Archive-name: acedb-faq
Last-modifed: 9/27/93
Version: 1.1
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Common Questions and Answers about ACEDB.
This is the zeroth posting of this document. Errors of
commission or omission are unintentional.
Please send comments and corrections to acedbfaq at s27w007.pswfs.gov.
Curators of ACEDB databases should take note of Question 4 and
keep me apprised of changes.
I will submit the next version of this FAQ for Usenet
archival storage.
--Bradley K. Sherman
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List of questions in the ACEDB FAQ:
Q0: What is ACEDB?
Q1: What is the current version of ACEDB?
Q2: What {hardware | software} do I need to run ACEDB?
Q3: Where can I get ACEDB?
Q4: What ACEDB databases exist?
Q5: What written documentation exists for ACEDB?
Q6: Where can I find further information about ACEDB?
Q7: How should ACEDB be cited?
Q8: Is ACEDB object-oriented?
Q411:Who contributed to this document?
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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 data about diverse species [see Q4].
ACEDB allows for automatic cross-referencing of items when loaded
and allows for hypertextual navigation of the links using a mouse.
Certain special purpose graphical displays have been integrated
into the software. These reflect the efforts 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 European integrated Genome
Project.
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.
Current display modes are:
TREE for text type objects: papers, authors, genes
etc.
GMAP genetic map
PMAP physical map (Sulston contig style)
SEQ DNA sequence - symbolic, features, sequence
and translation
GRID hybridisation patterns for a probe to a clone
grid
BIBLIO bibliography attached to any object display
modules under development:
CMAP whole chromosome physical map plot
GEL agarose gel simulation derived from sequence
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Q1: What is the current version of ACEDB?
A1: 1-10. It was released Summer 1993. The next release will be
2.0.
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Q2: What {hardware | software} do I need to run ACEDB?
A2: ACEDB currently runs on the following Unix sytems, under X11:
Sun SPARCstation 1, 1+, 2, IPC, IPX:
SPARCstation 10 running Solaris:
DEC DECstation3100, 5100 etc.
DEC Alpha/OSF-1
Silicon Graphics Iris series
PC 386/486 with Linux (public domain Unix)
Other Unix:
There exist, or have existed, ports onto Alliant, Hewlett-
Packard, IBM R6000, NeXT, Convex. You may have to contact
the developer responsible for the port to make these real.
Macintosh:
A port to the Macintosh may become available by the end of 1993.
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Q3: Where can I get ACEDB?
A3: All the files are available in the following public access
accounts (anonymous ftp sites) accessible via Internet:
lirmm.lirmm.fr (193.49.104.10) genome/acedb
cele.mrc-lmb.cam.ac.uk (131.11.84.1) pub/acedb
ncbi.nlm.nih.gov (130.14.20.1) repository/acedb
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Q4: What ACEDB databases exist?
A4: Database : ACeDB
Species : Caenorhabditis elegans
Availability :
Current version: 1-10
Curator : Jean Thierry-Mieg
Curator : Richard Durbin
Contact : rd at cele.mrc-lmb.cam.ac.uk
Contact : mieg at kaa.cnrs-mop.fr
Last_update : Sept. 1993
Database : AAtDB
Species : Arabadopsis thaliana
Availability :
Curator : John Morris
Current version: 1-5
Contact : curator at frodo.mgh.harvard.edu
Last_update : Sept. 1993
Database : GrainGenes
Species : Wheat, barley, oats, relatives
Availability : Gopher greengenes.cit.cornell.edu port 70
Availability : ACEDB version by ftp, on request from the curators
Curator : David E. Matthews
PI : Olin D. Anderson
Contact : matthews at greengenes.cit.cornell.edu
Contact : oandersn at wheat.usda.gov
Last_update : Sept. 1993
Database : SolGenes
Coverage: Solanaceae - tomato, potato, pepper (eventually)
Availability : Beta ACEDB via login or tar file
Curator : Edie Paul
Contact : epaul at nightshade.cit.cornell.edu
Last_update : Sept. 1993
Database : RiceGenes
Species : Rice (O. sative)
Availability : under development, login at own risk
Curator : Edie Paul
Contact : epaul at nightshade.cit.cornell.edu
Last_update : Sept. 1993
Database : SoyBase
Species : Soybeans
Curator : Lisa Lorenzen
PI : Randy Shoemaker
Contact : lorenzen at mendel.agron.iastate.edu
Last_update : Sept. 1993
Database : TreeGenes
Species : Forest trees, Pinus taeda
Availability : contact curator
Curator : Bradley K. Sherman
PI : David B. Neale
Contact : Dendrome at s27w007.pswfs.gov
Contact : bks at s27w007.pswfs.gov
Contact : dbn at s27w007.pswfs.gov
Last_update : Sept. 1993
Database : 21Bdb
Species : Homo sapiens
Availability : by request, via ftp, gopher
Curator : Donn F. Davy
Contact : DFDavy at lbl.gov
Contact : aggarwal at genome.lbl.gov
Focus : STS content mapping & sequencing of Human Chromosome 21
PI : Jasper Rine
PI : Michael Palazzolo
PI : Chris Martin
PI : Jan-Fang Cheng
Last_update : Sept. 1993
Database : Flydb
Species : Drosophila melanogaster
Availability : by request only, via ftp
Curator : Suzanna E. Lewis
Contact : SELewis at lbl.gov
Focus : STS content mapping project summary
PI : Gerald Rubin
PI : Mike Palazzolo
PI : Dan Hartl
PI : Alan Spradling
Last_update : Sept. 1993
Database : ChlamyDB
Species : Chlamydomonas
PI : Elizabeth Harris
Last_update : Sept. 1993
Database : AAnDB
Species : Aspergillus nidulans
PI : LeLand Ellis
Last_update : Sept. 1993
Species : Bovine
PI : LeLand Ellis
Last_update : Sept. 1993
Species : Sorghum
PI : LeLand Ellis
Last_update : Sept. 1993
Darabase : MycDB
Species : Mycobacterium
PI : Staffan Bergh
PI : Thierry Garnier
Last_update : Sept. 1993
Database : EcoDB
Species : E. coli
PI : Staffan Bergh
Last_update : Sept. 1993
PI : Scott Chasalow
Species : Potato
Contact : Scottish Crop Institute, Dundee
Last_update : Sept. 1993
PI : George Murphy
PI : David Flanders
Species : Arabidopsis t.
Contact : J. Innes Center, Norwich, England
Last_update : Sept. 1993
PI : David Bentley
Species : Homo sap.
Contact : Sanger Centre, Cambridge, England
Last_update : Sept. 1993
Database : MaizeDB
Species : Maize
Curator : Mary Polacco
Contact : University of Missouri, Columbia, MO
Last_update : Sept. 1993
[Curators: Please submit an entire paragraph in
this format for inclusion or update. --bks]
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Q5: What written documentation exists for ACEDB?
A5: The primary documents are included in the Software
distribution in the wdoc subdirectory:
acedb -- A C. elegans Database: I. Users' Guide.
acedb -- A C. elegans Database: II. Installation Guide.
acedb -- A C. elegans Database: III. Configurat
