From owner-acedb@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!CHPC.UTEXAS.EDU!mwitten From: mwitten@CHPC.UTEXAS.EDU Newsgroups: bionet.software.acedb Subject: URGENT: DEADLINE CHANGE FOR WORLD CONGRESS Message-ID: <9311031731.AA07924@morpheus.chpc.utexas.edu> Date: 3 Nov 93 17:31:08 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 68 UPDATE ON DEADLINES FIRST WORLD CONGRESS ON COMPUTATIONAL MEDICINE, PUBLIC HEALTH, AND BIOTECHNOLOGY 24-28 April 1994 Hyatt Regency Hotel Austin, Texas ----- (Feel Free To Cross Post This Announcement) ---- Due to a confusion in the electronic distribution of the congress announcement and deadlines, as well as incorrect deadlines appearing in a number of society newsletters and journals, we are extending the abstract submission deadline for this congress to 31 December 1993. We apologize to those who were confused over the differing deadline announcements and hope that this change will allow everyone to participate. For congress details: To contact the congress organizers for any reason use any of the following pathways: ELECTRONIC MAIL - compmed94@chpc.utexas.edu FAX (USA) - (512) 471-2445 PHONE (USA) - (512) 471-2472 GOPHER: log into the University of Texas System-CHPC select the Computational Medicine and Allied Health menu choice ANONYMOUS FTP: ftp.chpc.utexas.edu cd /pub/compmed94 (all documents and forms are stored here) POSTAL: Compmed 1994 University of Texas System CHPC Balcones Research Center 10100 Burnet Road, 1.154CMS Austin, Texas 78758-4497 SUBMISSION PROCEDURES: Authors must submit 5 copies of a single-page 50-100 word abstract clearly discussing the topic of their presentation. In addition, authors must clearly state their choice of poster, contributed paper, tutorial, exhibit, focused workshop or birds of a feather group along with a discussion of their presentation. Abstracts will be published as part of the preliminary conference material. To notify the congress organizing committee that you would like to participate and to be put on the congress mailing list, please fill out and return the form that follows this announcement. You may use any of the contact methods above. If you wish to organize a contributed paper session, tutorial session, focused workshop, or birds of a feather group, please contact the conference director at mwitten@chpc.utexas.edu . The abstract may be submitted electronically to compmed94@chpc.utexas.edu or by mail or fax. There is no official format. If you need further details, please contact me. Matthew Witten Congress Chair mwitten@chpc.utexas.edu From owner-acedb@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!S27W007.PSWFS.GOV!bks From: bks@S27W007.PSWFS.GOV (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Yet another gateway test Message-ID: <9311031810.AA21043@s27w007.pswfs.gov> Date: 3 Nov 93 18:10:15 GMT Sender: daemon@net.bio.net Distribution: biosci Lines: 26 Sorry, for the noise. I am once again testing to see if items mailed to acedb@net.bio.net will eventually appear in the Usenet conference biosci.software.acedb as they are supposed to. According to Kristofferson, et. al. this should have been happening but was not. I have been led to believe that it fixed but I have seen no traffic in the group. If you're still reading this, I use an nntp news reader rather than a subscription to the mailing list. I believe that articles in the conference *are* making it to the mailing list. If you're still there, I will be sending out an enhanced FAQ in a few days, once I have determined the status of the gateway. --bks Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-acedb@net.bio.net Tue Nov 02 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!rc1!ub4b!mcsun!uknet!pipex!howland.reston.ans.net!europa.eng.gtefsd.com!library.ucla.edu!csulb.edu!csus.edu!netcom.com!ead From: ead@netcom.com (Eric De Mund) Newsgroups: bionet.software.acedb Subject: test ignore Message-ID: Date: 3 Nov 93 18:59:40 GMT Sender: ead@netcom.com (Eric De Mund) Reply-To: Eric De Mund Organization: Netcom Online Communications Services Lines: 9 X-Reply-To: Eric De Mund This is a test posting. Date: Wed, 3 Nov 93 11:00:00 PST From: Eric De Mund Newsgroups: bionet.software.acedb Distribution: world Subject: test ignore Eric De Mund From owner-acedb@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!agate!doc.ic.ac.uk!daresbury!not-for-mail From: mieg@kaa.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: stepping in Message-ID: <2baigo$a6f@mserv1.dl.ac.uk> Date: 4 Nov 93 09:37:28 GMT Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Lines: 2 To: acedb@dl.ac.uk It seems that i may now receive the acedb newsgroup. Jean thierry-mieg From owner-acedb@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!news-feed-1.peachnet.edu!concert!duke!news.duke.edu!bio3.acpub.duke.edu!glh From: glh@bio3.acpub.duke.edu (Geoff Hughes) Newsgroups: bionet.software.acedb Subject: GenBank File Converters Message-ID: <23063@news.duke.edu> Date: 4 Nov 93 16:33:28 GMT Sender: news@news.duke.edu Reply-To: glh@bio3.acpub.duke.edu (Geoff Hughes) Lines: 10 Nntp-Posting-Host: bio3.acpub.duke.edu Hello all, Has anyone ported Mike Cherry's gb2ace.c program for VMS to a UNIX platform? It would be extraordinarily helpful to our efforts. Thanks, Geoff Hughes From owner-acedb@net.bio.net Wed Nov 03 22:00:00 1993 Path: biosci!S27W007.PSWFS.GOV!bks From: bks@S27W007.PSWFS.GOV (Bradley K. Sherman) Newsgroups: bionet.software.acedb Subject: Testing one two three four Message-ID: <9311041900.AA23595@s27w007.pswfs.gov> Date: 4 Nov 93 19:00:55 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 25 Apologies once again for the noise. Biosci claims to have fixed the problem and this message should appear in the USENET/BIOSCI conference bionet.software.acedb. Apparently the gateway was working for the BIOSCI computers but not for anyone else! It was mailed to mailing-list acedb@net.bio.net 11AM PST, 4 November 1993. For interested parties, the gateway from the conference to the mailing list seems robust. --bks A difference of taste in jokes is a great strain on the affections. --George Eliot Bradley K. Sherman P.O. Box 245 Computer Scientist Berkeley, CA, 94701 Dendrome Project 510-559-6437 FAX: 510-559-6440 Institute of Forest Genetics Internet: bks@s27w007.pswfs.gov From owner-acedb@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!kristoff From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.software.acedb Subject: Re: Yet another gateway test Message-ID: Date: 5 Nov 93 02:54:04 GMT References: <9311031810.AA21043@s27w007.pswfs.gov> Distribution: biosci Organization: BIOSCI International Newsgroups for Biology Lines: 11 Brad, Your test showed up in the news system here without a problem. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-acedb@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!FLY2.BERKELEY.EDU!gregg From: gregg@FLY2.BERKELEY.EDU (Gregg Helt) Newsgroups: bionet.software.acedb Subject: Re: GenBank File Converters Message-ID: <9311052042.AA20155@fly2.berkeley.edu.maggot> Date: 5 Nov 93 20:42:50 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 37 From Geoff Hughes: >Has anyone ported Mike Cherry's gb2ace.c program for VMS to a UNIX platform? >It would be extraordinarily helpful to our efforts. Hmm, well not exactly, but I've done some stuff that might be useful. I've been writing conversion code in Perl. This language was basicly designed to do just this kind of text manipulation/conversion, and I much prefer it over C for dealing with text. At the moment the only thing I've written that processes genbank info is part of a collection of short Perl programs called by a shell script. They are meant to periodicly search genbank for entries that match keywords (kept in a separate file), extract just the name and the sequence information, and append this info to a local blast-searchable database. For the Drosophila genome project, the keywords are various vectors, transposable elements, and repetitive stretches of DNA. Other programs in our data-flow then search this database any time new sequence information comes in, in order to filter out sequences that match these (presumably undesirable) sequences. However, this collection of programs is still rather rickety, so at the moment "periodicly" means when I get the chance to sit down and monitor its progress. Mainly this is necessary because the keywords are too inclusive, so once I write up a better interpreter of the keyword file (one that can recognize that some entries indicate _particular_ sequences to extract, rather than general keywords) we should be able to have the script run automaticly once a week or so to keep the filter database up to date. I've also written some perl scripts that extract basic info from blast output and put it in .ace format, and a few other similar conversions. Although Perl syntax can be odd, it is very powerful for this sort of thing. Gregg Helt From owner-acedb@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!agate!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Summary: Frequently Asked Questions about finding and getting started with the database system ACEDB. ACEDB is used to collect information regarding the molecular biology of the genome. Message-ID: <2becu0$5ch@overload.lbl.gov> Date: 5 Nov 93 20:26:40 GMT Reply-To: acedbfaq@s27w007.pswfs.gov Followup-To: bionet.software.acedb Organization: Dendrome, A genome database for forest trees Lines: 563 Approved: news-answers-request@MIT.Edu Xref: biosci bionet.software.acedb:107 news.answers:10896 NNTP-Posting-Host: s27w007.pswfs.gov Archive-name: acedb-faq Last-modifed: 11/5/93 Version: 1.5 ---------------------------------------------------------------------- Common Questions and Answers about ACEDB. This document will be posted monthly to the BIOSCI newsgroup bionet.software.acedb and to USENET conference news.answers. It is intended to be used as an index to ACEDB databases and to information about the database software. The latest version of the ACEDB FAQ should be available via anonymous ftp at net.bio.net as /pub/BIOSCI/ACEDB/ACEDB.FAQ and at rtfm.mit.edu as /pub/usenet/news.answers/ bionet.software.acedb/bionet.software.acedb.FAQ and via electronic mail from mail-server@rtfm.mit.edu [untried --bks]. Curators of ACEDB databases should take note of Question 4 and keep me apprised of changes. Errors of commission or omission are unintentional. If I have forgotten to give you credit please let me know. Please send comments and corrections to: acedbfaq@s27w007.pswfs.gov --Bradley K. Sherman ---------------------------------------------------------------------- List of questions in the ACEDB FAQ: Q0: What is ACEDB? Q1: What is the current version of ACEDB? Q2: What {hardware | software} do I need to run ACEDB? Q3: Where can I get ACEDB? Q4: What ACEDB databases exist? Q5: What written documentation exists for ACEDB? Q6: Where can I find further information about ACEDB? Q7: How should ACEDB be cited? Q8: Is ACEDB object-oriented? Q9: What's all this about Gopher/WAIS/Anonymous ftp/WWW ... Q10: How can I get on the ACEDB announcements mailing list? Q411:Who contributed to this document? ---------------------------------------------------------------------- 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 [see Q4]. 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 circa 1990. 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 [See Q3]. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups including Lawrence Berkeley Laboratory and the European integrated Genome Project. 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. Current display modes are: TREE for text type objects: papers, authors, genes etc. GMAP genetic map PMAP physical map (Sulston contig style) SEQ DNA sequence - symbolic, features, sequence and translation GRID hybridisation patterns for a probe to a clone grid BIBLIO bibliography attached to any object display modules under development: CMAP whole chromosome physical map plot GEL agarose gel simulation derived from sequence ---------------------------------------------------------------------- Q1: What is the current version of ACEDB? A1: 1-10. It was released Summer 1993. The next release will be 2.0. This refers to the version of the software, not the data. To be kept informed of new releases see Q10. ---------------------------------------------------------------------- Q2: What {hardware | software} do I need to run ACEDB? A2: ACEDB currently runs on the following Unix systems, under X11: Unix: Any machine running SunOS 4.x e.g. Sun SPARCstation 1, 1+, 2, IPC, IPX. SPARCstation 10 under Solaris [Probably all Solaris, then --bks] DEC DECstation3100, 5100 etc. DEC Alpha/OSF-1 Silicon Graphics Iris series PC 386/486 with Linux (public domain Unix) There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM R6000, NeXT, Convex. You may have to contact the developer responsible for the port to make these real. MSDOS/Windows/NT: A port to NT is rumored to be in the works. Macintosh: A port to the Macintosh may become available by the end of 1993. For cost savings, a combination of a high-end Intel platform with Linux appears very attractive. ---------------------------------------------------------------------- Q3: Where can I get ACEDB? A3: All the files are available in the following public access accounts (anonymous ftp sites) accessible via Internet: lirmm.lirmm.fr (193.49.104.10) genome/acedb cele.mrc-lmb.cam.ac.uk (131.11.84.1) pub/acedb ncbi.nlm.nih.gov (130.14.20.1) repository/acedb A typical session would be: ftp ncbi.nlm.nih.gov login: anonymous password: your email address cd repository/acedb binary ls get README get NOTES get INSTALL get bin.sparc.1_4.tar.Z quit ---------------------------------------------------------------------- Q4: What ACEDB databases exist? A4: [In alphabetic order by Database name --bks] Database : AAnDB Species : Aspergillus nidulans PI : Leland Ellis Last_update : Sept. 1993 Database : AAtDB Species : Arabidopsis thaliana Availability : Curator : John Morris Current version: 1-5 Contact : curator@frodo.mgh.harvard.edu Last_update : Sept. 1993 Database : ACeDB Species : Caenorhabditis elegans Availability : Current version: 1-21 Curator : Jean Thierry-Mieg Curator : Richard Durbin Contact : rd@cele.mrc-lmb.cam.ac.uk Contact : mieg@kaa.cnrs-mop.fr Last_update : Sept. 1993 Database : ChlamyDB Species : Chlamydomonas PI : Elizabeth Harris Contact : chlamy@acpub.duke.edu Availability : Still under construction Last_update : 30 Sept. 1993 Database : EcoDB Species : E. coli PI : Staffan Bergh Contact : staffan@biochem.kth.se Availability : Still under construction Last_update : 11 Oct. 1993 Database : Flydb Species : Drosophila melanogaster Availability : by request only, via ftp Curator : Suzanna E. Lewis Contact : SELewis@lbl.gov Focus : STS content mapping project summary PI : Gerald Rubin PI : Mike Palazzolo PI : Dan Hartl PI : Alan Spradling Last_update : Sept. 1993 Database : GrainGenes Species : Wheat, barley, oats, relatives Availability : Gopher greengenes.cit.cornell.edu port 70 Availability : ACEDB version by ftp, on request from the curators Curator : David E. Matthews PI : Olin D. Anderson Contact : matthews@greengenes.cit.cornell.edu Contact : oandersn@wheat.usda.gov Last_update : Sept. 1993 Database : Mace Species : Zea mays L. ssp. mays Focus : Maize genome Comment : Mace is the front end for maizedb, a relational (SYBASE) database. It is updated from maizedb by software written by Stan Letovsky. Maizedb is updated daily and will soon be accessible by public login. Curator : Ed Coe Curator : Pat Byrne Curator : Georgia Davis Curator : Mary Polacco Off-Site Curator : Marty Sachs Off-Site Curator : Christiane Fauron Off-Site Curator : Carolyn Wetzel Off-Site Curator : Steve Rodermel Off-Site Curator/Designer : Stan Letovsky Off-Site Curator/Designer : Mary Berlyn Systems Manager : Denis Hancock PI : Ed Coe Contact : maizedb@teosinte.agron.missouri.edu Last_update: 5 October 1993 Database : MycDB Species : Mycobacterium PI : Staffan Bergh PI : Thierry Garnier Contact : staffan@pasteur.fr Last_update : Sept. 1993 Database : RiceGenes Species : Rice (O. sative) Availability : under development, login at own risk Curator : Edie Paul Contact : epaul@nightshade.cit.cornell.edu Last_update : Sept. 1993 Database : SolGenes Coverage: Solanaceae - tomato, potato, pepper (eventually) Availability : Beta ACEDB via login or tar file Curator : Edie Paul Contact : epaul@nightshade.cit.cornell.edu Last_update : Sept. 1993 Database : SoyBase Species : Soybeans Curator : Lisa Lorenzen PI : Randy Shoemaker Contact : lorenzen@mendel.agron.iastate.edu Last_update : Sept. 1993 Database : TreeGenes Species : Forest trees, Pinus taeda Availability : contact curator Curator : Bradley K. Sherman PI : David B. Neale Contact : Dendrome@s27w007.pswfs.gov Contact : bks@s27w007.pswfs.gov Contact : dbn@s27w007.pswfs.gov Last_update : Sept. 1993 Database : 21Bdb Species : Homo sapiens Availability : by request, via ftp, gopher Curator : Donn F. Davy Contact : DFDavy@lbl.gov Contact : aggarwal@genome.lbl.gov Focus : STS content mapping & sequencing of Human Chromosome 21 PI : Jasper Rine PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng Last_update : Sept. 1993 Database : VoxPop Species : Populus spp. Availability : contact curator Curator : Carl G. Riches PI : Reinhard F. Stettler Contact : cgr@poplar1.cfr.washington.edu Contact : STETTLER@coyote.cfr.washington.edu Last_update : Sept. 1993 Database : ? Species : Bovine PI : Leland Ellis Last_update : Sept. 1993 Database : ? Species : Sorghum PI : Leland Ellis Last_update : Sept. 1993 Database : ? PI : Scott Chasalow Species : Potato Contact : Scottish Crop Institute, Dundee Last_update : Sept. 1993 Database : ? PI : George Murphy PI : David Flanders Species : Arabidopsis thaliana Contact : John Innes Center, Norwich, England Last_update : Sept. 1993 Database : ? Species : Homo sapiens Focus : Physical mapping of human chromosomes 22 and X Curator : Ian Dunham Contact : idunham@crc.ac.uk id1@sanger.ac.uk PI : Ian Dunham PI : David Bentley Last_update : 28 Sep 1993 [Curators: Please submit an entire paragraph in this format for inclusion or update. --bks] ---------------------------------------------------------------------- Q5: What written documentation exists for ACEDB? A5: The primary documents are included in the Software distribution in the wdoc subdirectory: acedb -- A C. elegans Database: I. Users' Guide. acedb -- A C. elegans Database: II. Installation Guide. acedb -- A C. elegans Database: III. Configuration Guide. Syntactic Definitions for the ACEDB Data Base Manager --Jean Thierry-Mieg and Richard Durbin (1991-) You will find other interesting documents in the wdoc subdirectory. By anonymous ftp from ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb: doc.1_9.tar.Z Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992) AAtDB, An Arabidopsis thaliana Database. Plant Molecular Biology Reporter 10 (4): 308-309,409-410 Tutorial manual for AAtDB: Cartinhour, S., Cherry, J.M., and Goodman, H.M. (1992) An Introduction to ACeDB: For AAtDB, An Arabidopsis thaliana Database. Massachusetts General Hospital. (Available on request in printed form from the AAtDB curator). A description of ACEDB: Cherry, J.M. and Cartinhour, S.W. (1993) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press (in press). [text is available through ftp or gopher from weeds.mgh.harvard.edu] Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1993) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. (Academic Press) (review, in press). [text is available through ftp or gopher from weeds.mgh.harvard.edu] ---------------------------------------------------------------------- Q6: Where can I find further information about ACEDB? A6: There is a Usenet/Biosci conference titled bionet.software.acedb. If you do not have access to the Biosci conferences via a newsreader (e.g. rn, trn) you can participate in the conference by electronic mail. To subscribe to the e-mail version of the conference send email to biosci-server@net.bio.net with no subject line and only the message subscribe ACEDB-SOFT in the body. To unsubscribe send the message unsubscribe ACEDB-SOFT to the same address. This is an automated service. Your e-mail address will be taken from the header of the message that you send. If you then send mail to acedb@net.bio.net the mail will be distributed to all subscribers and to the electronic conference. Mike Cherry has set up an ACEDB Developer's archive. For anonymous ftp use the hostname weeds.mgh.harvard.edu and look in the acedb_dev directory. If you wish to contribute you can put files in the incoming directory. Send a message to Mike (cherry@genome.stanford.edu) that you have put something in that directory then Mike will move it out for general access. For gopher you can connect to weeds.mgh.harvard.edu (132.183.190.21) and ... --> N. FTP Archives for Molecular Biology/ then --> M. ACEDB Developer's archive/ [N and M are integers which are subject to change.] The bionet.software. acedb.conference is archived and can be searched using WAIS. Here is a Gopher-style link to the WAIS archive. (This is also courtesy of Mike Cherry.): # Type=7 Name=ACEDB BioSci Electronic Conference Path=7/.index/acedb-biosci Host=genome-gopher.stanford.edu Port=70 The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes (see Q4) databases regularly submit data to the Plant Genome Database at the National Agricultural Library (NAL). Nal makes this data available using an WWW server (really http) with the Universal Resource Locator (URL) http://locus.nalusda.gov. You will also find a selection of models.wrm files (schemata) for the various databases here. You will want to get a "mosaic client" to examine this. [This section will be expanded in the next version. We hope to make this document available as hypertext on the NAL server --bks] Other URL's that readers with mosaic clients might want to examine are: http://moulon.inra.fr/acedb/acedb.html for C. elegans data http://moulon.inra.fr/acedb/mycdb.html for Mycobacterium data For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html" http://moulon.inra.fr/acedb_conf.html (en francais) The Genome Computing Group, Lawrence Berkeley Laboratory has an anonymous ftp service at machine genome.lbl.gov (131.243.224.80) which contains: flydb - LBL's Drosophila Acedb-style database 21bdb - LBL's Human Chromosome 21 Acedb-style database querdb - LBL's query-language extensions to Acedb metadata - LBL's compendium of Acedb database schema variants macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version There is also a repository of contributed software for data conversions and the like. Computer staff for the UC Berkeley Drosophila physical mapping project the LBL Human Chromosome 21 project, and the LBL plant genome projects meet regularly to coordinate their ACEDB extension and development efforts, along with Frank Eeckman, who is working on the Macintosh version of ACEDB (for further information, contact jlmccarthy@lbl.gov). They also keep in close touch (via email, personal visits, etc.) with their counterparts in Cambridge (Richard Durbin et al), Montpellier Jean Thierry-Mieg et al), and the Interated Genome Database project in Heidelburg (Otto Ritter, Detlef Wolf et al). ---------------------------------------------------------------------- Q7: How should ACEDB be cited? A7: 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 by Anonymous FTP from ... 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. ---------------------------------------------------------------------- Q8: Is ACEDB object-oriented? A8: From the ACEDB User's Guide. A major current vogue in computer languages and database design is for ``object-oriented'' systems. It's also a source of lots of argument. We are just trying to build a good system, and don't want to get caught in the crossfire, but we do talk about organising our data into objects and classes. We have undoubtedly been influenced by many of the ideas going around, but it isn't likely our system would be regarded as kosher by the object- oriented community. In particular there is no class hierarchy, nor inheritance, and it is written in a modular but non-ideological way in straight C. However display and disk storage methods are class dependent. In some ways the class hierarchy is replaced by our system of models and trees, which seems to be rather unusual. We think it is very natural for the representation of biological information, where for some members of a class a lot might be known about some aspect, but for most only a little is known. The advantages of our sytem over a relational database, such as Oracle or Sybase, is our ability to refine our descriptions without rebuilding the database and the possibility of organising the storage of data on disk according to their class, i.e. we store in a very different way the tree-objects and the long stretches of DNA sequence. ---------------------------------------------------------------------- Q9: What's all this about Gopher/WAIS/Anonymous ftp/WWW ... A9: These terms all refer to Internet protocols. An excellent introduction to the Internet is: _The Whole Internet User's Guide & Catalog_, by Ed Krol, O'Reilly & Associates, 1992. Or ask your system administrator to provide you with a gopher client or mosaic client and begin navigating on your own. ---------------------------------------------------------------------- Q10: How can I get on the ACEDB announcements mailing list? A10: To get on or off the mailing list send mail to rd@mrc-lmda.cam.ac.uk or mieg@kaa.cnrs-mop.fr. New releases of the software are announced to this list. ---------------------------------------------------------------------- Q411:Who contributed to this document? [Note to international readers: 411 is the phone number for information in the USA. --bks] A411: Major contributions in getting this FAQ off the ground were made by John McCarthy and Mike Cherry. Other contributors include: Lisa Lorenzen David Matthews Edie Paul Donn Davy Eric De Mund Sam Cartinhour To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov Bradley K. Sherman Dendrome Project Institute of Forest Genetics P.O. Box 245, Berkeley, CA, 94701 Phone: 510-559-6437 Fax: 510-559-6440 The Dendrome Project and TreeGenes are funded by the USDA-ARS Plant Genome Database Project. ---------------------End of file acedb-faq---------------------------- From owner-acedb@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!usenet.ins.cwru.edu!news.ysu.edu!yfn.ysu.edu!ar045 From: ar045@yfn.ysu.edu (Chad R. Knupp) Newsgroups: bionet.software.acedb Subject: HELP: INFO ON OS'S NEEDED Message-ID: <2beedc$8jr@news.ysu.edu> Date: 5 Nov 93 20:51:56 GMT Reply-To: ar045@yfn.ysu.edu (Chad R. Knupp) Organization: St. Elizabeth Hospital, Youngstown, OH Lines: 15 NNTP-Posting-Host: yfn.ysu.edu I know this post probably doesn't follow the topic of this group well...however, I'm posting to a lot of places in the hopes of finding a few people. I'm looking for people who can give me some info on OS9 and/or VRTX, both are supercomputer os's written by Microware. I need a # to Microware and/or a place to buy both of the affor mentioned products. Also, maybe someone has some info on Applied Inteligence Systems... I'm looking to purchase a virtual memory extention bus... I need to know what kind of drivers it requires and what kind of hardware is needed. If you work for either company or have been a customer, please contact me asap. Thanx much for your time. --cHad Knupp From owner-acedb@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!MENDEL.AGRON.IASTATE.EDU!lorenzen From: lorenzen@MENDEL.AGRON.IASTATE.EDU (Lisa Lorenzen) Newsgroups: bionet.software.acedb Subject: Re: Map models proposal from Jean Message-ID: <9311052129.AA18821@mendel.agron.iastate.edu> Date: 5 Nov 93 21:29:15 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 169 I have a question. Does ?Map refer to what are now called ?Chromosome and ?Linkage_Group ?? Thanks - Lisa :-) ----- Begin Included Message ----- From BIOSCI-REQUEST@net.bio.net Fri Nov 5 14:08:25 1993 Received: from net.bio.net by mendel.agron.iastate.edu (4.1/UW-NDC Revision: 2.21 ) id AA18460; Fri, 5 Nov 93 14:08:22 CST Received: by net.bio.net (5.65/IG-2.0) id AA04750; Fri, 5 Nov 93 12:02:15 -0800 Received: by net.bio.net (5.65/IG-2.0) id AA04730; Fri, 5 Nov 93 12:02:10 -0800 Message-Id: <9311052002.AA04730@net.bio.net> To: acedb@net.bio.net From: jlmccarthy@lbl.gov (John L. McCarthy) Subject: Map models proposal from Jean Date: 5 Nov 93 19:47:26 GMT Followup-To: bionet.software.acedb Nntp-Posting-Host: 128.3.140.95 Status: R I am delighted to see that Jean Thierry-Mieg is now receiving and contributing to this newsgroup (see "stepping in" 11/4/93). He just sent the following proposal for a more general map model and asked me to forward it to the newsgroup for discussion: -John McCarthy Received: from lbl.gov by ux5.lbl.gov (4.1/1.39) Date: Fri, 5 Nov 93 13:15:17 GMT From: mieg@kaa.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) November 6, 1993 A project for an Acedb model revision by J.T-M In collaboration with Otto, I came up with the following running prototype. Any feedback hartly welcome. the root of the matter is contained in this mini model. ?Map Type UNIQUE Genetic // this flag can be used to define subclasses Cytogenetic // Chromosome could be Map, filtered Cytogenetic Physical Contains Locus ?Locus XREF Map // to look tidy Also ANY XREF Map // Anything else ?map_location UNIQUE Position UNIQUE Float #map_error Multi_Position Float #map_error Ends Left UNIQUE Float #map_error Right UNIQUE Float #map_error ?map_error Error UNIQUE Float ?Locus Map ?Map XREF Locus #map_location Main_Marker ?Map XREF Main_Marker Inside Inside_YAC ?YAC XREF Contains Inside_Fragment ?Fragment XREF Locus Chrom_Band ?Chrom_Band XREF Locus ?Clone Position Map ?Map XREF Refers_to #map_location // position on vertical maps Inside Links ?Fragment XREF Link ?YAC Location Map ?Map XREF Refers_to #map_location Contains Locus ?Locus XREF Inside_YAC ************************************************************ RULE 1: MappingTags, governing the Map package behaviour are always 2 up from the actual objects. So far, i have defined this way: Contains, Inside, Outside i would consider Between, Does_Not_Contain RULE2: As far as the map display is concerned, anything in the Contains paragraph will appear on the map. In particular a Map may well contain another map. Its display will be specialised if it belongs to a class with a specialised display code (i.e.: Gene, Chrom_Band, Rearrangement, later submaps). Otherwise, any object containing the construction Map xxx Position 3.2 Error .3 will be displayed as a point locus (gMapDisplayAnyLocus) any with Map xxx Ends Left 4.2 Error .1 Right 4.8 Error .2 will be displeaed as a segment (gMapDisplayAnyInterval) RULE3: On firstpick (gMapSelect): a) The selected box, and all boxes refreeing to the same key turn lighblue. b) All neighbours (i.e. keys referred to in the selected obj) turn LIGHTGREEN c) All tags referred to via mappingTag (Inside, Outside etc) as obtained via a bsFlatten(mappingTag,2) recolor according to their relative position: GREEN if happy, RED if Problem, LIGHTRED if marginal. ************************************************************ Interesting properties: a) Every box on the map will be recolored according to the Inside, Outside etc mapping tags irrespective of their class, irrespective of their class and peculiar displays. b) I do not prerregister friends any more, i.e. sets of objetc coloring lightgreen in advance. This enormously simplifis the code. It also behaves much better because "friends" are not transitive. The overhead of accessing the object rather tahn a preregistered table is negligeable. It anticipates on the second pick(display) and is in fact faster than preregistering all sets of friends. c) Any new class will appear on the map if it XREF to a tag to the right of the Contains tag. In particular, in the runnig prototype i have a well behaved YAC/STS map, when the code was compiled before including these classes in the model files. This completely solves the problem of the Bentley database who had to call his YACs deficiencies and the like. d) The generic map making algorithms depend only on the mappingTags and thus run on arbitrary maps. e) As a side effect, you will note that the mappingTags are part of the models but will not appear in the ace files. Furthermore, a YAC say can be said to Contains other yacs, clones, STS, genes, i.e. any etherogeneous set you want, since you can define one level of tags under the mappingTag contains. f) As required by John McCarthy and others, the numbers defining the map position are now explicitelly qualified. ************************************************************** Again , i would welcome any sort of comments. -Jean -- posted by... +=====================================================================+ | John L. McCarthy. . | Internet:..JLMcCarthy@lbl.gov | | Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY@LBL | | Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 | | 1 Cyclotron Road . | | | BERKELEY, CA 94720, U.S.A. . | FAX: (510) 486-4004 | +=====================================================================+ ----- End Included Message ----- From owner-acedb@net.bio.net Thu Nov 04 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!news-feed-1.peachnet.edu!gatech!howland.reston.ans.net!agate!dog.ee.lbl.gov!csrgate3.lbl.gov!user From: jlmccarthy@lbl.gov (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: Map models proposal from Jean Message-ID: Date: 5 Nov 93 19:47:26 GMT Followup-To: bionet.software.acedb Organization: Lawrence Berkeley Laboratory Lines: 138 NNTP-Posting-Host: 128.3.140.95 I am delighted to see that Jean Thierry-Mieg is now receiving and contributing to this newsgroup (see "stepping in" 11/4/93). He just sent the following proposal for a more general map model and asked me to forward it to the newsgroup for discussion: -John McCarthy Received: from lbl.gov by ux5.lbl.gov (4.1/1.39) Date: Fri, 5 Nov 93 13:15:17 GMT From: mieg@kaa.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) November 6, 1993 A project for an Acedb model revision by J.T-M In collaboration with Otto, I came up with the following running prototype. Any feedback hartly welcome. the root of the matter is contained in this mini model. ?Map Type UNIQUE Genetic // this flag can be used to define subclasses Cytogenetic // Chromosome could be Map, filtered Cytogenetic Physical Contains Locus ?Locus XREF Map // to look tidy Also ANY XREF Map // Anything else ?map_location UNIQUE Position UNIQUE Float #map_error Multi_Position Float #map_error Ends Left UNIQUE Float #map_error Right UNIQUE Float #map_error ?map_error Error UNIQUE Float ?Locus Map ?Map XREF Locus #map_location Main_Marker ?Map XREF Main_Marker Inside Inside_YAC ?YAC XREF Contains Inside_Fragment ?Fragment XREF Locus Chrom_Band ?Chrom_Band XREF Locus ?Clone Position Map ?Map XREF Refers_to #map_location // position on vertical maps Inside Links ?Fragment XREF Link ?YAC Location Map ?Map XREF Refers_to #map_location Contains Locus ?Locus XREF Inside_YAC ************************************************************ RULE 1: MappingTags, governing the Map package behaviour are always 2 up from the actual objects. So far, i have defined this way: Contains, Inside, Outside i would consider Between, Does_Not_Contain RULE2: As far as the map display is concerned, anything in the Contains paragraph will appear on the map. In particular a Map may well contain another map. Its display will be specialised if it belongs to a class with a specialised display code (i.e.: Gene, Chrom_Band, Rearrangement, later submaps). Otherwise, any object containing the construction Map xxx Position 3.2 Error .3 will be displayed as a point locus (gMapDisplayAnyLocus) any with Map xxx Ends Left 4.2 Error .1 Right 4.8 Error .2 will be displeaed as a segment (gMapDisplayAnyInterval) RULE3: On firstpick (gMapSelect): a) The selected box, and all boxes refreeing to the same key turn lighblue. b) All neighbours (i.e. keys referred to in the selected obj) turn LIGHTGREEN c) All tags referred to via mappingTag (Inside, Outside etc) as obtained via a bsFlatten(mappingTag,2) recolor according to their relative position: GREEN if happy, RED if Problem, LIGHTRED if marginal. ************************************************************ Interesting properties: a) Every box on the map will be recolored according to the Inside, Outside etc mapping tags irrespective of their class, irrespective of their class and peculiar displays. b) I do not prerregister friends any more, i.e. sets of objetc coloring lightgreen in advance. This enormously simplifis the code. It also behaves much better because "friends" are not transitive. The overhead of accessing the object rather tahn a preregistered table is negligeable. It anticipates on the second pick(display) and is in fact faster than preregistering all sets of friends. c) Any new class will appear on the map if it XREF to a tag to the right of the Contains tag. In particular, in the runnig prototype i have a well behaved YAC/STS map, when the code was compiled before including these classes in the model files. This completely solves the problem of the Bentley database who had to call his YACs deficiencies and the like. d) The generic map making algorithms depend only on the mappingTags and thus run on arbitrary maps. e) As a side effect, you will note that the mappingTags are part of the models but will not appear in the ace files. Furthermore, a YAC say can be said to Contains other yacs, clones, STS, genes, i.e. any etherogeneous set you want, since you can define one level of tags under the mappingTag contains. f) As required by John McCarthy and others, the numbers defining the map position are now explicitelly qualified. ************************************************************** Again , i would welcome any sort of comments. -Jean -- posted by... +=====================================================================+ | John L. McCarthy. . | Internet:..JLMcCarthy@lbl.gov | | Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY@LBL | | Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 | | 1 Cyclotron Road . | | | BERKELEY, CA 94720, U.S.A. . | FAX: (510) 486-4004 | +=====================================================================+ From owner-acedb@net.bio.net Fri Nov 05 22:00:00 1993 Path: biosci!sanger.ac.uk!rd From: rd@sanger.ac.uk Newsgroups: bionet.software.acedb Subject: comments on Jean's models proposals Message-ID: <9311061538.AA06655@sanger.ac.uk> Date: 6 Nov 93 15:38:05 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 69 Here are some comments on Jean's ideas for the new models. First, in reply to Lisa, yes ?Map would replace ?Chromosome and ?Linkage_group. Also, I guess that Refers_to in the ?Clone and ?YAC models should be the same as Also in the ?Map model. I like the 2nd level map tag idea very much (RULE 1). Very natural. Better than any of the ideas we have discussed before. I support Inside, Outside. Is Contains the same as Inside, or does it refer to an interval within and interval? You could consider: Overlaps, Does_not_overlap for 2 intervals Requiring more thought: Order, taking a sequence of mappable objects left -> right after the next tag. Each sequence would have guaranteed order Minor point: as we discussed, you might have some other classes than Locus specifically in ?Map. I also strongly support ?map_location and ?map_error, though I would prefer to maintain upper case for models, i.e. ?Map_location and ?Map_error (a minor point since you never see them except in models.wrm). But I am not sure about Multi_position. What is that for, and how will it be used? The only area I disagree is over colours (RULE 3). I think there is no natural link from LIGHTBLUE to LIGHTGREEN, and it is a waste of a precious primary hue. I propose WHITE on BLUE for the object picked, and LIGHTBLUE background for neighbours. WHITE on BLUE (inverted) is much more striking, and I think the primary pick should be striking. I agree entirely that neighbours should be found on the fly. This is done a little in pmap and fmap already (e.g. the probes in pmap). The time is negligible. Also I disagree with the map data linked coloring scheme. We find it VERY useful to see the Inside-related objects coloured one colour, and Outside-related objects another colour. I liked LIGHTBLUE and LIGHTGREEN, but I guess we have preempted LIGHTBLUE. We could use CYAN and GREEN if you want. I would prefer to still see this primary information if objects are unhappy. Normally that allows you to assess why they are unhappy. What about changing the foreground colour to RED if things are unhappy? Alternatively, it would be fine to be able to switch on and off your proposed red colouring with a button. I see potential for the LIGHTRED variant, though I am not sure how it will be determined. The reason for being able to hide the red colouring is that red objects are very arresting, and often when working with raw data you want to be able to leave conflicting data in place without it dominating your field of view (cf Bob's approach to sequence editing during assembly). I agree we definitely want a map to be able to contain another Map (RULE 2). There are various ways this might work for display. I can imagine (1) giving a singular linear transformation, perhaps by defining where the endpoints of the contained map (Extent values) lie on the containing map. (2) piecewise linear interpolation, tying all shared loci in the contained map to their locations in the containing map, and interpolating in between (as with the physical map in the new worm gmap display). Note that there are likely to be conflicts when doing this. (3) more complicated things - like specifying explicitly a non-linear transformation (splines?). Richard From owner-acedb@net.bio.net Fri Nov 05 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!overload.lbl.gov!csrgate1.lbl.gov!user From: jlmccarthy@lbl.gov (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: Questions & Comments on Jean's Map models Message-ID: Date: 6 Nov 93 16:42:31 GMT References: Followup-To: bionet.software.acedb Organization: Lawrence Berkeley Laboratory Lines: 141 NNTP-Posting-Host: csrgate1.lbl.gov I am very glad to see Jean's proposal for making map representation more general in ACEDB. I have a few questions and comments, as indicated below, interspersed among the lines from Jean's proposal (which are indented and preceded by ">"). I also will follow up with a separate message (not thread) about map display. +=====================================================================+ | John L. McCarthy. . | Internet:..JLMcCarthy@lbl.gov | | Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY@LBL | | Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 | | 1 Cyclotron Road . | | | BERKELEY, CA 94720, U.S.A. . | FAX: (510) 486-4004 | +=====================================================================+ >?Map Type UNIQUE Genetic // this flag can be used to define subclasses > Cytogenetic // Chromosome could be Map, filtered Cytogenetic Please clarify the comment -- perhaps with an example > > Physical > Contains Locus ?Locus XREF Map // to look tidy > Also ANY XREF Map // Anything else Should "Also" be "Refers_to"? compare ?YAC/Location/Map/?Map XREF Refers_to > > >?map_location UNIQUE Position UNIQUE Float #map_error > Multi_Position Float #map_error > Ends Left UNIQUE Float #map_error > Right UNIQUE Float #map_error > >?map_error Error UNIQUE Float Why is this a separate object, rather than using Float Float in each above? Is it in order to have an explicit tag, or because of UNIQUE? Does this imply that postions can have multiple Errors? > > >?Locus Map ?Map XREF Locus #map_location > Main_Marker ?Map XREF Main_Marker > Inside Inside_YAC ?YAC XREF Contains > Inside_Fragment ?Fragment XREF Locus > Chrom_Band ?Chrom_Band XREF Locus > >?Clone Position Map ?Map XREF Refers_to #map_location // position on vertical maps Should be position on either vertical or horizontal (or other?) maps > Inside Links ?Fragment XREF Link Please explain what the ?Fragment object is supposed to be (not a clone?) > >?YAC Location Map ?Map XREF Refers_to #map_location Could you alternatively make ?YAC (P1, etc.) simply a sub-class of clone? > Contains Locus ?Locus XREF Inside_YAC > > >************************************************************ Suggest you add a heading here "MAP DISPLAY MODULE BEHAVIOR" > >RULE 1: >MappingTags, governing the Map package behaviour are always 2 up >from the actual objects. > >So far, i have defined this way: Contains, Inside, Outside > i would consider Between, Does_Not_Contain > >RULE2: >As far as the map display is concerned, anything in the Contains >paragraph will appear on the map. In particular a Map may well >contain another map. > >Its display will be specialised if it belongs to a class with a >specialised display code (i.e.: Gene, Chrom_Band, Rearrangement, >later submaps). > >Otherwise, any object containing the construction >Map xxx Position 3.2 Error .3 >will be displayed as a point locus (gMapDisplayAnyLocus) > >any with >Map xxx Ends Left 4.2 Error .1 > Right 4.8 Error .2 >will be displeaed as a segment (gMapDisplayAnyInterval) > >RULE3: >On firstpick (gMapSelect): >a) The selected box, and all boxes refreeing to the same key turn >lighblue. When will multiple boxes refer to the same key? (loci with multiple positons?) >b) All neighbours (i.e. keys referred to in the selected obj) turn >LIGHTGREEN >c) All tags referred to via mappingTag (Inside, Outside etc) as >obtained via a bsFlatten(mappingTag,2) recolor according to their Please explain what bsFlatten does >relative position: GREEN if happy, RED if Problem, LIGHTRED if marginal. > >************************************************************ > >Interesting properties: > >a) Every box on the map will be recolored according to the Inside, >Outside etc mapping tags irrespective of their class, irrespective >of their class and peculiar displays. > >b) I do not prerregister friends any more, i.e. sets of objetc >coloring lightgreen in advance. This enormously simplifis the code. >It also behaves much better because "friends" are not transitive. >The overhead of accessing the object rather tahn a preregistered >table is negligeable. It anticipates on the second pick(display) and >is in fact faster than preregistering all sets of friends. > >c) Any new class will appear on the map if it XREF to a tag to the >right of the Contains tag. In particular, in the runnig prototype i >have a well behaved YAC/STS map, when the code was compiled before >including these classes in the model files. This completely solves >the problem of the Bentley database who had to call his YACs >deficiencies and the like. > >d) The generic map making algorithms depend only on the mappingTags >and thus run on arbitrary maps. It would be good to have a separate discussion of these algorithms > >e) As a side effect, you will note that the mappingTags are part of >the models but will not appear in the ace files. Furthermore, a YAC >say can be said to Contains other yacs, clones, STS, genes, i.e. any >etherogeneous set you want, since you can define one level of tags HETEROGENEOUS? This is really good! >under the mappingTag contains. > >f) As required by John McCarthy and others, the numbers defining the >map position are now explicitelly qualified. +=====================================================================+ | John L. McCarthy. . | Internet:..JLMcCarthy@lbl.gov | | Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY@LBL | | Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 | | 1 Cyclotron Road . | | | BERKELEY, CA 94720, U.S.A. . | FAX: (510) 486-4004 | +=====================================================================+ From owner-acedb@net.bio.net Sat Nov 06 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!swrinde!gatech!howland.reston.ans.net!agate!overload.lbl.gov!csrgate1.lbl.gov!user From: jlmccarthy@lbl.gov (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: MappingTags Questions Message-ID: Date: 7 Nov 93 14:57:46 GMT References: Followup-To: bionet.software.acedb Organization: Lawrence Berkeley Laboratory Lines: 26 NNTP-Posting-Host: csrgate1.lbl.gov Here are a couple of additional questions about Jean's proposed mappingTags. > >RULE 1: >MappingTags, governing the Map package behaviour are always 2 up >from the actual objects. What does this mean? Please give an example or two. > >So far, i have defined this way: Contains, Inside, Outside > i would consider Between, Does_Not_Contain Please define what each of these means for another object. "Contains" and "Does_Not_Contain" seem pretty clear. "Inside" and "Outside" do not. Are they synonyms for "Inside" and "Outside"? If not, how do they differ? [I see Richard has some similar questions] What kinds of display behaviors do you see for each of these? >e) As a side effect, you will note that the mappingTags are part of >the models but will not appear in the ace files. I need an example here too. I see how Inside_YAC, Inside_Fragment, etc. could be automatically generated, so they do not NEED to part of input .ace .ace files. But once that happens, do you mean that you are going to specify that they NOT be SAVED in .ace files? If so, how? -John McCarthy From owner-acedb@net.bio.net Sat Nov 06 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!agate!overload.lbl.gov!csrgate1.lbl.gov!user From: jlmccarthy@lbl.gov (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: Map Display proposals from Jean Message-ID: Date: 7 Nov 93 15:00:36 GMT References: Followup-To: bionet.software.acedb Organization: Lawrence Berkeley Laboratory Lines: 121 NNTP-Posting-Host: csrgate1.lbl.gov I like Jean's proposals for making map representation and display more general in ACEDB. I'm also glad to see that Richard endorses most of them. Here are some further ideas on map DISPLAY, interspersed among lines from Jean's proposal (which are indented and preceded by ">"). > >RULE2: >As far as the map display is concerned, anything in the Contains >paragraph will appear on the map. In particular a Map may well >contain another map. > >Its display will be specialised if it belongs to a class with a >specialised display code (i.e.: Gene, Chrom_Band, Rearrangement, >later submaps). > >Otherwise, any object containing the construction >Map xxx Position 3.2 Error .3 >will be displayed as a point locus (gMapDisplayAnyLocus) > >any with >Map xxx Ends Left 4.2 Error .1 > Right 4.8 Error .2 >will be displeaed as a segment (gMapDisplayAnyInterval) > >RULE3: >On firstpick (gMapSelect): >a) The selected box, and all boxes refreeing to the same key turn >lighblue. >b) All neighbours (i.e. keys referred to in the selected obj) turn >LIGHTGREEN >c) All tags referred to via mappingTag (Inside, Outside etc) as >obtained via a bsFlatten(mappingTag,2) recolor according to their >relative position: GREEN if happy, RED if Problem, LIGHTRED if marginal. > Although these colours and behaviors seem reasonable for system-defaults, it would be nice to give individual database administrators and users more control to set their own visual characteristics for map displays. Richard's comments underscore the fact that people sometimes want different color coding. Some of our users want to be able to specify either vertical or horizontal display of any map. They also would like to have more user and/or data administrator control over setting display behaviors such as color [SEE ALSO MY SEPARATE NEWS ITEM ON COLOR IN GENERAL] pattern (so color is not always necessary) line width (for segments) symbol (for points) typography (for alphanumeric characters) visibility (i.e., whether object appears on map display) Each of these could start off with a well chosen set of defaults. Furthermore, we would like users to be able to reset some or all of these visual characteristics for abitrary subsets of map objects, depending on the results of arbitrary queries. For example, the flybase project wants to be able to visually distinguish those clones that have been verified by in-situ as well as PCR experiments. Sometimes they may want to ONLY display those clones, while hiding others. I can imagine some mechanism (like the table-definer window and display control windows) that would allow users to store a query along with a set of map display characteristics that would bring up the particular kind of map they want to see. At another level, perhaps we could let data administrators set global defaults in a configuration file (ala options.wrm), where they could assign database-specific map display defaults to particular classes, subclasses, "Inside", "Outside", etc. >************************************************************ > >Interesting properties: > >a) Every box on the map will be recolored according to the Inside, >Outside etc mapping tags irrespective of their class, irrespective >of their class and peculiar displays. Very good to do this in a general way. > >b) I do not prerregister friends any more, i.e. sets of objetc >coloring lightgreen in advance. This enormously simplifis the code. >It also behaves much better because "friends" are not transitive. >The overhead of accessing the object rather tahn a preregistered >table is negligeable. It anticipates on the second pick(display) and >is in fact faster than preregistering all sets of friends. > >c) Any new class will appear on the map if it XREF to a tag to the >right of the Contains tag. In particular, in the runnig prototype i >have a well behaved YAC/STS map, when the code was compiled before >including these classes in the model files. This completely solves >the problem of the Bentley database who had to call his YACs >deficiencies and the like. Excellent! > >d) The generic map making algorithms depend only on the mappingTags >and thus run on arbitrary maps. > >e) As a side effect, you will note that the mappingTags are part of >the models but will not appear in the ace files. Furthermore, a YAC >say can be said to Contains other yacs, clones, STS, genes, i.e. any >etherogeneous set you want, since you can define one level of tags >under the mappingTag contains. Is it possible to assign different default kinds of visual behavior for each type of mappingTag (Contains, etc.)? -- e.g., x for hits and o for misses? > >f) As required by John McCarthy and others, the numbers defining the >map position are now explicitelly qualified. What measurement units will be used for map positions? It probably needs to be something relative, like percent of the whole map, in order to support recursive nesting of maps. > +=====================================================================+ > | John L. McCarthy. . | Internet:..JLMcCarthy@lbl.gov | > | Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY@LBL | > | Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 | > | 1 Cyclotron Road . | | > | BERKELEY, CA 94720, U.S.A. . | FAX: (510) 486-4004 | > +=====================================================================+ From owner-acedb@net.bio.net Sat Nov 06 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!agate!overload.lbl.gov!csrgate1.lbl.gov!user From: jlmccarthy@lbl.gov (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: Color representation in ACEDB Message-ID: Date: 7 Nov 93 15:02:40 GMT References: Followup-To: bionet.software.acedb Organization: Lawrence Berkeley Laboratory Lines: 33 NNTP-Posting-Host: csrgate1.lbl.gov Recent discussion of map displays reminds me of a more general issue -- color. ACEDB currently relies too much on color to indicate different types of information in maps and other displays. Color can be very effective, but we should not be completely DEPENDENT on color encoding. Some people do not have color monitors on their workstations. Many do not have color printers easily at hand. Thus it is important to be able to redundantly encode information in typography, shape, thickness, and/or pattern -- as well as in color. The current ACEDB system attempts to make some mappings between different colors and patterns, but the current mappings often fail to produce good results. Many colors yield patterns that hide labels on monochrome displays and printers. It probably would be best to try to rethink the use of consistent colors and corresponding patterns throughout ACEDB, with the help of experts in the areas of color, graphic computer interface design, X-Windows color and pattern representation, Postscript color vs. pattern representation, etc. Are there any people with some of this expertise who we could get to volunteer? +=====================================================================+ | John L. McCarthy. . | Internet:..JLMcCarthy@lbl.gov | | Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY@LBL | | Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 | | 1 Cyclotron Road . | | | BERKELEY, CA 94720, U.S.A. . | FAX: (510) 486-4004 | +=====================================================================+ From owner-acedb@net.bio.net Sun Nov 07 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!pipex!sunic!kth.se!kiev.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb Subject: Re: GenBank File Converters Message-ID: <2bl0i5$6lh@kiev.physchem.kth.se> Date: 8 Nov 93 08:38:29 GMT References: <9311052042.AA20155@fly2.berkeley.edu.maggot> Sender: staffan@biochem.kth.se Distribution: bionet Organization: Biochemistry, KTH, Stockholm Lines: 24 Nntp-Posting-Host: kiev.physchem.kth.se In article <9311052042.AA20155@fly2.berkeley.edu.maggot> gregg@FLY2.BERKELEY.EDU (Gregg Helt) writes: > >From Geoff Hughes: > >>Has anyone ported Mike Cherry's gb2ace.c program for VMS to a UNIX platform? >>It would be extraordinarily helpful to our efforts. > >Hmm, well not exactly, but I've done some stuff that might be useful. >I've been writing conversion code in Perl. This language was basicly >designed to do just this kind of text manipulation/conversion, and I >much prefer it over C for dealing with text. [ ... the rest of Gregg's message deleted ... ] I second Gregg on that point, perl is very easy to get running and doing what you want... I've also written routines in perl for processing GenBank flatfiles into .ace, or one routine rather. It takes a file of flatfile entries and massages them into .ace, so Gregs seems a bit more flexible... There is an early, buggy(?), version available at weeds@mgh.harvard.edu, if you want to have a look. /staffan From owner-acedb@net.bio.net Tue Nov 09 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!psinntp!barilvm!kineret.huji.ac.il!wisipc.weizmann.ac.il!inherit4.weizmann.ac.il!lsprilus From: lsprilus@weizmann.weizmann.ac.il (Jaime Prilusky) Newsgroups: bionet.software.acedb Subject: Re: Testing one two three four Message-ID: <1993Nov10.060920.9445@wisipc.weizmann.ac.il> Date: 10 Nov 93 06:09:20 GMT References: <9311041900.AA23595@s27w007.pswfs.gov> Sender: news@wisipc.weizmann.ac.il (News User) Organization: Weizmann Institute of Science Lines: 12 X-Xxmessage-Id: X-Xxdate: Wed, 10 Nov 93 06:08:19 GMT X-Useragent: Version 1.1.3 In article <9311041900.AA23595@s27w007.pswfs.gov> Bradley K. Sherman, bks@S27W007.PSWFS.GOV writes: >Biosci claims to have fixed the problem and this >message should appear in the USENET/BIOSCI >conference bionet.software.acedb.... I got it from bionet.software.acedb. Dr Jaime Prilusky, Head Bioinformatics Unit ! LSPRILUS@WEIZMANN.WEIZMANN.AC.IL Weizmann Institute of Science ! fax: 972-8-344113 76100 Rehovot - Israel ! tel: 972-8-343456 From owner-acedb@net.bio.net Wed Nov 10 22:00:00 1993 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: ACEDB vs. Linux Message-ID: <9311112231.AA04228@greengenes.cit.cornell.edu> Date: 11 Nov 93 22:31:11 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 44 > Date: Wed, 3 Nov 93 14:00:13 PST > From: dbaillie@darwin.mbb.sfu.ca (David L. Baillie) > To: matthews@greengenes.cit.cornell.edu > Subject: Re: ACEDB vs. Linux > > No, what version of Linux are you running? And what release of ACeDB. > we have not put 1-10 on linux yet, as we cannot get the dataset to > assemble, we are not sure where the problem lies, I gather Solaris 2.0 > chokes on the new c. elegans data release also, so Linux is not alone. > I will forward your message to Ken Clark, who was the person who > did the port, he may be able to suggest something. > > dave Well, I fixed my problem. Don't know if it's related to yours or to the Solaris problem, but it looks like the kind of thing that might be. Fix: In models.wrm, change "Text" to "?Text" globally. Diagnosis: Apparently Linux can't handle long lines (e.g. 200 characters) as Text, only as ?Text. Symptoms: xace exits with a segmentation fault when an object containing a long Text line is picked, or when an attempt is made to delete the object, or to load another object that links to it. Notes: 1. The problem does not occur on the Sparc (xace 1.91 and 1-10), or SGI or DEC (xace 1.91; 1-10 not tested). 2. Freshly loaded objects usually can be manipulated without a problem. The program must be exited and restarted before the failures start happening. 3. The smallest dataset that was demonstrated to fail was two objects, not linked to each other. Versions and configurations: xace 1-9 or 1-10, CACHE1 800 to 10000, CACHE2 256 to 2000, DISK 10000 to 20000 Linux 0.99 patchlevel 13 8 MB RAM, 16 to 42 MB swap machine Texas Instruments 486DX2/50 MHz Dave, Ken, Jeff, thanks for your help in working on this. - Dave Matthews From owner-acedb@net.bio.net Thu Nov 11 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!howland.reston.ans.net!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!hsdndev!nmr-z!Frodo.MGH.Harvard.EDU!CHERRY From: cherry@Frodo.MGH.Harvard.EDU Newsgroups: bionet.software.acedb Subject: Re: ACEDB vs. Linux Message-ID: <1993Nov12.164359.21348@nmr-z.mgh.harvard.edu> Date: 12 Nov 93 16:43:59 GMT References: <9311112231.AA04228@greengenes.cit.cornell.edu> Sender: usenet@nmr-z.mgh.harvard.edu (User for USENET news postings) Reply-To: cherry@Frodo.MGH.Harvard.EDU Distribution: bionet Organization: Molecular Biology, Massachusetts General Hospital Lines: 16 Nntp-Posting-Host: frodo.mgh.harvard.edu >In article <9311112231.AA04228@greengenes.cit.cornell.edu>, matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") writes: >>Well, I fixed my problem. Don't know if it's related to yours or to the >>Solaris problem, but it looks like the kind of thing that might be. >> I recently received messages from Jean and Richard indicating that they have fixed the Solaris version of xace. I haven't tried it myself. We downgraded our SPARCClassic to SunOS 4.1.3C so that we are only running one OS on our SPARCs. This fixed version has not been placed on ncbi.nlm.nih.gov, I haven't looked at the other ftp archives. A message on ncbi.nlm.nih.gov says that if you want more information on the fixed Solaris version of ACEDB contact Jean (mieg@kaa.cnrs-mop.fr). Mike From owner-acedb@net.bio.net Mon Nov 15 22:00:00 1993 Path: biosci!daresbury!not-for-mail From: kirbym@har-rbu.mrc.ac.uk Newsgroups: bionet.software.acedb Subject: More on Jean's models Message-ID: <2cb00q$nb1@mserv1.dl.ac.uk> Date: 16 Nov 93 16:44:10 GMT Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Lines: 152 Original-To: acedb@dl.ac.uk Having been away for a week I see that there has been some discussion about the ACeDB ?Map model definition. As I had to get a demonstration ready recently for the mouse data I asked Richard for the new 2.0 map code. This linked in well with the rest of the ACeDB code but of course used the new (or a version of the new) model definitions. Having spent some considerable time implementing models and code for the cytogenetic map, the following comments are based on my own experience and how I see my data fitting in with the new ?Map model definition. The mouse cytogenetic data includes loci with locations derived mainly from hybridisation in situ (HIS) and somatic cell (SC) techniques and chromosomal anomalies (or rearrangements) with cytogenetic breakpoints. It is good that the ?Map can be defined as being of type Genetic, Cytogenetic or Physical. However for the cytogenetic map I feel the proposed definitions for ?Locus and ?Map_location need some more thought. > ?Locus Map ?Map XREF Locus #Map_location > Main_Marker ?Map XREF Main_Marker > Inside Inside_YAC ?YAC XREF Contains > Inside_Fragment ?Fragment XREF Locus > Chrom_Band ?Chrom_Band XREF Locus > ?Map_location UNIQUE Position UNIQUE Float #map_error > Multi_Position Float #map_error > Ends Left UNIQUE Float #map_error > Right UNIQUE Float #map_error 1. Presumably a Locus with a Chrom_Band tag defined will be referring to a cytogenetic location with the data coming from either HIS or SC or some other technique. How will this ?Locus definition handle genes whose locations have been determined by several different techniques and the results show different chromosome band(s)? Or even, what if you have data from several experiments of the same type, eg HIS, and the results differ? Using the 2.0 models and code, I ended up defining separate objects of class ?Interval for each locus location. Through appropriate tags and cross referencing, each location object could be linked back to its parent locus and each parent locus could list its cytogenetic location(s). One advantage of this is that you can add to the object relevant comments and references. 2. For purely semantic reasons I don't like the definition: Chrom_Band ?Chrom_Band XREF Locus If the location of a locus is uncertain, two bands may be given to specify the range of bands within which the locus may be located, eg Mouse_gene 12A1-A3 or Human_gene 1p35-p31. This definition will list the two bands at the ends of the range, thereby implicitly stating that the locus has two locations. I would prefer to see: Chrom_Band ?Chrom_Band ?Chrom_Band which to my mind says that the locus is located somewhere within the range specified by the two bands. If of course, the locus does have more than one location then they can still be listed. 3. Richard explained at the recent Boston ACeDB workshop that the new ?Map would have fewer data types. Many of the current data types would be composed of essentially two types - a Locus and an Interval. Does the proposed model definition do away with the ?Interval class, or even the concept? Maybe ?Map_location is replacing that functionality? 4. For chromosome anomalies, the ?Map_location may have to be modified to include chromosome bands. Chromosome anomalies with two breakpoints on the same chromosome can be treated as Intervals and placed on the genetic and/or cytogenetic maps as appropriate, eg deletions, insertions, transpositions, etc. (Chromosome anomalies have actually been defined with their own class structure but have links to these Intervals where appropriate. In this way complex anomalies involving several segments can be defined.) ie ?Map_location UNIQUE Position UNIQUE Float #map_error Multi_Position Float #map_error Ends Left_pos UNIQUE Float #map_error Left_band ?Chrom_Band ?Chrom_Band Right_pos UNIQUE Float #map_error Right_band ?Chrom_Band ?Chrom_Band Again the two Chrom_Bands are to specify the range if an end point is uncertain. However a breakpoint may fall "Within" a band (range) or at the "Junction" between two bands. So this is not adequate. In fact to properly define anomaly breakpoints you must know the anomaly, the anomaly type and which chromosome it falls on. Data may be available for both cytogenetic locations and genetic positions. The latter may include the loci with which the breakpoint was mapped by linkage experiments. To handle all this data for a single breakpoint I ended up defining a sub class called ?Anomaly_bkpt which could be used by both the parent chromosome anomaly object and the Interval object. The disadvantage of using a sub class for the breakpoint data is that the data is not easily accessible. 5. Perhaps, Jean would like to consider the tags "Within" and "Junction". Although "Within" and "Between" could be regarded as equivalent. Something else to consider (which I have not) are the wonderfully precise, yet imprecise definitions, such as "near the proximal end of band xxx"! 6. In answer to John McCarthy's comment about "when will multiple boxes refer to the same key?", it might be that an Interval of type anomaly is defined both genetically and cytogenetically. It is one object but would appear as two separate boxes on the same map - unless the cytogenetic map is a completely separate display. 7. Continuing with cytogenetic definitions. One of the things that I have done recently was to define some translocation breakpoints with both genetic and cytogenetic locations as class ?Locus so that they could appear as marker loci on the genetic map but with a line linking their genetic position to the chromosome band(s) they were located within. (Yes, this is a duplication of data as the translocations are also defined as chromosome anomalies but I knew no other way.) Of course, translocations have breakpoints on two chromosomes. The following does have some relevance to the new models if paralogous genes with locations on several different chromosomes are to eventually be considered. The ?Locus definition (Map ?Map Float) handles several chromosomes very well. However, because of the model tree structure, any ?Chrom_Band definition MUST immediately follow ?Map if the right band on the right chromosome on the right map is to be found for a particular locus (eg CytoMap ?Map ?Chrom_Band ?Chrom_Band). Because of this, ?Map was defined several times in the ?Locus model which I am not happy about. Any suggestions? Ideally of course, it should be defined once and in such a way that the routine in the gMapDisplay code which checks for a valid chromosome and position only has to check in one place. Is this relevant to Multi_Position? I am not sure what that is doing? 8. John McCarthy stated "What measurement units will be used for map positions? It probably needs to be something relative, like percent of the whole map, in order to support recursive nesting of maps." That's fine but the map should be able to suport different measurements, such as centiMorgans, kilobases, megabases and percent of total chromosome length. 9. Yes, I support the use of MappingTags and I like the idea of "Containing" heterogeneous data and other Maps or parts of Maps, if it can be done. But I would like to see how all this works in practice. Finally, one thing that does worry me, is that as time goes on more people will be developing code to fulfill functions not already covered by the main ACeDB code. With the main database in a constant state of flux (which is not altogether a bad thing), this could mean a lot of work just to maintain existing efforts, not to mention the reinventing the wheel syndrome. I personally don't mind if ACeDB provides me with all the functionality needed for my data. But I DO MIND if I spend time working on some aspect of it only to find two months later that it has all been a complete and utter waste of time and effort. Could we not have some coordination amongst the developers? Michelle Kirby Email: kirbym@uk.ac.mrc.har-rbu From owner-acedb@net.bio.net Tue Nov 23 22:00:00 1993 Path: biosci!CSR.LBL.GOV!victor From: victor@CSR.LBL.GOV (Victor Markowitz) Newsgroups: bionet.software.acedb Subject: ACEDB BNF & Parser Message-ID: <9311242221.AA29938@csr.lbl.gov> Date: 24 Nov 93 22:21:56 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 28 We intend to revisit the idea of mapping ACEDB models into OPM (Object-Protocol Model) schemas in order to allow having OPM `views' of ACEDB models. If nothing else, the OPM editor provides graphical browsing and documentation capabilities (postcript diagrams and latex document of classes) that may help documenting ACEDB models. We need for this an (independent) parser for ACEDB models based on the latest ACEDB BNF syntax. From discussions with Eric (LBL) and Detlef (DKFZ), it seems that no such parser exists. We have developed developed one with yacc & lex in Nov 1992. It would be nice to have an updated version developed with yacc++ (Detlef and others highly recommend yacc++). We are wondering if Jean or Richard ever cared to develop such a parser for ACEDB models that others can use. I think that such a parser is very desirable for keeping all ACEDB related efforts synchronized. We are also wondering what is the latest version of the BNF for ACEDB models- the last one we are aware of is dated Dec 1992 and was part of an incomplete document authored by Jean & Richard. I would appreciate anyone's help in clarifying our questions. Victor From owner-acedb@net.bio.net Tue Nov 23 22:00:00 1993 Path: biosci!agate!overload.lbl.gov!csrgate1.lbl.gov!user From: jlmccarthy@lbl.gov (John L. McCarthy) Newsgroups: bionet.software.acedb Subject: Questions & Comments on Jean's Map models Message-ID: Date: 6 Nov 93 16:42:31 GMT References: Followup-To: bionet.software.acedb Organization: Lawrence Berkeley Laboratory Lines: 141 NNTP-Posting-Host: csrgate1.lbl.gov I am very glad to see Jean's proposal for making map representation more general in ACEDB. I have a few questions and comments, as indicated below, interspersed among the lines from Jean's proposal (which are indented and preceded by ">"). I also will follow up with a separate message (not thread) about map display. +=====================================================================+ | John L. McCarthy. . | Internet:..JLMcCarthy@lbl.gov | | Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY@LBL | | Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 | | 1 Cyclotron Road . | | | BERKELEY, CA 94720, U.S.A. . | FAX: (510) 486-4004 | +=====================================================================+ >?Map Type UNIQUE Genetic // this flag can be used to define subclasses > Cytogenetic // Chromosome could be Map, filtered Cytogenetic Please clarify the comment -- perhaps with an example > > Physical > Contains Locus ?Locus XREF Map // to look tidy > Also ANY XREF Map // Anything else Should "Also" be "Refers_to"? compare ?YAC/Location/Map/?Map XREF Refers_to > > >?map_location UNIQUE Position UNIQUE Float #map_error > Multi_Position Float #map_error > Ends Left UNIQUE Float #map_error > Right UNIQUE Float #map_error > >?map_error Error UNIQUE Float Why is this a separate object, rather than using Float Float in each above? Is it in order to have an explicit tag, or because of UNIQUE? Does this imply that postions can have multiple Errors? > > >?Locus Map ?Map XREF Locus #map_location > Main_Marker ?Map XREF Main_Marker > Inside Inside_YAC ?YAC XREF Contains > Inside_Fragment ?Fragment XREF Locus > Chrom_Band ?Chrom_Band XREF Locus > >?Clone Position Map ?Map XREF Refers_to #map_location // position on vertical maps Should be position on either vertical or horizontal (or other?) maps > Inside Links ?Fragment XREF Link Please explain what the ?Fragment object is supposed to be (not a clone?) > >?YAC Location Map ?Map XREF Refers_to #map_location Could you alternatively make ?YAC (P1, etc.) simply a sub-class of clone? > Contains Locus ?Locus XREF Inside_YAC > > >************************************************************ Suggest you add a heading here "MAP DISPLAY MODULE BEHAVIOR" > >RULE 1: >MappingTags, governing the Map package behaviour are always 2 up >from the actual objects. > >So far, i have defined this way: Contains, Inside, Outside > i would consider Between, Does_Not_Contain > >RULE2: >As far as the map display is concerned, anything in the Contains >paragraph will appear on the map. In particular a Map may well >contain another map. > >Its display will be specialised if it belongs to a class with a >specialised display code (i.e.: Gene, Chrom_Band, Rearrangement, >later submaps). > >Otherwise, any object containing the construction >Map xxx Position 3.2 Error .3 >will be displayed as a point locus (gMapDisplayAnyLocus) > >any with >Map xxx Ends Left 4.2 Error .1 > Right 4.8 Error .2 >will be displeaed as a segment (gMapDisplayAnyInterval) > >RULE3: >On firstpick (gMapSelect): >a) The selected box, and all boxes refreeing to the same key turn >lighblue. When will multiple boxes refer to the same key? (loci with multiple positons?) >b) All neighbours (i.e. keys referred to in the selected obj) turn >LIGHTGREEN >c) All tags referred to via mappingTag (Inside, Outside etc) as >obtained via a bsFlatten(mappingTag,2) recolor according to their Please explain what bsFlatten does >relative position: GREEN if happy, RED if Problem, LIGHTRED if marginal. > >************************************************************ > >Interesting properties: > >a) Every box on the map will be recolored according to the Inside, >Outside etc mapping tags irrespective of their class, irrespective >of their class and peculiar displays. > >b) I do not prerregister friends any more, i.e. sets of objetc >coloring lightgreen in advance. This enormously simplifis the code. >It also behaves much better because "friends" are not transitive. >The overhead of accessing the object rather tahn a preregistered >table is negligeable. It anticipates on the second pick(display) and >is in fact faster than preregistering all sets of friends. > >c) Any new class will appear on the map if it XREF to a tag to the >right of the Contains tag. In particular, in the runnig prototype i >have a well behaved YAC/STS map, when the code was compiled before >including these classes in the model files. This completely solves >the problem of the Bentley database who had to call his YACs >deficiencies and the like. > >d) The generic map making algorithms depend only on the mappingTags >and thus run on arbitrary maps. It would be good to have a separate discussion of these algorithms > >e) As a side effect, you will note that the mappingTags are part of >the models but will not appear in the ace files. Furthermore, a YAC >say can be said to Contains other yacs, clones, STS, genes, i.e. any >etherogeneous set you want, since you can define one level of tags HETEROGENEOUS? This is really good! >under the mappingTag contains. > >f) As required by John McCarthy and others, the numbers defining the >map position are now explicitelly qualified. +=====================================================================+ | John L. McCarthy. . | Internet:..JLMcCarthy@lbl.gov | | Computer Science R&D MS 50B-3238 | Bitnet: ...JLMCCARTHY@LBL | | Lawrence Berkeley Laboratory .| telephone: (510) 486-5307 | | 1 Cyclotron Road . | | | BERKELEY, CA 94720, U.S.A. . | FAX: (510) 486-4004 | +=====================================================================+ From owner-acedb@net.bio.net Mon Nov 29 22:00:00 1993 Path: biosci!LBL.GOV!eademund From: eademund@LBL.GOV (Eric De Mund) Newsgroups: bionet.software.acedb Subject: acedb workshop Message-ID: <9311301754.AA03119@genome.lbl.gov> Date: 30 Nov 93 17:54:20 GMT Sender: daemon@net.bio.net Reply-To: Eric De Mund Distribution: bionet Organization: Lawrence Berkeley Laboratory, Genome Computing Group Lines: 54 People, I'm forwarding the following announcement from Jean Thierry-Mieg. Eric De Mund ------------------------------ Message-Id: <9311301823.AA25618@kaa.cnrs-mop.fr> Date: Tue, 30 Nov 93 18:23:31 GMT From: mieg@kaa.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) To: mcc@lirmm.fr Subject: acedb workshop I am proposing to organize the 1994 acedb workshop monday june 6, to saturday june 18 in Cargese, Corse (Corse is south of France, in the mediterranee) This place is equipped and used for summer school from may to october every year, this is the only slot yet available. The cost is around 3000F per person including lunch + lodging. Dinner is taken at the local village restaurant, or you can cook for yourself. It is possible to camp on site for free. The place is beautiful, nested on a private beach, with many trees around. And there is plenty of work space. I can find some funding to cover part of the local costs but certainly not pay for travels. The return ticket to Paris is around 1500 FF so 3000 + 1500 = 4500 FF around 900 US $ This can work if at least 40 people would come ideal is between 50 to 80. TYhis may be too large for us. Could you please let me know ASAP if you are interested. I do not need a full commitment, but I have to evaluate the number of participants roughly. I hope 2 weeks would: a) let us enjoy a very pleasant place b) give us time for actual programming to take place on many problems There would be, I hope, plenty of cpu around. Jean Thierry-Mieg mieg@kaa.cnrs-mop.fr ------------------------------ ****************************** From owner-acedb@net.bio.net Tue Nov 30 22:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.software.acedb Subject: IMPORTANT BIOSCI INFORMATION Message-ID: <9312011000.AA19172@net.bio.net> Date: 1 Dec 93 10:00:05 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 244 Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ. **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add your name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database is reindexed nightly for WAIS and waismail access (waismail is our WAIS e-mail server, more below) and will also be available for access via other gopher sites if they wish to permit it. The raw unindexed data is available for FTP from net.bio.net and is atomized sufficiently to allow import into your local RDBMS should you so desire. Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check our WAIS source or waismail e-mail server from time-to-time to see if your address information is still up-to-date. Send the message help to waismail@net.bio.net for instructions on using waismail. Leave the Subject: line in your message blank. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.gdb.org and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters) or alter any of the field identifiers such as "first name: ". Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 05-05-93 for 5 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 05-05-93, not 5-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIO-SOFTWARE bionet.software CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast Listing newsgroups on the comment: line is optional, of course. Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-acedb@net.bio.net Tue Nov 30 22:00:00 1993 Path: biosci!UX5.LBL.GOV!mccarthy From: mccarthy@UX5.LBL.GOV (John McCarthy) Newsgroups: bionet.software.acedb Subject: 1994 ACEDB Workshop Message-ID: <9312011312.AA28982@ux5.lbl.gov> Date: 1 Dec 93 13:14:12 GMT Sender: daemon@net.bio.net Reply-To: jlmccarthy@lbl.gov Distribution: bionet Lines: 51 Jean asked me to forward this message to the newsgroup. -John McCarthy, LBL Date: Tue, 30 Nov 93 18:23:31 GMT From: mieg@kaa.cnrs-mop.fr (Danielle et Jean Thierry-Mieg) Subject: acedb workshop I am proposing to organize the 1994 acedb workshop monday june 6, to saturday june 18 in Cargese, Corse (Corse is south of France, in the mediterranee) This place is equipped and used for summer school from may to october every year, this is the only slot yet available. The cost is around 3000F per person including lunch + lodging. Dinner is taken at the local village restaurant, or you can cook for yourself. It is possible to camp on site for free. The place is beautiful, nested on a private beach, with many trees around. And there is plenty of work space. I can find some funding to cover part of the local costs but certainly not pay for travels. The return ticket to Paris is around 1500 FF so 3000 + 1500 = 4500 FF around 900 US $ This can work if at least 40 people would come ideal is between 50 to 80. TYhis may be too large for us. Could you please let me know ASAP if you are interested. I do not need a full commitment, but I have to evaluate the number of participants roughly. I hope 2 weeks would: a) let us enjoy a very pleasant place b) give us time for actual programming to take place on many problems There would be, I hope, plenty of cpu around. Jean Thierry-Mieg mieg@kaa.cnrs-mop.fr From owner-acedb@net.bio.net Tue Nov 30 22:00:00 1993 Path: biosci!sanger.ac.uk!srk From: srk@sanger.ac.uk Newsgroups: bionet.software.acedb Subject: Re: acedb workshop Message-ID: <9312011412.AA08691@sanger.ac.uk> Date: 1 Dec 93 14:12:21 GMT References: <9311301754.AA03119@genome.lbl.gov> Sender: daemon@net.bio.net Distribution: bionet Lines: 2 ------------------------------------------------------------------------------- Simon Kelley. srk@sanger.ac.uk work: +44 223 494980 home: +44 223 832411