Announcing the WWW/ACEDB Documentation Server
National Agricultural Library
U. S. Department of Agriculture
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:
As ACEDB continues to evolve it is becomes increasingly urgent to
document its features. Fortunately there is widespread interest in
writing and editing documentation in the ACEDB community. We have
received permission from many authors to present their work on the
server. However, there is clearly room for much more writing to be
We would like to issue an open invitation to everyone writing
documentation to contact us when they are ready to release their
(finished or unfinished) work for public consumption. Our view of
documentation is that it can range from the formal to the informal,
long to short, and programmer-oriented to user-oriented. If you have
no experience with html (hypertext markup language) we can provide
Please contact Sam Cartinhour if you would like to participate in this
effort in any way (writing, markup, ideas, suggestions).
Sam Cartinhour (scartinh at vector.nalusda.gov)
Plant Genome Database Project
National Agricultural Library, USDA
10301 Baltimore Blvd.
Beltsville, MD 20705 USA
Brief description of ACEDB Documentation Server contents:
I. User's guide--Durbin and Thierry-Mieg's original user's
guide. Introduces ace and explains printing, help, window and mouse
behavior, queries, basic display types, super-user status and updates.
II. Installation guide--Durbin and 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--Durbin and Thierry-Mieg. wspec with emphasis
on the models, .ace and update file syntax.
ACEDB Frequently Asked Questions--The FAQ for the ACEDB
newsgroup. Maintained by Brad Sherman. Please contact Brad to update
an entry or include new material (acedbfaq at s27w007.pswfs.gov).
ACEDB, A Tool for biological information--Mike Cherry and Sam
Cartinhour. A non-technical introduction to ACEDB as a generic genome
The ACEDB Genome Database--Durbin and Thierry-Mieg. Introduction to
ACEDB. Discussion of software design issues.
Exploring Models Design and Structure--Sam Cartinhour. Model
components and how to modify them. Intended for new curators and
advanced users. This is a draft version undergoing revision.
***Forthcoming (manuscripts received and being marked up)
Syntactic Definitions--Thierry-Mieg and Durbin. Specification of
syntax of models, .ace files, and the query language.
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.
User guide--Mary O'Callaghan. Introduces ACEDB. Discusses major
display types, menu options, queries.
The ANGIS ACEDB manual--Bruno Gaeta, Australian Genomic Information
Centre, Sydney (gaeta at angis.su.oz.au). A detailed (and recently
written) introduction for ACEDB users. ANGIS is the Australian
National Genomic Information Service.
Working on ACEDB: Modeling and More--Lisa Lorenzen. Her handouts from
a minicourse taught at Iowa state University.
Source Code Documentation--Provided by Simon Kelley. Descriptions of
several ACEDB modules. For programmers.
**Ideas for Documentation
This is a call for contributions! Below are a few suggestions. If any
of these appeal to you, or if you are pursuing other ideas for
documentation projects, please let us know!
TableMaker--This powerful utility needs a good introduction.
Queries--We need documentation for query by example, the query
builder, and the original query interface.
Metabolic Pathways--Anticipating that this module (coded by Stan
Letovsky) will be included in the standard ACEDB release,
documentation is needed both for users and curators.
Hints--This area might consist of an unlimited series of small essays
contributed by many people dealing with very focused topics. You could
examine a particular feature in detail (constructed types,
attachments, acediff, keyset manipulation....the list goes on and
on). If you are reluctant to undertake a large documentation project,
try one of these.
Proposals--This area might include descriptions of modifications or
new features you would like to see.