From owner-acedb@hgmp.mrc.ac.uk Tue May 2 15:35:53 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 89BDA17B35; Tue, 2 May 2000 15:35:51 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 90D2217A9E; Tue, 2 May 2000 15:35:44 +0100 (BST) Received: from isgate.is (isgate.is [193.4.58.51]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id PAA01173 for ; Tue, 2 May 2000 15:30:32 +0100 (BST) Received: from mail.deja.com (mail.deja.com [205.238.143.34]) by isgate.is (8.9.3r/8.9.0Imo) with ESMTP id OAA01286 for ; Tue, 2 May 2000 14:30:28 GMT Received: from nnrp1.deja.com (nnrp1.deja.com [10.2.2.16]) by mail.deja.com (8.8.7/8.8.5) with ESMTP id JAA30806 for ; Tue, 2 May 2000 09:30:11 -0500 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id JAA02920; Tue, 2 May 2000 09:29:45 -0500 To: bionet-software-acedb@moderators.isc.org From: zgudmunt@my-deja.com Newsgroups: bionet.software.acedb Subject: re: performance problems in loading Organization: Deja.com - Before you buy. Message-ID: <8emoop$2r7$1@nnrp1.deja.com> References: <200004252039.QAA17217@greengenes.cit.cornell.edu> X-Article-Creation-Date: Tue May 02 14:30:09 2000 GMT X-Http-User-Agent: Mozilla/4.7 [en] (WinNT; I) X-Http-Proxy: 1.0 proxy.decode.is:8080 (Squid/2.2.STABLE5), 1.0 x40.deja.com:80 (Squid/1.1.22) for client 172.18.253.134, 193.4.196.222 X-MyDeja-Info: XMYDJUIDzgudmunt Date: Tue, 2 May 2000 15:35:44 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I am now running my Ace-s on a Linux server with 1 Gb of ram, but will move them to a dedicated Ace-machine soon, with only 500 Mb of ram. I was wondering about the cache-sizes and performance issues: should I use specific cachesizes for the small (few hundred Mb on disk) local-running Ace-s, accessed through Xace, different from cachesizes for the server(s) running on the same server? The small servers are pretty fast with the default values of 4000/4000, but the big ones (several Gb on disk) can be pretty slow. Shouldn't I be able to speed the big server and/or xace up significantly by increasing my caches? Mummi In article <200004252039.QAA17217@greengenes.cit.cornell.edu>, matthews@greengenes.cit.cornell.edu (Dave Matthews) wrote: > jean said: > > : Date: Wed, 19 Apr 2000 13:29:34 +0100 (BST) > : > : You fly while you fill the cache > : but then it should stay fast > : > : you describe gioing to 1 record/minute which ius ridiculously slow > : > : so i suppose you have defines a cachesize much larger than you actual > : memeory and are swapping > : acedb should not swap > : > : please check wspec/cachesize.wrm , the size declared should be a good > : proportion of your real ram > > Xiaowu Gai reported back that the problem was indeed his cache sizes, but > in the opposite direction. He originally had > CACHE1 = 4000 > CACHE2 = 4000 > on a machine with 0.5 GB memory. (I'm not sure if that's RAM or total.) > The fix: > > > I increased the cache sizes to the same as the ones that you listed [16000, > > 32000] and it solved the problem. I loaded the whole 53,000 sequences in 10 > > minutes. I also tried to increase them a little more and it became even > > faster. > > --- > > Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Wed May 3 09:13:54 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A529517AA1; Wed, 3 May 2000 09:13:53 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 4C4B117A64; Wed, 3 May 2000 09:13:51 +0100 (BST) Received: from news.uky.edu (news.uky.edu [128.163.2.26]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id UAA09790 for ; Tue, 2 May 2000 20:26:07 +0100 (BST) Received: (from news@localhost) by news.uky.edu (8.8.5/8.6.12) id PAA12945; Tue, 2 May 2000 15:25:30 -0400 (EDT) To: bionet-software-acedb@hgmp.mrc.ac.uk From: nasand00@sac.uky.edu (Nathaniel Sanders) Newsgroups: bionet.software.acedb Subject: A grammar or similar specification for the models Organization: University of Kentucky Computing Services Message-ID: <8ena3a$b1c$1@news.uky.edu> X-Newsreader: TIN [version 1.2 PL2] Date: Wed, 3 May 2000 09:13:51 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Can anyone point me in a good direction for a specification for the structure of a model ? I've read Sam Cartinhour's document called "Exploring Models Design and Structure", but I think I need something more in-depth. I'm working on a model broswer, similar to Lincoln Stein's Perl-based object-browswer. I need to know the lexical structure for legal labels in a model, among possible other things. -- ============================================================================== Nathaniel Sanders nasand00@cslab.uky.edu ============================================================================== From owner-acedb@hgmp.mrc.ac.uk Wed May 3 16:20:48 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C380517B75; Wed, 3 May 2000 16:20:46 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 517A917A83; Wed, 3 May 2000 16:20:45 +0100 (BST) Received: from jess.sanger.ac.uk (root@jess.sanger.ac.uk [193.60.84.61]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id OAA12357 for ; Wed, 3 May 2000 14:50:24 +0100 (BST) Received: from griffin.sanger.ac.uk (rd@griffin [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id OAA01824; Wed, 3 May 2000 14:50:14 +0100 (BST) From: Richard Durbin Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id OAA12452; Wed, 3 May 2000 14:50:13 +0100 (BST) Message-Id: <200005031350.OAA12452@griffin.sanger.ac.uk> To: bionet-software-acedb@hgmp.mrc.ac.uk, nasand00@sac.uky.edu Subject: Re: A grammar or similar specification for the models Newsgroups: bionet.software.acedb Date: Wed, 3 May 2000 16:20:45 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk There is a python validation program for model files in the current source code tree, wtools/modelcheck. If this is not in the standard source code distribution you can get it from ftp.sanger.ac.uk/pub/acedb_src/wtools/. Thank you Ralph Gauges for writing this. Richard From owner-acedb@hgmp.mrc.ac.uk Thu May 4 09:27:30 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 28C2C17ADB; Thu, 4 May 2000 09:27:30 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 277D917AAD; Thu, 4 May 2000 09:27:28 +0100 (BST) Received: from moderated.news.pipex.net (moderated.news.pipex.net [158.43.192.79]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with SMTP id SAA15988 for ; Wed, 3 May 2000 18:28:46 +0100 (BST) Received: (qmail 29663 invoked by alias); 3 May 2000 17:28:46 -0000 Received: (qmail 29659 invoked from network); 3 May 2000 17:28:45 -0000 Received: from pat.ccc.nottingham.ac.uk (HELO nottingham.ac.uk) (128.243.40.194) by moderated.news.pipex.net with SMTP; 3 May 2000 17:28:45 -0000 Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.13 #2) id 12n2wh-00039c-00 for bionet-software-acedb@moderators.isc.org; Wed, 03 May 2000 18:28:23 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 12n2wz-00069E-00; Wed, 3 May 2000 18:28:41 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Classes and subclasses 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 957374921 23634 128.243.116.150 (3 May 2000 17:28:41 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 3 May 2000 17:28:41 GMT X-Sender: keith@thale Date: Thu, 4 May 2000 09:27:28 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Is there some sort of inbuilt limit for subclasses? I seem to recall reading somewhere that there might be. I've started noticing weird behaviour as I try to create more than 8 subclasses for any one class. Also...should I be able to (apart from the above complication) be able to make subclasses within subclasses (e.g. 'c' is a subclass of 'b' is a subclass of 'a')? If so, then when specifying in subclasses.wrm, do I say that 'c' is a subclass of 'b' or of 'a'? Keith ~ Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR) ~ Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/ ~ University Park, University of Nottingham, NG7 2RD, UK ~ Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Thu May 4 13:40:05 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id DFE0817AE9; Thu, 4 May 2000 13:40:04 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id B261C17A62; Thu, 4 May 2000 13:40:02 +0100 (BST) Received: from mailbox2.ucsd.edu (mailbox2.ucsd.edu [132.239.1.54]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id KAA03245 for ; Thu, 4 May 2000 10:39:40 +0100 (BST) Received: from jess.sanger.ac.uk (jess.sanger.ac.uk [193.60.84.61]) by mailbox2.ucsd.edu (8.9.3/8.9.3) with ESMTP id CAA04597 for ; Thu, 4 May 2000 02:39:36 -0700 (PDT) Received: from griffin.sanger.ac.uk (rd@griffin [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id KAA14983; Thu, 4 May 2000 10:39:27 +0100 (BST) From: Richard Durbin Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id KAA09606; Thu, 4 May 2000 10:39:27 +0100 (BST) Message-Id: <200005040939.KAA09606@griffin.sanger.ac.uk> To: bionet-software-acedb@moderators.isc.org, keith@thale.life.nottingham.ac.uk Subject: Re: Classes and subclasses Newsgroups: bionet.software.acedb Date: Thu, 4 May 2000 13:40:02 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > Is there some sort of inbuilt limit for subclasses? I seem to recall > reading somewhere that there might be. I've started noticing weird > behaviour as I try to create more than 8 subclasses for any one class. There is a limit of 8 subclasses per top level class in older versions of acedb, including I suspect 4_7l, but the code was rewritten to remove that limit, so that in new versions (4_8 and future) there is no limit. > Also...should I be able to (apart from the above complication) be able to > make subclasses within subclasses (e.g. 'c' is a subclass of 'b' is a > subclass of 'a')? > > If so, then when specifying in subclasses.wrm, do I say that 'c' is a > subclass of 'b' or of 'a'? Yes, you should be able to have subclasses of subclasses. You should say 'c' is a subclass of 'b'. This still counts as a subclass of 'a' for the limit of 8 discussed above. Richard From owner-acedb@hgmp.mrc.ac.uk Mon May 8 08:19:56 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 413DA17A5D; Mon, 8 May 2000 08:19:56 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 994B517A5C; Mon, 8 May 2000 08:19:54 +0100 (BST) Received: from dns2.nrc.ca (dns2.nrc.ca [132.246.60.2]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA17229 for ; Fri, 5 May 2000 17:27:28 +0100 (BST) Received: (from news@localhost) by dns2.nrc.ca (8.9.0/8.9.0) id MAA21634; Fri, 5 May 2000 12:27:25 -0400 (EDT) To: bionet-software-acedb@hgmp.mrc.ac.uk From: Mark Wilkinson Newsgroups: bionet.software.acedb Subject: Bad display type GMAP... how bad is it?? Organization: PBI - NRC Message-ID: <3912E823.4AAB015B@gene.pbi.nrc.ca> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.73 [en] (Win98; I) X-Accept-Language: en Date: Mon, 8 May 2000 08:19:54 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi Group! I have been trying to install ACEdb (Windows) on my laptop and it wont initialize. It chokes on the options.wrm file with an error "Bad Display Type GMAP". I copied the entire wspec file directly from a working installation on my NT in the lab, so as far as I know the settings should be correct. I tried explaining to ACE that the GMAP display type *is* a little confusing sometimes, but that doesn't necessarily make it *bad* and that it should be a little more tolerant... ACE, however, remains unconvinced. Since I don't know how ACE decides what is a "good" display type and what is a "bad" display type I am a bit stuck. There are only two "notable" differences between the two installations: the working one is on an NT at 1024X768, the non-working one is on Win98(German) at 800X600... could either of these be the problem? Any advice appreciated! By the way, for those of you who know me, I have now left the Max Planck and am back in Canada working at the PBI in Saskatoon. My E-mail address remains the same however, and for the forseeable future I will continue to curate DragonDB in Cologne. Cheers all! Mark Wilkinson markw@cheerful.com Plant Biotechnology Institute National Research Council of Canada 110 Gymnasium Place Saskatoon, Saskatchewan Canada From owner-acedb@hgmp.mrc.ac.uk Mon May 8 13:06:42 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 718C217A89; Mon, 8 May 2000 13:06:41 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 91B4C17A43; Mon, 8 May 2000 13:06:39 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id IAA17685 for ; Mon, 8 May 2000 08:25:56 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA14347 for bionet-software-acedb@net.bio.net; Mon, 8 May 2000 08:25:55 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: Bad display type GMAP... how bad is it?? Organization: Sanger Centre Message-ID: <39166C03.3092D908@sanger.ac.uk> References: <3912E823.4AAB015B@gene.pbi.nrc.ca> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 957770755 14345 193.60.84.177 (8 May 2000 07:25:55 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 8 May 2000 07:25:55 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Mon, 8 May 2000 13:06:39 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Mark, > I have been trying to install ACEdb (Windows) on my laptop and it wont > initialize. It chokes on the options.wrm file with an error "Bad > Display Type GMAP". Sorry, sorry, sorry, this is a bug introduced by us into the latest code. The bug was introduced for the best reasons: to fix an existing hole in acedb, but... You would only notice this on reinitialising a database, otherwise everything would be OK. Simon Kelley (here at Sanger) has fixed this, the fix will be available in the next monthly build which will be done this week. If you need a binary quicker than this you could contact Simon direct (srk@sanger.ac.uk). Really sorry about this... cheers Ed ------------------------------------------------------------------------------ | Ed Griffiths, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 (switch +44 1223 834244) Fax: +44 1223 494919 | ------------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Mon May 8 17:23:32 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 195F817AD2; Mon, 8 May 2000 17:23:30 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id ECC9A17AD1; Mon, 8 May 2000 17:23:27 +0100 (BST) Received: from dns2.nrc.ca (dns2.nrc.ca [132.246.60.2]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA10610 for ; Mon, 8 May 2000 17:21:01 +0100 (BST) Received: (from news@localhost) by dns2.nrc.ca (8.9.0/8.9.0) id MAA25251; Mon, 8 May 2000 12:20:32 -0400 (EDT) To: bionet-software-acedb@hgmp.mrc.ac.uk From: Mark Wilkinson Newsgroups: bionet.software.acedb Subject: Re: Bad display type GMAP... how bad is it?? Organization: PBI - NRC Message-ID: <3916DAF8.A399595F@gene.pbi.nrc.ca> References: <3912E823.4AAB015B@gene.pbi.nrc.ca> <39166C03.3092D908@sanger.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.73 [en] (Win98; I) X-Accept-Language: en Date: Mon, 8 May 2000 17:23:27 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > Sorry, sorry, sorry, this is a bug introduced by us into the latest code. no panic :-) I'm just happy that it's a bug and not me being a dumb-arse! cheers! Mark From owner-acedb@hgmp.mrc.ac.uk Thu May 11 10:25:59 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BEE5817AA4; Thu, 11 May 2000 10:25:58 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 98A1C17A67; Thu, 11 May 2000 10:25:55 +0100 (BST) Received: from news.uky.edu (news.uky.edu [128.163.2.26]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id BAA07175 for ; Thu, 11 May 2000 01:46:47 +0100 (BST) Received: (from news@localhost) by news.uky.edu (8.8.5/8.6.12) id UAA16611; Wed, 10 May 2000 20:46:05 -0400 (EDT) To: bionet-software-acedb@hgmp.mrc.ac.uk From: nasand00@sac.uky.edu (Nathaniel Sanders) Newsgroups: bionet.software.acedb Subject: How xaceclient handles recursive specification of data Organization: University of Kentucky Computing Services Message-ID: <8fcvsc$g6f$1@news.uky.edu> X-Newsreader: TIN [version 1.2 PL2] Date: Thu, 11 May 2000 10:25:55 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk In the HTML document entitled "Syntactic Definitions for the ACEDB Data Base Manager", I learned that constructed types allow a recursive specification of data in models. An example of this is in the Paper class. There is a label called In_book whose type is #Paper. As constructed types are "grafted" onto the current class, this creates a potentially infinitely long class. This of course isn't a problem in terms of actual storage of data, as the In_book label won't exist for some paper. However, I was curious how xaceclient would deal with the visual display of the creation of a new Paper object. Maybe I'm not doing something correctly, but no "In_book" label comes up, and I checked the models file and found it there. I'd like to know how this is supposed to work, since I'm writing a web interface to a particular installation of ACEDB and I'm going to have to solve the same problem. Thanks, Nate -- ============================================================================== Nathaniel Sanders nasand00@cslab.uky.edu ============================================================================== From owner-acedb@hgmp.mrc.ac.uk Thu May 11 14:00:54 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 68F8817B66; Thu, 11 May 2000 14:00:53 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id BD39517A65; Thu, 11 May 2000 14:00:49 +0100 (BST) Received: from jess.sanger.ac.uk (root@jess.sanger.ac.uk [193.60.84.61]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id MAA00485 for ; Thu, 11 May 2000 12:58:43 +0100 (BST) Received: from griffin.sanger.ac.uk (rd@griffin.sanger.ac.uk [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id MAA27229; Thu, 11 May 2000 12:58:26 +0100 (BST) From: Richard Durbin Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id MAA17800; Thu, 11 May 2000 12:56:40 +0100 (BST) Message-Id: <200005111156.MAA17800@griffin.sanger.ac.uk> To: bionet-software-acedb@hgmp.mrc.ac.uk, nasand00@sac.uky.edu Subject: Re: How xaceclient handles recursive specification of data Newsgroups: bionet.software.acedb Date: Thu, 11 May 2000 14:00:49 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > In the HTML document entitled "Syntactic Definitions for the > ACEDB Data Base Manager", I learned that constructed types allow > a recursive specification of data in models. An example of this > is in the Paper class. There is a label called In_book whose > type is #Paper. As constructed types are "grafted" onto the > current class, this creates a potentially infinitely long class. > This of course isn't a problem in terms of actual storage of data, > as the In_book label won't exist for some paper. However, > I was curious how xaceclient would deal with the visual > display of the creation of a new Paper object. Maybe I'm not > doing something correctly, but no "In_book" label comes up, > and I checked the models file and found it there. > > I'd like to know how this is supposed to work, since I'm writing > a web interface to a particular installation of ACEDB and > I'm going to have to solve the same problem. It should work by showing the #Paper in green, rather than the places in the model that you can add data which are in blue. When you double click on the green #Paper cell, it will expand out into another (empty) model, with blue places you can add data and a new green #Paper cell that you can double click on again if neede, and so on recursively as long as you want (but never infinitely). I don't know why this didn't work for you - I assure you it has worked in general for a long time. Perhaps you changed the models and did not "Read Models" explicitly from the main window menu. Models are not updated from scratch when you restart the program. Richard From owner-acedb@hgmp.mrc.ac.uk Tue May 16 12:54:33 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 96FE317AEF; Tue, 16 May 2000 12:54:32 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id AB1FC17AEA; Tue, 16 May 2000 12:54:28 +0100 (BST) Received: from dfw7-1.relay.mail.uu.net (dfw7-1.relay.mail.uu.net [199.171.54.106]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id MAA21249 for ; Tue, 16 May 2000 12:31:45 +0100 (BST) Received: from nottingham.ac.uk by dfw7sosrv11.alter.net with ESMTP (peer crosschecked as: pat.ccc.nottingham.ac.uk [128.243.40.194]) id QQipko21474 for ; Tue, 16 May 2000 11:31:40 GMT Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.13 #2) id 12rfZ1-0003ZU-00 for bionet-software-acedb@moderators.isc.org; Tue, 16 May 2000 12:31:03 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 12rfZX-0005XG-00; Tue, 16 May 2000 12:31:35 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Problem characters in object names 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 958476695 21280 128.243.116.150 (16 May 2000 11:31:35 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 16 May 2000 11:31:35 GMT X-Sender: keith@thale Date: Tue, 16 May 2000 12:54:28 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Is there a reason why acedb doesn't seem to like colons in object names? In our database I prefix all sequence and protein objects with a descriptor of the relevant database. E.g. EMBL:A000001 SWISS:Q87878 TREMBL:P24878 I've noticed recently that if I have a keyset window which contains a number of sequences and I try to perform a query such as: TREMBL:P* then it will return no objects. The problem seems to be with the colon. I can return successful queries such as: TREMBL* TREMBL*P* but as soon as the colon appears in the query it fails...is this for a particular reason (does the colon perform a function similar to use of the semicolon?). It only does this when using a query from within a keyset window. Typing in TREMBL:* from the main window works fine. Anyone have any ideas? Keith ~ Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR) ~ Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/ ~ University Park, University of Nottingham, NG7 2RD, UK ~ Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Tue May 16 16:02:54 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 67C1317AF7; Tue, 16 May 2000 16:02:53 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 040E617A7F; Tue, 16 May 2000 16:02:51 +0100 (BST) Received: from briar.org (backdraft.briar.org [192.207.123.123]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA26703 for ; Tue, 16 May 2000 13:14:26 +0100 (BST) Received: (from smap@localhost) by briar.org (8.9.1b+Sun/8.6.12) id IAA10007 for ; Tue, 16 May 2000 08:14:22 -0400 (EDT) X-Authentication-Warning: backdraft.briar.org: smap set sender to using -f Received: from mail.deja.com(205.238.143.34) by backdraft via smap (V2.1) id xma010005; Tue, 16 May 00 08:14:10 -0400 Received: from nnrp1.deja.com (nnrp1.deja.com [10.2.2.16]) by mail.deja.com (8.8.7/8.8.5) with ESMTP id HAA06862 for ; Tue, 16 May 2000 07:14:10 -0500 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id HAA30262; Tue, 16 May 2000 07:13:55 -0500 To: bionet-software-acedb@moderators.isc.org From: zgudmunt@my-deja.com Newsgroups: bionet.software.acedb Subject: RE: Cache sizes, increasing from default values Organization: Deja.com - Before you buy. Message-ID: <8fre23$thl$1@nnrp1.deja.com> X-Article-Creation-Date: Tue May 16 12:14:07 2000 GMT X-Http-User-Agent: Mozilla/4.7 [en] (X11; I; Linux 2.2.14-15mdk i686) X-Http-Proxy: 1.0 proxy.decode.is:8080 (Squid/2.2.STABLE5), 1.0 x26.deja.com:80 (Squid/1.1.22) for client 172.18.2.4, 193.4.196.222 X-MyDeja-Info: XMYDJUIDzgudmunt Date: Tue, 16 May 2000 16:02:51 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I tried these values: CACHE1 = 32000 CACHE2 = 16000 as recommended in a message on the mailing list a couple of weeks ago. the big Ace seems a lot faster, but still takes a while to start up of course. I am however having trouble with reading in a very large acefile, over 500Mb in size, xace and tace keep crashing on me. Could this be due to the changes to the cache values? Should I try even larger values? I have just over 500Mb RAM in the machine now. Mummi >yes i think so >please test and let me know >I do not have so much ram on my own machine > > On Fri, 12 May 2000 19:09:38 Jean Thierre-Mieg wrote: > >> The small Ace-s that I am running are pretty fast with the default values of >>4000/4000, but the big ones (several Gb on disk) can be pretty slow. >>Shouldn't I be able to speed the big server and/or xace up significantly >>by increasing my caches? >> >> Mummi >> > > Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Tue May 23 09:42:05 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id F3BD917B25; Tue, 23 May 2000 09:42:04 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 0AF4117A76; Tue, 23 May 2000 09:42:02 +0100 (BST) Received: from mailbox1.ucsd.edu (mailbox1.ucsd.edu [132.239.1.53]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id RAA08069 for ; Thu, 18 May 2000 17:37:42 +0100 (BST) Received: from usintout01.net.bms.com (usintout01.bms.com [165.89.129.231]) by mailbox1.ucsd.edu (8.9.3/8.9.3) with ESMTP id JAA18572 for ; Thu, 18 May 2000 09:37:36 -0700 (PDT) Received: from news1.bms.com ([127.0.0.1]) by mochilla.bms.com (PMDF V5.2-32 #38481) with ESMTP id <0FUR0020BK2HOD@mochilla.bms.com> for bionet-software-acedb@moderators.isc.org; Thu, 18 May 2000 16:20:41 +0000 (GMT) Received: (from news@localhost) by news1.bms.com (8.8.8+Sun/8.8.8) id MAA07977; Thu, 18 May 2000 12:20:40 -0400 (EDT) From: nathan@dnase.hpw.pri.bms.com (Nathan O. Siemers) Subject: phredphrap ACE files to ACEDB interface? To: bionet-software-acedb@moderators.isc.org Reply-To: siemersn@bms.com Message-id: Organization: Bristol-Myers Squibb Company MIME-version: 1.0 Content-type: text/plain; charset=us-ascii User-Agent: Gnus/5.0803 (Gnus v5.8.3) Emacs/20.3 Cache-Post-Path: newsreader-hpw1.net.bms.com!nathan@dnase.hpw.pri.bms.com X-Cache: nntpcache 2.3.3 (see http://www.nntpcache.org/) Newsgroups: bionet.software.acedb Date: Tue, 23 May 2000 09:42:02 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Forgive me for my naive questions here. We use phred/phrap/consed for much of our in-house sequencing projects. We have a Projects directory, where all of our sequencing is sorted by project. Underneath these projects is the standard consed file hierarchies (phd_dir, edit_dir, etc) and the corresponding ace files. Is there a simple way to load all of this information into an acedb instance and let people browse results by project, look at alignments, etc? Has anyone written such an integration procedure? I would think it would be straightforward. Thanks for any pointers you have. nathan -- N a t h a n O . S i e m e r s Bioinformatics Division of Applied Genomics Bristol-Myers Squibb Pharmaceutical Research Institute Hopewell Building 3B, P.O. Box 5400, Princeton, NJ 08543-5400 609 818-6568 siemersn@bms.com From owner-acedb@hgmp.mrc.ac.uk Tue May 23 09:43:24 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8169117B26; Tue, 23 May 2000 09:43:23 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C08ED17B25; Tue, 23 May 2000 09:43:20 +0100 (BST) Received: from isgate.is (isgate.is [193.4.58.51]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id NAA07257 for ; Sun, 21 May 2000 13:30:37 +0100 (BST) Received: from mark.ucdavis.edu (mark.ucdavis.edu [169.237.105.49]) by isgate.is (8.9.3r/8.9.0Imo) with ESMTP id MAA09298 for ; Sun, 21 May 2000 12:30:35 GMT Received: (from usenet@localhost) by mark.ucdavis.edu (8.9.3/8.9.3/IT4.3.3) id FAA27900 for bionet-software-acedb@moderators.isc.org; Sun, 21 May 2000 05:30:33 -0700 (PDT) To: bionet-software-acedb@moderators.isc.org From: john doe Newsgroups: bionet.software.acedb Subject: AceDB gifaceserver/RPC problem Organization: University of California, Davis Message-ID: <3927D7E9.34F16921@ucdavis.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit X-Trace: mark.ucdavis.edu 958912233 27893 169.237.16.43 (21 May 2000 12:30:33 GMT) X-Complaints-To: usenet@ucdavis.edu NNTP-Posting-Date: 21 May 2000 12:30:33 GMT X-Mailer: Mozilla 4.61 (Macintosh; I; PPC) X-Accept-Language: en Date: Tue, 23 May 2000 09:43:20 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi - I have been running into a weird problem with the gifaceserver program that has me stumped... Basically, whenever gifaceserver is called (via webace or aceclient), it just hangs in memory, and stops responding to anything. From ps: 8 S 98 295 133 0 78 20 608f8020 1273 600c236e ? 0:01 gifacese 8 S 60001 296 271 1 49 20 60a3f628 598 600c30b6 ? 0:01 webace - gifaceserver is sleeping. The first error messages I found on this, from the syslog, were: May 15 02:48:07 pgfsun sshd2[9811]: FATAL ERROR: ssh_pty_get_exit_status called before the child has exited. May 15 03:51:28 pgfsun gifaceserver[10033]: svc_tp_create: Could not register prog 200001 vers 1 on tcp May 15 03:54:21 pgfsun inetd[133]: config: rstatd/rpc/udp still active and was not reconfigured. May 15 03:54:21 pgfsun inetd[133]: config: 100083/rpc/tcp still active and was not reconfigured. May 15 03:54:21 pgfsun inetd[133]: config: acedb/rpc/tcp still active and was not reconfigured. May 15 04:11:29 pgfsun gifaceserver[10079]: svc_tp_create: Could not register prog 200001 vers 1 on udp May 15 04:11:29 pgfsun gifaceserver[10079]: svc_tp_create: Could not register prog 200001 vers 1 on tcp May 15 04:11:29 pgfsun gifaceserver[10079]: svc_tp_create: Could not register prog 200001 vers 1 on ticlts May 15 04:11:29 pgfsun gifaceserver[10079]: svc_tp_create: Could not register prog 200001 vers 1 on ticotsord May 15 04:11:29 pgfsun gifaceserver[10079]: svc_tp_create: Could not register prog 200001 vers 1 on ticots >From the $ACEDB/server.log, I have a lot of entries like #### Server starts 2000-05-21_04:25:03 #### host=(unknown) port=200001 ACEDB=/var/local/acedb/compositdb/lettdb #### clientTimeout=600 serverTimeout=600 maxKbytes=50 autoSaveInterval=600 No more active clients, starting to count-down: 600 s // 2000-05-21_04:35:03 #### Server starts 2000-05-21_04:42:30 #### host=(unknown) port=200001 ACEDB=/var/local/acedb/compositdb/lettdb #### clientTimeout=600 serverTimeout=600 maxKbytes=50 autoSaveInterval=600 Apparently, gifaceserver starts fine, then tries to register its RPC port and fails. Now, the only significant things I did on the system before this was install an ssh2 server, but that shouldn't have affected any ace stuff or RPC calls. I even disabled the sshd2 daemon temporarily, with no effect. Webace was working fine up till this point. In my /etc/rpc, I have acedb 200001 (I also tried it with ' rpc.acedbd' appended to this line; no difference). In inetd.conf, I have acedb/1 stream rpc/tcp wait d-giface /usr/local/bin/rpc.acedbd rpc.acedbd /var/local/acedb/compositdb/lettdb 200001 600:600:50 So, if you have any words of wisdom, I'd appreciate it. Or point me to something incredibly obvious that I'm missing. Thanks in advance, steve edberg From owner-acedb@hgmp.mrc.ac.uk Tue May 23 09:45:50 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1CE6F17B29; Tue, 23 May 2000 09:45:48 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 2893517B28; Tue, 23 May 2000 09:45:45 +0100 (BST) Received: (from daemon@localhost) by hgmp.mrc.ac.uk (8.9.3/8.9.3) id CAA02601 for bionet-software-acedb@net.bio.net; Tue, 23 May 2000 02:26:58 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: janety@u.washington.edu (janety) Newsgroups: bionet.software.acedb Subject: view control - column width and horizontal scrolling Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <3929DE61.A7C40F1A@u.washington.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: from mxout2.cac.washington.edu (mxout2.cac.washington.edu [140.142.33.4]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id CAA02579 for ; Tue, 23 May 2000 02:26:54 +0100 (BST) X-Received: from mailhost2.u.washington.edu (mailhost2.u.washington.edu [140.142.33.2]) by mxout2.cac.washington.edu (8.9.3+UW00.02/8.9.3+UW99.09) with ESMTP id SAA09299 for ; Mon, 22 May 2000 18:26:51 -0700 X-Received: from u.washington.edu (pumpkin.mbt.washington.edu [128.95.231.119]) by mailhost2.u.washington.edu (8.9.3+UW00.02/8.9.3+UW00.01) with ESMTP id SAA05927 for ; Mon, 22 May 2000 18:26:51 -0700 X-Reply-To: janety@u.washington.edu X-Mailer: Mozilla 4.7 (Macintosh; I; PPC) X-Accept-Language: en X-To: acedb@hgmp.mrc.ac.uk Date: Tue, 23 May 2000 09:45:45 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi I have been playing with the Gmap display, adding some derived_tag columns. I'm having problems with stuff going off the right-hand edge of the screen. two problems: 1. no scroll bar in the Gmap window (ace4_7l, OSF1, openwindows). is there no scroll bar, or do I need to change something in displays.wrm, or is this just a problem with my windows manager? any ideas? 2. I don't understand the column width restriction control when defining columns - I change it but it doesn't seem to do anything to the way my map is displayed. maybe someone could explain column widths to me. thanks Janet Young ------------------------------------------------------------------- Dr. Janet Young Dept. Molecular Biotechnology University of Washington tel: (206) 685 9254 Health Sciences Building fax: (206) 685 7301 PO BOX 357730 email: janety@u.washington.edu Seattle, WA 98195, USA --- From owner-acedb@hgmp.mrc.ac.uk Tue May 23 09:45:58 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7159817B2A; Tue, 23 May 2000 09:45:57 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 7D22717B29; Tue, 23 May 2000 09:45:55 +0100 (BST) Received: (from daemon@localhost) by hgmp.mrc.ac.uk (8.9.3/8.9.3) id DAA05792 for bionet-software-acedb@net.bio.net; Tue, 23 May 2000 03:21:10 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: janety@u.washington.edu (janety) Newsgroups: bionet.software.acedb Subject: colours in gmap display Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <3929EB11.2701D88E@u.washington.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: from mxout1.cac.washington.edu (mxout1.cac.washington.edu [140.142.32.5]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id DAA05785 for ; Tue, 23 May 2000 03:21:06 +0100 (BST) X-Received: from mailhost2.u.washington.edu (mailhost2.u.washington.edu [140.142.33.2]) by mxout1.cac.washington.edu (8.9.3+UW00.02/8.9.3+UW99.09) with ESMTP id TAA03496 for ; Mon, 22 May 2000 19:20:59 -0700 X-Received: from u.washington.edu (pumpkin.mbt.washington.edu [128.95.231.119]) by mailhost2.u.washington.edu (8.9.3+UW00.02/8.9.3+UW00.01) with ESMTP id TAA09368 for ; Mon, 22 May 2000 19:20:59 -0700 X-Reply-To: janety@u.washington.edu X-Mailer: Mozilla 4.7 (Macintosh; I; PPC) X-Accept-Language: en X-To: acedb@hgmp.mrc.ac.uk Date: Tue, 23 May 2000 09:45:55 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello again I have a very simple question. Is it possible to change the colours used for highlighting parents and neighbours in the Gmap display? I find it very hard to see the light blue my copy of ace is using at the moment. thanks Janet --- From owner-acedb@hgmp.mrc.ac.uk Tue May 23 09:59:57 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B5EF117B2A; Tue, 23 May 2000 09:59:55 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C9CFE17B26; Tue, 23 May 2000 09:59:52 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA06038 for ; Tue, 23 May 2000 09:59:24 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA17838 for bionet-software-acedb@net.bio.net; Tue, 23 May 2000 09:59:23 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: AceDB gifaceserver/RPC problem Organization: Sanger Centre Message-ID: <392A486A.F58FD70F@sanger.ac.uk> References: <3927D7E9.34F16921@ucdavis.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 959072363 17836 193.60.84.177 (23 May 2000 08:59:23 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 23 May 2000 08:59:23 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Tue, 23 May 2000 09:59:52 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Steve, > The first error messages I found on this, from the syslog, were: > > May 15 02:48:07 pgfsun sshd2[9811]: FATAL ERROR: ssh_pty_get_exit_status > called before the child has exited. > May 15 03:51:28 pgfsun gifaceserver[10033]: svc_tp_create: Could not > register prog 200001 vers 1 on tcp > May 15 03:54:21 pgfsun inetd[133]: config: rstatd/rpc/udp still active > and was not reconfigured. > May 15 03:54:21 pgfsun inetd[133]: config: 100083/rpc/tcp still active > and was not reconfigured. > May 15 03:54:21 pgfsun inetd[133]: config: acedb/rpc/tcp still active > and was not reconfigured. > May 15 04:11:29 pgfsun gifaceserver[10079]: svc_tp_create: Could not > register prog 200001 vers 1 on udp > May 15 04:11:29 pgfsun gifaceserver[10079]: svc_tp_create: Could not > register prog 200001 vers 1 on tcp > May 15 04:11:29 pgfsun gifaceserver[10079]: svc_tp_create: Could not > register prog 200001 vers 1 on ticlts > May 15 04:11:29 pgfsun gifaceserver[10079]: svc_tp_create: Could not > register prog 200001 vers 1 on ticotsord > May 15 04:11:29 pgfsun gifaceserver[10079]: svc_tp_create: Could not > register prog 200001 vers 1 on ticots The above all suggests to me that there is a problem with your inetd configuration, it looks to me like 200001 might be in use by another program (perhaps ssh ?). > > >From the $ACEDB/server.log, I have a lot of entries like > > #### Server starts 2000-05-21_04:25:03 > #### host=(unknown) port=200001 > ACEDB=/var/local/acedb/compositdb/lettdb > #### clientTimeout=600 serverTimeout=600 maxKbytes=50 > autoSaveInterval=600 > > No more active clients, starting to count-down: 600 s // > 2000-05-21_04:35:03 > > #### Server starts 2000-05-21_04:42:30 > #### host=(unknown) port=200001 > ACEDB=/var/local/acedb/compositdb/lettdb > #### clientTimeout=600 serverTimeout=600 maxKbytes=50 > autoSaveInterval=600 > > Apparently, gifaceserver starts fine, then tries to register its RPC > port and fails. Now, the only significant things I did on the system > before this was install an ssh2 server, but that shouldn't have affected > any ace stuff or RPC calls. I even disabled the sshd2 daemon > temporarily, with no effect. Webace was working fine up till this point. > OK, this is possible if you started the server in the foreground from a terminal, but not if it was inetd started, inetd does all the port registering _before_ gifaceserver is even started. ssh may have affected the aceserver, what port is ssh using ?? Also, the port number you have chosen for the aceserver is in the range known as the ephemeral ports and its possible that ssh may temporarily have been using this port. This is all speculation and I really need a bit more information, see below. > In my /etc/rpc, I have > > acedb 200001 > > (I also tried it with ' rpc.acedbd' appended to this line; no > difference). > > In inetd.conf, I have > > acedb/1 stream rpc/tcp wait d-giface > /usr/local/bin/rpc.acedbd rpc.acedbd > /var/local/acedb/compositdb/lettdb 200001 600:600:50 > OK, what is missing here is what you had in /etc/services for gifaceserver and also what you had in /etc/services and /etc/inetd.conf for the ssh daemon. This is important because there may be a clash of ports. Its probably best if you send stuff directly to me from now on and if there is some basic problem that everyone needs to know about I will post it here. But for general reference for these types of problems: 1) please include in your note the result of typeing "uname -a" so we know what machine/level you are running on. 2) please try running the server in the foreground and see if that works, this is useful info. for us. 3) make sure you include entries from all /etc configuration files: /etc/servcies, /etc/rpc and /etc/inetd.conf Please do contact me direct and I'll see what I can do. cheers Ed ------------------------------------------------------------------------------ | Ed Griffiths, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 (switch +44 1223 834244) Fax: +44 1223 494919 | ------------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Tue May 23 16:28:36 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9007017A8D; Tue, 23 May 2000 16:28:35 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C6A7817A85; Tue, 23 May 2000 16:28:33 +0100 (BST) Received: from chx400.switch.ch (chx400.switch.ch [130.59.10.2]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id QAA16332 for ; Tue, 23 May 2000 16:16:35 +0100 (BST) Received: from mail.deja.com ([205.238.143.34]) by chx400.switch.ch with esmtp (Exim 3.12 #4) id 12uGPc-0007Fz-00 for bionet-software-acedb@moderators.isc.org; Tue, 23 May 2000 17:16:04 +0200 Received: from nnrp1.deja.com (nnrp1.deja.com [10.12.2.16] (may be forged)) by mail.deja.com (8.8.7/8.8.5) with ESMTP id KAA17161 for ; Tue, 23 May 2000 10:16:03 -0500 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id KAA19698; Tue, 23 May 2000 10:15:44 -0500 To: bionet-software-acedb@moderators.isc.org From: zgudmunt@my-deja.com Newsgroups: bionet.software.acedb Subject: Socked client/server issues: Xace and/or WinAce?? Organization: Deja.com - Before you buy. Message-ID: <8ge7b0$j7h$1@nnrp1.deja.com> X-Article-Creation-Date: Tue May 23 15:16:01 2000 GMT X-Http-User-Agent: Mozilla/4.7 [en] (X11; I; Linux 2.2.14-15mdk i686) X-Http-Proxy: 1.0 proxy.decode.is:8080 (Squid/2.2.STABLE5), 1.0 x54.deja.com:80 (Squid/1.1.22) for client 172.18.2.4, 193.4.196.222 X-MyDeja-Info: XMYDJUIDzgudmunt Date: Tue, 23 May 2000 16:28:33 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I was just wondering how things are going with the socket client/server. I have tried out the commandline-client and it worked fine, but what I am really interested in is the socket AcePerl interface and, of course, the socked graphical client. Is it possible that one you developers could give us users some info on that on the mailing list? I will definately ask those questions on the conference this summer! Mummi Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Wed May 24 09:18:19 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0D8F717AB6; Wed, 24 May 2000 09:18:18 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 4530517A77; Wed, 24 May 2000 09:18:17 +0100 (BST) Received: (from daemon@localhost) by hgmp.mrc.ac.uk (8.9.3/8.9.3) id EAA13283 for bionet-software-acedb@net.bio.net; Wed, 24 May 2000 04:37:36 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: janety@u.washington.edu (janety) Newsgroups: bionet.software.acedb Subject: table maker query Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <392B4E79.AF441AF8@u.washington.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: from mxout2.cac.washington.edu (mxout2.cac.washington.edu [140.142.33.4]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id EAA13275 for ; Wed, 24 May 2000 04:37:32 +0100 (BST) X-Received: from mailhost2.u.washington.edu (mailhost2.u.washington.edu [140.142.33.2]) by mxout2.cac.washington.edu (8.9.3+UW00.02/8.9.3+UW99.09) with ESMTP id UAA16943 for ; Tue, 23 May 2000 20:37:25 -0700 X-Received: from u.washington.edu (pumpkin.mbt.washington.edu [128.95.231.119]) by mailhost2.u.washington.edu (8.9.3+UW00.02/8.9.3+UW00.01) with ESMTP id UAA13052 for ; Tue, 23 May 2000 20:37:25 -0700 X-Reply-To: janety@u.washington.edu X-Mailer: Mozilla 4.7 (Macintosh; I; PPC) X-Accept-Language: en X-To: acedb@hgmp.mrc.ac.uk Date: Wed, 24 May 2000 09:18:17 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi I am trying to formulate a table maker query but am having problems. I have clone objects for which the In_situ tag appears up to three times: Clone : MB01A01 In_situ 6p21 In_situ 11p13 In_situ 8p24 and I am trying to display the three values in three columns, instead of on three separate lines in my table. Is this possible without redefining my model to have three fields In_situ1, In_situ2 and In_situ3? I did manage to make a table which displays all three values on one line BUT which displays them in all six possible orders (and complains many times about my use of brackets - this might be a bug?). my .def file is below. However, I have a feeling I am going about it completely the wrong way. can anybody help? thanks Janet // Spread sheet definition for the ACeDB software // Date: 2000-05-23_20:33:12 // %n (%%n in the graphic) are parameter to be given on the command line in tace // or by default by the Parameters given in this file // \%n (%n in the graphic) are substituted by the value of column n at run time // Line starting with // are ignored, starting with # are comments Sortcolumn 1 Colonne 1 Width 12 Optional Visible Class Class Clone >From 1 Colonne 2 Width 12 Mandatory Visible Class Class Chrom_Band >From 1 Tag In_situ Colonne 3 Width 12 Optional Visible Class Class Chrom_Band >From 1 Tag In_situ Condition (NOT (\%2)) Colonne 4 Width 12 Optional Visible Class Class Chrom_Band >From 1 Tag In_situ Condition ((NOT (\%2)) AND (NOT (\%3))) // End of these definitions --- From owner-acedb@hgmp.mrc.ac.uk Wed May 24 09:33:02 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A912E17ACB; Wed, 24 May 2000 09:33:01 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 47E6B17AB6; Wed, 24 May 2000 09:33:00 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id JAA05638 for ; Wed, 24 May 2000 09:31:27 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA13563 for bionet-software-acedb@net.bio.net; Wed, 24 May 2000 09:31:26 +0100 (BST) To: bionet-software-acedb@hgmp.mrc.ac.uk From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: Socked client/server issues: Xace and/or WinAce?? Organization: Sanger Centre Message-ID: <392B935D.7981481@sanger.ac.uk> References: <8ge7b0$j7h$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 959157086 13561 193.60.84.177 (24 May 2000 08:31:26 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 24 May 2000 08:31:26 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Wed, 24 May 2000 09:33:00 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Mummi, > I was just wondering how things are going with the socket > client/server. I have tried out the commandline-client and it worked > fine, but what I am really interested in is the socket AcePerl interface > and, of course, the socked graphical client. Is it possible that one you > developers could give us users some info on that on the mailing list? Lincoln Stein (lstein@cshl.org) is the one to answer the questions about AcePerl and I'm sure that he will very soon. Assuming that by "graphical client" you mean the application called xaceclient (i.e. a client/server version of xace), then I have produced a test version of this that uses sockets. I haven't done rigorous testing but I need to make this available very soon because I have had other requests for it. I'll announce when its available on this newsgroup in the next few days. cheers Ed ------------------------------------------------------------------------------ | Ed Griffiths, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 (switch +44 1223 834244) Fax: +44 1223 494919 | ------------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Wed May 24 14:58:03 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2441717A98; Wed, 24 May 2000 14:58:03 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 1DC5817A84; Wed, 24 May 2000 14:58:00 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 0151117B0E; Wed, 24 May 2000 12:45:05 +0100 (BST) Received: from rutgers.rutgers.edu (rutgers.edu [165.230.4.76]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 5AC96415E0 for ; Wed, 24 May 2000 12:45:03 +0100 (BST) Received: from mail.deja.com (mail.deja.com [205.238.143.34]) by rutgers.rutgers.edu (8.8.8/8.8.8) with ESMTP id HAA13016 for ; Wed, 24 May 2000 07:45:01 -0400 (EDT) Received: from nnrp1.deja.com (nnrp1.deja.com [10.12.2.16]) by mail.deja.com (8.8.7/8.8.5) with ESMTP id GAA20158 for ; Wed, 24 May 2000 06:44:30 -0500 Received: (news@localhost) by nnrp1.deja.com (8.7.6/8.6.12) id GAA05459; Wed, 24 May 2000 06:44:25 -0500 To: bionet-software-acedb@moderators.isc.org From: zgudmunt@my-deja.com Newsgroups: bionet.software.acedb Subject: Xace for Windows speculations, again Organization: Deja.com - Before you buy. Message-ID: <8ggfap$5ai$1@nnrp1.deja.com> X-Article-Creation-Date: Wed May 24 11:44:28 2000 GMT X-Http-User-Agent: Mozilla/4.7 [en] (X11; I; Linux 2.2.14-15mdk i686) X-Http-Proxy: 1.0 proxy.decode.is:8080 (Squid/2.2.STABLE5), 1.0 x65.deja.com:80 (Squid/1.1.22) for client 172.18.2.4, 193.4.196.222 X-MyDeja-Info: XMYDJUIDzgudmunt Date: Wed, 24 May 2000 14:58:00 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I wanted to ponder a bit more on the Xace f. Windows issue. I tried out the most recent version of the Windows-build, and it worked just fine. I even managed to get it to work over smb-mounts to my Linux Ace-server (hosting 35+ project Ace's). But there was a problem with saving procedure, since the database was owned by user ace (me) and the WinNT-user mummi was trying to write. The windows Xace was running in normal mode and not this Unix "setuid" mode as the Unix Xace, so I expect that is the problem. But if there is no way to run Win-Xace in setuid mode, how can I otherwise allow multiple users to write using the Win-version over the smb-mount? Will I have to wait for the socket Winclient-2-Unixserver system? Oh, I can just as well continue to use the Unix Xace over a Reflection terminal to the Ace-server as I have been doing so far. It's just that all those graphic Xace's are taking up so much server memory, instead of users using their own workstation resources in a true client/server dream :) I do have a feeling, however,(after reading the ACEDB2000 preliminary conference schedule) that I will know lots more about future development for ACeDB! Mummi Sent via Deja.com http://www.deja.com/ Before you buy. From owner-acedb@hgmp.mrc.ac.uk Fri May 26 17:40:38 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 48DBB17B18; Fri, 26 May 2000 17:34:06 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id E008617BB4; Fri, 26 May 2000 17:07:23 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id B63A217B70; Fri, 26 May 2000 15:25:40 +0100 (BST) Received: from isgate.is (isgate.is [193.4.58.51]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 56E46415DD for ; Fri, 26 May 2000 15:25:33 +0100 (BST) Received: from postfix1.free.fr (postfix@postfix1.free.fr [212.27.32.21]) by isgate.is (8.9.3r/8.9.0Imo) with ESMTP id OAA09723 for ; Fri, 26 May 2000 14:25:13 GMT Received: from nnrp3.proxad.net (nnrp3.proxad.net [212.27.32.20]) by postfix1.free.fr (Postfix) with ESMTP id 98DBD2809E for ; Fri, 26 May 2000 16:25:28 +0200 (MEST) Received: from localhost (localhost [[UNIX: localhost]]) by nnrp3.proxad.net (8.9.3/8.9.3/Debian 8.9.3-21) id QAA01769; Fri, 26 May 2000 16:25:28 +0200 To: bionet-software-acedb@moderators.isc.org Message-ID: <392E89E6.41BB9906@marseille.inserm.fr> From: "F. Coulier" Organization: INSERM X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.11 i686) X-Accept-Language: fr-FR, en MIME-Version: 1.0 Newsgroups: bionet.software.acedb Subject: Update to WS9: problems! Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Complaints-To: abuse@proxad.net X-Trace: nnrp3.proxad.net 959351127 195.220.67.155 (Fri, 26 May 2000 16:25:27 CEST) NNTP-Posting-Date: Fri, 26 May 2000 16:25:27 CEST Date: Fri, 26 May 2000 17:07:23 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi everybody! I just tried to upgrade to WS9, and got stuck with some problems, and I am seeking help. I downloaded database.WS9.4-x.-tar.Z (x from 0 to 8), plus INSTALL, from ftpsrv1.sanger.ac.uk. Then csh INSTALL from within acedb directory. I can run acedb from the command line. It says "ACEDB 4_7l, AutoAce 21/03/00 WS9" on the banner. Looks OK, then. The problem is with gifaceserver: web access is out (I get a "Software Error" message), and when I try to start gifaceserver from the command line: gifaceserver /home/Database/acedb 20000114 1200:1200:0 I get: FATAL ERROR reported by program gifaceserver, in file aceserver.c, at line 323: Server cannot create a magic file in the WRITE_ACCESS_DIRECTORY /nfs/disk100/wormpub/SERVER_WRITES // FATAL ERROR reported by program gifaceserver, in file aceserver.c, at line 323: Server cannot create a magic file in the WRITE_ACCESS_DIRECTORY /nfs/disk100/wormpub/SERVER_WRITES Any help or clues? François -- François Coulier, INSERM Unité 119, 27 bd Leï Roure, 13009 Marseille, France Tel: 33 (0) 4 91 75 84 11 Fax: 33 (0) 4 91 26 03 64 mél: coulier@marseille.inserm.fr Site ouaibe: http://olan.marseille.inserm.fr/ From owner-acedb@hgmp.mrc.ac.uk Fri May 26 17:40:37 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E9FDB17AFD; Fri, 26 May 2000 17:34:04 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 4DC3E17B23; Fri, 26 May 2000 17:07:23 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id B6F4017B29; Fri, 26 May 2000 12:32:33 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 05996415DD for ; Fri, 26 May 2000 12:32:32 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id MAA08590 for bionet-software-acedb@net.bio.net; Fri, 26 May 2000 12:32:32 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Sylvia Martinelli Newsgroups: bionet.software.acedb Subject: Re: colours in gmap display Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: References: <3929EB11.2701D88E@u.washington.edu> Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: niobium.hgmp.mrc.ac.uk 959340752 8588 193.60.84.46 (26 May 2000 11:32:32 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 26 May 2000 11:32:32 GMT To: janety Date: Fri, 26 May 2000 17:07:23 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk On a gmap display, click on the green box at the bottom of an interval column or a points column. you will get a "configure interval column window" go to each of the 4 coloured boxes. on a unix system the right mouse will give you a long menu of colours, when you slide to the one you want and let go, this will become the new colour. press apply and have a look at your gmap. sylvia On Tue, 23 May 2000, janety wrote: > Hello again > > I have a very simple question. Is it possible to change the colours used > for highlighting parents and neighbours in the Gmap display? I find it > very hard to see the light blue my copy of ace is using at the moment. > > thanks > > Janet > --- > > ++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr.Sylvia D. Martinelli phone 01223 494971 (C. elegans database) fax 01223 494919 Informatics Sanger Centre Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA URL http://www.sanger.ac.uk/Users/sylvia/ ++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-acedb@hgmp.mrc.ac.uk Tue May 30 13:50:55 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B26F417A9B; Tue, 30 May 2000 13:50:54 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3EC8317A9B; Tue, 30 May 2000 13:50:43 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id CBFD417A8D; Fri, 26 May 2000 21:46:35 +0100 (BST) Received: from rutgers.rutgers.edu (rutgers.edu [165.230.4.76]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D4F9D415D4 for ; Fri, 26 May 2000 21:46:33 +0100 (BST) 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 QAA28581 for ; Fri, 26 May 2000 16:46:32 -0400 (EDT) Received: from jove.nlm.nih.gov (jove [130.14.25.149]) by ncbi.nlm.nih.gov (8.9.3/8.9.3) with ESMTP id QAA24556; Fri, 26 May 2000 16:46:29 -0400 (EDT) Received: (from mieg@localhost) by jove.nlm.nih.gov (8.9.3+Sun/8.9.3) id QAA18332; Fri, 26 May 2000 16:46:29 -0400 (EDT) From: Jean Thierry-Mieg Message-Id: <200005262046.QAA18332@jove.nlm.nih.gov> To: bionet-software-acedb@moderators.isc.org, coulier@marseille.inserm.fr Subject: Re: Update to WS9: problems! Newsgroups: bionet.software.acedb Date: Tue, 30 May 2000 13:50:43 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk the problem is in the config of your server you must restore your previous wspec/server.wrm file so that WRITE_ACCESS_DIRECTORY /nfs/disk100/wormpub/SERVER_WRITES points to a directory belonging to you