From owner-acedb@hgmp.mrc.ac.uk Thu Feb 1 12:24:55 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4A42517AF5; Thu, 1 Feb 2001 12:24:54 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id D019C17AAF; Thu, 1 Feb 2001 12:24:52 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id A0B7C17AC4; Thu, 1 Feb 2001 10:51:24 +0000 (GMT) Received: from moderated.news.pipex.net (moderated.news.pipex.net [158.43.192.79]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 4100541602 for ; Thu, 1 Feb 2001 10:51:11 +0000 (GMT) Received: (qmail 697 invoked by alias); 1 Feb 2001 10:51:15 -0000 Received: (qmail 693 invoked from network); 1 Feb 2001 10:51:09 -0000 Received: from pat.ccc.nottingham.ac.uk (HELO nottingham.ac.uk) (128.243.40.194) by moderated.news.pipex.net with SMTP; 1 Feb 2001 10:51:09 -0000 Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.20 #2) id 14OHIl-0000QA-00 for bionet-software-acedb@moderators.isc.org; Thu, 01 Feb 2001 10:49:19 +0000 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 14OHKV-0004Dg-00; Thu, 1 Feb 2001 10:51:07 +0000 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Using giface to get Protein details 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 981024667 16222 128.243.116.150 (1 Feb 2001 10:51:07 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 1 Feb 2001 10:51:07 GMT X-Sender: keith@thale Date: Thu, 1 Feb 2001 12:24:52 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Using acedb 4.7l: I've just noticed that if I use giface (and then use the 'gif' command), I can then use the commands 'seqget' and 'seqfeatures' to retrieve the homology details for the specified sequence. But whilst there is a pepget command for fetching protein sequences, there is no equivalent pepfeatures command. Any chance of this being implemented in a new version or is there some reason why this is hard to do? Keith ~ Keith Bradnam - UK CropNet (http://ukcrop.net) webmaster and ~ Arabidopsis Genome Resource (http://ukcrop.net/agr) developer. ~ ~ Nottingham Arabidopsis Stock Centre, University Park, ~ University of Nottingham, NG7 2RD, UK. Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Mon Feb 5 09:54:47 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7ECC617AEC; Mon, 5 Feb 2001 09:54:45 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 210C617AD8; Mon, 5 Feb 2001 09:54:40 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 8010117B28; Fri, 2 Feb 2001 16:15:20 +0000 (GMT) Received: from rutgers.rutgers.edu (rutgers.edu [165.230.4.76]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C99294160A for ; Fri, 2 Feb 2001 16:15:14 +0000 (GMT) Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by rutgers.rutgers.edu (8.8.8/8.8.8) with ESMTP id LAA14709 for ; Fri, 2 Feb 2001 11:15:13 -0500 (EST) Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.20 #2) id 14Oipt-0002Bs-00 for bionet-software-acedb@moderators.isc.org; Fri, 02 Feb 2001 16:13:21 +0000 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 14Oire-00044U-00; Fri, 2 Feb 2001 16:15:10 +0000 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: new AceBrowser display for viewing proteins Organization: ACS, The University of Nottingham Message-ID: Reply-To: Keith Bradnam Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 981130510 15652 128.243.116.150 (2 Feb 2001 16:15:10 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 2 Feb 2001 16:15:10 GMT X-Sender: keith@thale Date: Mon, 5 Feb 2001 09:54:40 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi all, The standard AceBrowser package comes with a 'sequence' script which produces a neat 'Sequence report' page when viewing any sequence. No such display has been available for viewing proteins so I thought that I would try to create one based on the 'sequence' script to complement the standard 'tree display' view. I have now done this and whilst the script is heavily customised for our Arabidopsis database (AGR), anyone can have a copy if they want to. Some example pages from our database: http://ukcrop.net/perl/ace/AGR-protein/AGR?name=SWISS%3AP46600&class=Protein http://ukcrop.net/perl/ace/AGR-protein/AGR?name=SWISS%3AO04407&class=Protein http://ukcrop.net/perl/ace/AGR-protein/AGR?name=TREMBL%3AQ9SKS5&class=Protein The script makes use of some other customisations in our database, but could be easily hacked I think to suit other databases. Keith P.S. Whilst I thought it would be fairly simple to emulate the sequence script, I ended up spending a few days trying to copy the standard table of BLAST homologies from the 'tree display' into a neat table like the one that appears on the 'sequence' output. The problem being due to the fact that for DNA sequences, you can fire off the command: "gif seqget $s -coords $start $end ; seqdisplay ; seqfeatures" and the 'seqfeatures' part returns a nice hash array of all the features and homologies associated with that sequence. You can't do the same for proteins though as there is not 'pepfeatures' command (see my previous post). The solution was a lot of AcePerl navigation through the tree display (I presume there would be a more elegant solution, but my AcePerl skills are a bit weak really). ~ Keith Bradnam - UK CropNet (http://ukcrop.net) webmaster and ~ Arabidopsis Genome Resource (http://ukcrop.net/agr) developer. ~ ~ Nottingham Arabidopsis Stock Centre, University Park, ~ University of Nottingham, NG7 2RD, UK. Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Mon Feb 5 09:55:15 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B76FC17AEC; Mon, 5 Feb 2001 09:55:14 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 5407E17AD8; Mon, 5 Feb 2001 09:55:09 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 8471817B0B; Sun, 4 Feb 2001 07:17:02 +0000 (GMT) To: bionet-software-acedb@net.bio.net From: anna_tsykin@yahoo.com (=?iso-8859-1?q?Anna=20Tsykin?=) Newsgroups: bionet.software.acedb Subject: multiorganism single gene model Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <20010204071651.93881.qmail@web10106.mail.yahoo.com> MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 8EB8D17ADE; Sun, 4 Feb 2001 07:17:00 +0000 (GMT) X-Received: from web10106.mail.yahoo.com (web10106.mail.yahoo.com [216.136.130.56]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 1ADCB415F7 for ; Sun, 4 Feb 2001 07:16:53 +0000 (GMT) X-Received: from [134.7.134.20] by web10106.mail.yahoo.com; Sat, 03 Feb 2001 23:16:51 PST X-To: acedb@net.bio.net Date: Mon, 5 Feb 2001 09:55:09 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I'd like to set up an ACEDB to hold data on a single gene from a variety of organisms. The main source of data would be Genbank sequences. Does anybody have a similar DB? I'd love to borrow a simple model to adapt rather then work with the huge complete genome models. Anna Tsykin __________________________________________________ Get personalized email addresses from Yahoo! Mail - only $35 a year! http://personal.mail.yahoo.com/ --- From owner-acedb@hgmp.mrc.ac.uk Mon Feb 5 16:02:46 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 49C8317B1F; Mon, 5 Feb 2001 16:02:45 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 4C64C17B1E; Mon, 5 Feb 2001 16:02:42 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id E819E17B00; Mon, 5 Feb 2001 15:52:14 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 6DBC741632 for ; Mon, 5 Feb 2001 15:52:02 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA06885 for bionet-software-acedb@net.bio.net; Mon, 5 Feb 2001 15:52:02 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Acedb information... Organization: Sanger Centre Message-ID: <3A7ECC21.BAC6BADB@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 981388321 6883 193.60.84.177 (5 Feb 2001 15:52:01 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 5 Feb 2001 15:52:01 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Mon, 5 Feb 2001 16:02:42 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi all, Just a quick reminder about various ways to get acedb information: web site: http://www.acedb.org/ (note especially the search facility for finding useful acedb stuff) newsgroup: http://www.bio.net/hypermail/acedb/ newsletter: http://www.acedb.org/winfo/Newsletters/ (if you want this emailed to you every month, just send me a note) bug reporting: http://www.sanger.ac.uk/cgi-bin/webddts/WebDDTS.pl?Project=Acedb developers: email to acedb@sanger.ac.uk Hope that's useful, Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Tue Feb 6 09:19:36 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7A87317AAC; Tue, 6 Feb 2001 09:19:34 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 9543017A70; Tue, 6 Feb 2001 09:19:28 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id C1FE217B2D; Tue, 6 Feb 2001 00:51:28 +0000 (GMT) Received: from moderated.news.pipex.net (moderated.news.pipex.net [158.43.192.79]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id B2AC641736 for ; Tue, 6 Feb 2001 00:51:18 +0000 (GMT) Received: (qmail 24000 invoked by alias); 6 Feb 2001 00:51:18 -0000 Received: (qmail 23996 invoked from network); 6 Feb 2001 00:51:17 -0000 Received: from mailsrv1.sanger.ac.uk (193.62.207.19) by moderated.news.pipex.net with SMTP; 6 Feb 2001 00:51:17 -0000 Received: from sanger.ac.uk (dialup22 [193.62.203.151]) by mailsrv1.sanger.ac.uk (8.11.1/8.11.1) with ESMTP id f160phh06143; Tue, 6 Feb 2001 00:51:43 GMT Message-ID: <3A7F4C12.3A952DEE@sanger.ac.uk> From: Richard Durbin Organization: The Sanger Centre X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: Keith Bradnam Subject: Re: Using giface to get Protein details References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Newsgroups: bionet.software.acedb Date: Tue, 6 Feb 2001 09:19:28 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Ah. Good question. Unfortunately each giface command requires a little bit of adaptor code to be written. There isn't any yet to interface to the pep display functionality. Quite a lot would have to be put into place. Not a bad idea though. Richard Keith Bradnam wrote: > > Using acedb 4.7l: > > I've just noticed that if I use giface (and then use the 'gif' command), I > can then use the commands 'seqget' and 'seqfeatures' to retrieve the > homology details for the specified sequence. > > But whilst there is a pepget command for fetching protein sequences, there > is no equivalent pepfeatures command. > > Any chance of this being implemented in a new version or is there some > reason why this is hard to do? > > Keith From owner-acedb@hgmp.mrc.ac.uk Tue Feb 6 12:39:05 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id DA29F17B62; Tue, 6 Feb 2001 12:39:04 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 5EBBC17B60; Tue, 6 Feb 2001 12:39:03 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 1F22417B0A; Tue, 6 Feb 2001 09:31:59 +0000 (GMT) Received: from mailbox3.ucsd.edu (mailbox3.ucsd.edu [132.239.1.55]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A5B6841613 for ; Tue, 6 Feb 2001 09:31:53 +0000 (GMT) Received: from naranjo.sdi.uam.es (naranjo.sdi.uam.es [150.244.9.11]) by mailbox3.ucsd.edu (8.11.0/8.11.0) with ESMTP id f169VoY15701 for ; Tue, 6 Feb 2001 01:31:50 -0800 (PST) Received: from olivo.sdi.uam.es (olivo.sdi.uam.es [150.244.9.45]) by naranjo.sdi.uam.es (8.9.3/8.9.3/UAM) with ESMTP id KAA09425 for ; Tue, 6 Feb 2001 10:31:46 +0100 (MET) Received: from acebo.sdi.uam.es (acebo.sdi.uam.es [150.244.9.3]) by olivo.sdi.uam.es (8.9.3+Sun/8.9.3) with ESMTP id KAA03201 for ; Tue, 6 Feb 2001 10:31:46 +0100 (MET) Received: (from news@localhost) by acebo.sdi.uam.es (8.9.3+Sun/8.9.3) id KAA13531 for bionet-software-acedb@moderators.isc.org; Tue, 6 Feb 2001 10:31:31 +0100 (MET) To: bionet-software-acedb@moderators.isc.org From: jr@foxtrot.cnb.uam.es (José R. Valverde) Newsgroups: bionet.software.acedb Subject: II National Bioinformatics Network Organization: EMBnet/CNB Message-ID: <95og9i$d4u$3@acebo.sdi.uam.es> Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Trace: acebo.sdi.uam.es 981451890 13470 150.244.23.5 (6 Feb 2001 09:31:30 GMT) X-Complaints-To: abuse@uam.es NNTP-Posting-Date: Tue, 6 Feb 2001 09:31:30 +0000 (UTC) X-Newsreader: knews 1.0b.1 Date: Tue, 6 Feb 2001 12:39:03 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I'm forwarding this on behalf of the organisers. This is a call for submissions to the II Spanish National Meeting in Bioinformatics. The meeting is addressed mainly to Spanish Bioinformaticians, both resident in Spain and abroad, and is being organised by the Spanish National Tematic Network on Bioinformatics. -------------------------------------------------- II Spain National Bioinformatics Meeting (JBI2001) ************************************************** May 30,31, June 1, 2001 Malaga, Spain Organised by Departamento de Arquitectura de Computadores Departamento de Genetica, U.Malaga Unidad de Biocomputacion, CNB Red Nacional de Bioinformatica ================================================ http://www.ac.uma.es/~jbi2001 ================================================ There is more information in the above web page. Submissions: Deadline: Wednesday, 28 February 2001 Electronic submission: jbi2001@ac.uma.es Mail address: Oswaldo Trelles Arquitectura de Computadores Universidad de Malaga Campues de Teatinos 29071 Malaga, Spain WWW: http://www.ac.uma.es/~jbi2001 Questions: Oswaldo Trelles Tel: +34 952 13 2823 Fax: +34 952 13 2790 email: jbi2001@ac.uma.es / ots@ac.uma.es -- These opinions are mine and only mine. Hey man, I saw them first! José R. Valverde De nada sirve la Inteligencia Artificial cuando falta la Natural From owner-acedb@hgmp.mrc.ac.uk Wed Feb 7 12:08:16 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D824E17BD0; Wed, 7 Feb 2001 12:08:13 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 2268B17BC7; Wed, 7 Feb 2001 12:08:06 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 92DE217BBD; Wed, 7 Feb 2001 09:37:46 +0000 (GMT) Received: from mailsrv1.sanger.ac.uk (mailsrv1.sanger.ac.uk [193.62.207.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C1ABB415FF; Wed, 7 Feb 2001 09:36:26 +0000 (GMT) Received: from griffin.sanger.ac.uk (root@griffin [193.60.84.177]) by mailsrv1.sanger.ac.uk (8.11.1/8.11.1) with ESMTP id f179Wch18590; Wed, 7 Feb 2001 09:32:39 GMT Received: from localhost (edgrif@localhost [127.0.0.1]) by griffin.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id JAA08219; Wed, 7 Feb 2001 09:32:09 GMT From: Ed Griffiths To: Acedb Newsletter , acedb newsgroup on bionet , aratnasiri@ucdavis.edu, boberkfe@watson.wustl.edu, carson@mbt.washington.edu, colin.dolphin@kcl.ac.uk, dbaillie@gene.mbb.sfu.ca, dblasiar@watson.wustl.edu, Dennis.Knudson@colostate.edu, dgrant@iastate.edu, G.REYES@CGIAR.ORG, jayne.vallance@bbsrc.ac.uk, jayoung@fhcrc.org, jmh.neefs@pandora.be, jspieth@watson.wustl.edu, jurg@sanger.ac.uk, keith@thale.life.nottingham.ac.uk, Lincoln Stein , lnothake@watson.wustl.edu, lvandela@bccancer.bc.ca, Martien.Groenen@Alg.VF.WAU.NL, matthews@greengenes.cit.cornell.edu, mieg@sanger.ac.uk, mummi@decode.is, mwilkinson@gene.pbi.nrc.ca, r.bruskiewich@CGIAR.ORG, sjones@bcgsc.bc.ca, sness@bcgsc.bc.ca, syurman@spatialfocus.com, T.van_Wezel@lumc.nl Subject: Acedb January Newsletter Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Newsgroups: bionet.software.acedb Date: Wed, 7 Feb 2001 12:08:06 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk The January Newsletter, slightly late...sorry, you'll have to put it down to New Year tardiness. Do remember that contributions to the Newsletter would be most welcome, topic could be anything from "your favourite tip" to "your favourite bug" to "my wish list". Just send me a few paragraphs and I'll put it in the next newsletter. cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ACEDB User Group Newsletter - January 2001 ########################################## 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 is the post-Christmas/not that much has changed report. There are small but important changes to the acedb database log format, a short article about the introduction of better web-based downloads for acedb and a number of bug fixes. General News ************ File Chooser and selecting a directory ++++++++++++++++++++++++++++++++++++++ A number of users didn't see last months newsletter and wanted to know how to go directly to a directory using the 4_8c file chooser. I'll just repeat last months item about how to do this: * If you want to go directly to a directory using the file chooser window, you can do this by typing the directory name in the bottom "selection" window and pressing the key. This will point the file chooser to this directory so you can then choose files from there. * _Note_ that the key also does C-shell style filename completion just like you get when using an xterm window. So if you type part of a directory and press the rest will be filled in for you (as far as this can be done unambiguously). Hope that's useful. New Features ************ Acedb on windows ++++++++++++++++ The acedb locking/write access mechanism now works on Windows 95/98. Better information for signals ++++++++++++++++++++++++++++++ When an internal error happens in acedb or the system runs out of resources (e.g. program stack space), the operating system may send a "signal" to acedb which stops the program from running. When this happens acedb runs a special signal handling routine which attempts to terminate the acedb program with a message about what has happened. The message that acedb outputs has been improved in the following ways: * The message now includes an operating system defined message that identifies the cause of the signal. * The text of the message has been changed so more accurately indicate whether the signal is likely to have been caused by an acedb error or by a system resource error. So if one of the acedb programs you are using exits with a message like this: // ABORT : Fatal error, program received signal.... and you can remember/reproduce the sequence of actions that caused it then please get in touch with the acedb developers (acedb@sanger.ac.uk). "Preserve" behaviour restored +++++++++++++++++++++++++++++ Due to popular demand, the "preserve" button has been added back for the tree window display, selecting this item on a tree window menu will ensure that the window stays around until explicitly "quit". Articles ******** Rearrangements to acedb downloads Its possible to download acedb code in one of two ways: FTP site login to the sanger ftp site and go to /pub/acedb Web site visit http://www.acedb.org/Software/Downloads/ We've introduced the web pages to make it easier to navigate the acedb downloads directories and get the download package you want. On visiting http://www.acedb.org/Software/Downloads/ you will find there are three levels of code you can download and a quick summary of the current build status available at the bottom of the page. The three levels of code that can be downloaded are: _Public_ This is the most stable and supported code. It has the fewest bugs and should be used for critical databases. _Monthly_ This is a montly build of the development code and will have been tested by developers and with the overnight build/test system. This code will have most of the latest features/bug fixes in it. The code is widely used within the Sanger Centre and should be fairly bug free, if you find a bug in this code please report it as soon as possible. _Overnight_ This code is the very latest and is not guaranteed to compile/run or anything, its there only to allow other developers to see the latest acedb code and perhaps to allow some users to try out very new features. You shouldn't use this code without talking to the acedb developers first. If you visit the page for one of these levels of code you will see that there are various packages that can be downloaded ranging from the source code, to precompiled binaries for various platforms to a demonstration database. If you find any problems with any aspect of the download pages then please let the acedb developers know. Bugs Fixed ********** Drawing performance bug Drawing of some fmap/gmap displays was very slow because a bug in the acedb code was causing the displays to be drawn twice. This should now be fixed for all acedb displays, please email the acedb developers if this is not so in the latest monthly build code. A another smaller bug was that gmap code would try to map loci or regions even if they had no given map coordinates, this has also been fixed. In this case the loci/regions are displayed in a text window. Objects missing from active keyset after rename +++++++++++++++++++++++++++++++++++++++++++++++ Where a simple rename of an object was done via parsing an acefile, the object was not left in the active keyset. Now the renamed object will be in the active keyset allowing a quick check of renames. Log entries in database/log.wrm Logging information in acedb was not complete because although the start of a new user session was recorded, the end of the session was not. This meant that if acedb failed in a way that could not be caught by the error handling routines, there was no record in the log that this had happened. Now all session starts/ends shouid be bracketed by: SESSION_START - session information SESSION_END - where "session end type" can be one of: NORMAL EXIT acedb program exitted normally. ABNORMAL EXIT acedb program did not crash, but rather detected an error such as "database not found" and so could not continue. CRASH acedb detected an unrecoverable error such as an internal programming fault, or the system running out of memory. If a SESSION_START is found in the log without a corresponding SESSION_END, this means (assuming the acedb program is no longer running) that acedb crashed severely in a way that it could not detect (e.g. if the program was killed with "kill -9" or on some systems if it ran out of stack space). This type of crash _may_ have left the database corrupted if the program crashed while updating the database, and certainly if the database does become corrupted you should look in the log for either a SESSION_END - CRASH or an unmatched SESSION_START. Note that a little care is required in parsing the log file for these paired starts and ends, process ids can be reused by the operating system. This means that you need to first find the "SESSION_START/machine/process_id" and then look for both a new "SESSION_START/machine/same_process_id" and a "SESSION_END/machine/process_id". If you find the former, or don't find the latter it means the acedb program crashed severely. January monthly build now available. ************************************ You can pick up the monthly builds from: Sanger users ~acedb/RELEASE.DEVELOPMENT External users http://www.acedb.org/Software/Downloads/monthly.shtml Next User Group Meeting - D319, 2.30pm, Thursday 15th February 2001 ******************************************************************* !*! Please note changed venue !*! ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- Ed Griffiths Last modified: Tue Feb 6 12:55:14 GMT 2001 From owner-acedb@hgmp.mrc.ac.uk Wed Feb 7 14:32:52 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 44F1B17BE1; Wed, 7 Feb 2001 14:32:51 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 6D88017BDF; Wed, 7 Feb 2001 14:32:49 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 8E6EE17BC7; Wed, 7 Feb 2001 14:10:01 +0000 (GMT) Received: from chx400.switch.ch (chx400.switch.ch [130.59.10.2]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 077D5416AD for ; Wed, 7 Feb 2001 14:09:39 +0000 (GMT) Received: from pegasus.csx.cam.ac.uk ([131.111.8.69]) by chx400.switch.ch with esmtp (Exim 3.20 #1) id 14QVHv-0002bz-00 for bionet-software-acedb@moderators.isc.org; Wed, 07 Feb 2001 15:09:39 +0100 Received: from news by pegasus.csx.cam.ac.uk with local (Exim 2.05 #1) id 14QVHu-00027W-00 for bionet-software-acedb@moderators.isc.org; Wed, 7 Feb 2001 14:09:38 +0000 To: bionet-software-acedb@moderators.isc.org From: Lavinia Hyde Newsgroups: bionet.software.acedb Subject: ace.mbly. Organization: University of Cambridge, England Message-ID: References: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: lavinia@rigging Date: Wed, 7 Feb 2001 14:32:49 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi, I just wondered if ace.mbly was still being actively maintained/developed, and if anyone is using it/has used it? regards Lavinia Hyde Department of Medical Genetics Wellcome Trust Centre for Molecular Mechanisms in Disease Wellcome Trust/MRC Building Addenbrooke's Hospital Site Hills Road, Cambridge CB2 2XY Tel. 01223 762671 Fax. 01223 726102 Website: http://www-gene.cimr.cam.ac.uk/todd/ From owner-acedb@hgmp.mrc.ac.uk Thu Feb 8 09:52:02 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D742C17AE5; Thu, 8 Feb 2001 09:51:59 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 2738317AB8; Thu, 8 Feb 2001 09:51:53 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 7DF3417BFF; Wed, 7 Feb 2001 18:11:00 +0000 (GMT) Received: from moderated.news.pipex.net (moderated.news.pipex.net [158.43.192.79]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 7B436416DF for ; Wed, 7 Feb 2001 18:10:55 +0000 (GMT) Received: (qmail 24788 invoked by alias); 7 Feb 2001 18:10:54 -0000 Received: (qmail 24783 invoked from network); 7 Feb 2001 18:10:54 -0000 Received: from pat.ccc.nottingham.ac.uk (HELO nottingham.ac.uk) (128.243.40.194) by moderated.news.pipex.net with SMTP; 7 Feb 2001 18:10:54 -0000 Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.20 #2) id 14QZ1U-0000k9-00 for bionet-software-acedb@moderators.isc.org; Wed, 07 Feb 2001 18:08:56 +0000 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 14QZ3L-0005eY-00; Wed, 7 Feb 2001 18:10:51 +0000 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Jade interface development 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 981569451 21732 128.243.116.150 (7 Feb 2001 18:10:51 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 7 Feb 2001 18:10:51 GMT X-Sender: keith@thale Date: Thu, 8 Feb 2001 09:51:53 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi, Is there any life in the Jade project? Or did it reach a dead-end with version 1.0j (the latest version detailed on Lincoln Stein's site). No real reason for asking other than curiousity (keep seeing links to Jade dotted about the place). Regards, Keith ~ Keith Bradnam - UK CropNet (http://ukcrop.net) webmaster and ~ Arabidopsis Genome Resource (http://ukcrop.net/agr) developer. ~ ~ Nottingham Arabidopsis Stock Centre, University Park, ~ University of Nottingham, NG7 2RD, UK. Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Mon Feb 19 10:31:05 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0032817B44; Mon, 19 Feb 2001 10:31:04 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 7D4F317B31; Mon, 19 Feb 2001 10:31:00 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 530C017B99; Fri, 16 Feb 2001 17:15:48 +0000 (GMT) To: bionet-software-acedb@net.bio.net From: jhill@myriad.com (Jason Hill) Newsgroups: bionet.software.acedb Subject: acedb 4.7 and solaris 8 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <3A8D601F.5E271092@myriad.com> 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 A5C1617B95; Fri, 16 Feb 2001 17:15:43 +0000 (GMT) X-Received: from mail1.myriad.com (myriad.com [63.75.14.2]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 1637741655 for ; Fri, 16 Feb 2001 17:15:29 +0000 (GMT) X-Received: from dr.myriad.com by mail1.myriad.com via smtpd (for mercury.hgmp.mrc.ac.uk [193.62.192.80]) with SMTP; 16 Feb 2001 17:15:28 UT X-Received: from myriad.com (aqua.myriad.com [10.1.3.59]) by dr.myriad.com (8.9.2/8.9.2) with ESMTP id KAA11326 for ; Fri, 16 Feb 2001 10:15:26 -0700 (MST) X-Mailer: Mozilla 4.72 [en] (X11; U; SunOS 5.8 sun4u) X-Accept-Language: en X-To: acedb@net.bio.net Date: Mon, 19 Feb 2001 10:31:00 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I'm trying to get acedb 4.7 to run on Solaris 8, but when I when I try to read a .ace file, the "open file" dialog opens up and my machine then goes into a state of entropy -- all available memory (256Mb) fills up and it begins to swap (695Mb) until it fills up all available swap space, then acedb crashes and I have to login from another machine to kill my Xsession. 4.3 and earlier seem to work fine, 4.7_? has the above behavior. The same things happens if I try to do anything from the Admin or Edit buttons. I never get to the point of actually selecting which .ace file I want to import. This happens with the available 4.7 binary as well as recompiling the source. Any help would be greatly appreciated. Jason Hill Programmer III Myriad Genetics, Inc. --- From owner-acedb@hgmp.mrc.ac.uk Mon Feb 19 10:31:29 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0C4FE17B4A; Mon, 19 Feb 2001 10:31:28 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 7721A17B44; Mon, 19 Feb 2001 10:31:25 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 8A52D17B2D; Mon, 19 Feb 2001 05:55:51 +0000 (GMT) Received: from briar.org (backdraft.briar.org [192.207.123.123]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8B437415EE for ; Mon, 19 Feb 2001 05:55:43 +0000 (GMT) Received: (from smap@localhost) by briar.org (8.9.1b+Sun/8.6.12) id AAA20494 for ; Mon, 19 Feb 2001 00:55:21 -0500 (EST) X-Authentication-Warning: backdraft.briar.org: smap set sender to using -f Received: from news.cis.nctu.edu.tw(140.113.23.2) by backdraft via smap (V2.1) id xma020492; Mon, 19 Feb 01 00:55:03 -0500 Received: (from news@localhost) by news.cis.nctu.edu.tw (8.11.0/8.11.2) id f1J5sK075092 for bionet-software-acedb@moderators.isc.org; Mon, 19 Feb 2001 13:54:20 +0800 (CST) (envelope-from news) To: bionet-software-acedb@moderators.isc.org From: "Yuh-Jyh Hu" Newsgroups: bionet.software.acedb Subject: CFP: special session on Biological Data Mining and Management in METMBS'2001 Organization: Dept. of Computer & Information Science, NCTU, Taiwan Message-ID: <96qcec$29ah$1@news.cis.nctu.edu.tw> X-Trace: news.cis.nctu.edu.tw 982562060 75089 140.113.167.85 (19 Feb 2001 05:54:20 GMT) X-Complaints-To: usenet@news.cis.nctu.edu.tw NNTP-Posting-Date: Mon, 19 Feb 2001 05:54:20 +0000 (UTC) X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Date: Mon, 19 Feb 2001 10:31:25 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I apologize if you receive multiple copies of this call. Call for Papers ************************************************************************ Special Session on Biological Data Mining and Management in The 2001 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS' 2001) June 25 - 28, 2001 Monte Carlo Resort, Las Vegas, Nevada, USA ************************************************************************ The completion of genome sequences has produced sufficient data for biological experiments, and the advent of the microarray and genechip technology has resulted in the expanded ability of monitoring simultaneously the gene expression level changes on a genomic scale. Ever since efficient and relatively cheap methods were developed for the acquisition of biological data, analysis and management of biological data has become the primary problem in molecular biology. The purpose of this special session is to allow researchers to introduce their work or ideas on important issues regarding biological data mining and data management. Topics of interest include (but are not limited to): * biosequence alignment * motif detection in biosequences * gene finding * gene family classification * gene expression data management * protein structure and function prediction Prospective authors are invited to submit three copies of their draft paper (about 4 pages) to either of the following addresses by Thursday March 1, 2001: Dr. Yuh-Jyh Hu Computer and Information Science Dept. National Chiao-Tung University 1001 Ta Hsueh Rd., Hsinchu, Taiwan 300, R.O.C. Tel: +886-3-573-1795 Fax: +886-3-5721490 Email: yhu@cis.nctu.edu.tw or Dr. Faramarz Valafar, Chair METMBS Cognitive and Neural Systems Boston University 677 Beacon Street Boston, MA 02215 U.S.A. Tel: (617) 353-5134 Fax: (617) 353-7755 Email: faramarz@cns.bu.edu E-mail and Fax submissions are also acceptable. Papers must not have been previously published or currently submitted for publication elsewhere. See details on http://www.cns.bu.edu/metmbs/ From owner-acedb@hgmp.mrc.ac.uk Tue Feb 20 13:48:03 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BF8BE17B73; Tue, 20 Feb 2001 13:48:02 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 477FD17B6F; Tue, 20 Feb 2001 13:48:01 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id B111217A9B; Mon, 19 Feb 2001 10:51:01 +0000 (GMT) Received: from ncbi.nlm.nih.gov (ncbi.nlm.nih.gov [130.14.25.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 377E7415CF for ; Mon, 19 Feb 2001 10:50:52 +0000 (GMT) Received: from ray.nlm.nih.gov (ray [130.14.25.2]) by ncbi.nlm.nih.gov (8.9.3/8.9.3) with ESMTP id FAA28451; Mon, 19 Feb 2001 05:50:45 -0500 (EST) Received: (from mieg@localhost) by ray.nlm.nih.gov (8.9.3+Sun/8.9.3) id FAA28042; Mon, 19 Feb 2001 05:50:44 -0500 (EST) From: Jean Thierry-Mieg Message-Id: <200102191050.FAA28042@ray.nlm.nih.gov> To: bionet-software-acedb@net.bio.net, jhill@myriad.com Subject: Re: acedb 4.7 and solaris 8 Newsgroups: bionet.software.acedb Date: Tue, 20 Feb 2001 13:48:01 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk please download the fixed version from www.acedb.org (i amne the version that runs ok on soalris 4_8 sun changed something in their X11 server) From owner-acedb@hgmp.mrc.ac.uk Wed Feb 21 14:52:41 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1807C17AF9; Wed, 21 Feb 2001 14:52:40 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id EB1FE17AE3; Wed, 21 Feb 2001 14:52:33 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id CD8CB17AF7; Wed, 21 Feb 2001 14:48:19 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 57CC14164A for ; Wed, 21 Feb 2001 14:46:50 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA09354 for bionet-software-acedb@net.bio.net; Wed, 21 Feb 2001 14:46:49 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: Jade interface development Organization: Sanger Centre Message-ID: <3A93D4D9.620817FB@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 982766809 9234 193.60.84.177 (21 Feb 2001 14:46:49 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 21 Feb 2001 14:46:49 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Wed, 21 Feb 2001 14:52:33 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Keith, > Is there any life in the Jade project? Or did it reach a dead-end with > version 1.0j (the latest version detailed on Lincoln Stein's site). > > No real reason for asking other than curiousity (keep seeing links to Jade > dotted about the place). There is no active work going on with Jade as far as I know, there is however some effort going on in BioJava to interface to the acedb socket server. You should contact Matthew Pocock (mrp@sanger.ac.uk) for more info. cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Wed Feb 21 14:52:49 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id AB5B917AF9; Wed, 21 Feb 2001 14:52:47 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C34C817AFB; Wed, 21 Feb 2001 14:52:42 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 32D4A17AE3; Wed, 21 Feb 2001 14:45:04 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 33A714164B for ; Wed, 21 Feb 2001 14:44:51 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA09242 for bionet-software-acedb@net.bio.net; Wed, 21 Feb 2001 14:44:50 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: ace.mbly. Organization: Sanger Centre Message-ID: <3A93D462.24F5EB94@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 982766690 9234 193.60.84.177 (21 Feb 2001 14:44:50 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 21 Feb 2001 14:44:50 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Wed, 21 Feb 2001 14:52:42 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Lavinia, > Hi, I just wondered if ace.mbly was still being actively > maintained/developed, and if anyone is using it/has used it? You should contact Jean (Thierry-Mieg) as he is the acembly maestro. Perhaps he has already contacted you, if not you can mail him at: mieg@nlm.nih.gov cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Wed Feb 21 14:53:11 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 6BF5717B0F; Wed, 21 Feb 2001 14:53:10 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 0621F17AF9; Wed, 21 Feb 2001 14:53:05 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id BC9E717AE3; Wed, 21 Feb 2001 14:49:42 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4A1314164A for ; Wed, 21 Feb 2001 14:49:21 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA09367 for bionet-software-acedb@net.bio.net; Wed, 21 Feb 2001 14:49:20 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: acedb 4.7 and solaris 8 Organization: Sanger Centre Message-ID: <3A93D570.81BA4AC@sanger.ac.uk> References: <3A8D601F.5E271092@myriad.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 982766960 9234 193.60.84.177 (21 Feb 2001 14:49:20 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 21 Feb 2001 14:49:20 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Wed, 21 Feb 2001 14:53:05 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Jason, > I never get to the point of actually selecting which .ace file I want to > import. This happens with the available 4.7 binary as well as recompiling > the source. > > Any help would be greatly appreciated. You could alternatively move to acedb 4_8 by downloading the monthly build from our web site. This code is stable and is being used by lots of people at Sanger. As far as we know it does not have problems with the Solaris 8 X server. cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Wed Feb 21 17:26:59 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 6CFC817BA7; Wed, 21 Feb 2001 17:26:58 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 2739717A4E; Wed, 21 Feb 2001 17:26:57 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id BF61717BA9; Wed, 21 Feb 2001 15:51:42 +0000 (GMT) Received: from formaggio.cshl.org (formaggio.cshl.org [143.48.31.42]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A1BF041684 for ; Wed, 21 Feb 2001 15:51:22 +0000 (GMT) Received: (from lstein@localhost) by formaggio.cshl.org (8.9.3/8.8.7) id KAA22975; Wed, 21 Feb 2001 10:50:18 -0500 From: Lincoln Stein MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14995.58298.397656.174861@formaggio.cshl.org> To: Jean Thierry-Mieg , lstein@cshl.org, wugm@cshl.org Subject: Re: Jade interface development References: <200102211528.KAA19124@ray.nlm.nih.gov> X-Mailer: VM 6.71 under 21.1 "20 Minutes to Nikko" XEmacs Lucid (patch 2) Reply-To: lstein@cshl.org Newsgroups: bionet.software.acedb Date: Wed, 21 Feb 2001 17:26:57 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Actually, Jade rides again. It has been reincarnated as Jadex, uses the socket server, and has graphical displays for genetic and physical maps. Unfortunately, I just lost Guanming Wu, the brilliant software developer who worked on Jadex, and so it might be going to sleep again. However, I'll put Jadex up on the web site for people to download and play with. Lincoln Jean Thierry-Mieg writes: > yes jade is asleep > > we may revive it someday but are globally very happy > with acep[erl > jean Thierry-Mieg -- ======================================================================== Lincoln D. Stein Cold Spring Harbor Laboratory lstein@cshl.org Cold Spring Harbor, NY NOW HIRING BIOINFORMATICS POSTDOCTORAL FELLOWS AND PROGRAMMERS. PLEASE WRITE FOR DETAILS. ======================================================================== From owner-acedb@hgmp.mrc.ac.uk Wed Feb 21 17:27:07 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2ED7817AFE; Wed, 21 Feb 2001 17:27:06 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C6F4A17AAC; Wed, 21 Feb 2001 17:27:04 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id E510C17AF7; Wed, 21 Feb 2001 15:28:56 +0000 (GMT) Received: from ncbi.nlm.nih.gov (ncbi.nlm.nih.gov [130.14.25.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id ADCDF415DA for ; Wed, 21 Feb 2001 15:28:47 +0000 (GMT) Received: from ray.nlm.nih.gov (ray [130.14.25.2]) by ncbi.nlm.nih.gov (8.9.3/8.9.3) with ESMTP id KAA01769; Wed, 21 Feb 2001 10:28:43 -0500 (EST) Received: from cetus (cetus [130.14.25.107]) by ray.nlm.nih.gov (8.9.3+Sun/8.9.3) with SMTP id KAA19124; Wed, 21 Feb 2001 10:28:42 -0500 (EST) Message-Id: <200102211528.KAA19124@ray.nlm.nih.gov> From: Jean Thierry-Mieg Reply-To: Jean Thierry-Mieg Subject: Re: Jade interface development To: bionet-software-acedb@net.bio.net, edgrif@sanger.ac.uk, lstein@cshl.org MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: b8cc2xy2ynY6PF5/yMmGHg== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.3.5 SunOS 5.7 sun4u sparc Newsgroups: bionet.software.acedb Date: Wed, 21 Feb 2001 17:27:04 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk yes jade is asleep we may revive it someday but are globally very happy with acep[erl jean Thierry-Mieg From owner-acedb@hgmp.mrc.ac.uk Thu Feb 22 09:18:21 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4909C17B28; Thu, 22 Feb 2001 09:18:20 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 60AE817B28; Thu, 22 Feb 2001 09:18:17 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 16B4017B11; Wed, 21 Feb 2001 21:19:40 +0000 (GMT) To: bionet-software-acedb@net.bio.net From: YUE_YONG@LILLY.COM Newsgroups: bionet.software.acedb Subject: installation error from 4.8c Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: Content-return: prohibited MIME-version: 1.0 Content-type: multipart/alternative; boundary="=_alternative 0075246B052569FA_=" X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 2B41117A69; Wed, 21 Feb 2001 21:19:39 +0000 (GMT) X-Received: from Lilly.com (inet.d48.lilly.com [40.33.1.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id CFECD416F2 for ; Wed, 21 Feb 2001 21:19:33 +0000 (GMT) X-Received: from LILLY.COM ([40.59.1.39]) by INET.D48.LILLY.COM (PMDF V5.2-31 #34229) with ESMTP id <01K0DMMI5DM4006CKU@INET.D48.LILLY.COM> for acedb@net.bio.net; Wed, 21 Feb 2001 16:19:31 EST X-Received: from mcntusmail11.d51.lilly.com (mcntusmail11.d51.lilly.com [40.1.129.132]) by NEWMAN.D52.LILLY.COM (PMDF V5.2-31 #34229) with ESMTP id <01K0DMMHVMDO008XLR@NEWMAN.D52.LILLY.COM> for acedb@net.bio.net; Wed, 21 Feb 2001 16:19:31 +0000 (GMT) X-To: acedb@net.bio.net X-Mailer: Lotus Notes Release 5.0.4a July 24, 2000 X-MIMETrack: Serialize by Router on USMAIL11/AM/LLY(Release 5.0.3 (Intl)|21 March 2000) at 02/21/2001 04:18:54 PM, Serialize complete at 02/21/2001 04:18:54 PM Date: Thu, 22 Feb 2001 09:18:17 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk This is a multipart message in MIME format. --=_alternative 0075246B052569FA_= Content-Type: text/plain; charset="us-ascii" I got a "directory checksum error" message during AceDB4.8c installation. It occured while taring 'ACEDB-binarySOLARIS.4_8c.tar.gz', which I downloaded from ftp.sanger.ac.uk/pub/acedb/MONTHLY. Any help will be appreciated. Yong Yue --=_alternative 0075246B052569FA_= Content-Type: text/html; charset="us-ascii"
I got a "directory checksum error" message during AceDB4.8c installation.  It occured while taring 'ACEDB-binarySOLARIS.4_8c.tar.gz', which I downloaded from ftp.sanger.ac.uk/pub/acedb/MONTHLY.  Any help will be appreciated.  

Yong Yue --=_alternative 0075246B052569FA_=-- --- From owner-acedb@hgmp.mrc.ac.uk Thu Feb 22 09:58:47 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 583B317B35; Thu, 22 Feb 2001 09:58:46 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C26D417B34; Thu, 22 Feb 2001 09:58:44 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id AA72617B32; Thu, 22 Feb 2001 09:45:31 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 627C5415FB for ; Thu, 22 Feb 2001 09:45:16 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA02112 for bionet-software-acedb@net.bio.net; Thu, 22 Feb 2001 09:45:15 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: installation error from 4.8c Organization: Sanger Centre Message-ID: <3A94DFAB.BC62BA98@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 982835115 2107 193.60.84.177 (22 Feb 2001 09:45:15 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 22 Feb 2001 09:45:15 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 22 Feb 2001 09:58:44 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Yong Yue, > I got a "directory checksum error" message during AceDB4.8c installation. It > occured while taring 'ACEDB-binarySOLARIS.4_8c.tar.gz', which I downloaded > from ftp.sanger.ac.uk/pub/acedb/MONTHLY. Any help will be appreciated. Sorry, we sometimes have network problems that cause the tar files to get corrupted. I will redo them. cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Thu Feb 22 16:15:12 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BF16F17B1A; Thu, 22 Feb 2001 16:15:11 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 7439617AF5; Thu, 22 Feb 2001 16:15:10 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 75B7B17A81; Thu, 22 Feb 2001 14:51:33 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 26D1441640 for ; Thu, 22 Feb 2001 14:51:11 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA06045 for bionet-software-acedb@net.bio.net; Thu, 22 Feb 2001 14:51:10 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: installation error from 4.8c Organization: Sanger Centre Message-ID: <3A95275E.4F6242BC@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 982853470 5934 193.60.84.177 (22 Feb 2001 14:51:10 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 22 Feb 2001 14:51:10 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 22 Feb 2001 16:15:10 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Yong Yue, I think you should find that the tar files are OK now. In fact the problem is to do with a broken version of tar that has come with an upgrade to some of our systems here...sigh... cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Fri Feb 23 09:37:42 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5C63817B62; Fri, 23 Feb 2001 09:37:42 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 1378B17B60; Fri, 23 Feb 2001 09:37:40 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id E109E17BDF; Thu, 22 Feb 2001 17:18:00 +0000 (GMT) Received: from dfw7-1.relay.mail.uu.net (dfw7-1.relay.mail.uu.net [199.171.54.106]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B559C41673 for ; Thu, 22 Feb 2001 17:17:36 +0000 (GMT) Received: from electra.cc.umanitoba.ca by dfw7sosrv11.alter.net with ESMTP (peer crosschecked as: electra.cc.umanitoba.ca [130.179.16.23]) id QQkdmr18157 for ; Thu, 22 Feb 2001 17:17:34 GMT Received: from canopus.cc.umanitoba.ca (news@canopus.cc.umanitoba.ca [130.179.16.24]) by electra.cc.umanitoba.ca (8.9.0/8.9.0) with ESMTP id LAA11914 for ; Thu, 22 Feb 2001 11:17:32 -0600 (CST) Received: (from news@localhost) by canopus.cc.umanitoba.ca (8.9.0/8.9.0) id LAA20345 for bionet-software-acedb@moderators.isc.org; Thu, 22 Feb 2001 11:17:32 -0600 (CST) To: bionet-software-acedb@moderators.isc.org From: frist@cc.UManitoba.CA (Brian Fristensky) Newsgroups: bionet.software.acedb Subject: Call for Votes: bionet.molbio.genearrays Followup-To: bionet.general Organization: University of Manitoba, Winnipeg, Manitoba, Canada Message-ID: <973hjc$jrn$1@canopus.cc.umanitoba.ca> X-Trace: canopus.cc.umanitoba.ca 982862252 20343 130.179.16.120 (22 Feb 2001 17:17:32 GMT) X-Complaints-To: Postmaster@cc.umanitoba.ca NNTP-Posting-Date: 22 Feb 2001 17:17:32 GMT Date: Fri, 23 Feb 2001 09:37:40 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Call for votes ARRAYS/bionet.molbio.genearrays Voting on the following proposal will now be open until the 25th of March. To vote send an email to biovote@net.bio.net with either of the following two lines (only) in the body of the email. YES to arrays NO to arrays ---------------------------------------------------------------------- Proposal to establish ARRAYS/bionet.molbio.genearrays Proposed USENET name: bionet.molbio.genearrays Proposed mailing list name: ARRAYS Proposed email addresses: arrays@net.bio.net Discussion leader: Brian Fristensky University of Manitoba frist@cc.umanitoba.ca Newsgroup charter: The group bionet.molbio.genearrays is for the discussion of topics relating to gene array/micro array technology. This includes but is not limited to: - making filter arrays or slide arrays - strategies eg. normalization - quality control, quality assurance - array software and databases - theory and data mining - arrays, reagents or equipment commercially available - Product announcements The bionet.molbio.genearrays newsgroup will not be moderated. ============================================================================= Brian Fristensky | Department of Plant Science | A special place in Hell is reserved for University of Manitoba | the inventors of correct-as-you-type Winnipeg, MB R3T 2N2 CANADA | features in word processors. frist@cc.umanitoba.ca | Office phone: 204-474-6085 | FAX: 204-474-7528 | http://home.cc.umanitoba.ca/~frist/ =============================================================================