ACEDB Documentation Library
ACEDB Documentation Library
Welcome to the ACEDB documentation library. This repository is for
developers, curators, and end-users wanting to learn more about the ACEDB
software. ACEDB is freely
available and should be cited
when used.
ACEDB has undergone many versions since it was first created in 1990.
The ACEDB version and document date are being added for each
resource in this library. Documents that are particularly helpful to
ACEDB newcomers are indicated with a 
. Some materials
are also available (as html and other format) from the
via downloads page.
For more information or to contribute documentation, contact
the AceDB developers at:
acedb@sanger.ac.uk.
Contents
General Resources
- ACEDB Frequently Asked Questions
- Dave Matthews
The FAQ for the ACEDB newsgroup that is updated monthly. Contact Dave to contribute new material.
- ACEDB newsgroup
- Search messages posted to the ACEDB newsgroup (bionet.software.acedb conference archives).
- The Sanger Center ACEDB Site
- Source for ACEDB software at major ace development site. Some links below are directly to
documents at this site.
- The CNRS-MOP
ACEDB Site at Montpellier
- Source for ACEDB software
at major ace development site. Some links below are directly to
documents at this site.
- The future of ACEDB
- Proposals and plans for ACEDB by the developers.
ACEDB Conference and Workshop
- ACEDB 2000
- Reports from the 2000 meeting June 12-16 at Simon Fraser University, B.C., Canada
- 1997 ACEDB Conference and Workshop Proceedings
- Reports from the 1997 meeting July 27-August 9 at Cornell
University, Ithaca, New York, USA.
- 1995
ACEDB Conference and Workshop Proceedings
- Agenda, participant list, working group papers and other
information from the 1995 ACEDB Conference and Workshop held in
Geyserville, California May 15-27. See the participants hard at work in
photographs by
Frank
Eeckman and Nomi Harris and Dave Matthews.
- 1994 ACEDB Conference and Workshop, Photos
Overviews and Introductory Guides
- The ACEDB Genome Database
- Richard Durbin and Jean Thierry-Mieg
Introduction to ACEDB. Discussion of software design issues.
- ACEDB, A Tool for biological information
- Mike Cherry and Sam Cartinhour
A non-technical introduction to ACEDB as a generic genome database.
- ACEDB Summary
- Gary Aochi
Introduction to ACEDB for programmers. (July 1993)
ACEDB Query Language
- AQL - Acedb Query Language
- AQL is the new query language for the Acedb database system
to be implemented fully in ACEDB version 5.
- Searching an ACeDB database
- Dave Matthews and Suzanna Lewis
Intended for end users and curators. Query tools, query language syntax,
many examples. Includes screen dumps. (version 4, May 1995)
- Using TableMaker
- Dave Matthews
Tutorial for the TableMaker, a powerful query tool which can construct
relational tables. Illustrated with screendumps. (version 4, May 1995)
- Introduction to Table-maker on the WWW
- JD Barnett
An introduction to the AGIS WWW interface to Table-maker.
(December 1995)
- Help for ACEDB Queries
- Staffan Bergh
Guide to ACEDB queries, with examples using MycDB. Discusses differences in
syntax between queries submitted via tace and the Moulon ACEDB-WWW server.
(May 1995)
- About ACEDB Queries
- Gail Juvik
Discussion of query syntax with examples from AGIS WWW-ACEDB interface
(October 1995)
- ACEDB Query Language Examples
- JD Barnett
Over 40 sample queries using the ACEDB Query Language. (December 1995)
Technical Guides
- Jade
- Home page for Jade, a Java library providing access to ACEDB
databases. See also the Jade site
maintained by Lincoln Stein at CSHL.
- Data Conversion Tools
- Pointers to tools designed to help ACEDB curators reformat and process data.
- Loading data into ACEDB
- Dave Matthews and Suzanna Lewis
Reading data into ACEDB via .ace files using both xace and tace. Includes
a discussion of the acediff utility; hints on how to reformat and validate
data. (version 3, May 1995)
- II. Installation guide
- Richard Durbin and Jean Thierry-Mieg
Discusses installation of ACEDB (automatic and by hand) and setting up
for more than one organism. How to initialise the database and recompile.
- III. Configuration guide
- Richard Durbin and Jean Thierry-Mieg
Discusses wspec with emphasis on the models, .ace and update file syntax.
(December 1992)
- Syntactic Definitions
- Jean Thierry-Mieg and Richard Durbin
Specification of syntax of models, .ace files, and the query language.
(December 1992)
- Tace
- John Morris
Guide to Tace, including use of scripts. (version 3, August 1994)
- On-line ACEDB Help
- The on-line help (whelp) for ACEDB maintained at the Sanger Centre.
- Source Code Documentation
- Ed Griffiths and Fred Wobus
Descriptions of ACEDB modules for programmers. Maintained at the Sanger Centre (no screen dumps).
- AboutDB
- Staffan Bergh
ACEDB database information on developers, bug reports, tools, and more.
See also about AboutDB for additional information.
(August 1995)
- Webace
- Webace is used to connect ACEDB to the WWW and is maintained at
the Sanger Center. This version supercedes AceWWW and webace developed
by GIG.
- AcePerl
- AcePerl is an object-oriented Perl interface for the ACEDB database
under development by Lincoln Stein at Cold Spring Harbor Laboratory.
- AceBrowser
- AceBrowser is a set of CGI scripts that work with AcePerl to provide a browsable interface to ACEDB.
- aceclient and
aceserver
- Doug Bigwood
Setting up an acedb (4.x) server or client, and compiling the client code
into Perl. See
also the distribution
information. (August 1995)
- Aceobj.pm and
AceWWW.pm
- JD Barnett
Perl modules for manipulating acedb objects and formatting in html. See
also the distribution information.
(version 4, August 1995)
- wwwace
- JD Barnett
Modifications to the ACEDB source and accompanying perl scripts to provide
ACEDB graphics on the WWW. wwwace is available by
ftp.
(version 4, October 1995)
- webace
- JD Barnett
Latest incarnation of the www <-> acedb interface, for version 4.3.
(ftp)
- comment
- Christophe Caron
Adding a user-feedback form ("_Submit comment/correction") to webace records.
- TextConvert
- Joachim Baumann
A general tool for converting data to ACEDB format input files.
ACEDB Models
- Magic Tags
- Descriptions of the "Magic" tags which support various
displays in ACEDB version 4 (includes many screen dumps). (May 1995)
- A Guide to Models and Ace Files
- Mary O'Callaghan
Describes model elements and function. Detailed look at ace files,
including deletion, renaming, and comment options (no screen dumps).
(October 1993)
- Exploring Models
Design and Structure
- Sam Cartinhour
Model components and how to modify them. Intended for new curators and
advanced users (includes screen dumps). (July, 1997)
- Introduction to ACEDB
- JD Barnett
An introduction to ACEDB databases and models on AGIS.
(December 1995)
- A Note about Constructed Types
- JD Barnett
Describes constructed types in ACEDB models. (December 1995)
- Selected Models
- Models.wrm from databases deposited at the National Agricultural Library.
Tutorials and User Guides
- DictyDB_Help
- Doug Smith
User manual for the MacAce version of DictyDB, a database for Dictyostelium discoideum. Very detailed;
uses ACEDB v. 4. (screen dumps). (May, 1996)
- Acembly
- Acembly home site (Mieg) including software.
- ACE-mbly
- John Morris
Tutorial for ACE-mbly, an ACEDB extension for displaying and
editing data from an ABI sequencer. (screen dumps). (June 1995)
- The Genetic Map Display
- Dave Matthews
Introduction to the genetic map display with particular emphasis
on the "columns" feature, new in ACEDB version 4. (screen dumps).
(May 1995)
- SampleDB
- Dave Matthews
A sample database to demonstrate features of ACEDB, especially map and
sequence displays. SampleDB 1.0 is available via
ftp and
with a SunOS 4.x executable of ACEDB version 4_0b4. (June 1995)
- I. User's guide
- Richard Durbin and Jean Thierry-Mieg
The original user's guide. Introduces ace and explains printing, help,
window and mouse behavior, queries, basic display types, super-user
status and updates. (January 1993)
- User guide
- Mary O'Callaghan
Introduces ACEDB and discusses major display types, menu options,
queries (no screen dumps). (October 1993)
- An Introduction to ACeDB:
For AAtDB, An Arabidopsis thaliana Database
- Sam Cartinhour, Mike Cherry, and Howard Goodman
Recently updated for ACEDB version 3.x by John Morris (screen dumps).
(January 1995)
- The ANGIS ACEDB manual
- Bruno Gaeta, Australian Genomic Information Centre, Sydney
(gaeta@angis.su.oz.au)
A detailed (and recently written) introduction for ACEDB users.
Contains many screen dumps; we recommend setting your WWW browser to
delay image loading.
- An
Introduction to SacchDB for the Macintosh
- Mike Cherry
Although based on the Macintosh version, demonstrates general features
available with any ACEDB software. Contains screen dumps.
Last update 10 Feb 00
maria_nemchuk@genome.cornell.edu