----------------------------------------------------------------------
Common Questions, with Answers, about ACEDB.
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?
Q9: What's all this about Gopher|WAIS|ftp|WWW|URL ...
Q10: How can I get on/off the ACEDB announcements mailing list?
Q11: When and where is the next ACEDB Workshop?
Q411:Who prepared this document & where is the current version?
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 [see Q4].
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 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.
----------------------------------------------------------------------
Q1: What is the current version of ACEDB?
A1: As of January 1994, ACEDB has undergone a bifurcation. Those
involved with C. elegans will want to to track the 2.x series
under the stewardship of Richard Durbin and all other groups
should probably track the 3.x series of Jean Thierry-Mieg.
Thierry-Mieg writes "... 2 and 3 differ only at the level of
displays ..." Version 2.0 was released in December, 1993 and
version 3.0 was released in January, 1994.
To retrieve the software see Q3.
To be kept informed of new releases see Q10.
[This question refers to the software not the C. elegans data.]
----------------------------------------------------------------------
Q2: What hardware/software do I need to run ACEDB?
A2:
Unix and X11:
Any machine running SunOS 4.x
SPARCstation 10 under Solaris [Probably all Solaris, then --bks]
DEC DECstation3100, 5100 etc.
DEC Alpha/OSF-1
Silicon Graphics Iris series
PC 386/486 with Linux (free Unix)
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.
NeXT: contact Patrick Phillips at University of Texas,
NeXTmail: patrick at wbar.uta.edu
email: phil at decster.uta.edu
MSDOS/Windows/NT:
A port to NT is rumored to be in the works.
Macintosh:
[Contributed by Frank Eeckman]
macace 2.0 is now available from genome.lbl.gov
(131.243.224.80) under ftp/pub/macace. 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 from the same source. Please send all questions/bug
reports to eeckman at llnl.gov 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 eeckman at 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.
For cost savings, a combination of a high-end Intel platform
with Linux appears very attractive.
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. [This section should
be expanded to have a more thorough discussion of X11
interactions. --bks]
----------------------------------------------------------------------
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) in pub/acedb
cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb
ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb
(version 1-10 is available in repository/aatdb)
bioinformatics.weizmann.ac.il (132.76.55.12) in
pub/databases/acedb.
A typical session would be:
ftp ncbi.nlm.nih.gov
login: anonymous
password: your email address
cd repository/acedb/ace3
binary
ls
get README_3
get NOTES
get INSTALL
get bin.sparc.3.0.tar.Z
quit
----------------------------------------------------------------------
Q4: What ACEDB databases exist?
A4: [In alphabetic order by Database name.
Curators, submit changes as new paragraphs.--bks]
Database : AAnDB-1.0
Species : Aspergillus nidulans
PI : Leland Ellis
Last_update : February 1994
ACEDB_version : 3.0
Contact : leland at stralight.tamu.edu
URL : http://keck.tamu.edu/ibt.html
Comment : defunct, See AGsDB
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 : ABtDB-1.0
Species : Bovine, Bos taurus
ACEDB_version : 3.0 extended
PI : Leland Ellis
Last_update : February 1994
Contact : leland at stralight.tamu.edu
URL : http://keck.tamu.edu/ibt.html
Comment : defunct, See AGsDB
Database : ACeDB
Species : Caenorhabditis elegans
Current version: 2-9
Curator : Jean Thierry-Mieg
Curator : Richard Durbin
Contact : rd at mrc-lmb.cam.ac.uk
Contact : mieg at kaa.crbm.cnrs-mop.fr
Last_update : March 1994
Database : AceMap
Species : Homo Sapiens (Saccaromyces Pombe, Mus musculus in development)
Focus : Physical mapping of human chromosomes X and 21
Curator : Hugues Roest Crollius
Contact : hrc at gea.lif.icnet.uk
PI : Hans Lehrach
PI : Hugues Roest Crollius
Last_update : 22 Feb 1994
Database : AGhDB
Species : Gossipium hirsutum (cotton)
PI : Russ Klhel
Curator : Stephanie Crouch
Last_update : March 1994
Contact : scrouch at tamsun.tamu.edu
Database : AGsDB A Genus species Database
Species : Aspergillus nidulans
Species : Neurospora crassa
Species : cow w/ human anchor loci
Species : cotton (demo)
Species : Homologs of Aspergillus cell cycle loci
for budding and fission yeast
PI : Leland Ellis
Curator : Leland Ellis
Last_update : March 1994
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
Models : as of 3.13.94
Data : as of 3.13.94
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.
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 at moulon.inra.fr).
URL : http://keck.tamu.edu/ibt.html
Contact : leland at straylight.tamu.edu
Database : ASbDB
Species : Sorghum bicolor
PI : Keith Schertz
Curator : Stephanie Crouch
Last_update : March 1994
Contact : scrouch at tamsum.tamu.edu
Database : ChlamyDB
Species : Chlamydomonas
PI : Elizabeth Harris
Contact : chlamy at acpub.duke.edu
Availability : Still under construction
Phone : 919-684-5243 (till 6/94)
Fax : 919-684-5412 (till 6/94)
Last_update : 30 Sept. 1993
Database : EcoDB
Species : E. coli
PI : Staffan Bergh
Contact : staffan at biochem.kth.se
Availability : Still under construction
Last_update : 11 Oct. 1993
Database : FlyBase
Species : Drosophila melanogaster
Availability : gopher or gopher+ ftp.bio.indiana.edu
Availability : ACeDB-style interface to SyBase server
due by end of 1994
Curator : Edward Welbourne
Contact : eddy at gen.cam.ac.uk
Contact : flybase at morgan.harvard.edu
PI : William Gelbart
PI : Michael Ashburner
PI : Thomas Kaufman
PI : Kathy Matthews
PI : John Merriam
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 : Anonymous ftp from probe.nalusda.gov:pub/grains
Availability : Gopher greengenes.cit.cornell.edu port 70
Availability : Gopher probe.nalusda.gov port 7002
Curator : David E. Matthews
PI : Olin D. Anderson
Contact : matthews at greengenes.cit.cornell.edu
Contact : oandersn at wheat.usda.gov
URL : gopher://greengenes.cit.cornell.edu/1/
Data_version : 1.3
Released : 12 Jan 1994
Based_on : acedb.1-10
Availability : See following WWW URL
URL : http://probe.nalusda.gov:8000/acedbs/acedbs/graingenes/index.html
Last_update : Feb. 1994
Database : human.c17
Species : Homo sapiens
Availability : the database is under development
Contact : lsprilus at weizmann.weizmann.ac.il
Focus : mapping & sequencing of Human Chromosome 17
Based_on: acedb.3-0
Last_update : Jan. 1994
Database : Maize
Species : Zea mays L. ssp. mays
Focus : Maize genome
Acedb_version : 1.9
FTP : probe.nalusda.gov, pub directory; anonymous ftp
Comment : Maize is an acedb front end for the Maize Genome
Database, MaizeDB, a SYBASE database.
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).
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.
Gopher : host = teosinte.agron.missouri.edu, port = 70
Telnet : telnet teosinte.agron.missouri.edu
login as guest, use password 'corncob'
HTTP : http://teosinte.agron.missouri/top.html
HTTP : http://probe.nalusda.gov:8000/acedbs/index.html
via PGD, the Plant Genome Database
Comment : Genera is a software toolkit for creating and
extracting data from Sybase databases; used to
create MaizeDB and Worldwide Web connectivity.
HTTP : Genera Info http://cgsc.biology.yale.edu/genera.html
Funding : MaizeDB USDA/ARS to E. Coe
Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn
Curator/PI : Ed Coe ed at teosinte.agron.missouri.edu
Curator : Pat Byrne byrne at teosinte.agron.missouri.edu
Curator : Georgia Davis gdavis at teosinte.agron.missouri.edu
Curator : Mary Polacco maryp at teosinte.agron.missouri.edu
Curator : Marty Sachs, Maize Stock Center, msachs at uiuc.edu
Curator : Christiane Fauron FAURON at GENE1.med.utah.edu
Curator : Carolyn Wetzel cmwetzel at iastate.edu
Curator : Steve Rodermel S1SRR at ISUVAX.IASTATE.EDU
Design : Stan Letovsky letovsky-stan at CS.YALE.EDU
Design : Mary Berlyn mary at fetalpig.biology.yale.edu
Systems Manager : Denis Hancock
dhancock at teosinte.agron.missouri.edu
Contact : db_request at teosinte.agron.missouri.edu
Last_update : 25 April 1994
Database : MycDB
Species : Mycobacteria
Comment : MycDB is a collation of data on the mycobacteria,
causative agents of tuberculosis and leprosy. It
is centered on the mapping and sequencing projects
under way in M.leprae and M.tuberculosis.
PI : Staffan Bergh
PI : Stewart Cole
PI : Doug Smith
Curator : Staffan Bergh
Contact : staffan at biochem.kth.se
Last_update : Apr. 1994
WWW : http://kiev.physchem.kth.se/MycDB.html
ftp : ftp.pasteur.fr (157.99.64.12) in pub/MycDB
ftp : kiev.physchem.kth.se (130.237.52.64) in pub/MycDB
ftp : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb
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
Phone : 515-294-0421
Fax : 515-294-2299
Last_update : Sept. 1993
Database : TreeGenes
Species : Forest trees
Availability : alpha, contact curator
ACEDB_version : 1-10
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 : March 1994
URL : gopher://s27w007.pswfs.gov/
URL : http://s27w007.pswfs.gov/
URL : ftp://probe.nalusda.gov/pub/trees
Database : 21Bdb
Species : Homo sapiens
Availability : by request, via ftp, world-wide-web
Based_on : acedb.1-10 plus moulon server
URL : ftp://genome.lbl.gov/pub/21Bdb-v1.1.tar.Z
URL : http://genome.lbl.gov/Genome/acepage.html
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 : Michael Palazzolo
PI : Chris Martin
PI : Jan-Fang Cheng
Last_update : Apr. 1994
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 : ?
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
----------------------------------------------------------------------
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:
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-)
Get By anonymous ftp from ncbi.nlm.nih.gov (130.14.20.1)
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 and postscript. [I have had
some difficulty printing these. Jean Thierry-Mieg
suggests latex xxxx.tex, dvi2ps xxxx.dvi > xxxx.ps,
lpr xxxx.ps.]
You will find interesting documents in the wdoc
subdirectory of the ACEDB distribution.
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. (1993) ACEDB, A tool for
biological information. in Automated DNA Sequencing and
Analysis, edited by M. Adams, C. Fields, and C. Venter.
Academic Press (in press). [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. (1993)
Physical mapping projects and ACEDB, in Guide to Human
Genome Computing. Ed. Bishop, M.J. (Academic Press)
(review, in press). [text is available through ftp or
gopher from weeds.mgh.harvard.edu]
----------------------------------------------------------------------
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) you can participate in the conference
by electronic mail. To subscribe to the e-mail version of the
conference send email to biosci-server at net.bio.net (UK, European
readers use biosci at 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 at net.bio.net the mail will be distributed to all
subscribers and to the electronic conference.
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. (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.
Other URL's that readers with mosaic clients might want to
examine are:
http://moulon.inra.fr/acedb/acedb.html for C. elegans data
http://moulon.inra.fr/acedb/mycdb.html for Mycobacterium data
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.htmlhttp://moulon.inra.fr/acedb_conf.html (en francais)
The Genome Computing Group, Lawrence Berkeley Laboratory
has an anonymous ftp service at machine genome.lbl.gov
(131.243.224.80) which contains:
flydb - LBL's Drosophila Acedb-style database
21bdb - LBL's Human Chromosome 21 Acedb-style database
querdb - LBL's query-language extensions to Acedb
metadata - LBL's compendium of Acedb database schema variants
macace-aatdb-demo.hqx - pre-release Acedb MacIntosh version
There is also a repository of contributed software for
data conversions and the like.
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 at 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).
----------------------------------------------------------------------
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.
----------------------------------------------------------------------
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.
----------------------------------------------------------------------
Q9: What's all this about Gopher/WAIS/ftp/WWW ...
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.
----------------------------------------------------------------------
Q10: How can I get on/off the ACEDB announcements mailing list?
A10: To get on or off the mailing list send mail to
rd at mrc-lmb.cam.ac.uk or mieg at kaa.crbm.cnrs-mop.fr.
New releases of the software are announced to
this list.
----------------------------------------------------------------------
Q11: When and where is the Next ACEDB Workshop?
From Jean Thierry-Mieg:
DATES:
The acedb '94 workshop will be held july 2 to 16, in Saint Matthieu
de Treviers, a small village, 20 km north of Montpellier, at the
foot of the Pic Saint Loup.
HOUSING:
We have booked a place meant for family vacations which includes
ample space, a nice conference room and ten studios meant for 5
people (bathroom, shower, kitchenette, terrace, all nice and clean)
that we plan to share among 3 to 4 participants. Meals will be
taken at a local restaurant.
The place is ideal for work and informal discussions and will be
well equiped with computers. The situation is nice for hiking and
allows volley-ball, ping-pong, tennis and petanque.
We can provide lists of possible hotels for those who would prefer
more privacy or find ways of accomodating families if you let us
know very soon (school ends early july in France).
Cost for 2 weeks is 1000 FF (about 200 US dollars) for housing on
site plus 2500 FF for full meals. We may get enough funding to
reduce this cost, but cannot pay for travel.
PROGRAM:
Formal presentations and general discussions will take place in the
mornings and the evenings, alternating network aspects, data handling,
displays and genome data analaysis.
The afternoons will be dedicated to data manipulation, programming
and writing documentation. The idea is to actually implement during
the meeting many of the ideas that will come up, to fuse and
coallesce the now numerous acedb-based applications into a working
modular package, and to import and consolidate large sets of
additional data.
Towards this goal, we will broadcast the following announcement
ACEDB'94 Genome Database Workshop.
Montpellier, July 2-16, 1994
This meeting will cover the use and development of the
ACEDB database manager central to several major genome projects,
including C.elegans, A.thaliana, human, and a number of
other plant and animal species.
We wish to encourage people with large sets of data on other
organisms to attend this workshop. They will be helped to build,
during the meeting, a friendly graphic presentation of their own
data, in return for discussing their own experience.
*******************************************************************
FORMAT:
This meeting will be much longer than the 2 previous acedb workshops
(Cambridge 92 and Boston 93), in the hope of initiating new
collaborations and allowing concrete results. This format is usual in
physics summer schools and often very productive.
The workshop may be coupled to a 2 days presentation of acedb, open
to the general audience, and yet to be organised.
We anticipate at least the participation of people from: Berkeley,
Boston, Cambridge, Heidelberg and Montpellier, including Richard
Durbin (LMB and Sanger Centre, Cambridge), John McCarthy (LBL,
Berkeley), Otto Ritter (DKFZ, Heidelberg), Danielle and Jean
Thierry-Mieg (CNRS, Montpellier).
Please confirm your participation and forward this announcement to
your colleagues.
Danielle and Jean Thierry-Mieg
CNRS-CRBM
BP 5051,
34033 Montpellier, France.
email mieg at kaa.crbm.cnrs-mop.fr
(if this address fails, fall back on mieg at ncbi.nlm.nih.gov)
Tel: (33) 67 61 33 24
Fax: (33) 67 52 15 59
----------------------------------------------------------------------
Q411:Who prepared this document & where is the current version?
[Note to international readers: 411 is the phone number for
information in the USA. --bks]
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 (134.172.2.69) as
file pub/BIOSCI/ACEDB/ACEDB.FAQ or at rtfm.mit.edu
(18.70.0.209) as pub/usenet/news.answers/acedb-faq. Answer 3
demonstrates a sample FTP session. If you only have
electronic mail, the FAQ can be retrieved from
mail-server at 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.htmlhttp://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: acedbfaq at s27w007.pswfs.gov
Major contributions in getting this FAQ 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
Please cite as:
Sherman, Bradley K. (1994) "ACEDB Genome Database FAQ."
Usenet news.answers. Available via Universal Resource
Locator ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq
To add or modify information in this document, please
send mail to: acedbfaq at 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.
--bks
---------------------End of file acedb-faq----------------------------
