Archive-name: acedb-faq
Last-modifed: 10/6/93
Version: 1.2
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Common Questions and Answers about ACEDB.
This document will be posted monthly to the Usenet newsgroup
bionet.software.acedb. It is intended to be used as an index
to ACEDB databases and to information about the database
software.
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.
This FAQ has been submitted for approval for Usenet archival
storage. It has also been submitted to the Bionet curator.
--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. (This refers to the software package.)
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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:
Any machine running SunOS 4.x.
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: [In alpha order by Database name --bks]
Database : AAnDB
Species : Aspergillus nidulans
PI : Leland Ellis
Last_update : Sept. 1993
Database : AAtDB
Species : Arabidopsis thaliana
Availability :
Curator : John Morris
Current version: 1-5
Contact : curator at frodo.mgh.harvard.edu
Last_update : Sept. 1993
Database : ACeDB
Species : Caenorhabditis elegans
Availability :
Current version: 1-21
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 : ChlamyDB
Species : Chlamydomonas
PI : Elizabeth Harris
Contact : chlamy at acpub.duke.edu
Availability : Still under construction
Last_update : 30 Sept. 1993
Database : EcoDB
Species : E. coli
PI : Staffan Bergh
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 : 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 : Mace
Species : Zea mays L. ssp. mays
Focus : Maize genome
Comment : Mace is the frontend for maizedb, a relational\
(SYBASE) database. It isupdated from maizedb by\
Stan Letovsky. Maizedb is updated daily and\
will soon beaccessible by guest login.
Curator : Ed Coe
Curator : Pat Byrne
Curator : Georgia Davis
Curator : Mary Polacco
Off-Site Curator : Marty Sachs
Off-Site Curator : Christiane Fauron
Off-Site Curator : Carolyn Wetzel
Off-Site Curator : Steve Rodermel
Off-Site Curator/Designer : Stan Letovsky
Off-Site Curator/Designer : Mary Berlyn
Systems Manager : Denis Hancock
PI : Ed Coe
Contact : maizedb at teosinte.agron.missouri.edu
Last_update: 5 October 1993
Database : MycDB
Species : Mycobacterium
PI : Staffan Bergh
PI : Thierry Garnier
Contact : staffan at pasteur.fr
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 : 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 : 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 : VoxPop
Species : Populus spp.
Availability : contact curator
Curator : Carl G. Riches
PI : Reinhard F. Stettler
Contact : cgr at poplar1.cfr.washington.edu
Contact : STETTLER at coyote.cfr.washington.edu
Last_update : Sept. 1993
Database : ?
Species : Bovine
PI : Leland Ellis
Last_update : Sept. 1993
Database : ?
Species : Sorghum
PI : Leland Ellis
Last_update : Sept. 1993
Database : ?
PI : Scott Chasalow
Species : Potato
Contact : Scottish Crop Institute, Dundee
Last_update : Sept. 1993
Database : ?
PI : George Murphy
PI : David Flanders
Species : Arabidopsis thaliana
Contact : John Innes Center, Norwich, England
Last_update : Sept. 1993
Database : ?
Species : Homo sapiens
Focus : Physical mapping of human chromosomes 22 and X
Curator : Ian Dunham
Contact : idunham at crc.ac.ukid1 at sanger.ac.uk
PI : Ian Dunham
PI : David Bentley
Last_update : 28 Sep 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. Configuration Guide.
Syntactic Definitions for the ACEDB Data Base Manager
--Jean Thierry-Mieg and Richard Durbin (1991-)
By anonymous ftp:
doc.1_9.tar.Z
--ncbi.nlm.nih.gov (130.14.20.1) repository/acedb
You will find other interesting documents in the wdoc subdirectory.
"An Introduction to ACeDB: For MycDB a Mycobacterium DataBase"
is available. Try anonymous ftp at ftp.pasteur.fr (157.99.64.2)
in pub/MycDB. [I could not find this document at first glance,
so it may be part of the distribution itself which is in the
same directory. Clarification from the curator would be helpful
--bks.]
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Q6: Where can I find further information about ACEDB?
A6: There is a Usenet Biosci conference titled bionet.software.acedb.
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
(cherry at genome.stanford.edu) 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:
#
Type=7
Name=ACEDB BioSci Electronic Conference
Path=7/.index/acedb-biosci
Host=genome-gopher.stanford.edu
Port=70
(This is also courtesy of Mike Cherry.)
If you do not have access to the Usenet you may receive the
conference messages by e-mail. To subscribe to this service send
email to biosci at net.bio.net requesting inclusion in the
acedb-soft list and explicitly stating the e-mail address at which
you wish to receive the mail.
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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 by Anonymous FTP from ...
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.
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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.
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Q411:Who contributed to this document?
A411: Bradley K. Sherman (bks at s27w007.pswfs.gov) is currently
managing this FAQ. Major contributions in getting it
off the ground were made by John McCarthy and Mike
Cherry. Other contributors include:
Lisa Lorenzen
David Matthews
Edie Paul
Donn Davy
Eric De Mund
Sam Cartinhour
To add or modify information in this document, please
send mail to: acedbfaq at s27w007.pswfs.gov
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