ACEDB Genome Database Software FAQ

ACEDB FAQ Curator acedbfaq at s27w007.pswfs.gov
Tue May 27 17:31:22 EST 1997


URL: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html
Archive-name: acedb-faq
Last-modified: 27 May 97
Version: 1.37

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ACEDB FAQ

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Curated by: Dave Matthews
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Frequently Asked Questions about ACEDB

   * Q0 : What is ACEDB?
   * Q1 : What is the current version of ACEDB?
   * Q2 : What hardware/software do I need to run ACEDB?
   * Q3a : Where can I get ACEDB?
   * Q3b : + Where can I get the graphic ace client?
   * Q4 : How does ACEDB compare to commercial relational DBMS's?
   * Q5 : Is ACEDB object-oriented?
   * Q6 : What documentation exists for ACEDB?
   * Q7 : What other resources are available for ACEDB?
   * Q8 : How should ACEDB be cited?
   * Q9 : How does one get on/off the ACEDB announcements mailing list?
   * Q10 : ! When and where is the next ACEDB Workshop?
   * Q11 : ! What ACEDB databases exist?
   * Q12 : Who prepared this document & where is the current version?

Questions marked with '+' are new, those with '!' have substantially changed
answers.
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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 molecular biology
data about the genomes of diverse species [Q11 gives contact information].

ACEDB allows for automatic cross-referencing of items during loading and
allows for hypertextual navigation of the links using a graphical user
interface and mouse. Certain special purpose graphical displays have been
integrated into the software. These reflect the needs of molecular
biologists in constructing genetic and physical maps of genomes.

ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge,
England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning circa
1990. It is written in the C programming language and uses the X11 windowing
system to provide a platform independent graphical user interface. The
source code is publicly available [See Q3]. Durbin & Thierry-Mieg continue
to develop the system, with contributions from other groups including
Lawrence Berkeley Laboratory and the Integrated Genomic Database (IGD)
project headed by Otto Ritter.

A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying
relational database schema, but a system we wrote ourselves in which data
are stored in objects that belong in classes. This is nevertheless a general
database management system using caches, session control, and a powerful
query language. Typical objects are clones, genes, alleles, papers,
sequences, etc. Each object is stored as a tree, following a hierarchical
structure for the class (called the "model"). Maps are derived from data
stored in tree objects, but precomputed and stored as tables for efficiency.
The system of models allows flexibility and efficiency of storage --missing
data are not stored. A major advantage is that the models can be extended
and refined without invalidating an existing database. Comments can be added
to any node of an object.

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Q1: What is the current version of ACEDB?

A1:

(This answer refers to the software, not the C. elegans data.)

Current Unix version is 4_3 (as of May 1996) and is identical to the test
version test.4_3i.

A Macintosh version is available as version 4.1b1.

A Windows 95/NT version is available as version beta960927.

To retrieve the software see Q3.
To be kept informed of new releases see Q9.

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Q2: What hardware/software do I need to run ACEDB?

A2:

The software is available as source code, so you may be able to get it
working on any machine, with effort. It is also available in binary
(pre-compiled) format for a variety of machines. To retrieve the software
see Q3.

   * Unix:
        o Sun/SunOS 4.x
        o Sun/Solaris
        o DEC DECstation3100, 5100 etc.
        o DEC Alpha/OSF-1
        o Silicon Graphics Iris series 4, 5, 6
        o IBM RS-6000
        o PC 386/486/Pentium with Linux
        o NEC EWS4800
        o NeXT: contact Patrick Phillips at University of Texas, NeXTmail:
          patrick at wbar.uta.edu email: phil at decster.uta.edu
        o There exist, or have existed, ports onto Alliant, Hewlett-
          Packard, Convex. You may have to contact the developer responsible
          for the port to make these real.
   * Windows 95/NT
   * Macintosh (not currently supported)

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Q3a: Where can I get ACEDB?

A3a:

Source code and Unix binaries are available in the following anonymous ftp
sites:

   * lirmm.lirmm.fr in pub/acedb
   * ftp.sanger.ac.uk in pub/acedb
   * ncbi.nlm.nih.gov in repository/acedb
   * bioinformatics.weizmann.ac.il in pub/databases/acedb

Linux binaries in ELF and a.out format, from Jeff Bryer:

   * ncbi.nlm.nih.gov in repository/acedb
   * bioinformatics.weizmann.ac.il in pub/databases/acedb

NEC EWS4800 binaries:

   * http://www.labs.nec.co.jp/freesoft/freesofte.html

Windows 95/NT 3.51, from Richard Bruskiewich:
(Note: This is a development version, not fully debugged.)

   * ftp.sanger.ac.uk in pub/winace
   * bioinformatics.weizmann.ac.il in pub/databases/acedb

MacAce, from Frank Eeckman, Cyrus Harmon and Richard Durbin:
(Note: The authors are not currently able to support MacAce. Latest version
was 4.1b1.)

   * genome.lbl.gov in pub/macace
   * ncbi.nlm.nih.gov in repository/acedb/macace
   * bioinformatics.weizmann.ac.il in pub/databases/acedb

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NEW!

Q3b: Where can I get the graphic ace client?

A3b:

from Jean 15apr97:
I have now a graphic client with read write access and i would be happy to
have people test it, it runs off any unix platform, including linux and is
good if several people want to update in parallel or to have distant users

To obtain the client, send mail to Jean, mieg at kaa.crbm.cnrs-mop.fr.

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Q4: How does ACEDB compare to commercial relational DBMS's?

A4:




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