From owner-acedb@hgmp.mrc.ac.uk Thu Jan 4 09:30:44 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E713C17B2A; Thu, 4 Jan 2001 09:30:43 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 6821517AA3; Thu, 4 Jan 2001 09:30:42 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id F044317AFB; Wed, 3 Jan 2001 20:45:43 +0000 (GMT) Received: from ashd1-1.relay.mail.uu.net (ashd1-1.relay.mail.uu.net [199.171.54.245]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4F483415E4 for ; Wed, 3 Jan 2001 20:45:38 +0000 (GMT) Received: from mail.deja.com by mr0.ash.ops.us.uu.net with ESMTP (peer crosschecked as: mail.deja.com [64.57.170.34]) id QQjwkp27772 for ; Wed, 3 Jan 2001 20:45:54 GMT Received: from nnrp1.deja.com (nnrp1.deja.com [10.12.2.16]) by mail.deja.com (8.11.1/8.11.1) with ESMTP id f03Kjan17673 for ; Wed, 3 Jan 2001 14:45:36 -0600 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id OAA24089; Wed, 3 Jan 2001 14:45:31 -0600 To: bionet-software-acedb@moderators.isc.org From: syurman@my-deja.com Newsgroups: bionet.software.acedb Subject: doggerel Organization: Deja.com Message-ID: <93031b$ngo$1@nnrp1.deja.com> X-Article-Creation-Date: Wed Jan 03 20:45:34 2001 GMT X-Http-User-Agent: Mozilla/4.76 [en] (X11; U; Linux 2.2.17 i686) X-Http-Proxy: 1.0 x53.deja.com:80 (Squid/1.1.22) for client 216.175.66.5 X-MyDeja-Info: XMYDJUIDsyurman Date: Thu, 4 Jan 2001 09:30:42 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk We're geographers in private practice, and have been using ACEDB quite happily for a couple of years. For some reason we started a new project in a relational database instead. Why? I don't have an excuse really. Must have taken leave of my senses. After a particularly nasty bout with the stuff my partner sent me this, and I couldn't resist passing it on. never again will we relate it makes us late, objects are the only way stones and worms are where we play Yes, we're shifting this project to ACEDB and BoulderIO immediately. With apologies, Sara Sent via Deja.com http://www.deja.com/ From owner-acedb@hgmp.mrc.ac.uk Thu Jan 4 09:30:51 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 69BF517B2A; Thu, 4 Jan 2001 09:30:50 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 29B0017A5B; Thu, 4 Jan 2001 09:30:42 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id C2B9617AD1; Wed, 3 Jan 2001 17:05:50 +0000 (GMT) To: bionet-software-acedb@net.bio.net From: BrathwaiteMg@grc.nia.nih.gov ("Brathwaite, Mgavi (NIA/IRP)") Newsgroups: bionet.software.acedb Subject: Sequence Annotation Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id E243E17AED; Wed, 3 Jan 2001 17:05:42 +0000 (GMT) X-Received: from ims.hub.nih.gov (ims.hub.nih.gov [128.231.90.111]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8F6DD41610 for ; Wed, 3 Jan 2001 17:05:06 +0000 (GMT) X-Received: by ims.hub.nih.gov with Internet Mail Service (5.5.2653.19) id ; Wed, 3 Jan 2001 12:05:03 -0500 X-To: "'acedb@net.bio.net'" X-Mailer: Internet Mail Service (5.5.2653.19) Date: Thu, 4 Jan 2001 09:30:42 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello, I am new to ACEDB. I need to annotate my sequence data, repeat data and CpG islands, in a hi-throughput fashion. Mgavi --- From owner-acedb@hgmp.mrc.ac.uk Thu Jan 4 10:14:14 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1672217B2F; Thu, 4 Jan 2001 10:14:12 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C897817B2C; Thu, 4 Jan 2001 10:14:06 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 05FF317B2A; Thu, 4 Jan 2001 09:43:23 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8CE1141672 for ; Thu, 4 Jan 2001 09:43:19 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA05972 for bionet-software-acedb@net.bio.net; Thu, 4 Jan 2001 09:43:19 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: Sequence Annotation Organization: Sanger Centre Message-ID: <3A5445B6.3CE759D6@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 978601398 5958 193.60.84.177 (4 Jan 2001 09:43:18 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 4 Jan 2001 09:43:18 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 4 Jan 2001 10:14:06 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Mgavi, > I am new to ACEDB. I need to annotate my sequence data, repeat data and CpG > islands, in a hi-throughput fashion. Sorry, I don't mean to be obtuse but could you expand on this, what is it that you want to know ? 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 Jan 4 10:14:18 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id AA78717B2C; Thu, 4 Jan 2001 10:14:17 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id E95B317B31; Thu, 4 Jan 2001 10:14:13 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 455C117B2F; Thu, 4 Jan 2001 10:13:18 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 0568641677 for ; Thu, 4 Jan 2001 10:12:55 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id KAA06358 for bionet-software-acedb@net.bio.net; Thu, 4 Jan 2001 10:12:50 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: as postscript file: related Organization: Sanger Centre Message-ID: <3A544CA1.944DCCBC@sanger.ac.uk> References: <396350AE.60D3DCD6@marseille.inserm.fr> <8kfbor$ku4$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 978603169 6356 193.60.84.177 (4 Jan 2001 10:12:49 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 4 Jan 2001 10:12:49 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 4 Jan 2001 10:14:13 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Mummi, > I think that when reorganizing the the documentation for the new > acedb.org, it should definately be an issue to make all of it available > in more formats than HTML only, portions clustered together. If the docs > are maintained as, say, Latex, they can easily by converted to HTML by > Latex2HTML, or converted to Postscript for printing. Have you guys > thought about this, Ed? > > Mummi This came up at the Vancouver conference last year, there is certainly a _MASSIVE_ case for improving the documentation for acedb. I seem to remember that the concensus was that we really needed a funded person whose job it was to take existing docs and sort this out. Does anyone have any suggestions for who could be approached for funding ? I would make the following points: 1) I don't think the approach of having one base type of document (e.g. latex) from which all others will be derived will work. Some people like to use Word, others emacs etc. We need to let people write documentation in whatever form they want. 2) There are however some recognised ways of doing things, many sites offer the following: - the original document (be it html, word or whatever) - an html version for online browsing - various printable versions (postscript, pdf or whatever) I expect there are some tools that help with preparing printable versions from browsable documents. We've certainly thought about it but we don't have the resources to do this at the moment as there are a number of other higher priority tasks in the pipeline. 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 Jan 4 10:14:21 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D3BA317B2C; Thu, 4 Jan 2001 10:14:19 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 74BF617A5E; Thu, 4 Jan 2001 10:14:06 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 8B4DA17B2A; Thu, 4 Jan 2001 09:42:05 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 43E8741672 for ; Thu, 4 Jan 2001 09:42:01 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA05968 for bionet-software-acedb@net.bio.net; Thu, 4 Jan 2001 09:42:00 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: doggerel Organization: Sanger Centre Message-ID: <3A544568.BC427109@sanger.ac.uk> References: <93031b$ngo$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 978601320 5958 193.60.84.177 (4 Jan 2001 09:42:00 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 4 Jan 2001 09:42:00 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 4 Jan 2001 10:14:06 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Sara, > We're geographers in private practice, and have been using ACEDB quite > happily for a couple of years. For some reason we started a new project > in a relational database instead. Why? I don't have an excuse really. > Must have taken leave of my senses. After a particularly nasty bout > with the stuff my partner sent me this, and I couldn't resist passing it > on. This is great, if you know of anyone else who uses acedb in this kind of way do let us know. Do you want to receive the acedb newsletter each month ? If so just send me a note. 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 Jan 4 15:37:11 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D76CF17A6D; Thu, 4 Jan 2001 15:37:10 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id F382017A58; Thu, 4 Jan 2001 15:37:05 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 991F617A6D; Thu, 4 Jan 2001 15:08:22 +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 4567241681 for ; Thu, 4 Jan 2001 15:08:12 +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 KAA06714; Thu, 4 Jan 2001 10:07:35 -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 KAA10779; Thu, 4 Jan 2001 10:07:34 -0500 (EST) Message-Id: <200101041507.KAA10779@ray.nlm.nih.gov> From: Jean Thierry-Mieg Reply-To: Jean Thierry-Mieg Subject: Re: as postscript file: related To: bionet-software-acedb@net.bio.net, edgrif@sanger.ac.uk MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: mHDAdO1WBSY/uWBqExHNXA== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.3.5 SunOS 5.7 sun4u sparc Newsgroups: bionet.software.acedb Date: Thu, 4 Jan 2001 15:37:05 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk in my expereince, Latex that i used a lot in the 80's is or at least was, quite heavy Lincoln once recommended to me to use a simple perl tool, what do you expect of Lincoln, to convert from there in other forms From owner-acedb@hgmp.mrc.ac.uk Thu Jan 4 15:37:17 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BCEFB17A74; Thu, 4 Jan 2001 15:37:16 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 29D7117A6D; Thu, 4 Jan 2001 15:37:14 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 4045817A6D; Thu, 4 Jan 2001 15:12:46 +0000 (GMT) Received: from rutgers.rutgers.edu (rutgers.edu [165.230.4.76]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B3F57415E5 for ; Thu, 4 Jan 2001 15:12:18 +0000 (GMT) Received: from ncbi.nlm.nih.gov (ncbi.nlm.nih.gov [130.14.25.1]) by rutgers.rutgers.edu (8.8.8/8.8.8) with ESMTP id KAA23659 for ; Thu, 4 Jan 2001 10:12:05 -0500 (EST) 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 KAA08220; Thu, 4 Jan 2001 10:11:57 -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 KAA11694; Thu, 4 Jan 2001 10:11:55 -0500 (EST) Message-Id: <200101041511.KAA11694@ray.nlm.nih.gov> From: Jean Thierry-Mieg Reply-To: Jean Thierry-Mieg Subject: Re: doggerel To: bionet-software-acedb@moderators.isc.org, syurman@my-deja.com MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: 1V4Fpfx+Zsl7dSxS4FDyYw== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.3.5 SunOS 5.7 sun4u sparc Newsgroups: bionet.software.acedb Date: Thu, 4 Jan 2001 15:37:14 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Thank you very much for these nice appreciations. The perfect Happy New year greeting card It will make our day ! Merci jean From owner-acedb@hgmp.mrc.ac.uk Fri Jan 5 12:41:51 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 261B117A70; Fri, 5 Jan 2001 12:41:51 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 50B1317A9F; Fri, 5 Jan 2001 12:41:49 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id EA85117B66; Fri, 5 Jan 2001 10:14:28 +0000 (GMT) Received: from briar.org (backdraft.briar.org [192.207.123.123]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 877CD415EF for ; Fri, 5 Jan 2001 10:14:19 +0000 (GMT) Received: (from smap@localhost) by briar.org (8.9.1b+Sun/8.6.12) id FAA20744 for ; Fri, 5 Jan 2001 05:14:07 -0500 (EST) X-Authentication-Warning: backdraft.briar.org: smap set sender to using -f Received: from pat.ccc.nottingham.ac.uk(128.243.40.194) by backdraft via smap (V2.1) id xma020742; Fri, 5 Jan 01 05:13:52 -0500 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 14ETrG-0002Ba-00 for bionet-software-acedb@moderators.isc.org; Fri, 05 Jan 2001 10:12:26 +0000 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 14ETsb-00071d-00; Fri, 5 Jan 2001 10:13:49 +0000 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Re: doggerel Organization: ACS, The University of Nottingham Message-ID: References: <93031b$ngo$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 978689629 27007 128.243.116.150 (5 Jan 2001 10:13:49 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 5 Jan 2001 10:13:49 GMT X-Sender: keith@thale Date: Fri, 5 Jan 2001 12:41:49 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk On 4 Jan 2001 syurman@my-deja.com wrote: > We're geographers in private practice, and have been using ACEDB quite > happily for a couple of years. For some reason we started a new project > in a relational database instead. Why? I don't have an excuse really. > Must have taken leave of my senses. After a particularly nasty bout > with the stuff my partner sent me this, and I couldn't resist passing it > on. Could I enquire as to what problems you had using a relational database? Our group heavily uses acedb at the moment but we are looking into the *possibilities* of whether our data could also be stored in a relational database. Were there any *general* problems with relational databases that you were having where acedb proved superior? 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 Fri Jan 5 15:53:59 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2B01317AA7; Fri, 5 Jan 2001 15:53:58 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id A984217A85; Fri, 5 Jan 2001 15:53:55 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 4F53717A81; Fri, 5 Jan 2001 15:20:58 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 513B941628 for ; Fri, 5 Jan 2001 15:20:28 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA06765 for bionet-software-acedb@net.bio.net; Fri, 5 Jan 2001 15:20:27 GMT To: bionet-software-acedb@net.bio.net From: John Sturdy Newsgroups: bionet.software.acedb Subject: Re: as postscript file: related Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: References: <396350AE.60D3DCD6@marseille.inserm.fr> <8kfbor$ku4$1@nnrp1.deja.com> <3A544CA1.944DCCBC@sanger.ac.uk> X-Trace: niobium.hgmp.mrc.ac.uk 978708027 6643 193.62.207.28 (5 Jan 2001 15:20:27 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 5 Jan 2001 15:20:27 GMT X-Newsreader: Gnus v5.5/Emacs 20.3 Date: Fri, 5 Jan 2001 15:53:55 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Rather than looking at how to provide documents in multiple formats, I'd rather track down the underlying problems, i.e. what's not good enough about HTML? I suspect that the problem is largely that HTML browsers tend not to produce good printed output (e.g. PostScript); also, web pages tend to have navigational things on them that are not wanted in a printed paper. I don't think it's logically part of the AceDB output to fix browser printing problems ;-) but we can help with the other part of it by making the server capable of outputting a "de-navigationalized" version of each page. If anyone knows of good tools for printing web pages (better than the browsers do) -- or tips for setting up browser printing -- let me know and I'll set up a page of "advice for printing documents from this site". I will make some enquiries in this domain myself. If, however, I'm wrong about why other formats are wanted, let me know about that instead. -- Dr John Sturdy jcgs@sanger.ac.uk Informatics Division Sanger Centre From owner-acedb@hgmp.mrc.ac.uk Tue Jan 9 15:47:51 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 3B2BB17B50; Tue, 9 Jan 2001 15:47:49 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 8779A17B4F; Tue, 9 Jan 2001 15:47:43 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id A6D5517ACE; Tue, 9 Jan 2001 11:34:54 +0000 (GMT) Received: from mailbox3.ucsd.edu (mailbox3.ucsd.edu [132.239.1.55]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 840E94160A for ; Tue, 9 Jan 2001 11:34:41 +0000 (GMT) Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by mailbox3.ucsd.edu (8.11.0/8.11.0) with ESMTP id f09BYSC21139 for ; Tue, 9 Jan 2001 03:34:29 -0800 (PST) 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 14Fx1P-0006ct-00 for bionet-software-acedb@moderators.isc.org; Tue, 09 Jan 2001 11:32:59 +0000 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 14Fx2o-0004lh-00; Tue, 9 Jan 2001 11:34:26 +0000 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: AcePerl question 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 979040066 18331 128.243.116.150 (9 Jan 2001 11:34:26 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 9 Jan 2001 11:34:26 GMT X-Sender: keith@thale Date: Tue, 9 Jan 2001 15:47:43 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Here's hoping someone can help. I have a niggly (non-life-threatening) problem in that if anyone uses any AceBrowser interface (text search, class browser, query etc.) to access any acedb database on our server, then it generates the following line in the web error log on our server. ERROR: failed to read file It has taken me a long time to track down what is causing this message. It appears to be the OpenDatabase() function call that is usually present in every AceBrowser script. E.g. if you take the standard 'grep' script that comes as part of AceBrowser and strip away most of it to just leave: #!/usr/bin/perl use strict 'vars'; use vars qw/$DB $URL %PAPERS/; use Ace 1.51; use CGI 2.42 qw/:standard :html3 escape/; use CGI::Carp qw/fatalsToBrowser/; use AceSubs qw(:DEFAULT :search); $DB = OpenDatabase(); print "DB is $DB\n"; #--------------------------- Then calling this script still produces the 'ERROR: failed to read file' web log message. The OpenDatabase() function is part of AceSubs.pm and is simply: sub OpenDatabase { my $name = shift || get_symbolic(); my $db = $DB{$name}; unless ($db and $db->ping) { my ($host,$port) = getDatabase($name); return $DB{$name} = Ace->connect(-host=>$host,-port=>$port,-timeout=>50); } return $db; } Can anyone suggest why this function produces these error messages? It's not doing any damage as far as I can tell, but it is starting to clog up our web error log file. We have AceBrowser 2.10, Apache 1.3.12 running on Tru64 UNIX. Thanks in advance, 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 Wed Jan 10 10:46:01 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id CA16417B72; Wed, 10 Jan 2001 10:46:00 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id EC0B317B71; Wed, 10 Jan 2001 10:45:58 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 55DFC17B71; Wed, 10 Jan 2001 10:17:36 +0000 (GMT) Received: from postfix1.free.fr (postfix1.free.fr [212.27.32.21]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C220D415E3 for ; Wed, 10 Jan 2001 10:17:12 +0000 (GMT) Received: from nnrp3.proxad.net (nnrp3-2.proxad.net [213.228.0.134]) by postfix1.free.fr (Postfix) with ESMTP id D160328170 for ; Wed, 10 Jan 2001 11:16:59 +0100 (MET) Received: from localhost (localhost [[UNIX: localhost]]) by nnrp3.proxad.net (8.9.3/8.9.3/Debian 8.9.3-21) id LAA27809; Wed, 10 Jan 2001 11:16:58 +0100 To: bionet-software-acedb@net.bio.net Message-ID: <3A5C381A.F98089F5@marseille.inserm.fr> From: "F. Coulier" Organization: INSERM X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.11 i686) X-Accept-Language: fr-FR, en MIME-Version: 1.0 Newsgroups: bionet.software.acedb Subject: Re: AcePerl question References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Complaints-To: abuse@proxad.net X-Trace: nnrp3.proxad.net 979121818 195.220.67.155 (Wed, 10 Jan 2001 11:16:58 CET) NNTP-Posting-Date: Wed, 10 Jan 2001 11:16:58 CET Date: Wed, 10 Jan 2001 10:45:58 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I don't know if my (old) problem is related. Maybe. Briefly, I have installed acedb on a PC (Linux Mandrake 7.1). Acedb works fine, but not the web interface, I get a "Couldn't open database." error message. Your post gave me the idea to try to find out where that message come from: if I look into the cgi-bin/ace/simple script (the one I (try to) launch from the web page): # fetch database handle $DB = OpenDatabase() || AceError("Couldn't open database."); However, I am still not able to solve my problem from there. Can anyone help me on this? François -- François Coulier, mél: coulier@marseille.inserm.fr INSERM Unité 119, 27 bd Leï Roure, 13009 Marseille, France Tel: 33 (0) 4 91 26 04 26 (temporaire) Fax: 33 (0) 4 91 26 03 64 Site ouaibe: http://olan.marseille.inserm.fr/ From owner-acedb@hgmp.mrc.ac.uk Wed Jan 10 16:35:19 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9931617B83; Wed, 10 Jan 2001 16:35:18 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 45BC017B7E; Wed, 10 Jan 2001 16:35:14 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id CF03F17B6F; Wed, 10 Jan 2001 14:21:56 +0000 (GMT) Received: from sprettur.isnet.is (sprettur.isnet.is [193.4.58.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id DE5BF415ED for ; Wed, 10 Jan 2001 14:21:50 +0000 (GMT) Received: from mail.deja.com (mail.deja.com [64.57.170.34]) by sprettur.isnet.is (8.11.1/8.11.0/isnet) with ESMTP id f0AELmG94858 for ; Wed, 10 Jan 2001 14:21:49 GMT (envelope-from news@dejanews.com) Received: from nnrp1.deja.com (nnrp1.deja.com [10.12.2.16]) by mail.deja.com (8.11.1/8.11.1) with ESMTP id f0AELlf07301 for ; Wed, 10 Jan 2001 08:21:47 -0600 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id IAA25321; Wed, 10 Jan 2001 08:21:34 -0600 To: bionet-software-acedb@moderators.isc.org From: syurman@my-deja.com Newsgroups: bionet.software.acedb Subject: Re: doggerel Organization: Deja.com Message-ID: <93hr5e$on8$1@nnrp1.deja.com> References: <93031b$ngo$1@nnrp1.deja.com> X-Article-Creation-Date: Wed Jan 10 14:21:45 2001 GMT X-Http-User-Agent: Mozilla/4.76 [en] (X11; U; Linux 2.2.17 i686) X-Http-Proxy: 1.0 x55.deja.com:80 (Squid/1.1.22) for client 216.175.67.227 X-MyDeja-Info: XMYDJUIDsyurman Date: Wed, 10 Jan 2001 16:35:14 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi Keith and list, The "problem" was in efficiency, not operation. The data could be configured and managed in a relational system but we had to write absolutely baroque SQL in order to get the equivalent of a single find...follow statement. Flexibility is also an important element of efficiency for us. The nature of our projects can be fairly fluid. We haven't found an equivalent to changing our acedb model in order to morph the database in the relational world. Our concept of how to accomplish this project had changed substantially since the original pilot and it caused major dislocations. Hope that helps, Sara > Could I enquire as to what problems you had using a relational database? > Our group heavily uses acedb at the moment but we are looking into the > *possibilities* of whether our data could also be stored in a relational > database. > > Were there any *general* problems with relational databases that you were > having where acedb proved superior? > > 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 > > Sent via Deja.com http://www.deja.com/ From owner-acedb@hgmp.mrc.ac.uk Thu Jan 11 12:27:43 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B573517AD3; Thu, 11 Jan 2001 12:27:42 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 7F6B017A71; Thu, 11 Jan 2001 12:27:41 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id EAD3917A71; Thu, 11 Jan 2001 12:22:05 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id AA39B4160B for ; Thu, 11 Jan 2001 12:21:40 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id MAA13394 for bionet-software-acedb@net.bio.net; Thu, 11 Jan 2001 12:21:40 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: as postscript file: related Organization: Sanger Centre Message-ID: <3A5DA553.FD567FDD@sanger.ac.uk> References: <396350AE.60D3DCD6@marseille.inserm.fr> <8kfbor$ku4$1@nnrp1.deja.com> <3A544CA1.944DCCBC@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 979215700 13392 193.60.84.177 (11 Jan 2001 12:21:40 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 11 Jan 2001 12:21:40 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 11 Jan 2001 12:27:41 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk John, > Rather than looking at how to provide documents in multiple formats, > I'd rather track down the underlying problems, i.e. what's not good > enough about HTML? The problem is that many people who might write about acedb want to do so in their favourite word processor and they (quite rightly) don't want to waste time battling with html or anything else. We should be clear about providing two sorts of docs: - those viewable online, where html/web based the clear favourite - printable docs which could be viewed via ghostscript, acrobat etc. but can also be printed out. I agree about your other points. 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 Jan 11 12:28:00 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id ADB3A17AD3; Thu, 11 Jan 2001 12:27:59 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 7563917AC9; Thu, 11 Jan 2001 12:27:57 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id CE85317A71; Thu, 11 Jan 2001 12:27:11 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id CC2C941616 for ; Thu, 11 Jan 2001 12:27:05 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id MAA13516 for bionet-software-acedb@net.bio.net; Thu, 11 Jan 2001 12:27:05 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: doggerel Organization: Sanger Centre Message-ID: <3A5DA699.5B0B63CA@sanger.ac.uk> References: <93031b$ngo$1@nnrp1.deja.com> <93hr5e$on8$1@nnrp1.deja.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 979216025 13514 193.60.84.177 (11 Jan 2001 12:27:05 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 11 Jan 2001 12:27:05 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 11 Jan 2001 12:27:57 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > The "problem" was in efficiency, not operation. The data could be > configured and managed in a relational system but we had to write > absolutely baroque SQL in order to get the equivalent of a single > find...follow statement. Interesting, this is something that I've often heard said, but because I am not an expert on SQL I've never known if its really true or not. > Flexibility is also an important element of > efficiency for us. The nature of our projects can be fairly fluid. We > haven't found an equivalent to changing our acedb model in order to > morph the database in the relational world. Our concept of how to > accomplish this project had changed substantially since the original > pilot and it caused major dislocations. Yes, this comes up in the acedb courses that are run at the Sanger Centre: - people are usually _very_ surprised at the idea that you can (within certain limits) just edit the models file to add stuff on a live database. - people really like the fact that the models file is just a simple text file. A real plus for acedb. Thanks for the feedback. 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 Mon Jan 15 16:01:06 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8854717B12; Mon, 15 Jan 2001 16:01:05 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3140C17AC3; Mon, 15 Jan 2001 16:01:02 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id BB5C317AF5; Mon, 15 Jan 2001 15:02:56 +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 8C89A41615 for ; Mon, 15 Jan 2001 15:02:35 +0000 (GMT) Received: (qmail 8825 invoked by alias); 15 Jan 2001 15:02:31 -0000 Received: (qmail 8821 invoked from network); 15 Jan 2001 15:02:30 -0000 Received: from pat.ccc.nottingham.ac.uk (HELO nottingham.ac.uk) (128.243.40.194) by moderated.news.pipex.net with SMTP; 15 Jan 2001 15:02:30 -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 14IB7u-0003JQ-00 for bionet-software-acedb@moderators.isc.org; Mon, 15 Jan 2001 15:00:54 +0000 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 14IB9O-0005UK-00; Mon, 15 Jan 2001 15:02:27 +0000 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Fix for LongText display problem (in AceBrowser) 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 979570945 21098 128.243.116.150 (15 Jan 2001 15:02:25 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 15 Jan 2001 15:02:25 GMT Dave Matthews X-Sender: keith@thale Date: Mon, 15 Jan 2001 16:01:02 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi all, The default display of LongText objects using AceBrowser isn't very pretty. Any formatting of spaces and tabs are lost as text is converted to HTML (which doesn't allow multiple spaces). A lot of acedb databases - including ours - contain the original EMBL entries of sequences as LongText objects and they look terrible unless you try viewing them as a graphic. E.g. try looking at this WormBase record: http://www.wormbase.org/perl/ace/elegans/misc/etree?name=EMBL%3AAB006659&class=LongText A quick fix can be made though by editing the AceBrowser 'tree' script which handles the initial display of most acedb objects. Find the line in the tree script which starts: print $obj->asHTML(\&to_href) || strong('No more text... This is the line which normally displays the contents of any object using the 'asHTML' function. Replace this line with: if ($class eq 'LongText'){ print $obj->asHTML(\&format_longtext); } else{ print $obj->asHTML(\&to_href) || strong('No more text information about this object in the database'), "\n"; } You will also need to add a subroutine somewhere in the tree script. This is simply: sub format_longtext{ my $obj = shift; return pre($obj); } Basically you are telling AceBrowser to check whether the object is a LongText object and if so display it using the 'format_longtext' subroutine which does nothing but return the text using the equivalent of the HTML 
 tag (which preserves formatting).  If it isn't a LongText
object, the object is displayed as normal.

There is probably an even simpler way of getting around this, but this
method seems to work and might be helpful for people who use AceBrowser.


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  Wed Jan 17 09:32:37 2001
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To: bionet-software-acedb@moderators.isc.org
From: Keith Bradnam 
Newsgroups: bionet.software.acedb
Subject: Adding a class count facility to AceBrowser
Organization: ACS, The University of Nottingham
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Hi,

Those of you who like the ability of WebAce to show you how many objects
are in each class and bemoan the fact that AceBrowser doesn't do this, can
now breathe a sigh of relief.

I've made a quick hack to remedy the situation. E.g. see

http://ukcrop.net/perl/ace/search/AGR

Anyone wanting details, just ask.


Now to try to make it list subclasses next to parent classes!

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 Jan 22 09:31:22 2001
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To: bionet-software-acedb@net.bio.net
From: Ed Griffiths 
Newsgroups: bionet.software.acedb
Subject: acedb ftp site change
Organization: Sanger Centre
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Precedence: bulk


This will probably only affect a few people.....

Here at Sanger we have had two ftp directories for acedb: /pub/acedb and
/pub/acedb_src. The latter was used to hold an up to date copy of the source
code plus back versions, it was updated every night.

As part of the rationalisation/reorganisation of the acedb ftp site,
/pub/acedb_src will disappear this week and instead the source/code/binaries
will be copied into /pub/acedb each night into /pub/acedb/DAILY.

You should note that /pub/acedb/DAILY contains a snapshot of development code
and as a rule you should _not_ download this code. It is there mainly to
continue the policy of acedb being "open source", to provide up to date source
for fellow developers and perhaps to provide a quick fix for particular users.

If this change will cause you any problems then please mail acedb@sanger.ac.uk
or post to this newsgroup.

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  Tue Jan 23 14:21:25 2001
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To: bionet-software-acedb@moderators.isc.org
From: Keith Bradnam 
Newsgroups: bionet.software.acedb
Subject: xace crash
Organization: ACS, The University of Nottingham
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I have just found a reliable way of crashing xace...which is nice.

We run 4.7l on Tru64 UNIX. 

I have a simple 'Species' class in my database which mostly contains
details of Proteins and Sequences for each species represented in the
database. For 'Arabidopsis thaliana' there is (as you would expect) a lot
of sequences (over 183,000). 

In the default tree display for the 'Arabidopsis thaliana' species it
lists that there are 183,000 sequences, but as you would expect,
it collapses the branch that leads to these 183,000 sequences. If I try to
expand it xace crashes with the error:

Stack overflow: pid 6745, proc xace, addr 0x11dffffb0, pc 0x1201afa1c
Segmentation fault (core dumped)


This happens even if I try running 'unlimit' first.  We do have 2 Gb
memory on this machine, so memory shouldn't really be a problem.  Is there
some upper limit of objects that can be 'expanded' from a collapsed branch
in this manner?  The same display will let me expand the 24,000 or so
Protein sequences without crashing.


Food for thought.


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  Tue Jan 23 16:06:46 2001
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To: bionet-software-acedb@net.bio.net
From: Ed Griffiths 
Newsgroups: bionet.software.acedb
Subject: Re: xace crash
Organization: Sanger Centre
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Keith,

> Stack overflow: pid 6745, proc xace, addr 0x11dffffb0, pc 0x1201afa1c
> Segmentation fault (core dumped)
> 
> This happens even if I try running 'unlimit' first.  We do have 2 Gb
> memory on this machine, so memory shouldn't really be a problem.  Is there
> some upper limit of objects that can be 'expanded' from a collapsed branch
> in this manner?  The same display will let me expand the 24,000 or so
> Protein sequences without crashing.

Running unlimit will not necessarily give you unlimited stack space, all unix
users have a "hard" limit for each of the process resources such as "core",
"data", "stack" etc. If you use unlimit, the resource will only be allowed to
use up to this hard limit.

e.g. on my DEC:

griffin[edgrif]59: ulimit -s             # current stack limit
2048
griffin[edgrif]60: ulimit -Hs            # hard stack limit
32768
griffin[edgrif]63: unlimit               # unlimit stack
griffin[edgrif]64: ulimit -s             # new stack limit
32768

Although I used unlimit, my stack is still limited to the level set by the hard
level. You need to check what this is for your system, note that only root can
change hard limits.

You have a large number of objects so running out of stack space is a
possibility.

Let us know what you find.

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 Jan 24 09:54:32 2001
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> Stack overflow: pid 6745, proc xace, addr 0x11dffffb0, pc 0x1201afa1c
> Segmentation fault (core dumped)

As Ed pointed out, there is a hard limit.  So you can't use your 2Gb
all as stack space.

But I think we have to acknowledge that this is an acedb bug.  A few
years ago we rewrote most code that looks at acedb tree objects to
only recurse going right, not when going down lists.  This speeds
things up as well as avoiding stack overflow problems.  My guess is
that the tree display code still has a downwards recursion (it is
simpler to write that way), which is causing this problem.  We should
remove it.

Richard





From owner-acedb@hgmp.mrc.ac.uk  Fri Jan 26 16:49:40 2001
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From: jayoung@fhcrc.org (Janet Young)
Newsgroups: bionet.software.acedb
Subject: table maker - hidden columns
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
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Hi all

If I remember rightly, in the table maker in an old version of acedb I was
using (I think 4.7l), when I hid a column, then if all the information in
the other columns was identical, identical rows would only be shown once.
But now I've updated to acedb 4_8c I get the identical rows multiple times
(because information in hidden columns is different for these rows).

Is this something I can do anything about or is it something which has
changed in the acedb code? or maybe I'm remembering wrongly anyway? It would
be more helpful for me to not show identical rows - I don't know what other
people think...

thanks

Janet

-------------------------------------------------------------------
                              Dr. Janet Young
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N.                    tel: (206) 667 1471
C3-168                                     fax: (206) 667 6524
P.O. Box 19024                             email: jayoung@fhcrc.org
Seattle, WA 98109-1024, USA.



---




From owner-acedb@hgmp.mrc.ac.uk  Mon Jan 29 08:46:07 2001
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From: Angela Baldo 
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Hi Janet,

I pointed the same thing out to Richard Bruskiewich last November, and
he agreed that it was strange.  I recall, we emailed a bug report about
it to Ed.  You can see the message here:
http://ars-genome.cornell.edu/BugDB/Notes?id=186;user=guest;selectid=186

Glad it's not just me!  :-)

anja

Janet Young wrote:
> 
> Hi all
> 
> If I remember rightly, in the table maker in an old version of acedb I was
> using (I think 4.7l), when I hid a column, then if all the information in
> the other columns was identical, identical rows would only be shown once.
> But now I've updated to acedb 4_8c I get the identical rows multiple times
> (because information in hidden columns is different for these rows).
> 
> Is this something I can do anything about or is it something which has
> changed in the acedb code? or maybe I'm remembering wrongly anyway? It would
> be more helpful for me to not show identical rows - I don't know what other
> people think...
> 
> thanks
> 
> Janet
> 
> -------------------------------------------------------------------
>                               Dr. Janet Young
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Avenue N.                    tel: (206) 667 1471
> C3-168                                     fax: (206) 667 6524
> P.O. Box 19024                             email: jayoung@fhcrc.org
> Seattle, WA 98109-1024, USA.
> 
> ---

-- 
NOW HIRING INFORMATICS POSTDOCS, GRAIN BREEDING EXPERTS!
http://ars-genome.cornell.edu/rice/employment.html
_______________________________________________________________
Angela M. Baldo, PhD    RiceGenes / Gramene
USDA-ARS CAB            http://ars-genome.cornell.edu/rice
622 Rhodes Hall         http://www.gramene.org
Cornell Theory Center     
Cornell University      phone   (607) 254-1230
Ithaca, NY 14853 USA    fax     (607) 255-0323
_______________________________________________________________





From owner-acedb@hgmp.mrc.ac.uk  Mon Jan 29 08:46:10 2001
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From: matthews@greengenes.cit.cornell.edu (Dave Matthews)
Newsgroups: bionet.software.acedb
Subject: Can we limit XREFs? Please? (re: xace crash)
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
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Keith Bradnam said:

: I have a simple 'Species' class in my database which mostly contains
: details of Proteins and Sequences for each species represented in the
: database. For 'Arabidopsis thaliana' there is (as you would expect) a lot
: of sequences (over 183,000).

Many of us have a similar problem if not so extreme.  Some few records get
filled with a huge number of links, too many to be conceivably useful.  Not
only is browsing the record a ridiculous notion, even the performance
efficiency of a "follow" query ("find species 'Arabidopsis thaliana';
follow sequence") has no utility, no reason you would want a result set
that large.  Even when such records aren't big enough to actually crash the
system they can be a performance problem and a user-ugliness.

On the other hand in the record for Species 'Arabidopsis arenosa' which has
only four sequence entries, these might be quite interesting to somebody.

Such unbalanced situations almost always arise from loading sequences into
a model like Keith's:

   ?Sequence ...
             Species ?Species XREF Sequence

Which is a natural way to process input from Genbank/EMBL records.  Of
course the input could be balanced better by parsing otherwise, eschewing
the XREF and loading the data from the other side:

   Species : X
   Sequence Y

, but this would still require additional code to filter which Species
should be excluded.

The ACEDB code already has a trigger that detects when loading such XREFs
creates an unuseful result.  You can read it in database/log.wrm:

: 2001-01-20_00:30:20 genome 20042	Class Sequence, object
:  BCD421_WHE1B0042 has 4280 > 3000 cells.  This is just a warning, acedb
:  has no hard limits on the mumber of cells per object, but the
:  performances degrade on very large objects
:  Either, you are cross referencing many entries into a single object, it
:  may not be useful, and you could drop the XREF in the model and get the
:  same info via an occasional query or, continually, via a subclass, or
:  This object is Class:?Text, and you should rather use plain Text in the
:  model or define a controlled vocabulary by giving an explicit list of
:  tags


REQUEST

My request is, can the code be extended to allow the database owner to
set a hard limit on XREFs?  A configuration in a wspec/ file?  When the
limit is exceeded all the links could be deleted and replaced with an
object like Sequence : "More than 10,000, not shown".


APPRECIATION

One of ACEDB's strengths is its ability to handle efficiently large numbers
of sparse many-to-many relations.  My database has hundreds of these, yours
probably does too.  In a relational DBMS any of these with a sparseness
above about 10:1 would need to be implemented with a separate relationship
table, each of which would itself have a cost in performance, data size and
mainly complexity.  In ACEDB I don't see any cost up to at least 100:1.  I
estimate about half my records fall in this range, and nearly all the rest
are below.  This is a big win for the ACEDB data structure.

The place where we're having problems is beyond 1000:1.  Here a properly
structured RDBMS could be quite efficient whereas ACEDB isn't.  The question
is, how often is it useful?  If we could just truncate such records wouldn't
that be what we really want?

- Dave


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David E. Matthews                       USDA-ARS Plant Genome Database Curator
Adjunct Associate Professor         
Department of Plant Breeding        Email: matthews@greengenes.cit.cornell.edu
Cornell University                                         Phone: 607-255-9951
Ithaca, New York 14853, USA                                  Fax: 607-255-6683


---




From owner-acedb@hgmp.mrc.ac.uk  Mon Jan 29 08:46:15 2001
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To: bionet-software-acedb@net.bio.net
From: jayoung@fhcrc.org (Janet Young)
Newsgroups: bionet.software.acedb
Subject: aceperl question - parse_file
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
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Hi

I'm trying to get the parse_file method of aceperl to work but I am doing
something wrong. This is probably a very simple question for someone who
knows aceperl.

here's my test script:

#!/usr/bin/perl
use warnings;
use Ace;
my @files = @ARGV;
foreach my $file (@files) {
   print "reading file $file\n";
   my $db = Ace->connect(-path =>'/shared1/traskdata/janet/OLFace',
                         -program
=>'/shared1/traskdata/janet/OLFace/tacedb');
   $db->auto_save(1);
   my $check = $db -> fetch (Sequence=> 'AC000096');
   print "check " . $check->asString;
   my @objects = $db->parse_file('dummy.ace');
   my $noobjs = @objects;
   print "$noobjs read into database\n";
   print "objects " . $objects[0]->asString . "\n";
}

here's the dummy.ace file:
Clone : dummyclone
Sequence dummyseq
Remark "this item not a real database object"

and here's the output:
reading file dummy.ace
check AC000096  Visible  Clone  CT7-98D3
1 read into database
objects dummyclone;

and a clone called dummyclone; appears in my database but without any tags.

Questions: where did the semi-colon in the object name come from, and why
does my object have no tags? (the input file gets read fine if I use xace to
read it in)


thanks for any help

Janet 

-------------------------------------------------------------------
                              Dr. Janet Young
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N.                    tel: (206) 667 1471
C3-168                                     fax: (206) 667 6524
P.O. Box 19024                             email: jayoung@fhcrc.org
Seattle, WA 98109-1024, USA.



---




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From: Jean Thierry-Mieg 
Reply-To: Jean Thierry-Mieg 
Subject: Re: table maker - hidden columns
To: bionet-software-acedb@net.bio.net, jayoung@fhcrc.org,
	srk@sanger.ac.uk
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Thsi of course an ESSENTIAL feature of table maker
we sue it all the time

please srk fix that !
and at the same time the possibility to switch not just
rotate columns if that is not yet fixed in 4.8c

both functions where destroyed for no good reason by fred
at some point.

please janet, revert to previous version 4.7m
in the mean time


>Hi all
>
>If I remember rightly, in the table maker in an old version of acedb I was
>using (I think 4.7l), when I hid a column, then if all the information in
>the other columns was identical, identical rows would only be shown once.
>But now I've updated to acedb 4_8c I get the identical rows multiple times
>(because information in hidden columns is different for these rows).
>
>Is this something I can do anything about or is it something which has
>changed in the acedb code? or maybe I'm remembering wrongly anyway? It would
>be more helpful for me to not show identical rows - I don't know what other
>people think...
>
>thanks
>
>Janet
>
>-------------------------------------------------------------------
>                              Dr. Janet Young
>Fred Hutchinson Cancer Research Center
>1100 Fairview Avenue N.                    tel: (206) 667 1471
>C3-168                                     fax: (206) 667 6524
>P.O. Box 19024                             email: jayoung@fhcrc.org
>Seattle, WA 98109-1024, USA.
>
>
>
>---
>
>

Danielle Thierry-Mieg
NCBI. NLM. NIH Bldg 38A
8600 Rockville Pike
Bethesda, MD 20894, USA
email   mieg@ncbi.nlm.nih.gov
Tel   1 (301) 594 70 92   Fax   1 (301) 480 92 41





From owner-acedb@hgmp.mrc.ac.uk  Mon Jan 29 15:53:56 2001
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From: Keith Bradnam 
Newsgroups: bionet.software.acedb
Subject: Re: Can we limit XREFs? Please? (re: xace crash)
Organization: ACS, The University of Nottingham
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On 29 Jan 2001, Dave Matthews wrote:

> Such unbalanced situations almost always arise from loading sequences into
> a model like Keith's:
> 
>    ?Sequence ...
>              Species ?Species XREF Sequence
> 
> Which is a natural way to process input from Genbank/EMBL records.  Of
> course the input could be balanced better by parsing otherwise, eschewing
> the XREF and loading the data from the other side:
> 
>    Species : X
>    Sequence Y
> 
> , but this would still require additional code to filter which Species
> should be excluded.

I think this is a good point Dave and I am probably guilty of always using
XREFs in our database when a conventional link may be more appropriate.
In most cases there is no real use in looking at a list of thousands of
objects, but would limiting the use of XREFs affect the way in which you
could query the data?

E.g. if I wanted to find out ATP genes in Arabidopsis or Brassica species
I could formulate a query like:

Find Species "Arabidopsis*" || "Brassica*"; Follow Protein; Gene_name =
"ATP*"

Would I still be able to do this if I didn't have the XREFs between
Species and Protein (admittedly I could rework the query starting from
Gene_name, but there may be reasons where you want to query in this way) ?

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  Wed Jan 31 14:23:33 2001
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Janet,

First things first, I am not a perl guru and don't have any suggestions about
the trailing ";" on the dummyclone object.

> here's the dummy.ace file:
> Clone : dummyclone
> Sequence dummyseq
> Remark "this item not a real database object"
> 
> and here's the output:
> reading file dummy.ace
> check AC000096  Visible  Clone  CT7-98D3
> 1 read into database
> objects dummyclone;
> 
> and a clone called dummyclone; appears in my database but without any tags.

Oh dear, well I tried your dummy ace file with tace and it worked fine producing
a dummyclone object with the correct tags and also an xreffed dummyseq object.

One thing does occur to me though, we have had problems with the underlying code
that does xreffing/aliasing/blending of objects. What version of acedb are you
using ?

If its not the latest monthly build then perhaps you should get hold of that and
try the above again because we believe that the xref code now works correctly.

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 |
 ------------------------------------------------------------------------