:44:07 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA21105 for bionet-software-acedb@net.bio.net; Thu, 13 Apr 2000 09:44:06 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: compiling ace for Mac OSX Organization: Sanger Centre Message-ID: <38F588D5.7BDB1F08@sanger.ac.uk> References: <38F3C368.AAB7F985@brown.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 955615445 21103 193.60.84.177 (13 Apr 2000 08:44:05 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 13 Apr 2000 08:44:05 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 13 Apr 2000 13:33:23 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > Has anyone had any luck compiling aceserver for Mac OS X (~Nextstep)? > There aren't any Xlibs, but I don't think that aceserver needs them. > Anyone with ideas, please send them my way! We haven't tried this but I think you will have the best chance with saceserver (the socket server) rather than aceserver (the RPC server). saceserver uses straight TCP sockets and has already been compiled in one go on Windows. I'm not sure what your compilation environment is on Mac OS X, contact me direct if you like and we can see if between us we can get it running. cheers Ed ------------------------------------------------------------------------------ | Ed Griffiths, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 (switch +44 1223 834244) Fax: +44 1223 494919 | ------------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Thu Apr 13 13:34:22 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 418E017B3A; Thu, 13 Apr 2000 13:34:22 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 2F37717AFC; Thu, 13 Apr 2000 13:34:19 +0100 (BST) Received: (from daemon@localhost) by hgmp.mrc.ac.uk (8.9.3/8.9.3) id LAA16221 for bionet-software-acedb@net.bio.net; Thu, 13 Apr 2000 11:34:57 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: mieg@beta.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: mac OS X Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200004131936.VAA06849@beta.crbm.cnrs-mop.fr> X-Received: from xerxes.crbm.cnrs-mop.fr (IDENT:root@xerxes.crbm.cnrs-mop.fr [193.49.189.10]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA16199 for ; Thu, 13 Apr 2000 11:34:53 +0100 (BST) X-Received: from eta.crbm.cnrs-mop.fr (IDENT:root@eta [193.49.189.67]) by xerxes.crbm.cnrs-mop.fr (8.9.3/jtpda-5.3.1) with ESMTP id MAA02896 ; Thu, 13 Apr 2000 12:37:46 +0200 X-Received: from beta.crbm.cnrs-mop.fr (beta.crbm.cnrs-mop.fr [193.49.189.62]) by eta.crbm.cnrs-mop.fr (8.9.1a/jtpda-5.3.1) with ESMTP id MAA23036 ; Thu, 13 Apr 2000 12:34:37 +0200 X-Received: from (mieg@localhost) by beta.crbm.cnrs-mop.fr (8.9.3/jtpda-5.3.1) id VAA06849 ; Thu, 13 Apr 2000 21:36:24 +0200 (MET DST) X-To: acedb@dl.ac.uk, acedb@hgmp.mrc.ac.uk X-Cc: srk@sanger.ac.uk Date: Thu, 13 Apr 2000 13:34:19 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk if this is a posix system you can try setenv ACEDB_MACHINE POSIX_4 make tace aceserver but aceserver uses rpc it would also be interesting to test the beta version of acedb.4_8 available at sanger which comes with GTK libraries and see if that compiles on you mac may be srk can discuss that with you --- From owner-acedb@hgmp.mrc.ac.uk Thu Apr 13 13:34:28 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8B06317B41; Thu, 13 Apr 2000 13:34:27 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id EB85117B3A; Thu, 13 Apr 2000 13:34:24 +0100 (BST) Received: (from daemon@localhost) by hgmp.mrc.ac.uk (8.9.3/8.9.3) id NAA28572 for bionet-software-acedb@net.bio.net; Thu, 13 Apr 2000 13:31:59 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: srk@sanger.ac.uk (Simon Kelley) Newsgroups: bionet.software.acedb Subject: Re: mac OS X Organization: Sanger Centre, Hinxton Hall, England. Message-ID: <38F5BE34.F76D96CF@sanger.ac.uk> References: <200004131936.VAA06849@beta.crbm.cnrs-mop.fr> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: from jess.sanger.ac.uk (root@jess.sanger.ac.uk [193.60.84.61]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA28550 for ; Thu, 13 Apr 2000 13:31:52 +0100 (BST) X-Received: from sanger.ac.uk (srk@danah [172.25.16.59]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id NAA08687; Thu, 13 Apr 2000 13:31:49 +0100 (BST) X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.0.36 i686) X-Accept-Language: en X-To: Danielle et jean Thierry-Mieg X-CC: acedb@dl.ac.uk, acedb@hgmp.mrc.ac.uk Date: Thu, 13 Apr 2000 13:34:24 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Danielle et jean Thierry-Mieg wrote: > > if this is a posix system you can try > > setenv ACEDB_MACHINE POSIX_4 > make tace aceserver > > but aceserver uses rpc > > it would also be interesting to test the beta version of acedb.4_8 available at sanger > which comes with GTK libraries and see if that compiles on you mac > > may be srk can discuss that with you It won't unless you can find or do a port of GTK/GDK to the mac, or find an Xserver for MacOS X. I believe Joen Carmack is porting XFree86, but I don't know the details. It would be interesting to know if the non-graphical code works...... Simon -- ------------------------------------------------------------------------------- Simon Kelley. srk@sanger.ac.uk simon.kelley@bigfoot.com +44 1223 494991 --- From owner-acedb@hgmp.mrc.ac.uk Mon Apr 17 09:22:20 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1234917A67; Mon, 17 Apr 2000 09:22:19 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id E909017A5B; Mon, 17 Apr 2000 09:22:17 +0100 (BST) Received: from beaver.cs.washington.edu (beaver.cs.washington.edu [128.95.1.1]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA15001 for ; Thu, 13 Apr 2000 21:38:17 +0100 (BST) Received: from nntp4.u.washington.edu (root@nntp4.u.washington.edu [140.142.17.38]) by beaver.cs.washington.edu (8.9.3/8.9.3/0.3) with ESMTP id NAA14820 for ; Thu, 13 Apr 2000 13:38:14 -0700 (PDT) (envelope-from root@nntp4.u.washington.edu) Received: (from root@localhost) by nntp4.u.washington.edu (8.9.3+UW99.09/8.9.3+UW00.01) id NAA19412 for bionet-software-acedb@beaver.cs.washington.edu; Thu, 13 Apr 2000 13:38:13 -0700 To: bionet-software-acedb@cs.washington.edu From: Carson Thoreen Newsgroups: bionet.software.acedb Subject: Re: mac OS X Organization: Dept. of Molecular Biotechnology Message-ID: <38F630DB.45E93166@brown.edu> References: <200004131936.VAA06849@beta.crbm.cnrs-mop.fr> <38F5BE34.F76D96CF@sanger.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Trace: nntp4.u.washington.edu 955658293 8402 (None) 140.142.17.35 X-Complaints-To: help@cac.washington.edu X-Mailer: Mozilla 4.72 (Macintosh; I; PPC) X-Accept-Language: en,pdf Date: Mon, 17 Apr 2000 09:22:17 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > > > It won't unless you can find or do a port of GTK/GDK to the mac, or find > an Xserver for MacOS X. I believe Joen Carmack is porting XFree86, but I > don't know the details. > > It would be interesting to know if the non-graphical code works...... > > Simon I can run the client on an alpha, so all that needs to work is saceserver and tace (for AcePerl). Given that OS X runs on top of a BDS layer, I think it should be possible, and maybe even trivial, to get it working but I don't know quite where to begin. Ideas? -Carson From owner-acedb@hgmp.mrc.ac.uk Mon Apr 17 09:23:17 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0A18B17AB3; Mon, 17 Apr 2000 09:23:15 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 4A5BC17A67; Mon, 17 Apr 2000 09:23:13 +0100 (BST) Received: from jess.sanger.ac.uk (root@jess.sanger.ac.uk [193.60.84.61]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id CAA20251 for ; Sat, 15 Apr 2000 02:59:56 +0100 (BST) Received: from griffin.sanger.ac.uk (rd@griffin [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id CAA10624; Sat, 15 Apr 2000 02:59:53 +0100 (BST) From: Richard Durbin Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id CAA08513; Sat, 15 Apr 2000 02:59:52 +0100 (BST) Message-Id: <200004150159.CAA08513@griffin.sanger.ac.uk> To: bionet-software-acedb@hgmp.mrc.ac.uk, matthews@greengenes.cit.cornell.edu Subject: Re: case-sensitivity of Keywords Newsgroups: bionet.software.acedb Date: Mon, 17 Apr 2000 09:23:13 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > Is it possible to make the ?Keyword class non-Case-Sensitive? It appears > to be a System class and not controlled by wspec/options.wrm. I don't > see any way to turn the case-sensitivity off. (in ace4_7m or 4_8c) > - Dave I can see the point here, but I can't advise making this change except protected by #ifdef ACEDB5 (i.e. only for the next major version), because otherwise all existing databases with case-dependent keywords would be in a confused state. Does anyone remember why we made this case sensitive? Richard From owner-acedb@hgmp.mrc.ac.uk Mon Apr 17 17:09:14 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id ED0A917B16; Mon, 17 Apr 2000 17:09:13 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id E823017AC2; Mon, 17 Apr 2000 17:09:11 +0100 (BST) Received: from isgate.is (isgate.is [193.4.58.51]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA27694 for ; Mon, 17 Apr 2000 13:12:43 +0100 (BST) Received: from mail.deja.com (mail.deja.com [205.238.143.34]) by isgate.is (8.9.3r/8.9.0Imo) with ESMTP id LAA06755 for ; Mon, 17 Apr 2000 11:51:26 GMT Received: from nnrp1.deja.com (nnrp1.deja.com [10.2.2.16]) by mail.deja.com (8.8.7/8.8.5) with ESMTP id GAA09332 for ; Mon, 17 Apr 2000 06:51:10 -0500 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id GAA13470; Mon, 17 Apr 2000 06:51:04 -0500 To: bionet-software-acedb@moderators.isc.org From: zgudmunt@my-deja.com Newsgroups: bionet.software.acedb Subject: On new socket client/server Organization: Deja.com - Before you buy. Message-ID: <8detr8$d4t$1@nnrp1.deja.com> X-Article-Creation-Date: Mon Apr 17 11:51:08 2000 GMT X-Http-User-Agent: Mozilla/4.7 [en] (WinNT; I) X-Http-Proxy: 1.0 proxy.decode.is:8080 (Squid/2.2.STABLE5), 1.0 x33.deja.com:80 (Squid/1.1.22) for client 172.18.253.134, 193.4.196.222 X-MyDeja-Info: XMYDJUIDzgudmunt Date: Mon, 17 Apr 2000 17:09:11 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I have been trying out the new socket server and the text client. Seems work fine for my setup. But how about the graphic client, Unix and/or Windows; what's new on that (Simon...?) And how will AcePerl fit into all of this, can we expect a new release that uses the socket server? Mummi Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Tue Apr 18 10:32:44 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7408317A88; Tue, 18 Apr 2000 10:32:43 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 336EC17A58; Tue, 18 Apr 2000 10:32:40 +0100 (BST) Received: (from daemon@localhost) by hgmp.mrc.ac.uk (8.9.3/8.9.3) id BAA18611 for bionet-software-acedb@net.bio.net; Tue, 18 Apr 2000 01:57:26 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: matthews@greengenes.cit.cornell.edu (Dave Matthews) Newsgroups: bionet.software.acedb Subject: performance problems in loading Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200004180057.UAA06408@greengenes.cit.cornell.edu> X-Received: from greengenes.cit.cornell.edu (GREENGENES.CIT.CORNELL.EDU [128.253.246.43]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id BAA18586 for ; Tue, 18 Apr 2000 01:57:19 +0100 (BST) X-Received: (from matthews@localhost) by greengenes.cit.cornell.edu (8.9.3/8.9.3) id UAA06408; Mon, 17 Apr 2000 20:57:17 -0400 (EDT) X-To: ACEDB newsgroup X-Cc: xgai@iastate.edu Date: Tue, 18 Apr 2000 10:32:40 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Apologies for forwarding a raw dialog, but there are several interesting issues scattered in it. ZmDB is at www.zmdb.iastate.edu/. - Dave ~~~~~~~~~~~~~ Date: Mon, 17 Apr 2000 14:37:51 -0500 From: xgai Subject: Re: slow loading ACEDB Dear Dr. Matthews: Thank you for your quick response. I checked the memory usage and xace uses only 8% of the memory. Our server has 0.5 GB memory. As you noticed, the Sequence model that I built is a very simple model, it is much less complicated than the model used by ACeDB. I actually wondered how people who maintain the ACeDB did to load the large amount of data. Their database is much larger and much more complicated. I tried to divide the big .ace file into several smaller files. I tried to load the database by phases and quit, save the data and reopen it in between. It does not solve the problem. The total number of the sequence objects seems to be the magical number. I realized that it should take longer and longer to update the index file when the index got much larger. However, it is the precipitous drop of performance that puzzles me. In fact, this time the sequences that I am trying to load do not have "EST" as the keyword (I found it is not that useful anyway since all my sequences are ESTs). One more question: Do you know any good ACEDB documents that are more like an ACEDB database manager's guide? It has been very frustrating for me to try to figure a lot of things out and I can not find such a document for reference on all of the acedb links or web sites that I can find. I am really thankful that you spent time answering my questions. I greatly appreciate it. Best wishes, At 03:01 PM 4/17/00 -0400, you wrote: >Hi Xiaowu, > >Interesting question. Looks like a good one for the ACEDB newsgroup. >Lots of folks are building bigger databases nowadays, and no doubt starting >to hit performance problems. I have two thoughts/suggestions: > >1. machine > >The symptoms sound like you're running out of RAM and starting to use the >swap space (virtual memory). This would always slow things down hugely. >Even worse if your swap space is on the same disk with database/block*wrm >and/or the .ace file. You can monitor memory usage while the database is >loading with "ps" and "vmstat". I like "top" even better; it's usually >included with Linux. > >I noticed this with GrainGenes when the number of Sequence records went >past about 30K. On my old Sparc2 with 64 MB RAM it now takes over two hours >to load the whole database. On a newer machine with 1 GB RAM (Intel Solaris) >it's 4 minutes. > >2. ACEDB > >One thing ACEDB doesn't handle very well is records that have huge numbers >of links from them, tens of thousands. I just looked at the Sequence model >for the online ZmDB, and it looks like you've cleaned it of XREFs that >might cause this kind of trouble. But I notice many of your Sequences have >Keyword "EST". The ?Keyword class is usually automatically XREF'd; I don't >know how to prevent it. Also, trying to query or browse ZmDB for Keyword >EST, or 'find Sequence keyword=est', all fail. > >Did you look in database/log.wrm for complaints? As you may know, this one >is common: > >2000-04-14_10:20:10 genome 16041 Class Text, object 93.09 has >8729 > 3000 cells. > This is just a warning, acedb has no hard limits on the mumber of cells > per object, but the performances degrade on very large objects > Either, you are cross referencing many entries into a single object, > it may not be useful, and you could drop the XREF in the model and get the > same info via an occasional query or, continually, via a subclass, > or This object is Class:?Text, and you should rather use plain Text in > the model > or define a controlled vocabulary by giving an explicit list of tags > This message is issued once per offending class and per code run > > >I'd be interested to hear if you identify any smoking guns. > >cheers, >- Dave > > > > From xgai@iastate.edu Mon Apr 17 10:56:30 2000 > > Subject: Please help > > > > I need your help. Our database, ZmDB, is an ACEDB database. I found an > > interesting problem with ACEDB that confuses and frustrates me. When I used > > the Ace parser to load a large .ace file, it first was flying (relatively) > > and parsed thousands of records in a few minutes. However, after a while , > > it seemed reach to a critical point where it becomes terribly slow (about > > one record per minute). I am very frustrated and puzzled. I can not find > > anywhere in ACEDB documents that says anything about it? Can you shed some > > lights on it? Thank you. > > > > Some details: we are running ACEDB on a linux box (RedHat5.2). The number > > of records that I tried to load is about 50,000 of the same type sequence > > data. Xiaowu Gai 2104 Molecular Biology Building Department of Zoology & Genetics Iowa State University Ames, IA 50010 Tel: (515)-2940022 --- From owner-acedb@hgmp.mrc.ac.uk Tue Apr 18 13:08:59 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1705517ADB; Tue, 18 Apr 2000 13:08:59 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id D198F17AB0; Tue, 18 Apr 2000 13:08:56 +0100 (BST) Received: from wodc7-1.relay.mail.uu.net (wodc7-1.relay.mail.uu.net [199.171.54.114]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA08888 for ; Tue, 18 Apr 2000 13:07:18 +0100 (BST) Received: from mail.deja.com by wodc7mr0.ffx.ops.us.uu.net with ESMTP (peer crosschecked as: mail.deja.com [205.238.143.34]) id QQillg16881 for ; Tue, 18 Apr 2000 12:07:16 GMT Received: from nnrp1.deja.com (nnrp1.deja.com [10.2.2.16]) by mail.deja.com (8.8.7/8.8.5) with ESMTP id HAA15960 for ; Tue, 18 Apr 2000 07:07:16 -0500 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id HAA11688; Tue, 18 Apr 2000 07:07:06 -0500 To: bionet-software-acedb@moderators.isc.org From: syurman@spatialfocus.com Newsgroups: bionet.software.acedb Subject: Our dumps are diving Organization: Deja.com - Before you buy. Message-ID: <8dhj5a$bd7$1@nnrp1.deja.com> X-Article-Creation-Date: Tue Apr 18 12:07:13 2000 GMT X-Http-User-Agent: Mozilla/4.7 [en] (X11; I; Linux 2.2.14 i686) X-Http-Proxy: 1.0 x30.deja.com:80 (Squid/1.1.22) for client 209.86.45.245 X-MyDeja-Info: XMYDJUIDsyurman Date: Tue, 18 Apr 2000 13:08:56 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk My partner and I are using ACEDB to construct photogrammetric database definitions, and store geographic metadata in general. We are having trouble finishing the project because ACEDB has repeatedly come to a screeching halt in the process of doing a dump. It then promptly loses all the input since the previous dump. We have been using ACEDB for about a year, and haven't run into this before. Any suggestions? Thanks in advance, Sara Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Tue Apr 18 15:20:39 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 285F017A81; Tue, 18 Apr 2000 15:20:39 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 0128A17A64; Tue, 18 Apr 2000 15:20:36 +0100 (BST) Received: from briar.org (backdraft.briar.org [192.207.123.123]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id OAA17774 for ; Tue, 18 Apr 2000 14:16:45 +0100 (BST) Received: (from smap@localhost) by briar.org (8.9.1b+Sun/8.6.12) id JAA05152 for ; Tue, 18 Apr 2000 09:16:35 -0400 (EDT) X-Authentication-Warning: backdraft.briar.org: smap set sender to using -f Received: from mail.deja.com(205.238.143.34) by backdraft via smap (V2.1) id xma005150; Tue, 18 Apr 00 09:16:12 -0400 Received: from nnrp1.deja.com (nnrp1.deja.com [10.2.2.16]) by mail.deja.com (8.8.7/8.8.5) with ESMTP id IAA19742 for ; Tue, 18 Apr 2000 08:16:12 -0500 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id IAA16365; Tue, 18 Apr 2000 08:15:56 -0500 To: bionet-software-acedb@moderators.isc.org From: zgudmunt@my-deja.com Newsgroups: bionet.software.acedb Subject: Re: performance problems in loading Organization: Deja.com - Before you buy. Message-ID: <8dhn6c$fvc$1@nnrp1.deja.com> References: <200004180057.UAA06408@greengenes.cit.cornell.edu> X-Article-Creation-Date: Tue Apr 18 13:16:10 2000 GMT X-Http-User-Agent: Mozilla/4.7 [en] (WinNT; I) X-Http-Proxy: 1.0 proxy.decode.is:8080 (Squid/2.2.STABLE5), 1.0 x28.deja.com:80 (Squid/1.1.22) for client 172.18.253.134, 193.4.196.222 X-MyDeja-Info: XMYDJUIDzgudmunt Date: Tue, 18 Apr 2000 15:20:36 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I would like to pitch in some information about my own experience with rather large (from my viewpoint) Ace-dbases. I maintain, among other things, a local version of the human BAC ends collection. These are between 700 and 800 thousand sequence objects, each linking back to a BAC-parent, (just over 400 thousand BACs). The whole thing is taking almost 2 Gb on disk but did, admittedly, take a while to load from the 500 Mb Acefile. My hardware is a 450 MHz PIII with around 500 Mb RAM. When querying the thing, it performs quite well and only slows down when I do something silly like querying ALL the Sequence-objects by some of their tags, so all access-methods (AcePerl mostly) are designed to NOT make that sort of queries! My way around that sort of problem, like when looking for a sequence with a particular GenBank-accession, is to make a model and GenBank_accession-object that links back to the sequence itself, elimating the need to ask check and every sequence for its accession. Quite similar to indexing a column in a relational table. But, this may be old news to veteran Ace-ers :I So, I hope this helps with the hardware/performance-discussion. I will soon expand this setup to incorporate other BAC-data (ePCR, hybridizations etc) which will increase my cross-reference count great deal. IŽll keep you posted on how it affects my performancs. And one more thing; I came across some documentation on a benchmarking utility called Aquila. Is that still supported and used? I had trouble finding the software to download. Can someone help me on that one? Thanks, Mummi, Iceland In article <200004180057.UAA06408@greengenes.cit.cornell.edu>, matthews@greengenes.cit.cornell.edu (Dave Matthews) wrote: > Apologies for forwarding a raw dialog, but there are several interesting > issues scattered in it. ZmDB is at www.zmdb.iastate.edu/. > - Dave > > ~~~~~~~~~~~~~ > Date: Mon, 17 Apr 2000 14:37:51 -0500 > From: xgai > Subject: Re: slow loading ACEDB > > Dear Dr. Matthews: > > Thank you for your quick response. > > I checked the memory usage and xace uses only 8% of the memory. Our server > has 0.5 GB memory. As you noticed, the Sequence model that I built is a > very simple model, it is much less complicated than the model used by > ACeDB. I actually wondered how people who maintain the ACeDB did to load > the large amount of data. Their database is much larger and much more > complicated. > > I tried to divide the big .ace file into several smaller files. I tried to > load the database by phases and quit, save the data and reopen it in > between. It does not solve the problem. The total number of the sequence > objects seems to be the magical number. I realized that it should take > longer and longer to update the index file when the index got much larger. > However, it is the precipitous drop of performance that puzzles me. > > In fact, this time the sequences that I am trying to load do not have "EST" > as the keyword (I found it is not that useful anyway since all my sequences > are ESTs). > > One more question: Do you know any good ACEDB documents that are more like > an ACEDB database manager's guide? It has been very frustrating for me to > try to figure a lot of things out and I can not find such a document for > reference on all of the acedb links or web sites that I can find. > > I am really thankful that you spent time answering my questions. I greatly > appreciate it. > > Best wishes, > > At 03:01 PM 4/17/00 -0400, you wrote: > >Hi Xiaowu, > > > >Interesting question. Looks like a good one for the ACEDB newsgroup. > >Lots of folks are building bigger databases nowadays, and no doubt starting > >to hit performance problems. I have two thoughts/suggestions: > > > >1. machine > > > >The symptoms sound like you're running out of RAM and starting to use the > >swap space (virtual memory). This would always slow things down hugely. > >Even worse if your swap space is on the same disk with database/block*wrm > >and/or the .ace file. You can monitor memory usage while the database is > >loading with "ps" and "vmstat". I like "top" even better; it's usually > >included with Linux. > > > >I noticed this with GrainGenes when the number of Sequence records went > >past about 30K. On my old Sparc2 with 64 MB RAM it now takes over two hours > >to load the whole database. On a newer machine with 1 GB RAM (Intel Solaris) > >it's 4 minutes. > > > >2. ACEDB > > > >One thing ACEDB doesn't handle very well is records that have huge numbers > >of links from them, tens of thousands. I just looked at the Sequence model > >for the online ZmDB, and it looks like you've cleaned it of XREFs that > >might cause this kind of trouble. But I notice many of your Sequences have > >Keyword "EST". The ?Keyword class is usually automatically XREF'd; I don't > >know how to prevent it. Also, trying to query or browse ZmDB for Keyword > >EST, or 'find Sequence keyword=est', all fail. > > > >Did you look in database/log.wrm for complaints? As you may know, this one > >is common: > > > >2000-04-14_10:20:10 genome 16041 Class Text, object 93.09 has > >8729 > 3000 cells. > > This is just a warning, acedb has no hard limits on the mumber of cells > > per object, but the performances degrade on very large objects > > Either, you are cross referencing many entries into a single object, > > it may not be useful, and you could drop the XREF in the model and get the > > same info via an occasional query or, continually, via a subclass, > > or This object is Class:?Text, and you should rather use plain Text in > > the model > > or define a controlled vocabulary by giving an explicit list of tags > > This message is issued once per offending class and per code run > > > > > >I'd be interested to hear if you identify any smoking guns. > > > >cheers, > >- Dave > > > > > > > From xgai@iastate.edu Mon Apr 17 10:56:30 2000 > > > Subject: Please help > > > > > > I need your help. Our database, ZmDB, is an ACEDB database. I found an > > > interesting problem with ACEDB that confuses and frustrates me. When I used > > > the Ace parser to load a large .ace file, it first was flying (relatively) > > > and parsed thousands of records in a few minutes. However, after a while , > > > it seemed reach to a critical point where it becomes terribly slow (about > > > one record per minute). I am very frustrated and puzzled. I can not find > > > anywhere in ACEDB documents that says anything about it? Can you shed some > > > lights on it? Thank you. > > > > > > Some details: we are running ACEDB on a linux box (RedHat5.2). The number > > > of records that I tried to load is about 50,000 of the same type sequence > > > data. > > Xiaowu Gai > 2104 Molecular Biology Building > Department of Zoology & Genetics > Iowa State University > Ames, IA 50010 > Tel: (515)-2940022 > --- > > Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Wed Apr 19 10:37:58 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5ED6417B1D; Wed, 19 Apr 2000 10:37:58 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 77EF617AE4; Wed, 19 Apr 2000 10:37:56 +0100 (BST) Received: from mailbox3.ucsd.edu (mailbox3.ucsd.edu [132.239.1.55]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA27503 for ; Wed, 19 Apr 2000 09:38:26 +0100 (BST) Received: from jess.sanger.ac.uk (jess.sanger.ac.uk [193.60.84.61]) by mailbox3.ucsd.edu (8.9.3/8.9.3) with ESMTP id BAA12214 for ; Wed, 19 Apr 2000 01:38:24 -0700 (PDT) Received: from griffin.sanger.ac.uk (rd@griffin [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id JAA04801; Wed, 19 Apr 2000 09:38:20 +0100 (BST) From: Richard Durbin Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id JAA11133; Wed, 19 Apr 2000 09:38:20 +0100 (BST) Message-Id: <200004190838.JAA11133@griffin.sanger.ac.uk> To: bionet-software-acedb@moderators.isc.org, zgudmunt@my-deja.com Subject: Re: performance problems in loading Newsgroups: bionet.software.acedb Date: Wed, 19 Apr 2000 10:37:56 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I would guess that Xiaowu Gai's problem is with disk access. Everything is very fast while filling up cache, but when the kernel's object cache gets full objects need writing to disk (which they all will eventually) and if the disk connection is not good then this will slow things way down. This type of behaviour would be typical of any database. Richard > From xgai@iastate.edu Mon Apr 17 10:56:30 2000 > Subject: Please help > > I need your help. Our database, ZmDB, is an ACEDB database. I found an > interesting problem with ACEDB that confuses and frustrates me. When I used > the Ace parser to load a large .ace file, it first was flying (relatively) > and parsed thousands of records in a few minutes. However, after a while , > it seemed reach to a critical point where it becomes terribly slow (about > one record per minute). I am very frustrated and puzzled. I can not find > anywhere in ACEDB documents that says anything about it? Can you shed some > lights on it? Thank you. From owner-acedb@hgmp.mrc.ac.uk Wed Apr 19 13:29:36 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C16A117AAE; Wed, 19 Apr 2000 13:29:35 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 4C3AC17A98; Wed, 19 Apr 2000 13:29:34 +0100 (BST) Received: (from daemon@localhost) by hgmp.mrc.ac.uk (8.9.3/8.9.3) id KAA04760 for bionet-software-acedb@net.bio.net; Wed, 19 Apr 2000 10:50:57 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: mieg@alpha.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: performance problems in loading Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200004191852.UAA06727@alpha.crbm.cnrs-mop.fr> X-Received: from xerxes.crbm.cnrs-mop.fr (IDENT:root@xerxes.crbm.cnrs-mop.fr [193.49.189.10]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA04753 for ; Wed, 19 Apr 2000 10:50:54 +0100 (BST) X-Received: from eta.crbm.cnrs-mop.fr (IDENT:root@eta [193.49.189.67]) by xerxes.crbm.cnrs-mop.fr (8.9.3/jtpda-5.3.1) with ESMTP id LAA12321 ; Wed, 19 Apr 2000 11:53:38 +0200 X-Received: from alpha.crbm.cnrs-mop.fr (alpha.crbm.cnrs-mop.fr [193.49.189.71]) by eta.crbm.cnrs-mop.fr (8.9.1a/jtpda-5.3.1) with ESMTP id LAA31742 ; Wed, 19 Apr 2000 11:50:41 +0200 X-Received: from (mieg@localhost) by alpha.crbm.cnrs-mop.fr (8.9.3/jtpda-5.3.1) id UAA06727 ; Wed, 19 Apr 2000 20:52:31 +0200 (MET DST) X-To: acedb@dl.ac.uk, acedb@hgmp.mrc.ac.uk Date: Wed, 19 Apr 2000 13:29:34 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk You fly while you fill the cache but then it should stay fast you describe gioing to 1 record/minute which ius ridiculously slow so i suppose you have defines a cachesize much larger than you actual memeory and are swapping acedb should not swap please check wspec/cachesize.wrm , the size declared should be a good proportion of your real ram other explanation, as proposed by richard, your database disk is not locally mounted please what is you architecture, and your disk drive --- From owner-acedb@hgmp.mrc.ac.uk Wed Apr 19 15:36:16 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 83F2917B3A; Wed, 19 Apr 2000 15:36:15 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 8574D17B37; Wed, 19 Apr 2000 15:36:13 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA21507 for ; Wed, 19 Apr 2000 13:40:36 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA05350 for bionet-software-acedb@net.bio.net; Wed, 19 Apr 2000 13:40:35 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: Our dumps are diving Organization: Sanger Centre Message-ID: <38FDA943.2DC28E13@sanger.ac.uk> References: <8dhj5a$bd7$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 956148035 5335 193.60.84.177 (19 Apr 2000 12:40:35 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 19 Apr 2000 12:40:35 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Wed, 19 Apr 2000 15:36:13 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Sara, > My partner and I are using ACEDB to construct photogrammetric database > definitions, and store geographic metadata in general. We are having > trouble finishing the project because ACEDB has repeatedly come to a > screeching halt in the process of doing a dump. It then promptly loses > all the input since the previous dump. We have been using ACEDB for > about a year, and haven't run into this before. Please could you send some information about the following: which version of acedb are you using ? what machine are you running on ? how big is your database ? are there any error messages ? If you are not sure about how to collect any of this information then mail me direct. Thanks Ed ------------------------------------------------------------------------------ | Ed Griffiths, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 (switch +44 1223 834244) Fax: +44 1223 494919 | ------------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Thu Apr 20 09:19:20 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A419617B21; Thu, 20 Apr 2000 09:19:19 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 2DB6B17B17; Thu, 20 Apr 2000 09:19:17 +0100 (BST) Received: (from daemon@localhost) by hgmp.mrc.ac.uk (8.9.3/8.9.3) id TAA23482 for bionet-software-acedb@net.bio.net; Wed, 19 Apr 2000 19:22:49 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: mieg@alpha.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: performances Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200004200324.FAA07183@alpha.crbm.cnrs-mop.fr> X-Received: from xerxes.crbm.cnrs-mop.fr (IDENT:root@xerxes.crbm.cnrs-mop.fr [193.49.189.10]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA23471 for ; Wed, 19 Apr 2000 19:22:46 +0100 (BST) X-Received: from eta.crbm.cnrs-mop.fr (IDENT:root@eta [193.49.189.67]) by xerxes.crbm.cnrs-mop.fr (8.9.3/jtpda-5.3.1) with ESMTP id UAA17193 ; Wed, 19 Apr 2000 20:25:31 +0200 X-Received: from alpha.crbm.cnrs-mop.fr (alpha.crbm.cnrs-mop.fr [193.49.189.71]) by eta.crbm.cnrs-mop.fr (8.9.1a/jtpda-5.3.1) with ESMTP id UAA32267 ; Wed, 19 Apr 2000 20:22:35 +0200 X-Received: from (mieg@localhost) by alpha.crbm.cnrs-mop.fr (8.9.3/jtpda-5.3.1) id FAA07183 ; Thu, 20 Apr 2000 05:24:25 +0200 (MET DST) X-To: acedb@dl.ac.uk, acedb@hgmp.mrc.ac.uk Date: Thu, 20 Apr 2000 09:19:17 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk my database has 150 thousands sequences, i run it on a linux pc 350 MHz i load all data in may be 10 minutes the index all work via hashing so insertion time is independant of size what is a real kill is as Dave says XREF to many enties including ?Text entries which are all the same could i have a copy of the models used and a sample of tyhe data file if they all look the same for example if you have a chromosoeme with very many balst hits it can become heavy what we do in the worm is to split the chromosome in cosmids and each has not so many blast hits --- From owner-acedb@hgmp.mrc.ac.uk Thu Apr 20 10:03:22 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A863B17A8D; Thu, 20 Apr 2000 10:03:21 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 54AD917A67; Thu, 20 Apr 2000 10:03:20 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA06722 for ; Thu, 20 Apr 2000 10:00:38 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA28867 for bionet-software-acedb@net.bio.net; Thu, 20 Apr 2000 10:00:37 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: On new socket client/server Organization: Sanger Centre Message-ID: <38FEC734.76F4C15F@sanger.ac.uk> References: <8detr8$d4t$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 956221237 28865 193.60.84.177 (20 Apr 2000 09:00:37 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 20 Apr 2000 09:00:37 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 20 Apr 2000 10:03:20 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Mummi, > I have been trying out the new socket server and the text client. > Seems work fine for my setup. But how about the graphic client, Unix > and/or Windows; what's new on that (Simon...?) And how will AcePerl fit > into all of this, can we expect a new release that uses the socket > server? I am just looking at the graphical client code now as there have been other requests for it to work with the socket server. I get the feeling that this will either be a 5 minute job or 5 weeks...watch this space... AcePerl is currently being changed by its author (Lincoln Stein) so that it will talk directly to the socket server rather than via the intermediate acedb code which used to be necessary to handle the RPC stuff. I expect that Lincoln will post here when this work is done. cheers Ed ------------------------------------------------------------------------------ | Ed Griffiths, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 (switch +44 1223 834244) Fax: +44 1223 494919 | ------------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Thu Apr 20 11:36:11 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 6826117A8D; Thu, 20 Apr 2000 11:36:10 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 0775417A7B; Thu, 20 Apr 2000 11:36:08 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id LAA14888 for ; Thu, 20 Apr 2000 11:35:22 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA00096 for bionet-software-acedb@net.bio.net; Thu, 20 Apr 2000 11:35:21 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: ACeDB 4.8: availability??? Organization: Sanger Centre Message-ID: <38FEDD68.58152A41@sanger.ac.uk> References: <895t9m$m3v$1@news.uky.edu> <38BA66FF.71AF4A2E@sanger.ac.uk> <8bp46c$g50$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 956226920 94 193.60.84.177 (20 Apr 2000 10:35:20 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 20 Apr 2000 10:35:20 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 20 Apr 2000 11:36:08 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Several people have asked where they can get new versions of acedb code. If you go to the acedb ftp site (ftp://ftp.sanger.ac.uk/pub/acedb/) you will find a tar/gzip file called: Sanger-release.2000_03_08.tar.gz this is our last monthly build of the 4_8c development code. The montly builds are intended to be reasonably stable development code that we get internal users at the Sanger centre to try out. You are welcome to try out this code BUT NOTE THE FOLLOWING: - this is development code, please don't use it on your prized database (unless you are ready to restore the database yourself). Experiment with a copy ! - interfaces/code behaviour will change from month to month. - there may be obvious bugs or performance problems which won't be fixed until the next monthly release - if you find a problem then do report it to us (either through this newsgroup or via email, best to email acedb@sanger.ac.uk). I will be updating the ftp site, especially the README, and will put new monthly builds on the site as they are done. cheers Ed ------------------------------------------------------------------------------ | Ed Griffiths, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 (switch +44 1223 834244) Fax: +44 1223 494919 | ------------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Thu Apr 20 17:03:55 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D1D2417ADD; Thu, 20 Apr 2000 17:03:54 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3B29417A63; Thu, 20 Apr 2000 17:03:53 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA22936 for ; Thu, 20 Apr 2000 17:03:03 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA04464 for bionet-software-acedb@net.bio.net; Thu, 20 Apr 2000 17:03:02 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: aquila Organization: Sanger Centre Message-ID: <38FF2A36.93B57AD3@sanger.ac.uk> References: <200004180057.UAA06408@greengenes.cit.cornell.edu> <8dhn6c$fvc$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 956246582 4462 193.60.84.177 (20 Apr 2000 16:03:02 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 20 Apr 2000 16:03:02 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 20 Apr 2000 17:03:53 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Mummi, > And one more thing; I came across some documentation on a > benchmarking utility called Aquila. Is that still supported and used? I > had trouble finding the software to download. Can someone help me on > that one? Thanks, According to the header in the aquila perl script this is the person who wrote aquila: # Author: Detlef Wolf (D.Wolf@dkfz-heidelberg.de) # Copyright (C) European Data Resource, 1995 #-------------------------------------------------------------------- # This file is part of the IGD project I don't know if there have been any updates sicne 1995, perhaps if D.Wolf follows this newsgroup they will send in a note. We use aquila for testing the overnight build of acedb. It can be used to test the commandline versions of acedb: tace, giface, aceclient. You write script files of the acedb commands you want to use for testing and aquila squirts these into stdin and captures acedbs output. You can then use aquila to compare the output from previous acedb executables with the current one and look for differences. NOTE that if finds differences, not necessarily errors, it for instance find any comment output that has changed. Never-the-less it is very useful for flagging code changes that have broken acedb. I can tar up our test stuff if this is useful, if you manage to contact the owner of aquila and find that it has been updated, perhaps you could let me know. cheers Ed ------------------------------------------------------------------------------ | Ed Griffiths, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 (switch +44 1223 834244) Fax: +44 1223 494919 | ------------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Tue Apr 25 09:30:45 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 42BDA17A59; Tue, 25 Apr 2000 09:30:45 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 88D2A17A62; Tue, 25 Apr 2000 09:30:41 +0100 (BST) Received: (from daemon@localhost) by hgmp.mrc.ac.uk (8.9.3/8.9.3) id SAA03510 for bionet-software-acedb@net.bio.net; Thu, 20 Apr 2000 18:47:41 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: mieg@alpha.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: aquila Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200004210249.EAA08252@alpha.crbm.cnrs-mop.fr> X-Received: from xerxes.crbm.cnrs-mop.fr (IDENT:root@xerxes.crbm.cnrs-mop.fr [193.49.189.10]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id SAA03493 for ; Thu, 20 Apr 2000 18:47:37 +0100 (BST) X-Received: from eta.crbm.cnrs-mop.fr (IDENT:root@eta [193.49.189.67]) by xerxes.crbm.cnrs-mop.fr (8.9.3/jtpda-5.3.1) with ESMTP id TAA25261 ; Thu, 20 Apr 2000 19:50:15 +0200 X-Received: from alpha.crbm.cnrs-mop.fr (alpha.crbm.cnrs-mop.fr [193.49.189.71]) by eta.crbm.cnrs-mop.fr (8.9.1a/jtpda-5.3.1) with ESMTP id TAA02975 ; Thu, 20 Apr 2000 19:47:21 +0200 X-Received: from (mieg@localhost) by alpha.crbm.cnrs-mop.fr (8.9.3/jtpda-5.3.1) id EAA08252 ; Fri, 21 Apr 2000 04:49:08 +0200 (MET DST) X-To: acedb@dl.ac.uk, acedb@hgmp.mrc.ac.uk X-Cc: Detlef.Wolf@Roche.com Date: Tue, 25 Apr 2000 09:30:41 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Detlef Wolf, who wrote aquila is now in Swiss working for a bio company I am taking care of the package I will put the latest package on the ncbi and sanger site Aquila can be used to find differences and to compare compilation options and machine speed It produces a very large amount of output files but has an excellent facility to summarize the results Detlef.Wolf@Roche.com is his mail --- From owner-acedb@hgmp.mrc.ac.uk Tue Apr 25 09:31:05 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 431E817A68; Tue, 25 Apr 2000 09:31:04 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id B95CD17A65; Tue, 25 Apr 2000 09:31:02 +0100 (BST) Received: from isgate.is (isgate.is [193.4.58.51]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA15322 for ; Thu, 20 Apr 2000 21:06:17 +0100 (BST) Received: from mail.deja.com (mail.deja.com [205.238.143.34]) by isgate.is (8.9.3r/8.9.0Imo) with ESMTP id UAA20827 for ; Thu, 20 Apr 2000 20:06:09 GMT Received: from nnrp1.deja.com (nnrp1.deja.com [10.2.2.16]) by mail.deja.com (8.8.7/8.8.5) with ESMTP id PAA08993 for ; Thu, 20 Apr 2000 15:05:50 -0500 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id PAA08800; Thu, 20 Apr 2000 15:05:37 -0500 To: bionet-software-acedb@moderators.isc.org From: syurman@my-deja.com Newsgroups: bionet.software.acedb Subject: Re: Our dumps are diving Organization: Deja.com - Before you buy. Message-ID: <8dnnuh$8iv$1@nnrp1.deja.com> References: <8dhj5a$bd7$1@nnrp1.deja.com> <38FDA943.2DC28E13@sanger.ac.uk> X-Article-Creation-Date: Thu Apr 20 20:05:50 2000 GMT X-Http-User-Agent: Mozilla/4.7 [en] (X11; I; Linux 2.2.14 i686) X-Http-Proxy: 1.0 x33.deja.com:80 (Squid/1.1.22) for client 209.86.45.245 X-MyDeja-Info: XMYDJUIDsyurman Date: Tue, 25 Apr 2000 09:31:02 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi Ed, My apologies to all. The problem turned out to be the documentation I'd given my colleague. Our applications are way off the beaten track for most of the ACEDB stuff, so we tend to do our own documentation. I'm responsible for it, and made way too many assumptions. I'm reworking it and am sure the problem will solve itself post haste. Many thanks for such wonderful software. Cheers, Sara > Please could you send some information about the following: -------------------------------------------------------------------- > | Ed Griffiths, Informatics Group, | > | The Sanger Centre, Wellcome Trust Genome Campus, | > | Hinxton, Cambridge CB10 1SA, UK | > | | > | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | > | Tel: +44-1223-494780 (switch +44 1223 834244) Fax: +44 1223 494919 | > ------------------------------------------------------------------------------ > > Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Tue Apr 25 09:31:53 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id CED6C17A69; Tue, 25 Apr 2000 09:31:52 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 63C0317A68; Tue, 25 Apr 2000 09:31:51 +0100 (BST) Received: (from daemon@localhost) by hgmp.mrc.ac.uk (8.9.3/8.9.3) id TAA05158 for bionet-software-acedb@net.bio.net; Mon, 24 Apr 2000 19:34:03 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: bswanson@cmdmail.amd.com Newsgroups: bionet.software.acedb Subject: AcePerl 'add_row' Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200004241833.LAA17504@ultrasrvr9> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: j2bk9RDJE1F0HtBmUpUa6A== X-Received: from amdext.amd.com (amdext.amd.com [139.95.251.1]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id TAA05151 for ; Mon, 24 Apr 2000 19:33:59 +0100 (BST) X-Received: from amdint.amd.com (amdint.amd.com [139.95.250.1]) by amdext.amd.com (8.9.3/8.9.3/AMD) with ESMTP id LAA02802 for ; Mon, 24 Apr 2000 11:33:28 -0700 (PDT) X-Received: from cmdmail.amd.com (cmdmail.amd.com [172.28.14.226]) by amdint.amd.com (8.9.3/8.9.3/AMD) with ESMTP id LAA13966 for ; Mon, 24 Apr 2000 11:33:26 -0700 (PDT) X-Received: from ultrasrvr9 (ultrasrvr9.amd.com [172.28.14.122]) by cmdmail.amd.com (8.9.1a-LCCHA/8.9.0/lccha 1.5) with ESMTP id LAA10803 for ; Mon, 24 Apr 2000 11:33:25 -0700 (PDT) X-Received: by ultrasrvr9 (8.8.8+Sun) id LAA17504; Mon, 24 Apr 2000 11:33:22 -0700 (PDT) X-To: acedb@hgmp.mrc.ac.uk Date: Tue, 25 Apr 2000 09:31:51 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Using AcePerl, I'm trying to add data to an object created in my script. The 'add_row' (and 'add_tree') methods do not appear to be capable of handling a tag without an associated value (e.g. using the existence of the tag in the object as a flag.) Is it possible to add just a tag that has no associated value in the model using AcePerl? (importing a .ace file works fine) Thanks. Brian --- From owner-acedb@hgmp.mrc.ac.uk Wed Apr 26 12:51:50 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8AFBA17A9F; Wed, 26 Apr 2000 12:51:48 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 2099217A5B; Wed, 26 Apr 2000 12:51:44 +0100 (BST) Received: (from daemon@localhost) by hgmp.mrc.ac.uk (8.9.3/8.9.3) id VAA21621 for bionet-software-acedb@net.bio.net; Tue, 25 Apr 2000 21:39:53 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: matthews@greengenes.cit.cornell.edu (Dave Matthews) Newsgroups: bionet.software.acedb Subject: re: performance problems in loading Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200004252039.QAA17217@greengenes.cit.cornell.edu> X-Received: from greengenes.cit.cornell.edu (GREENGENES.CIT.CORNELL.EDU [128.253.246.43]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id VAA21602 for ; Tue, 25 Apr 2000 21:39:47 +0100 (BST) X-Received: (from matthews@localhost) by greengenes.cit.cornell.edu (8.9.3/8.9.3) id QAA17217 for ACEDB newsgroup ; Tue, 25 Apr 2000 16:39:45 -0400 (EDT) X-To: ACEDB newsgroup Date: Wed, 26 Apr 2000 12:51:44 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk jean said: : Date: Wed, 19 Apr 2000 13:29:34 +0100 (BST) : : You fly while you fill the cache : but then it should stay fast : : you describe gioing to 1 record/minute which ius ridiculously slow : : so i suppose you have defines a cachesize much larger than you actual : memeory and are swapping : acedb should not swap : : please check wspec/cachesize.wrm , the size declared should be a good : proportion of your real ram Xiaowu Gai reported back that the problem was indeed his cache sizes, but in the opposite direction. He originally had CACHE1 = 4000 CACHE2 = 4000 on a machine with 0.5 GB memory. (I'm not sure if that's RAM or total.) The fix: > I increased the cache sizes to the same as the ones that you listed [16000, > 32000] and it solved the problem. I loaded the whole 53,000 sequences in 10 > minutes. I also tried to increase them a little more and it became even > faster. --- From owner-acedb@hgmp.mrc.ac.uk Wed Apr 26 15:46:36 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id AA13017ACE; Wed, 26 Apr 2000 15:46:34 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 1EAAC17A72; Wed, 26 Apr 2000 15:46:27 +0100 (BST) Received: (from daemon@localhost) by hgmp.mrc.ac.uk (8.9.3/8.9.3) id NAA10461 for bionet-software-acedb@net.bio.net; Wed, 26 Apr 2000 13:36:38 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: mieg@alpha.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: direction Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200004260703.JAA00965@alpha.crbm.cnrs-mop.fr> X-Received: from xerxes.crbm.cnrs-mop.fr (IDENT:root@xerxes.crbm.cnrs-mop.fr [193.49.189.10]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA10454 for ; Wed, 26 Apr 2000 13:36:35 +0100 (BST) X-Received: from eta.crbm.cnrs-mop.fr (IDENT:root@eta [193.49.189.67]) by xerxes.crbm.cnrs-mop.fr (8.9.3/jtpda-5.3.1) with ESMTP id OAA12919 ; Wed, 26 Apr 2000 14:38:43 +0200 X-Received: from alpha.crbm.cnrs-mop.fr (alpha.crbm.cnrs-mop.fr [193.49.189.71]) by eta.crbm.cnrs-mop.fr (8.9.1a/jtpda-5.3.1) with ESMTP id NAA03884 ; Wed, 26 Apr 2000 13:47:42 +0200 X-Received: from (mieg@localhost) by alpha.crbm.cnrs-mop.fr (8.9.3/jtpda-5.3.1) id JAA00965 ; Wed, 26 Apr 2000 09:03:47 +0200 (MET DST) X-To: edgrif@sanger.ac.uk X-Cc: acedb@dl.ac.uk, acedb@hgmp.mrc.ac.uk Date: Wed, 26 Apr 2000 15:46:27 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk this is the direction i proned ! : please check wspec/cachesize.wrm , the size declared should be a good : proportion of your real ram to me good propportion means 30% ---