From owner-acedb@net.bio.net Wed Jun 05 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: ACEDB class definitions Date: 6 Jun 1996 15:16:57 +0100 Lines: 16 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4p6p8p$84c@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk ?Object is ANY this is an idea of Otto to defeat acedb strong typing myself I object to using ANY except at kernel level if i had been able to do it, i would have make it disapper^Har from the user interface, but at the beginning, i could not separate the needs of the kernel (which does require ANY) from the user interface techniclly: -?Collection is UNIQUE ?Object XREF is means that in a given collection there may be one or zero Object after the tag is and that the Collection is pointed back automatically (xrefed) in Object From owner-acedb@net.bio.net Wed Jun 05 23:00:00 1996 Path: biosci!rutgers!uwm.edu!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!fu-berlin.de!rag100.rz-berlin.mpg.DE!hunt_e From: Ela Pustulka-Hunt Newsgroups: bionet.software.acedb Subject: ACEDB class definitions Date: Thu, 06 Jun 1996 13:49:33 +0200 Lines: 30 Message-ID: <31B6C5CD.41C6@rag100.rz-berlin.mpg.de> NNTP-Posting-Host: rag100.rz-berlin.mpg.de (141.14.130.78) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-User: hunt_e X-Access: 16 25 816 X-Mailer: Mozilla 2.0 (X11; I; OSF1 V3.0 alpha) What is the meaning of "is UNIQUE ?Object XREF is" -?Collection is UNIQUE ?Object XREF is owner UNIQUE ?Object description UNIQUE Text set ?Object keyset ?KeySet n_array Int UNIQUE ?Object a_array Text UNIQUE ?Object binary_rel ?Object ?Object Text ternary_rel ?Object ?Object ?Object Text list UNIQUE ?Object REPEAT graph ?Object ?Object Text generic_properties #Generic_properties with reference to the ?Object below. Why are generic_properties defined in both? -?Object is ANY aux Text Text REPEAT generic_properties #Generic_properties _______________________________________________________________________________ Ela Pustulka-Hunt hunt_e@rag100.rz-berlin.mpg.de Database Administrator tel. 030 - 8413-1356 Max Planck Institut fuer Molekulare Genetik, Abtl. Lehrach Ihnestrasse 73, 14195 Berlin, Germany _____________________________________________________________________________ From owner-acedb@net.bio.net Thu Jun 06 23:00:00 1996 Path: biosci!rutgers!uwm.edu!chi-news.cic.net!nntp.coast.net!swidir.switch.ch!scsing.switch.ch!news.belwue.de!fu-berlin.de!rag2.rz-berlin.mpg.DE!leser From: Ulf Leser Newsgroups: bionet.software.acedb Subject: ACEDB 4.3 update Date: Fri, 07 Jun 1996 12:09:31 +0200 Organization: MPI: "Molekulare Genetik", Berlin, Dahlem Lines: 8 Message-ID: <31B7FFDB.167E@mpimg-berlin-dahlem.mpg.de> NNTP-Posting-Host: rag2.rz-berlin.mpg.de (141.14.130.102) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-User: leser X-Access: 16 25 816 X-Mailer: Mozilla 2.0 (X11; I; OSF1 V3.0 alpha) Hello, I've downloaded and installed the update to 4.3. Works good. My question is: is it enough just to exchange the binaries ? (from 4.1 to 4.3). I tried it, it seems to work, but maybe there are hidden conflicts. Thank's, Ulf From owner-acedb@net.bio.net Sun Jun 09 23:00:00 1996 Path: biosci!rutgers!uwm.edu!fnnews.fnal.gov!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 Jun 1996 20:14:12 GMT Organization: Dendrome, A genome database for forest trees Lines: 1169 Approved: news-answers-request@MIT.Edu Message-ID: <4phvmk$kf2@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:918 news.answers:67746 Archive-name: acedb-faq Last-modified: 6/10/96 Version: 1.29 ------------------------------------------------------------------------------- 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 4.2 and a complete C. elegans data set at trog.mbb.sfu.ca in /pub/acedb as bin.linux.4_1.tar.Z and in ELF binary as ftp://trog.mbb.sfu.ca/pub/acedb/bin.linux.4_2.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 4.1 (and earlier versions) for Linux 2-10: * trog.mbb.sfu.ca /pub/acedb as bin.linux.4_1.tar.Z. ACEDB for The NEC EWS4800: * ftp.nec.co.jp[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. Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/other/ WWW : http://keck.tamu.edu/cgi/agsdb/agsdbserver.html 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 Fool 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 : EofD (Encyclopaedia of the Drosophila) Species : Drosophilidae (primarily D. melanogaster) Availability : Macintosh CD-ROM and SunOS executables via anonymous ftp Last_update : November 1995 ACEDB_version : 4.1 Developer : Suzanna Lewis, suzi@fly2.berkeley.edu Developer : Cyrus Harmon, sly@fly2.berkeley.edu Developer : Edward Welbourne, eddy@gen.cam.ac.uk Collaborator : The FlyBase Consortium, flybase-help@morgan.harvard.edu Collaborator : The Berkeley Drosophila Genome Project, flygenome@maillink.berkeley.edu FTP : fruitfly.berkeley.edu in pub/EofD Gopher : fly.bio.indiana.edu:70+/11/Flybase WWW : http://shoofly.berkeley.edu WWW : http://fly2.berkeley.edu:3512/EofD.html Database : EthnobotDB (orldwide 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, relatives Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu PI : Olin D. Anderson, oandersn@pw.usda.gov ACEDB_version : 4_1 Data_version : 1.5+ Last_update : November 1995 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 : Leishmaia 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 : Musculus 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 occurence, 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 a tool set for integrating version 4 of ACEDB with perl and the World-Wide Web. The archive is 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 96. There is a tutorial 19-21 June 1996 in Cambridge. Consult http://www.hgmp.mrc.ac.uk . 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 is 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, 1993,1994,1995,1996 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 Mon Jun 10 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: acedb WS-1-8, enzymes missing. Date: 11 Jun 1996 10:57:51 +0100 Lines: 26 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4pjfuv$5g4@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Jeff Bryer just noticed that the list of restriction enzymes is missing in the new C.elegans dataset WS-1-8 It should be part both of the complete dataset WS and the smaller genetic dataset, but we left it out by error. Sorry. The code ace.4_3 is identical to ace.4-1 for this functionality. To recover the restriction enzymes you may dump them out of the previous data distribution with the tace query acedb> Query Find Motif Restriction acedb> write restriction.enzymes.ace and then read them in the new code using: acedb> parse restriction.enzymes.ace acedb> save alternativelly, you can read save this mail as /var/tmp/restriction.enzymes.ace clean the top of the message and read it finally you can import a clean file restriction.enzymes.ace from ftp://ncbi.nlm.nih.gov/repository/acedb/restriction.enzymes.ace The restriction.enzymes.ace file will be in the next mail Jean From owner-acedb@net.bio.net Wed Jun 12 23:00:00 1996 Path: biosci!har.mrc.ac.uk!mark From: mark@har.mrc.ac.uk (Mark Strivens) Newsgroups: bionet.software.acedb Subject: ACESERVER Problems Date: 13 Jun 1996 10:14:18 -0700 Organization: MRC Lines: 50 Sender: daemon@net.bio.net Distribution: world Message-ID: <31C0599E.7982@har.mrc.ac.uk> NNTP-Posting-Host: net.bio.net I'm having problems installing an ACE 4.1 aceserver on a SPARC 5 running Solaris 2.5. I have done the following according to the instructions. 1) Compiled Aceserver/client using gcc 2.7.2 (I did get a complaint about a redefinition of RPC_ANYSOCK (between a gcc include file and rpcace.h 2) Entered in /etc/rpc : acedbd 20000116 rpc.acedbd 3) Entered (as one line fields separated by tabs) in /etc/inet/inetd.conf : 20000116/1 stream rpc/tcp wait mark /opt/local/bin/rpc.acedbd rpc.acedbd /opt/www/acedb/xg 20000116 600:600:100 4) done kill -HUP [inetd_pid]. 5) I also have the line in my /etc.services: acedbd 20000116/tcp rpc.acedbd also the line nsswitch.conf : services: files I tried three other things : - rebooting the machine (at least once) - starting the aceserver as a foreground process (I get the message !! internal system error: No valid port specified) - edited the wspec/server.wrm file This is most frustrating I have had this working today and now it refuses to work for love nor money, can anyone help?? Many thanks in advance Mark ------------------------------------------------------------------ Mark Strivens Telephone : 01235-824 536 (direct line) Informatics Group, 01235-834 393 (switchboard) MRC Mouse Genome Centre, Fax : 01235-824 540 Harwell, Didcot, email : mark@har.mrc.ac.uk Oxfordshire, OX11 0RD. mstriven@hgmp.mrc.ac.uk United Kingdom. URL : http://www.mgc.har.mrc.ac.uk/ ==================================================================== From owner-acedb@net.bio.net Wed Jun 12 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: aceserver Date: 13 Jun 1996 21:44:21 +0100 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4ppuj5$r2n@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk you did not quite follow the intsructions: you should have: /etc/services astrid_server 20000300/tcp rpc.acedbd /etc/rpc astrid_server 20000300 rpc.acedbd astrid_server/1 stream rpc/tcp wait menes /usr/local/bin/rpc.acedbd rpc.acedbd /local1/astrid 20000300 1200:1200:0 all on a single line this is diffrent from what you report: 20000116/1 stream rpc/tcp wait..... that is i declare in inetd by name not by number, you have no name link However, i am having trouble on a SGI, there the server works nicly in foreground, but not as a daemon, it keeps forking on each request From owner-acedb@net.bio.net Thu Jun 13 23:00:00 1996 Path: biosci!har.mrc.ac.uk!mark From: mark@har.mrc.ac.uk (Mark Strivens) Newsgroups: bionet.software.acedb Subject: Re: aceserver Date: 14 Jun 1996 00:40:51 -0700 Organization: MRC Lines: 50 Sender: daemon@net.bio.net Distribution: world Message-ID: <31C124BF.6CA0@har.mrc.ac.uk> References: <4ppuj5$r2n@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net Your observation is correct about the line in inetd.conf, > astrid_server/1 stream rpc/tcp wait menes /usr/local/bin/rpc.acedbd rpc.acedbd /local1/astrid 20000300 1200:1200:0 > > all on a single line > > this is diffrent from what you report: 20000116/1 stream rpc/tcp wait..... > that is i declare in inetd by name not by number, you have no name link but I have never got the aceserver to work on either a SunOS 4.1.3 or Solaris 2.5 machine by specifying the service name at the beginning of the inetd.conf line. It has only ever worked using the rpc # instead, this according to the man pages for inetd.conf is quite valid. service-name The name of a valid service listed in the services file. For RPC services, the value of the service-name field con- sists of the RPC service name or program number, followed by a '/' (slash) and either a version number or a range of version numbers (for example, rstatd/2- 4). if try to restart inetd using 'kill -HUP' specifying the service name rather than it's id in inetd.conf I get message like: inetd[116]: acedbd/rpc/tcp: unknown service > However, i am having trouble on a SGI, there the server works nicly in foreground, but not > as a daemon, it keeps forking on each request What do you think...?? I can't get it to run as a foreground process either I get an error like: !! internal system error : No valid port specified Many thanks Mark -------------------------------------------------------------------- Mark Strivens Telephone : 01235-824 536 (direct line) Informatics Group, 01235-834 393 (switchboard) MRC Mouse Genome Centre, Fax : 01235-824 540 Harwell, Didcot, email : mark@har.mrc.ac.uk Oxfordshire, OX11 0RD. mstriven@hgmp.mrc.ac.uk United Kingdom. URL : http://www.mgc.har.mrc.ac.uk/ ==================================================================== From owner-acedb@net.bio.net Thu Jun 13 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!news2.cais.net!news.cais.net!nntp.uio.no!news.kth.se!sibirien.physchem.kth.se!not-for-mail From: staffan@biochem.kth.se (Staffan Bergh) Newsgroups: bionet.software.acedb Subject: Re: ACEDB 4.1 Client/Server Date: 14 Jun 1996 17:04:56 +0200 Organization: Biochemistry, KTH, Stockholm Lines: 40 Sender: staffan@biochem.kth.se Distribution: bionet Message-ID: <4prv2o$mb2@sibirien.physchem.kth.se> References: <4pr9he$hee@mserv1.dl.ac.uk> NNTP-Posting-Host: sibirien.physchem.kth.se Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit In article <4pr9he$hee@mserv1.dl.ac.uk> Dr Mike Arnold writes: [some stuff deleted] >Also, multiple client connections are forked from one session. For >example, if I query classes and then click a returned link, another >client connection is established - this eats into CPU and is probably >not what was intended! Excuse me if this is really basic ... If you make sure to do a closeServer call at the end of each 'transaction' this problem will go away - in fact I think the openServer and closeServer calls in Aceclient are a bit misnamed: they actually pertain to _clients_, not the server. With the rpc setup, if you start a new client (with the openServer call) then if no server is running a new server will be started (by inetd) *and* a new client (although I've seen some problems with that bit - it seems the first client just hangs ...). The following openServer calls will just connect to the already running server. closeServer will close the active _client_, not the server. The server will kill idle clients after a while (one of the timeouts in the command line for the server tells how long a while) but if you have lots of openServer calls in the script and don't close the clients as you go, it's easy to overload the server - on my machine, when it gets up to a hundred active clients or so, the server starts to return errors. Cheers /staffan Staffan Bergh Biochemistry, KTH, S-100 44 Stockholm, Sweden email: staffan@biochem.kth.se + Don't let that horse eat that violin phone: int+46 8 790 9230 + cried Chagall's mother fax: int+46 8 24 54 52 + but he kept right on painting + -- Lawrence Ferlinghetti Webmaster and MycDB maintainer From owner-acedb@net.bio.net Thu Jun 13 23:00:00 1996 Path: biosci!CUTTER.LBL.GOV!davy From: davy@CUTTER.LBL.GOV (Donn Davy) Newsgroups: bionet.software.acedb Subject: Re: ACEDB 4.1 Client/Server Date: 14 Jun 1996 07:46:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <4pr9he$hee@mserv1.dl.ac.uk> Reply-To: Donn Davy NNTP-Posting-Host: net.bio.net There is a trick that works on my Solaris 2.5 system to get the inetd to fire up the aceserver. It also worked, and was sometimes necessary in SunOS 4.1.x. It is the following: 1) start the aceclient using the */etc/services* number as the port. This will fail, but 2) now starting the aceclient with the inetd.conf port will succeed. Example: %tail /etc/services acecot117 1117/tcp rpc.acedbd acecot117 acecotprod %tail /etc/inetd.conf 1117/1 stream rpc/tcp wait davy /usr/local/bin/rpc.acedbd rpc.acedbd /home2/zorn/data1/users/davy/acecot/acecot1.7 20000117 600:600:0 %aceclient donn.lbl.gov -port 1117 Sol2.5: [hangs] ^C SunOS: //! cannot establish connection //! usage: aceclient host [-port port_num] [-time_out nn_in_seconds] [-ace_out] [-ace_in] [-f reportfile parameters] [but now,] %aceclient donn.lbl.gov -port 20000117 acedb@donn.lbl.gov> [works!] Like Mark Strivens, I have never gotten the server to start from inetd.conf by mentioning the service *name* there, but have had success using the services *number*, as in the above example. --------------------------------------------+------------------ Donn F. Davy, Computer Systems Engineer / (510) 486-4162 Lawrence Berkeley National Laboratory \ MS 50F-129, One Cyclotron Rd / Berkeley, CA 94720 \ fax (510) 486-5548 -----------------------------------------+--------------------- Home page: http://donn.lbl.gov/misc/dfd/dfdhome.html -----------------------------------------+--------------------- From owner-acedb@net.bio.net Thu Jun 13 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Dr Mike Arnold Newsgroups: bionet.software.acedb Subject: ACEDB 4.1 Client/Server Date: 14 Jun 1996 09:57:18 +0100 Organization: NASC Lines: 101 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4pr9he$hee@mserv1.dl.ac.uk> MIME-Version: 1.0 Original-To: acedb@dl.ac.uk I have just got wind of a current thread concerning the aceserver/client setup that comes with ACEDB 4.1. Basically, people seem to be having the same problems that I have experienced. I am running the ACE stuff on a SPARCStation20 under Solaris 2.5. I have compiled the full ace setup using gcc 2.7.2 without too much fuss (just the usual three days of linker errors!) and re-compiled Perl5.002 with the Aceclient extension statically linked. (This bit was - well - typically UNIX - frustrating and time consuming). So now I have a perl executable with the ace extension, an aceserver/client compiled for this machine and the following entries in the /etc files: /etc/inetd.conf > # > # AceServer daemon for communicating AatDB over a WWW interface > # > # > aatdb/1 stream tcp wait root /usr/local/bin/rpc.aatdb rpc.aatdb /catalogue2/aatdb/ace4.1/aatdb/ 4000001 /etc/services > ## > # Mike's addition for aatdb > ## > ### > aatdb/1 4000001/tcp rpc.aatdb > (In here I HAVE to put aatdb/1 otherwise I get an error message saying > aatdb/1/tcp : Unknown service ) /etc/rpc > aatdb 4000001 rpc.aatdb OK, so now we test the setup with the dbinfo.pl file looking like this :- > #!/usr/local/bin/perl > > # everything you wanted to know about our acedb's > # but were afraid to ask > > %main::dbinfo = ( > 'aatdb' => {'title'=>"AatDB", > 'sub'=>"Arabidopsis thaliana", > 'group'=>'other', > 'version'=>4.1, > 'portmap'=>{'thale.nott.ac.uk'=>4000001}} > ); I'm not sure where the version bit is used, but I have also tried version 1 here as well! The aceserver has been renamed to /usr/local/bin/rpc.aatdb and the following command issued from the command line starts the server running : > /usr/local/bin/rpc.aatdb /catalogue2/aatdb/ace4.1/aatdb -port 4000001 with the usual splash screen stuff and the correct port settings, etc. The URL: http://thale.nott.ac.uk/cgi-bin/aatdb?classes then generates the classes output nicely wrapped in HTML etc., and you can browse the classes nicely until you want to actually look at an object. The object then just comes back > "Object empty:" even though this same object can be viewed properly from Ace4.1 But, that aside, the problem of not running under daemon experienced by others stands for my configuration also, and no matter how I tweak the entries in the /etc files I have not yet successfully managed to run from under inetd. Also, multiple client connections are forked from one session. For example, if I query classes and then click a returned link, another client connection is established - this eats into CPU and is probably not what was intended! I have also noticed that the little blue bar at the bottom of the screen on Netscape (3.0b3) remains at 100% for as long as this screen is displayed, suggesting that the connection with the server is being maintained even after information has stopped being transmitted. -- Mike Arnold NASC Dept. Life Science University of Nottingham Nottingham e-mail : mike@thale.life.nottingham.ac.uk URL: http://thale.nott.ac.uk/ Mike's URL (still under const.!) http://thale.nott.ac.uk/~mike From owner-acedb@net.bio.net Fri Jun 14 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Danielle et jean Thierry-Mieg Newsgroups: bionet.software.acedb Subject: staffan's 100 clients Date: 15 Jun 1996 13:22:14 +0100 Lines: 10 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4pu9tm$7n6@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk there is another limitation, hte server maintains one active list per client so a 100 open cleints meean a reather large memory consumption on the server the active list is needed because of the semantiocs of follow etc the client could retransmit his own lit, but this is costly we couls have a command, clean or something like that, to tell the server to zero the active list maybe "Clear" From owner-acedb@net.bio.net Sat Jun 15 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.software.acedb Subject: Macace versions of latest ACEDB release Date: 16 Jun 1996 15:05:57 +0100 Lines: 9 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <4q14c5$9p9@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk, celegans@dl.ac.uk Macintosh versions of the most recent C.elegans acedb release are now available as self-extracting archives from the following two locations: ftp://ftp.sanger.ac.uk/pub/acedb/macace ftp://ncbi.nih.gov/repository/acedb/macace Richard Durbin From owner-acedb@net.bio.net Sun Jun 16 23:00:00 1996 Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!munnari.OZ.AU!news.mel.connect.com.au!news.mel.aone.net.au!usenet From: Matt O'Donnell Newsgroups: bionet.software.acedb Subject: Re: ACEDB Genome Database Software FAQ Date: Mon, 17 Jun 1996 22:50:49 +0000 Lines: 1 Message-ID: <31C5E149.6E45@s054.aone.net.au> References: <4phvmk$kf2@overload.lbl.gov> Reply-To: odonnellm@s054.aone.net.au NNTP-Posting-Host: d22-2.cpe.sydney.aone.net.au Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01E (Macintosh; I; 68K) What the fuck is all this shit From owner-acedb@net.bio.net Sun Jun 16 23:00:00 1996 Path: biosci!agate!ihnp4.ucsd.edu!swrinde!newsfeed.internetmci.com!tank.news.pipex.net!pipex!dish.news.pipex.net!pipex!news.ukpats.org.uk!lade.news.pipex.net!pipex!ggr.co.uk!ussun2n.glaxo.com!usenet From: G S Miller Newsgroups: bionet.software.acedb Subject: unable to share ace databases between Solaris 2.4 & Irix 5.3 Date: Wed, 12 Jun 1996 16:44:52 -0400 Organization: Glaxo Wellcome Bioinformatics Lines: 51 Message-ID: <31BF2C44.41C6@glaxo.com> NNTP-Posting-Host: ussg2t.glaxo.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP22) CC: gsm15414@glaxo.com We have recently tried to install ACEdb in a heterogeneous environment. Two different machine types each access an identical file system. We have found that the system is not able to function properly between the two platforms involved -- a database created by ACEDB on one architecture cannot be read by the other. a summary: we built acedb from scratch: On SGIs: -------- setenv ACEDB /pub/bioinfo/apps/ace4.3 setenv ACEDB_SRC $ACEDB setenv ACEDB_MACHINE SGI cd $ACEDB/wmake make -------- No problems, and binaries are eventually placed in $ACEDB/bin.SGI On Solaris: ----------- setenv ACEDB /pub/bioinfo/apps/ace4.3 setenv ACEDB_SRC $ACEDB setenv ACEDB_MACHINE SOLARIS_4_RELEASE cd $ACEDB/wmake make -------- Also no problems. Running xace/tace/aceserver/aceclient on a single machine/architecture works fine. Trying to run xace on a machine with a different architecture gives the following immediately on startup: !! FATAL ERROR: system error 2 No such file or directory !! arrayGet(_lexi1) read an array of incorrect size 20 != 12 It doesn't matter whether I run on an SGI first or a SUN first, as soon as I try to run on the complementary machine type, BOOM! Any insights would be greatly appreciated. Greg Miller Programmer Analyst II Glaxo Wellcome Bioinformatics From owner-acedb@net.bio.net Sun Jun 16 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!usc!howland.reston.ans.net!nntp.coast.net!oleane!jussieu.fr!orstom.fr!usenet From: Thierry VALERO Newsgroups: bionet.software.acedb,sci.geo.eos,sci.geo.hydrology,sci.geo.meteorology,sci.data.formats Subject: ACEDB in others fields than 'genetic'? Date: Mon, 17 Jun 1996 18:08:30 +0100 Organization: ORSTOM Lines: 36 Message-ID: <31C5910E.2FBA@orstom.rio.net> NNTP-Posting-Host: pchydro1.mpl.orstom.fr Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 2.02 (Win16; I) CC: AAAA C'est moi Xref: biosci bionet.software.acedb:932 sci.geo.eos:1589 sci.geo.hydrology:4670 sci.geo.meteorology:21602 sci.data.formats:1461 Bonjour, Is there any implementation of ACEDB (http://probe.nalusda.gov) in others = fields than 'genetic'? I ask myself if ACEDB has been used for climat/hydrology database or climat/hydrology catalog database. Thierry VALERO 'Computer Engineer at ORSTOM', one of guys involved in HAPEX-SAHEL Information System (http://www.orstom.fr/hapex). +------------------------------------------------------+ ! Thierry VALERO Tel. +33 67.61.74.35 ! ! ORSTOM Fax. +33 67.41.18.06 ! ! BP 5045 E-Mail valero@orstom.fr ! ! F-34032 MONTPELLIER CEDEX ! ! FRANCE ! +------------------------------------------------------+ -- = =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=3D=3D=3D Une partie des messages arriv=E9s sur mon micro-ordinateur le 4 juin 1996 a =E9t=E9 =E9truite. = +------------------------------------------------------+ ! Thierry VALERO Tel. +33 67.61.74.35 ! ! ORSTOM Fax. +33 67.41.18.06 ! ! BP 5045 E-Mail valero@orstom.fr ! ! F-34032 MONTPELLIER CEDEX ! ! FRANCE ! +------------------------------------------------------+ From owner-acedb@net.bio.net Mon Jun 17 23:00:00 1996 Newsgroups: bionet.software.acedb Path: biosci!rutgers!uwm.edu!news-res.gsl.net!news.gsl.net!nntp.coast.net!howland.reston.ans.net!world1.bawave.com!news.clark.net!mr.net!news.mid.net!tin.monsanto.com!newspump.wustl.edu!news.cellbio.wustl.edu!not-for-mail From: eddy@wol.wustl.edu (Sean Eddy) Subject: Re: ACEDB Genome Database Software FAQ Sender: eddy@wol.wustl.edu Message-ID: Date: 18 Jun 1996 06:44:01 -0500 References: <4phvmk$kf2@overload.lbl.gov> <31C5E149.6E45@s054.aone.net.au> In-reply-to: Matt O'Donnell's message of Mon, 17 Jun 1996 22:50:49 +0000 X-Newsreader: Gnus v5.1 Lines: 5 In article <31C5E149.6E45@s054.aone.net.au> Matt O'Donnell writes: > What the fuck is all this shit Ah, obviously a disgruntled Sybase user :) -- - Sean Eddy - Dept. of Genetics, Washington University School of Medicine - 660 S. Euclid Box 8232, St. Louis MO 63110, USA - mailto://eddy@genetics.wustl.edu http://genome.wustl.edu/eddy From owner-acedb@net.bio.net Mon Jun 17 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!nntp.coast.net!fu-berlin.de!news.dfn.de!news.embl-heidelberg.de!bioftp.unibas.ch!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: Ewan Birney Newsgroups: bionet.software.acedb Subject: Re: ACEDB Genome Database Software FAQ Date: Tue, 18 Jun 1996 22:29:53 +0100 Organization: Oxford University Lines: 17 Message-ID: <31C71FD1.41C6@molbiol.ox.ac.uk> References: <4phvmk$kf2@overload.lbl.gov> <31C5E149.6E45@s054.aone.net.au> NNTP-Posting-Host: nmrd.ocms.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (X11; I; IRIX 5.3 IP22) Sean Eddy wrote: > > In article <31C5E149.6E45@s054.aone.net.au> Matt O'Donnell writes: > > What the fuck is all this shit > > Ah, obviously a disgruntled Sybase user :) > > -- > - Sean Eddy > - Dept. of Genetics, Washington University School of Medicine > - 660 S. Euclid Box 8232, St. Louis MO 63110, USA > - mailto://eddy@genetics.wustl.edu http://genome.wustl.edu/eddy Yeah - maybe it was an SQL too far.... e. From owner-acedb@net.bio.net Tue Jun 18 23:00:00 1996 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!news.uoregon.edu!arclight.uoregon.edu!news.bc.net!news.sfu.ca!trog.mbb.sfu.ca!jbryer From: jbryer@trog.mbb.sfu.ca (Jeff Bryer) Newsgroups: bionet.software.acedb,bionet.celegans Subject: ANNOUNCE: ACEDB 4.3 for Linux Date: 19 Jun 1996 20:58:27 GMT Organization: IMBB, Simon Fraser University Lines: 46 Distribution: world Message-ID: <4q9plj$cd7@morgoth.sfu.ca> NNTP-Posting-Host: trog.mbb.sfu.ca Xref: biosci bionet.software.acedb:935 bionet.celegans:952 I have now compiled a version of ACEDB v4.3 for Linux. Sorry for the delay in this. a.out and elf binaries are both available and for the C. elegans community an entire package containing the precompiled WS4-8 database is also available (in 5 parts). The readme file follows: Jeff Bryer jbryer@darwin.mbb.sfu.ca -----include readme README.LINUX.4_3 June 18, 1996 This is the a.out binary version of ACEDB v4.3 for Linux and can be found at ftp://trog.mbb.sfu.ca/pub/acedb/bin.linux.4_3.tar.gz and soon at ftp://ncbi.nlm.nih.gov/repository/acedb/ace4/bin.linux.4_3.tar.gz If your Linux system cannot handle the a.out format, an ELF version is also available. ftp://trob.mbb.sfu.ca/pub/acedb/bin.linux.4_3.elf.tar.gz Linux is a free Unix-like OS available for the Intel [3456]86 platform. You can find out more about Linux in the comp.os.linux.* groups on usenet. Acedb runs very well on Linux, but you will need a fairly loaded system. I recommend at _least_ 16MB of RAM and a 486/33. You will also want a large disk that can accomodate the database's growth. More RAM is much better than a faster processor. A 486/66 with 32MB RAM will blow the doors off a Pentium/100 with 8M. You should have 32MB of swap for updates. You should be running Linux 1.0 or better and either the a.out shared libraries (I am using libc 4.5.26) or the ELF libraries (I am using libc 5.0.9). Other versions should work, but are untested. Jeff Bryer jbryer@darwin.mbb.sfu.ca -- ------- Jeff Bryer | "Maybe VR.12 turns you into Fabio." jbryer@darwin.mbb.sfu.ca | -Duncan in Parallel Lives (VR.5) From owner-acedb@net.bio.net Mon Jun 24 23:00:00 1996 Path: biosci!daresbury!lyra.csx.cam.ac.uk!sunsite.doc.ic.ac.uk!yama.mcc.ac.uk!usenet From: you@stud.man.ac.uk (PUT Your Name Here) Newsgroups: bionet.software.acedb Subject: embl2ace.perl - ace.txt [1/1] Date: 25 Jun 1996 09:02:43 GMT Organization: University of Manchester Lines: 8 Message-ID: <4qo9vj$rca@yama.mcc.ac.uk> NNTP-Posting-Host: m345.sbs.man.ac.uk Mime-Version: 1.0 Content-Type: Application/octet-stream; name=ace.txt Content-Transfer-Encoding: Base64 X-Newsreader: WinVN 0.99.2 SSBoYXZlIGJlZW4gdHJ5aW5nIHRvIHVzZSBlbWJsMmFjZS5wZXJsIHRvIHBy b2R1Y2UgQUNFIA0KZnJvbSBFTUJMIGZpbGVzIGZvciBBQ0VEQi4gQWx0aG91 Z2ggdGhlIHByb2dyYW0gZ2V0cyBhcw0KZmFyIGFzIGNyZWF0aW5nIGEgemVy byBsZW5ndGggb3V0cHV0IGZpbGUgbm90aGluZyBlbHNlDQpzZWVtcyB0byBo YXBwZW4uIEhhcyBhbnlvbmUgYW55IGlkZWFzIHBsZWFzZT8NCg0KUm9nZXIg SG9ydG9uDQpTY2hvb2wgb2YgQmlvbG9naWNhbCBTY2llbmNlDQpVbml2ZXJz aXR5IG9mIE1hbmNoZXN0ZXINCg0KbW9iZmVyaDFAc3R1ZC5tYW4uYWMudWs= From owner-acedb@net.bio.net Sun Jun 30 23:00:00 1996 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: $DBDIR Date: 1 Jul 1996 10:40:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 12 Sender: daemon@net.bio.net Distribution: world Message-ID: <9607011735.AA10690@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net A user complained that the xace startup script I gave him doesn't include the "setenv DBDIR" line, which I omitted because it didn't have any effect as far as I could tell. He said, > The DBDIR varaible seems only necessary for the loading of the databases > in xace, not for consultation. True? It isn't necessary for data loading either when I do it, using ace4_3c under SunOS, Solaris or Linux. He is using a DEC Alpha with OSF/1, which I don't have access to any of. - Dave