Subject: ACEDB Genome Database Software FAQ
ACEDB is used to collect information regarding the molecular biology
of the genome.
Archive-name: acedb-faq
Last-modified: 8/7/95
Version: 1.23
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 doe 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.)
Most production sites are using 3.0 (or 2.0) binaries. The most recent beta
source code distribution (3/95) is test.source.3.7.tar.gz.
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) [note from Jeff Bryer,
jbryer@darwin.mbb.sfu.ca] I have just made available via ftp the Linux
binary for version 4 of ACEDB. Thanks immensely to Ken Clark for doing the
actual port. You can pick up the binary from trog.mbb.sfu.ca in /pub/acedb
as bin.linux.4_0.tar.Z. This is based on the source code for the beta
version 4 available from ncbi.nlm.nih.gov. We intend to make available a
release version of the Linux binary once ACEDB ver 4 final has been
released.
As usual, for the C. elegans community I have compiled in the current set
of updates (4-6) and will be making available an archive containing the
Linux ACEDB 4 binary and the C. elegans dataset (so you don't have to wait
a few hours compiling in the data yourself). The filename is
linux.4_6.tar.Z and is in the same location as the linux binary.
Uncompressed this archive is about 170MBs in size. I don't actually have
access to the machine that has this archive on it right now but I will
place it on trog Monday the 10th at the latest. If you need the archive in
smaller chunks (for ftp'ing) please let me know.
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 2.0 for Linux 2-10:
o trog.mbb.sfu.ca /pub/acedb as bin.linux.4_0.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, dknudson@lamar.colostate.edu
o Curator : Martin Ferguson, martinf@lamar.colostate.edu
o Curator : Dave Severson, dave@aedes.vetsci.wisc.edu
o Contact : aaedbmgr@klab.agsci.colostate.edu
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 : leland@stralight.tamu.edu
o URL: http://keck.tamu.edu/ibt.html
o Comment : defunct, See AGsDB
o Database : AAtDB
o Species : Arabidopsis thaliana
o Current version : 3-5
o Last_update : March 1995
o Curator : John Morris
o Contact : curator@frodo.mgh.harvard.edu
o Availability : ftp weeds.mgh.harvard.edu/aatdb/aatdb.3x
o Availability : Macintosh version in /aatdb/MacAAtDB directory
o FTP : URL : ftp://weeds.mgh.harvard.edu/aatdb
o Gopher : gopher://weeds.mgh.harvard.edu/
o WWW : http://weeds.mgh.harvard.edu:80/index.html
o WWW : 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 : leland@stralight.tamu.edu
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 : staffan@biochem.kth.se
o URL : http://www.biochem.kth.se/AboutDB.html
o Database : ACeDB
o Species : Caenorhabditis elegans
o Current version: 2-18
o Curator : Jean Thierry-Mieg
o Curator : Richard Durbin
o Contact : rd@mrc-lmb.cam.ac.uk
o Contact : mieg@kaa.crbm.cnrs-mop.fr
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 : hrc@gea.lif.icnet.uk (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
(ducoux@moulon.inra.fr).
o URL : http://keck.tamu.edu/ibt.html
o Contact : leland@straylight.tamu.edu
o Database : Alfagenes
o Species : Medicago sativa (Alfalfa, Lucerne)
o Availability : Under development
o Curator : D. Z. Skinner
o Contact : dzolek@ksu.ksu.edu
o Telephone : (913) 532-7247
o Database : BeanGenes
o Species : Phaseolus and Vigna species
o PI : Phillip E. McClean
o Email : mcclean@beangenes.cws.ndsu.nodak.edu
o WWW : http://probe.nalusda.gov:8300
o Gopher: probe.nalusda.gov
o Database : ChlamyDB
o Species : Chlamydomonas
o PI : Elizabeth Harris
o Contact : chlamy@acpub.duke.edu
o Availability : ChlamyDB 1.1, 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/chlamy directory. A Macintosh version is
avaliable in ftp://ftp.duke.edu/pub/chlamy/MacChlamy
o URL : http://probe.nalusda.gov:8300
o Last_update : 14 April 1995
o Database : CottonDB
o Species : Gossypium hirsutum (cotton) and related species
o PI : Russell J. Kohel, USDA-ARS, Southern Crops Research Laboratory, 2765 F&B
Road, 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 : lazo@tamu.edu (Gerard R. Lazo)
o Contact : rjk0339@acs.tamu.edu (Russell J. Kohel)
o URL : http://probe.nalusda.gov:8000/index.html
o Data_submission_form : http://algodon.tamu.edu/
o Phone : 409-260-9311
o Fax : 409-260-9333
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 taka@nihs.go.jp
o Database : EcoDB
o Species : E. coli
o PI : Staffan Bergh
o Contact : staffan@biochem.kth.se
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 b.arnold@ic.ac.uk
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 : suzi@fly2.berkeley.edu
o Developer : Cyrus Harmon
o Contact : sly@fly2.berkeley.edu
o Developer : Edward Welbourne
o Contact : eddy@gen.cam.ac.uk
o Curation : Data is provided by the collaborating organisations:
o Collaborator : The FlyBase Consortium, flybase@morgan.harvard.edu
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 : suzi@fly2.berkeley.edu
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 : matthews@greengenes.cit.cornell.edu
o Contact : oandersn@wheat.usda.gov
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 : lsprilus@weizmann.weizmann.ac.il
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 [ o.ritter@dkfz-heidelberg.de ]
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 giudi@ligm.crbm.cnrs-mop.fr
o Database : Maize
o Species : Zea mays L. ssp. mays and related
o Focus : Maize genome
o Latest_release : April 1995
o Acedb_version : 3.3
o FTP : probe.nalusda.gov, pub/maize directory
o Comment : Maize is a periodically extracted ACeDB front end for the Maize
Genome Database, MaizeDB, a SYBASE database, implemented using Genera
software, developed by Stan Letovsky.
o 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.
o 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.
o 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.
o Gopher : host = gopher.agron.missouri.edu, port = 70 .
o Telnet : telnet teosinte.agron.missouri.edu login as guest, use password:
corncob
o HTTP : http://www.agron.missouri.edu/top.html
o HTTP : http://probe.nalusda.gov:8000/acedbs/index.html via PGD, the Plant
Genome Database - Moulon WWW gateway to several ACeDB databases
o HTTP : Genera information http://gdbdoc.gdb.org/letovsky/genera/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 ed@teosinte.agron.missouri.edu
o Curator : Mary Polacco maryp@teosinte.agron.missouri.edu
o Assoc Curator : Pat Byrne byrne@teosinte.agron.missouri.edu QTL data
o Assoc Curator : Georgia Davis gdavis@teosinte.agron.missouri.edu Map data
o Assoc Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu Genetic
Stock data
o Assoc Curator : Christiane Fauron FAURON@GENE1.med.utah.edu Mitochondrion
genome
o Assoc Curator : Carolyn Wetzel cmwetzel@iastate.edu Chloroplast genome
o Assoc Curator : Steve Rodermel S1SRR@ISUVAX.IASTATE.EDU Chloroplast genome
o Design : Stan Letovsky letovsky@gdb.org
o Design : Mary Berlyn mary@fetalpig.biology.yale.edu
o Systems Manager : Denis Hancock dhancock@teosinte.agron.missouri.edu
o Contact : db_request@teosinte.agron.missouri.edu
o Last_update : 11 April 1995
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 Curator : Staffan Bergh
o Contact : staffan@biochem.kth.se
o Last_update : July 1995
o ACEDB_version : 3.0
o Data_version : 3-8 (June 18, 1995)
o WWW : http://www.biochem.kth.se/MycDB.html
o WWW : http://probe.nalusda.gov:8300/other/index.html
o ftp : www.biochem.kth.se (130.237.52.64) in pub/MycDB
o ftp : ftp.pasteur.fr (157.99.64.12) 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 : svw@sanger.ac.uk
o Contact : barrell@sanger.ac.uk
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 : 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: (+44) 1223 494520 Fax: (+44) 1223 494510 For other information
contact Rachael Selley.
o Contact : rselley@har-rbu.mrc.ac.uk, MRC Radiobiology Unit, Chilton, Didcot,
Oxon OX11 ORD
o Last_update : July 1995
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 : epaul@nightshade.cit.cornell.edu
o ACEDB_version : 3.0
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, botstein@genome.stanford.edu
o Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu
o Curator : Selena Dwight, dwight@genome.stanford.edu
o Curator : Cathy Ball, ball@genome.stanford.edu
o Curator : Rita Schmidt, bleb@genome.stanford.edu
o Curator : Barbara Dunn, bdunn@genome.stanford.edu
o Curator : Caroline Adler, adler@genome.stanford.edu
o Programmer : Karen Davis, karen@genome.stanford.edu
o Sys. Admin : Mark Schroeder, mark@genome.stanford.edu
o Contact : yeast-curator@genome.stanford.edu
o Data_Submission : yeast-curator@genome.stanford.edu
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 : cnelson@nightshade.cit.cornell.edu
o Release : ACEDB 3.0
o Last_update : May 1995
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 : (409) 260-9252 FAX : (409)
845-0456 E_mail : schertz@tamvm1.tamu.edu
o Curator : Najeeb U. Siddiqui Southern Crop Improvement Facility Crop
Biotechnology Center Texas A&M University College Station, TX 77843-2123
Phone : (409) 862-1523 FAX : (409) 862-4790 E_mail : nus6389@tamsun.tamu.edu
o Last_update : July 1994
o ACEDB_version : 3.0
o Availability : Under Development
o Database : SoyBase
o Species : Soybeans
o Curator : Marica Imsamde
o PI : Randy Shoemaker
o Contact : mimsande@mendel.agron.iastate.edu
o Phone : 515-294-1297
o Contact : schrader@mendel.agron.iastate.edu
o Phone : 515-294-0421
o Fax : 515-294-2299
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 : D.Wolf@dfkz-heidelberg.de
o See_also : IGD
o Database : Syndb
o Species : Homo sapiens, Mus musculus
o Focus : STS content mapping & directed sequencing of Human Chromosomes 21,5
with Mouse for syntenic comparison
o Availability : by request, via ftp, world-wide-web
o Based_on : acedb v3.3 plus moulon server
o URL: ftp://genome.lbl.gov/pub/acedb/syndb.tar.Z
o URL: http://genome.lbl.gov/Genome/acepage.html
o Curator : Donn F. Davy
o Contact : DFDavy@lbl.gov
o Contact : aggarwal@genome.lbl.gov
o Focus : STS content mapping & directed sequencing of Human Chromosomes 21 and
5, with Mouse data for syntenic comparison
o PI : Michael Palazzolo
o PI : Chris Martin
o PI : Jan-Fang Cheng
o Last_update : Oct. 1994
o Database : TreeGenes
o Species : Forest trees
o ACEDB_version : 3.0
o Curator : Bradley K. Sherman
o PI : David B. Neale
o Contact : Dendrome@s27w007.pswfs.gov
o Contact : bks@s27w007.pswfs.gov
o Contact : dbn@s27w007.pswfs.gov
o Last_update : March 1994
o Gopher: s27w007.pswfs.gov
o WWW: http://probe.nalusda.gov:8300/plant/index.html .
o WWW: http://s27w007.pswfs.gov/
o FTP: probe.nalusda.gov in /pub/trees
o Database : Trypbase
o Species : Trypanosoma brucei
o ACEDB_version : 3.0
o PI : Sara Malville
o Contact : sm160@mole.cam.ac.uk
o Comment : Under development, feedback welcome.
o ACEDB_version : 3.0 and 4.0
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 : DFDavy@lbl.gov
o Contact : aggarwal@genome.lbl.gov
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. id1@sanger.ac.uk
o Database : VoxPop
o Species : Populus spp.
o Availability : contact curator
o Curator : Carl G. Riches
o PI : Reinhard F. Stettler
o Contact : cgr@poplar1.cfr.washington.edu
o Contact : STETTLER@coyote.cfr.washington.edu
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.
glm@sanger.ac.uk
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 swood@unixg.ubc.cq
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.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). 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:
+++
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).
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/TextConvert
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 Bigwoody. 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