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New AAtDB version 3-5 update available

John Morris john.morris at FRODO.MGH.HARVARD.EDU
Tue Mar 28 13:39:08 EST 1995

AAtDB, An Arabidopsis thaliana Database

A new release of AAtDB is now available for Unix workstations. Perhaps you
read about it in Weeds World yesterday, now you can down load it today. To
get your own copy of the software for UNIX connect via ftp to
weeds.mgh.harvard.edu.  More details below.  An updated Macintosh version
should be available on the ftp server shortly. The information is also
available through the Internet using the Gopher and WAIS software clients.

Special features of this new release include:
*       Over 600 new image files from the Nottingham Arabidopsis Stock Centre

*       Updated Recombinant Inbred, and Visibile Marker genetic maps with
additional 2-point recombination data.

*       Sequence updates from GenBank including over 5000 new EST entries.

*       New GeneFinder tables for Arabidopsis from Stefan Klostermann and
Colin Wilson

*       New bibliographic information from Agricola and Medline

Numbers of Objects in selected Classes for version 3-4:

   Map                  31         Locus                 1926
   Allele             1295         Map_Population          26
   Author             5425         Motif                  343
   Clone             19163         Paper                 4192
   Contact            1419         Probe                  528
   DNA_Resource       2869         Sequence             34686
   Gene_Class          244             Sequence_EST     14915
   Gene_Product        791             Sequence_Homol   17257
   Germplasm_Resource 3520             Sequence_Genomic+ 2495
   Image               819         Source                  60
   Journal             395         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 3-5.

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 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 (Feb 95)

-- 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 now 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:

Detailed information about how to retrieve the Unix update information is
included in the file AAtDB.Retrieval_Installation on the
weeds.mgh.harvard.edu (in the aatdb directory) via anonymous ftp. You can
also obtain this file via our Gopher from the "AAtDB FTP Archive" folder.
You will need to obtain the INSTALL script, the compressed binary for your
machine and the upddate files.  currently we have binaries for Sun Sparc
running Sun OS or  Solaris, DEC mips and alpha and SGI.  You will need
approximately 380 Mb of disk space to load and install, approximately 300
Mb final if you download all the image files.

How to obtain the Macintosh version

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.  After decoding
the binhex file to produce the .sea file, double clicking on the file to
launch the extraction process.

Please send submissions of new information (mapping and colleague listing
or any of the other types of information provided) to the AAtDB Project via
electronic mail at curator at frodo.mgh.harvard.edu or via FAX at
617-726-6893. Please help us make this resource better by providing some of
your data and information.  Special thanks to all those that have submitted

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

The AAtDB project is staffed by members of the Department of Molecular
Biology at Massachusetts General Hospital and Harvard Medical School,
Boston USA.

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