From owner-acedb@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!rutgers!uwm.edu!news-peer.gsl.net!news.gsl.net!news.uoregon.edu!newsfeed.orst.edu!newshub.tc.umn.edu!fu-berlin.de!sheep.rz-berlin.mpg.DE!not-for-mail From: Ela Hunt Newsgroups: bionet.software.acedb Subject: error while trying to use views Date: Thu, 05 Sep 1996 09:37:04 +0200 Organization: Max-Planck Institut fuer Molekulare Genetik Lines: 15 Message-ID: <322E8320.167E@sheep.rz-berlin.mpg.de> NNTP-Posting-Host: sheep.rz-berlin.mpg.de (141.14.131.90) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Access: 16 25 816 X-Mailer: Mozilla 2.0 (X11; I; OSF1 V3.2 alpha) Can anyone help? ERROR: Internal error: condMatch could not parse follow I am trying to add hybrids to my map display: I have clones in the Intervals column (Query: >yac) I added Interval_SRK to the right of Loci with Query for display: >hybrid, queries: >hybrid When I try to redraw the map (pressing OK)I get the message above, around 50 times (probably twice for every hybrid) and the map gets drawn finally, but the color I chose for the hybrids does not show (they show white inside). Ela From owner-acedb@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: >hybrid Date: 5 Sep 1996 09:08:56 +0100 Lines: 10 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <50m1qo$qsi@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk i suppose hybrid is a class, not a tag in the map in which case, you would have to say >?hybrid Note: >hybrid is an abbreviation for Follow Hybrid i.e. ou are on a set of obj and follow the hybrid tag to whatever is on the right of that tag >?hybrid is an abbreviation for Find hybrid , i.e. you all memebers of class hybrid From owner-acedb@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!kazusa.or.jp!miyajima From: miyajima@kazusa.or.jp (Nobuyuki Miyajima) Newsgroups: bionet.software.acedb Subject: ACEDB data of Cyanobacterium Date: 5 Sep 1996 01:38:39 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <199609050838.RAA11110@not1.kazusa.or.jp> NNTP-Posting-Host: net.bio.net Colleagues, We have just released a preliminary version of ACEDB data of Cyanobacterium synechocystis sp. Strain PCC680 based on the complete 3573470bp sequence. It is available from ftp://ftp.kazusa.or.jp/pub/acedb/ Any suggestion would be greatly appreciated. WWW version is also available from http://www.kazusa.or.jp/cyanobase/ which uses Java enhanced clickable maps. Comments about the acedb version should be sent to miyajima@kazusa.or.jp Comments about WWW version should be sent to cyanobase@kazusa.or.jp Thanks in advance for your interest. ----------------------------------------------- Nobuyuki Miyajima Kazusa DNA Research Institute Department of Genome Informatics, Chief Researcher 1532-3 Yana, Kisarazu, Chiba 292, Japan TEL: +81-438-52-3917 FAX: +81-438-52-3918 E-mail: miyajima@kazusa.or.jp From owner-acedb@net.bio.net Thu Sep 05 23:00:00 1996 Path: biosci!agate!news.ucdavis.edu!info.ucla.edu!newsfeed.internetmci.com!news.sgi.com!enews.sgi.com!mcsun!EU.net!main.Germany.EU.net!fu-berlin.de!sheep.rz-berlin.mpg.DE!not-for-mail From: Ela Hunt Newsgroups: bionet.software.acedb Subject: Re: Please take minute to read this. Date: Fri, 06 Sep 1996 10:24:22 +0200 Organization: Max-Planck Institut fuer Molekulare Genetik Lines: 9 Message-ID: <322FDFB6.41C6@sheep.rz-berlin.mpg.de> References: <322f4447.5342159@news.tip.nl> NNTP-Posting-Host: sheep.rz-berlin.mpg.de (141.14.131.90) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Access: 16 25 816 X-Mailer: Mozilla 2.0 (X11; I; OSF1 V3.2 alpha) To: BiMi Hi Mike, I think you should really post such rubbish in gamblers.math.ignoramus.world. Or take a course in basic combinatorics, to see how long this kind of chain list can live without hitting all the inhabitants of your town. Cheers, Ela From owner-acedb@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!CCR.DSI.UANL.MX!pearl From: pearl@CCR.DSI.UANL.MX ("Dr. Paul R.Earl") Newsgroups: bionet.software.acedb Subject: BIOMX-----Call for papers Date: 9 Sep 1996 07:33:08 -0700 Organization: UANL Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <32344777.4C03@ccr.dsi.uanl.mx> NNTP-Posting-Host: net.bio.net Please enter BIOMX under Yahoo search to see the HomePage. Thank you, Dr Paul R. Earl PS HTTP://WWW.UANL.MX/BIOMX From owner-acedb@net.bio.net Mon Sep 09 23:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!news.emf.net!overload.lbl.gov!acedbfaq From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser) Newsgroups: bionet.software.acedb,news.answers Subject: ACEDB Genome Database Software FAQ Followup-To: bionet.software.acedb Date: 10 Sep 1996 17:45:43 GMT Organization: Dendrome, A genome database for forest trees Lines: 1161 Approved: news-answers-request@MIT.Edu Message-ID: <5149g8$78g@overload.lbl.gov> Reply-To: acedbfaq@s27w007.pswfs.gov NNTP-Posting-Host: s27w007.pswfs.gov 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. Xref: biosci bionet.software.acedb:969 news.answers:74240 Archive-name: acedb-faq Last-modified: 9/10/96 Version: 1.30 ------------------------------------------------------------------------------- ACEDB FAQ ------------------------------------------------------------------------------- Curated by: Bradley K. Sherman ------------------------------------------------------------------------------- Frequently Asked Questions about ACEDB * 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 documentation exists for ACEDB? * Q6 : !What other resources are available for ACEDB? * Q7 : How should ACEDB be cited? * Q8 : Is ACEDB object-oriented? * Q9 : How does one get on/off the ACEDB announcements mailing list? * Q10 : When and where is the next ACEDB Workshop? * Q11 : Who prepared this document & where is the current version? Questions marked with '+' are new, those with '!' have substantially changed answers. ------------------------------------------------------------------------------- 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 [Q4 gives contact information]. 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 Integrated Genomic Database (IGD) project headed by Otto Ritter. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage --missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions ------------------------------------------------------------------------------- Q1: What is the current version of ACEDB? A1: (This answer refers to the software not the C. elegans data.) Current version is 4_3 (as of May 1996) and is identical to the test version test.4_3i. A Macintosh version is available as version 2.0b4. To retrieve the software see Q3. To be kept informed of new releases see Q9. Return to List of Questions ------------------------------------------------------------------------------- Q2: What hardware/software do I need to run ACEDB? A2: The software is available as source code, so you may be able to get it working on any machine, with effort. It is also available in binary (pre-compiled) format for a variety of machines. To retrieve the software see Q3. * Unix and X11: o Sun/SunOS 4.x o Sun/Solaris o DEC DECstation3100, 5100 etc. o DEC Alpha/OSF-1 o Silicon Graphics Iris series 4, 5, 6 o IBM RS-6000 o PC 386/486/Pentium with Linux (free Unix) Jeff Bryer, jbryer@darwin.mbb.sfu.ca and Ken Clark provide a linux version of 4.3 and a complete C. elegans data set at trog.mbb.sfu.ca in /pub/acedb as bin.linux.4_3.tar.Z and in ELF binary as ftp://trog.mbb.sfu.ca/pub/acedb/bin.linux.4_3.elf.tar.gz . o There exist, or have existed, ports onto Alliant, Hewlett- Packard, Convex. You may have to contact the developer responsible for the port to make these real. o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu * Macintosh: o [Contributed by Frank Eeckman] Macace is distributed as a self-extracting archive that contains the application, the wspec files, and a fully up to date database. macace 3.0 is available with an updated 21bdb database. Please send all questions/bug reports to eeckman@llnl.gov A native powerPC version is available as well. Macace needs a macintosh with > 16 MBytes of RAM, and a 17" color monitor is preferred. System 7 or greater is required. For the multimedia extensions Quicktime 1.0 is required. Please add your name to our mailing list by sending email to eeckman@llnl.gov. It is our belief that for cost savings a powerPC mac will beat the advertised linux-intel combination. Macace is fully compatible with xace, but includes some multimedia extensions (picture and movie support) not found in the unix versions. * ACEDB for The NEC EWS4800 is available via anonymous ftp at ftp.nec.co.jp (192.135.93.2) in /pub/packages/acedb/ace2. Contact Tohru Sano Fundamental Research Laboratories NEC Corporation Tsukuba, 305, JAPAN, e-mail: sano@exp.cl.nec.co.jp, FAX: +81-298-56-6136, VOICE: +81-298-50-1507 (Here at the Institute of Forest Genetics we run ACEDB on a Sun Microsystems SPARCstation II, and users can interact using Macintoshes and PC-clones by using X11 implementations for the personal computers and a LAN. --bks) X11 fonts note: ACEDB uses fonts listed in the xfonts.wrm file. If you install new fonts on your machine be sure to run bldfamily(1) so that they are available. Return to List of Questions ------------------------------------------------------------------------------- Q3: Where can I get ACEDB? A3: The standard ACEDB source and binaries are available in the following public access accounts (anonymous ftp sites) accessible via Internet: * lirmm.lirmm.fr in pub/acedb * cele.mrc-lmb.cam.ac.uk in pub/acedb * ncbi.nlm.nih.gov in repository/acedb * bioinformatics.weizmann.ac.il in pub/databases/acedb. MacAce is available from: * genome.lbl.gov in pub/macace * cele.mrc-lmb.cam.ac.uk in pub/acedb/macace Linux; ACEDB version 4.3 (and earlier versions) for Linux 1.0+: * trog.mbb.sfu.ca /pub/acedb as bin.linux.4_3.tar.Z. ACEDB for The NEC EWS4800: * ftp.nec.co.jp [may be obsolete? --bks] in /pub/packages/acedb/ace2. Return to List of Questions ------------------------------------------------------------------------------- Q4: What ACEDB databases exist? A4: In alphabetic order by Database name [Curators, please submit changes as new paragraphs] Database : AaeDB Species : Aedes aegypti (Mosquito) Last_update : December 1994 ACEDB_version : 3.0 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Curator : Martin Ferguson, martinf@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Database : AAtDB Species : Arabidopsis thaliana Current version : 3-5 Last_update : August 1995 PI : J. Michael Cherry Curator : David Flanders Contact : arab-curator@genome.stanford.edu Availability : UNIX and Macintosh versions via anonymous ftp FTP : genome-ftp.stanford.edu in arabidopsis/aatdb FTP : ncbi.nlm.nih.gov in repository/aatdb FTP : probe.nalusda.gov in pub/aatdb Gopher : genome-gopher.stanford.edu/11/Arabidopsis Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://genome-www.stanford.edu WWW : http://probe.nalusda.gov:8300/plant/ Database : AboutDB Curator : Staffan Bergh, staffan@biochem.kth.se Subject : ACEDB itself (meta-meta-metadata) ACEDB_version: 3.0 Last_update : July 1995 WWW : http://www.biochem.kth.se/AboutDB.html Database : ACeDB Species : Caenorhabditis elegans Current version: 4-8 Curator : Jean Thierry-Mieg, mieg@kaa.crbm.cnrs-mop.fr Curator : Richard Durbin, rd@mrc-lmb.cam.ac.u Curator : Sylvia Martinelli, sylvia@sanger.ac.uk Last_update : August 1995 Availability: Unix and Macintosh versions via anonymous ftp FTP: USA - ncbi.nlm.nih.gov in repository/acedb FTP: England - ftp.sanger.ac.uk in pub/acedb FTP: France - lirmm.lirmm.fr in genome/acedb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/other/ Database : IXDB (Integrated X chromosome DataBase) Species: Homo sapiens Subject: Chromosome X Acedb_version : 4.1 Data: The YAC map constructed by the Max-Planck-Institut fuer Molekulare Genetik in Berlin, with all the attached experimental data necessary to reconstruct the map. Information on each of 9000 YAC clones mapped to the X chromosome, and constituting the YAC collection assembled with clone sets from 14 different laboratories worldwide. Latest_release:March 1996 Curator: Hugues Roest Crollius, roest@mpimg-berlin-dahlem.mpg.de Contact: Ulf Leser, leser@mpimg-berlin-dahlem.mpg.de PI: Hans Lehrach FTP: ftp.mpimg-berlin-dahlem.mpg.de in directory pub/lehrach/x-map WWW: http://www.mpimg-berlin-dahlem.mpg.de/~xteam Database : AGsDB (A Genus species Database) Species : Aspergillus nidulans Species : Neurospora crassa Species : Bos taurus (cow) Species : Homo sapiens anchor loci Species : Gossypium hirsutum (cotton) Species : Neurospora crassa Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast Curator : Leland Ellis, leland@straylight.tamu.edu Last_update : March 1994 ACeDB_version : 3.0 Subject: Contains extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe yeast); interacting loci via defined Interactions for each locus Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. WWW : http://keck.tamu.edu/cgi/agsdb/agsdbserver.html FTP: ftp://keck.tamu.edu/pub/agsdb/agsdb1_0_acedb3_0_solaris2.3.tar.Z Database : Alfagenes Species : Medicago sativa (alfalfa) Curator : D. Z. Skinner, dzolek@ksu.ksu.edu Telephone : (913) 532-7247 ACEDB_version : 3.0 Last_Update : July 1995 FTP : probe.nalusda.gov in pub/alfagenes Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : BeanGenes Species : Phaseolus and Vigna Curator : Phillip E. McClean, mcclean@beangenes.cws.ndsu.nodak.edu ACEDB_version : 4.1 Last_updated : September 1995 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : ChlamyDB Species : Chlamydomonas Curator : Elizabeth Harris Contact : chlamy@acpub.duke.edu ACEDB_version : 3.0 Data_version : 1.2 Last_update : August 1995 Availability : Macintosh and UNIX versions via anonymous ftp FTP : probe.nalusda.gov in pub/chlamydb Gopher : ftp.duke.edu/11/pub/chlamy Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : CIMMYT (Wheat International Nursery Data) Species : Triticum spp. ACEDB_version : 4.0 Last_update : September 1995 Curator : Hector Sanchez, hsanchez@cimmyt.mx FTP : probe.nalusda.gov in pub/cimmyt Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : CoolGenes Species : Cool Season Food Legumes; Pisum, Lens, Cicer, Lathyrus, Vicia faba Curator : Fred Muehlbauer, muehlbau@wsu.edubr> ACEDB_version : 3.0 Last_update : January 1996 Gopher : gopher://probe.nalusda.gov:7000/11/genome.databases/coolgenes/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : CottonDB Species : Gossypium hirsutum (cotton) and related species PI : Russell J. Kohel (rjk0339@acs.tamu.edu), USDA-ARS, Southern Crops Research Laboratory, 2765 F&B Road, College Station, Texas 77845 Curator : Gerard R. Lazo, lazo@tamu.edu Curator : Sridhar Madhavan, msridhar@tamu.edu Phone : 409-260-9311 Fax : 409-260-9333 Last_update : January 1995 (version 95.1) ACEDB_version : 3.0 FTP : probe.nalusda.gov in pub/cottondb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Data_submission_form : http://algodon.tamu.edu/ Database : CSNDB Focus : Cell Signaling Networks Species : human Curator : Takako Igarashi, taka@nihs.go.jp Curator : Tsuguchika Kaminuma, kaminuma@nihs.go.jp Assistant_Curator : Masumi Yukawa, yukawa@nihs.go.jp Assistant_Curator : Shikiko Hasegawa, shasegaw@nihs.go.jp Contact : Takako Igarashi, taka@nihs.go.jp ACeDB_version : 4.1 Data : molecular data of signal molecules, molecular data of signal transductions, signal transduction pathways, domain structure and function of signal molecules, and three dimensional structures of signal molecules. Availability : CSNDB is on WWW. WWW-browser is required to attach molecular viewer RasMol ( ftp: colonsay.dcs.ed.ac.uk ) for displaying three dimensional structure of protein. WWW : http://geo.nihs.go.jp/csndb.html Database : Cyanobase Species : Cyanobacterium synechocytstis sp. Strain PCC680 Last_update : September 1996 Developer : Nobuyuki Miyajima miyajima@kazusa.or.jp FTP : ftp://ftp.kazusa.or.jp/pub/acedb/ WWW : http://www.kazusa.or.jp/cyanobase/ Remark : WWW interface Uses Java enhanced clickable maps. Database : EthnobotDB (worldwide plant uses) Species : wide range of plant species ACEDB_version : 4.0 Last_update : June 1995 Comment : Converted to ACEDB from the original SQL database. Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : FoodplantDB (Native American Food Plants) Species : Over 1,100 plant species ACEDB_version : 4.0 Last_update : May 1995 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Comment : Converted to ACEDB from ORACLE. Comment : Data originally from a publication by Yanovsky, Elias. 1936. Food Plants of the North American Indians. USDA Miscellaneous Publication Number 237. Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : GrainGenes Species : Wheat, barley, oats, sugarcane, relatives Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu PI : Olin D. Anderson, oandersn@pw.usda.gov ACEDB_version : 4_3 Data_version : 1.6 Last_update : April 1996 FTP : probe.nalusda.gov in pub/graingenes Gopher : greengenes.cit.cornell.edu/ Gopher : probe.nalusda.gov:7002 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://wheat.pw.usda.gov/graingenes.html Database : IGD (Integrated Genomic Database) Species : Homo sapiens Subject : Chromosome 21 Availability : September 1994 by ftp, on-line server October 1994 Contact : Otto Ritter, o.ritter@dkfz-heidelberg.de Contact : Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr Contact : Nicole Creau-Goldberg, creau@arthur.citi2.fr Contact : Jean-Maurice Delabar, delabar@arthur.citi2.fr WWW : http://moulon.inra.fr/acedb/igd.html Description : IGD (Integrated Genomic Database) aims to integrate multiple public general molecular biology and human genome specific databases into single logical database with unified interface to existing analysis tools. From data produced by the 4th International Workshop on Chromosome 21 (Genomics,1993,18,735-744) and from data provided by or taken from the following databases and data repositories: GDB, OMIM, EMBL, CEPH, Genethon, UKProbeBank, and RLDB. Database : LeishDB Species : Leishmania major, L. infantum, L. peruviana, L. donovani and others PI : Jennie Blackwell PI : Al Ivens Last_update : September 1995 ACEDB_version : 4.1 Contact : Matin Aslett, ma10025@cus.cam.ac.uk FTP : ftp://parsun1.path.cam.ac.uk [obsolete? --bks] WWW : http://parsun1.path.cam.ac.uk/ Curator : Martin Aslett Curator : Howard Cobb Database : LIGM-DB Curator : Veronique Giudicelli Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors PI : Marie-Paule Lefranc Contact : Veronique Giudicelli LIGM IGMM UMR CNRS 9942 BP 5051 Rte de Mende 34000 Montpellier giudi@ligm.crbm.cnrs-mop.fr Database : MaizeDB Species : Zea mays L. ssp. mays and related species Latest_release : April 1995 Acedb_version : 3.3 Comment : MaizeDB is a periodically extracted ACeDB front end for the Maize Genome Database, MaizeDB, a SYBASE database, implemented using Genera software, developed by Stan Letovsky. Comment : Genera provides (1) up-to-the-minute form internet access to SYBASE databases, both for query (WWW and APT) and data entry (APT only); (2) database design alterations by systems administrators; (3) gopher file extraction. Comment: MaizeDB uses WWW record-to-record hard-links to 16 external databases for (1) annotated sequences: GenBank, dbEST, GenoBase, PIR, SwissProt, Prosite, ENZYME; (2) other species genome information: AAtDB(Arabidopsis), RiceGenes, GrainGenes, SaachDB (yeast), CGSC(E. coli), XLocus, RiceGenes, GrainGenes (3) germplasm: GRIN. Data : Over 100,000 records include: 6513 mapped loci (located to chromosome or better) including 1081 mapped genes and 1937 mapped probed sites (gene candidates); 2448 probes; 2460 map scores; 1551 gel patterns (Probe/Enzyme/Stock); 8777 stocks; 18,100 Variations (alleles, DNA polymorphisms, rearrangements, etc); 596 phenotypes; 317 traits; 715 gene products; 6158 bibliographic references; 2200 researchers with addresses. FTP : probe.nalusda.gov in pub/maizedb Gopher : gopher.agron.missouri.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ Telnet : telnet teosinte.agron.missouri.edu login as guest, use password: corncob WWW : http://www.agron.missouri.edu/top.html WWW : http://probe.nalusda.gov:8300/plant/ WWW Genera information : http://gdbdoc.gdb.org/letovsky/genera/genera.html Funding : MaizeDB USDA/ARS to E. Coe Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn Curator/PI : Ed Coe, ed@teosinte.agron.missouri.edu Curator : Mary Polacco, maryp@teosinte.agron.missouri.edu Assoc Curator : Pat Byrne, byrne@teosinte.agron.missouri.edu QTL data Assoc Curator : Georgia Davis, gdavis@teosinte.agron.missouri.edu Map data Assoc Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Genetic Stock data Assoc Curator : Christiane Fauron, FAURON@GENE1.med.utah.edu Mitochondrion genome Assoc Curator : Carolyn Wetzel, cmwetzel@iastate.edu Chloroplast genome Assoc Curator : Steve Rodermel, S1SRR@ISUVAX.IASTATE.EDU Chloroplast genome Design : Stan Letovsky, letovsky@gdb.org Design : Mary Berlyn, mary@fetalpig.biology.yale.edu Systems Manager : Denis Hancock, dhancock@teosinte.agron.missouri.edu Contact : db_request@teosinte.agron.missouri.edu Last_update : 11 April 1995 Database : Mendel (plant wide gene names) Species : wide range of plant species Subject : standardized designations for sequenced genes Comment : The purpose is to provide a common system of nomenclature for substantially similar genes across the plant kingdom. Mendel is maintained by the Commission on Plant Gene Nomenclature. ACEDB_version : 4.0 Last_update : July 1995 Curator : Carl Price, price@mbcl.rutgers.edu Curator : Ellen Reardon, reardon@mbcl.rutgers.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : Millet Genes Species : Pennisetum Glaucum (Pearl Millet) ACEDB_version : 4.1 Availablity : Local Curator : Matt Couchman, couchman@bbsrc.ac.uk Curator : Katrien Devos, devos@bbsrc.ac.uk DataBase : Mousedb Species : Mus Musculus Species : Homo Sapiens ACEDB_version : 3.0 with extensions to define and display cytogenetic data. Description : Mouse genome data from the published literature, including mouse genes with phenotypic effects, chromosome anomalies, imprinted regions and man-mouse homologies with associated pathological disorders. The maps are consensus ones. They use data, such as the HIS and anomaly data, to show alignments between the genetic and cytogenetic maps. Curator : Rachael Selley, rselley@har-rbu.mrc.ac.uk PI : Mary Lyon PI : Jo Peters Availability : Mousedb is available publicly from the UK HGMP Resource Centre's computing service via the INTERNET. For user id. please contact Administration, HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ, UK. Tel: (+44) 1223 494520 Fax: (+44) 1223 494510 Contact : Rachael Selley, MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD Last_update : July 1995 Database : MPNADB (Medicinal Plants of Native America) Species : Over 2,100 plant species Curator : Daniel E. Moerman, dmoerman@umich.edu Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov - ACEDB version Comment : MPNADB is based on a two-volume book of the same name published in 1986 by the Museum of Anthropology of the University of Michigan. MPNADB was first developed at the University of Michigan in DBase II. ACEDB_vertion : 4.0 Last_update : June 1995 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : MsqDB Species : Interspecies Mosquito database Last_update : March 1996 ACEDB_version : 4.1 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Curator : Martin Ferguson, martinf@lamar.colostate.edu Contact : aaedbmgr@klab.agsci.colostate.edu Database : MycDB Species : Mycobacteria Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. Curator : Staffan Bergh, staffan@biochem.kth.se Curator : Stewart Cole, stcole@pasteur.fr Last_update : November 1995 ACEDB_version : 4.1 Data_version : 4-9 (November 1995) FTP : www.biochem.kth.se (130.237.52.64) in pub/MycDB FTP : ftp.pasteur.fr (157.99.64.12) in pub/MycDB FTP : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://www.biochem.kth.se/MycDB.html WWW : http://probe.nalusda.gov:8300/other/ Database : OMIA (Online Mendelian Inheritance in Animals) Species : wide range of animal species Subject : gene and phene (familial trait or phenotype) information Comment : MIA is modeled after Victor McKusick's Mendelian Inheritance in Man (MIM) database and was developed at the University of Sydney, Australia, in Advanced Revelation. Curator : Frank Nicholas, frankn@doolittle.vetsci.su.oz.au Curator : Gail Juvik, gjuvik@nalusda.gov - ACEDB version ACEDB_vertion : 4.0 Last_update : September 1995 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/animal/ WWW : http://morgan.angis.su.oz.au/BIRX/phenes_form.html Database : PhytochemDB (Plant Chemicals) Species : wide range of plant species Subject : Consists primarily of plant chemical data, including quantity, taxonomic occurrence, and chemical activity. Comment : Converted to ACEDB from the original SQL database. ACEDB_version : 4.0 Last_update : June 1995 Data_version : July 1994 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : PomBase Curator : Sean Walsh, svw@sanger.ac.uk Curator : Marie-Adele Rajendream PI : Bart Barrell, barrell@sanger.ac.uk Species : Schizosaccharomyces pombe ACEDB_version : 4.1 Last_update : September 1995 FTP : ftp.sanger.ac.uk in pub/PomBase Database : PVP (Plant Variety Protection) Species : Glycine max (soybeans) Subject : Data about plant varieties that have been granted a Certificate of Protection by the Plant Variety Protection Office. Curator : Stephen M. Beckstrom-Sternberg, sbeckstr@nalusda.gov - ACEDB version ACEDB_version : 4.0 Last_update : June 1995 Contact: The Plant Variety Protection Office, Room. 500, National Agriculture Library, 10301 Baltimore Blvd., Beltsville, Maryland 20705 Telephone : 301-504-5518 Fax : 301-504-5291 Email : Jeff Strachan, strachan@locus.nalusda.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ Database : RiceGenes Species : Oryza sativa Curator : Edie Paul, epaul@nightshade.cit.cornell.edu PI : Susan McCouch ACEDB_version : 4.1 Last_update : November 1995 FTP : probe.nalusda.gov in pub/ricegenes Gopher : nightshade.cit.cornell.edu Gopher : probe.nalusda.gov:7007 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : SacchDB Species : Saccharomyces cerevisiae Subject : Budding (common baker's) Yeast Genome ACEDB_version : UNIX 2.0, MacAce 2.0b4 Last_update : September 1995 Data_version : 2.4.12 Data : All Saccharomyces genes contained in the Registry of Gene Names. Results of the completed chromosomal sequencing projects have been integrated into the database. Physical Maps based on DNA sequencing projects, hybridization to the Olson/Riles prime filter grids, and restriction mapping. For the completely sequenced chromosomes the Olson prime clones have been re-mapped (on the computer) to the DNA sequence. Saccharomyces DNA sequences contained within GenBank are incorporated. Literature references, most including abstracts, for the information contained within the database. Gene protein product information obtained from the YPD database (Garrels and Latter, CSHL) and the literature. Genetic Maps including the underlying two point tetrad data. Including all tetrad data reported in previous additions of the Mortimer Yeast Maps. FTP : genome-ftp.stanford.edu in pub/yeast/SacchDB FTP : ncbi.nlm.nih.gov in repository/SacchDB Gopher : genome-gopher.stanford.edu WWW : http://genome-www.stanford.edu/ Funding : National Center for Human Genome Research, NIH PI : David Botstein, botstein@genome.stanford.edu Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu Curator : Selena Dwight, dwight@genome.stanford.edu Curator : Cathy Ball, ball@genome.stanford.edu Curator : Rita Schmidt, bleb@genome.stanford.edu Curator : Barbara Dunn, bdunn@genome.stanford.edu Curator : Caroline Adler, adler@genome.stanford.edu Programmer : Karen Davis, karen@genome.stanford.edu Sys. Admin : Mark Schroeder, mark@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu Database : SolGenes Subject : Solanaceae - tomato, potato, pepper Curator : Clare Nelson, cnelson@nightshade.cit.cornell.edu PI : Steve Tanksley Release : ACEDB 4.3 Last_update : April 1996 FTP : probe.nalusda.gov in pub/solgenes Gopher : nightshade.cit.cornell.edu:71 Gopher : probe.nalusda.gov:7006 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : SorghumDB Species : Sorghum bicolor (L.) Moench PI : Keith F. Schertz, schertz@tamvm1.tamu.edu USDA-ARS, Dept. of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 Curator : Najeeb U. Siddiqui, nus6389@tam2000.tamu.edu Southern Crop Improvement Facility, Crop Biotechnology Center, Texas A&M University, College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 Last_update : September 1995 ACEDB_version : 3.0 Data_version : 2.0 FTP : probe.nalusda.gov in pub/sorghumdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Database : SoyBase Species : Glycine max (Soybeans) and related species PI : Randy Shoemaker Curator : David Grant, dgrant@iastate.edu Assistant_curator : Marica Imsamde, mimsande@mendel.agron.iastate.edu Contact : David Grant, dgrant@iastate.edu ACEDB-Version : 3.7 Last_update : October 1995 FTP : probe.nalusda.gov in pub/soybase Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://mendel.agron.iastate.edu:8000/main.html Database : Syndb Species : Homo sapiens, Mus musculus Subject : STS content mapping & directed sequencing of Human Chromosomes 21,5 with Mouse for syntenic comparison ACEDB_version : acedb v3.3 plus moulon server Last_update : October 1994 FTP : genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov Database : Toxo Species : Toxoplasma gondii PI : Jennie Blackwell PI : Jim Ajioka Last_update : September 1995 ACEDB_version : 4.1 Contact : Martin Aslett, ma10025@cus.cam.ac.uk FTP : parsun1.path.cam.ac.uk WWW : http://parsun1.path.cam.ac.uk/ Curator : Martin Aslett Curator : Howard Cobb Database : TreeGenes Species : Forest trees ACEDB_version : 4.3 Last_update : May 1996 Curator : Bradley K. Sherman, bks@s27w007.pswfs.gov PI : David B. Neale, dbn@s27w007.pswfs.gov Contact : Dendrome@s27w007.pswfs.gov FTP : probe.nalusda.gov in /pub/treegenes Gopher : s27w007.pswfs.gov/ Gopher : probe.nalusda.gov:7508/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://s27w007.pswfs.gov/ Database : Trypbase Species : Trypanosoma brucei PI : Sara Melville Curator : Martin Aslett, ma10025@cus.cam.ac.uk Curator : Howard Cobb, hc102@econ.cam.ac.uk Contact : sm160@mole.bio.cam.ac.uk ACEDB_version : 4.1 (Sun and Linux) FTP : parsun1.path.cam.ac.uk WWW : http://parsun1.path.cam.ac.uk Database : 21Bdb Species : Homo sapiens Subject : STS content mapping and sequencing of Human Chromosome 21 ACEDB_version : acedb.1-10 plus moulon server Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov Last_update : April 1994 FTP : ftp://genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Database : 11Db Species : Homo sapiens Subject : Physical and Genetic mapping of Human Chromosome 11 Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Contact : Benedict Arnold (b.arnold@bc.ic.ac.uk) PI : Peter Little (p.little@bc.ic.ac.uk) ACEDB_version : based on 4_1 with added map displays. ACEDB_version : based on 3_6 with added map displays. Data version : 1.0 Last Update : December 1995 WWW : http://chr11.bc.ic.ac.uk FTP : ftp.cc.ic.ac.uk Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Database : 22ace Species : Homo sapiens Subject : Physical map of human chromosome 22, genomic sequencing and more ACEDB_version : 4.1 Curator : Ian Dunham, id1@sanger.ac.uk Curator : Gareth Maslen, glm@sanger.ac.uk PI : Ian Dunham Last_update : August 1995 FTP : ftp.sanger.ac.uk in pub/human/chr22/physical_map/ WWW : http://www.sanger.ac.uk/hum22/ Database : VoxPop Species : Populus species Curator : Carl G. Riches, cgr@poplar1.cfr.washington.edu PI : Reinhard F. Stettler, STETTLER@coyote.cfr.washington.edu Last_update : September 1993 ACEDB_version : 1.9 FTP : poplar1.cfr.washington.edu in /pub/ Gopher : poplar1.crf.washington.edu Return to List of Questions ------------------------------------------------------------------------------- Q5: What documentation exists for ACEDB? A5: From Sam Cartinhour: The ACEDB Documentation Server is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. Eventually we hope to offer all kinds of documentation, from reprints to (technical) gossip. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The documentation server is listed on the home page for the Agricultural Genome World Wide Web Server at http://probe.nalusda.gov:8000 . Primary documents from the developers are: * 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-) Get By anonymous ftp from ncbi.nlm.nih.gov in repository/acedb: ftp://ncbi.nlm.nih.gov/respository/acedb/doc*tar.Z . The files are in TeX (Jean Thierry-Mieg suggests latex xxx.tex; dvi2ps xxx.dvi > xxx.ps; lpr xxx.ps) and PostScript. The Proceedings from the May 1995 ACEDB Conference are available at http://probe.nalusda.gov:8000/acedocs/ace95/index.html A final summary report is available at http://probe.nalusda.gov:8000/acedocs/ace95/ace95.final.html . Japanese language guides: _Japanese ACEDB Guide Ver.1.2._ _ACEDB ver.2 for NEC engineering workstation EWS4800 series_ are available in PostScript via anonymous ftp at ftp.nec.co.jp as /pub/packages/acedb/acemanjp.1_2.ps.Z . There is a Japanese language ACEDB FAQ available at http://www.cbi.or.jp/~sano/acemanjp12/index.html SampleDB, by Dave Matthews, is an ACEDB database constructed to demonstrate features of ACEDB, especially map and sequence displays. Anonymous ftp to probe.nalusda.gov:pub/acedocs/sampledb You will find interesting documents in the wdoc subdirectory of the ACEDB distribution. The Australian National Genomic Information Service has prepared good documentation of the C. elegans version as Angistute.ps and angistute.hqx available by anonymous ftp at ncbi.nih.gov in repository/acedb/ace2. 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). URL : http://genome-www.stanford.edu/docs/aatdb_man.html . A description of ACEDB: Cherry, J.M. and Cartinhour, S.W. (1994) ACEDB, A tool for biological information. in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press, pages 347-356. URL : http://probe.nalusda.gov:8000/acedocs/overview.html . Another description of ACEDB for physical mapping projects: Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994) Physical mapping projects and ACEDB, in Guide to Human Genome Computing. Ed. Bishop, M.J. Academic Press, pages 111-158. Return to List of Questions ------------------------------------------------------------------------------- Q6: What other resources are available for ACEDB? A6: Perl and WWW tools The AGIS server at the National Agricultural Library provides tools for integrating version ACEDB with perl and the World-Wide Web. A WWW interface to 4.3 ia available as ftp://probe.nal.usda.gov/pub/tools/webace.tar.gz Instructions for this interface can be found at http://probe.nal.usda.gov:8000/acedocs/webace.html (An earlier tool set is available as ftp://probe.nalusda.gov/pub/tools/acelib.tar.gz) For a general tool for converting data to ACEDB format input files, Joachim Baumann (joachim.baumann@informatik.uni-stuttgart.de) has written the Perl program TextConvert, available at ftp.informatic.uni.stuttgart.de/pub/DART/ . Java Interface A Java interface to acedb is under active development. Involved people are Lincoln Stein, Jean Thierry-Mieg, Doug Bigwood, Jonh Barnett, Sam Cartinhour. A test system can be seen at http://alpha.crbm.cnrs-mop.fr If you are interested in this approach, please contact mieg@kaa.crbm.cnrs-mop.fr X-client The 4_3 distribution contains the source code for a new version of the code called xclient. You need to recompile it (make xclient). Then, you create an empty database with the nematode models and strat xclient. It will automatically retrieve data from the server declared in wspec/server.wrm (the montpellier server in the distrib server.wrm). The data will be saved locally and can then be viewed with a normal xace. The control of which data should be imported is very crude. In anay session, every object will be imported once. This should be rationalised, please let us know if this approach seems useful, and how it should be configured. (mieg@kaa.crbm.cnrs-mop.fr) The Developers' Archive Mike Cherry maintains an archive of tools that may be useful in curating ACEDB databases via gopher at gopher://genome-gopher.stanford.edu:70/11/ftp If you have a contribution send a message to Mike (cherry@genome.stanford.edu). The Biosci conference bionet.software.acedb There is a USENET/Biosci conference titled bionet.software.acedb created expressly for discussion of ACEDB. The best way to interact with the Biosci conferences is via a newsreader like rn, trn, tin or a WWW browser. Consult your system administrator for more information. If you do not have access to the Biosci conferences via a newsreader (e.g. rn, trn, tin) 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 (UK, European readers use biosci@uk.ac.daresbury or biosci.daresbury.ac.uk) 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. All of the articles in biosci.software.acedb are archived by Biosci at http://www.bio.net:80/hypermail/ACEDB/ and by Mike Cherry at http://genome-www.stanford.edu/cgi-bin/biosci_acedb. If your WWW browser is configured properly you may be able to read the newsgroup at news:biosci.software.acedb . And more 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 via the WWW using an http server with URL: http://probe.nalusda.gov:8000/index.html 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. AboutDB is a stab at an integrated info and project tracking database for the 'Greater ACEDB Community'. It was conceived and implemented by Staffan Bergh (staffan@biochem.kth.se), the 'coordinator', during the ace94 workshop in Montpellier, based on an earlier effort by John McCarthy. The aim is to collect information on all aspects of ACEDB use as a database manager. Currently it contains information on Databases implemented in ACEDB, Colleagues in the community, some Tools for >curators of ACEDB databases and some of the information on 'magic tags' collected during the ace94 workshop. AboutDB can be reached at URL: http://kiev.physchem.kth.se/AboutDB.html 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://kiev.physchem.kth.se/MycDB.html for Mycobacterium data * http://moulon.inra.fr:8001/acedb/igd.html for an integrated genome database. For information on how these were created see http://moulon.inra.fr/acedb_conf_eng.html and en francais http://moulon.inra.fr/acedb_conf.html A how-to manual on the Moulon server is available at http://keck.tamu.edu/cgi/staff/ace-mosaic-howto.html The Genome Computing Group, Lawrence Berkeley Laboratory, has an anonymous ftp service at machine genome.lbl.gov 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. [From Otto Ritter] IGD - the Integrated Genomic Database - is an international project of DKFZ, Heidelberg (Germany), CNRS, Montpellier (France), ICRF, London (UK), LBL, Berkeley (USA), and MRC, London/Cambridge, (UK). IGD is an extensible object-oriented distributed information management system with one global schema, physical data integration at the back-end, and local data management at the front-end. It supports local schema evolution and local data integration, and has a potential for truly virtual "on-the-fly" integration (federation) of its resource databases. Beside data integration, IGD provides graphical user interface, client/server communication, and seamless interface to a growing number of tools for structure, sequence, genetic, physical and comparative mapping analysis. ACEDB is the IGD main software component for data management. As a database, IGD integrates and references genome related data from public sources. As an analysis tool, IGD provides uniform interface to existing programs and program packages for tructure and sequence analysis, genetic and physical map construction and analysis, etc. In addition to the major human and mouse databases already planned SWISS-PROT/PIR, PDB, GDB, OMIM, CitDB, CEPH, CHLC, CEPH-Genethon, Genbase, UK DNA ProbeBank, RLDB2, CAD, MGD, MouseBackcross DB), crossreferences will be maintained to dataabases established around specific model organisms (C.elegans, D. melanogaster, S. cerevisiae, pombe etc.). Refs: * 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). * 2/ Ritter,O., Kocab,P., Senger,M., Wolf,D., and Suhai,S.: Prototype Implementation of the Integrated Genomic Database, Computers and Biomedical Research, 27, 97-115 (1994) 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). Return to List of Questions ------------------------------------------------------------------------------- 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 via anonymous ftp. Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions ------------------------------------------------------------------------------- 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. Return to List of Questions ------------------------------------------------------------------------------- Q9: How can I get on/off the ACEDB announcements mailing list? A9: To get on or off the mailing list send mail to rd@mrc-lmb.cam.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. New releases of the software are announced to this list and very little else. The BIOSCI newsgroup bionet.software.acedb [See Q6 for details] is on the mailing list. Return to List of Questions ------------------------------------------------------------------------------- Q10: When and where is the Next ACEDB Workshop? A10: The 1996 Workshop scheduled in Heidelberg has been cancelled, a smaller meeting may be organised in England at the end of 1996. . If you would like to see some pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers, there are online collections: * by Mike Cherry at http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; * by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; * and by Brad Sherman at ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html Return to List of Questions ------------------------------------------------------------------------------- Q11:Who prepared this document & where is the current version? A11: 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 text version of the ACEDB FAQ should be available via anonymous ftp at machine net.bio.net as file pub/BIOSCI/ACEDB/ACEDB.FAQ or at rtfm.mit.edu as pub/usenet/news.answers/acedb-faq . If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. There is an HyperText Markup Language (HTML) version of this document available on the World Wide Web: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html and http://s27w007.pswfs.gov/Homepage/acedbfaq.html There might be a Japanese language FAQ available at http://www.cbi.or.jp/~sano/acemanjp12/index.html 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 Major contributions in getting this FAQ off the ground were made by Mike Cherry, John McCarthy, and Doug Bigwood. Other contributors include: * Lisa Lorenzen * David Matthews * Edie Paul * Donn Davy * Eric De Mund * Sam Cartinhour Please cite as: Sherman,B.K., ACEDB Genome Database Software FAQ, ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993-1996, approx. 50K bytes. 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 Research Program. Return to List of Questions ------------------------------------------------------------------------------- End of ACEDB FAQ --bks ------------------------------------------------------------------------------- From owner-acedb@net.bio.net Tue Sep 10 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!howland.erols.net!newsfeed.internetmci.com!in2.uu.net!netnews.worldnet.att.net!news.u.washington.edu!root From: "Peter J. Myler" Newsgroups: bionet.software.acedb Subject: Win95 version of AceDB Date: 11 Sep 1996 17:18:37 GMT Organization: SBRI Lines: 51 Message-ID: <01bba005$c5c62b40$0bb58e8c@mylerpj> NNTP-Posting-Host: cs113-9.u.washington.edu Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_01BB9FCB.19707B00" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Internet News 4.70.1155 This is a multi-part message in MIME format. ------=_NextPart_000_01BB9FCB.19707B00 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi folks: Is there an existing Windows version of AceDB or is there one in the pipeline? If so where can I get it? If not, what are the system requirements (CPU, RAM, HDD etc) for installing and running the Linux version on a PC. Thanks Peter ===================================================== Peter J. Myler Seattle Biomedical Research Institute 4 Nickerson Street Seattle, WA 98109-1651 phone: (206) 284-8846x332 FAX: (206) 284-0313 e-mail: MYLERPJ@U.WASHINGTON.EDU ===================================================== ------=_NextPart_000_01BB9FCB.19707B00 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hi folks:

Is there an existing = Windows version of AceDB or is there one in the pipeline?
If so where = can I get it?
If not, what are the system requirements (CPU, RAM, HDD = etc) for installing and running the Linux version on a = PC.

Thanks

Peter =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D
Peter J. Myler
Seattle Biomedical Research = Institute
4 Nickerson Street
Seattle, WA =  98109-1651
phone: (206) 284-8846x332
FAX: (206) = 284-0313
e-mail: MYLERPJ@U.WASHINGTON.EDU
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D


------=_NextPart_000_01BB9FCB.19707B00-- From owner-acedb@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!nntp-serv.cam.ac.uk!srk From: srk@handa.sanger.ac.uk (Simon Kelley) Newsgroups: bionet.software.acedb Subject: problem with gMap cacheing in Acedb 4.3 Date: 13 Sep 1996 12:01:26 GMT Organization: Sanger Centre, Hinxton Hall, England. Lines: 25 Distribution: world Message-ID: NNTP-Posting-Host: handa.sanger.ac.uk Acedb 4.3 re-introduced the facility for cacheing genetic maps as arrays in class gMap for fast access and display. There is a bug which is seen when trying to update the cached version of the map to reflect changes in the database. This can be done in two ways, either by using the "recalculate" function on the menu in a gMap window, or the "Make gMaps" button in the align maps window (from the menu in the main window.) The bug is that using "Make gMaps" works fine to create the cached version the first time, but will _not_ overwrite an existing cached version with a new one. The work-around is to use "Recalculate" instead, but beware that if you do not have write access when you do the re-calculate, it will appear to work, but silently fail to store the new version of the map back into the database. The out-of-date version will re-appear next time you display the map. This is fixed in the next release (4.4) Simon. ------------------------------------------------------------------------------- Simon Kelley. srk@sanger.ac.uk work: +44 1223 494980 home: +44 1223 832411 -- ------------------------------------------------------------------------------- Simon Kelley. srk@sanger.ac.uk work: +44 1223 494980 home: +44 1223 832411 From owner-acedb@net.bio.net Thu Sep 12 23:00:00 1996 Path: biosci!agate!spool.mu.edu!newspump.sol.net!news.inc.net!arclight.uoregon.edu!news.sprintlink.net!news-peer.sprintlink.net!rain.fr!news.remcomp.fr!invivo!eWattel.lille From: eWattel.lille@invivo.remcomp.fr (Eric Wattel) Reply-To: eWattel.lille@invivo.remcomp.fr Newsgroups: bionet.software.acedb Distribution: world Subject: search program macintosh Date: 13 Sep 1996 09:33:50 GMT Message-ID: <1170083735.256710@invivo.remcomp.fr> Organization: inVivo Lines: 12 Hello, I was wondering if anybody knows a nice sequence alignmment and PCR (to select primers and probes) program that runs on a MACINTOSH? Thanks for your help! EW eWattel.lille@invivo.edu end ******************************************************************** Sent by inVivo. The BBS of Life Sciences, Paris, France, info@invivo.edu From owner-acedb@net.bio.net Fri Sep 13 23:00:00 1996 Path: biosci!ERI.UCHSC.EDU!clancy From: clancy@ERI.UCHSC.EDU (Kevin Clancy PhD) Newsgroups: bionet.software.acedb Subject: Acessing databases by browsers Date: 13 Sep 1996 17:35:23 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear All I am working with a group that has an AceDB database. I would like to make this accessible to the web. Is there any software/programs available that could be used for this? I was thinking of something like the SybPerl extension modules that can be used to access Sybase databases. Thanks for your help Kevin Clancy From owner-acedb@net.bio.net Fri Sep 13 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: web access to acedb in java Date: 14 Sep 1996 11:15:06 +0100 Lines: 20 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <51e0ja$ble@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk, clancy@ERI.UCHSC.EDU In collaboration with Lincoln Stein, we have develloped a generic Java library. The idea was to write a communication layer between reusable jave displays, often borrowed from collaborators, and various servers. So far, we wrote a jade access to the acedb data server, the corresponding code is available at ftp:://ftp.crbm.cnrs-mop.fr/pub/unix/jade info and demos at http://alpha.crbm.cnrs-mop.fr the nematode demos includes an incomplete reuse of a sequence display by Gregg Holt, the grass demo, several displays from Bigwood, Barnett, Cartinhour Jade can access several servers in parallel (Grass demo) and we would be happy to collaborate on accessing other sorts of servers than acedb From owner-acedb@net.bio.net Sun Sep 15 23:00:00 1996 Path: biosci!faseb.org!cpk-news-feed1.bbnplanet.com!sprout.nal.usda.gov!usenet From: Doug Bigwood Newsgroups: bionet.jobs,bionet.software.acedb,misc.jobs.offered Subject: Programmer/Analysts - Java/Perl Date: Mon, 16 Sep 1996 10:35:09 -0400 Organization: Genome Informatics Group, University of Maryland Lines: 21 Message-ID: <323D659D.2FFD@gig.usda.gov> NNTP-Posting-Host: locus.gig.usda.gov Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; SunOS 5.5 sun4m) Xref: biosci bionet.software.acedb:976 misc.jobs.offered:1260055 Two programmer/analyst positions are available immediately for the Agricultural Genome Information Service (AGIS) project. This project, an ongoing cooperative effort between the University of Maryland and the USDA, provides genome data to scientists and other users throughout the world. If hired, you will be working in a state-of-the-art environment developing the next generation of software for Internet access of our databases and other information. Most of the development will be in Java and Perl 5 (and perhaps C) on Sun/Solaris and DEC Alpha systems. Experience in these languages in a real-world situation is strongly preferred and Unix experience is essential. Some knowledge of biology is helpful. You must be able to work cooperatively with group members. Excellent benefits. Positions will be filled as soon as suitable candidates are found. For full consideration submit resume and names/addresses of 3 references to Dr. Paul Bottino, H.J. Patterson Hall, Dept. of Plant Biology, University of Maryland, College Park, MD 20742-7011. You may also fax to 310-314-9082 or e-mail to pb23@umail.umd.edu. THE UNIVERSITY OF MARYLAND IS AN EQUAL OPPORTUNITY EMPLOYER. From owner-acedb@net.bio.net Wed Sep 18 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: ACEDB for EWS4800 and User's guide written in Japanese (v.1.3) Date: 19 Sep 1996 09:26:15 +0100 Lines: 25 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <51r037$fhd@mserv1.dl.ac.uk> Original-To: arab-gen@net.bio.net, celegans@dl.ac.uk, acedb@dl.ac.uk (1) We compiled a version of ACEDB(4.3) for NEC-EWS4800. This package is available. Please take it from Freesoft Page of http://www.labs.nec.co.jp/ (2) ACEDB User's guide written in Japanese (v.1.3) is also available. http://www.cbi.or.jp/~sano/ (HTML) http://www.labs.nec.co.jp/ (PostScript) Many thanks to Dr. Durbin and Dr. Thierry-Mieg. -=-=-=-=-=-=-=-=-=-=- Tohru Sano NEC Corporation sano@exp.cl.nec.co.jp From owner-acedb@net.bio.net Thu Sep 19 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: acedb query language proposals Date: 20 Sep 1996 18:55:13 +0100 Lines: 473 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <51ulq1$nna@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk, acedbg@ppsw.cam.ac.uk, lhillier@watson.wustl.edu This mail contains a draft proposal for a new query language for acedb. The background to this is that Prof. Stefan Wiesmann is visiting the Sanger Centre for 6 months on sabbatical from the Darmstadt University, Germany, and during his visit is working on this aspect of acedb. What you see below is the result of our joint endeavours. Most of the good ideas are his. I have retained some acedb "close-to-the-implementation" habits in places, for which he should not be blamed. Jean has only given preliminary (supportive) comments so far, so shouldn't be blamed for anything. We are sending this out as a discussion document. Please comment, particularly on points where we have expressed uncertainty, but also on any topic you choose. We are also accumulating a set of examples, and would value suggestions for this. These could either be exisiting queries/table definitions to be rephrased, or queries that you find hard or impossible with the current tools. Comment by email is welcome (Stefan's email address is wiesmann@sanger.ac.uk). I am also sending this to the little-used bionet.software.acedb newsgroup and suggest that could be a forum for wider discussion. I'll be away from Sunday 22/9 to Wednesday 2/10, but Stefan will be here. Richard Durbin ---------------------------------------------------------------------------- Proposals for a new ACEDB query language ======================================== The aims include the following: 1) Subsume existing query language and table-maker functionality. 2) Provide a clean guaranteed non-ambiguous parser from a query string, preferably based on lex/yacc or equivalent. 3) Give a programmer interface for use in C code inside ACEDB, as well as a user one in tace/aceclient and a (new) graphical one. 4) Incorporate the existing notion of an active keyset, which is used productively all over the place. The underlying idea is that the user process maintains state of one query result/input, which can be used for other actions (displaying, dumping etc.) 5) Follow where possible syntax and ideas from the mainstream of database query languages, as exemplified in OQL. Note that we do are not aiming to provide all OQL/SQL funcionality. 6) Avoid being so ambitious that we can not implement it. A clear starting point is to decide on the nature of the result of a query. We propose that this is an ordered list (acedb Array) of structures, with fields that can be typed as either objects (class not specified) or basic types. The structures (rows) are distinct. This is like a relational table, and corresponds to the output of table-maker. The current notion of a keyset is a special case. BNF for syntax, with notes ========================== query ::== list_expr { ; list_expr } ; // The ACTIVE list for the first list_expr is determined extrinsically. For // subsequent list_expr's it is the result of the previous one. The result // of the entire query is the result of the final list_expr. This becomes // the new ACTIVE list. list_expr ::== clean_list_expr | [ SELECT ] [field_name:] field { , [field_name:] field } [ FROM declaration { , declaration } ] [ WHERE bool_expr ] | // default field names are f1, f2 ... clean_list_expr set_op clean_list_expr | // for this option the list field types must be the same list_expr ORDER_BY sort_criterion {, sort_criterion } // default order is ascending, left to right on fields clean_list_expr.field_name // projection to a single list of just this field // Lists have a width, given by the number of fields in the // defining SELECT expressions. // SELECT is not necessary for parsing, and is perhaps a little clumsy, // especially when embedded in FIRST etc. constructions. However it is // required in other languages. // Similarly, the FROM clause could potentially be omitted, either where // only references to ACTIVE are used, or in embedded queries where // identifiers are inherited from the parents. XX One of us would like SELECT and FROM mandatory, the other not. clean_list_expr ::== ( list_expr ) | ACTIVE // The distinction between clean_list_expr and list_expr is a parsing hack. // The reason is that we need to put SELECT_FROM_WHERE statements in // brackets in some places, e.g. where we want to set_op the result, or // extract a field from it. set_op ::== OR | AND | DIFF // DIFF is a more standard term for set diferencing than MINUS. Should we // also allow MINUS? What about XOR? sort_criterion ::== field_name [ordering] // Default is as for previous sort_criteria in the list if they exist, else ASC ordering ::== ASC | DESC field ::== * | // represents the default identifier (see below) expr declaration ::== ACTIVE[.field_name] [[AS] identifier] | CLASS class_name [[AS] identifier] | locator [[AS] identifier] // The left hand side of these declarations defines a list, which becomes // the range of values held by the identifier. All the items in the // list must have the same basic type (KEY, Int etc.). Also, when a list // is generated by a locator, in general it carries with it a cursor // position within a parent object. // An identifier of any type can have a null value (testable using EXISTS). // The identifier can be omitted for one declaration only, with the effect // that a default identifier is created. // Scope of identifiers: identifiers have scope throughout the // SELECT_FROM_WHERE in which they are defined. In particular this // means they can be used in embedded SELECT_FROM_WHERE clauses. ++ e.g. SELECT s FROM Sequence AS s ++ WHERE YEARDIFF(LAST(s.Edit_date),NOW) > 0 ++ finds all the sequences not edited this year. locator ::== identifier[[number]] | // number defaults to 0 locator#tag_name[[number]] | // number defaults to 1 locator.tag_name[[number]] | // number defaults to 1 [number] | // as above for default identifier #tag_name[[number]] | // as above for default identifier .tag_name[[number]] // as above for default identifier // The number in the compound forms is how far right to move the cursor. // When present it should be enclosed in literal square brackets (a // bit messy in this informal bnf notation - sorry). // The forms "x[number]" and "x#tag_name[number]" move the cursor in the // current object -- a cursor must already exist for x. // The "x.tag_name" form requires that x represents an object, and // establishes a new cursor in that object. // Interestingly, these 3 lines capture the tree-based acedb data model. ++ example to illustrate this ++ Models: ++ ?Paper Title UNIQUE ?Text ++ Author ?Author #Address ++ #Address Email UNIQUE Text ++ ?Author Email UNIQUE Text ++ Data: ++ Paper Paper1 ++ Author Durbin_R Email rd@mrc-lmb.cam.ac.uk ++ Author Durbin_R ++ Email rd@sanger.ac.uk ++ Queries: ++ SELECT *, a, a#Email FROM CLASS Paper, .Author AS a ++ gives back { Paper1, Durbin_R, rd@mrc-lmb.cam.ac.uk } ++ SELECT *, a, a.Email FROM CLASS Paper, .Author AS a ++ gives back { Paper1, Durbin_R, rd@sanger.ac.uk } // Alternative to the above. We can in fact eliminate the # symbol, as // follows. The idea is that we think of a pseudo-object where // #constructed_type comes in the model, and dot into that using '.'. // The first example above then becomes: ++ SELECT *, a, a[1].Email FROM CLASS Paper, .Author AS a // One advantage of this is that it emphasizes the "lightweight object" // view of subobject data. In fact, if we switch to true Address objects // then the query does not change. What is a:1 itself? // This could be a run-time error, or could take value null. No, it must // take values over the first column of the subobject (normally tags). // As well as these arguments, this also reduces the syntactic complexity. // Could allow '->' as alternative syntax for '.'. This indicates nicely // the concept of going into an object. Also, it is valid alternative // syntax for OQL (not SQL). // We changed the current notation x:2 to x[2], to make it conform better // to other standards, and because ':' is already used for field name // declaration (though the parser could have distinguished the two uses). bool_expr ::== EXISTS locator | // test for not null NOT bool_expr | ( bool_expr ) | bool_expr bool_op bool_expr | expr comparator expr // expr's must be type compatible. // Any comparison involving a null expr is FALSE. // When testing identity of two objects, say a and b, standard OO semantics // would say that "(a = b)" tests by content, i.e. that the contents are // the same, while "(a.ID = b.ID)" or something similar tests that the // two indentifiers are referring to the same actual object. // In acedb, even if two different objects have the same contents, they // have different names, so there are no complete duplicates, so this // difference is less important. ?? Question: should we use the syntax (a = b), more obvious, or ?? (a.ID = b.ID), more correct for what we actually do bool_op ::== AND | OR | XOR expr ::== locator | // type determined implicitly // As with the field definition, all compound locators in // expressions are treated functionally as though they // declare a new identifier. In many cases this identifier // will range over a set of multiple values. If the expr // is used in a condition, the effect will be that if there // is any value in the set that satisfies the condition then // the result is true. string_literal | // include *, ? for regexp int_literal | float_literal | date_literal | locator.ID | // something needed for comparisons? locator.NAME | // name of an object, result type Text locator.CLASS | // returns a main class object, null if not an object COUNT ( list_expr ) | list_func ( list_expr ) | // result just from first column of list. Use // list_expr ::== clean_list_expr .field_name // for other fields date_diff_func ( expr, expr ) | // both expr's must be dates, returns an Int // units depend on which func (see below) ( expr ) | expr num_op expr // both expr's must be numerical ?? otherwise null, or an error comparator ::== < |<= | > | >= | = | != num_op ::== + | - | * | / list_func ::== FIRST | LAST | SUM | MIN | MAX | AVG // defined on Int, Float only date_diff_func ::== YEARDIFF | MONTHDIFF | WEEKDIFF | DAYDIFF | HOURDIFF | MINDIFF | SECDIFF string_literal ::== "{char}" int_literal ::== [-]digit{digit} float_literal ::== int_literal.{digit}[Eint_literal] date_literal ::== `yyyy[-mm[-dd[_hh[:mm[:ss]]]]] | `yy[-mm[-dd[_hh[:mm[:ss]]]]] | // All letters here represent digits. This is sloppy syntax // to let you see the order as in 1996-09-18_20:35:10 NOW Types ===== The basic types for fields and identifiers are { Int, Float, Text, DateType, KEY, TAG }. KEY is the type for an object identifier. We have separated out TAG as a formally distinct type, which it is not inside the acedb kernel. We do not otherwise treat different classes as different types, because we want to allow columns of mixed classes. We can allow automatic type conversion/promotion as follows: Int -> Float where combined in expressions/comparisons KEY -> Text use the name of an object where required TAG -> Text Alternatives, extensions ======================== We could extend the list_expr syntax in various ways. Named lists ----------- Another way to go is to allow named lists. These would I guess be stored in an acedb class that would record their field names and types in a tree object, and the actual list/table in an associated array class object. i.e. they would permanent scope if the user had write access. Syntax could be to use a '$' prefix, e.g. list_expr ::+= $list_id := list_expr // assignment clean_list_expr ::+= $list_id // retrieval Then I guess you would also have to allow in the FROM clause either declaration ::+= $list_id [.field_name] [AS identifier] or even declaration ::+= clean_list_expr [.field_name] [AS identifier] ::-= ACTIVE [.field_name] [AS identifier] which is very general indeed. Why not? Methods ------- It would be nice to have a general handle for methods, to allow domain specific extension. What type of methods/extensions do we envisage? 1) more operators like SUM, MIN etc. 2) class specfic operations on members, particularly on array classes, e.g. x.length() where x is a dna object (or any array class object) 3) possible member specific operations on tree classes? e.g. things to test interval overlap/containment for maps and sequences. Perhaps we might even want interval objects? Implementation issues ===================== We need a null value for each type. Many are already available: Object 0 Text 0 Float NaN DateType 0 Int // we must make this up The result of a query would be accessible from acedb C code via: Array a = newQuery ("....") ; with members being accessible by arr (a, irow*nfield + jfield, BSunit).? This requires the user to know the field positions, the total number of fields and the type (for the '?'), but that seems unavoidable unless we subvert the C compiler. We would want a function to set the current active list. I think this would just deactivate the interactive active keyset window, not overwrite it (it does not support more complex lists anyway). Discussion about typing by syntax, or at run time ================================================= We have had to make some difficult decisions about expression typing, in particular whether to determine type by the syntax, or at run time. Associated with this, we had to decide whether list elements come with a type or not. Nodes inside objects do come with a type, but that can only be determined at run time. There are two options for specfying list element types. In the proposal above we state that each field (column) has a type. An alternative is that each element in each column (i.e. every element in the table) has its type attached. The latter allows mixed entries of for example Ints and Text in one field. It seems unnecessarily general, though there are plausible acedb models and queries that would construct these. We propose that these generate run time errors. A key advantage of syntactic type checking is obviously better error reporting to the user. The disadvantage is complexity of comparator and operator notation, and consequent likelihood of an error. The version given above contains an untyped expr syntax, requiring dynamic typing. Here is an alternative that would type tightly at compile time. Note the multiplicity of comparators, and of list_funcs. It is not fully thought out, and would not work as is. Note that in the dynamic typing version of the main proposal, it is easier to type promote automatically where wanted, e.g. Int + Float -> Float. bool_expr ::== EXISTS locator | NOT bool_expr | ( bool_expr ) | bool_expr bool_op bool_expr | ob_expr ob_comparator ob_exp | str_expr str_comparator str_expr | num_expr num_comparator num_expr bool_op ::== AND | OR | XOR ob_expr ::== locator ob_comparator ::== == str_expr ::== "regexp" | // string literal locator | ob_expr.ID | // name of an object FIRSTS ( list_expr ) [.field_name] | LASTS ( list_expr ) [.field_name] // field_name needed if more than 1 field, default f1 str_comparator ::== <~ |<=~ | >~ | >=~ | =~ | !~ num_expr ::== number_literal | locator | // type convert if int ( num_expr ) | num_expr num_op num_expr | COUNT ( list_expr ) | num_func ( list_expr ) [.field_name] // field_name needed if more than 1 field, default f1 date_diff_func ( date_expr, date_expr ) // All num_expr have result type Float. num_op ::== + | - | * | / num_func ::== SUMF | MINF | MAXF | AVGF | FIRSTF | LASTF | SUMI | MINI | MAXI | AVGI | FIRSTI | LASTI // The F or I suffix determines whether to treat as Float or Int numm_comparator ::== < |<= | > | >= | = | != date_expr ::== `yyyy[-mm[-dd[_hh[:mm[:ss]]]]] | // literal `yy[-mm[-dd[_hh[:mm[:ss]]]]] | // literal NOW | locator | FIRSTD ( list_expr ) [.field_name] | LASTD ( list_expr ) [.field_name] // field_name needed if more than 1 field, default f1 date_diff_func ::== YEARDIFF | MONTHDIFF | WEEKDIFF | DAYDIFF | HOURDIFF | MINDIFF | SECDIFF Examples ======== There are a few examples in the text. Here are a couple more to illustrate particular points. 1) Find all sequences that are on more than one chromosome map. SELECT * FROM CLASS Sequence WHERE COUNT(m FROM .Map m WHERE m = "Chr*") > 1 This search can not be done just now. 2) Show all predicted coding genes that have brief identifications (i.e. that have functional homology) belonging to cosmids on the specified sequence map, in the correct order on the map. SELECT g, g.Brief_identification, 0.5*(c#Left +c#Right), 0.5*(g[1] + g[2]) FROM CLASS Map a, a.Clone b b.Map c, b.Sequence.Subsequence g WHERE a = "Sequence-%1" AND c = a AND EXISTS g.Brief_identification ORDER_BY f3, f4 This search can be done, but requires a table with at least 10 columns. Note that we must declare an identifier b to tie the map position, derived from c, to the predicted genes g. ------------------------------------------------------------------------------- From owner-acedb@net.bio.net Fri Sep 20 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: Re: # . : -> Date: 21 Sep 1996 19:40:27 +0100 Lines: 15 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <521cqr$d7j@mserv1.dl.ac.uk> Original-To: mieg@kaa.crbm.cnrs-mop.fr, rd@sanger.ac.uk i rather like the proposal FOO f tag a b tag c d tag3 e where tag3 is in a submodel, then ee = ff.tag[2][tag3] i have to get used to it, but i think it is natural and if i want what is right of c i would have to do it as a constraint WHERE tag[1]=c, i suppose ? From owner-acedb@net.bio.net Fri Sep 20 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: Re: # . : -> Date: 21 Sep 1996 19:10:56 +0100 Lines: 49 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <521b3g$b9u@mserv1.dl.ac.uk> Original-To: mieg@kaa.crbm.cnrs-mop.fr Given data in ace file format: FOO f tag a b tag c d I would expect FROM ff = CLASS FOO, // line 1 dd = ff->tag[2] // line 2 would get the two pairs (f,a) and (f,d) ff->tag->tag2 would get whatever is after tag2 inside objects a and c, not something in f at all. I think -> should definitely dereference a pointer. It is also natural to use . for this. NB ff is a KEY, i.e. an object pointer. Line 1 gives it no context of being in an object. You can not move right. So ff#tag[2] is meaningless. In order to eliminate #, we need to have imagine another node in each object where the '#' symbol is in the model. This gives the pseudo-object-id that is dereferenced. One problem is that there is no NAME or CLASS of this pseudo-object-id. If we do not imagine this extra node, we can have ambiguous queries. In fact the difference between # and . in our original proposal is exactly what is needed to disambiguate: do you go into the object referred to by this KEY (.), or do you move right in the same object (#). In fact, you could have the syntax [tag] to mean #tag, i.e. stay in the same object, e.g. given FOO f tag a b tag c d tag3 e where tag3 is in a submodel, then ee = ff.tag[2][tag3] would access e? This is sort of natural. A bit like associative array dereferencing in perl, which are the foundation of GDB's tag:value system. Richard From owner-acedb@net.bio.net Fri Sep 20 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: Re: # . : -> Date: 21 Sep 1996 19:48:33 +0100 Lines: 28 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <521da1$do0@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk, lstein@genome.wi.mit.edu, scartinh@vector.gig.usda.gov, wiesmann@sanger.ac.uk > > i rather like the proposal > > > FOO f > tag a b > tag c d tag3 e > > where tag3 is in a submodel, then > > ee = ff.tag[2][tag3] > > i have to get used to it, but i think it is natural > > and if i want what is right of c i would have to do it > as a constraint WHERE tag[1]=c, i suppose ? > No, "WHERE tag[1] = c" will not work. There is nothing tying that to the ee line. You need FROM cc = ff.tag, ee = cc[1][tag3] WHERE cc = c This binds cc to match c, and hence ee only ranges over things right of that. From owner-acedb@net.bio.net Fri Sep 20 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: bnf Date: 21 Sep 1996 19:41:03 +0100 Lines: 16 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <521crv$d8n@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk, lstein@genome.wi.mit.edu, mieg@kaa.crbm.cnrs-mop.fr, rd@sanger.ac.uk, scartinh@vector.gig.usda.gov, wiesmann@sanger.ac.uk i rather like the proposal FOO f tag a b tag c d tag3 e where tag3 is in a submodel, then ee = ff.tag[2][tag3] i have to get used to it, but i think it is natural and if i want what is right of c i would have to do it as a constraint WHERE tag[1]=c, i suppose ? From owner-acedb@net.bio.net Fri Sep 20 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: mieg@kaa.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg) Newsgroups: bionet.software.acedb Subject: query bug Date: 21 Sep 1996 12:11:31 +0100 Lines: 77 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <520ih3$la4@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk The proposed BNF stress that: 1) Find all sequences that are on more than one chromosome map. SELECT * FROM CLASS Sequence WHERE COUNT(m FROM .Map m WHERE m = "Chr*") > 1 This search can not be done just now. *********** true, a bug in the code, i try to fix it ! the correct present syntax is FIND Sequence ; COUNT { FOLLOW Map chr* } > 1 note the {} casting the inside FOLLOW Map chr* to an embedded query *** this query does NOT work in distributed 4.3 i have not tested deeper recursions with several embeded {{ }} but the present syntax allows that in principle finally, there is a parsing problem, semicolumns embeded inside the {} arere allowed by the syntax but do break the parser ******** what i am aiming at is that one should distinguish 2 concepts a) the bnf syntax b) bugs in the implementations that is, on this particular case, the new query is not better but an implementation bug was noticed ******* As long as the expected result of the query is just a set of objects, it is not clear that the proposed system has real superiority, i think it is less concise and no more expressive however, there is a big advantage when we come to tables, I was never able to write down the BNF for the table maker, because i always thought it was too clumsy and I welcome the notion of a unified query/table definition my comments on the document by rd and weisman is: some little details of style an interogation about casting i think explict casting should be allowed, so checking of the query against the model would give much better messages while compiling the query finally i would prefer the syntax WHERE p = Paper a = p->author to the syntax WHERE Paper p p.author a and also would prefer class casting, possibly to subclasses WHERE p = Paper a = (Prolific_author) p->a ****** PS: i got an empty result with the query FIND Sequence ; COUNT {FOLLOW Map chr*} > 1 but i think this is normal, but i did verify that the query FIND Sequence zk* ; COUNT {FOLLOW Subsequence *6} > 0 which has the same grammar, does yield the expected 44 answers in the nematode data distrib Jean From owner-acedb@net.bio.net Sat Sep 21 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: rd@mrc-lmb.cam.ac.uk (Richard Durbin) Newsgroups: bionet.software.acedb Subject: ACEDB data updates for C.elegans Date: 22 Sep 1996 05:12:41 +0100 Lines: 101 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <522ebp$alc@mserv1.dl.ac.uk> Original-To: acedb_distrib@ppsw.cam.ac.uk This is a broadcast message to the ACEDB mailing list and related newsgroups. If you are on the explicit mailing list and do not want to be, please send email to rd@sanger.ac.uk. ACEDB data updates WG1.4-6 and WS1.4-17 to 4-20 for C. elegans ============================================================= You should be using these in conjunction with release 4_3 of the acedb software. Reminder: there are now two versions of the C.elegans database. The WS1 update series contains everything, whereas WG1 update series contains all data except sequences and directly related material (proteins, motifs etc.), for those with limited resources. The additions since WG1.4-5 and WS1.4-16 are: for both types of update - a physical map update with a few changes (mid Sept) - accumulated genetic data including new gene_classes, loci and mapping data - expression data from 2 new labs, Naples and Strasbourg. - some old Cell mistakes have been corrected and for just the complete database including sequences (WS1.4-20) Data fom St Louis and Sanger Sequence databases taken in mid-Sept: - There are now 1714 (1586 before) cosmids totalling 51,655,842 (47,908,858 before) bases. - We are switching from using the PIR protein database for homology searches to the TREMBL database, hence many PIR homologies are being deleted and TR ones added. The total database sizes after adding these updates are around 390Mb for the WS1 database (we said it would grow!) and around 65Mb for the WG1 database. It will take a long time to read in the WS1 updates, particularly WS1.4-19. All four updates took us several hours. Instructions for obtaining updates/the whole thing ================================================== All the files are available in the following public access accounts (anonymous ftp sites) accessible over internet: ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb ftp.sanger.ac.uk (193.60.84.11) in England, in pub/acedb lirmm.lirmm.fr (193.49.104.10) in France, in directory genome/acedb In each case, log in as user "anonymous" and give a user identifier as password. Remember to transfer the files in BINARY mode by typing the word "binary" at the start of your ftp session. Many thanks to NCBI for letting us share in their excellent resource. Example: ftp ncbi.nlm.nih.gov login: anonymous password: your user id or email address cd repository/acedb # change to relevant directoy binary # IMPORTANT dir # display files in this directory get README get NOTES get INSTALL cd ace4 # change to ace4 directory get bin.sunos.4_3.tar.Z # get program cd ../celegans # change to worm data directory mget update.WS1.* # get all WS1 update files quit -------------------------------- Get any update files that you do not have already and read the file NOTES before proceeding further. Always get a copy of the INSTALL script. Move it and the .tar.Z files into the home directory in which you are installing ACEDB. Type "source INSTALL". Start acedb (normally by typing "acedb"), click "Yes" to accept initialising the database if starting from scratch, then choose "Add Update File" from the menu (right button), and press "All updates" with the left mouse button. If you have a problem making the program work, look at the section on problems in NOTES, and if that fails to help, let us know. ****************************************************************** Comments about the data should be sent to the data curator, Sylvia Martinelli (sylvia@sanger.ac.uk). Comments about the program, or the installation procedure, should be sent to one of us: Richard Durbin (rd@sanger.ac.uk) Jean Thierry-Mieg (mieg@kaa.cnrs-mop.fr) -------------------- end of message -------------------- From owner-acedb@net.bio.net Sat Sep 21 23:00:00 1996 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!news.sgi.com!enews.sgi.com!insync!pornstorm.eit.com!news.sprintlink.net!news-chi-13.sprintlink.net!ratty.wolfe.net!usenet From: jjones@wolfenet.com (Jeronimo Jones) Newsgroups: bionet.software.acedb Subject: Re: MONEY (and the IRS) Date: 22 Sep 1996 19:53:44 GMT Organization: Wolfe Internet Access, L.L.C. Lines: 17 Message-ID: <5245g8$96b@ratty.wolfe.net> References: <3242B36F.7F69@wing.rug.nl> NNTP-Posting-Host: yak-ts1-p05.wolfenet.com Mime-Version: 1.0 X-Newsreader: WinVN 0.99.4 In article <3242B36F.7F69@wing.rug.nl>, bounce@wing.rug.nl says... > >Taking 5 minutes to read what follows can change your life : > > Two weeks later, I began receiving money in the mail! I > could not believe it! Soon, hundreds, and then thousands of > dollars began to roll in. Within 4 weeks, I had received a > total of $32,445! How much of this $32445 has to be reported to the IRS? How do they keep track of all this money that people send to you? How do you claim it on your 1040? Inquiring minds want to know... From owner-acedb@net.bio.net Sun Sep 29 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Joanne Dicks Newsgroups: bionet.software.acedb Subject: bioinformatics post Date: 30 Sep 1996 16:37:26 +0100 Lines: 43 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <52opfm$h17@mserv1.dl.ac.uk> X-Sender: jld@topaz MIME-Version: 1.0 Original-To: acedb@dl.ac.uk UK CROP BIOINFORMATICS NETWORK ------------------------------ The Biotechnology and Biological Sciences Research Council (BBSRC) has initiated a programme involving several posts to develop and apply plant genome bioinformatics in the UK. The following position at the John Innes Centre is available :- Ref : BIONET.2 -------------- To develop software for the analysis and display of comparative genome data. The successful applicant will have the opportunity to work under his/her own initiative and should be strongly motivated. The position will also involve the co-ordination and integration of the Network, which comprises the Arabidopsis, Brassica and cereal databases. Communication with other bioinformatics groups in the UK and worldwide will be a priority of the project. The role of the Network will be to develop bioinformatics as a research tool. Accordingly, the successful applicant will be given the opportunity to design and implement software using novel computer tools and languages such as Java. The appointment will be for a fixed term of three years within Pay Band 6 within the salary range 13,951 to 24,174 per annum (UK pounds sterling). The John Innes Centre is an Equal Opportunities Employer and operates a non-contributory superannuation scheme. A first degree in computer science or biology and some relevant postgraduate qualification is preferable. Previous experience of bioinformatics, in particular knowledge of UNIX, ACeDB, WWW and programming in C or Perl would be an advantage. Application forms can be obtained by writing to the Personnel Officer, John Innes Centre, Norwich Research Park, Colney, Norwich, Norfolk, NR4 7UH quoting reference BIONET2. The closing data for completed applications is 11 October 1996. The John Innes Centre is a Registered Charity (No 511709), grant aided by the Biotechnology and Biological Sciences Research Council. From owner-acedb@net.bio.net Mon Sep 30 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.acedb Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 1 Oct 1996 02:00:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199610010900.CAA25653@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net