From owner-acedb@hgmp.mrc.ac.uk Tue Aug 1 11:48:24 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9FA6C17B11; Tue, 1 Aug 2000 11:48:23 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id D9C3017B09; Tue, 1 Aug 2000 11:48:21 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 2FE0A17B5F; Fri, 28 Jul 2000 21:34:13 +0100 (BST) To: bionet-software-acedb@net.bio.net From: matthews@greengenes.cit.cornell.edu (Dave Matthews) Newsgroups: bionet.software.acedb Subject: ACEDB FAQ Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200007282034.QAA22467@greengenes.cit.cornell.edu> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id A9E0417B59; Fri, 28 Jul 2000 21:34:10 +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 A056F415DE for ; Fri, 28 Jul 2000 21:34:08 +0100 (BST) X-Received: (from matthews@localhost) by greengenes.cit.cornell.edu (8.9.3/8.9.3) id QAA22467 for ACEDB newsgroup ; Fri, 28 Jul 2000 16:34:07 -0400 (EDT) X-To: ACEDB newsgroup Date: Tue, 1 Aug 2000 11:48:21 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Newsgroups: bionet.software.acedb Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Reply-To: matthews@greengenes.cit.cornell.edu Distribution: world Organization: USDA-ARS, Dept. Plant Breeding, Cornell University Summary: Frequently Asked Questions about the genome database software ACEDB. URL: htp://ars-genome.cornell.edu/acedocs/acedbfaq.html Archive-name: acedb-faq Last-modified: 27 Jul 00 Version: 1.43 _________________________________________________________________ ACEDB FAQ _________________________________________________________________ Curated by: Dave Matthews _________________________________________________________________ Frequently Asked Questions about ACEDB * Q0 : What is ACEDB? * Q1 : ! What is the current version of ACEDB? * Q2 : ! Where can I get ACEDB? * Q3 : What hardware/software do I need to run ACEDB? * Q4 : ! Can ACEDB be networked? * Q5 : ! What documentation exists for ACEDB? * Q6 : Can I subscribe to the ACEDB newsgroup by mail? * Q7 : Is there a repository of software tools for ACEDB curators? * Q8 : ! When and where is the next ACEDB Workshop? * Q9 : How does ACEDB compare to commercial relational DBMS's? * Q10 : How should ACEDB be cited? * Q11 : What ACEDB databases exist? * Q12 : Who prepared this document & where is the current version? Questions marked with '!' have substantially changed answers since the last update of the FAQ. _________________________________________________________________ Q0: What is ACEDB? A0: ACEDB is an acronym for "A Caenorhabditis elegans Database". It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning in 1989. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage --missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions _________________________________________________________________ Q1: What is the current version of the ACEDB software? A1: Development versions of the source code are released ca. monthly at ftp://ftp.sanger.ac.uk/pub/acedb/. Compiled executables: * Unix -- version ace.4_7l, July 1999 * Windows -- version Acedb.4_8c.beta.14, May 2000 * Macintosh -- version 4.1b1, August 1995 WWW interfaces: (See "Can ACEDB be networked?".) * AcePerl -- version 1.62, May 2000 * AceBrowser -- version 2.10, September 1999 * webace2K (Cornell) -- May 2000 * webace2 (Sanger) -- version 2.0a5, March 1998 * CITA -- May 2000 * Jade -- version 1.0j, Apr 1998 Return to List of Questions _________________________________________________________________ Q2: Where can I get ACEDB? A2: Source code and Unix binaries are available by anonymous ftp at the following sites: * ftp.sanger.ac.uk in pub/acedb * ncbi.nlm.nih.gov in repository/acedb * http://alpha.crbm.cnrs-mop.fr/acedb/distrib/ (http, not ftp) Windows 95/98/NT/2000, from Simon Kelley: * ftp.sanger.ac.uk in pub/acedb/winace * Documentation: http://www.sanger.ac.uk/Software/Acedb/WinAce.shtml MacAce, from Frank Eeckman, Cyrus Harmon and Richard Durbin: (Note: The authors are not currently able to support MacAce. Latest version was 4.1b1.) * ftp.sanger.ac.uk in pub/acedb/macace * ncbi.nlm.nih.gov in repository/acedb/macace Return to List of Questions _________________________________________________________________ Q3: What hardware/software do I need to run ACEDB? A3: The software is available in binary (pre-compiled) format for a variety of machines. * Unix: + Sun/SunOS 4.x + Sun/Solaris + DEC DECstation3100, 5100 etc. + DEC Alpha/OSF-1 + Silicon Graphics Iris series 4, 5, 6 + IBM RS-6000 + PC 386/486/Pentium with Linux + NEC EWS4800 + NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu + There exist, or have existed, ports onto Alliant, Hewlett- Packard, Convex. You may have to contact the developer responsible for the port to make these real. * Windows 95/98/NT/2000 * Macintosh (not currently supported) The software is also available as source code, so you may be able to get it working on any machine. Memory requirements (from Richard Durbin, aug 97) The amount of memory you require for ACEDB depends very much on how big the database is (i.e. the disk space used by the database/ subdirectory). Our rule of thumb is that one typically uses 5-10Mb plus up to 10% of the disk space size of the database. So with a 200Mb database perhaps 25Mb memory, and with a 500Mb database (e.g. the C. elegans one) up to 50-60Mb. In fact for short sessions less memory is used -- it is only when all classes are explored, or for example when parsing big files that these amounts of memory get used. Return to List of Questions _________________________________________________________________ Q4: Can ACEDB be networked? A4: ACEDB Client / Server Computing (from Doug Bigwood, aug97) There are several client/server models for ACEDB computing and several more are in development. The start of the ACEDB client/server age began with the inclusion of aceclient and aceserver in version 4.0. These are C - based and use the RPC protocol for communication. These executables can be made from the standard ACEDB distributions. Starting in version 4.5 an xaceclient is also included with ACEDB. Xaceclient provides remote read/write access to an aceserver while providing the user with the same X displays that are found in xace. To use it, you create an empty database with the appropriate models and start xaceclient. It will automatically retrieve data from the server declared in wspec/server.wrm (the Montpellier server in the distribution server.wrm). The data will be saved locally and can then be viewed with a normal xace. A perl extension which provides aceclient functionality to Perl 5.x was developed at ACE95. The files necessary for this perl extension are now (ACEDB 4.5 and later) included in the wrpc directory of the ACEDB directory hierarchy. Documentation about how to extend perl is found at http://ars-genome.cornell.edu/acedocs/ace97/perlace/perlacecl.html. WWWAce and its successor webace were developed to provide a World Wide Web interface for ACEDB. Webace instructions can be found at http://ars-genome.cornell.edu/acedocs/webace.html, and http://ars-genome.cornell.edu/acedocs/ace97/webace.html and the program itself at ftp://ars-genome.cornell.edu/pub/tools/webace.tar.gz. A Java-based client called Jade allows communication via sockets to an aceserver. Jade installation instructions and information on downloading can be found at http://stein.cshl.org/jade/. There are now development efforts underway to provide additional client/server functionality to ACEDB including a CORBA server and socket-based communications. These will likely be included in future versions of ACEDB. A new C library interface to ACEDB internals will greatly ease the development of new clients and servers that will support additional protocols. Subsequent developments (from Dave Matthews, jul00) A new version of webace, sometimes called webace2, was developed at the Sanger Centre. It makes use of the new gifaceserver instead of aceserver to improve interactive response of the graphical displays, Javascript, Java, and a new Aceclient.pm module which can be installed into Perl without recompiling. It also supports the ACEDB ?URL class. The home page is at http://webace.sanger.ac.uk/. Its authors currently consider it "deprecated", preferring AceBrowser. AcePerl, from Lincoln Stein, is an object-oriented Perl interface to ACEDB. It can connect to remote ACEDB databases, perform queries, fetch ACE objects, and update databases. The programmer's API is compatible with the Jade Java API. Home page at http://stein.cshl.org/AcePerl/. New! AceBrowser, from Lincoln Stein, is a ready-to-use WWW gateway to ACEDB databases built on AcePerl. It has most of the functionality of webace. http://stein.cshl.org/AcePerl/AceBrowser/. New! webace2K is an enhancement of webace2, from Maria Nemchuk. http://ars-genome.cornell.edu/webace/webace_install.html New! CITA is a CORBA Interface To ACEDB, from UK CropNet. http://jic-bioinfo.bbsrc.ac.uk/BrassicaDB/CITA/ Return to List of Questions _________________________________________________________________ Q5: What documentation exists for ACEDB? A5: In the ACEDB Documentation Library, http://ars-genome.cornell.edu/acedocs/ * The original documentation from the developers Durbin & Thierry-Mieg, ca. 1992. + acedb -- A C. elegans Database: I. Users' Guide + acedb -- A C. elegans Database: II. Installation Guide + acedb -- A C. elegans Database: III. Configuration Guide + acedb -- A C. elegans Database: Syntactic Definitions for the ACEDB Data Base Manager * Tutorials and technical guides, for users, curators and programmers * Documentation written at the ACEDB Workshops * Documents in Postscript, wordprocessor and other non-html formats, at ftp://ars-genome.cornell.edu/pub/acedocs/. * Some curator tools * A selection of models.wrm files from various databases * SampleDB, a sample database to demonstrate some ACEDB features, 1995 * This FAQ in html format At the Sanger Centre, www.acedb.org * Proceedings of the ACEDB2000 Conference * A recent (jan00) user tutorial by Sylvia Martinelli, http://www.acedb.org/embtut/ * Archive of the monthly ACEDB User Group Newsletter from Ed Griffiths, http://www.acedb.org/winfo/Newsletters/ * WebDDTS for ACEDB bug reporting and tracking * WWW copies of the ACEDB online help (see below), http://www.acedb.org/whelp/TOC.html Other * The ACEDB online help, available from the Help buttons in xace. A context-sensitive hypertext reader for the contents of the whelp directory of the ACEDB software distribution. * Contents of the wdoc, wtools, and wscripts directories. * Searchable archives of the bionet.software.acedb newsgroup + http://www.bio.net/hypermail/ACEDB/, from BIOSCI + http://genome-www.stanford.edu/cgi-bin/biosci_acedb, from the Saccharomyces Genome Database site * ACEDB User's Guide in Japanese, from Tohru Sano, NEC, sano@exp.cl.nec.co.jp, http://www.cbi.or.jp/~sano/. (Postscript at http://www.labs.nec.co.jp/ . Follow the prompts to register and "download the software".) * Paper publications + 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. Return to List of Questions _________________________________________________________________ Q6: Can I subscribe to the ACEDB newsgroup by mail? A6: Yes! Just send the message "subscribe acedb" to biosci-server@net.bio.net. You can also post to the newsgroup by mail, write to acedb@net.bio.net. Or you can access it with a standard newsreader like rn or tin at bionet.software.acedb, or with a WWW browser at news:bionet.software.acedb. The articles are archived by BIOSCI at http://www.bio.net/archives.html and by Mike Cherry at http://genome-www.stanford.edu/cgi-bin/biosci_acedb. Both archives are indexed for searching. This is the place to find the Questions that really are Frequently Asked! Return to List of Questions _________________________________________________________________ Q7 : Is there a repository of software tools for ACEDB curators? A7: Not really, but there are several partial ones. The main tools available are for converting data from other formats to .ace format. The USDA-ARS Center for Bioinformatics and Comparative Genomics has some useful tools at http://ars-genome.cornell.edu/acedocs/conversion.html. Some additional ones were contributed at the ACE97 Workshop and can be found in the Proceedings, http://ars-genome.cornell.edu/acedocs/ace97/tools/. Mike Cherry maintains an archive of tools at ftp://genome-ftp.stanford.edu/pub/acedb_dev/utilities/ For a general tool for converting data to ACEDB format input files, Joachim Baumann (joachim.baumann@informatik.uni-stuttgart.de) has written the Perl program TextConvert, available at ftp.informatic.uni.stuttgart.de/pub/DART/. Return to List of Questions _________________________________________________________________ Q8: When and where is the next ACEDB Workshop? A8: The ACEDB2000 Workshop was held June 10-16 at Simon Fraser University, B.C., Canada. The Proceedings are at http://www.acedb.org/winfo/Conferences/acedb2000/. The ACE97 Conference and Workshop was held July 27 - August 9 at Cornell University, Ithaca, New York, USA. See the ACE97 Proceedings Page, http://ars-genome.cornell.edu/acedocs/ace97/proceedings.html for the results. The Proceedings from the May 1995 ACEDB Conference are available at http://ars-genome.cornell.edu/acedocs/ace95/. A final summary report is available at http://ars-genome.cornell.edu/acedocs/ace95/ace95.final.html. Also available online are collections of snapshots taken during the conference by Frank Eeckman and by Dave Matthews. For pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers, see the online collections: * by Mike Cherry at http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; * by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; * and by Brad Sherman at ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html Return to List of Questions _________________________________________________________________ Q9: How does ACEDB compare to commercial relational DBMS's? A9: From Jean Thierry-Mieg, 4/97: Obviously, i have a biased opinion, but i would say that acedb is to be recommended if the following criteria are met: 1) A very complex schema, that cannot be developed at once, but will need continuous refinement in parallel with the accumulation of the data 2) The type of questions that will be asked are rather complex, with rather fuzzy answers, that one tries to refine progressively. The acedb browsing capacities are useful in this case and have no equivalent in a relational dbms ______________ I would rather recommend sybase in the following case 1) Simple schema, that can be designed from the start and does not contain too many n.n relations and does not need recursivity 2) The type of questions that will be asked is: succession of de-correlated simple questions with simple answers ____________________ Within this context, i would then list the following goodies of acedb: 1) The ace file format, which is a powerful system to prepare and exchange data between data curators. 2) The existence of an easy graphic browsing interface 3) The availability of a biology-layer, if the application is about genetics 4) Portability (any unix machine), mac (with some limitations), windows (in development) and price (ace is a freeware). This implies that you can actually redistribute the complete system, say on a CD, something impossible with sybase. 5) Ease of use, i seriously believe that ace is much easier to configure and use than sybase. _____________________ Finally one should consider the following question: concurrency. Sybase has a well designed transaction system, which will allow roll backs and refined lockings. This is essential for an application like a booking agency, with many users in simultaneous write access. Ace is much simpler minded. The graphic acedb creates a global lock allowing a single user with write access at the time, and the modifications are not echoed to the other "read access" users in real time. The non graphic client server system allows parallel downloading of data by many users, it is intended for example for collection of robots sending their independent data in parallel. This is now well tested. A graphic client system is being developed and now runs in our hands, but is not yet released. -- Therefore, if you do need real time simultaneous write access with partial locks, and roll backs, use sybase/oracle ________________ Last issue is speed and quantities of data. In principle, sybase/oracle is unlimited, whereas acedb needs to keep around 5-10% of the data in ram. But this apparent difference is misleading. On a 32 Meg machine, you can run ace with around 300.000 objects with a complex schema at high speed. With say 1M objects, you will need more memory or the performance would totally degrade because of swapping. However, this is really a lot of data. On a similar machine, your sybase oracle will work with that amount or more data only if you do not perform too many joins. This implies that you are asking simple questions from a simple schema which was indeed our first criterion to choose sybase. If you start asking complex questions and make joins, acedb is actually much more powerful. During tests run on a big dec alpha server by Otto Ritter in decembre 1995 on several million biological objects with a complex schema, acedb was about 10 times faster than sybase, both to load the data and to answer queries. I would therefore conclude that the quantity of data is not a criterion pushing one way or the other, it is the complexity of the schema that matters. Return to List of Questions _________________________________________________________________ Q10: How should ACEDB be cited? A10: From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit available via anonymous ftp. Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions _________________________________________________________________ Q11: What ACEDB databases exist? A11: Too many to maintain an up-to-date listing. A list as of mid-1998 is available at http://ars-genome.cornell.edu/acedocs/acedbfaq.dbs.html A repository of many of these databases is maintained by CBCG, both for anonymous ftp at ftp://ars-genome.cornell.edu/pub and for WWW access via Webace at http://ars-genome.cornell.edu/. Return to List of Questions _________________________________________________________________ Q12: Who prepared this document & where is the current version? A12: This document is posted monthly to the BIOSCI newsgroup bionet.software.acedb. The WWW version is at http://ars-genome.cornell.edu/acedocs/acedbfaq.html. This FAQ was created and maintained from 1993 - 1996 by Bradley K. Sherman. Major contributions in getting it off the ground were made by Mike Cherry, John McCarthy, and Doug Bigwood. Other contributors include: * Lisa Lorenzen * David Matthews * Edie Paul * Donn Davy * Eric De Mund * Sam Cartinhour It is currently maintained by Dave Matthews. Please cite as: Matthews, D.E., and B.K. Sherman, ACEDB Genome Database Software FAQ, http://ars-genome.cornell.edu/acedocs/acedbfaq.html, 1993-2000, approx. 30K bytes. To add or modify information in this document, please send mail to: matthews@greengenes.cit.cornell.edu The GrainGenes Project is funded by the USDA ARS Plant Genome Research Program. Return to List of Questions _________________________________________________________________ --- From owner-acedb@hgmp.mrc.ac.uk Tue Aug 1 11:49:01 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id DA2F317B13; Tue, 1 Aug 2000 11:49:00 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3B3DD17B12; Tue, 1 Aug 2000 11:48:59 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 06D6517B03; Tue, 1 Aug 2000 10:55:14 +0100 (BST) Received: from mailbox3.ucsd.edu (mailbox3.ucsd.edu [132.239.1.55]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id E9AEA415DE for ; Tue, 1 Aug 2000 10:55:12 +0100 (BST) Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by mailbox3.ucsd.edu (8.9.3/8.9.3) with ESMTP id CAA05494 for ; Tue, 1 Aug 2000 02:55:10 -0700 (PDT) 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 13JYl3-0003U2-00 for bionet-software-acedb@moderators.isc.org; Tue, 01 Aug 2000 10:54:45 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13JYlP-00002Q-00; Tue, 1 Aug 2000 10:55:07 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: 4.8 ready yet? 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 965123706 148 128.243.116.150 (1 Aug 2000 09:55:06 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 1 Aug 2000 09:55:06 GMT X-Sender: keith@thale Date: Tue, 1 Aug 2000 11:48:59 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk How far away are we from a full, working release of 4.8??? 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 Aug 4 08:29:33 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 3A0AA17A9F; Fri, 4 Aug 2000 08:29:33 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id E88EC17A7A; Fri, 4 Aug 2000 08:29:31 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id C191717B1C; Thu, 3 Aug 2000 17:17:20 +0100 (BST) To: bionet-software-acedb@net.bio.net From: ashwin@har.mrc.ac.uk (Ashwin) Newsgroups: bionet.software.acedb Subject: Which file? Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <39899B04.37111ACC@har.mrc.ac.uk> 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 3AFBF17A70; Thu, 3 Aug 2000 17:17:12 +0100 (BST) X-Received: from jerry.har.mrc.ac.uk.har.mrc.ac.uk (jerry.har.mrc.ac.uk [193.63.70.145]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 2A8C3415DD for ; Thu, 3 Aug 2000 17:17:11 +0100 (BST) X-Received: from har.mrc.ac.uk (cheetera [130.246.241.12]) by jerry.har.mrc.ac.uk.har.mrc.ac.uk (8.9.3/8.9.1) with ESMTP id RAA29043 for ; Thu, 3 Aug 2000 17:17:06 +0100 (BST) X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en X-To: acedb@net.bio.net Date: Fri, 4 Aug 2000 08:29:31 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I am attempting to edit an existing models.wrm to fit our data, which has an extra class compared to the data for which the model was intended. After my first attempt at opening Acedb (I am opening an empty database with the intention of parsing an .ace file) I am getting the message EXIT: Model screwup: impossible level line 6 Do you know which file this would be referring to? I did not alter line 6 of models.wrm or any other file. --- From owner-acedb@hgmp.mrc.ac.uk Fri Aug 4 08:49:33 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D8B5317A79; Fri, 4 Aug 2000 08:49:32 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 9DE1F17A70; Fri, 4 Aug 2000 08:49:31 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 7AB8A17A70; Fri, 4 Aug 2000 08:48:59 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id DD3B9415DE for ; Fri, 4 Aug 2000 08:48:58 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id IAA06142 for bionet-software-acedb@net.bio.net; Fri, 4 Aug 2000 08:48:58 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: Which file? Organization: Sanger Centre Message-ID: <398A756A.97F8D037@sanger.ac.uk> References: <39899B04.37111ACC@har.mrc.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 965375338 6140 193.60.84.177 (4 Aug 2000 07:48:58 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 4 Aug 2000 07:48:58 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Fri, 4 Aug 2000 08:49:31 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Ashwin, > EXIT: Model screwup: impossible level line 6 > > Do you know which file this would be referring to? I did not alter line > 6 of > models.wrm or any other file. the code issues this message at the line in the models file where it runs into trouble, BUT just as when compiling C code etc. the original problem may be elsewhere. Without seeing the original models file and your changes its not possible to diagnose this. I will be away now for 2 weeks but you can send a note (with models file + changes attached) to acedb@sanger.ac.uk and one of the developers will take a look sometime over the next couple of weeks. Otherwise, perhaps some kind soul will volunteer to look at this more quickly ? 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 Mon Aug 21 15:38:47 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 6BF0817B1D; Mon, 21 Aug 2000 15:38:45 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id E61A017AC4; Mon, 21 Aug 2000 15:38:42 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 88A9E17AE0; Mon, 14 Aug 2000 13:22:05 +0100 (BST) Received: from moderated.news.pipex.net (moderated.news.pipex.net [158.43.192.79]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 5FEF4415DA for ; Mon, 14 Aug 2000 13:22:03 +0100 (BST) Received: (qmail 22757 invoked by alias); 14 Aug 2000 12:22:02 -0000 Received: (qmail 22753 invoked from network); 14 Aug 2000 12:22:01 -0000 Received: from gwdu67.gwdg.de (134.76.98.67) by moderated.news.pipex.net with SMTP; 14 Aug 2000 12:22:01 -0000 Received: (from news@localhost) by gwdu67.gwdg.de (8.9.2/8.9.2) id OAA90423 for bionet-software-acedb@moderators.isc.org; Mon, 14 Aug 2000 14:22:00 +0200 (CEST) (envelope-from news) To: bionet-software-acedb@moderators.isc.org From: Kurt Stueber Newsgroups: bionet.software.acedb Subject: how to record blast results? Organization: Max-Planck-Institut fuer Zuechtungsforchung Message-ID: <3997E288.15B7F617@mpiz-koeln.mpg.de> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: gwdu67.gwdg.de 966255720 90421 193.174.239.26 (14 Aug 2000 12:22:00 GMT) X-Complaints-To: news@gwdg.de NNTP-Posting-Date: 14 Aug 2000 12:22:00 GMT To: stueber@gwdu67.gwdg.de X-Mailer: Mozilla 4.51 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Mon, 21 Aug 2000 15:38:42 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Dear colleages, I would like to record the results of blastn searches in acedb. Looking at the models.wrm file I found the line in the model for "sequence": homol DNA_homol ?sequence XREF DNA_homol ?Method Float Int Int Int Int #Homol_info This looks like the place to store homologies. Is there a place where I can find out what the five number (one float and 4 integers) are designed to stand for? Greetings Kurt stueber@mpiz-koeln.mpg.de From owner-acedb@hgmp.mrc.ac.uk Mon Aug 21 15:38:48 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D805C17AC4; Mon, 21 Aug 2000 15:38:46 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id BDB4F17B0E; Mon, 21 Aug 2000 15:38:44 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 16D6617AAE; Wed, 16 Aug 2000 20:14:13 +0100 (BST) Received: from rutgers.rutgers.edu (bsd.rutgers.edu [165.230.4.71]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 23AFB415DD for ; Wed, 16 Aug 2000 20:14:11 +0100 (BST) Received: from electra.cc.umanitoba.ca (root@electra.cc.umanitoba.ca [130.179.16.23]) by rutgers.rutgers.edu (8.8.8/8.8.8) with ESMTP id PAA03693 for ; Wed, 16 Aug 2000 15:14:09 -0400 (EDT) Received: from canopus.cc.umanitoba.ca (news@canopus.cc.umanitoba.ca [130.179.16.24]) by electra.cc.umanitoba.ca (8.9.0/8.9.0) with ESMTP id OAA26485 for ; Wed, 16 Aug 2000 14:14:06 -0500 (CDT) Received: (from news@localhost) by canopus.cc.umanitoba.ca (8.9.0/8.9.0) id OAA24255 for bionet-software-acedb@moderators.isc.org; Wed, 16 Aug 2000 14:14:05 -0500 (CDT) To: bionet-software-acedb@moderators.isc.org From: Brian Fristensky Newsgroups: bionet.software.acedb Subject: Resurrection of pop-up bug? Organization: University of Manitoba Message-ID: <399AE7FB.A7F8C87A@cc.umanitoba.ca> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: canopus.cc.umanitoba.ca 966453244 24253 130.179.16.30 (16 Aug 2000 19:14:04 GMT) X-Complaints-To: Postmaster@cc.umanitoba.ca NNTP-Posting-Date: 16 Aug 2000 19:14:04 GMT X-Mailer: Mozilla 4.7 [en] (X11; U; SunOS 5.8 sun4m) X-Accept-Language: en Date: Mon, 21 Aug 2000 15:38:44 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > Subject: Re: ACeDB bug in Solaris 7? > From: Ed Griffiths (edgrif@sanger.ac.uk) > Date: Thu 23 Dec 1999 - 08:53:05 GMT > > Jody, > > > I've developed a horrible bug with ACeDB 4.7e. I have a new Ultra60 > > which got Solaris 7 (MU 4) installed on it. Something is now terribly > > wrong. When I try to do anything at all, the ready on the main menu > > starts to flicker, ACeDB takes over the entire window manager and > > freezes the screen. It has to be killed from another terminal. When > > you look at the processes running, dtwm and Xsun are taking up all the > > processor and ACeDB is gobbling up memory. I got the newest GCC > > compiler and recompiled ACeDB. Same problem. > > > > I can answer this one, around this time someone inadvertantly intrduced a bug > into the code that controls acedb's version of pop-up dialogs. Basically this > bug tried to keep the dialog on top of all other windows on the screen by > calling an X routine to raise the window. Unfortunately the call to this routine ... stuff deleted... > > Later versions of 4_7 (I think we are to 4_7l) do not have this problem, I know, > I fixed it. I would suggest you get the latest 4_7 code and try it. If you still > have a problem then come back to me. > > ------------------------------------------------------------------------------ > > | Ed Griffiths, Informatics Group, | > | The Sanger Centre, Wellcome Trust Genome Campus, | > | Hinxton, Cambridge CB10 1SA, UK | > | | > | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | > | Tel: +44-1223-494780 (switch +44 1223 834244) Fax: +44 1223 494919 | > ------------------------------------------------------------------------------ We are now testing Solaris 8 using the CDE window manager. I have seen this exact problem with xace 4.71. Apparently, there is still a problem lurking somewhere. We never installed Solaris 7 here, so I can't verify the previous fix. -- =============================================================================== Brian Fristensky | To put genomics projects in perspective: Department of Plant Science | The Large Hadron Collider will "write University of Manitoba | data to a disk-based database at 100Mb/sec Winnipeg, MB R3T 2N2 CANADA | ... for 10 to 15 years... that's over frist@cc.umanitoba.ca | 100 petabytes of data, roughly the equiv- Office phone: 204-474-6085 | alent of 10 milllion PC hard disks." FAX: 204-474-7528 | http://home.cc.umanitoba.ca/~frist/ Science 286:1840 (1999) =============================================================================== From owner-acedb@hgmp.mrc.ac.uk Mon Aug 21 15:39:07 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0C6B917AC4; Mon, 21 Aug 2000 15:39:04 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 2FEBE17AC4; Mon, 21 Aug 2000 15:39:00 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id C06A817B6C; Wed, 16 Aug 2000 11:52:30 +0100 (BST) To: bionet-software-acedb@net.bio.net From: gwilliam@hgmp.mrc.ac.uk Newsgroups: bionet.software.acedb Subject: 1 Day ACeDB Training Course Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200008161052.LAA25084@tin.hgmp.mrc.ac.uk> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id C757917B68; Wed, 16 Aug 2000 11:52:28 +0100 (BST) X-Received: from tin.hgmp.mrc.ac.uk (tin [193.62.192.50]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 31C3E415DC for ; Wed, 16 Aug 2000 11:52:28 +0100 (BST) X-Received: (from gwilliam@localhost) by tin.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA25084 for acedb@hgmp.mrc.ac.uk; Wed, 16 Aug 2000 11:52:27 +0100 (BST) X-To: acedb@hgmp.mrc.ac.uk Date: Mon, 21 Aug 2000 15:39:00 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk The MRC HGMP is giving a 1-day training course on the use of ACeDB. Date: 7 September 2000 Venue: Cambridge University, UK Cost: 50 Pounds +VAT for registered academic users Contact: http://www.hgmp.mrc.ac.uk/About/Courses/comp.regist.html 1-Day course brief description ------------------------------ An Introduction to ACEDB software using C. elegans and human genome databases. The course will be run on UNIX-based computers. USING THE XACE EXECUTABLE Navigating around the various window displays : text, genetic map, physical map, sequence display, pepmap, grids, forest display, pathways, dendrograms, bibliography tool, DNA analysis, blixem and dotter alignment tools. Dumping out data. Reading in data. Keyset manipulation. Query Language. Table-Maker. Configuring displays. Genefinder. INTRODUCTION TO OTHER EXECUTABLES Brief overview of tace, giface, AceBrowser. ACEDB RESOURCES ACEDB homepages, newsgroups, bug reports. ftp site. code versions. Teachers : Sylvia Martinelli Adam Butler Queries about the teaching material to : sylvia@sanger.ac.uk apb@sanger.ac.uk Course Registration Contact : http://www.hgmp.mrc.ac.uk/About/Courses/comp.regist.html --- From owner-acedb@hgmp.mrc.ac.uk Mon Aug 21 15:39:14 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id BD26617B1D; Mon, 21 Aug 2000 15:39:13 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 6DD2117AC4; Mon, 21 Aug 2000 15:39:12 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 62F6017A9A; Sun, 20 Aug 2000 02:09:56 +0100 (BST) Received: from moderated.news.pipex.net (moderated.news.pipex.net [158.43.192.79]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 675DC415DA for ; Sun, 20 Aug 2000 02:09:55 +0100 (BST) Received: (qmail 8810 invoked by alias); 20 Aug 2000 01:09:54 -0000 Received: (qmail 8806 invoked from network); 20 Aug 2000 01:09:54 -0000 Received: from electra.cc.umanitoba.ca (130.179.16.23) by moderated.news.pipex.net with SMTP; 20 Aug 2000 01:09:54 -0000 Received: from canopus.cc.umanitoba.ca (news@canopus.cc.umanitoba.ca [130.179.16.24]) by electra.cc.umanitoba.ca (8.9.0/8.9.0) with ESMTP id UAA14523 for ; Sat, 19 Aug 2000 20:09:51 -0500 (CDT) Received: (from news@localhost) by canopus.cc.umanitoba.ca (8.9.0/8.9.0) id UAA25402 for bionet-software-acedb@moderators.isc.org; Sat, 19 Aug 2000 20:09:51 -0500 (CDT) To: bionet-software-acedb@moderators.isc.org From: Brian Fristensky Newsgroups: bionet.software.acedb Subject: Re: xace looping on solaris 7 Organization: University of Manitoba Message-ID: <399F2FDE.BBE0CB37@cc.umanitoba.ca> References: <200007140313.XAA18851@ray.nlm.nih.gov> <397567DA.D5C94EB6@sanger.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: canopus.cc.umanitoba.ca 966733791 25400 130.179.16.120 (20 Aug 2000 01:09:51 GMT) X-Complaints-To: Postmaster@cc.umanitoba.ca NNTP-Posting-Date: 20 Aug 2000 01:09:51 GMT X-Mailer: Mozilla 4.7 [en] (X11; U; SunOS 5.6 sun4u) X-Accept-Language: en Date: Mon, 21 Aug 2000 15:39:12 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Ed Griffiths wrote: > > Probably worth noting: > > > Ed and I have just fixed a bug that plagued > > all versions of acedb (4.7 and 4.8) on recent solaris > > machine (sparc and intel alike) > > the behaviour was: when you covered the mainwindow > > the whole screen would freze because of acedb creating > > an X11 event loop. > > you had essentially to kill xace and restart the window > > manager. > > > > the fix is simple and i will update the 4.7 distrib > > As far as we know this does not affect the 4_8c version, if you have Solaris 5.7 > and could test xace from acedb 4_8c we would be grateful (download the July > build available as Sanger-release.2000_07_14.tar.gz from the ftp site). > > > i just fixed also a simple bug that prevents the > > development release of aceserver to work. may be nobody saw > > that bug but the behavious was a message 'cannot connect' > > from the client > > Yup, I also fixed this, it was a trivial mistake in both 4_7 and 4_8 code. > I just observed similar behavior on Solaris 8, with xace 4.71. In my case, if I went to the main keyset and clicked on an object, the 'Ready' box would keep flashing and lockup the screen. The entire CDE session would have to be killed remotely. It works fine on machines running Solaris 6. (We skipped Solaris 7 entirely, so I have no data on 7). Is xace 4.8 close enough to being a "production release" that I should install that, or should I wait for a fix in 4.7? -- =============================================================================== Brian Fristensky | To put genomics projects in perspective: Department of Plant Science | The Large Hadron Collider will "write University of Manitoba | data to a disk-based database at 100Mb/sec Winnipeg, MB R3T 2N2 CANADA | ... for 10 to 15 years... that's over frist@cc.umanitoba.ca | 100 petabytes of data, roughly the equiv- Office phone: 204-474-6085 | alent of 10 milllion PC hard disks." FAX: 204-474-7528 | http://home.cc.umanitoba.ca/~frist/ Science 286:1840 (1999) =============================================================================== From owner-acedb@hgmp.mrc.ac.uk Tue Aug 22 13:51:29 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 81A6317B3D; Tue, 22 Aug 2000 13:51:28 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 08B7F17B3B; Tue, 22 Aug 2000 13:51:26 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id A752D17A69; Tue, 22 Aug 2000 10:35:08 +0100 (BST) Received: from rutgers.rutgers.edu (bsd.rutgers.edu [165.230.4.71]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id F0599415D4 for ; Tue, 22 Aug 2000 10:35:06 +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 FAA08743 for ; Tue, 22 Aug 2000 05:35:05 -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 13RASG-0003K0-00 for bionet-software-acedb@moderators.isc.org; Tue, 22 Aug 2000 10:34:48 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13RASS-0003V2-00; Tue, 22 Aug 2000 10:35:00 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Re: how to record blast results? Organization: ACS, The University of Nottingham Message-ID: References: <3997E288.15B7F617@mpiz-koeln.mpg.de> Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 966936900 13442 128.243.116.150 (22 Aug 2000 09:35:00 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 22 Aug 2000 09:35:00 GMT To: Kurt Stueber X-Sender: keith@thale Date: Tue, 22 Aug 2000 13:51:26 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk On 21 Aug 2000, Kurt Stueber wrote: > Dear colleages, > > I would like to record the results of blastn searches in acedb. > Looking at the models.wrm file I found the line > in the model for "sequence": > > homol DNA_homol ?sequence XREF DNA_homol ?Method Float Int Int Int Int > #Homol_info > > This looks like the place to store homologies. Is there > a place where I can find out what the five number > (one float and 4 integers) are designed to stand for? The floating point number holds the actual blast score. Most blast programs give you two scores for how good a match is. One of these scores is the raw score and is an integer. The second is a score measured in 'bits' (a unit of information content) and is a floating point number. This score allows you to make comparisons between blast results from different datasets...the raw score on its own is not that useful if you want to make comparisons. You should probably use the score in bits for the 'Float' field of the DNA homology info, but that's up to you. The remaining four numbers simply specify two sets of coordinates for the query and matched sequence. E.g. consider the following (very short) ace file: Sequence : "EMBL:AI618741" DNA_homol "EMBL:AC009513" "BLASTN_EST" 547 4 279 47153 47428 This query sequence (AI618741) has a match to AC009513. The blast score is 547, the actual match is between bases 4..279 on the query sequence and 47,153..47,428 on the other sequence. Hope this helps, 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 Aug 22 17:51:21 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B453D17B54; Tue, 22 Aug 2000 17:51:20 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 23BC517B5A; Tue, 22 Aug 2000 17:51:18 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 937D517B54; Tue, 22 Aug 2000 17:49:59 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 1AF57415D5 for ; Tue, 22 Aug 2000 17:49:59 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA02108 for bionet-software-acedb@net.bio.net; Tue, 22 Aug 2000 17:49:58 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: xace looping on solaris 7 Organization: Sanger Centre Message-ID: <39A2AF36.FDFBB5C4@sanger.ac.uk> References: <200007140313.XAA18851@ray.nlm.nih.gov> <397567DA.D5C94EB6@sanger.ac.uk> <399F2FDE.BBE0CB37@cc.umanitoba.ca> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 966962998 2106 193.60.84.177 (22 Aug 2000 16:49:58 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 22 Aug 2000 16:49:58 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Tue, 22 Aug 2000 17:51:18 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk OK, as Jean wrote: > > > Ed and I have just fixed a bug that plagued > > > all versions of acedb (4.7 and 4.8) on recent solaris > > > machine (sparc and intel alike) > > > the behaviour was: when you covered the mainwindow > > > the whole screen would freze because of acedb creating > > > an X11 event loop. > > > you had essentially to kill xace and restart the window > > > manager. > > > > > > the fix is simple and i will update the 4.7 distrib --------------------------------- So as Brian has observerd, the bug is in 4_7: > I just observed similar behavior on Solaris 8, with xace 4.71. > Is xace 4.8 close enough to being a "production release" that > I should install that, or should I wait for a fix > in 4.7? but the fix is not yet out there !! We hope that 4.8 will be out this month or early next month, in the meantime I will try to put the fixed code on the ftp site this week. 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 Aug 22 17:51:29 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id CA52617B54; Tue, 22 Aug 2000 17:51:28 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id BD08017B57; Tue, 22 Aug 2000 17:51:18 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 352FE17B4A; Tue, 22 Aug 2000 17:16:07 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 94656415DA for ; Tue, 22 Aug 2000 17:16:06 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id RAA01738 for bionet-software-acedb@net.bio.net; Tue, 22 Aug 2000 17:16:06 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: Which file? Organization: Sanger Centre Message-ID: <39A2A745.AACE3B14@sanger.ac.uk> References: <39899B04.37111ACC@har.mrc.ac.uk> <398A756A.97F8D037@sanger.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 966960965 1735 193.60.84.177 (22 Aug 2000 16:16:05 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 22 Aug 2000 16:16:05 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Tue, 22 Aug 2000 17:51:18 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk More on the below problem.... > > EXIT: Model screwup: impossible level line 6 > > > > Do you know which file this would be referring to? I did not alter line > > 6 of > > models.wrm or any other file. > Just had this suggestion from Luc Ducazu: > I had the same problem a few months ago. If I can remember correctly, this > was a DOS/UNIX related 'line feed - carriage return' problem. You may want to check that the models file has not got mashed with DOS style end of lines...?? 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 Aug 23 15:18:49 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2597517B07; Wed, 23 Aug 2000 15:18:46 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C645A17ADA; Wed, 23 Aug 2000 15:18:42 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 04C3D17ADA; Wed, 23 Aug 2000 15:18:04 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 6F277415D5 for ; Wed, 23 Aug 2000 15:18:04 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA26421 for bionet-software-acedb@net.bio.net; Wed, 23 Aug 2000 15:18:04 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Acedb Monthly Newsletter Organization: Sanger Centre Message-ID: <39A3DD1B.913A3EBD@sanger.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 967040283 26419 193.60.84.177 (23 Aug 2000 14:18:03 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 23 Aug 2000 14:18:03 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Wed, 23 Aug 2000 15:18:42 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Just a gentle reminder that each month I put out a newsletter about acedb and would welcome contributions to it, e.g. perhaps a few paragraphs on your favourite model, database recovery or whatever... 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 Aug 25 09:09:18 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0281617B09; Fri, 25 Aug 2000 09:09:17 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 527C417B06; Fri, 25 Aug 2000 09:09:16 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 65C8217AE3; Thu, 24 Aug 2000 18:42:41 +0100 (BST) Received: from chx400.switch.ch (chx400.switch.ch [130.59.10.2]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A05F6415DA for ; Thu, 24 Aug 2000 18:42:40 +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 13S11T-0004us-00 for bionet-software-acedb@moderators.isc.org; Thu, 24 Aug 2000 19:42:39 +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 13S10w-0003pt-00 for bionet-software-acedb@moderators.isc.org; Thu, 24 Aug 2000 18:42:06 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13S11C-0002HV-00; Thu, 24 Aug 2000 18:42:22 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: AceBrowser/gifaceserver problem viewing maps 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 967138942 8771 128.243.116.150 (24 Aug 2000 17:42:22 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 24 Aug 2000 17:42:22 GMT X-Sender: keith@thale Date: Fri, 25 Aug 2000 09:09:16 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello, I've been in the process of moving our acedb databases to a new system. After many headaches, I seemed to reach the point where AceBrowser was behaving normally. However, I then noticed that I can't view certain map objects as pictures without getting the error: "The ACEDB server was unable to generate a picture of this object, please return to text mode". What is confusing me is that everything else seems to be ok and I can view other images (e.g. sequences), I can also view some of the other maps in our database with no problems. E.g. go to: http://flora.nottingham.ac.uk/perl/ace/search/AGR and select the 'Map' class and then any of the 'classical' maps. It is only our 'Physical' and 'Recombinant Inbred' maps which exhibit this behaviour. I assume that the error message is being generated by the following subroutine in the AceBrowser 'pic' script: unless (-e $image_file && -M $image_file < 0) { local(*F); open (F,">$image_file") || AceError("Can't open image file $image_file for writing: $!\n"); print F $gif || unpack("u",ERROR_GIF); close F; } Has anyone else experienced anything similar??? I can't see why it is failing for just one type of image. I've checked the server.log file and nothing appears as unusual. Regardless of which map you choose and whether the map appears or not, you get the same type of output, e.g. Client 1 (1 active). Query: Client 1 (1 active). Query: find Map "Physical-III" Client 1 (1 active). Query: list -j -b 0 Client 1 (1 active). Query: gif display Map "Physical-III" ; Dimensions 1024 768 ; gifdump - gifaceserver seems to try and generate the image and our /ace_images folder on our web server contains the appropriately named files in the /AGR/Map subdirectory, only these images are the error message gif rather than a gif of the map. Any ideas??? We have all the latest software, e.g. Perl 5.6.0 acedb 4.7l (server and client) AcePerl 1.62 AceBrowser 2.10 mod_perl 1.24 all running on Tru64 UNIX 5.0a. Any help welcome, 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 Aug 25 09:09:29 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 09BC617B0B; Fri, 25 Aug 2000 09:09:28 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3C7E617B09; Fri, 25 Aug 2000 09:09:27 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 3773517AF7; Thu, 24 Aug 2000 19:46:38 +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 1B562415DC for ; Thu, 24 Aug 2000 19:46:37 +0100 (BST) Received: from tpsmtp1.mail.portal by chi6sosrv11.alter.net with ESMTP (peer crosschecked as: olemail.terra.es [213.4.90.160]) id QQjdqx18076 for ; Thu, 24 Aug 2000 18:45:46 GMT Received: from telenews.teleline.es ([172.27.200.11]) by tpsmtp1.mail.portal (Netscape Messaging Server 4.1) with ESMTP id FZT82L01.R6D for ; Thu, 24 Aug 2000 20:44:45 +0200 Received: (from newsuser@localhost) by telenews.teleline.es (8.8.8+Sun/8.8.8) id UAA05917; Thu, 24 Aug 2000 20:46:56 +0200 (MET DST) To: bionet-software-acedb@moderators.isc.org From: tykvmg@e.com Newsgroups: bionet.software.acedb Subject: Is this for you? Message-ID: X-Complaints-To: usenet@teleline.es X-Trace: telenews.teleline.es 967142792 62.82.120.100 (Thu, 24 Aug 2000 20:46:32 MET DST) NNTP-Posting-Date: Thu, 24 Aug 2000 20:46:32 MET DST Organization: Clientes_Teleline Date: Fri, 25 Aug 2000 09:09:27 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Go to: http://usuarios.tripod.es/revistapandora From owner-acedb@hgmp.mrc.ac.uk Fri Aug 25 09:09:43 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 61A3917B0C; Fri, 25 Aug 2000 09:09:42 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id B19B917B0B; Fri, 25 Aug 2000 09:09:40 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 265A517AFD; Fri, 25 Aug 2000 08:17:37 +0100 (BST) Received: from jerry.har.mrc.ac.uk.har.mrc.ac.uk (jerry.har.mrc.ac.uk [193.63.70.145]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 0FAAA415E0 for ; Fri, 25 Aug 2000 08:17:35 +0100 (BST) Received: from har.mrc.ac.uk (cheetera [130.246.241.12]) by jerry.har.mrc.ac.uk.har.mrc.ac.uk (8.9.3/8.9.1) with ESMTP id IAA02169; Fri, 25 Aug 2000 08:17:28 +0100 (BST) Message-ID: <39A61D89.E288D042@har.mrc.ac.uk> From: Ashwin X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Ed Griffiths , bionet-software-acedb@net.bio.net Subject: Re: Which file? References: <39899B04.37111ACC@har.mrc.ac.uk> <398A756A.97F8D037@sanger.ac.uk> <39A2A745.AACE3B14@sanger.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Newsgroups: bionet.software.acedb Date: Fri, 25 Aug 2000 09:09:40 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi, That seems familiar- we were finding that editing the models in MS word kept putting "^M" at the end of every line. We've worked out how to get rid of them (zip and unzip into UNIX). It turned out in the end that revising the model needed a two line insertion, rather that the grand scheme that I was attempting! Thanks to everyone for their help, Ashwin Ed Griffiths wrote: > More on the below problem.... > > > > EXIT: Model screwup: impossible level line 6 > > > > > > Do you know which file this would be referring to? I did not alter line > > > 6 of > > > models.wrm or any other file. > > > > Just had this suggestion from Luc Ducazu: > > > I had the same problem a few months ago. If I can remember correctly, this > > was a DOS/UNIX related 'line feed - carriage return' problem. > > You may want to check that the models file has not got mashed with DOS style end > of lines...?? > > 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 Aug 25 12:27:59 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7A37B17B0E; Fri, 25 Aug 2000 12:27:58 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 2C49617ADF; Fri, 25 Aug 2000 12:27:57 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id A2F9317A61; Fri, 25 Aug 2000 12:10:53 +0100 (BST) Received: from isgate.is (isgate.is [193.4.58.51]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B5330415DF for ; Fri, 25 Aug 2000 12:10:51 +0100 (BST) Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by isgate.is (8.9.3r/8.9.0Imo) with ESMTP id LAA01170 for ; Fri, 25 Aug 2000 11:10:47 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 13SHNU-0002dJ-00 for bionet-software-acedb@moderators.isc.org; Fri, 25 Aug 2000 12:10:28 +0100 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 13SHNk-00023G-00; Fri, 25 Aug 2000 12:10:44 +0100 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: Re: AceBrowser/gifaceserver problem viewing maps Organization: ACS, The University of Nottingham Message-ID: References: Reply-To: Keith Bradnam Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 967201844 7888 128.243.116.150 (25 Aug 2000 11:10:44 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 25 Aug 2000 11:10:44 GMT X-Sender: keith@thale Date: Fri, 25 Aug 2000 12:27:57 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk OK, I've fixed the problem so I guess I should say what the problem was just in case anybody else runs into it. gifaceserver seemed to be falling over when generating certain images because of memory problems. If I tried viewing the same images using xace then it crashes reporting a memory error (took me a while to realise this as I usually have run xace after first using the unlimit command). Raising the datasize limit to about 150000 kb seems to be enough to cope, but I've raised it to about 500000 kb to be sure. As gifaceserver runs from my user account, I had to modify .cshrc to specify the new limit. Not sure whether I should also modify the stacksize limit as well and increase it from the default 8192 kb?? 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 Aug 25 12:48:34 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id F3C6217B0F; Fri, 25 Aug 2000 12:48:33 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 9B51017B01; Fri, 25 Aug 2000 12:48:32 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id B6BFE17B0F; Fri, 25 Aug 2000 12:46:49 +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 7EC2C415D4; Fri, 25 Aug 2000 12:46:48 +0100 (BST) Received: from griffin.sanger.ac.uk (root@griffin [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id MAA28840; Fri, 25 Aug 2000 12:46:41 +0100 (BST) Received: from localhost (edgrif@localhost [127.0.0.1]) by griffin.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id MAA15141; Fri, 25 Aug 2000 12:46:40 +0100 (BST) From: Ed Griffiths To: Acedb Development Team , acedb user group , informaticsg@sanger.ac.uk, bionet-software-acedb@net.bio.net Subject: CDS tags.... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Newsgroups: bionet.software.acedb Date: Fri, 25 Aug 2000 12:48:32 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk All, In fixing a couple of bugs to do with protein display from xace I came across an inconsistency that would be worth fixing: If you are looking at some sequence object such as a supported CDS, then it will have a series of exons specified something like this: Structure From Source bA404F10 Source_Exons 1 82 26575 26877 30296 30562 The model/code allows you to specify the CDS start/end within the source_exons: Properties Coding CDS BUT currently the start/end values must be specified in the coordinate system of the spliced dna, not the above coordinate system. If you specified 30500 as the coordinate where you wanted the coding to stop you would get a surprise as this will lead the protein display window to display vast numbers of 'X's where it has run off the end of the spliced DNA, in the above example the spliced DNA is only 652 long.... It would make more sense to me if you could specify a start/end in the coordinate frame of the Source_Exons and then the code did the translation to the spliced dna. I don't want to make this change however until I've got your opinions on it because I know that people often store values in acedb that they later extract via ace dumps and perl script filtering and I don't want to mess that up. Pleass send me a note if you have an opinion on this... cheers Ed p.s. please restrict yourself to this very specific problem, if you think the model should all be completely different, that's a separate matter. (I don't want to stifle discussion, but I don't want to start off a landslide of discussion either...) ------------------------------------------------------------------------ | 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 Aug 25 13:49:00 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5F8C017B16; Fri, 25 Aug 2000 13:48:59 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 2A39117B12; Fri, 25 Aug 2000 13:48:58 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 6DDA917B0D; Fri, 25 Aug 2000 13:41:37 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id A362F415D5 for ; Fri, 25 Aug 2000 13:41:36 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id NAA17391 for bionet-software-acedb@net.bio.net; Fri, 25 Aug 2000 13:41:36 +0100 (BST) To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: AceBrowser/gifaceserver problem viewing maps Organization: Sanger Centre Message-ID: <39A6697F.6EA40C5E@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 967207296 17389 193.60.84.177 (25 Aug 2000 12:41:36 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 25 Aug 2000 12:41:36 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Fri, 25 Aug 2000 13:48:58 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Keith, > Raising the datasize limit to about 150000 kb seems to be enough to cope, > but I've raised it to about 500000 kb to be sure. As gifaceserver runs > from my user account, I had to modify .cshrc to specify the new limit. > Not sure whether I should also modify the stacksize limit as well and > increase it from the default 8192 kb?? The below is for unix, I don't know what happens on Windows... OK, this is a fairly common problem, for large databases acedb can be fairly memory intensive both in terms of how much heap and stack space it uses. The former is restricted by the data segment limit and the latter by the stacksize limit for a users process. The initial values for these are set up by whoever installed the system, from the shell you can use the limit or ulimit commands to change these limits. We can insert some code so that when a malloc call fails (= heap allocation) then we could see what the users datasize limit is and check to see if this is the problem, then our error message could be more informative. This won't be possible on all systems because it needs the get/setrlimit calls to be available. The situation for running out of stack space is not easily remedied, the process will probably receive a SIGSEGV which is the same as when we have a program error due to messed up pointers. The only thing we could do is check for a very small stack size but I'm not happy to mask potential coding errors with a confusing error message. I'll put some code in to try and give a better error message for when mallocs fail. 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 Aug 25 16:37:56 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0762117B1E; Fri, 25 Aug 2000 16:37:55 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 4C83A17A79; Fri, 25 Aug 2000 16:37:54 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 9B2E917B22; Fri, 25 Aug 2000 15:40:37 +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 ADAA3415DD; Fri, 25 Aug 2000 15:40:36 +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 PAA12314; Fri, 25 Aug 2000 15:40:31 +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 PAA22013; Fri, 25 Aug 2000 15:40:31 +0100 (BST) From: James Gilbert To: Ed Griffiths acedb user group , informaticsg@sanger.ac.uk, bionet-software-acedb@net.bio.net Subject: Re: CDS tags.... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Newsgroups: bionet.software.acedb Date: Fri, 25 Aug 2000 16:37:54 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Changing to unspliced coordinates would be a good plan as far as I'm concerned. James On Fri, 25 Aug 2000, Ed Griffiths wrote: > All, > > In fixing a couple of bugs to do with protein display from xace I came across an > inconsistency that would be worth fixing: > > If you are looking at some sequence object such as a supported CDS, then it will > have a series of exons specified something like this: > > > Structure From Source bA404F10 > Source_Exons 1 82 > 26575 26877 > 30296 30562 > > > The model/code allows you to specify the CDS start/end within the source_exons: > > Properties > Coding CDS > > BUT currently the start/end values must be specified in the coordinate system > of the spliced dna, not the above coordinate system. If you specified 30500 as > the coordinate where you wanted the coding to stop you would get a surprise as > this will lead the protein display window to display vast numbers of 'X's where > it has run off the end of the spliced DNA, in the above example the spliced DNA > is only 652 long.... > > It would make more sense to me if you could specify a start/end in the > coordinate frame of the Source_Exons and then the code did the translation to > the spliced dna. > > I don't want to make this change however until I've got your opinions on it > because I know that people often store values in acedb that they later extract > via ace dumps and perl script filtering and I don't want to mess that up. > > Pleass send me a note if you have an opinion on this... > > cheers Ed > > p.s. please restrict yourself to this very specific problem, if you think the > model should all be completely different, that's a separate matter. (I don't > want to stifle discussion, but I don't want to start off a landslide of > discussion either...) > > ------------------------------------------------------------------------ > | 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 | > ------------------------------------------------------------------------ > 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 Mon Aug 28 09:09:50 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id AE0B817ABC; Mon, 28 Aug 2000 09:09:49 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 908C017A9E; Mon, 28 Aug 2000 09:09:48 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id D87CB17A63; Sat, 26 Aug 2000 00:02:26 +0100 (BST) Received: from rutgers.rutgers.edu (bsd.rutgers.edu [165.230.4.71]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 508DE415DA for ; Sat, 26 Aug 2000 00:02:25 +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 TAA19301 for ; Fri, 25 Aug 2000 19:02:23 -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 TAA17945; Fri, 25 Aug 2000 19:02:21 -0400 (EDT) Received: (from mieg@localhost) by ray.nlm.nih.gov (8.9.3+Sun/8.9.3) id TAA01154; Fri, 25 Aug 2000 19:02:20 -0400 (EDT) From: Jean Thierry-Mieg Message-Id: <200008252302.TAA01154@ray.nlm.nih.gov> To: bionet-software-acedb@moderators.isc.org, keith@thale.life.nottingham.ac.uk Subject: Re: AceBrowser/gifaceserver problem viewing maps Newsgroups: bionet.software.acedb Date: Mon, 28 Aug 2000 09:09:48 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk i recommend limit datasize unlimited limit stacksize 20000 limit coredumpsize 0 From owner-acedb@hgmp.mrc.ac.uk Mon Aug 28 09:10:00 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 130C717AC0; Mon, 28 Aug 2000 09:09:59 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id D202D17ABC; Mon, 28 Aug 2000 09:09:58 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 21C6417A63; Sat, 26 Aug 2000 00:05:59 +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 8E17F415DF for ; Sat, 26 Aug 2000 00:05:48 +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 TAA18602; Fri, 25 Aug 2000 19:05:44 -0400 (EDT) Received: (from mieg@localhost) by ray.nlm.nih.gov (8.9.3+Sun/8.9.3) id TAA01538; Fri, 25 Aug 2000 19:05:43 -0400 (EDT) From: Jean Thierry-Mieg Message-Id: <200008252305.TAA01538@ray.nlm.nih.gov> To: acedb@sanger.ac.uk, acedbg@sanger.ac.uk, bionet-software-acedb@net.bio.net, edgrif@sanger.ac.uk, informaticsg@sanger.ac.uk Subject: Re: CDS tags.... Newsgroups: bionet.software.acedb Date: Mon, 28 Aug 2000 09:09:58 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk no if we keep everything nearly as is then the splicing gives a mrna and the CDS must be (as it is now) in spliced coordinates it is meeningless biologically to give in in unspliced coords although i agree it is nasty for the programmer really we would need an additional levl of obj or ebe even 2 leles gen, mrna (the currnet ill named genes), CDS, protein From owner-acedb@hgmp.mrc.ac.uk Mon Aug 28 17:26:56 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B50DF17AB0; Mon, 28 Aug 2000 17:26:55 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 9ACC517AA6; Mon, 28 Aug 2000 17:26:54 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 6BA2C17AC9; Mon, 28 Aug 2000 13:03:32 +0100 (BST) To: bionet-software-acedb@net.bio.net From: ralph.gauges@eml.villa-bosch.de (Ralph Gauges) Newsgroups: bionet.software.acedb Subject: Uniqueness of tags? Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <39AA550F.25B214C9@eml.villa-bosch.de> 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 205F817AC1; Mon, 28 Aug 2000 13:03:30 +0100 (BST) X-Received: from ktaemail01.villa-bosch.de (tigershark.villa-bosch.de [195.185.79.56]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 54611415DD for ; Mon, 28 Aug 2000 13:03:29 +0100 (BST) X-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 RLBTRSWP; Mon, 28 Aug 2000 13:59:47 +0200 X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.16 i686) X-Accept-Language: en X-To: acedb@net.bio.net Date: Mon, 28 Aug 2000 17:26:54 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi, I am currently trying to automate the process of generating an acedb model file from an object oriented database model. Since acedb does not provide inheritance, I have to find a way around this. What I tried to do is instead of having a pointer to the base class, (which could only hold a pointer to the base class and not to all subclasses, as I need it) I use a UNIQUE List of pointers to the base class and all subclasses which looks something like this: ?BaseClass1 sometags.... ?Sub1BaseClass1 get all attributes from BaseClass1 + some extra ?Sub2BaseClass1 get all attributes from BaseClass1 + some extra ?BaseClass2 UNIQUE PointsTo ?BaseClass1 PointsTo ?Sub1BaseClass1 PointsTo ?Sub2BaseClass1 But in some document it was stated that all tag names have to be unique within a model. What I was wondering now is if those tag names would be considered unique, since there would be only one in an actual instance, or is something like this forbidden? If this is not allowed, how could I solve the inheritance problem? Thanks a lot Ralph --- From owner-acedb@hgmp.mrc.ac.uk Tue Aug 29 09:41:53 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 533A817B01; Tue, 29 Aug 2000 09:41:52 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3F7F117AFA; Tue, 29 Aug 2000 09:41:50 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 88E5317B02; Tue, 29 Aug 2000 09:39:00 +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 18F23415DE; Tue, 29 Aug 2000 09:38:58 +0100 (BST) Received: from griffin.sanger.ac.uk (rd@griffin [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id JAA01146; Tue, 29 Aug 2000 09:36:17 +0100 (BST) From: Richard Durbin Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id JAA28727; Tue, 29 Aug 2000 09:36:17 +0100 (BST) Message-Id: <200008290836.JAA28727@griffin.sanger.ac.uk> To: acedb@sanger.ac.uk, acedbg@sanger.ac.uk, bionet-software-acedb@net.bio.net, edgrif@sanger.ac.uk, informaticsg@sanger.ac.uk Subject: Re: CDS tags.... Newsgroups: bionet.software.acedb Date: Tue, 29 Aug 2000 09:41:50 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > BUT currently the start/end values must be specified in the coordinate system > of the spliced dna, not the above coordinate system. This was intentional. In fact it is more work to do it this way than by specifying start/end in the coordinate frame of the Source_Exons. The principle is that coordinates in an acedb sequence object should be with respect to the DNA that is represented by the object. In my view, the Source_exons information is in the wrong place (should be in the parent, or done with Exon/Intron objects), but that is another story, as Ed says. Richard From owner-acedb@hgmp.mrc.ac.uk Tue Aug 29 14:18:05 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C7B1E17B0F; Tue, 29 Aug 2000 14:18:04 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 8152B17A9F; Tue, 29 Aug 2000 14:18:03 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 7DA1717B0F; Tue, 29 Aug 2000 13:49:12 +0100 (BST) Received: from dfw7-1.relay.mail.uu.net (dfw7-1.relay.mail.uu.net [199.171.54.106]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 49EB5415D4 for ; Tue, 29 Aug 2000 13:49:10 +0100 (BST) Received: from chiark.greenend.org.uk by dfw7sosrv11.alter.net with ESMTP (peer crosschecked as: chiark.greenend.org.uk [195.224.76.132]) id QQjeil17742 for ; Tue, 29 Aug 2000 12:49:08 GMT Received: from news by chiark.greenend.org.uk with local (Exim 2.05 #1) id 13Tkp9-0002LV-00 (Debian); Tue, 29 Aug 2000 13:49:07 +0100 To: bionet-software-acedb@uunet.uu.net From: Tim Cutts Newsgroups: bionet.software.acedb Subject: Re: CDS tags.... Organization: Linux Unlimited Message-ID: References: <200008290836.JAA28727@griffin.sanger.ac.uk> X-Newsreader: trn 4.0-test70 (17 January 1999) Date: Tue, 29 Aug 2000 14:18:03 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk In article <200008290836.JAA28727@griffin.sanger.ac.uk>, Richard Durbin wrote: >> BUT currently the start/end values must be specified in the coordinate system >> of the spliced dna, not the above coordinate system. > >This was intentional. In fact it is more work to do it this way than by >specifying >start/end in the coordinate frame of the Source_Exons. The principle is that >coordinates in an acedb sequence object should be with respect to the >DNA that is >represented by the object. In my view, the Source_exons information is in the >wrong place (should be in the parent, or done with Exon/Intron objects), >but that >is another story, as Ed says. I agree. The ideal solution would be distinct intron-exon objects (which could then, perhaps, be shared by transcripts, which would probably give a clearer picture of alternative splicing). As it is, I'd rather keep the spliced coordinates. I do a lot of processing with CDSs in perl, and once I've constructed the mRNA using the Source_Exon values, finding the CDS sequence is trivial using spliced coordinates. Leave it the way it is, Ed! Tim. From owner-acedb@hgmp.mrc.ac.uk Tue Aug 29 14:18:15 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 9671917B0F; Tue, 29 Aug 2000 14:18:14 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 54BF017B0C; Tue, 29 Aug 2000 14:18:13 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 27A7217B03; Tue, 29 Aug 2000 11:11:35 +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 2A769415DC; Tue, 29 Aug 2000 11:11:32 +0100 (BST) Received: from rock.sanger.ac.uk (root@rock [193.60.84.238]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id LAA12964; Tue, 29 Aug 2000 11:07:12 +0100 (BST) Received: from localhost (id1@localhost [127.0.0.1]) by rock.sanger.ac.uk (8.8.7/8.8.7) with SMTP id LAA26435; Tue, 29 Aug 2000 11:07:06 +0100 (BST) Message-Id: <200008291007.LAA26435@rock.sanger.ac.uk> X-Authentication-Warning: rock.sanger.ac.uk: id1@localhost [127.0.0.1] didn't use HELO protocol To: rd@sanger.ac.uk Subject: Re: CDS tags.... bionet-software-acedb@net.bio.net, edgrif@sanger.ac.uk, informaticsg@sanger.ac.uk From: id1@sanger.ac.uk X-Mts: smtp Newsgroups: bionet.software.acedb Date: Tue, 29 Aug 2000 14:18:13 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk 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). 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. 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 believe that this must be what was originally intended but it isn't getting used like this in the human databases at least. Cheers Ian From owner-acedb@hgmp.mrc.ac.uk Tue Aug 29 14:30:16 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 5C8DF17B14; Tue, 29 Aug 2000 14:30:16 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 97E4A17B10; Tue, 29 Aug 2000 14:30:14 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 292BB17B13; Tue, 29 Aug 2000 14:25:12 +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 9F741415D4; Tue, 29 Aug 2000 14:25:11 +0100 (BST) Received: from griffin.sanger.ac.uk (root@griffin [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id OAA32578; Tue, 29 Aug 2000 14:22:01 +0100 (BST) Received: from localhost (edgrif@localhost [127.0.0.1]) by griffin.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id OAA28476; Tue, 29 Aug 2000 14:22:01 +0100 (BST) From: Ed Griffiths To: id1@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, 29 Aug 2000 14:30:14 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk 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. > 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.... 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 Aug 29 14:30:26 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1C27217B13; Tue, 29 Aug 2000 14:30:26 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id EB6A717B14; Tue, 29 Aug 2000 14:30:24 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id F0A6717B10; Tue, 29 Aug 2000 14:29:21 +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 5E23A415D4 for ; Tue, 29 Aug 2000 14:29:20 +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 QQjein28844 for ; Tue, 29 Aug 2000 13:29:14 GMT Received: from griffin.sanger.ac.uk (root@griffin [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id OAA32726; Tue, 29 Aug 2000 14:29:12 +0100 (BST) Received: from localhost (edgrif@localhost [127.0.0.1]) by griffin.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id OAA29816; Tue, 29 Aug 2000 14:29:12 +0100 (BST) From: Ed Griffiths To: Tim Cutts Subject: Re: CDS tags.... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Newsgroups: bionet.software.acedb Date: Tue, 29 Aug 2000 14:30:24 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Tim, > I agree. The ideal solution would be distinct intron-exon objects > (which could then, perhaps, be shared by transcripts, which would > probably give a clearer picture of alternative splicing). OK, I think everyone would like to see this... > As it is, I'd rather keep the spliced coordinates. I do a lot of > processing with CDSs in perl, and once I've constructed the mRNA using > the Source_Exon values, finding the CDS sequence is trivial using > spliced coordinates. Leave it the way it is, Ed! Let me emphasise that no change has been made to the coordinate frame for the CDSs, its all just as it was... What I have done is fix a bug whereby, for reverse strand CDS objects, if you wished to specify a start position, you were forced to specify both the start and end positions of the CDS before the fmap code recognised the new start position. This fix is in Augusts build. 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 Aug 30 09:49:45 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A632317AB8; Wed, 30 Aug 2000 09:49:44 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id CDE8817AB8; Wed, 30 Aug 2000 09:49:41 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id EE4F117A77; Wed, 30 Aug 2000 07:46:19 +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 024B5415DA for ; Wed, 30 Aug 2000 07:46:18 +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 RLBTRT85; Wed, 30 Aug 2000 08:42:35 +0200 Message-ID: <39ACADB6.24BE9700@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: bionet-software-acedb@net.bio.net Subject: Re: Uniqueness of tags? References: <200008291654.RAA30570@griffin.sanger.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Newsgroups: bionet.software.acedb Date: Wed, 30 Aug 2000 09:49:41 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Thank you that you took the time to look into my problem. You were wondering why this didn't look like natural acedb style (and in fact isn't) and I will try to explain it in a litle more detail (see below). > > ?BaseClass2 UNIQUE PointsTo ?BaseClass1 > PointsTo ?Sub1BaseClass1 > PointsTo ?Sub2BaseClass1 > > is not legal, but > > ?BaseClass2 Points_to UNIQUE Points_to_BaseClass1 ?BaseClass1 > Points_to_Sub1BaseClass1 ?Sub1BaseClass1 > ... > > is, and probably does what you want. Yes, I thought of this as well, but this seems to be a litle awkward to me. > > But I don't really understand your approach, which certainly does not > look natural acedb style to me. Yes you are right again. The best way certainly would be to do the whole model in acedb from the start, but database people have their modeling tools and those normaly do not generate ACEDB models. But since we want other people to use and test our model, we would like to distribute it as an ACEDB model as well. Now I am faced with the problem to port an object oriented data model to an ACEDB model that has no notion of inheritance. Just imagine, we would like to have the notion of a reaction in the model, this reaction has e.g. substrates which are of the type compound. Now compound is a baseclass and has lots of subclasses like simple_molecule, peptide, dna, rna etc. and those subclasses might have subclasses of their own. So how would I define this reaction. The easiest would have been, if ACEDB knew abou inheritance than I would just say: ?Reaction Substrate ?Compound O.K., but since we all know, this does not work, so I thought about using the Unique construct above which just lists all subclasses: ?Reaction Unique Substrate ?Compound Substrate ?SimpleMolecule Substrate ?..... Now you suggest to do it like this: ?Reaction Substrate UNIQUE CompoundSubstrate ?Compound SimpleMoleculeSubstrate ?SimpleMolecule ... Although this works, it adds another level of complexety when you want to query a reaction. To bad, but since this seems to be the only way to do it, I guess I wil have to do it this way. But I hope, I could clearify why I tried to do it the other way first. How would one define ?Reaction the "ACEDB way"? I am still facing the problem that a substrate can be a peptide, a dna, a rna etc. How could this be solved besides using ID numbers? > > I suggest one of the following approaches: > > - if the subclass only inherits from one base class, then incorporate > all of its model additions into the base class model as a branch > under some tag such as SubClass1. Next make an acedb subclass of all > objects for which that tag is set. As soon as objects contain data > on the branch they will become part of the subclass, whereas > objects for which there is no data in that branch will not be in the > subclass. > I have not thought of this. That also might be an option as well, I have to think it over. Thank you very much for your help Ralph From owner-acedb@hgmp.mrc.ac.uk Wed Aug 30 09:49:49 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id D4CCB17AB8; Wed, 30 Aug 2000 09:49:48 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 1D58217ABF; Wed, 30 Aug 2000 09:49:41 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id BED4C17B1E; Tue, 29 Aug 2000 17:54:56 +0100 (BST) Received: from jess.sanger.ac.uk (jess.sanger.ac.uk [193.60.84.61]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C403E415D5 for ; Tue, 29 Aug 2000 17:54:55 +0100 (BST) Received: from griffin.sanger.ac.uk (rd@griffin [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id RAA20216; Tue, 29 Aug 2000 17:54:54 +0100 (BST) From: Richard Durbin Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id RAA30570; Tue, 29 Aug 2000 17:54:54 +0100 (BST) Message-Id: <200008291654.RAA30570@griffin.sanger.ac.uk> To: bionet-software-acedb@net.bio.net, ralph.gauges@eml.villa-bosch.de Subject: Re: Uniqueness of tags? Newsgroups: bionet.software.acedb Date: Wed, 30 Aug 2000 09:49:41 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk ?BaseClass2 UNIQUE PointsTo ?BaseClass1 PointsTo ?Sub1BaseClass1 PointsTo ?Sub2BaseClass1 is not legal, but ?BaseClass2 Points_to UNIQUE Points_to_BaseClass1 ?BaseClass1 Points_to_Sub1BaseClass1 ?Sub1BaseClass1 ... is, and probably does what you want. You can get to the thing you are pointing to by Points_to:2 (old query syntax) or Points_to[2] (AQL syntax), while you can load data by Points_to_XXX. But I don't really understand your approach, which certainly does not look natural acedb style to me. I suggest one of the following approaches: - if the subclass only inherits from one base class, then incorporate all of its model additions into the base class model as a branch under some tag such as SubClass1. Next make an acedb subclass of all objects for which that tag is set. As soon as objects contain data on the branch they will become part of the subclass, whereas objects for which there is no data in that branch will not be in the subclass. - if you want to inherit multiple interfaces, then make models for them not associated to any class, then incorporate this model either by copying or by #Model consrtruction into all the models which you want to have these properties. See for example the usage of the model fragment Map ?Map #Map_info in the model set distributed with the code, which allows objects to be placed on map displays. This can (and is) used in the models of many classes. Richard From owner-acedb@hgmp.mrc.ac.uk Wed Aug 30 12:38:41 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id E053817B4A; Wed, 30 Aug 2000 12:38:40 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 696C317B04; Wed, 30 Aug 2000 12:38:39 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 3558417ACF; Wed, 30 Aug 2000 10:45:36 +0100 (BST) Received: from moderated.news.pipex.net (moderated.news.pipex.net [158.43.192.79]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 685C8415DC for ; Wed, 30 Aug 2000 10:45:35 +0100 (BST) Received: (qmail 3267 invoked by alias); 30 Aug 2000 09:45:34 -0000 Received: (qmail 3263 invoked from network); 30 Aug 2000 09:45:34 -0000 Received: from resu1.ulb.ac.be (164.15.59.200) by moderated.news.pipex.net with SMTP; 30 Aug 2000 09:45:34 -0000 Received: from snic.vub.ac.be (snic.ulb.ac.be [164.15.128.20]) by resu1.ulb.ac.be (8.8.8/3.17.0.ap (resu)) id LAA00517; Wed, 30 Aug 2000 11:46:08 +0200 (MET DST) for Received: (news@localhost) by snic.vub.ac.be (8.9.3/%I%.0.ap (snic.test)) id LAA07808; Wed, 30 Aug 2000 11:45:26 +0200 (MET DST) for bionet-software-acedb@moderators.isc.org To: bionet-software-acedb@moderators.isc.org From: Guy Bottu Newsgroups: bionet.software.acedb Subject: question about AceBrowser Class Browser Organization: Belgian EMBnet Node Message-ID: <8oil3m$78h$1@snic.vub.ac.be> X-Trace: snic.vub.ac.be 967628726 7441 134.184.15.23 (30 Aug 2000 09:45:26 GMT) X-Complaints-To: usenet@snic.vub.ac.be NNTP-Posting-Date: 30 Aug 2000 09:45:26 GMT User-Agent: tin/1.4.3-20000502 ("Marian") (UNIX) (SunOS/5.7 (sun4u)) Date: Wed, 30 Aug 2000 12:38:39 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I have recently installed an AceBrowser server on our new computer. When testing the retrieval of external images, I noticed the following : the databank GrainGenes contains 2124 objects of type "Image" and in the page "Class Browser" Image appears in the selector, so far, so good. But the databank ACeDB contains 351 objects of type "Picture" and Picture does not appear in the selector. And AceBrowser was precisely supposed to be developed optimized for ACeDB. Does someone know how you can make "Picture" and other missing object type names appear in the selector ? Guy Bottu From owner-acedb@hgmp.mrc.ac.uk Thu Aug 31 09:11:48 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id DCC4A17AAB; Thu, 31 Aug 2000 09:11:46 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 5627F17A96; Thu, 31 Aug 2000 09:11:44 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 1EFBE17A6C; Wed, 30 Aug 2000 14:03:58 +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 4994A415DA for ; Wed, 30 Aug 2000 14:03:57 +0100 (BST) Received: from griffin.sanger.ac.uk (rd@griffin [193.60.84.177]) by jess.sanger.ac.uk (8.8.8/8.8.7) with ESMTP id OAA22822; Wed, 30 Aug 2000 14:03:54 +0100 (BST) From: Richard Durbin Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id OAA01725; Wed, 30 Aug 2000 14:03:54 +0100 (BST) Message-Id: <200008301303.OAA01725@griffin.sanger.ac.uk> To: bionet-software-acedb@net.bio.net, ralph.gauges@eml.villa-bosch.de Subject: Re: Uniqueness of tags? Newsgroups: bionet.software.acedb Date: Thu, 31 Aug 2000 09:11:44 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > Just imagine, we would like to have the notion of a reaction > in the model, this reaction has e.g. substrates which are of > the type compound. Now compound is a baseclass and has lots > of subclasses like simple_molecule, peptide, dna, rna etc. > and those subclasses might have subclasses of their own. So > how would I define this reaction. The easiest would have > been, if ACEDB knew abou inheritance than I would just say: > > ?Reaction Substrate ?Compound > > O.K., but since we all know, this does not work, so I > thought about using the Unique construct above which just > lists all subclasses: Aha, but I think it does work. See below. > ?Reaction Unique Substrate ?Compound > Substrate ?SimpleMolecule > Substrate ?..... > > Now you suggest to do it like this: > > ?Reaction Substrate UNIQUE CompoundSubstrate ?Compound > SimpleMoleculeSubstrate > ?SimpleMolecule > ... > > Although this works, it adds another level of complexety > when you want to query a reaction. To bad, but since this > seems to be the only way to do it, I guess I wil have to do > it this way. But I hope, I could clearify why I tried to do > it the other way first. > How would one define ?Reaction the "ACEDB way"? I am still > facing the problem that a substrate can be a peptide, a dna, > a rna etc. How could this be solved besides using ID > numbers? I would have ?Reaction Substrate ?Compound XREF Reaction ?Compound Type UNIQUE Peptide Nucleic_acid UNIQUE DNA RNA Small_molecule Reaction ?Reaction XREF Substrate Then define subclasses of Compound as follows in subclasses.wrm Class Peptide Is_a_subclass_of Compound Filter Peptide Class Nucleic_acid Is_a_subclass_of Compound Filter Nucleic_acid Class DNA_compound Is_a_subclass_of Nucleic_acid Filter DNA etc. Does this do what you want? Note that I say DNA_compound because DNA is a reserved class. Richard From owner-acedb@hgmp.mrc.ac.uk Thu Aug 31 09:11:50 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 1E85717A96; Thu, 31 Aug 2000 09:11:48 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 47C4A17AA8; Thu, 31 Aug 2000 09:11:46 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 1609A17AE2; Wed, 30 Aug 2000 16:14:02 +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 1AFF9415D5 for ; Wed, 30 Aug 2000 16:14:02 +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 RLBTR43Q; Wed, 30 Aug 2000 17:10:17 +0200 Message-ID: <39AD24B8.100DD7AF@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: bionet-software-acedb@net.bio.net Subject: Re: Uniqueness of tags? References: <200008301303.OAA01725@griffin.sanger.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Newsgroups: bionet.software.acedb Date: Thu, 31 Aug 2000 09:11:46 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk > > I would have > > ?Reaction Substrate ?Compound XREF Reaction > > ?Compound Type UNIQUE Peptide > Nucleic_acid UNIQUE DNA > RNA > Small_molecule > Reaction ?Reaction XREF Substrate > > Then define subclasses of Compound as follows in subclasses.wrm > > Class Peptide > Is_a_subclass_of Compound > Filter Peptide > > Class Nucleic_acid > Is_a_subclass_of Compound > Filter Nucleic_acid > > Class DNA_compound > Is_a_subclass_of Nucleic_acid > Filter DNA > > etc. > > Does this do what you want? Note that I say DNA_compound because DNA > is a reserved class. > > Richard If I would add all the extra attributes that e.g. peptide has compared to Compound, it might work. If I get this right, it might look something like ?Reaction Substrate ?Compound XREF Reaction ?Compound Type UNIQUE Peptide Sequence TEXT Function TEXT .... Nucleic_acid Type UNIQUE DNA RNA Sequence TEXT ... Small_molecule ... Reaction ?Reaction XREF Substrate To be honest, I have not looked at subclasses in detail yet. But I assume that the filters could also be made more restrictive. Like Filter Type.DNA instead of just DNA. But again, what if I have subclasses of subclasses and so on. This would get very complicated if I put everything in the Compound model. But this mailinglist is no substitute for reading the documentation, so I don't want to bother you with more questions that I might get answers to from the manual. I think I will read the stuff about subclassing. Thanks again for putting me on this track, maybe this will help me to find the optimal solution for the problem. Ralph From owner-acedb@hgmp.mrc.ac.uk Thu Aug 31 09:11:53 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id EB41717A96; Thu, 31 Aug 2000 09:11:52 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 2D0C917A8E; Thu, 31 Aug 2000 09:11:44 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 3A73B17B53; Wed, 30 Aug 2000 13:37:14 +0100 (BST) To: bionet-software-acedb@net.bio.net From: matthews@greengenes.cit.cornell.edu (Dave Matthews) Newsgroups: bionet.software.acedb Subject: re: question about AceBrowser Class Browser Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <200008301237.IAA14902@greengenes.cit.cornell.edu> X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id D33D717B4A; Wed, 30 Aug 2000 13:37:11 +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 6BA3E415D5 for ; Wed, 30 Aug 2000 13:37:10 +0100 (BST) X-Received: (from matthews@localhost) by greengenes.cit.cornell.edu (8.9.3/8.9.3) id IAA14902 for ACEDB newsgroup ; Wed, 30 Aug 2000 08:37:05 -0400 (EDT) X-To: ACEDB newsgroup Date: Thu, 31 Aug 2000 09:11:44 +0100 (BST) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hi Guy, This is controlled in wspec/options.wrm. Each class may be set to either -Visible or -Hidden. (After changing this you'll have to kill your rpc.acedbd process for the results to show through to AceBrowser.) - Dave > From: Guy Bottu > Date: Wed, 30 Aug 2000 12:38:39 +0100 (BST) > > I have recently installed an AceBrowser server on our new computer. When > testing the retrieval of external images, I noticed the following : the > databank GrainGenes contains 2124 objects of type "Image" and in the > page "Class Browser" Image appears in the selector, so far, so good. But > the databank ACeDB contains 351 objects of type "Picture" and Picture > does not appear in the selector. And AceBrowser was precisely supposed > to be developed optimized for ACeDB. Does someone know how you can make > "Picture" and other missing object type names appear in the selector ? > > Guy Bottu ---