928 lines
37 KiB
Plaintext
928 lines
37 KiB
Plaintext
Path: bloom-beacon.mit.edu!gatech!news.byu.edu!news.kei.com!hookup!swrinde!ihnp4.ucsd.edu!agate!overload.lbl.gov!acedbfaq
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From: acedbfaq@s27w007.pswfs.gov (ACEDB FAQ Pseudouser)
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Newsgroups: bionet.software.acedb,news.answers
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Subject: ACEDB Genome Database Software FAQ
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Followup-To: bionet.software.acedb
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Date: 6 May 1994 17:52:21 GMT
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Organization: Dendrome, A genome database for forest trees
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Lines: 906
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Approved: news-answers-request@MIT.Edu
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Message-ID: <2qe04l$shd@overload.lbl.gov>
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Reply-To: acedbfaq@s27w007.pswfs.gov
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NNTP-Posting-Host: s27w007.pswfs.gov
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Summary: Frequently Asked Questions about finding and getting
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started with the database system ACEDB. ACEDB is used
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to collect information regarding the molecular biology
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of the genome.
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Archive-name: acedb-faq
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Last-modified: 5/6/94
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Version: 1.11
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Xref: bloom-beacon.mit.edu bionet.software.acedb:219 news.answers:19222
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----------------------------------------------------------------------
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Common Questions, with Answers, about ACEDB.
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Q0: What is ACEDB?
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Q1: What is the current version of ACEDB?
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Q2: !What hardware/software do I need to run ACEDB?
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Q3: Where can I get ACEDB?
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Q4: !What ACEDB databases exist?
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Q5: What written documentation exists for ACEDB?
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Q6: Where can I find further information about ACEDB?
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Q7: How should ACEDB be cited?
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Q8: Is ACEDB object-oriented?
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Q9: What's all this about Gopher|WAIS|ftp|WWW|URL ...
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Q10: How can I get on/off the ACEDB announcements mailing list?
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Q11: When and where is the next ACEDB Workshop?
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Q411:Who prepared this document & where is the current version?
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Questions marked with + are new, those with !
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have substantially changed answers.
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----------------------------------------------------------------------
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Q0: What is ACEDB?
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A0: ACEDB is an acronym for A Caenorhabditis elegans Database. It can
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refer to a database and data concerning the nematode C. elegans,
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or to the database software alone. This document is concerned
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primarily with the latter meaning. ACEDB is being adapted by many
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groups to organize molecular biology data about the genomes of
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diverse species [see Q4].
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ACEDB allows for automatic cross-referencing of items during
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loading and allows for hypertextual navigation of the links
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using a graphical user interface and mouse. Certain special
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purpose graphical displays have been integrated into the
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software. These reflect the needs of molecular biologists
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in constructing genetic and physical maps of genomes.
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ACEDB was written and developed by Richard Durbin (MRC LMB
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Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier,
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France), beginning circa 1990. It is written in the C programming
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language and uses the X11 windowing system to provide a platform
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independent graphical user interface. The source code is publicly
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available [See Q3]. Durbin & Thierry-Mieg continue to develop
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the system, with contributions from other groups including
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Lawrence Berkeley Laboratory and the European integrated Genome
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Project.
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A description by Durbin & Thierry-Mieg:
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ACEDB does not use an underlying relational database
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schema, but a system we wrote ourselves in which data
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are stored in objects that belong in classes. This is
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nevertheless a general database management system using
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caches, session control, and a powerful query language.
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Typical objects are clones, genes, alleles, papers,
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sequences, etc. Each object is stored as a tree,
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following a hierarchical structure for the class (called
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the "model"). Maps are derived from data stored in tree
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objects, but precomputed and stored as tables for
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efficiency. The system of models allows flexibility
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and efficiency of storage -missing data are not stored.
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A major advantage is that the models can be extended
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and refined without invalidating an existing database.
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Comments can be added to any node of an object.
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----------------------------------------------------------------------
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Q1: What is the current version of ACEDB?
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A1: As of January 1994, ACEDB has undergone a bifurcation. Those
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involved with C. elegans will want to to track the 2.x series
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under the stewardship of Richard Durbin and all other groups
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should probably track the 3.x series of Jean Thierry-Mieg.
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Thierry-Mieg writes "... 2 and 3 differ only at the level of
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displays ..." Version 2.0 was released in December, 1993 and
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version 3.0 was released in January, 1994.
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To retrieve the software see Q3.
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To be kept informed of new releases see Q10.
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[This question refers to the software not the C. elegans data.]
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Q2: What hardware/software do I need to run ACEDB?
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A2:
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Unix and X11:
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Any machine running SunOS 4.x
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SPARCstation 10 under Solaris [Probably all Solaris, then --bks]
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DEC DECstation3100, 5100 etc.
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DEC Alpha/OSF-1
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Silicon Graphics Iris series
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PC 386/486 with Linux (free Unix)
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There exist, or have existed, ports onto Alliant, Hewlett-
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Packard, IBM R6000, Convex. You may have to contact
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the developer responsible for the port to make these real.
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NeXT: contact Patrick Phillips at University of Texas,
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NeXTmail: patrick@wbar.uta.edu
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email: phil@decster.uta.edu
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MSDOS/Windows/NT:
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A port to NT is rumored to be in the works.
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Macintosh:
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[Contributed by Frank Eeckman]
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macace 2.0 is now available from genome.lbl.gov
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(131.243.224.80) under ftp/pub/macace. Macace is
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distributed as a self-extracting archive that contains the
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application, the wspec files, and a fully up to date
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database. macace 3.0 is available with an updated 21bdb
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database from the same source. Please send all questions/bug
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reports to eeckman@llnl.gov A native powerPC version is
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available as well. Macace needs a macintosh with > 16 MBytes
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of RAM, and a decent color monitor is preferred. System 7 or
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greater is required. For the multimedia extensions Quicktime
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1.0 is required. Please add your name to our mailing list by
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sending email to eeckman@llnl.gov.
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It is our belief that for cost savings a powerPC mac will beat
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the advertised linux-intel combination.
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Macace is fully compatible with xace, but includes some
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multimedia extensions (picture and movie support) not found
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in the unix versions.
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For cost savings, a combination of a high-end Intel platform
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with Linux appears very attractive.
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Here at the Institute of Forest Genetics we run ACEDB on a
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Sun Microsystems SPARCstation II, and users can interact
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using Macintoshes and PC-clones by using X11 implementations
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for the personal computers and a LAN. [This section should
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be expanded to have a more thorough discussion of X11
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interactions. --bks]
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----------------------------------------------------------------------
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Q3: Where can I get ACEDB?
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A3: All the files are available in the following public access
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accounts (anonymous ftp sites) accessible via Internet:
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lirmm.lirmm.fr (193.49.104.10) in pub/acedb
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cele.mrc-lmb.cam.ac.uk (131.111.84.1) in pub/acedb
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ncbi.nlm.nih.gov (130.14.20.1) in repository/acedb
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(version 1-10 is available in repository/aatdb)
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bioinformatics.weizmann.ac.il (132.76.55.12) in
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pub/databases/acedb.
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A typical session would be:
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ftp ncbi.nlm.nih.gov
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login: anonymous
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password: your email address
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cd repository/acedb/ace3
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binary
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ls
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get README_3
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get NOTES
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get INSTALL
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get bin.sparc.3.0.tar.Z
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quit
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----------------------------------------------------------------------
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Q4: What ACEDB databases exist?
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A4: [In alphabetic order by Database name.
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Curators, submit changes as new paragraphs.--bks]
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Database : AAnDB-1.0
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Species : Aspergillus nidulans
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PI : Leland Ellis
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Last_update : February 1994
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ACEDB_version : 3.0
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Contact : leland@stralight.tamu.edu
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URL : http://keck.tamu.edu/ibt.html
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Comment : defunct, See AGsDB
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Database : AAtDB
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Species : Arabidopsis thaliana
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Availability :
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Curator : John Morris
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Current version: 1-5
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Contact : curator@frodo.mgh.harvard.edu
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Last_update : Sept. 1993
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Database : ABtDB-1.0
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Species : Bovine, Bos taurus
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ACEDB_version : 3.0 extended
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PI : Leland Ellis
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Last_update : February 1994
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Contact : leland@stralight.tamu.edu
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URL : http://keck.tamu.edu/ibt.html
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Comment : defunct, See AGsDB
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Database : ACeDB
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Species : Caenorhabditis elegans
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Current version: 2-9
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Curator : Jean Thierry-Mieg
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Curator : Richard Durbin
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Contact : rd@mrc-lmb.cam.ac.uk
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Contact : mieg@kaa.crbm.cnrs-mop.fr
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Last_update : March 1994
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Database : AceMap
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Species : Homo Sapiens (Saccaromyces Pombe, Mus musculus in development)
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Focus : Physical mapping of human chromosomes X and 21
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Curator : Hugues Roest Crollius
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Contact : hrc@gea.lif.icnet.uk
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PI : Hans Lehrach
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PI : Hugues Roest Crollius
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Last_update : 22 Feb 1994
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Database : AGhDB
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Species : Gossipium hirsutum (cotton)
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PI : Russ Klhel
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Curator : Stephanie Crouch
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Last_update : March 1994
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Contact : scrouch@tamsun.tamu.edu
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Database : AGsDB A Genus species Database
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Species : Aspergillus nidulans
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Species : Neurospora crassa
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Species : cow w/ human anchor loci
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Species : cotton (demo)
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Species : Homologs of Aspergillus cell cycle loci
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for budding and fission yeast
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PI : Leland Ellis
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Curator : Leland Ellis
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Last_update : March 1994
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ACeDB_version : 3.0 (beta still), with extensions to the Human
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C21 Models to provide for multiple species, and queries
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between species via Homologs (e.g., cell cycle loci with
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links via Homologs between Aspergillus and budding
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C. cerevisiae) and fission (S. pombe) yeast);
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interacting loci via defined Interactions for each locus
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Models : as of 3.13.94
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Data : as of 3.13.94
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Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus
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(cow) have been folded into AGsDB, and are not being
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developed futher as individual species databases.
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WWW : WWW-AGsDB is an interface of AGsDB with the World-Wide Web,
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and utilizes the WWW-ACeDB Server (nph-acedb3) of Guy Ducoux
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(ducoux@moulon.inra.fr).
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URL : http://keck.tamu.edu/ibt.html
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Contact : leland@straylight.tamu.edu
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Database : ASbDB
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Species : Sorghum bicolor
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PI : Keith Schertz
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Curator : Stephanie Crouch
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Last_update : March 1994
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Contact : scrouch@tamsum.tamu.edu
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Database : ChlamyDB
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Species : Chlamydomonas
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PI : Elizabeth Harris
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Contact : chlamy@acpub.duke.edu
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Availability : Still under construction
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Phone : 919-684-5243 (till 6/94)
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Fax : 919-684-5412 (till 6/94)
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Last_update : 30 Sept. 1993
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Database : EcoDB
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Species : E. coli
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PI : Staffan Bergh
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Contact : staffan@biochem.kth.se
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Availability : Still under construction
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Last_update : 11 Oct. 1993
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Database : FlyBase
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Species : Drosophila melanogaster
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Availability : gopher or gopher+ ftp.bio.indiana.edu
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Availability : ACeDB-style interface to SyBase server
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due by end of 1994
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Curator : Edward Welbourne
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Contact : eddy@gen.cam.ac.uk
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Contact : flybase@morgan.harvard.edu
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PI : William Gelbart
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PI : Michael Ashburner
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PI : Thomas Kaufman
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PI : Kathy Matthews
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PI : John Merriam
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Database : Flydb
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Species : Drosophila melanogaster
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Availability : by request only, via ftp
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Curator : Suzanna E. Lewis
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Contact : SELewis@lbl.gov
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Focus : STS content mapping project summary
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PI : Gerald Rubin
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PI : Mike Palazzolo
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PI : Dan Hartl
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PI : Alan Spradling
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Last_update : Sept. 1993
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Database : GrainGenes
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Species : Wheat, barley, oats, relatives
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Availability : Anonymous ftp from probe.nalusda.gov:pub/grains
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Availability : Gopher greengenes.cit.cornell.edu port 70
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Availability : Gopher probe.nalusda.gov port 7002
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Curator : David E. Matthews
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PI : Olin D. Anderson
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Contact : matthews@greengenes.cit.cornell.edu
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Contact : oandersn@wheat.usda.gov
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URL : gopher://greengenes.cit.cornell.edu/1/
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Data_version : 1.3
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Released : 12 Jan 1994
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Based_on : acedb.1-10
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Availability : See following WWW URL
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URL : http://probe.nalusda.gov:8000/acedbs/acedbs/graingenes/index.html
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Last_update : Feb. 1994
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Database : human.c17
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Species : Homo sapiens
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Availability : the database is under development
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Contact : lsprilus@weizmann.weizmann.ac.il
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Focus : mapping & sequencing of Human Chromosome 17
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Based_on: acedb.3-0
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Last_update : Jan. 1994
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Database : Maize
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Species : Zea mays L. ssp. mays
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Focus : Maize genome
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Acedb_version : 1.9
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FTP : probe.nalusda.gov, pub directory; anonymous ftp
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Comment : Maize is an acedb front end for the Maize Genome
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Database, MaizeDB, a SYBASE database.
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Comment : MaizeDB is updated daily and has WWW connectivity
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to external databases: GenBank (loci, alleles and
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probes), SwissProt (gene products) and the E. coli
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Stock Center (loci).
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Data : Major data categories: 4522 mapped loci (located to
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chromosome or better) including 684 mapped genes and
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1423 mapped probed sites (gene candidates); 982
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probes; 1850 map scores; 1533 gel patterns
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(Probe/Enzyme/Stock); 4231 stocks; 5105 Variations
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(alleles, DNA polymorphisms, rearrangements, etc);
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465 phenotypes; 223 traits; 547 gene products;
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5314 bibliographic references; 1979 persons with
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addresses.
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Gopher : host = teosinte.agron.missouri.edu, port = 70
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Telnet : telnet teosinte.agron.missouri.edu
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login as guest, use password 'corncob'
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HTTP : http://teosinte.agron.missouri/top.html
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HTTP : http://probe.nalusda.gov:8000/acedbs/index.html
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via PGD, the Plant Genome Database
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Comment : Genera is a software toolkit for creating and
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extracting data from Sybase databases; used to
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create MaizeDB and Worldwide Web connectivity.
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HTTP : Genera Info http://cgsc.biology.yale.edu/genera.html
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Funding : MaizeDB USDA/ARS to E. Coe
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Funding : Genera NSF BIR 92-01652 to S. Letovsky and M. Berlyn
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Curator/PI : Ed Coe ed@teosinte.agron.missouri.edu
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Curator : Pat Byrne byrne@teosinte.agron.missouri.edu
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Curator : Georgia Davis gdavis@teosinte.agron.missouri.edu
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Curator : Mary Polacco maryp@teosinte.agron.missouri.edu
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Curator : Marty Sachs, Maize Stock Center, msachs@uiuc.edu
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Curator : Christiane Fauron FAURON@GENE1.med.utah.edu
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Curator : Carolyn Wetzel cmwetzel@iastate.edu
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Curator : Steve Rodermel S1SRR@ISUVAX.IASTATE.EDU
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Design : Stan Letovsky letovsky-stan@CS.YALE.EDU
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Design : Mary Berlyn mary@fetalpig.biology.yale.edu
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Systems Manager : Denis Hancock
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dhancock@teosinte.agron.missouri.edu
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Contact : db_request@teosinte.agron.missouri.edu
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Last_update : 25 April 1994
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Database : MycDB
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Species : Mycobacteria
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Comment : MycDB is a collation of data on the mycobacteria,
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causative agents of tuberculosis and leprosy. It
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is centered on the mapping and sequencing projects
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under way in M.leprae and M.tuberculosis.
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PI : Staffan Bergh
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PI : Stewart Cole
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PI : Doug Smith
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Curator : Staffan Bergh
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Contact : staffan@biochem.kth.se
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Last_update : Apr. 1994
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WWW : http://kiev.physchem.kth.se/MycDB.html
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ftp : ftp.pasteur.fr (157.99.64.12) in pub/MycDB
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ftp : kiev.physchem.kth.se (130.237.52.64) in pub/MycDB
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ftp : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/mycdb
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Database : RiceGenes
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Species : Rice (O. sative)
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Availability : under development, login at own risk
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Curator : Edie Paul
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Contact : epaul@nightshade.cit.cornell.edu
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Last_update : Sept. 1993
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Database : SolGenes
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Coverage: Solanaceae - tomato, potato, pepper (eventually)
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Availability : Beta ACEDB via login or tar file
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Curator : Edie Paul
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Contact : epaul@nightshade.cit.cornell.edu
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Last_update : Sept. 1993
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Database : SoyBase
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Species : Soybeans
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Curator : Lisa Lorenzen
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PI : Randy Shoemaker
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Contact : lorenzen@mendel.agron.iastate.edu
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Phone : 515-294-0421
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Fax : 515-294-2299
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Last_update : Sept. 1993
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Database : TreeGenes
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Species : Forest trees
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Availability : alpha, contact curator
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ACEDB_version : 1-10
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Curator : Bradley K. Sherman
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PI : David B. Neale
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Contact : Dendrome@s27w007.pswfs.gov
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Contact : bks@s27w007.pswfs.gov
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Contact : dbn@s27w007.pswfs.gov
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Last_update : March 1994
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URL : gopher://s27w007.pswfs.gov/
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URL : http://s27w007.pswfs.gov/
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URL : ftp://probe.nalusda.gov/pub/trees
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Database : 21Bdb
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Species : Homo sapiens
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Availability : by request, via ftp, world-wide-web
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Based_on : acedb.1-10 plus moulon server
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URL : ftp://genome.lbl.gov/pub/21Bdb-v1.1.tar.Z
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URL : http://genome.lbl.gov/Genome/acepage.html
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Curator : Donn F. Davy
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Contact : DFDavy@lbl.gov
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Contact : aggarwal@genome.lbl.gov
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Focus : STS content mapping & sequencing of Human Chromosome 21
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PI : Michael Palazzolo
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PI : Chris Martin
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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@poplar1.cfr.washington.edu
|
|
Contact : STETTLER@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@crc.ac.uk id1@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@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.
|
|
|
|
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@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.html
|
|
|
|
|
|
http://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@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@mrc-lmb.cam.ac.uk or mieg@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@kaa.crbm.cnrs-mop.fr
|
|
(if this address fails, fall back on mieg@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@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
|
|
http://s27w007.pswfs.gov/Homepage/acedbfaq.html
|
|
|
|
Curators of ACEDB databases should take note of Question 4 and
|
|
keep me apprised of changes.
|
|
|
|
Errors of commission or omission are unintentional. If I have
|
|
forgotten to give you credit please let me know. Please
|
|
send comments and corrections to: acedbfaq@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@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----------------------------
|