Amiga Plus 1995 #2/Amiga Plus CD - 1995 - No. 2.iso/internet/faq/englisch/acedb-genomedatabasesoftware

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Archive-name: acedb-faq
Last-modified: 3/7/95
Version: 1.19




Common Questions, with Answers, 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 written documentation exists for ACEDB?
 o +++++++++++++++++++++++++++++++++++++++++++++++++
 o Q6: Where can I find further information about ACEDB?
 o ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 o Q7: How should ACEDB be cited?
 o +++++++++++++++++++++++++++++++
 o Q8: Is ACEDB object-oriented?
 o ++++++++++++++++++++++++++++++
 o Q9: What's all this about Gopher, WAIS, FTP, WWW, URL, ...
 o +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 o Q10: How can I get on/off the ACEDB announcements mailing list?
 o ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 o Q11: When and where is the next ACEDB Workshop?
 o ++++++++++++++++++++++++++++++++++++++++++++++++
 o Q411: 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.)
Most production sites are using 3.0 (or 2.0) binaries. The most recent beta
source code distribution (1/95) is test.source.3.6a.tar.gz.

A Macintosh version is available as version 2.0b4.

To retrieve the software see Q3.
To be kept informed of new releases see Q10.

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 with Linux (free Unix) [note from Jeff Bryer,
      [e-mail]] I just installed up Linux yesterday and today
      spent the many hours to compile in the C. elegans data for ACEDB v2.0 So
      to save other people the trouble of doing the same the entire package
      ACEDB for Linux 2-10 is available on trog.mbb.sfu.ca in /pub/acedb as
      linux.2_10.tar.Z
      The data was compiled in on a 486DX-33 with 16MBs of RAM running Linux
      1.1.18 (Slackware 2.0.0 distribution) and a 32MB swap device (and it
      chugged away for a couple hours chewing up all 16MBs and half the swap
      space). File size is about 73MBs uncompressed, 26MBs compressed.
      This is based on the ACEDB v2.0 port for Linux that Ken Clark
      ([e-mail]) did.
    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:
      [e-mail] email: [e-mail]
 o MSDOS/Windows/NT:
    o A port to NT is rumored to be in the works.
 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 [e-mail] A native powerPC
      version is available as well. Macace needs a macintosh with > 16 MBytes of
      RAM, and a decent 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 [e-mail]. 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:
   [e-mail], FAX: [phone], VOICE: [phone]

(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 2.0 for Linux 2-10:

 o trog.mbb.sfu.ca /pub/acedb as linux.2_10.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]

 o Database : AaeDB
 o Species : Aedes aegypti
 o Last_update : December 1994
 o ACEDB_version : 3.0
 o WWW : http://klab.agsci.colostate.edu/index.html
 o PI : Dennis Knudson, [e-mail]
 o Curator : Martin Ferguson, [e-mail]
 o Curator : Dave Severson, [e-mail]
 o Contact : [e-mail]

 o Database : AAnDB-1.0
 o Species : Aspergillus nidulans
 o PI : Leland Ellis
 o Last_update : February 1994
 o ACEDB_version : 3.0
 o Contact : [e-mail]
 o URL: http://keck.tamu.edu/ibt.html
 o Comment : defunct, See AGsDB

 o Database : AAtDB
 o Species : Arabidopsis thaliana
 o Current version : 3-4
 o Last_update : November 1994
 o Curator : John Morris
 o Contact : [e-mail]
 o Availability : ftp weeds.mgh.harvard.edu/aatdb/aatdb.3x
 o Availability : Macintosh version in /aatdb/MacAAtDB directory
 o URL : gopher://weeds.mgh.harvard.edu/
 o URL : http://weeds.mgh.harvard.edu:80/index.html
 o URL : http://probe.nalusda.gov:8300/

 o Database : ABtDB-1.0
 o Species : Bovine, Bos taurus
 o ACEDB_version : 3.0 extended
 o PI : Leland Ellis
 o Last_update : February 1994
 o Contact : [e-mail]
 o URL : http://keck.tamu.edu/ibt.html
 o Comment : defunct, See AGsDB

 o Database : AboutDB
 o Curator : Staffan Bergh
 o PI : Staffan Bergh
 o Subject : ACEDB itself (Is this meta-meta-metadata)
 o ACEDB 3.0
 o Contact : [e-mail]
 o URL : http://kiev.physchem.kth.se/AboutDB.html

 o Database : ACeDB
 o Species : Caenorhabditis elegans
 o Current version: 2-10
 o Curator : Jean Thierry-Mieg
 o Curator : Richard Durbin
 o Contact : [e-mail]
 o Contact : [e-mail]
 o Last_update : May 1994

 o DataBase : AceMap
 o Species : Homo sapiens (Mus musculus under development)
 o Focus : Physical mapping of human chromsome X and 21
 o ACEDB_version : 3.0
 o Curator : Hugues Roest Crollius
 o PI : Hans Lehrach
 o Availability : beta release of the X chr. data/models by anonymous ftp to
   ftp.icnet.uk in icrf-public/GenomeAnalysis/X/acemap. Get the README file in
   the directory above.
 o Contact : [e-mail] (Hugues Roest Crollius) ICRF, Lincoln's Inn
   Fields London, UK.
 o Last_update : August 94

 o Database : AGsDB A Genus species Database
 o Species : Aspergillus nidulans
 o Species : Neurospora crassa
 o Species : cow w/ human anchor loci
 o Species : cotton (demo)
 o Species : Homologs of Aspergillus cell cycle loci for budding and fission
   yeast
 o PI : Leland Ellis
 o Curator : Leland Ellis
 o Last_update : March 1994
 o ACeDB_version : 3.0 (beta still), with 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
 o Models : as of 3.13.94
 o Data : as of 3.13.94
 o 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.
 o WWW : WWW-AGsDB is an interface of AGsDB with the World-Wide Web, and
   utilizes the WWW-ACeDB Server (nph-acedb3) of Guy Ducoux
   ([e-mail]).
 o URL : http://keck.tamu.edu/ibt.html
 o Contact : [e-mail]

 o Database : BeanGenes
 o Species : Phaseolus and Vigna species
 o PI : Phillip E. McCLean
 o Email : [e-mail]
 o WWW : http://probe.nalusda.gov:8300
 o Gopher: probe.nalusda.gov

 o Database : ChlamyDB
 o Species : Chlamydomonas
 o PI : Elizabeth Harris
 o Contact : [e-mail]
 o Availability : ChlamyDB 1.0, using ACEDB 3.0, is now on WWW and gopher
   (probe.nalusda.gov). Complete version using ACECB 3.0 now available by ftp
   from probe.nalusda.gov in the pub/chlamydirectory.
 o URL : http://probe.nalusda.gov:8300
 o Last_update : 25 Oct, 1994

 o Database : CottonDB
 o Species : Gossypium hirsutum (cotton) and related species
 o PI : Russell J. Kohel USDA-ARS Southern Crops Research Laboratory Route 5,
   Box 805, College Station, Texas 77845
 o Curator : Gerard R. Lazo
 o Curator : Sridhar Madhavan
 o Last_update : January, 1995 (version 95.1)
 o ACEDB_version : 3.0
 o Contact : [e-mail] (Gerard R. Lazo)
 o Contact : [e-mail] (Russell J. Kohel)
 o URL : http://probe.nalusda.gov:8000/index.html
 o Phone : [phone]
 o Fax : [phone]

 o Database : CSNDB
 o Focus : Cell Signalling Molecules and Interactions
 o Contact : Takako Igarashi National Insitute of Health Sciences Division of
   Chem-Bio Informatics Setagaya-ku, Tokyo, Japan 158 [e-mail]

 o Database : EcoDB
 o Species : E. coli
 o PI : Staffan Bergh
 o Contact : [e-mail]
 o Availability : Proposed
 o Last_update : Aug. 1994

 o Database : 11DB
 o Species : Homo sapiens
 o Focus : Physical mapping of chromosome 11
 o Availability : under development
 o Curator : Benedict Arnold
 o PI : Peter Little
 o Contact : Benedict Arnold Dept. Biochemistry, Imperial College, London, SW7
   2AZ [e-mail]

 o Database : The Encyclopaedia of the Drosophila Genome.
 o Acronym : (none)
 o Species : Drosophilidae (primarily D. melanogaster)
 o Availability : MacFly/FlyDB-based distribution by ftp and CD-ROM due early
   1995
 o Developer : Suzanna Lewis
 o Contact : [e-mail]
 o Developer : Cyrus Harmon
 o Contact : [e-mail]
 o Developer : Edward Welbourne
 o Contact : [e-mail]
 o Curation : Data is provided by the collaborating organisations:
 o Collaborator : The FlyBase Consortium, [e-mail]
 o Collaborator : The Berkeley Drosophila Genome Project
 o URL : gopher://fly.bio.indiana.edu:70+/11/Flybase

 o Database : Flydb
 o Species : Drosophila melanogaster
 o Curator : Suzanna Lewis
 o Contact : [e-mail]

 o Database : GrainGenes
 o Species : Wheat, barley, oats, relatives
 o Availability : Anonymous ftp from probe.nalusda.gov:pub/grains
 o Availability : Gopher greengenes.cit.cornell.edu port 70
 o Availability : Gopher probe.nalusda.gov port 7002
 o Curator : David E. Matthews
 o PI : Olin D. Anderson
 o Contact : [e-mail]
 o Contact : [e-mail]
 o URL : gopher://greengenes.cit.cornell.edu/1/
 o Data_version : 1.3
 o Released : 12 Jan 1994
 o Based_on : acedb.1-10
 o Availability : See following WWW URL
 o URL : http://probe.nalusda.gov:8300
 o Last_update : Feb. 1994

 o Database : human.c17
 o Species : Homo sapiens
 o Availability : the database is under development
 o Contact : [e-mail]
 o Focus : mapping & sequencing of Human Chromosome 17
 o Based_on: acedb.3-0
 o Last_update : Jan. 1994

 o Database : IGD - the Integrated Genomic Database
 o Species : Homo sapiens (later mouse and other mammalian species)
 o Availability : September 1994 by ftp, on-line server October 1994
 o Contact : Otto Ritter [ [e-mail] ]
 o Curator : tba
 o Description : IGD - the 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.

 o Database : LIGM-DB
 o Curator : Veronique Giudicelli
 o Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell
   receptors
 o PI : Marie_paule Lefranc
 o Contact : Veronique Giudicelli LIGM IGMM UMR CNRS 9942 BP 5051 Rte de Mende
   34000 Montpellier [e-mail]

 o Database : Maize
 o Species : Zea mays L. ssp. mays
 o Focus : Maize genome
 o Acedb_version : 1.9
 o FTP : probe.nalusda.gov, pub directory; anonymous ftp
 o Comment : Maize is an acedb front end for the Maize Genome Database, MaizeDB,
   a SYBASE database.
 o Comment : MaizeDB is updated daily and has WWW connectivity to external
   databases: GenBank (loci, alleles and probes), SwissProt (gene products) and
   the E. coli Stock Center (loci).
 o Data : Major data categories: 4522 mapped loci (located to chromosome or
   better) including 684 mapped genes and 1423 mapped probed sites (gene
   candidates); 982 probes; 1850 map scores; 1533 gel patterns
   (Probe/Enzyme/Stock); 4231 stocks; 5105 Variations (alleles, DNA
   polymorphisms, rearrangements, etc); 465 phenotypes; 223 traits; 547 gene
   products; 5314 bibliographic references; 1979 persons with addresses.
 o Gopher : host = teosinte.agron.missouri.edu, port = 70
 o Telnet : telnet teosinte.agron.missouri.edu login as guest, use password
   'corncob'
 o HTTP : http://teosinte.agron.missouri/top.html
 o HTTP : http://probe.nalusda.gov:8000/acedbs/index.html via PGD, the Plant
   Genome Database
 o Comment : Genera is a software toolkit for creating and extracting data from
   Sybase databases; used to create MaizeDB and Worldwide Web connectivity.
 o HTTP : Genera Info http://cgsc.biology.yale.edu/genera.html
 o Funding : MaizeDB USDA/ARS to E. Coe
 o Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn
 o Curator/PI : Ed Coe [e-mail]
 o Curator : Pat Byrne [e-mail]
 o Curator : Georgia Davis [e-mail]
 o Curator : Mary Polacco [e-mail]
 o Curator : Marty Sachs, Maize Stock Center, [e-mail]
 o Curator : Christiane Fauron [e-mail]
 o Curator : Carolyn Wetzel [e-mail]
 o Curator : Steve Rodermel [e-mail]
 o Design : Stan Letovsky [e-mail]
 o Design : Mary Berlyn [e-mail]
 o Systems Manager : Denis Hancock [e-mail]
 o Contact : [e-mail]
 o Last_update : 25 April 1994

 o Database : MycDB
 o Species : Mycobacteria
 o 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.
 o PI : Staffan Bergh
 o PI : Stewart Cole
 o PI : Doug Smith
 o Curator : Staffan Bergh
 o Contact : [e-mail]
 o Last_update : Apr. 1994
 o WWW : http://kiev.physchem.kth.se/MycDB.html
 o ftp : ftp.pasteur.fr (157.99.64.12) in pub/MycDB
 o ftp : kiev.physchem.kth.se (130.237.52.64) in pub/MycDB
 o ftp : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb

 o Database : PomBase
 o Curator : Sean Walsh
 o Curator : Marie-Adele Rajendream
 o PI : Bart Barrell
 o Species : Schizosaccharomyces pombe
 o Contact : [e-mail]
 o Contact : [e-mail]
 o Comment : Not yet available for distribution

 o DataBase : Mousedb
 o Species : Musculus Musculus
 o Species : Homo Sapiens
 o ACEDB_version : 3.0 with extensions to define and display cytogenetic data.
 o 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.
 o Curator : Michelle Kirby
 o Curator : Rachael Selley
 o PI : Mary Lyon
 o PI : Jo Peters
 o 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: [phone] Fax: [phone] For other information
   contact Michelle Kirby.
 o Contact : [e-mail] (or [e-mail])
   [e-mail] MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11
   ORD
 o Last_update : October 1994

 o Database : RiceGenes
 o Species : Rice (O. sativa)
 o Availability : Anonymous ftp from probe.nalusda.gov:pub/rice
 o Availability : Gopher nightshade.cit.cornell.edu port 70
 o Availability : Gopher probe.nalusda.gov port 7007
 o Curator : Edie Paul
 o PI : Susah McCouch
 o Contact : [e-mail]
 o Release : ACEDB 1-10
 o Last_update : May 1994

 o Database : SacchDB
 o Species : Saccharomyces cerevisiae
 o Focus : Budding (common baker's) Yeast Genome
 o ACEDB_version : UNIX 2.0, MacAce 2.0b4
 o FTP : genome-ftp.stanford.edu in /pub/SacchDB
 o FTP : ncbi.nlm.nih.gov in /repository/SacchDB
 o 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.
 o Gopher : host = genome-gopher.stanford.edu, port = 70
 o HTTP : http://genome-www.stanford.edu/
 o Funding : National Center for Human Genome Research, NIH
 o PI : David Botstein, [e-mail]
 o Project Manager/Curator : Mike Cherry, [e-mail]
 o Curator : Selena Dwight, [e-mail]
 o Curator : Cathy Ball, [e-mail]
 o Curator : Rita Schmidt, [e-mail]
 o Programmer : Karen Davis, [e-mail]
 o Sys. Admin : Mark Schroeder, [e-mail]
 o Contact : [e-mail]
 o Data_Submission : [e-mail]
 o Last_update : 2 February 1995

 o Database : SolGenes
 o Coverage: Solanaceae - tomato, potato, pepper
 o Availability : Anonymous ftp from probe.nalusda.gov:pub/solgenes
 o Availability : Gopher nightshade.cit.cornell.edu port 71
 o Availability : Gopher probe.nalusda.gov port 7006
 o Curator : Clare Nelson
 o PI : Steve Tanksley
 o Contact : [e-mail]
 o Release : ACEDB 3.0
 o Last_update : May 1994

 o Database : SorghumDB
 o Species : Sorghum bicolor (L.) Moench
 o PI : Keith F. Schertz USDA-ARS Dept. of Soil & Crop Sciences Texas A&M
   University College Station, TX 77843-2474 Phone : [phone] FAX : (409)
   845-0456 E_mail : [e-mail]
 o Curator : Najeeb U. Siddiqui Southern Crop Improvement Facility Crop
   Biotechnology Center Texas A&M University College Station, TX 77843-2123
   Phone : [phone] FAX : [phone] E_mail : [e-mail]
 o Last_update : July 1994
 o ACEDB_version : 3.0
 o Availability : Under Development

 o Database : SoyBase
 o Species : Soybeans
 o Curator : Lisa Lorenzen
 o PI : Randy Shoemaker
 o Contact : [e-mail]
 o Phone : [phone]
 o Fax : [phone]
 o Last_update : Sept. 1993
 o Gopher : probe.nalusda.gov port 7005

 o Database : Sybace
 o Species : Homo sapiens
 o Creator : Detlef Wolf
 o Comment : Custom software --ACEDB front-end to SYBASE data
 o Contact : [e-mail]
 o See_also : IGD

 o Database : TreeGenes
 o Species : Forest trees
 o ACEDB_version : 3.0
 o Curator : Bradley K. Sherman
 o PI : David B. Neale
 o Contact : [e-mail]
 o Contact : [e-mail]
 o Contact : [e-mail]
 o Last_update : March 1994
 o Gopher: s27w007.pswfs.gov
 o WWW: http://s27w007.pswfs.gov/
 o FTP: probe.nalusda.gov in /pub/trees

 o Database : 21Bdb
 o Species : Homo sapiens
 o Focus : STS content mapping & sequencing of Human Chromosome 21
 o Availability : by request, via ftp, world-wide-web
 o Based_on : acedb.1-10 plus moulon server
 o URL: ftp://genome.lbl.gov/pub/21Bdb-v1.1.tar.Z
 o URL: http://genome.lbl.gov/Genome/acepage.html
 o Curator : Donn F. Davy
 o Contact : [e-mail]
 o Contact : [e-mail]
 o Focus : STS content mapping & sequencing of Human Chromosome 21
 o PI : Michael Palazzolo
 o PI : Chris Martin
 o PI : Jan-Fang Cheng
 o Last_update : Apr. 1994

 o Database : 22ace
 o Species : Homo sapiens
 o Curator : Ian Dunham
 o Focus : Physical mapping of chromosome 22
 o PI : Ian Dunham
 o Contact : Ian Dunham Sanger Centre Hinxton Hall, Cambs. UK. [e-mail]

 o Database : VoxPop
 o Species : Populus spp.
 o Availability : contact curator
 o Curator : Carl G. Riches
 o PI : Reinhard F. Stettler
 o Contact : [e-mail]
 o Contact : [e-mail]
 o Gopher : poplar1.crf.washington.edu
 o Last_update : Sept. 1993

 o Database : Xace
 o Species : Homo sapiens
 o Curator : Gareth Maslen
 o Focus : Physical mapping of chromosome X
 o PI : David Bentley
 o Contact : Gareth Maslen Sanger Centre Hinxton Hall, Cambs. UK.
   [e-mail]

 o Database : ?
 o Species : Homo sapiens
 o Focus : Physical mapping of human chromosome 6.
 o Curator : Ioannis Ragoussis
 o Availability : Unknown
 o Contact : Guy's hospital

 o Database : ?
 o PI : Scott Chasalow
 o Species : Potato
 o Contact : Scottish Crop Institute, Dundee
 o Last_update : Sept. 1993

 o Database : ?
 o PI : George Murphy
 o PI : David Flanders
 o Species : Arabidopsis thaliana
 o Contact : John Innes Center, Norwich, England
 o Last_update : Sept. 1993

 o Database : ?
 o Species : Homo Sapiens
 o Focus : Physical and linkage mapping of chromosome 8
 o Availability :
 o Curator : Stephen Wood
 o PI : Stephen Wood
 o Contact : Stephen Wood Dept. Medical Genetics University of B. C. Vancouver,
   B. C. Canada [e-mail]

Return to List of Questions


Q5: What written 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.

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 .

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 Angisturte.ps and angistute.hqx
available by anonymous ftp at ncbi.hih.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).

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]

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: Where can I find further information about ACEDB?
=====================================================

A6: There is a Usenet/Biosci conference titled bionet.software.acedb. If you do
not have access to the Biosci conferences via a newsreader (e.g. rn, trn, tin)
you can participate in the conference by electronic mail. To subscribe to the
e-mail version of the conference send email to [e-mail] (UK,
European readers use [e-mail] 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 [e-mail] the mail will
be distributed to all subscribers and to the electronic conference. All of the
articles are archived on the gopher at net.bio.net .

Mike Cherry has set up an ACEDB Developer's archive. For anonymous ftp use the
hostname weeds.mgh.harvard.edu and look in the acedb_dev directory. If you wish
to contribute you can put files in the incoming directory. Send a message to
Mike ([e-mail]) that you have put something in that directory
then Mike will move it out for general access. For gopher you can connect to
weeds.mgh.harvard.edu (132.183.190.21) and ...

--> N. FTP Archives for Molecular Biology/

then

--> M. ACEDB Developer's archive/

[N and M are integers which are subject to change.]

The bionet.software. acedb.conference is archived and can be searched using
WAIS. Here is a Gopher-style link to the WAIS archive. (This is also courtesy of
Mike Cherry.):
#
Type=7
Name=ACEDB BioSci Electronic Conference
Path=7/.index/acedb-biosci
Host=genome-gopher.stanford.edu
Port=70

The AAtDB, Soybase, GrainGenes, Mace, and TreeGenes [see Q4] databases regularly
submit data to the Plant Genome Database at the National Agricultural Library
(NAL). Nal makes this data available 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
([e-mail]), 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

The Genome Computing Group, Lawrence Berkeley Laboratory has an anonymous ftp
service at machine genome.lbl.gov (131.243.224.80) 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 [e-mail]). 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: What's all this about Gopher, WAIS, FTP, WWW, URL, ...
==========================================================

A9: These terms all refer to Internet protocols. An excellent introduction to
the Internet is: _The Whole Internet User's Guide & Catalog_, by Ed Krol,
O'Reilly & Associates, 1992. Or ask your system administrator to provide you
with a gopher client or mosaic client and begin navigating on your own.

URL is a Universal Resource Locator on the World-Wide Web (WWW). There are many
free Internet browsers available that allow you to use an Internet connection
and a URL to access services. Mosaic may be the most popular and it is available
for Mac, PC or Unix via anonymous ftp from ftp.ncsa.uiuc.edu.

Return to List of Questions


Q10: How can I get on/off the ACEDB announcements mailing list?
===============================================================

A10: To get on or off the mailing list send mail to [e-mail] or
[e-mail]. 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


Q11: When and where is the Next ACEDB Workshop?
===============================================

The 1995 ACEDB Conference and Workshop will be held May 14-27, 1995, at the Isis
Oasis, a small retreat center in Geyserville, about 80 miles north of
SanFrancisco in Sonoma County, California. We will have exclusive use of the
entire retreat center, including the theater (for workstations and primary
sessions), dining room, lodge, and other residential facilities.

For more information send email to [e-mail] or vist URL
http://genome.lbl.gov/ace95.html on the WWW.

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


Q411:Who prepared this document & where is the current version?
===============================================================

A411: (Note to international readers: 411 is the phone number for information in
the USA.)

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 [e-mail].

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

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:
[e-mail]

Major contributions in getting this FAQ off the ground were made by John
McCarthy and Mike Cherry. 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:
[e-mail]

Bradley K. Sherman
Dendrome Project
Institute of Forest Genetics
P.O. Box 245, Berkeley, CA, 94701
Phone: [phone] Fax: [phone]

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