Subject: ACEDB Genome Database Software FAQ
Date: 6 Feb 1996 00:16:19 GMT
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.

Version: 1.27




ACEDB FAQ
*********


Curated by: Bradley K. Sherman 


Frequently Asked Questions about ACEDB
++++++++++++++++++++++++++++++++++++++

 o Q0 : What is ACEDB? 
 o --------------------
 o Q1 : What is the current version of ACEDB? 
 o -------------------------------------------
 o Q2 : What hardware/software do I need to run ACEDB? 
 o ----------------------------------------------------
 o Q3 : Where can I get ACEDB? 
 o ----------------------------
 o Q4 : !What ACEDB databases exist? 
 o ----------------------------------
 o Q5 : What documentation exists for ACEDB? 
 o ------------------------------------------
 o Q6 : What other resources are available for ACEDB? 
 o ---------------------------------------------------
 o Q7 : How should ACEDB be cited? 
 o --------------------------------
 o Q8 : Is ACEDB object-oriented? 
 o -------------------------------
 o Q9 : How does one get on/off the ACEDB announcements mailing list? 
 o -------------------------------------------------------------------
 o Q10 : When and where is the next ACEDB Workshop? 
 o -------------------------------------------------
 o Q11 : Who prepared this document & where is the current version? 
 o -----------------------------------------------------------------

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_1 (as of 10 August 1995). 

A test (beta) version of ACEDB 4.0b4 (5/95) is available. 

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. 

 o 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 
    o PC 386/486/Pentium with Linux (free Unix) Jeff Bryer,
      jbryer@darwin.mbb.sfu.ca and Ken Clark provide a linux version of 4.1 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_1.elf.tar.gz . 
    o There exist, or have existed, ports onto Alliant, Hewlett- Packard, IBM
      R6000, 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 
 o 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. 
 o 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: 

 o lirmm.lirmm.fr in pub/acedb 
 o cele.mrc-lmb.cam.ac.uk in pub/acedb 
 o ncbi.nlm.nih.gov in repository/acedb 
 o bioinformatics.weizmann.ac.il in pub/databases/acedb. 

MacAce is available from: 

 o genome.lbl.gov in pub/macace 
 o cele.mrc-lmb.cam.ac.uk in pub/acedb/macace 

Linux; ACEDB version 4.1 (and earlier versions) for Linux 2-10: 

 o trog.mbb.sfu.ca /pub/acedb as bin.linux.4_1.tar.Z. 

ACEDB for The NEC EWS4800: 

 o ftp.nec.co.jp 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 : AceMap
Species : Homo sapiens
Subject : Physical mapping data for human chromsome X
ACEDB_version : 4.1
Curator : Hugues Roest Crollius, croillius@mpimg-berlin-dahlem.mpg.de
PI : Hans Lehrach
FTP : ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap
Comment: Get the README file in the directory above.
Contact : Max-Planck-Institut fur Moleulare Genetic, Ihnestrasse 73, 14195
Berlin, Germany
Availability : beta release of the X chromosome data/models via anonymous ftp
FTP : ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap 
Last_update : August 1994 

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 : 1.0
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 Signalling Molecules and Interactions
Contact : Takako Igarashi, National Insitute of Health Sciences, Division of
Chem-Bio Informatics, Setagaya-ku, Tokyo, Japan 158, taka@nihs.go.jp 

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
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 : 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 : Susah 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 3.0
Last_update : May 1995
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 : 3.0
Last_update : July 1995
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: 

 o acedb -- A C. elegans Database: I. Users' Guide. 
 o acedb -- A C. elegans Database: II. Installation Guide. 
 o acedb -- A C. elegans Database: III. Configuration Guide. 
 o 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 and 
ftp://weeds.mgh.harvard.edu/acedb_doc . 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. [text is
available through ftp or gopher from weeds.mgh.harvard.edu] 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.
[text is available through ftp or gopher from weeds.mgh.harvard.edu] 

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/ . 

The Developers' Archive
+++++++++++++++++++++++

Mike Cherry maintains an archive of tools that may be useful in curating ACEDB
databases. It can be reached by anonymous ftp at URL 
ftp://weeds.mgh.harvard.edu/acedb_dev/ or via gopher at 
gopher://genome-gopher.stanford.edu:70/11/ftp 

If you have a contribution place it in
ftp://weeds.mgh.harvard.edu/acedb_dev/incoming/ and 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. 

 o All of the articles in biosci.software.acedb are archived by Biosci at 
   gopher://gopher.bio.net/1/ACEDB 
 o Mike Cherry makes it possible to search past articles in
   biosci.software.acedb using WAIS at 
   gopher://genome-gopher.stanford.edu:80/77/.index/acedb-biosci and at URL 
   http://genome-www.stanford.edu/biosci_acedb.html . 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:

 o http://moulon.inra.fr/acedb/acedb.html for C. elegans data 
 o http://kiev.physchem.kth.se/MycDB.html for Mycobacterium data 
 o 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: 

 o flydb - LBL's Drosophila Acedb-style database 
 o 21bdb - LBL's Human Chromosome 21 Acedb-style database 
 o querdb - LBL's query-language extensions to Acedb 
 o metadata - LBL's compendium of Acedb database schema variants 
 o macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version 
 o 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: 

 o 1/ Ritter,O.: The Integrated Genomic Database. in Computational Methods in
   Genome Research, edited by S.Suhai, Plenum, 57-73 (1994). 
 o 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 is not yet scheduled. 

If you would like to see some pictures of the ACEDB '94 Workshop in St. Matthieu
de Treviers, there are online collections: 

 o by Mike Cherry at
   http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; 
 o by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; 
 o 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: 

 o Lisa Lorenzen 
 o David Matthews 
 o Edie Paul 
 o Donn Davy 
 o Eric De Mund 
 o 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 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 

