What ACeDB is (?)

Don Gilbert gilbertd at bio.indiana.edu
Thu Jun 24 16:03:43 EST 1993


I've had a request to explain what ACeDB is.  I'm not a developer
nor primary user of ACeDB, so my explanation here is limited
to copying a segment of the documents that come with the software.
Someone else may want to better answer this.

--- from acedb/wdoc/users_guide.tex ----------------------------
\title{acedb --- A C.\ elegans Database \\I. Users' guide}

\author{Richard Durbin\thanks{MRC Laboratory for Molecular Biology,
Hills Road, Cambridge, CB2 2QH, UK.  Email: rd at lmba.cam.ac.uk} and
Jean Thierry-Mieg\thanks{CNRS--CRBM, Route de Mende, BP 5051, 34033
Montpellier, France.  Email: mieg at frmop11.bitnet}}

Acedb is the database system that we are writing to meet the needs of
the nematode genome project.
It is graphic, flexible and portable. As of february 1992, it has
been tested on various Unix workstations (SUN, DEC, NEXT, SGI ...),
on all sorts of X terminals
and under several different windowing systems (X11, Sunview, Mac).

The system contains its own portable graphic library, an original
object oriented database manager, a series of applications and a set
of configuration file corresponding to the nematode data.


---- this is from AAtDB_1-1.Announcement ----------------------

AAtDB, An Arabidopsis thaliana Data Base, uses the excellent database
software written by Richard Durbin (MCR-LMB, UK) and Jean Thierry-Mieg
(CNRS, France).  AAtDB is funded by the U. S. Department of
Agriculture Plant Genome Research Program through the National
Agricultural Library and is maintained by a group at the Massachusetts
General Hospital and Harvard Medical School. 

AAtDB is available free of charge via Internet network transfer.  A
complete description of the procedure to retrieve the software and
database is included in a separate message. 

The ACeDB software allows the user to browse information by simply
pointing and clicking with the workstation mouse.  A powerful query
facility is also available. However, our experience is that most users
choose the mouse interface to find the information they are interested in.

Currently AAtDB contains:

	- The Hauge/Goodman cosmid/YAC physical map including >14,000
          cosmid clones.
        - Genetic markers, both RFLP and classical markers.
        - Unified Genetic Map. Including both the Goodman and Meyerowitz
          RFLP markers and classical genetic markers.
        - Primary F2 mapping database from the Goodman and Meyerowitz RFLP
          mapping projects.
        - Primary two point recombination data from M. Koornneef.
        - A strain catalog including all strains and clones available
          from the Nottingham Stock Centre and the ABRC at Ohio State
          University.
        - Bibliographic citations from 1964 to present, currently
          numbering over 2,600.
        - List of Arabidopsis researchers including mail address, phone
          number, FAX number and electronic mail address. Currently
          information on over 500 colleagues is included.
        - Green Book. The Green Book by Meyerowitz and Pruitt has been
          updated and integrated into many parts of the database,
          including phenotype and allele descriptions.
        - All Arabidopsis DNA sequences from GenBank, currently there are
          over 300 sequences.
        - BLASTX defined amino acid sequence similarities for all
          Arabidopsis sequences against the SwissProt, PIR and GenPept
          protein sequence databases.
        - REBASE restriction enzyme database maintained by R. Roberts,
          CSHL.
        - Graphical displays of all Genetic Maps, Physical Maps, and DNA
          Sequence features and similarities.
        - Scanned images of photographs showing mutant phenotypes.

As much as possible all information is connected to other information in
the database.  The database presents the information in separate windows
that allow many parts of the database to be viewed at one time.  There
are also many paths to any piece of information, allowing the user to
easily navigate the connections between the various types of
information. 

This is just the starting point.  Just as the known Arabidopsis genome
information is always being expanded AAtDB is also being extended and
enhanced via periodic updates.  There is much more information that we
are working to include in subsequent updates of AAtDB. 

The database currently requires a Unix workstation running X-Windows. 
Versions of the ACeDB database software are available for Sun
Microsystems SPARCstations, Digital Equipment's DECstation, Silicon
Graphics Iris series and NeXT workstations. 


--
Don Gilbert                                     gilbert at bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405




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