From owner-acedb@hgmp.mrc.ac.uk Tue Sep 5 10:12:37 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 27F7E17AD0; Tue, 5 Sep 2000 10:12:36 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id A085F17ACD; Tue, 5 Sep 2000 10:12:34 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id EB39517B82; Thu, 31 Aug 2000 17:55:46 +0100 (BST) Received: from jess.sanger.ac.uk (jess.sanger.ac.uk [193.60.84.61]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 19A4C415DA; Thu, 31 Aug 2000 17:55:43 +0100 (BST) Received: from obi-wan.sanger.ac.uk (root@obi-wan [193.62.207.144]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id RAA14957; Thu, 31 Aug 2000 17:51:13 +0100 (BST) Received: from localhost (jgrg@localhost [127.0.0.1]) by obi-wan.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id RAA01783; Thu, 31 Aug 2000 17:51:13 +0100 (BST) From: James Gilbert To: Ed Griffiths , acedbg@sanger.ac.uk, bionet-software-acedb@net.bio.net, informaticsg@sanger.ac.uk Subject: Re: CDS tags.... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Newsgroups: bionet.software.acedb Date: Tue, 5 Sep 2000 10:12:34 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Ed, On Tue, 29 Aug 2000, Ed Griffiths wrote: > Ian, > > > I don't really have any great feeling either way about in which coordinate set > > the CDS description should be (although working in coordinates of what is > > essentially a subsequence of a subsequence, while more correctly representing > > the biology, is harder to get your head around). > > Current concensus seems to favour having spliced-DNA coords. > > > What I would like is to see this all properly implemented so that we can get > > around the awful fudge that is prevalent now in the sanger human acedbs whereby > > to describe the translated portion of a transcript two subsequence objects are > > made, the transcript itself and then the translated (CDS) object. To make this > > look nice the views of the two objects are tweaked so that they are in different > > colours and the translation lies on top. > > I don't see why we can't do this, it will require some changes to fmap code and > maybe a new tag, I'm not sure at the moment, but basically the code is all there > to do it. I'd just __LOVE__ to see this happen! > > What seems nicer to me would be to only make transcript subsequences, and to > > describe the translation of these using CDS Int Int in whatever coordinates are > > deemed appropriate, and to add in a function to colour or fill in the translated > > portion of the transcript in the fmap display. (BTW I presume that the system > > allows description of the translation of polycistronic messages?) > > I don't see why we can't do this. My only doubts are that I don't know what > polycistronic means.... Polycistronic is where you have several translations along an mRNA. This is common in bacteria, but I guess it probably happens in human as well??? (Most things than can happen seem to happen somewhere.) James James G.R. Gilbert The Sanger Centre Wellcome Trust Genome Campus Hinxton Cambridge Tel: 01223 494906 CB10 1SA Fax: 01223 494919 From owner-acedb@hgmp.mrc.ac.uk Tue Sep 5 10:12:39 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 36AC117ACD; Tue, 5 Sep 2000 10:12:37 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id DEAE217ACE; Tue, 5 Sep 2000 10:12:34 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id E8A4017A8E; Mon, 4 Sep 2000 06:32:37 +0100 (BST) Received: from ktaemail01.villa-bosch.de (tigershark.villa-bosch.de [195.185.79.56]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id DE671415D4 for ; Mon, 4 Sep 2000 06:32:36 +0100 (BST) Received: from eml.villa-bosch.de (l44.eml.org [195.185.79.53]) by ktaemail01.villa-bosch.de with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id RLBTRWHW; Mon, 4 Sep 2000 07:28:45 +0200 Message-ID: <39B333EF.3262EBC5@eml.villa-bosch.de> From: Ralph Gauges X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: Jean Thierry-Mieg Subject: Re: Uniqueness of tags? References: <200009022014.QAA24388@ray.nlm.nih.gov> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Newsgroups: bionet.software.acedb Date: Tue, 5 Sep 2000 10:12:34 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Jean Thierry-Mieg wrote: > > if the idea is to generate something automatic > then the best is rd's suggestion of #types > this is functionaly the way in acedb to > do what java calls interface and implements > > can you do something in this direction > > consider the famous example > > Person id Number > > Student Inherits person > studies history > > Teacher Inherits person > teaches history > > assistant Inherits student,teacher > > ===== > > in acedb that could be > > #anybody id Int > > #Student Studies ?Lecture > > #Teacher Teaches ?Lecture > > ?person Anybody #Anybody > Student #student > Teacher #teacher > > > Class Assistant > subclass_of Person > Filter "Student AND Teacher" This seems to be going in the same direction that Richard already pointed, only that some of the attributes are put in their own model. This would look more readable and more maintainable once it has been generated. Thanks for this suggestion as well, now I will have think of a straight foreward theme on how to do this conversion automatically. So that just the finetuning has to be done manualy. A great many thanks for all the help and I hope I can work it out from here Ralph From owner-acedb@hgmp.mrc.ac.uk Tue Sep 5 10:12:48 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 65B7417ACD; Tue, 5 Sep 2000 10:12:46 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id D090B17ACD; Tue, 5 Sep 2000 10:12:43 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id AC56B17A9B; Mon, 4 Sep 2000 09:50:34 +0100 (BST) To: bionet-software-acedb@net.bio.net From: birney@ebi.ac.uk (Ewan Birney) Newsgroups: bionet.software.acedb Subject: acedb future? Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 304F017A99; Mon, 4 Sep 2000 09:50:32 +0100 (BST) X-Received: from alpha1.ebi.ac.uk (alpha1.ebi.ac.uk [193.62.196.122]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 68BC7415D5 for ; Mon, 4 Sep 2000 09:50:31 +0100 (BST) X-Received: from riker.ebi.ac.uk (birney@riker.ebi.ac.uk [193.62.196.38]) by alpha1.ebi.ac.uk (8.8.8/8.8.7) with ESMTP id JAA08057 for ; Mon, 4 Sep 2000 09:50:30 +0100 (BST) X-To: acedb@hgmp.mrc.ac.uk Date: Tue, 5 Sep 2000 10:12:43 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk (for the people who don't get constantly hassled by my email, I am one of the technical leads for the Ensembl project and also the bioperl coordinator. I played with acedb about 4 years ago; as my letter says, I like some things and hate others in acedb...) Where should ACEDB go? ACeDB is a loveable, annoying, integrated genome database with many great features and many large faults. A hard question is where acedb should go over the next 2 to 3 years. These are my views, as biased as always: (a) componentise heavily. ACeDB should become 4-5 separate projects, with their own release schedules and cvs modules, being something like: (i) database kernel (ii) bioobject layer (iii) graphics library (iv) fmap (v) other viewers I would take the "chain saw" approach for componentising these things, ie, having some pretty brutal tearing apart of the code, potentially copying large amounts of files so that projects can be separated appropiately. The new projects, in my mind, would not be run via the classic ACeDB source code management system + makefile, but a more vanilla cvs with autoconf style configurations, lowering the problems of entry for new developers to work with you guys. >From the little that I know of ACeDB, I think the code perhaps reuses code *too much* at a fine granularity, which then causes problems in reusing large components. (b) plot a course for each component such that the end point is to be "one of the best open projects" in this area. Take note of what is out there already, and decide whether it is better to merge with other open source projects, discard projects or forge ahead. Here are some ideas: - make the database kernel the best open source XML database; reading/writing XML and XMLSchema; Bindings to perl/python/java; JDBC bindings if it is mappeable. - there are XML databases out there but I don't know if they are that good (the open source ones). Is XMLSchema good? Or established? Certainly DTD support would have to be put in. - make the bio objects lean, mean tight objects able to sit on top of acedb or another database; able to coexist with other schemes well - there is EMBOSS, an established C bio-objects system. There are the bioperl/biopython/biojava projects. - make fmap the world's best, fast, large genome viewer. Look at the apollo server IDL and leverage that. Discuss what people like and hate about fmap. Integrate GAZE and other 3rd party programs using everything from a stanardised GFF system call-out to CORBA based services. I would hate to use ACEDB at the moment, but that doesn't mean I can't see the potential for many aspects of the software. I believe that it is time for your guys to be bold and go forward. I have no doubt that this is going to be difficult in many areas; some tough decisions await you guys, but it is better to make bold moves than none at all. ewan (an acedb admirer) Apollo IDL http://www.ensembl.org/Docs/wiki/html/EnsemblDocs/ApolloIDL.html EMBOSS http://www.sanger.ac.uk/Software/EMBOSS bioperl/biojava/biopython bio.perl.org biojava.org biopython.org ----------------------------------------------------------------- Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420 . ----------------------------------------------------------------- --- From owner-acedb@hgmp.mrc.ac.uk Tue Sep 5 10:13:01 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B323317AD0; Tue, 5 Sep 2000 10:13:00 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 167A117ACD; Tue, 5 Sep 2000 10:12:58 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 1071117A7E; Mon, 4 Sep 2000 17:19:05 +0100 (BST) Received: from wodc7-1.relay.mail.uu.net (wodc7-1.relay.mail.uu.net [199.171.54.114]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 95077415D5 for ; Mon, 4 Sep 2000 17:19:04 +0100 (BST) Received: from chiark.greenend.org.uk by wodc7mr0.ffx.ops.us.uu.net with ESMTP (peer crosschecked as: chiark.greenend.org.uk [195.224.76.132]) id QQjffd26537 for ; Mon, 4 Sep 2000 16:19:03 GMT Received: from news by chiark.greenend.org.uk with local (Exim 3.12 #2) id 13Vyxa-0004kk-00 (Debian); Mon, 04 Sep 2000 17:19:02 +0100 To: bionet-software-acedb@uunet.uu.net From: Tim Cutts Newsgroups: bionet.software.acedb Subject: Adding partitions Organization: Linux Unlimited Message-ID: X-Newsreader: trn 4.0-test70 (17 January 1999) Date: Tue, 5 Sep 2000 10:12:58 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk If I add partitions to database.wrm, what does it take to make ACeDB notice them? Re-reading models doesn't seem to do it, and I don't want to have to dump and re-load the database - surely I don't have to do that? Thanks in advance... Tim. From owner-acedb@hgmp.mrc.ac.uk Tue Sep 5 13:26:24 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5E83117ADF; Tue, 5 Sep 2000 13:26:23 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 9E14F17AD7; Tue, 5 Sep 2000 13:26:21 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 2D98117ADC; Tue, 5 Sep 2000 11:41:12 +0100 (BST) Received: from chi6-1.relay.mail.uu.net (chi6-1.relay.mail.uu.net [199.171.54.98]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C1ED8415D4 for ; Tue, 5 Sep 2000 11:41:10 +0100 (BST) Received: from chiark.greenend.org.uk by chi6sosrv11.alter.net with ESMTP (peer crosschecked as: chiark.greenend.org.uk [195.224.76.132]) id QQjfhy05840 for ; Tue, 5 Sep 2000 10:41:04 GMT Received: from news by chiark.greenend.org.uk with local (Exim 3.12 #2) id 13WGA2-0006Sb-00 (Debian); Tue, 05 Sep 2000 11:41:02 +0100 To: bionet-software-acedb@uunet.uu.net From: Tim Cutts Newsgroups: bionet.software.acedb Subject: Re: Adding partitions Organization: Linux Unlimited Message-ID: <3py*UntBo@news.chiark.greenend.org.uk> References: X-Newsreader: trn 4.0-test70 (17 January 1999) Date: Tue, 5 Sep 2000 13:26:21 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk In article , Tim Cutts wrote: >If I add partitions to database.wrm, what does it take to make ACeDB >notice them? Re-reading models doesn't seem to do it, and I don't want >to have to dump and re-load the database - surely I don't have to do >that? > >Thanks in advance... Hmm... re-reading models in tace rather than xace seemed to work. Odd. Tim. From owner-acedb@hgmp.mrc.ac.uk Tue Sep 5 13:26:24 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id CD97317A84; Tue, 5 Sep 2000 13:26:23 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 5FE0017A84; Tue, 5 Sep 2000 13:26:21 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 4439817ADC; Tue, 5 Sep 2000 11:40:24 +0100 (BST) Received: from wodc7-1.relay.mail.uu.net (wodc7-1.relay.mail.uu.net [199.171.54.114]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id EE110415D4 for ; Tue, 5 Sep 2000 11:40:22 +0100 (BST) Received: from chiark.greenend.org.uk by wodc7mr0.ffx.ops.us.uu.net with ESMTP (peer crosschecked as: chiark.greenend.org.uk [195.224.76.132]) id QQjfhy16426 for ; Tue, 5 Sep 2000 10:40:11 GMT Received: from news by chiark.greenend.org.uk with local (Exim 3.12 #2) id 13WG9B-0006Qz-00 (Debian); Tue, 05 Sep 2000 11:40:09 +0100 To: bionet-software-acedb@uunet.uu.net From: Tim Cutts Newsgroups: bionet.software.acedb Subject: Re: acedb future? Organization: Linux Unlimited Message-ID: References: X-Newsreader: trn 4.0-test70 (17 January 1999) Date: Tue, 5 Sep 2000 13:26:21 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk In article , Ewan Birney wrote: > >(a) componentise heavily. ACeDB should become 4-5 separate projects, >with their own release schedules and cvs modules, being something like: > > (i) database kernel In my view the current database kernel should be thrown out entirely (or at least made just one possible kernel people can use), and the remaining components below, thanks to the bioobject layer, made kernel independent. That would allow people to bind the superb visualisation features that ACeDB has to other databases. > (ii) bioobject layer > > (iii) graphics library > > (iv) fmap > > (v) other viewers Sounds very sensible. I find the current architecture of ACeDB really awkward - the massive code duplication between tace, giface and xace, without even using shared libraries is really scary. >The new projects, in my mind, would not be run via the classic ACeDB >source code management system + makefile, but a more vanilla cvs with >autoconf style configurations, lowering the problems of entry for new >developers to work with you guys. I agree with this, too. The current ACeDB build system is, erm, shall we say idiosyncratic? :-) > - make fmap the world's best, fast, large genome viewer. Look at the >apollo server IDL and leverage that. Discuss what people like and hate >about fmap. Integrate GAZE and other 3rd party programs using everything >from a stanardised GFF system call-out to CORBA based services. I'm certainly keen on this idea; fmap is still the best genome annotation display I have seen, if only because it display vertically. I don't know why no other annotation viewer authors have cottoned onto this idea; it allows you to view a sequence on a large scale, and still be able to read labels on the annotation, something that becomes impossible as soon as you display sequences horizontally, when you have to make decisions about what labels you can and cannot show. I suspect the principal barrier at the moment is that the various components of ACeDB are not well separated, and that large chunks of the fmap code are hard-wired, and will be difficult to separate from the database. Not that this is impossible, of course, but I would imagine it will be fairly painful. Depending on how painful it is, it might be simpler to just take the FMAP display as a good idea, and re-implement it from scratch on top of your bioobjects layer. The simplistic Java viewer that Matt showed us at the BOSC conference was a good move in the right direction; like FMAP, it divided the display up into rectangles (sadly they were rows rather than columns) into which each type of annotation was responsible for drawing itself. That kind of modular architecture is a real win, in my view. I'd like to make the plea though that we should from the beginning not look at this as purely a viewer, but think of it as a read-write interface to the underlying data from the word go. Hand annotation is one thing that most genomic viewers currently don't handle well, with the exception of FMAP, Artemis and possibly others that I'm not aware of. Re-reading this message, it sounds like I'm attacking ACeDB. I'm not, I still think it's the leader for hand annotation, but I agree with Ewan that it really does need some major re-working to bind it to up-and-coming database and annotation strategies; interoperability between tools is the key! Phew... rant over. :-) Tim. From owner-acedb@hgmp.mrc.ac.uk Wed Sep 6 09:29:00 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 189B817B14; Wed, 6 Sep 2000 09:28:58 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 644D617AB2; Wed, 6 Sep 2000 09:28:55 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 38D4F17B02; Wed, 6 Sep 2000 00:23:52 +0100 (BST) Received: from rutgers.rutgers.edu (bsd.rutgers.edu [165.230.4.71]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 676DF415D4 for ; Wed, 6 Sep 2000 00:23:50 +0100 (BST) Received: from news1.ucsd.edu (news1.ucsd.edu [132.239.1.221]) by rutgers.rutgers.edu (8.8.8/8.8.8) with ESMTP id TAA07121 for ; Tue, 5 Sep 2000 19:23:48 -0400 (EDT) Received: by news1.ucsd.edu (8.11.0/8.9.3) id e85NNla28275 for bionet-software-acedb@moderators.isc.org; Tue, 5 Sep 2000 16:23:47 -0700 (PDT) To: bionet-software-acedb@moderators.isc.org From: Kevin Coakley Newsgroups: bionet.software.acedb Subject: Getting Sanger-release.2000_07_14 To Compile On Solaris 2.6 Organization: Univ of Calif San Diego Message-ID: <39B58082.EAAF5A3D@sdcc12.ucsd.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news1.ucsd.edu 968196227 28273 132.239.50.79 (5 Sep 2000 23:23:47 GMT) X-Complaints-To: usenet@news1.ucsd.edu NNTP-Posting-Date: Tue, 5 Sep 2000 23:23:47 +0000 (UTC) X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en Date: Wed, 6 Sep 2000 09:28:55 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello, I work for UCSD and I am trying to get Sanger-release.2000_07_14 to compile on a Solaris 2.6 server. When I use SOLARIS_4_DEF or SOLARIS_4_RELEASE_DEF, it produces binaries that core dump. I was able to compile version 4.7l on the server using SOLARIS_4_OPT_DEF but now Sanger-release.2000_07_14.tar.gz does not include SOLARIS_4_OPT_DEF. Anyone have any insight into how I could get Sanger-release.2000_07_14 to compile on Solaris 2.6 without core dumping? btw: I did get the source to compile on a Linux server. Thanks -Kevin zz1kc@sdcc12.ucsd.edu From owner-acedb@hgmp.mrc.ac.uk Wed Sep 6 09:29:03 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 761C317B18; Wed, 6 Sep 2000 09:29:00 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id A5C9717ADA; Wed, 6 Sep 2000 09:28:57 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 2452017AD6; Tue, 5 Sep 2000 13:50:49 +0100 (BST) Received: from chi6-1.relay.mail.uu.net (chi6-1.relay.mail.uu.net [199.171.54.98]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 82581415D5 for ; Tue, 5 Sep 2000 13:50:46 +0100 (BST) Received: from jess.sanger.ac.uk by chi6sosrv11.alter.net with ESMTP (peer crosschecked as: jess.sanger.ac.uk [193.60.84.61]) id QQjfih13912 for ; Tue, 5 Sep 2000 12:50:40 GMT 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 NAA11408; Tue, 5 Sep 2000 13:50:27 +0100 (BST) From: Richard Durbin Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id NAA26978; Tue, 5 Sep 2000 13:50:27 +0100 (BST) Message-Id: <200009051250.NAA26978@griffin.sanger.ac.uk> To: bionet-software-acedb@uunet.uu.net, timc@chiark.greenend.org.uk Subject: Re: Adding partitions Newsgroups: bionet.software.acedb Date: Wed, 6 Sep 2000 09:28:57 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > >If I add partitions to database.wrm, what does it take to make ACeDB > >notice them? Re-reading models doesn't seem to do it, and I don't want > >to have to dump and re-load the database - surely I don't have to do > >that? > > > >Thanks in advance... > > Hmm... re-reading models in tace rather than xace seemed to work. Odd. I believe that new versions of the code will recognize changes to database.wrm, so maybe your xace and tace have slightly different kernel versions. If you are stuck with an old version, then you can avoid reloading the entire database by adding lines to database/database.map directly. This breaks the rule that you should never manually touch the database/ directory, but is a workaround for the problem that Tim had which has been tested many times and will not have adverse consequences. Don't change anything else in database/! Richard From owner-acedb@hgmp.mrc.ac.uk Wed Sep 6 09:29:05 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2E59817B14; Wed, 6 Sep 2000 09:29:02 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 8FA6717AB2; Wed, 6 Sep 2000 09:28:59 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id A1B0417AF3; Tue, 5 Sep 2000 17:57:13 +0100 (BST) Received: from wodc7-1.relay.mail.uu.net (wodc7-1.relay.mail.uu.net [199.171.54.114]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4AA2A415D5 for ; Tue, 5 Sep 2000 17:57:12 +0100 (BST) Received: from ncbi.nlm.nih.gov by wodc7mr0.ffx.ops.us.uu.net with ESMTP (peer crosschecked as: ncbi.nlm.nih.gov [130.14.25.1]) id QQjfix12688 for ; Tue, 5 Sep 2000 16:57:11 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 MAA04861; Tue, 5 Sep 2000 12:56:59 -0400 (EDT) Received: (from mieg@localhost) by ray.nlm.nih.gov (8.9.3+Sun/8.9.3) id MAA21967; Tue, 5 Sep 2000 12:56:58 -0400 (EDT) From: Jean Thierry-Mieg Message-Id: <200009051656.MAA21967@ray.nlm.nih.gov> To: bionet-software-acedb@uunet.uu.net, timc@chiark.greenend.org.uk Subject: Re: Adding partitions Newsgroups: bionet.software.acedb Date: Wed, 6 Sep 2000 09:28:59 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk >Hmm... re-reading models in tace rather than xace seemed to work. Odd. taht cannot possibly make a difference From owner-acedb@hgmp.mrc.ac.uk Wed Sep 6 09:29:06 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 31B6417B18; Wed, 6 Sep 2000 09:29:05 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 07DC617B16; Wed, 6 Sep 2000 09:28:59 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id D980617AF4; Tue, 5 Sep 2000 18:59:25 +0100 (BST) Received: from chi6-1.relay.mail.uu.net (chi6-1.relay.mail.uu.net [199.171.54.98]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 92986415DA for ; Tue, 5 Sep 2000 18:59:24 +0100 (BST) Received: from ncbi.nlm.nih.gov by chi6sosrv11.alter.net with ESMTP (peer crosschecked as: ncbi.nlm.nih.gov [130.14.25.1]) id QQjfjb04507 for ; Tue, 5 Sep 2000 17:59:23 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 NAA15210; Tue, 5 Sep 2000 13:59:22 -0400 (EDT) Received: from cetus (cetus [130.14.25.107]) by ray.nlm.nih.gov (8.9.3+Sun/8.9.3) with SMTP id NAA10163; Tue, 5 Sep 2000 13:59:21 -0400 (EDT) Message-Id: <200009051759.NAA10163@ray.nlm.nih.gov> From: Jean Thierry-Mieg Reply-To: Jean Thierry-Mieg Subject: Re: acedb architecture To: timc@chiark.greenend.org.uk, bionet-software-acedb@uunet.uu.net MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: Duza41mhVp9l3UEvyKTPBw== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.3.5 SunOS 5.7 sun4u sparc Newsgroups: bionet.software.acedb Date: Wed, 6 Sep 2000 09:28:59 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Tim Cutts says: > I find the current architecture of ACeDB really >awkward - the massive code duplication between tace, giface and xace, >without even using shared libraries is really scary. > there is no code duplication the exact same .o module are linked in different executables essentilay they are included as part of acelib.a From owner-acedb@hgmp.mrc.ac.uk Wed Sep 6 15:13:08 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1067817B2B; Wed, 6 Sep 2000 15:13:07 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id D61BB17ACF; Wed, 6 Sep 2000 15:13:05 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id AFC8017ACF; Wed, 6 Sep 2000 15:12:48 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 1F6E6415D5 for ; Wed, 6 Sep 2000 15:12:48 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA00672 for bionet-software-acedb@net.bio.net; Wed, 6 Sep 2000 15:12:47 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: acedb future? Organization: Sanger Centre Message-ID: <39B650DF.BB7B57BE@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 968249567 670 193.60.84.177 (6 Sep 2000 14:12:47 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 6 Sep 2000 14:12:47 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Wed, 6 Sep 2000 15:13:05 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk A reply to Ewans points... > (a) componentise heavily. ACeDB should become 4-5 separate projects, > with their own release schedules and cvs modules, being something like: > > (i) database kernel > > (ii) bioobject layer > > (iii) graphics library > > (iv) fmap > > (v) other viewers > > I would take the "chain saw" approach for componentising these things, > ie, having some pretty brutal tearing apart of the code, potentially > copying large amounts of files so that projects can be separated > appropiately. OK, there are several points here..... 1) large parts of acedb have been carved up into separately compiled libraries, we started at the bottom and produced a library of utilities that just about all of acedb makes use of. Next we attacked the graphics library and this is also completely separate (its actually the basis of the Sanger Centres "image" programs for gel analysis/display which have nothing to do with acedb). This is not to say that there isn't a lot that could be done, see following points: 2) I think its worth adding the following split to the kernel: kernel ----- models/class code (i.e. the bit that makes acedb what it | is) | ---- storage of objects (read/write to disk) The kernel is not cleanly divided into routines that implement the models/class like stuff that makes acedb what it is as a database, and the underlying code to store/retrieve objects from disk. We have been thinking about this a lot recently. It may make sense to allow the storage bit to be something else, e.g. BerkleyDB, MySQL etc., but it doesn't make sense to throw out the models/class stuff which is precisely what many people like and treasure about acedb. If we did use a different backend it would enable us to add transactions, multiple concurrent writing etc. and enable us to make use of a load of existing database code. 3) bio-object layer - I'm not sure what is meant here, if it means "provide a layer that serves up sequences, exons etc. in some standard format", then this doesn't exist at the moment. To take the example of fmap, fmap in doing its display does a whole of operations on the database to gather all the information that it needs to do the display. The intelligence about what to do with exon-like data etc. resides in fmap. fmap could be changed to split out bits of code that prepared the sequence from the code that displayed it but this would be an extremely non-trivial task and would require an excellent description of what bio-objects were required to make this worthwhile (volunteers ?). 4) CVS stuff... > The new projects, in my mind, would not be run via the classic ACeDB > source code management system + makefile, but a more vanilla cvs with > autoconf style configurations, lowering the problems of entry for new > developers to work with you guys. the acedb cvs stuff _is_ completely standard, we do use cover scripts which issue cvs calls but this is to stop screw-ups in the way people create, destroy, move, edit etc. files within the source tree. To access cvs directly people need to contact us to get ssh access to the Sanger Centre, thats all. The build is not standard, it was produced to allow fast/quick building on many architectures simultaneously. We need to use autoconf badly and we've more or less worked out how to get the best of both worlds. Autoconf is a must to help users with install/compile on machines for which we don't provide binaries. > >From the little that I know of ACeDB, I think the code perhaps reuses code > *too much* at a fine granularity, which then causes problems in reusing > large components. No, this is not the problem. Code structure has been the main problem, acedb did not have a clear enough separation between libraries and the applications using them. It used #defines to munge the code into different behaviours for different applications which completely blurred application and library. This has made reuse difficult but is a situation that has improved enormously over the last 2 years, but it is still not possible to take fmap as a separate component for instance. > (b) plot a course for each component such that the end point is to be "one > of the best open projects" in this area. Take note of what is out there > already, and decide whether it is better to merge with other open > source projects, discard projects or forge ahead. Here are some ideas: > > - make the database kernel the best open source XML database; > reading/writing XML and XMLSchema; Bindings to perl/python/java; JDBC > bindings if it is mappeable. > > - there are XML databases out there but I don't know if they are > that good (the open source ones). Is XMLSchema good? Or established? > Certainly DTD support would have to be put in. xml output is on the way but I am still not sure what exactly we want from xml output, we could quickly/cheaply do an xml version of an ace file which I guess we will do, but what does this buy you apart from a warm, fuzzy feeling.... > - make the bio objects lean, mean tight objects able to sit on top of > acedb or another database; able to coexist with other schemes well hmmmm, the thought of fmap on top of Oracle, warms the cockles of your heart, or something like that... > - there is EMBOSS, an established C bio-objects system. There are > the bioperl/biopython/biojava projects. OK, I don't know about EMBOSS, someone else could comment on that. biojava already has sophisticated links to acedb, biopython is on the way, aceperl provides access to acedb but I don't know what the links between bioperl and aceperl are (over to you Ewan and Lincoln). > I would hate to use ACEDB at the moment, but that doesn't mean I can't see > the potential for many aspects of the software. I believe that it is time > for your guys to be bold and go forward. I have no doubt that this is > going to be difficult in many areas; some tough decisions await you guys, > but it is better to make bold moves than none at all. Well I guess that acedb does have some difficult decisions coming up but its worth noting that many criticisms of acedb centre around: 1) It won't scale 2) It doesn't have concurrent write access 3) It doesn't support transactions 4) It doesn't run on Macs 5) The docs are not good enough i.e. a totally different set of problems from the ones identified by Ewan. Comments ?? 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 URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Wed Sep 6 15:30:58 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 32A3C17B30; Wed, 6 Sep 2000 15:30:56 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 4E64317B2E; Wed, 6 Sep 2000 15:30:55 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id BB5A417B2F; Wed, 6 Sep 2000 15:30:16 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 388BD415D5 for ; Wed, 6 Sep 2000 15:30:16 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA00924 for bionet-software-acedb@net.bio.net; Wed, 6 Sep 2000 15:30:15 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: acedb future? Organization: Sanger Centre Message-ID: <39B654F7.BE5FA0B6@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 968250615 922 193.60.84.177 (6 Sep 2000 14:30:15 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 6 Sep 2000 14:30:15 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Wed, 6 Sep 2000 15:30:55 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > In my view the current database kernel should be thrown out entirely (or > at least made just one possible kernel people can use), and the > remaining components below, thanks to the bioobject layer, made kernel > independent. That would allow people to bind the superb visualisation > features that ACeDB has to other databases. I can see what you are getting at but we will need to import a couple more good programmers to do this, we have our hands full with supporting/extending acedb as it is. I also don't think that this will be at all straight forward, much of the power of fmap comes from the combination of the sequence model(s) and the fmap code combined. I don't know enough about sequence representation in other databases to say if it would work to simply shove a different database on the back of fmap.... > Sounds very sensible. I find the current architecture of ACeDB really > awkward - the massive code duplication between tace, giface and xace, > without even using shared libraries is really scary. Why ?? Unix shares executable images between processes.... Shared libraries are OK but they can cause a lot of grief for users who just want to pick up an executable and use it......this is why we have avoided them so far. > I agree with this, too. The current ACeDB build system is, erm, shall > we say idiosyncratic? :-) I think the build system is fine for developers but not good for users, certainly neither Simon or I would argue against the introduction of autoconf. > I suspect the principal barrier at the moment is that the various > components of ACeDB are not well separated, and that large chunks of the > fmap code are hard-wired, and will be difficult to separate from the > database. Not that this is impossible, of course, but I would imagine > it will be fairly painful. ok, this is the problem exactly..... A "component" fmap sounds like a great idea but the devil is in the detail, how many databases support the kind of information that acedb does ?? I don't know the answer, I'm just saying that all this effort would only be worthwhile if there really were other databases that could be efficiently queried to retrieve this information. 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 URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Thu Sep 7 09:24:20 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E92B017B7D; Thu, 7 Sep 2000 09:24:19 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id B3B3E17B78; Thu, 7 Sep 2000 09:24:18 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 1638817B4C; Wed, 6 Sep 2000 19:29:17 +0100 (BST) Received: from supernews.com (unknown [207.126.101.36]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 40F27415D5 for ; Wed, 6 Sep 2000 19:29:13 +0100 (BST) Received: from localhost ([127.0.0.1] helo=post-01.supernews.net) by supernews.com with smtp (Exim 3.02 #1) id 13WjvW-00076d-00 for bionet-software-acedb@net.bio.net; Wed, 06 Sep 2000 11:28:02 -0700 To: bionet-software-acedb@net.bio.net From: bks@emf.emf.net (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Re: acedb future? Organization: DNA + Sunlight Message-ID: References: X-Complaints-To: newsabuse@supernews.com Date: Thu, 7 Sep 2000 09:24:18 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk In article , Ewan Birney wrote: > >Where should ACEDB go? > More documentation, rich in examples. Tutorials at major conferences. ACeDB is still the only system where middle-aged, tenured Molecular Biologists sit down and understand the interaction quickly. Please spare the world an objectified, Corba-ready, OMG sanctioned, UML specified, Java-rich, multi-tiered, component-heavy, ORB-funky, multiply-inherited, polymorphic, open-source, ontolological yet hermeneutic, slow-as-molasses, non-functional ACeDB. --bks p.s. Genes are verbs not objects. From owner-acedb@hgmp.mrc.ac.uk Thu Sep 7 09:36:55 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1C97717B7F; Thu, 7 Sep 2000 09:36:55 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id D8CC717B7E; Thu, 7 Sep 2000 09:36:53 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 03EA017B7F; Thu, 7 Sep 2000 09:36:28 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4F539415DE for ; Thu, 7 Sep 2000 09:36:28 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA22683 for bionet-software-acedb@net.bio.net; Thu, 7 Sep 2000 09:36:27 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: Getting Sanger-release.2000_07_14 To Compile On Solaris 2.6 Organization: Sanger Centre Message-ID: <39B7538B.42BCFBF3@sanger.ac.uk> References: <39B58082.EAAF5A3D@sdcc12.ucsd.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 968315787 22681 193.60.84.177 (7 Sep 2000 08:36:27 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 7 Sep 2000 08:36:27 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 7 Sep 2000 09:36:53 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Kevin, We've had problems with aceserver not running under inetd on Solaris 2.6/2.7 but never with what you describe below (as far as I am aware...). Please can you do several things: 1) send me the output of "uname -a" on your machine 2) tell me which binaries you tried to compile and run and we'll take it from there. (send the stuff direct to me) cheers Ed Kevin Coakley wrote: > > Hello, > > I work for UCSD and I am trying to get Sanger-release.2000_07_14 to > compile on a Solaris 2.6 server. When I use SOLARIS_4_DEF or > SOLARIS_4_RELEASE_DEF, it produces binaries that core dump. I was able > to compile version 4.7l on the server using SOLARIS_4_OPT_DEF but now > Sanger-release.2000_07_14.tar.gz does not include SOLARIS_4_OPT_DEF. > Anyone have any insight into how I could get Sanger-release.2000_07_14 > to compile on Solaris 2.6 without core dumping? > > btw: I did get the source to compile on a Linux server. > > Thanks > -Kevin > zz1kc@sdcc12.ucsd.edu -- ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, 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 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Thu Sep 7 13:16:27 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 81AD717A5D; Thu, 7 Sep 2000 13:16:26 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id E93BC17A59; Thu, 7 Sep 2000 13:16:24 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 69B6C17A7B; Thu, 7 Sep 2000 12:36:31 +0100 (BST) Received: from ncbi.nlm.nih.gov (ncbi.nlm.nih.gov [130.14.25.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8E0D4415DF for ; Thu, 7 Sep 2000 12:36:29 +0100 (BST) 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 HAA26822; Thu, 7 Sep 2000 07:36:28 -0400 (EDT) Received: from cetus (cetus [130.14.25.107]) by ray.nlm.nih.gov (8.9.3+Sun/8.9.3) with SMTP id HAA26591; Thu, 7 Sep 2000 07:36:26 -0400 (EDT) Message-Id: <200009071136.HAA26591@ray.nlm.nih.gov> From: Jean Thierry-Mieg Reply-To: Jean Thierry-Mieg Subject: Re: acedb future? To: bks@emf.emf.net, bionet-software-acedb@net.bio.net MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: 4YtxPrdy0M7MzZk8Qqowbw== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.3.5 SunOS 5.7 sun4u sparc Newsgroups: bionet.software.acedb Date: Thu, 7 Sep 2000 13:16:24 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk You can count on me to maintain a functional acedb whatever other people do Jean >To: bionet-software-acedb@net.bio.net >From: bks@emf.emf.net (Bradley K. Sherman) >Subject: Re: acedb future? >X-Complaints-To: newsabuse@supernews.com >Date: Thu, 7 Sep 2000 09:24:18 +0100 (BST) > >In article , >Ewan Birney wrote: >> >>Where should ACEDB go? >> > >More documentation, rich in examples. Tutorials at >major conferences. > >ACeDB is still the only system where middle-aged, >tenured Molecular Biologists sit down and understand >the interaction quickly. > >Please spare the world an objectified, Corba-ready, >OMG sanctioned, UML specified, Java-rich, multi-tiered, >component-heavy, ORB-funky, multiply-inherited, >polymorphic, open-source, ontolological yet hermeneutic, >slow-as-molasses, non-functional ACeDB. > > --bks > >p.s. Genes are verbs not objects. > > > From owner-acedb@hgmp.mrc.ac.uk Thu Sep 7 13:16:36 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id EEDA817A5D; Thu, 7 Sep 2000 13:16:35 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id A694817A5C; Thu, 7 Sep 2000 13:16:34 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id A01FA17A84; Thu, 7 Sep 2000 12:41:13 +0100 (BST) Received: from ncbi.nlm.nih.gov (ncbi.nlm.nih.gov [130.14.25.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 30924415DD for ; Thu, 7 Sep 2000 12:41:12 +0100 (BST) 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 HAA27352; Thu, 7 Sep 2000 07:41:10 -0400 (EDT) Received: from cetus (cetus [130.14.25.107]) by ray.nlm.nih.gov (8.9.3+Sun/8.9.3) with SMTP id HAA27533; Thu, 7 Sep 2000 07:41:09 -0400 (EDT) Message-Id: <200009071141.HAA27533@ray.nlm.nih.gov> From: Jean Thierry-Mieg Reply-To: Jean Thierry-Mieg Subject: Re: Getting Sanger-release.2000_07_14 To Compile On Solaris 2.6 To: edgrif@sanger.ac.uk, bionet-software-acedb@net.bio.net MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: LzHj7k/KsKpNLbGqJ2/SsQ== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.3.5 SunOS 5.7 sun4u sparc Newsgroups: bionet.software.acedb Date: Thu, 7 Sep 2000 13:16:34 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk i have compiled on soplaris 2.6 and 2.7 without prtoblem but not run the server under inetd on that machine is that the problem ? >To: >From: Ed Griffiths >Subject: Re: Getting Sanger-release.2000_07_14 To Compile On Solaris 2.6 >Mime-Version: 1.0 >Content-Transfer-Encoding: 7bit >X-Trace: niobium.hgmp.mrc.ac.uk 968315787 22681 193.60.84.177 (7 Sep 2000 08:36:27 GMT) >X-Complaints-To: news@net.bio.net >NNTP-Posting-Date: 7 Sep 2000 08:36:27 GMT >X-Accept-Language: en >Date: Thu, 7 Sep 2000 09:36:53 +0100 (BST) > >Kevin, > >We've had problems with aceserver not running under inetd on Solaris 2.6/2.7 but >never with what you describe below (as far as I am aware...). > >Please can you do several things: > >1) send me the output of "uname -a" on your machine > >2) tell me which binaries you tried to compile and run > >and we'll take it from there. (send the stuff direct to me) > >cheers Ed > >Kevin Coakley wrote: >> >> Hello, >> >> I work for UCSD and I am trying to get Sanger-release.2000_07_14 to >> compile on a Solaris 2.6 server. When I use SOLARIS_4_DEF or >> SOLARIS_4_RELEASE_DEF, it produces binaries that core dump. I was able >> to compile version 4.7l on the server using SOLARIS_4_OPT_DEF but now >> Sanger-release.2000_07_14.tar.gz does not include SOLARIS_4_OPT_DEF. >> Anyone have any insight into how I could get Sanger-release.2000_07_14 >> to compile on Solaris 2.6 without core dumping? >> >> btw: I did get the source to compile on a Linux server. >> >> Thanks >> -Kevin >> > >-- > ------------------------------------------------------------------------ >| Ed Griffiths, Acedb development, 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 Fax: +44 1223 494919 | > ------------------------------------------------------------------------ > > > From owner-acedb@hgmp.mrc.ac.uk Mon Sep 11 12:11:18 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1CD4E17B15; Mon, 11 Sep 2000 12:11:16 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3882817ABD; Mon, 11 Sep 2000 12:11:15 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 2BEC217B1A; Mon, 11 Sep 2000 11:48:41 +0100 (BST) Received: from chx400.switch.ch (chx400.switch.ch [130.59.10.2]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 1238B415DA for ; Mon, 11 Sep 2000 11:48:36 +0100 (BST) Received: from pat.ccc.nottingham.ac.uk ([128.243.40.194] helo=nottingham.ac.uk) by chx400.switch.ch with esmtp (Exim 3.15 #3) id 13YR8e-0003hh-00 for bionet-software-acedb@moderators.isc.org; Mon, 11 Sep 2000 12:48:36 +0200 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 13YR8T-00035M-00 for bionet-software-acedb@moderators.isc.org; Mon, 11 Sep 2000 11:48:25 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13YR8a-0002Yd-00; Mon, 11 Sep 2000 11:48:32 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: 8 subclass limit in acedb 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 968669312 9833 128.243.116.150 (11 Sep 2000 10:48:32 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 11 Sep 2000 10:48:32 GMT X-Sender: keith@thale Date: Mon, 11 Sep 2000 12:11:15 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I've asked in the past whether the release of acedb 4.8 will enable you to exceed the current 8 subclass limit for any class. I recall hearing different answer with someone (Richard?) telling me that 4.8 (beta) already has this capacity. A beta version that I downloaded a while ago, didn't have this facility but I haven't tried any more recent betas. Any more news about this? I would find it exceptionally useful if you could have (at least) a doubling of this subclass limit. My database currently has nearly a quarter of a million sequences, and even when you divide that into 8 subclasses (Genomic, EST, GSS, mitochondrial etc.) you still have some hefty classes which I could ideally subdivide again if there wasn't the 8 subclass limit. 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 Mon Sep 11 12:11:31 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 20E1A17B15; Mon, 11 Sep 2000 12:11:30 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C30A817B15; Mon, 11 Sep 2000 12:11:27 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id BDD0817ABD; Mon, 11 Sep 2000 11:43:47 +0100 (BST) Received: from rutgers.rutgers.edu (bsd.rutgers.edu [165.230.4.71]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 2DBE7415CF for ; Mon, 11 Sep 2000 11:43:46 +0100 (BST) Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by rutgers.rutgers.edu (8.8.8/8.8.8) with ESMTP id GAA13591 for ; Mon, 11 Sep 2000 06:43:44 -0400 (EDT) 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 13YR3l-0002un-00 for bionet-software-acedb@moderators.isc.org; Mon, 11 Sep 2000 11:43:33 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13YR3s-0002Vx-00; Mon, 11 Sep 2000 11:43:40 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Re: acedb future? Organization: ACS, The University of Nottingham Message-ID: References: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 968669020 9667 128.243.116.150 (11 Sep 2000 10:43:40 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 11 Sep 2000 10:43:40 GMT X-Sender: keith@thale Date: Mon, 11 Sep 2000 12:11:27 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk On 7 Sep 2000, Bradley K. Sherman wrote: > In article , > Ewan Birney wrote: > > > >Where should ACEDB go? > > > > More documentation, rich in examples. Tutorials at > major conferences. > > ACeDB is still the only system where middle-aged, > tenured Molecular Biologists sit down and understand > the interaction quickly. I've been an acedb database curator now for almost a year (managing an Arabidopsis genome database as part of a network of crop plant databases). Part of my job is also to run training sessions for existing and potential users of these databases. It seems to me that very few end users will bother/have bothered to download databases to install locally. Many people might only want to occasionally use one of these databases, invariably to find out more about their sequence of interest (particularly in a genomic context). I'm not sure how much the windows port of acedb will encourage people to install it locally, but the problems remain that some of these databases are getting very big now. My database (AGR) has reached about 2.5 Gb in total (partly caused by the problem (bug?) that acedb 'puts on weight' when you keep on updating entries, even if you remove entries! - I've found that dumping out the entire database and reloading can shed up to 0.5 Gb). I guess the C. elegans database is reaching a similar size. I can't envisage many people setting up these databases if they have to first download so much data. Therefore it seems that a web based approach will become increasingly more popular, but then you run into the limitations of AcePerl, AceBrowser, and WebAce - particularly when interacting with images from gifaceserver. I think having a decent manual (downloadable as a pdf?) would help a lot, the current collection of online manuals and guides are often woefully out of date, and a centrally maintained, regularly updated, manual at the Sanger Centre would be a useful resource to point potential and existing users to. If acedb wants to remain a popular and practical choice for managing biological, and particularly genomic data then it must (at the least) be able to handle the torrent of data that is starting to be produced by various post-genomics projects (esp. microarray data). As these data, along with the ever increasing amounts of sequence data, mean that acedb databases will just get bigger and bigger, then it seems to me that it will become harder to expect people to download and install databases locally...I guess this all hinges on whether growth of genomic data exceeds growth in bandwidth capacity/disk storage. Just my two-penneth-worth. 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 Sep 19 09:37:42 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id F17BC17AE5; Tue, 19 Sep 2000 09:37:40 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id D1DB017AEE; Tue, 19 Sep 2000 09:37:37 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 7337D17B09; Fri, 15 Sep 2000 18:53:33 +0100 (BST) To: bionet-software-acedb@net.bio.net From: bswanson@sibyte.com (Brian Swanson) Newsgroups: bionet.software.acedb Subject: xace problem Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200009151751.KAA29155@oakland.sibyte.com> MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: 48crzr0vAeNxhIUY1xRN6w== X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 45CE017AC6; Fri, 15 Sep 2000 18:53:31 +0100 (BST) X-Received: from pobox.sibyte.com (pobox.sibyte.com [208.12.96.20]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A299B415E0 for ; Fri, 15 Sep 2000 18:53:26 +0100 (BST) X-Received: from postal.sibyte.com (moat.sibyte.com [208.12.96.21]) by pobox.sibyte.com (Postfix) with SMTP id A2ED6205FE for ; Fri, 15 Sep 2000 10:51:32 -0700 (PDT) X-Received: from SMTP agent by mail gateway Fri, 15 Sep 2000 10:48:53 -0800 X-Received: from oakland.sibyte.com (oakland.sibyte.com [192.168.202.24]) by postal.sibyte.com (Postfix) with ESMTP id B2FDA159A3 for ; Fri, 15 Sep 2000 10:51:32 -0700 (PDT) X-Received: from oakland.sibyte.com (oakland.sibyte.com [192.168.202.24]) by oakland.sibyte.com (8.9.3+Sun/8.9.1) with SMTP id KAA29155 for ; Fri, 15 Sep 2000 10:51:31 -0700 (PDT) X-Reply-To: Brian Swanson X-To: acedb@hgmp.mrc.ac.uk X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.3.4p_5 SunOS 5.7 sun4u sparc Date: Tue, 19 Sep 2000 09:37:37 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I hope someone can point me the right direction: xace runs its initial window with no problem. The next window I launch takes a little longer. By the 3rd or 4th window, xace seems to be stuck in the event loop: The window manager (CDE) and Xsun processes swamp the cpu. The 'Ready' label in the main window flashes. Also, if I interrupt the process, the top of the function stack is '_poll'. tace and AcePerl seem to access the db with no problems, so it seems to be an X thing. I tried to compile with both the SOLARIS_4 and SOLARIS_4_RELEASE make files (both result in the same problem). I also tried the binary from one of the download sites (bin.solaris_5_6.4_7l.tar.Z), again with the same result. So, I'm looking for hints - Solaris rev/build?, window manager? acedb? operator headspace? Thanks. Brian SunOS 5.7 Generic_106541-08 sun4u sparc SUNW,Ultra-5_10 acedb version is 4.7l --- From owner-acedb@hgmp.mrc.ac.uk Tue Sep 19 09:37:42 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8A58117AEE; Tue, 19 Sep 2000 09:37:41 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 54F2717AF2; Tue, 19 Sep 2000 09:37:37 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id CD47517A68; Mon, 18 Sep 2000 14:56:43 +0100 (BST) To: bionet-software-acedb@net.bio.net From: mln10@cornell.edu ("Maria Nemchuk") Newsgroups: bionet.software.acedb Subject: Fw: What research articles have been published on ACEDB? Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <00ab01c02178$611df800$bdf65b18@nemchuk> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 5522D17A68; Mon, 18 Sep 2000 14:56:41 +0100 (BST) X-Received: from cornell.edu (cornell.edu [132.236.56.6]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 2FDA9415D4 for ; Mon, 18 Sep 2000 14:56:40 +0100 (BST) X-Received: from nemchuk (h00104bcddaa8.ne.mediaone.net [24.91.246.189]) by cornell.edu (8.9.3/8.9.3) with SMTP id JAA15214; Mon, 18 Sep 2000 09:55:42 -0400 (EDT) X-To: "ACEDB mail group" X-Cc: X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Date: Tue, 19 Sep 2000 09:37:37 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi everyone, I just got following question and curios myself. I remember one ACEDB-related article by Lincoln Stein in Perl Journal. Is there anything else published? Thanks, Maria Nemchuk > I am a graduate student studying data-modeling and am very interested in > ACEDB. Can you tell me which, if any, research articles have been > publishied about it? > > Thanks very much, > Martin Brandon > mbrandon@gen.emory.edu --- From owner-acedb@hgmp.mrc.ac.uk Tue Sep 19 09:37:55 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7212E17AF7; Tue, 19 Sep 2000 09:37:54 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 2360F17AE5; Tue, 19 Sep 2000 09:37:50 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 0B16717AD7; Tue, 19 Sep 2000 01:20:08 +0100 (BST) To: bionet-software-acedb@net.bio.net From: bswanson@sibyte.com (Brian Swanson) Newsgroups: bionet.software.acedb Subject: xace problem Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200009190020.RAA11055@oakland.sibyte.com> MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: 6zct5usdoh95mnPno4jRrg== X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id EB63A17AAC; Tue, 19 Sep 2000 01:20:05 +0100 (BST) X-Received: from pobox.sibyte.com (pobox.sibyte.com [208.12.96.20]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id E76C8415CF for ; Tue, 19 Sep 2000 01:20:03 +0100 (BST) X-Received: from postal.sibyte.com (moat.sibyte.com [208.12.96.21]) by pobox.sibyte.com (Postfix) with SMTP id 1BF9D205FB for ; Mon, 18 Sep 2000 17:20:02 -0700 (PDT) X-Received: from SMTP agent by mail gateway Mon, 18 Sep 2000 17:17:17 -0800 X-Received: from oakland.sibyte.com (oakland.sibyte.com [192.168.202.24]) by postal.sibyte.com (Postfix) with ESMTP id 4C42F15963 for ; Mon, 18 Sep 2000 17:20:01 -0700 (PDT) X-Received: from oakland.sibyte.com (oakland.sibyte.com [192.168.202.24]) by oakland.sibyte.com (8.9.3+Sun/8.9.1) with SMTP id RAA11055 for ; Mon, 18 Sep 2000 17:20:01 -0700 (PDT) X-Reply-To: Brian Swanson X-To: acedb@net.bio.net X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.3.4p_5 SunOS 5.7 sun4u sparc Date: Tue, 19 Sep 2000 09:37:50 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I hope someone can point me the right direction: xace runs its initial window with no problem. The next window I launch takes a little longer. By the 3rd or 4th window, xace seems to be stuck in the event loop: The window manager (CDE) and Xsun processes swamp the cpu. The 'Ready' label in the main window flashes. Also, if I interrupt the process, the top of the function stack is '_poll'. tace and AcePerl seem to access the db with no problems, so it seems to be an X thing. I tried to compile with both the SOLARIS_4 and SOLARIS_4_RELEASE make files (both result in the same problem). I also tried the binary from one of the download sites (bin.solaris_5_6.4_7l.tar.Z), again with the same result. So, I'm looking for hints - Solaris rev/build?, window manager? acedb? operator headspace? Thanks. Brian SunOS 5.7 Generic_106541-08 sun4u sparc SUNW,Ultra-5_10 acedb version is 4.7l and m --------------- Brian Swanson SiByte Inc. www.sibyte.com (408)845-6615 --- From owner-acedb@hgmp.mrc.ac.uk Tue Sep 19 09:37:56 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id ED58B17AE5; Tue, 19 Sep 2000 09:37:54 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 36F8817AEE; Tue, 19 Sep 2000 09:37:51 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id D3C5617B0A; Fri, 15 Sep 2000 21:14:09 +0100 (BST) To: bionet-software-acedb@net.bio.net From: matthews@greengenes.cit.cornell.edu (Dave Matthews) Newsgroups: bionet.software.acedb Subject: Re: What research articles have been published on ACEDB? Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200009152014.QAA10311@greengenes.cit.cornell.edu> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 08DDE17AEB; Fri, 15 Sep 2000 21:14:07 +0100 (BST) X-Received: from greengenes.cit.cornell.edu (greengenes.cit.cornell.edu [128.253.246.43]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A5DC1415DA for ; Fri, 15 Sep 2000 21:14:06 +0100 (BST) X-Received: (from matthews@localhost) by greengenes.cit.cornell.edu (8.9.3/8.9.3) id QAA10311; Fri, 15 Sep 2000 16:14:05 -0400 (EDT) X-To: mbrando@emory.edu X-Cc: ACEDB newsgroup Date: Tue, 19 Sep 2000 09:37:51 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi Martin, > I am a graduate student studying data-modeling and am very interested in > ACEDB. Can you tell me which, if any, research articles have been > published about it. > > Thanks very much, > Martin Brandon > mbrandon@gen.emory.edu The only ones I know of are what's listed in the ACEDB FAQ: Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992). AAtDB, an Arabidopsis thaliana database. Plant Molecular Biology Reporter 10: 308-309, 409-410. Cherry, J.M. and Cartinhour, S.W. (1994). ACEDB, A tool for biological information. Pp. 347-356 in: Automated DNA Sequencing and Analysis, M. Adams, C. Fields, and C. Venter (Eds.). Academic Press. Online version: http://ars-genome.cornell.edu/acedocs/overview.html. Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994). Physical mapping projects and ACEDB. Pp. 111-158 in: Guide to Human Genome Computing. Bishop, M.J (Ed.). Academic Press. Does anyone else out there have an updated bibliography? - Dave --- From owner-acedb@hgmp.mrc.ac.uk Tue Sep 19 09:57:37 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5AF8217AF5; Tue, 19 Sep 2000 09:57:36 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id DD9D317AE5; Tue, 19 Sep 2000 09:57:34 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id E4D2217AE5; Tue, 19 Sep 2000 09:55:53 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 3A612415D4 for ; Tue, 19 Sep 2000 09:55:53 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA05941 for bionet-software-acedb@net.bio.net; Tue, 19 Sep 2000 09:55:52 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: xace problem Organization: Sanger Centre Message-ID: <39C72A17.12C20D58@sanger.ac.uk> References: <200009151751.KAA29155@oakland.sibyte.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 969353752 5939 193.60.84.177 (19 Sep 2000 08:55:52 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 19 Sep 2000 08:55:52 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Tue, 19 Sep 2000 09:57:34 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Brian, > so it seems to be an X thing. Yup, I'm afraid this is a known problem with later versions of Solaris (5.6), our code is wrong but our error only shows up with certain window manager behaviour and Suns window manager has changed its behaviour. The net is that this is our problem and should be fixed, and so it has in acedb 4_8. I don't think this was fixed in 4_7l. There is a beta version of 4_8 (which many people in Sanger are using) on the ftp site as: Sanger-release.2000_07_14.tar.gz Can you try this and see if there is still a problem ?? I am loathe to spend time fixing 4_7 as we plan to release a pucker version of 4_8 (which will be released as 4_9) next month. 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 URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Tue Sep 19 13:09:40 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D66B017B05; Tue, 19 Sep 2000 13:09:39 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 854FB17AFB; Tue, 19 Sep 2000 13:09:38 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 2188117B06; Tue, 19 Sep 2000 11:55:01 +0100 (BST) To: bionet-software-acedb@net.bio.net From: james.o.mcinerney@may.ie (James McInerney) Newsgroups: bionet.software.acedb Subject: Molecular Systematics and Evolution Website Organization: http://www.may.ie/academic/biology/jmbioinformatics.shtml Message-ID: <39C747B0.46906861@may.ie> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 54F7517B04; Tue, 19 Sep 2000 11:54:55 +0100 (BST) X-Received: from ailm.may.ie (ailm.may.ie [149.157.1.20]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 573C6415CF; Tue, 19 Sep 2000 11:54:48 +0100 (BST) X-Received: from may.ie (macbl23.may.ie [149.157.201.23]) by ailm.may.ie (PMDF V5.2-33 #38649) with ESMTP id <01JUCU7CJ9960002CL@ailm.may.ie>; Tue, 19 Sep 2000 11:54:29 WET X-To: James McInerney X-Mailer: Mozilla 4.72 (Macintosh; I; PPC) X-Accept-Language: en Date: Tue, 19 Sep 2000 13:09:38 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Dear all, Just to let you know that our updated website is now available: http://www.bioinf.org/molsys/index.html or http://www.dbbm.fiocruz.br/james You may freely use this website as a resource for teaching molecular systematics and evolution. You may download the slides (344 in total), use the self-paced tutorials and practicals and generally take whatever you might wish from the website. This is completely free to you, its development has been funded by various organisations (see website). The old address: http://www.may.ie/academic/biology/james will soon contain a redirect page that will point you to either of the other two addresses. -- Dr. T. Martin Embley, Dr. Mark Wilkinson, Department of Zoology, Department of Zoology, The Natural History Museum, The Natural History Museum, Cromwell Road, Cromwell Road, london SW7 5BD, London SW7 5BD, UK. UK. Dr. James O. McInerney, Dr. Robert Hirt, Dept. Biology, Department of Zoology, Natl. Univ. Ireland, The Natural History Museum, Maynooth, Co. Kildare, Cromwell Road, Ireland London SW7 5BD, UK. --- From owner-acedb@hgmp.mrc.ac.uk Tue Sep 19 15:40:13 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 061DD17B1A; Tue, 19 Sep 2000 15:40:12 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3322217A69; Tue, 19 Sep 2000 15:40:11 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id AB71517B13; Tue, 19 Sep 2000 14:31:16 +0100 (BST) Received: from wodc7-1.relay.mail.uu.net (wodc7-1.relay.mail.uu.net [199.171.54.114]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 1087E415DA for ; Tue, 19 Sep 2000 14:31:15 +0100 (BST) Received: from chiark.greenend.org.uk by wodc7mr0.ffx.ops.us.uu.net with ESMTP (peer crosschecked as: chiark.greenend.org.uk [195.224.76.132]) id QQjhic23034 for ; Tue, 19 Sep 2000 13:31:13 GMT Received: from news by chiark.greenend.org.uk with local (Exim 3.12 #2) id 13bNUO-0006l8-00 (Debian); Tue, 19 Sep 2000 14:31:12 +0100 To: bionet-software-acedb@uunet.uu.net From: Tim Cutts Newsgroups: bionet.software.acedb Subject: Re: xace problem Organization: Linux Unlimited Message-ID: References: <200009151751.KAA29155@oakland.sibyte.com> <39C72A17.12C20D58@sanger.ac.uk> X-Newsreader: trn 4.0-test70 (17 January 1999) Date: Tue, 19 Sep 2000 15:40:11 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk In article <39C72A17.12C20D58@sanger.ac.uk>, Ed Griffiths wrote: >Brian, > >> so it seems to be an X thing. > >Yup, I'm afraid this is a known problem with later versions of Solaris (5.6), >our code is wrong but our error only shows up with certain window manager >behaviour and Suns window manager has changed its behaviour. On our Solaris boxes it's fine with the fvwm2 and AfterStep window managers. Haven't tried any others. Tim. From owner-acedb@hgmp.mrc.ac.uk Thu Sep 21 09:21:55 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 97A9E17BD4; Thu, 21 Sep 2000 09:21:54 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3E94417BD2; Thu, 21 Sep 2000 09:21:53 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id D1EBB17BBB; Wed, 20 Sep 2000 23:05:15 +0100 (BST) To: bionet-software-acedb@net.bio.net From: janety@u.washington.edu (janety) Newsgroups: bionet.software.acedb Subject: tacedb/xace Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <39C93497.1577173B@u.washington.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 5E52817A66; Wed, 20 Sep 2000 23:05:11 +0100 (BST) X-Received: from mxout1.cac.washington.edu (mxout1.cac.washington.edu [140.142.32.5]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 5E2D8415DD for ; Wed, 20 Sep 2000 23:05:09 +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 PAA02016 for ; Wed, 20 Sep 2000 15:05:07 -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 PAA24763 for ; Wed, 20 Sep 2000 15:05:07 -0700 X-Reply-To: janety@u.washington.edu X-Mailer: Mozilla 4.7 (Macintosh; I; PPC) X-Accept-Language: en X-To: acedb Date: Thu, 21 Sep 2000 09:21:53 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi this is a simple problem - I am mostly using xace (alpha, ace 4.7l) but I have a couple of aceperl scripts which query my database via tacedb. these scripts only query the database (->fetch) and do not try to write to it. the problem is that after I have run the script, I try to update the database (e.g. read and ace file, which is actually the output of my aceperl script) but I get this error: 'Sorry, while you were reading the database, another process updated it.// You can go on reading, but to write, you must quit and rerun' how did this happen? I am pretty sure I didn't update the database any other way. Is there a way in aceperl of connecting to the database in a read only way to make sure I don't do something by accident? thanks for any ideas Janet ------------------------------------------------------------------- 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 Thu Sep 21 10:49:20 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 321DB17AA6; Thu, 21 Sep 2000 10:49:20 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C7BEC17A62; Thu, 21 Sep 2000 10:49:18 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id D839117BD6; Thu, 21 Sep 2000 09:48:06 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4272E415E0 for ; Thu, 21 Sep 2000 09:48:06 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id JAA28434 for bionet-software-acedb@net.bio.net; Thu, 21 Sep 2000 09:48:05 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: tacedb/xace Organization: Sanger Centre Message-ID: <39C9CB45.F6E091CB@sanger.ac.uk> References: <39C93497.1577173B@u.washington.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 969526085 28432 193.60.84.177 (21 Sep 2000 08:48:05 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 21 Sep 2000 08:48:05 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Thu, 21 Sep 2000 10:49:18 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Janet, > this is a simple problem - I am mostly using xace (alpha, ace 4.7l) but > I have a couple of aceperl scripts which query my database via tacedb. > these scripts only query the database (->fetch) and do not try to write > to it. the problem is that after I have run the script, I try to update > the database (e.g. read and ace file, which is actually the output of my > aceperl script) but I get this error: > 'Sorry, while you were reading the database, another process updated > it.// You can go on reading, but to write, you must quit and rerun' > > how did this happen? I am pretty sure I didn't update the database any > other way. Is there a way in aceperl of connecting to the database in a > read only way to make sure I don't do something by accident? Let me just check with you what actually happens, is this the scenario: 1) start xace 2) run aceperl scripts which produce an ace file 3) try to parse in the ace file from xace 4) xace reports that above error Is that correct ?? Could you describe what operations your perl scripts do and in particular how they exit (they may inadvertantly be doing a 'save'). 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 URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Fri Sep 22 08:19:06 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2D61717A7F; Fri, 22 Sep 2000 08:19:06 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id E386E17A79; Fri, 22 Sep 2000 08:19:04 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 6B63017BF4; Thu, 21 Sep 2000 17:47:05 +0100 (BST) Received: from chi6-1.relay.mail.uu.net (chi6-1.relay.mail.uu.net [199.171.54.98]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id E7107415DE for ; Thu, 21 Sep 2000 17:47:03 +0100 (BST) Received: from nottingham.ac.uk by chi6sosrv11.alter.net with ESMTP (peer crosschecked as: pat.ccc.nottingham.ac.uk [128.243.40.194]) id QQjhpz04771 for ; Thu, 21 Sep 2000 16:47:01 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 13c9Ut-0002fd-00 for bionet-software-acedb@moderators.isc.org; Thu, 21 Sep 2000 17:46:55 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13c9Ux-00025Y-00; Thu, 21 Sep 2000 17:46:59 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: x-rated acedb 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 969554819 8030 128.243.116.150 (21 Sep 2000 16:46:59 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 21 Sep 2000 16:46:59 GMT X-Sender: keith@thale Date: Fri, 22 Sep 2000 08:19:04 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi all, I've just discovered that tf you read a sequence into Acedb which contains an 'x' (representing an unspecified base) it seems to convert it into an insertion ('-'). It also messes up the format of the sequence in tree display (at least in AceBrowser). I know that 'N's are 'allowed' by acedb, but this made me start thinking whether acedb recognises any of the other internationally agreed symbols, e.g. 'w' for weak (A or T) etc. Anyone know any more about this - is acedb just misbehaving here, or is there any sort of reason for converting 'x' into '-'??? 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 Fri Sep 22 11:27:34 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 688A717BDC; Fri, 22 Sep 2000 11:27:33 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 50EB817BDB; Fri, 22 Sep 2000 11:27:31 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id DF52717A83; Fri, 22 Sep 2000 08:23:24 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 33DC5415DE for ; Fri, 22 Sep 2000 08:23:24 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA23613 for bionet-software-acedb@net.bio.net; Fri, 22 Sep 2000 08:23:23 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: tacedb/xace Organization: Sanger Centre Message-ID: <39CB08EA.99B01DB3@sanger.ac.uk> References: <39C93497.1577173B@u.washington.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 969607403 23611 193.60.84.177 (22 Sep 2000 07:23:23 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 22 Sep 2000 07:23:23 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Fri, 22 Sep 2000 11:27:31 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Janet, Hope you don't mind me posting the answer to your problem with aceperl so that others can benefit from it: >> Could you describe what operations your perl scripts do and in particular how >> they exit (they may inadvertantly be doing a 'save'). > > you are right - the script was inadvertantly saving when it exit. your > question prompted me to delve deeper into the aceperl donumentation, and > I added a line to my perl script: > > $db->auto_save(0); > >which seems to have solved the problem. thanks for the suggestion! OK, so that's probably worth noting, Lincoln (Stein) may may like to comment on this. 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 URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Fri Sep 22 18:50:14 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9FC5217B02; Fri, 22 Sep 2000 18:50:13 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 18B3A17AEA; Fri, 22 Sep 2000 18:50:12 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 9387817AF5; Fri, 22 Sep 2000 14:57:31 +0100 (BST) Received: from rutgers.rutgers.edu (bsd.rutgers.edu [165.230.4.71]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D1992415DD for ; Fri, 22 Sep 2000 14:57:29 +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 JAA07534 for ; Fri, 22 Sep 2000 09:57:28 -0400 (EDT) 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 JAA07281; Fri, 22 Sep 2000 09:57:24 -0400 (EDT) Received: from cetus (cetus [130.14.25.107]) by ray.nlm.nih.gov (8.9.3+Sun/8.9.3) with SMTP id JAA16713; Fri, 22 Sep 2000 09:57:23 -0400 (EDT) Message-Id: <200009221357.JAA16713@ray.nlm.nih.gov> From: Jean Thierry-Mieg Reply-To: Jean Thierry-Mieg Subject: Re: x-rated acedb To: bionet-software-acedb@moderators.isc.org, keith@thale.life.nottingham.ac.uk MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: 1xT4ARrlP9fbyscKOqaS8g== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.3.5 SunOS 5.7 sun4u sparc Newsgroups: bionet.software.acedb Date: Fri, 22 Sep 2000 18:50:12 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk acedb recognisez the upac code n is sometimes shown as - in displays w, s etc are recognized and used by acedb in numerous cases like in non matching ovelapping cosmids x is NOT a UPAC letter so this whole letter is just creating confusion and should have been removed by the moderator jean thierry-mieg >To: bionet-software-acedb@moderators.isc.org >From: Keith Bradnam >Subject: x-rated acedb >Mime-Version: 1.0 >X-Trace: oyez.ccc.nottingham.ac.uk 969554819 8030 128.243.116.150 (21 Sep 2000 16:46:59 GMT) >X-Complaints-To: usenet@news.nottingham.ac.uk >NNTP-Posting-Date: 21 Sep 2000 16:46:59 GMT >X-Sender: keith@thale >Date: Fri, 22 Sep 2000 08:19:04 +0100 (BST) > > >Hi all, > >I've just discovered that tf you read a sequence into Acedb which contains >an 'x' (representing an unspecified base) it seems to convert it into an >insertion ('-'). It also messes up the format of the sequence in tree display >(at least in AceBrowser). > >I know that 'N's are 'allowed' by acedb, but this made me start thinking >whether acedb recognises any of the other internationally agreed symbols, >e.g. 'w' for weak (A or T) etc. > >Anyone know any more about this - is acedb just misbehaving here, or is >there any sort of reason for converting 'x' into '-'??? > >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 Mon Sep 25 13:47:33 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1E9EC17A91; Mon, 25 Sep 2000 13:47:33 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 4EC4D17A8D; Mon, 25 Sep 2000 13:47:31 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id C658217A5B; Mon, 25 Sep 2000 13:31:24 +0100 (BST) To: bionet-software-acedb@net.bio.net From: rd@sanger.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Re: x-rated acedb Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200009251231.NAA26275@griffin.sanger.ac.uk> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 930C517A43; Mon, 25 Sep 2000 13:31:22 +0100 (BST) X-Received: from jess.sanger.ac.uk (jess.sanger.ac.uk [193.60.84.61]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id F4204415D5 for ; Mon, 25 Sep 2000 13:31:21 +0100 (BST) X-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 NAA01534; Mon, 25 Sep 2000 13:31:18 +0100 (BST) X-Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id NAA26275; Mon, 25 Sep 2000 13:31:18 +0100 (BST) X-To: mieg@ncbi.nlm.nih.gov X-Cc: acedb@hgmp.mrc.ac.uk Date: Mon, 25 Sep 2000 13:47:31 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk It is a bit harsh to say that Keith's letter should have been removed by the moderator. I believe moderation of this news group should be to keep junk mail and off topic messages out of the group, not to remove misunderstanding, which would be a daunting duty. In fact I would like to clarify Jean's reply, which is (of course) correct in saying that we handle the whole IUPAC code for nucleic acid ambiguitities (parsing and displaying), and that 'X' is not an IUPAC nucleotide ambiguity code (I think it is the protein ambiguity code). But > n is sometimes shown as - in displays might create some confusion. We store four binary bits per DNA position, one for each of A, C, G, T. 'n' is used for 1111, i.e. could be anything, whereas '-' is used for 0000, i.e. nothing. Strictly this is a gap character - a good use for exammple would be to indicate gaps in multiple alignments. But we also use it when no data has been added. Perhaps acedb should initialise all DNA arrays to 1111, so that if no data is added you get a sequence of n's not of dashes? Richard character, which could be used for e.g. padded alignment display. We do use it for regions where we have not been given any sequence. --- From owner-acedb@hgmp.mrc.ac.uk Mon Sep 25 16:43:26 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4717517AD4; Mon, 25 Sep 2000 16:43:26 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id F262A17AD3; Mon, 25 Sep 2000 16:43:24 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id E33B617AB8; Mon, 25 Sep 2000 14:44:54 +0100 (BST) To: bionet-software-acedb@net.bio.net From: james.o.mcinerney@may.ie (James McInerney) Newsgroups: bionet.software.acedb Subject: Website for Molecular Systematics and Evolution Organization: http://www.may.ie/academic/biology/jmbioinformatics.shtml Message-ID: <39CF587A.7B55152C@may.ie> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 1DBF317AAC; Mon, 25 Sep 2000 14:44:53 +0100 (BST) X-Received: from ailm.may.ie (ailm.may.ie [149.157.1.20]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 69250415DA for ; Mon, 25 Sep 2000 14:44:52 +0100 (BST) X-Received: from may.ie (macbl23.may.ie [149.157.201.23]) by ailm.may.ie (PMDF V5.2-33 #38649) with ESMTP id <01JULDVE972G000UEC@ailm.may.ie> for acedb@net.bio.net; Mon, 25 Sep 2000 14:44:37 WET X-To: acedb X-Mailer: Mozilla 4.75 (Macintosh; U; PPC) X-Accept-Language: en Date: Mon, 25 Sep 2000 16:43:24 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Dear all, Just to let you know that our updated website is now available: http://www.bioinf.org/molsys/index.html or http://www.dbbm.fiocruz.br/james You may freely use this website as a resource for teaching molecular systematics and evolution. You may download the slides (344 in total), use the self-paced tutorials and practicals and generally take whatever you might wish from the website. This is completely free to you, its development has been funded by various organisations (see website). The old address: http://www.may.ie/academic/biology/james will soon contain a redirect page that will point you to either of the other two addresses. -- Dr. T. Martin Embley, Dr. Mark Wilkinson, Department of Zoology, Department of Zoology, The Natural History Museum, The Natural History Museum, Cromwell Road, Cromwell Road, london SW7 5BD, London SW7 5BD, UK. UK. Dr. James O. McInerney, Dr. Robert Hirt, Dept. Biology, Department of Zoology, Natl. Univ. Ireland, The Natural History Museum, Maynooth, Co. Kildare, Cromwell Road, Ireland London SW7 5BD, UK. --- From owner-acedb@hgmp.mrc.ac.uk Tue Sep 26 13:55:18 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E1C3517B51; Tue, 26 Sep 2000 13:55:17 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id A677317B4E; Tue, 26 Sep 2000 13:55:16 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 1181C17B4A; Tue, 26 Sep 2000 10:45:50 +0100 (BST) Received: from briar.org (backdraft.briar.org [192.207.123.123]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 04AB2415D5 for ; Tue, 26 Sep 2000 10:45:45 +0100 (BST) Received: (from smap@localhost) by briar.org (8.9.1b+Sun/8.6.12) id FAA05066 for ; Tue, 26 Sep 2000 05:45:44 -0400 (EDT) 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 xma005064; Tue, 26 Sep 00 05:45:17 -0400 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 13drIQ-00039U-00 for bionet-software-acedb@moderators.isc.org; Tue, 26 Sep 2000 10:45:06 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13drIZ-0002YQ-00; Tue, 26 Sep 2000 10:45:15 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Re: x-rated acedb Organization: ACS, The University of Nottingham Message-ID: References: <200009251231.NAA26275@griffin.sanger.ac.uk> Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 969961515 9820 128.243.116.150 (26 Sep 2000 09:45:15 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 26 Sep 2000 09:45:15 GMT X-Sender: keith@thale Date: Tue, 26 Sep 2000 13:55:16 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > It is a bit harsh to say that Keith's letter should have been removed > by the moderator. I believe moderation of this news group should be > to keep junk mail and off topic messages out of the group, not to > remove misunderstanding, which would be a daunting duty. Maybe I should elaborate on why I asked the question. In addition to reading in many 1000's of EMBL sequences into my ACEDB database, we also have started to receive many 'insert sequences' from groups, which have not yet been published in GenBank or EMBL. These (usually short) sequences reflect the sequencing of genomic DNA adjacent to (deliberately engineered) transposon insertions. We recently received a lot of these sequences and checked them (by eye) and they looked ok (i.e. just A,T,C,G, and N's) but we later found that some of them contained X's. I guess this is because some researchers who are not familiar with the IUPAC code just use 'X' to represent any base. I believe as well (but am not certain) that some (old) sequencing machines can return an 'X' in their output??? We only found this out when we noticed that AceBrowser was treating them strangely. So whilst 'X' may not be a standart IUPAC code, it is the case that some researchers will use 'X'...maybe acedb could run a simple check when sequences are loaded and not accept sequences with any non-standard code...or at least inform the curator when something non-standard is read in. > 'X' is not an IUPAC > nucleotide ambiguity code (I think it is the protein ambiguity code). And I've also seen it used to represent a stop codon in a peptide sequence (along with asterisks). 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 Wed Sep 27 09:58:41 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B6D5F17AEF; Wed, 27 Sep 2000 09:58:40 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 44CC617A8A; Wed, 27 Sep 2000 09:58:38 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 2511D17A4E; Wed, 27 Sep 2000 03:35:14 +0100 (BST) Received: from sprettur.isnet.is (sprettur.isnet.is [193.4.58.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D84A8415DA for ; Wed, 27 Sep 2000 03:35:12 +0100 (BST) Received: from ncbi.nlm.nih.gov (ncbi.nlm.nih.gov [130.14.25.1]) by sprettur.isnet.is (8.11.0/8.11.0/isnet) with ESMTP id e8R2ZBC17317 for ; Wed, 27 Sep 2000 02:35:12 GMT (envelope-from mieg@ncbi.nlm.nih.gov) 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 WAA29198; Tue, 26 Sep 2000 22:35:00 -0400 (EDT) Received: from cetus (cetus [130.14.25.107]) by ray.nlm.nih.gov (8.9.3+Sun/8.9.3) with SMTP id WAA20180; Tue, 26 Sep 2000 22:34:59 -0400 (EDT) Message-Id: <200009270234.WAA20180@ray.nlm.nih.gov> From: Jean Thierry-Mieg Reply-To: Jean Thierry-Mieg Subject: Re: x-rated acedb To: bionet-software-acedb@moderators.isc.org, keith@thale.life.nottingham.ac.uk MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: COv09SLhYf3hLcbtaR7jQA== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.3.5 SunOS 5.7 sun4u sparc Newsgroups: bionet.software.acedb Date: Wed, 27 Sep 2000 09:58:38 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk >So whilst 'X' may not be a standart IUPAC code, it is the case that some >researchers will use 'X'...maybe acedb could run a simple check when >sequences are loaded and not accept sequences with any non-standard >code...or at least inform the curator when something non-standard is read >in. > > >> 'X' is not an IUPAC >> nucleotide ambiguity code (I think it is the protein ambiguity code). > > acedb> parse // Type in your data in .ace format, then CTRL-D to finish DNA toto atgc axgc // 1 objects read with 0 errors // 1 Active Objects acedb> find dna toto // Found 1 objects in this class // 1 Active Objects acedb> show DNA : "toto" atgca-gc so x is treated as a place holder which is probably what yuo want considering that some biologists may use it i apologize for my letter of 2 days ago, i guess i was in a bad mood jean From owner-acedb@hgmp.mrc.ac.uk Wed Sep 27 09:58:47 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 331D517AF5; Wed, 27 Sep 2000 09:58:47 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 38C1617AEF; Wed, 27 Sep 2000 09:58:45 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id DE58D17A64; Tue, 26 Sep 2000 19:01:36 +0100 (BST) Received: from sprettur.isnet.is (sprettur.isnet.is [193.4.58.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4105F415D5 for ; Tue, 26 Sep 2000 19:01:34 +0100 (BST) Received: from mark.ucdavis.edu (mark.ucdavis.edu [169.237.105.49]) by sprettur.isnet.is (8.11.0/8.11.0/isnet) with ESMTP id e8QI1WC72209 for ; Tue, 26 Sep 2000 18:01:32 GMT (envelope-from usenet@mark.ucdavis.edu) Received: (from usenet@localhost) by mark.ucdavis.edu (8.9.3/8.9.3/IT4.3.4) id LAA04153 for bionet-software-acedb@moderators.isc.org; Tue, 26 Sep 2000 11:01:28 -0700 (PDT) To: bionet-software-acedb@moderators.isc.org From: Kim Marshall Newsgroups: bionet.software.acedb Subject: object is empty and other fine stuff Organization: US Forest Service Message-ID: <39D0E40C.4199CE65@ucdavis.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: mark.ucdavis.edu 969991288 4150 169.237.8.29 (26 Sep 2000 18:01:28 GMT) X-Complaints-To: usenet@ucdavis.edu NNTP-Posting-Date: 26 Sep 2000 18:01:28 GMT X-Mailer: Mozilla 4.72 [en] (X11; U; SunOS 5.6 sun4u) X-Accept-Language: en Date: Wed, 27 Sep 2000 09:58:45 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi everyone, I have been having a very weird problem that is driving me crazy. When I initialize our database (TreeGenes), the first class I click on through webace most often says object is empty even though I know that object is there. I can then go and clean out the javacache and click on the object and its information will show up. It was suggested to me that I may need to upgrade the memory on our server, which I did to 1 gig, but I still have that same problem. Any ideas? Is it a RPC problem? I am running Solaris 2.6 with Acedb 4.7g. Also, this weekend I was considering upgrading our server to Solaris 8 and was wondering how well acedb, webace and acebrowser run with this operating system. I am considering the socket version of webace but I am open to other ideas to keep things up and running. And finally, how can I include URLS in our data. Currently, if I use the full URL http:// the rest of the information gets commented out. I believe there are solutions to this but I have no idea what. thanks for any help. Kim Dendrome Project Institute of Forest Genetics US Forest Service kmarshal@dendrome.ucdavis.edu http://dendrome.ucdavis.edu From owner-acedb@hgmp.mrc.ac.uk Wed Sep 27 11:44:07 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 22D3B17B03; Wed, 27 Sep 2000 11:44:07 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 7DEB417B07; Wed, 27 Sep 2000 11:44:05 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 0EC4C17B07; Wed, 27 Sep 2000 11:09:28 +0100 (BST) To: bionet-software-acedb@net.bio.net From: rd@sanger.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: Re: x-rated acedb Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200009271009.LAA13179@griffin.sanger.ac.uk> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id CF4D517AF5; Wed, 27 Sep 2000 11:09:26 +0100 (BST) X-Received: from jess.sanger.ac.uk (jess.sanger.ac.uk [193.60.84.61]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D4FBA415DA for ; Wed, 27 Sep 2000 11:09:25 +0100 (BST) X-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 LAA08016; Wed, 27 Sep 2000 11:09:23 +0100 (BST) X-Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id LAA13179; Wed, 27 Sep 2000 11:09:23 +0100 (BST) X-To: mieg@ncbi.nlm.nih.gov X-Cc: acedb@hgmp.mrc.ac.uk Date: Wed, 27 Sep 2000 11:44:05 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I think we should create an error if a non IUPAC letter, non white-space letter is parsed. To be specific, we should reject the entire sequence, and create a parse error message like for lines in standard objects that do not match the model. Could anyone who objects to this write before the end of this week, after which we will make the change here unless there is consensus otherwise. Given we do this, Keith will have to replace x by n (e.g. with a perl script) before parsing into acedb. I think that is reasonable. Does anyone else rely on being able to read non IUPAC characters? Richard ... > acedb> parse > // Type in your data in .ace format, then CTRL-D to finish > DNA toto > atgc > axgc > > // 1 objects read with 0 errors > // 1 Active Objects > acedb> find dna toto > > // Found 1 objects in this class > // 1 Active Objects > acedb> show > > DNA : "toto" > atgca-gc > > so x is treated as a place holder > which is probably what yuo want > considering that some biologists may use it ... --- From owner-acedb@hgmp.mrc.ac.uk Wed Sep 27 11:44:15 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1D88417B11; Wed, 27 Sep 2000 11:44:14 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 69FD317B03; Wed, 27 Sep 2000 11:44:13 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 12A1817B11; Wed, 27 Sep 2000 11:17:05 +0100 (BST) Received: from mailbox2.ucsd.edu (mailbox2.ucsd.edu [132.239.1.54]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 1799D415DA for ; Wed, 27 Sep 2000 11:17:04 +0100 (BST) Received: from jess.sanger.ac.uk (jess.sanger.ac.uk [193.60.84.61]) by mailbox2.ucsd.edu (8.11.0/8.11.0) with ESMTP id e8RAHfY16500 for ; Wed, 27 Sep 2000 03:17:41 -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 LAA09447; Wed, 27 Sep 2000 11:16:48 +0100 (BST) From: Richard Durbin Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id LAA07266; Wed, 27 Sep 2000 11:16:47 +0100 (BST) Message-Id: <200009271016.LAA07266@griffin.sanger.ac.uk> To: bionet-software-acedb@moderators.isc.org, kamarshall@ucdavis.edu Subject: Re: object is empty and other fine stuff Newsgroups: bionet.software.acedb Date: Wed, 27 Sep 2000 11:44:13 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > And finally, how can I include URLS in our data. Currently, if I use the > full URL http:// the rest of the information gets commented out. I > believe there are solutions to this but I have no idea what. the string "//" means a comment in a .ace file, as in some languages. You can parse them in by escaping the slash characters, as in http:\/\/www.sanger.ac.uk Richard From owner-acedb@hgmp.mrc.ac.uk Wed Sep 27 13:01:47 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0BB9F17B12; Wed, 27 Sep 2000 13:01:45 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 02E2B17AA6; Wed, 27 Sep 2000 13:01:43 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 70C8617B11; Wed, 27 Sep 2000 12:10:38 +0100 (BST) Received: from postfix1.free.fr (postfix1.free.fr [212.27.32.21]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id E2687415DE for ; Wed, 27 Sep 2000 12:10:36 +0100 (BST) Received: from nnrp6.proxad.net (nnrp6.proxad.net [212.27.32.78]) by postfix1.free.fr (Postfix) with ESMTP id 553B828040 for ; Wed, 27 Sep 2000 13:10:17 +0200 (MEST) Received: from localhost (localhost [[UNIX: localhost]]) by nnrp6.proxad.net (8.9.3/8.9.3/Debian 8.9.3-21) id NAA03658; Wed, 27 Sep 2000 13:10:17 +0200 To: bionet-software-acedb@net.bio.net Message-ID: <39D1D6A9.19128494@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: Help needed for install Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Complaints-To: abuse@proxad.net X-Trace: nnrp6.proxad.net 970053017 195.220.67.155 (Wed, 27 Sep 2000 13:10:17 CEST) NNTP-Posting-Date: Wed, 27 Sep 2000 13:10:17 CEST Date: Wed, 27 Sep 2000 13:01:43 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Bonjour, I have been running acedb for about a year on my computer (under Linux); the install process went well at this time. I now want to install it on another computer that should become the server of the lab (still under Linux). I guess I need some help, although I think the problem lies not in AceDB, but in my system (see below). I put the database.WS9.4-*.tar.Z, bin.linux_libc6.4_7l.tar.Z as well as the INSTALL script (all files gotten anew from Sanger) in a directory (I have write access to this directory), and tried to run csh INSTALL It starts fine, ask me whether or not to proceed, starts the installation, and starts reporting errors: chmod: No match. grep: Command not found. (same for zcat, mkdir, touch and tar) Of course, all these commands are there (under /bin), and are exceutable by anyone. Now, what puzzled me (and I guess this is where I need your help), is that these commands work ok in bash (the default shell) as well as sh, but not in csh (and hence, I guess, why the INSTALL script cannot work). When I su to root, these commands will work, even under csh (but of course, I cannot install acedb under root). Any idea where I went wrong? Thanks for your help! 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 Sep 27 13:01:49 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1FEC317B13; Wed, 27 Sep 2000 13:01:47 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 69CC817B11; Wed, 27 Sep 2000 13:01:43 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 0B1E017AA3; Wed, 27 Sep 2000 12:34:59 +0100 (BST) To: bionet-software-acedb@net.bio.net From: matthews@greengenes.cit.cornell.edu (Dave Matthews) Newsgroups: bionet.software.acedb Subject: \/\/ vs. acediff Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200009271134.HAA25400@greengenes.cit.cornell.edu> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 9375517A73; Wed, 27 Sep 2000 12:34:57 +0100 (BST) X-Received: from greengenes.cit.cornell.edu (greengenes.cit.cornell.edu [128.253.246.43]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D44DD415DA for ; Wed, 27 Sep 2000 12:34:55 +0100 (BST) X-Received: (from matthews@localhost) by greengenes.cit.cornell.edu (8.9.3/8.9.3) id HAA25400 for ACEDB newsgroup ; Wed, 27 Sep 2000 07:34:54 -0400 (EDT) X-To: ACEDB newsgroup Date: Wed, 27 Sep 2000 13:01:43 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk That reminds me, I've been meaning for a long time to complain: This isn't working in acediff. It treats "\/\/" as a comment too. - Dave > From: Richard Durbin > the string "//" means a comment in a .ace file, as in some languages. > You can parse them in by escaping the slash characters, as in > > http:\/\/www.sanger.ac.uk --- From owner-acedb@hgmp.mrc.ac.uk Thu Sep 28 13:28:39 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 83ADF17AD0; Thu, 28 Sep 2000 13:28:38 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3E21517AB2; Thu, 28 Sep 2000 13:28:37 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 82A7917AB0; Thu, 28 Sep 2000 11:49:22 +0100 (BST) To: bionet-software-acedb@net.bio.net From: crepinau@sb-roscoff.fr (Florent Crepineau) Newsgroups: bionet.software.acedb Subject: Re : what future ? Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <39D33F52.20E5@sb-roscoff.fr> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id ED40D17A92; Thu, 28 Sep 2000 11:49:19 +0100 (BST) X-Received: from hp-lc3-2.igr.fr (hp-lc3-2.igr.fr [194.167.111.66]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 10F6D415DD for ; Thu, 28 Sep 2000 11:49:18 +0100 (BST) X-Received: from hp-lc3-4.igr.fr ([194.167.111.194]) by hp-lc3-2.igr.fr (Netscape Messaging Server 3.62) with ESMTP id 366 for ; Thu, 28 Sep 2000 12:49:20 +0200 X-Received: from hp-lc3-4.igr.fr ([194.167.111.194]) by hp-lc3-4.igr.fr (Netscape Messaging Server 3.62) with SMTP id 323; Thu, 28 Sep 2000 12:47:20 +0200 X-Received: from 172.16.1.233 by hp-lc3-4.igr.fr (InterScan E-Mail VirusWall NT); Thu, 28 Sep 2000 12:47:19 +0200 (Paris, Madrid (heure d'été)) X-Reply-To: crepinau@sb-roscoff.fr X-Mailer: Mozilla 3.01 (Macintosh; I; 68K) X-To: acedb@net.bio.net X-Cc: crepinau@sb-roscoff.fr Date: Thu, 28 Sep 2000 13:28:37 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk In article , Ewan Birney wrote: > >Where should ACEDB go? > More documentation, rich in examples. Tutorials at major conferences. ______________________________________________________________ I would like ACeDB to become a LIMS (Laboratory Information Managment System) for biology project. I have used it for an EST project and I am considering its use in a SAGE project to handle sequences information. The biggest problem I found is intefacing with other softwares especially analysis software such as motif/domain searching software. What I would like to see is a common motif/domain format ( similar to the CAF format developed to share assemblies ) with the translating softwares to go back and forth from ACeDB to pfamm MEME or whatever. ( I read such a project about 2 years ago but I can't remember where, about a common descriptive langage for motif, domains... but have not seen anything yet) Just my 2 cents. Florent ps : I also would like to see translating software between ACEDB and multiple alignment programs. --- From owner-acedb@hgmp.mrc.ac.uk Thu Sep 28 16:28:54 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8837417A91; Thu, 28 Sep 2000 16:28:53 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3E1BF17A8D; Thu, 28 Sep 2000 16:28:51 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id C936017A8C; Thu, 28 Sep 2000 14:39:06 +0100 (BST) Received: from ncbi.nlm.nih.gov (ncbi.nlm.nih.gov [130.14.25.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 41440415DC for ; Thu, 28 Sep 2000 14:39:05 +0100 (BST) 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 JAA08669; Thu, 28 Sep 2000 09:39:00 -0400 (EDT) Received: from cetus (cetus [130.14.25.107]) by ray.nlm.nih.gov (8.9.3+Sun/8.9.3) with SMTP id JAA19237; Thu, 28 Sep 2000 09:38:59 -0400 (EDT) Message-Id: <200009281338.JAA19237@ray.nlm.nih.gov> From: Jean Thierry-Mieg Reply-To: Jean Thierry-Mieg Subject: Re: Help needed for install To: bionet-software-acedb@net.bio.net, coulier@marseille.inserm.fr Content-MD5: rFc9d03mFp8ZE8TTXi+2dA== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.3.5 SunOS 5.7 sun4u sparc Newsgroups: bionet.software.acedb Date: Thu, 28 Sep 2000 16:28:51 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk try (as the readme says) chmod 755 INSTALL ./INSTALL this is not really equivalent to csh INSTALL are you running this as root (i bet a beer you are) i bet also that the following happens you should always say csh stuff -f otherwise you read $USER/.cshrc in this case i bet ~root/.cshrc and that .cshrc says path = null and you do not picck standard unix commands that is a lot of beers i am betting >To: bionet-software-acedb@net.bio.net >From: "F. Coulier" >X-Accept-Language: fr-FR, en >MIME-Version: 1.0 >Subject: Help needed for install >Content-Transfer-Encoding: 8bit >X-Complaints-To: abuse@proxad.net >X-Trace: nnrp6.proxad.net 970053017 195.220.67.155 (Wed, 27 Sep 2000 13:10:17 CEST) >NNTP-Posting-Date: Wed, 27 Sep 2000 13:10:17 CEST >Date: Wed, 27 Sep 2000 13:01:43 +0100 (BST) > >Bonjour, > >I have been running acedb for about a year on my computer (under Linux); >the install process went well at this time. I now want to install it on >another computer that should become the server of the lab (still under >Linux). > >I guess I need some help, although I think the problem lies not in >AceDB, but in my system (see below). > >I put the database.WS9.4-*.tar.Z, bin.linux_libc6.4_7l.tar.Z as well as >the INSTALL script (all files gotten anew from Sanger) in a directory >(I have write access to this directory), and tried to run csh INSTALL > >It starts fine, ask me whether or not to proceed, starts the >installation, and starts reporting errors: > >chmod: No match. >grep: Command not found. (same for zcat, mkdir, touch and tar) > >Of course, all these commands are there (under /bin), and are exceutable >by anyone. > >Now, what puzzled me (and I guess this is where I need your help), is >that these commands work ok in bash (the default shell) as well as sh, >but not in csh (and hence, I guess, why the INSTALL script cannot work). >When I su to root, these commands will work, even under csh (but of >course, I cannot install acedb under root). > >Any idea where I went wrong? > >Thanks for your help! > >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 Thu Sep 28 16:29:03 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B619B17AC2; Thu, 28 Sep 2000 16:29:02 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix,