From owner-acedb@hgmp.mrc.ac.uk Fri Jun 2 09:19:07 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 74DA817B5D; Fri, 2 Jun 2000 09:19:06 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 98A4017B5C; Fri, 2 Jun 2000 09:19:04 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 4934917ACE; Thu, 1 Jun 2000 23:25:39 +0100 (BST) Received: from beaver.cs.washington.edu (beaver.cs.washington.edu [128.95.1.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 7D82F415D4 for ; Thu, 1 Jun 2000 23:25:37 +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 PAA24654 for ; Thu, 1 Jun 2000 15:25:35 -0700 (PDT) (envelope-from root@nntp4.u.washington.edu) Received: (from root@localhost) by nntp4.u.washington.edu (8.9.3+UW00.05/8.9.3+UW00.01) id PAA77168 for bionet-software-acedb@beaver.cs.washington.edu; Thu, 1 Jun 2000 15:25:34 -0700 To: bionet-software-acedb@cs.washington.edu From: Carson Thoreen Newsgroups: bionet.software.acedb Subject: Chromosome band objects... Organization: University of Washington Message-ID: X-Trace: nntp4.u.washington.edu 959898334 58990 (None) 140.142.17.35 X-Complaints-To: help@cac.washington.edu User-Agent: MT-NewsWatcher/3.0 (PPC) Date: Fri, 2 Jun 2000 09:19:04 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello, I'm configuring my database to display clone-FISH data on a human cytogenetic map using the Chrom_Band and Map objects. Has anyone already entered all of the band->Map_position information and would you mind emailing me an ace file describing those objects? Thanks very much, Carson Carson_Thoreen@brown.edu From owner-acedb@hgmp.mrc.ac.uk Mon Jun 5 09:10:08 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 57FE117AFC; Mon, 5 Jun 2000 09:10:08 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 0F75417ADE; Mon, 5 Jun 2000 09:10:06 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 53AD417B19; Sat, 3 Jun 2000 15:44:16 +0100 (BST) Received: from wodc7-2.relay.mail.uu.net (wodc7-2.relay.mail.uu.net [199.171.54.115]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 05A2B415D5 for ; Sat, 3 Jun 2000 15:44:14 +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 QQirzm21204 for ; Sat, 3 Jun 2000 14:44:13 GMT Received: from nnrp1.deja.com (nnrp1.deja.com [10.12.2.16]) by mail.deja.com (8.8.7/8.8.5) with ESMTP id JAA01021 for ; Sat, 3 Jun 2000 09:44:12 -0500 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id JAA18645; Sat, 3 Jun 2000 09:44:08 -0500 To: bionet-software-acedb@moderators.isc.org From: zgudmunt@my-deja.com Newsgroups: bionet.software.acedb Subject: Re: Chromosome band objects... Organization: Deja.com - Before you buy. Message-ID: <8hb5jo$i6k$1@nnrp1.deja.com> References: X-Article-Creation-Date: Sat Jun 03 14:44:10 2000 GMT X-Http-User-Agent: Mozilla/4.7 [en] (X11; I; Linux 2.2.14-15mdk i686) X-Http-Proxy: 1.0 proxy.decode.is:8080 (Squid/2.2.STABLE5), 1.0 x71.deja.com:80 (Squid/1.1.22) for client 172.18.2.4, 193.4.196.222 X-MyDeja-Info: XMYDJUIDzgudmunt Date: Mon, 5 Jun 2000 09:10:06 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I have all the bands listed in Weizmann's UDB (see examply below) list of chromosome bands in my Ace. I just parsed the tables that they supply with my little Perl-script and added (most of) the Dark-tag by hand afterwards. Do you want to use those band-data? In that case IŽd be happy to share it with you. I know it's tedious to do by hand, that's why I wrote a script to do it :) Mummi, Bioinformatics Table example: Band Mb Start Mb End Mb Size pter 0.000 0.000 0.000 p16.3 0.000 4.231 4.231 p16.2 4.231 7.405 3.174 ...etc.. In article , Carson Thoreen wrote: > Hello, > I'm configuring my database to display clone-FISH data on a human > cytogenetic map using the Chrom_Band and Map objects. Has anyone already > entered all of the band->Map_position information and would you mind > emailing me an ace file describing those objects? > > Thanks very much, > Carson > > Carson_Thoreen@brown.edu > > Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Mon Jun 5 18:30:03 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C356317AA5; Mon, 5 Jun 2000 18:30:02 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 7AB6317AA1; Mon, 5 Jun 2000 18:30:01 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 888A617AB9; Mon, 5 Jun 2000 14:58:03 +0100 (BST) Received: from moderated.news.pipex.net (moderated.news.pipex.net [158.43.192.79]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 66F16415D4 for ; Mon, 5 Jun 2000 14:58:02 +0100 (BST) Received: (qmail 20366 invoked by alias); 5 Jun 2000 13:58:01 -0000 Received: (qmail 20362 invoked from network); 5 Jun 2000 13:58:00 -0000 Received: from pat.ccc.nottingham.ac.uk (HELO nottingham.ac.uk) (128.243.40.194) by moderated.news.pipex.net with SMTP; 5 Jun 2000 13:58:00 -0000 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 12yxNC-0000N3-00 for bionet-software-acedb@moderators.isc.org; Mon, 05 Jun 2000 14:56:58 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 12yxO3-0005lC-00; Mon, 5 Jun 2000 14:57:51 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: problem with peptide display 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 960213471 22144 128.243.116.150 (5 Jun 2000 13:57:51 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 5 Jun 2000 13:57:51 GMT X-Sender: keith@thale Date: Mon, 5 Jun 2000 18:30:01 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi, I've just noticed that the peptide viewer (blixem?) in xace (4.7l) handles BLASTX and BLASTP homologies but won't handle a TBLASTN homology. This seems to be due to the view control only allowing a set number of columns (the view control display box does seem to allow for a 'Homol' column but I couldn't seem to get this to display anything). Is there anyway around this or will there be support for TBLASTN homologies in 4.8??? I can read these homologies in as BLASTX homologies to get them to display but this would be a little misleading to anybody using our database. Regards, Keith ~ Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR) ~ Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/ ~ University Park, University of Nottingham, NG7 2RD, UK ~ Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Tue Jun 6 15:55:31 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 986AD17B48; Tue, 6 Jun 2000 15:55:30 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id F3F7D17B3E; Tue, 6 Jun 2000 15:55:27 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 5D90F17B0A; Tue, 6 Jun 2000 15:34:26 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Estann@hotmail.com (Cyril) Newsgroups: bionet.software.acedb Subject: Re : phredphrap ACE files to ACEDB interface? Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <393D1AF8.C1889AF3@hotmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 4C4DD17AD4; Tue, 6 Jun 2000 15:34:24 +0100 (BST) X-Received: from iznogoud.sb-roscoff.fr (iznogoud.sb-roscoff.fr [193.52.39.103]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 0589E415CA for ; Tue, 6 Jun 2000 15:34:22 +0100 (BST) X-Received: from hotmail.com (mac1-resto.sb-roscoff.fr [193.52.39.92]) by iznogoud.sb-roscoff.fr (8.9.3/8.9.3) with ESMTP id QAA12952; Tue, 6 Jun 2000 16:32:21 +0100 (WET DST) X-Mailer: Mozilla 4.7 (Macintosh; I; PPC) X-Accept-Language: en X-To: acedb@net.bio.net, nathan@dnase.hpw.pri.bms.com Date: Tue, 6 Jun 2000 15:55:27 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello, have a look at the CAF package that you will find at the Sanger center. I have used it to reformat the ACE file from phred/phrap/consed and tigr assembler as well to the ACE file from ACEDB. It works fine. Best regards Florent --- From owner-acedb@hgmp.mrc.ac.uk Tue Jun 13 16:41:25 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B68CA17AF0; Tue, 13 Jun 2000 16:41:24 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 43D6C17A68; Tue, 13 Jun 2000 16:41:23 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id D768917A78; Tue, 13 Jun 2000 07:21:23 +0100 (BST) Received: from isgate.is (isgate.is [193.4.58.51]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 97A0E415DE for ; Tue, 13 Jun 2000 07:21:22 +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 GAA02565 for ; Tue, 13 Jun 2000 06:19:47 GMT Received: from nnrp1.deja.com (nnrp1.deja.com [10.12.2.16]) by mail.deja.com (8.8.7/8.8.5) with ESMTP id BAA30107 for ; Tue, 13 Jun 2000 01:20:59 -0500 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id BAA13008; Tue, 13 Jun 2000 01:20:49 -0500 To: bionet-software-acedb@moderators.isc.org From: zgudmunt@my-deja.com Newsgroups: bionet.software.acedb Subject: ACeDB2000 Conference proceedings: news from Vancouver Organization: Deja.com - Before you buy. Message-ID: <8i4js0$cmd$1@nnrp1.deja.com> X-Article-Creation-Date: Tue Jun 13 06:20:56 2000 GMT X-Http-User-Agent: Mozilla/4.7 [en] (X11; I; Linux 2.2.14-15mdk i686) X-Http-Proxy: 1.0 x57.deja.com:80 (Squid/1.1.22) for client 142.58.237.11 X-MyDeja-Info: XMYDJUIDzgudmunt Date: Tue, 13 Jun 2000 16:41:23 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk For those who are interested in what is happening this week at the ACeDB conference/workshop in Vancouver, BC: The following URL leads to the official news homepage for the conference: http://www.acedb2000.bcgsc.bc.ca/ You are welcome to contribute suggestions on topics, schedules and general conference affairs and in that way participate indirectly in the conference. Mummi Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Tue Jun 13 18:50:33 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1B8DF17B1B; Tue, 13 Jun 2000 18:50:31 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 63B7017ABC; Tue, 13 Jun 2000 18:50:30 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 0483217B0F; Tue, 13 Jun 2000 17:46:57 +0100 (BST) Received: from moderated.news.pipex.net (moderated.news.pipex.net [158.43.192.79]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 2DB16415DC for ; Tue, 13 Jun 2000 17:46:57 +0100 (BST) Received: (qmail 21119 invoked by alias); 13 Jun 2000 16:46:56 -0000 Received: (qmail 21115 invoked from network); 13 Jun 2000 16:46:55 -0000 Received: from mail.deja.com (205.238.143.34) by moderated.news.pipex.net with SMTP; 13 Jun 2000 16:46:55 -0000 Received: from nnrp1.deja.com (nnrp1.deja.com [10.12.2.16]) by mail.deja.com (8.8.7/8.8.5) with ESMTP id LAA05971 for ; Tue, 13 Jun 2000 11:46:08 -0500 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id LAA06043; Tue, 13 Jun 2000 11:46:02 -0500 To: bionet-software-acedb@moderators.isc.org From: zgudmunt@my-deja.com Newsgroups: bionet.software.acedb Subject: ACeDB2000 proceedings: news center Organization: Deja.com - Before you buy. Message-ID: <8i5oga$5sq$1@nnrp1.deja.com> X-Article-Creation-Date: Tue Jun 13 16:46:06 2000 GMT X-Http-User-Agent: Mozilla/4.7 [en] (X11; I; Linux 2.2.14-15mdk i686) X-Http-Proxy: 1.0 x65.deja.com:80 (Squid/1.1.22) for client 142.58.237.11 X-MyDeja-Info: XMYDJUIDzgudmunt Date: Tue, 13 Jun 2000 18:50:30 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk For those interested in what's going on at the ACeDB2000 conference currently in session here in Vancouver BC, the following homepage is the official news center for daily conference information: http://www.acedb2000.bcgsc.bc.ca/ People who are interested but unable to attend are encouraged to send in comments, suggestions or other material and thus contribute to the conference. Gudmundur, appointed conference reporter. Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Fri Jun 16 16:20:57 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0743617AE8; Fri, 16 Jun 2000 16:20:56 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C513B17ADE; Fri, 16 Jun 2000 16:20:55 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 890CC17A84; Fri, 16 Jun 2000 10:04:19 +0100 (BST) Received: from chi6-1.relay.mail.uu.net (chi6-1.relay.mail.uu.net [199.171.54.98]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 22EB3415DA for ; Fri, 16 Jun 2000 10:04:18 +0100 (BST) Received: from nottingham.ac.uk by chi6sosrv11.alter.net with ESMTP (peer crosschecked as: pat.ccc.nottingham.ac.uk [128.243.40.194]) id QQituq14379 for ; Fri, 16 Jun 2000 09:04:16 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 132s1r-0004Kv-00 for bionet-software-acedb@moderators.isc.org; Fri, 16 Jun 2000 10:03:07 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 132s2v-0002vk-00; Fri, 16 Jun 2000 10:04:13 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: How big is yours? 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 961146253 11266 128.243.116.150 (16 Jun 2000 09:04:13 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 16 Jun 2000 09:04:13 GMT X-Sender: keith@thale Date: Fri, 16 Jun 2000 16:20:55 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Just curious? What are the largest ace databases that people have worked with (in either size Mb (or even Gb), or number of objects) and have people found any performance problems with very large databases (obviously this is dependent on the computer hosting and accessing the database). Are there any theoretical limits on the number of objects an ace db could hold? Keith ~ Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR) ~ Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/ ~ University Park, University of Nottingham, NG7 2RD, UK ~ Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Tue Jun 20 11:24:15 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9515717AB3; Tue, 20 Jun 2000 11:24:14 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 08CE617A5D; Tue, 20 Jun 2000 11:24:12 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 3B5CA17B1C; Mon, 19 Jun 2000 15:45:43 +0100 (BST) To: bionet-software-acedb@net.bio.net From: crepinau@sb-roscoff.fr (Crepineau) Newsgroups: bionet.software.acedb Subject: Re: problem with peptide display Organization: Station Biologique de Roscoff Message-ID: <394E3097.E7998A75@sb-roscoff.fr> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 3B77617B1A; Mon, 19 Jun 2000 15:45:40 +0100 (BST) X-Received: from iznogoud.sb-roscoff.fr (iznogoud.sb-roscoff.fr [193.52.39.103]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 2A3F8415DC for ; Mon, 19 Jun 2000 15:45:39 +0100 (BST) X-Received: from jaffar.sb-roscoff.fr (jaffar.sb-roscoff.fr [193.52.39.107]) by iznogoud.sb-roscoff.fr (8.9.3/8.9.3) with ESMTP id QAA20716; Mon, 19 Jun 2000 16:43:44 +0100 (WET DST) X-Received: from sb-roscoff.fr (localhost [127.0.0.1]) by jaffar.sb-roscoff.fr (8.9.3+Sun/8.9.1) with ESMTP id PAA04362; Mon, 19 Jun 2000 15:39:20 +0100 (WET DST) X-Mailer: Mozilla 4.5 [fr] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en X-To: keith@thale.life.nottingham.ac.uk, acedb@net.bio.net Date: Tue, 20 Jun 2000 11:24:12 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello, just in case you did not get any answer, I think it is in method.ace that you define how homologies are presented on screen, for example for Blastn this is the definition find in the distibution of ACeDB : // data dumped from keyset display Method : "BLASTN" Display Colour LIGHTBLUE Score_by_width Score_bounds 100.000000 400.000000 Right_priority 5.200000 Strand_sensitive Show_Up_Strand Blastn Blixem_N Best Regards Florent --- From owner-acedb@hgmp.mrc.ac.uk Tue Jun 20 11:24:57 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8420C17AB5; Tue, 20 Jun 2000 11:24:56 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 32CA817AB3; Tue, 20 Jun 2000 11:24:55 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 6C9B417ABC; Tue, 20 Jun 2000 01:37:57 +0100 (BST) To: bionet-software-acedb@net.bio.net From: lvandela@bccancer.bc.ca (Louie van de Lagemaat) Newsgroups: bionet.software.acedb Subject: Dendrograms in acedb Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <394EBF6E.7C338FF3@bccancer.bc.ca> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 29B9117A77; Tue, 20 Jun 2000 01:37:54 +0100 (BST) X-Received: from fw-bccancer.bc.tac.net (fw-bccancer.bc.tac.net [208.181.69.245]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 81BC7415DA for ; Tue, 20 Jun 2000 01:37:52 +0100 (BST) X-Received: (qmail 29133 invoked from network); 20 Jun 2000 00:37:50 -0000 X-Received: from unknown (HELO bccancer.bc.ca) (205.233.171.159) by m160-129.bc-cancer.pxy with SMTP; 20 Jun 2000 00:37:50 -0000 X-Mailer: Mozilla 4.6 [en] (X11; I; Linux 2.2.7-1.15smp i686) X-Accept-Language: en X-To: acedb@net.bio.net Date: Tue, 20 Jun 2000 11:24:55 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Newbie question here I've been trying to read in a dendrogram in New Hampshire format with acedb ver 4.8c. I tried various trees, including the example given in the help pages. I got the error: Improperly formed tree structure or missing semicolon for every tree I tried to read in. Any clues as to what might be wrong? Thanks. --- From owner-acedb@hgmp.mrc.ac.uk Wed Jun 21 09:28:17 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7328117B1F; Wed, 21 Jun 2000 09:28:16 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 45DAC17B1B; Wed, 21 Jun 2000 09:28:15 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 7F4F517B14; Tue, 20 Jun 2000 14:41:47 +0100 (BST) To: bionet-software-acedb@net.bio.net From: crepinau@sb-roscoff.fr (Crepineau) Newsgroups: bionet.software.acedb Subject: svc_tli_create: could not do t_sync: Illegal file descriptor Organization: Station Biologique de Roscoff Message-ID: <394F7319.B8C2A356@sb-roscoff.fr> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id B39ED17AED; Tue, 20 Jun 2000 14:41:44 +0100 (BST) X-Received: from iznogoud.sb-roscoff.fr (iznogoud.sb-roscoff.fr [193.52.39.103]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id CD64A415DE for ; Tue, 20 Jun 2000 14:41:42 +0100 (BST) X-Received: from jaffar.sb-roscoff.fr (jaffar.sb-roscoff.fr [193.52.39.107]) by iznogoud.sb-roscoff.fr (8.9.3/8.9.3) with ESMTP id PAA27559 for ; Tue, 20 Jun 2000 15:39:48 +0100 (WET DST) X-Received: from sb-roscoff.fr (localhost [127.0.0.1]) by jaffar.sb-roscoff.fr (8.9.3+Sun/8.9.1) with ESMTP id OAA21371 for ; Tue, 20 Jun 2000 14:35:21 +0100 (WET DST) X-Mailer: Mozilla 4.5 [fr] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en X-To: acedb@net.bio.net Date: Wed, 21 Jun 2000 09:28:15 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello, I wrought six month ago about problems with solaris 2.7 and going on the net. Has anybody managed to find an answer to this problem ? Or should I wait for the socket ? jaffar [11]%uname -a SunOS jaffar 5.7 Generic_106541-04 sun4u sparc SUNW,Ultra-1 jaffar [12]%tail /var/adm/messages Jun 20 14:27:38 jaffar inetd[183]: /usr/local/bin/rpc.acedb: Hangup Jun 20 14:27:48 jaffar rpcace[21134]: svc_tli_create: could not do t_sync: Illegal file descriptor Jun 20 14:27:48 jaffar rpcace[21134]: cannot create tcp service. Jun 20 14:27:48 jaffar inetd[183]: /usr/local/bin/rpc.acedb: Hangup Jun 20 14:27:58 jaffar rpcace[21140]: svc_tli_create: could not do t_sync: Illegal file descriptor Jun 20 14:27:58 jaffar rpcace[21140]: cannot create tcp service. Jun 20 14:27:58 jaffar inetd[183]: /usr/local/bin/rpc.acedb: Hangup Jun 20 14:28:08 jaffar rpcace[21145]: svc_tli_create: could not do t_sync: Illegal file descriptor Jun 20 14:28:08 jaffar rpcace[21145]: cannot create tcp service. Jun 20 14:28:08 jaffar inetd[183]: /usr/local/bin/rpc.acedb: Hangup jaffar [13]% Thank you for reading my message. Florent --- From owner-acedb@hgmp.mrc.ac.uk Wed Jun 21 10:38:29 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BEF0417B28; Wed, 21 Jun 2000 10:38:28 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 2C82317B25; Wed, 21 Jun 2000 10:38:26 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 26D4617B1D; Wed, 21 Jun 2000 10:37:20 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8699B415DA for ; Wed, 21 Jun 2000 10:37:20 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA21343 for bionet-software-acedb@net.bio.net; Wed, 21 Jun 2000 10:37:19 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: svc_tli_create: could not do t_sync: Illegal file descriptor Organization: Sanger Centre Message-ID: <39508CCF.9FEC7E08@sanger.ac.uk> References: <394F7319.B8C2A356@sb-roscoff.fr> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 961580239 21341 193.60.84.177 (21 Jun 2000 09:37:19 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 21 Jun 2000 09:37:19 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Wed, 21 Jun 2000 10:38:26 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > I wrought six month ago about problems with solaris 2.7 and going on the > net. Has anybody managed to find an answer to this problem ? Or should I > wait for the socket ? Uuuuggghhh, this just seems to be the same old stuff, sun boxes are the only boxes we have problems with, every time someone updates their operating system on a sun the RPC server breaks....sigh... The problems are very hard to debug because of course we don't have the source code for the sun libraries so This is a sorry tale, I have been putting my efforts into making the socket server work and I would suggest that you try using that. You can pick up the latest monthly development build from: ftp://ftp.sanger.ac.uk/pub/acedb/Sanger-release.2000_05_09.tar.gz and you can see documentation on how to set the server up at: http://www.acedb.org/Development/wdoc/SOCKET_aceserver.html Send me email if you have problems or need help. I really recommend just dropping the RPC server and going for the sockets version. 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 Wed Jun 21 10:38:39 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4F7E417B27; Wed, 21 Jun 2000 10:38:39 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id F06B917B1D; Wed, 21 Jun 2000 10:38:37 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 734A817A43; Wed, 21 Jun 2000 10:16:06 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B6C06415DD for ; Wed, 21 Jun 2000 10:16:04 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA21090 for bionet-software-acedb@net.bio.net; Wed, 21 Jun 2000 10:16:04 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: How big is yours? Organization: Sanger Centre Message-ID: <395087D3.288CE1E8@sanger.ac.uk> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 961578964 21088 193.60.84.177 (21 Jun 2000 09:16:04 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 21 Jun 2000 09:16:04 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Wed, 21 Jun 2000 10:38:37 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > What are the largest ace databases that people have worked with (in either > size Mb (or even Gb), or number of objects) and have people found any > performance problems with very large databases (obviously this is > dependent on the computer hosting and accessing the database). > > Are there any theoretical limits on the number of objects an ace db could > hold? This is, unfortunately, a "how long is a piece of string" like question. The number of objects you can stuff into an ace database will be dependent on the size of those objects. I'm sure you can appreciate that the size can be just about anything (allowing for various bits of house-keeping information that every object stored will need). If you mean "can I have a really large number of objects ?", then the answer is yes, you are likely to run out of disk space before acedb runs out of index space. In terms of performance, again its a bit tricky to be specific, there are two pathological extremes: - if you have very big objects in your database then they will take a long time to load and use up lots of memory. - if you have lots of tiny objects and want to search through them all without using acedbs indexes, then each object must be loaded and explored and again this will lead to poor performance. Most databases sit in between these two and acedbs indexing allows many queries to be done without the need to load objects and look through them, thus giving very good query performance. In terms of how big a database can get, well this is (as far as we know) only dependent on the biggest file size that can be supported by a system. The file position is usually given by a "long" which could mean anything from a 32 to a 64 bit signed integer. This implies that EACH of the database blockN.wrm files could be huge. In practice operating systems usually only allow file sizes somewhat smaller than the theoretical maximum allowed by the file position size. Its unlikely that this is going to present problems at the moment. hope this helps a bit...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 Jun 22 09:39:57 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 63AE017B30; Thu, 22 Jun 2000 09:39:56 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id A932217B2E; Thu, 22 Jun 2000 09:39:54 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id F404C17AC7; Wed, 21 Jun 2000 17:08:56 +0100 (BST) Received: from jess.sanger.ac.uk (jess.sanger.ac.uk [193.60.84.61]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 446A6415DA for ; Wed, 21 Jun 2000 17:08:56 +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 RAA15355; Wed, 21 Jun 2000 17:08:54 +0100 (BST) From: Richard Durbin Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id RAA07454; Wed, 21 Jun 2000 17:08:54 +0100 (BST) Message-Id: <200006211608.RAA07454@griffin.sanger.ac.uk> To: bionet-software-acedb@net.bio.net, edgrif@sanger.ac.uk Subject: Re: How big is yours? Newsgroups: bionet.software.acedb Date: Thu, 22 Jun 2000 09:39:54 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > What are the largest ace databases that people have worked with (in either > size Mb (or even Gb), or number of objects) and have people found any > performance problems with very large databases (obviously this is > dependent on the computer hosting and accessing the database). > > Are there any theoretical limits on the number of objects an ace db could > hold? There are databases of several GB that people use daily. There is currently a theoretical limit of 2^24 (approx 16,000,000) objects per class, and 256 main classes (i.e. not counting subclasses). We are thinking about ways one day in the future to remove those limits, but in practice they have never approached being a problem. You can certainly live with several million objects on a reasonable computer. As Ed says, the total disk usage possible is very large (possibly 1k x 2^32 = 4 TB because blocks are determined by a 32bit integer now). Richard From owner-acedb@hgmp.mrc.ac.uk Tue Jun 27 13:04:45 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8FB6517B39; Tue, 27 Jun 2000 13:04:44 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 243C617AA1; Tue, 27 Jun 2000 13:04:43 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 86AF317A77; Fri, 23 Jun 2000 12:06:21 +0100 (BST) Received: from isgate.is (isgate.is [193.4.58.51]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 24AA0415D5 for ; Fri, 23 Jun 2000 12:06:16 +0100 (BST) Received: from mail.deja.com (mail.deja.com [64.57.170.34]) by isgate.is (8.9.3r/8.9.0Imo) with ESMTP id LAA15748 for ; Fri, 23 Jun 2000 11:06:10 GMT Received: from nnrp1.deja.com (nnrp1.deja.com [10.12.2.16]) by mail.deja.com (8.8.7/8.8.5) with ESMTP id GAA05059 for ; Fri, 23 Jun 2000 06:06:11 -0500 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id GAA25921; Fri, 23 Jun 2000 06:06:03 -0500 To: bionet-software-acedb@moderators.isc.org From: zgudmunt@my-deja.com Newsgroups: bionet.software.acedb Subject: Re: How big is yours? Organization: Deja.com - Before you buy. Message-ID: <8ivgar$pa0$1@nnrp1.deja.com> References: <395087D3.288CE1E8@sanger.ac.uk> X-Article-Creation-Date: Fri Jun 23 11:06:09 2000 GMT X-Http-User-Agent: Mozilla/4.7 [en] (X11; I; Linux 2.2.14-15mdk i686) X-Http-Proxy: 1.0 proxy.decode.is:8080 (Squid/2.2.STABLE5), 1.0 x58.deja.com:80 (Squid/1.1.22) for client 172.18.2.4, 213.167.128.100 X-MyDeja-Info: XMYDJUIDzgudmunt Date: Tue, 27 Jun 2000 13:04:43 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hey, guys, thanks for last time. I have noticed what Ed mentioned about looking through each of very many objects in a large database leading to poor performance. I am mirroring the GDB-database amplimer objects over to my local Ace, with each amplimer being represented by an STS-object, with up to 15 aliases each (talk about redundancy!) as a Text tag. I had a problem at first when I was looking for markers by aliases if they were not found by name; looking through each of those 100.000+arkers and check their alias was of course mindboggingly slow. But when I changed the Alias from Text to a XREF to an Alias-object and queried the Alias-class instead, all was well and fast. It did however give my over 600.000 Alias objects and increased my dbase size !:) Mummi In article <395087D3.288CE1E8@sanger.ac.uk>, Ed Griffiths wrote: > > What are the largest ace databases that people have worked with (in either > > size Mb (or even Gb), or number of objects) and have people found any > > performance problems with very large databases (obviously this is > > dependent on the computer hosting and accessing the database). > > > > Are there any theoretical limits on the number of objects an ace db could > > hold? > > This is, unfortunately, a "how long is a piece of string" like question. The > number of objects you can stuff into an ace database will be dependent on the > size of those objects. I'm sure you can appreciate that the size can be just > about anything (allowing for various bits of house-keeping information that > every object stored will need). If you mean "can I have a really large number of > objects ?", then the answer is yes, you are likely to run out of disk space > before acedb runs out of index space. > > In terms of performance, again its a bit tricky to be specific, there are two > pathological extremes: > > - if you have very big objects in your database then they will take a long time > to load and use up lots of memory. > > - if you have lots of tiny objects and want to search through them all without > using acedbs indexes, then each object must be loaded and explored and again > this will lead to poor performance. > > Most databases sit in between these two and acedbs indexing allows many queries > to be done without the need to load objects and look through them, thus giving > very good query performance. > > In terms of how big a database can get, well this is (as far as we know) only > dependent on the biggest file size that can be supported by a system. The file > position is usually given by a "long" which could mean anything from a 32 to a > 64 bit signed integer. This implies that EACH of the database blockN.wrm files > could be huge. In practice operating systems usually only allow file sizes > somewhat smaller than the theoretical maximum allowed by the file position size. > Its unlikely that this is going to present problems at the moment. > > hope this helps a bit...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 | > ------------------------------------------------------------------------------ > > Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Thu Jun 29 11:32:36 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 757FB17B7D; Thu, 29 Jun 2000 11:32:35 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 1C68A17AD5; Thu, 29 Jun 2000 11:32:34 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id B75BE17B67; Thu, 29 Jun 2000 09:03:03 +0100 (BST) To: bionet-software-acedb@net.bio.net From: crepinau@sb-roscoff.fr ("Florent.Crepineau") Newsgroups: bionet.software.acedb Subject: xaceclient ? Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200006290756.IAA11435@jaffar.sb-roscoff.fr> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id D11AC17AB2; Thu, 29 Jun 2000 09:03:00 +0100 (BST) X-Received: from iznogoud.sb-roscoff.fr (iznogoud.sb-roscoff.fr [193.52.39.103]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id F26F9415D5 for ; Thu, 29 Jun 2000 09:02:59 +0100 (BST) X-Received: from jaffar.sb-roscoff.fr (jaffar.sb-roscoff.fr [193.52.39.107]) by iznogoud.sb-roscoff.fr (8.9.3/8.9.3) with ESMTP id KAA08046 for ; Thu, 29 Jun 2000 10:01:04 +0100 (WET DST) X-Received: (from crepinau@localhost) by jaffar.sb-roscoff.fr (8.9.3+Sun/8.9.1) id IAA11435 for acedb@net.bio.net; Thu, 29 Jun 2000 08:56:29 +0100 (WET DST) X-To: acedb@net.bio.net X-Sun-Charset: US-ASCII Date: Thu, 29 Jun 2000 11:32:34 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello, I would like to know what one can do with the xaceclient. Can one connect from a windows box with the xaceclient over the net to a saceserver running on a unix box? How can I do that ? Thank you for reading my message Best Regards Florent --- From owner-acedb@hgmp.mrc.ac.uk Thu Jun 29 11:32:44 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 3DE5017B7D; Thu, 29 Jun 2000 11:32:44 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C180D17B76; Thu, 29 Jun 2000 11:32:41 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 3D5E417B10; Wed, 28 Jun 2000 19:43:12 +0100 (BST) Received: from beaver.cs.washington.edu (beaver.cs.washington.edu [128.95.1.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 90201415CF for ; Wed, 28 Jun 2000 19:43:10 +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 LAA29610 for ; Wed, 28 Jun 2000 11:43:08 -0700 (PDT) (envelope-from root@nntp4.u.washington.edu) Received: (from root@localhost) by nntp4.u.washington.edu (8.9.3+UW00.05/8.9.3+UW00.01) id LAA74172 for bionet-software-acedb@beaver.cs.washington.edu; Wed, 28 Jun 2000 11:43:07 -0700 To: bionet-software-acedb@cs.washington.edu From: Carson Thoreen Newsgroups: bionet.software.acedb Subject: Constructed types in Ace 5 Organization: University of Washington Message-ID: X-Trace: nntp4.u.washington.edu 962217787 91066 (None) 140.142.17.38 X-Complaints-To: help@cac.washington.edu User-Agent: MT-NewsWatcher/3.0 (PPC) Date: Thu, 29 Jun 2000 11:32:41 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello -- I'm using the 5/9 development release and have found a couple problems that may or may not be my fault: 1. If I construct a model like this: ?Dog BelongsTo Text DogHouse Text #Yard ?Yard Frontyard Backyard InTheGarden and then try to import an .ace file like this: Dog : Rufus DogHouse "Deluxe" Frontyard I get an error claiming Frontyard doesn't exist in the model. When I create a Dog object through the edit menu and then choose to update it, the constructed type shows up as "DogHouse Text #SomeOtherClass"! If I open the "Model" class and examine the "Dog" model, I see "DogHouse Text #Yard". So I think there's a problem in the way ace is parsing the models for creating objects. Ideas? 2. In the last newsletter, there was mention that indexing in ace 5 was a little screwy so that queries wouldn't work correctly unless the database was re-indexed. I've had this problem with AQL -- the objects returned meet the query criteria, but the data from tags isn't right ie. in a database with lots of "Dog" objects, "Rufus" might correctly returned, but Rufus->BelongsTo column often shows data that isn't connected to "Rufus". Even when I choose "read models and reindex" the problem remains. Is there another way to re-index, or should I wait until the next release? 3. When I try to go to www.acedb2000.bcgsc.bc.ca to see what I've missed, my browser can't find the server. Is this the correct URL? Any help is very much appreciated! Thanks, Carson --------------------- Carson Thoreen Dept. of Molecular Biotechnology University of Washington Carson_Thoreen@brown.edu From owner-acedb@hgmp.mrc.ac.uk Thu Jun 29 11:52:22 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 3801B17B7A; Thu, 29 Jun 2000 11:52:22 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id A6E3D17AE8; Thu, 29 Jun 2000 11:52:20 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 96DC317AE8; Thu, 29 Jun 2000 11:51:51 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 16165415D4 for ; Thu, 29 Jun 2000 11:51:51 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA20554 for bionet-software-acedb@net.bio.net; Thu, 29 Jun 2000 11:51:50 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Calling all Acedb'ers... Organization: Sanger Centre Message-ID: <395B2A46.938359C5@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 962275910 20552 193.60.84.177 (29 Jun 2000 10:51:50 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 29 Jun 2000 10:51:50 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 29 Jun 2000 11:52:20 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk As I announced in an earlier append, I have been producing a monthly Newsletter for acedb users in the Sanger Centre. At Acedb2000 we agreed that I would append this newsletter to this newsgroup, I will be doing this later today. If you would also like to receive the letter in text form via email then send me a note at edgrif@sanger.ac.uk, remember that you can also access all the newsletters at: http://www.acedb.org/winfo/Newsletters/ Currently I write the Newsletter and put in it whatever I think is of interest to Sanger users. If you would like to contribute a short article about something you have discovered or find useful in acedb then please send it to me and I will include it in a future Newsletter. I want the Newsletter to be of general interest to as many acedb users as possible. The idea of the Newsletter is to keep users/developers in touch with what's going on in acedb, i.e. to provide more feedback. I also want it to include hints/tips/how-to type articles as well. Comments are welcome, but articles are even more welcome !! 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 Jun 29 13:11:26 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8583017AF3; Thu, 29 Jun 2000 13:11:25 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3B90B17AE0; Thu, 29 Jun 2000 13:11:24 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 029E317AE3; Thu, 29 Jun 2000 12:51:45 +0100 (BST) To: bionet-software-acedb@net.bio.net From: matthews@greengenes.cit.cornell.edu (Dave Matthews) Newsgroups: bionet.software.acedb Subject: Re: Constructed types in Ace 5 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200006291151.HAA01732@greengenes.cit.cornell.edu> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id C3FBF17AE0; Thu, 29 Jun 2000 12:51:43 +0100 (BST) X-Received: from greengenes.cit.cornell.edu (greengenes.cit.cornell.edu [128.253.246.43]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D52E6415D5 for ; Thu, 29 Jun 2000 12:51:42 +0100 (BST) X-Received: (from matthews@localhost) by greengenes.cit.cornell.edu (8.9.3/8.9.3) id HAA01732; Thu, 29 Jun 2000 07:51:41 -0400 (EDT) X-To: Carson_Thoreen@brown.edu X-Cc: ACEDB newsgroup , Ed Griffiths , Richard Bruskiewich , matthews@greengenes.cit.cornell.edu Date: Thu, 29 Jun 2000 13:11:24 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi Carson, Sorry, that host turned into a pumpkin at the end of the meeting. The stuff that was there is supposed to go onto www.acedb.org. I guess there'll be an announcement when it's online. - Dave > From: Carson Thoreen > Newsgroups: bionet.software.acedb > Date: Thu, 29 Jun 2000 11:32:41 +0100 (BST) > > When I try to go to www.acedb2000.bcgsc.bc.ca to see what I've > missed, my browser can't find the server. Is this the correct URL? --- From owner-acedb@hgmp.mrc.ac.uk Thu Jun 29 14:14:32 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BCC0017AF5; Thu, 29 Jun 2000 14:14:31 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 01FC117AE9; Thu, 29 Jun 2000 14:14:29 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 3C67917AEE; Thu, 29 Jun 2000 13:34:17 +0100 (BST) To: bionet-software-acedb@net.bio.net From: rbsk@sanger.ac.uk (Richard Bruskiewich) Newsgroups: bionet.software.acedb Subject: Re: Constructed types in Ace 5 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: References: <200006291151.HAA01732@greengenes.cit.cornell.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id ACB7B17AE9; Thu, 29 Jun 2000 13:34:14 +0100 (BST) X-Received: from jess.sanger.ac.uk (jess.sanger.ac.uk [193.60.84.61]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A5390415DA for ; Thu, 29 Jun 2000 13:34:13 +0100 (BST) X-Received: from kanga.sanger.ac.uk (kanga [193.62.207.226]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id NAA06442; Thu, 29 Jun 2000 13:34:11 +0100 (BST) X-Received: from localhost (localhost [127.0.0.1]) by kanga.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id NAA18216; Thu, 29 Jun 2000 13:29:11 +0100 (BST) X-To: Dave Matthews X-Cc: Carson_Thoreen@brown.edu, ACEDB newsgroup , Ed Griffiths X-In-Reply-To: <200006291151.HAA01732@greengenes.cit.cornell.edu> Date: Thu, 29 Jun 2000 14:14:29 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi Dave, As you can imagine, acedb has taken back seat to the working draft and EnsEMBL for the moment. I'm sure Ed will get some of the www.acedb.org updates in place once the dust has settled around here and he can engage a few of the team web to do the magic. I've had an initial chat with the wiki people here about the docs service. again, we'll have to wait our turn at the time slicing of web expertise. cheers, richard b. ps. Mummi has promised us a draft of his edited Acedb '2000 proceedings notes sometime soon. On Thu, 29 Jun 2000, Dave Matthews wrote: > Hi Carson, > > Sorry, that host turned into a pumpkin at the end of the meeting. > The stuff that was there is supposed to go onto www.acedb.org. I guess > there'll be an announcement when it's online. > - Dave > > > From: Carson Thoreen > > Newsgroups: bionet.software.acedb > > Date: Thu, 29 Jun 2000 11:32:41 +0100 (BST) > > > > When I try to go to www.acedb2000.bcgsc.bc.ca to see what I've > > missed, my browser can't find the server. Is this the correct URL? > ======================================================== Dr. Richard Bruskiewich WWW: http://www.sanger.ac.uk/Users/rbsk/ Human Analysis/Bioinformatics The Sanger Centre Tel: +44-(0)1223-834244 Wellcome Trust Genome Campus, Fax: +44-(0)1223-494919 Hinxton, Cambridge CB10 1SA United Kingdom ======================================================== --- From owner-acedb@hgmp.mrc.ac.uk Thu Jun 29 14:14:33 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 23A4117AE9; Thu, 29 Jun 2000 14:14:32 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 6B7A017AF3; Thu, 29 Jun 2000 14:14:30 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 3F71717AF3; Thu, 29 Jun 2000 14:13:55 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 9EF64415D5 for ; Thu, 29 Jun 2000 14:13:54 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA22334 for bionet-software-acedb@net.bio.net; Thu, 29 Jun 2000 14:13:54 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Acedb - June Newsletter Organization: Sanger Centre Message-ID: <395B4B91.C5E977A5@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 962284433 22332 193.60.84.177 (29 Jun 2000 13:13:53 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 29 Jun 2000 13:13:53 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 29 Jun 2000 14:14:30 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Below is Junes Acedb Newsletter. Please note that the newsletter is biased towards Sanger Centre users, I'm happy to see this emphasis change a but will need articles (of a few paragraphs) from other people. I can't undertake to do a "world-wide" newsletter on my own !! 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 | ------------------------------------------------------------------------------ ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ACEDB User Group Newsletter - June 2000 ####################################### If you want to have this newsletter mailed to you _or_ you want to make comments/suggestions about the format/content then send an email to acedb@sanger.ac.uk. This month saw the first Acedb Workshop since 1997, which took place in Vancouver. Thanks go to Richard Bruskiewich and Steve Jones (a former Sanger person, who now works at the Genome Sequence Centre, Vancouver) for their efforts in organising the workshop. This issue will be about the conference and what happened there. General News ************ Apologies +++++++++ Apologies for no Acedb Users meeting this month, in the end there just was not time to organise one. There will be a meeting in July, if you have issues you want to raise before then, please come and see the acedb developers in our new room (D2-12) which is just down from reception, near personnel/accounts etc. The Newsletter ++++++++++++++ Partly as a result of requests at the conference and partly because of independent requests from acedb users at other sites, this newsletter is now being added to the acedb newsgroup each month and is also being sent out to users at other sites. I hope to solicit some useful articles from contacts made at the conference. Acedb2000 at Vancouver ********************** I'm not going to cover everything that happened at Vancouver, the following sections deal with subjects most relevant to the Sanger Centre. A fuller description of the conference will appear on the acedb web site in due course. Grid ++++ Gudmund Thorission from Iceland gave a short presentation on how he hopes to use the grid models/display for micro-array data. The main points for discussion were: * scale - can acedb hold the amount of data that micro-arrays would produce. * colours - is it possible to colour code the squares in the grid display so that they look meaningful to the user. * intelligent display - can the grid display be made to work to allow reasonable scrolling across a micro-array but not need to load in the data for the entire array at once (as this may require prohibitive amounts of memory). This conversation mirrors several that have happened in the Sanger Centre over at least the last year (e.g. with Dan Lawson and Adam Butler). What's required now is an initial specification which includes: * expected size of micro-arrays * amount of data per micro-array element * some typical colour schemes Adam Butler is going to take an initial stab at this, but if you are interested in seeing this done then don't sit back, either start a discussion on the acedb newsgroup or email the acedb developers direct (acedb@sanger.ac.uk). Zacedb ++++++ Richard Durbin spent much of his time at Vancouver working on a new storage layer for acedb. This is the part of acedb that stores/retrieves objects to/from disk. The idea here would to allow a choice of "backends", perhaps including free (e.g. mySQL, BerkeleyDB, the original acedb system) or commercial (e.g. Oracle, Sysbase) systems to be used. The backend would not "know" about acedb objects, it would only be used to store/retrieve them and provide other services such as locking. The rationale for doing this is that the backend system could be used to allow truly concurrent reading/writing via threading and more reliability via support for transactions. This would be a great advance for acedb and would supply features requested by Sanger and external users. This work is currently only at the "broken prototype" stage, much work needs to be done on further prototyping, in particular to assess whether performance would be good enough with a different backend. The acedb web site ++++++++++++++++++ The session on the format/usability of the acedb web site produced one main conclusion: it's not very user friendly. Fortunately there were also a lot of suggestions for improvements including: * completely revamping the downloads section * less developer, more user stuff * provide search facilities for acedb keywords * sort the documentation out ! and a host of other good suggestions. We plan to substantially reorganise the web site over the next few weeks. socket server +++++++++++++ There were a number of talks/tutorials on how to use/set up the new sockets-based version of the acedb server/client (available now in Acedb 4_8c in ~acedb/RELEASE.DEVELOPMENT/bin.XXX directories). If you would like more information or a tutorial on the new server/client system (how to set up user passwords etc.) then contact Ed Griffiths (edgrif@sanger.ac.uk). Other important developments related to the socket server included: * AcePerl - Lincoln Stein has produced a new version of AcePerl that now talks directly to the socket server, you can get more information on this from: http://stein.cshl.org/AcePerl/. Note that because AcePerl can now talk directly to the server you will be able to use AcePerl from Windows and Apple Macs because AcePerl is now purely in Perl with no C code compilation required. * AcePython - Sean Powell & Siegfried Schloissnig wrote a python interface to the socket server whilst at the conference. If you want access to this code send a note to Ed Griffiths (edgrif@sanger.ac.uk). Note that you can also interface to the socket server from Java: (http://www.biojava.org/docs/api/. SMAP - a new way to construct sequences +++++++++++++++++++++++++++++++++++++++ There has been a lot of discussion at Sanger over how to construct larger sequences up to whole chromosome level. There was a whole session devoted to this with an introductory talk by Richard Bruskiewich, followed by a talk by Richard Durbin which gave an overview of the proposed model for SMAP and a model for exons. A fair summary would probably be that the SMAP model should solve a lot of the problems that were experienced with chromosome 22 and with large sequence construction in general. The difficult bit of the code still needs writing but that should happen over the next few weeks. What to do about building haplotype sequences remains unsolved however. AQL +++ There was a lot of interest in AQL as a more powerful replacement for the Query language and TableMaker. We would welcome more reports about how people find AQL to use, any performance problems etc. A major requirement for AQL is some kind of query builder and also more tutorial documentation of the "how to..." type. Anyone fancy writing an article on how to use AQL ?? Acedb and the Mac +++++++++++++++++ There were a significant number of users who would like to see a more up to date copy of acedb available on the Mac. Simon Kelley has made some headway with obtaining a software environment in which to build acedb on the Mac. The basic problem here is that we do not have the resources to maintain code that requires a completely different build environment, graphics routines etc. Things look hopeful but no more than that. Next User Group Meeting - D213, 2.30pm, Thursday, 13th July *********************************************************** ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- Ed Griffiths Last modified: Thu Jun 29 14:03:23 BST 2000