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