AAtDB update 3-6 release

John Morris john.morris at FRODO.MGH.HARVARD.EDU
Thu Aug 3 11:09:52 EST 1995

AAtDB, An Arabidopsis thaliana Database

A new release of AAtDB is now available for UNIX and Macintosh operating
systems. To get your own copy of the software, connect via ftp to
weeds.mgh.harvard.edu.  Other sites are listed below. The information is
also available through the Internet using the Gopher and WAIS software

Special features of this new release include:

*       Updated Chromosome Maps with the new Recombinant Inbred Maps from
Clare Lister and Caroline Dean.

*       Updated Contact information from nearly 200 people on the
Arabidopsis BioSci email news list.

*       yUP Hybridization data from the ATGC web server.

*       CAPS markers from Drenkard and Ausubel are now included.

*       Sequence updates from GenBank including over 4000 new EST entries.

*       New bibliographic information from Agricola and Medline

Numbers of Objects in selected Classes for version 3-6:

   Map                  31         Locus                 1988
   Allele             1334         Map_Population          26
   Author             5981         Motif                  349
   Clone             23168         Paper                 4441
   Contact            1447         Probe                  528
   DNA_Resource       2869         Sequence             41755
   Gene_Class          244             Sequence_EST     18277
   Gene_Product        830             Sequence_Homol   20780
   Germplasm_Resource 3520             Sequence_Genomic+ 2665
   Image               819         Source                  61
   Journal             411         2_point_data          4877

AAtDB features a wide variety of public information that is presented using
graphical, text, and tabular formats. The user interface, which was
designed to invite browsing, allows users to explore information by
pointing and clicking with the workstation mouse or by using a versatile
query facility. This UNIX release of AAtDB runs using the ACEDB 3.0
software.  ACEDB allows all parts of the database to be cross-referenced
with each other. The large number of interconnections provides a dense
navigable network in which information can be located from many different
starting points.

All information contained within AAtDB was obtained directly from the
original authors or from publicly available collections and databases.
Updates to AAtDB are periodically distributed, the current version of the
database is 3-6.

The database features:

-- The Hauge/Goodman cosmid physical map including greater than 14,000
cosmid clones. The contigs of the physical map are associated with the
genetic maps.

-- Genetic markers, including CAPS, RFLP, RAPD, and "classical" visible markers.

-- Genetic maps, including an update to the RI map of Lister and Dean
(1993) The Plant Journal, the Integrated map from Hauge et al. (1993) The
Plant Journal. The "Classical" marker map from Koornneef (1994) in;
Arabidopsis, Meyerowitz and Somerville editors, Cold Spring Harbor Labs,

-- Primary F2 and RI population recombination data from the Goodman,
Meyerowitz, Scolnik, and Dean laboratories.

-- Primary 2-point data from M. Koorneef, D. Meinke, and others.

-- Stock lists, maintained and entered for AAtDB by Mary Anderson at the
Nottingham Arabidopsis Stock Centre.

-- List of Arabidopsis researchers, including postal mail address,
telephone and FAX numbers, electronic mail address, publications, research
interests, and research associates.

-- All Arabidopsis DNA sequences from GenBank and EMBL DNA sequence
databases (GenBank version 89, June 1995)

-- NCBI BLASTX (six frame translations searched against the NCBI
non-redundant peptide database) defined peptide sequence homologies for all
DNA sequences included in AAtDB.

-- Phenotype descriptions from the Green Book by Meyerowitz and Pruitt,
updated with descriptions from the Nottingham and Ohio State stock centers.

-- Scanned images of RFLP autoradiograms from the Goodman lab, photographs
of mutant plants from G. Redei and M. Anderson, and ethidum bromide-stained
restriction enzyme digests of RFLP probes distributed by the ABRC.

-- Bibliographic citations, including references for all articles from the
Arabidopsis Information Service.

 AAtDB uses the ACEDB software developed by Richard Durbin (MRC-LMB,
Cambridge, U.K.) and Jean Thierry-Mieg (CNRS, Montpellier, France).
Precompiled executables of ACEDB are available for Sun SPARC (SunOS and
Solaris), DEC Alpha, and Silicon Graphics workstations under the X-windows
environment. Source code is available for compilation with other computer

All the AAtDB information in text form is available via the Arabidopsis
Research Companion, an Internet Gopher server at Massachusetts General
Hospital.  The images obtained from the ABRC at Ohio State University are
available as GIF files. All these files are available via Gopher and
anonymous ftp from the host weeds.mgh.harvard.edu (IP

 Using Gopher to search AAtDB and retrieve information:

Internet Gopher was developed by the University of Minnesota. It requires a
computer that is connected to the worldwide Internet network. Software
referred to as a Gopher client is available for most types of computer,
most of these are available via anonymous ftp from boombox.micro.umn.edu.

If your computer manager cannot provide you with one of the free Gopher
clients but you have access to telnet you can use a public access account
provided by the Department of Molecular Biology at Massachusetts General
Hospital. Simply telnet to the host weeds.mgh.harvard.edu (IP, use the username gopher, there is no password. A Gopher
client will start that automatically connects with the AAtDB Research
Companion. Text information can be mailed from the public gopher account by
using the "m" option. However the images cannot be viewed using the public
telnet account. A Gopher client on your local computer is required to view
images, or you can transfer the images via an ftp or Gopher client to an
intermediate computer subsequently transferring the image to a workstation
or personal computer that can display GIF and JPEG images.

The AAtDB Research Companion Gopher is also connected to the World Wide
Web.  The URL is http://weeds.mgh.harvard.edu:80/index.html   If you are
unfamiliar with ACEDB software, there is a revised version of the primer
"An Introduction to ACEDB for AAtDB, which is available through the Web
server (URL=http://weeds.mgh.harvard.edu/introaatdb/index.html).  This
manual is approximately 20 pages of text and graphics which briefly
describes the data and how to use the database.

 Remote Access to the Unix AAtDB database using X-windows

Remote access to the full Unix version of AAtDB is available to computers
with a good Internet network connection and X-windows software. This means
that most Unix workstations using OpenWindows, Motif, or any of a large
number of other windowing environments based on MIT's X-windows can access
a remote server that will display the graphic interface of AAtDB on the
local computer's display. For personal computers a variety of commercial
X-windows emulation software is available.

If you are on a Unix X-windows workstation you will need to issue the
following command before connecting with the server:

% xhost weeds.mgh.harvard.edu

If you are using X-window software on a DEC Vax  you need to set the
security options window to:
Node; weeds.mgh.harvard.edu
User; ?
Transport; TCPIP

The above commands are required to allow the AAtDB server to create and
display windows on your computer.

The basic procedure is to login on the host weeds.mgh.harvard.edu using the
username 'aatdb'; no password is required. After login you will be asked
two questions about your computer: (1) do you have a color monitor, and (2)
do you need to change the hostname. If you are using an X-terminal, a
special device that displays X-windows graphics, you will need to change
the hostname to the hostname of the X-terminal.

If your computer has a color monitor and is not an X-terminal you can use
the login name "c-aatdb". This login name is also useful for some of the
X-windows software on personal computers.

 How to obtain the Unix version of AAtDB:

UNIX files are available via anonymous FTP from three sites.  Note the new
UK site at the European Bioinformatics Institute, the URLs are:

Detailed information about how to retrieve the Unix update information is
included in the file AAtDB_Retrieval_Installation available via anonymous
ftp on the AAtDB server (weeds.mgh.harvard.edu, in the /aatdb/aatdb.3x
directory) .   You will need to obtain the INSTALL script, the compressed
binary for your machine and the update files.  currently we have binaries
for Sun Sparc running Sun OS or  Solaris, DEC mips and alpha and SGI.  You
will need approximately 400 Mb of disk space to load and install,
approximately 310 Mb final if you download all the image files.

How to obtain the Macintosh version

Macintosh files are available from;

To install the Macintosh version you need only retrieve the file
MacAAtDB.sea.bin (using binary mode if you are retrieving with ftp).  On
the anonymous ftp server, the file is in /aatdb/MacAAtDB.  Double clicking
on the file should launch the extraction process. Two version are
available; one with EST sequences and homology data, and one without.  The
'full' version requires 142,456 kb of disk space and the 'demo' version
requires 52,587 kb of disk space.  Neither version has the entire set of
Stock Center images due to space limitations.

This is the last update from Mass General Hospital.  Special thanks to all
those that have submitted information, and the people at the USDA and the
National Agricultural Library who provided funding.

John W. Morris and Howard M. Goodman, Department of Molecular Biology,
Massachusetts General Hospital, 50 Blossom Street, Boston, MA 02114 USA

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