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Release of AAtDB update 3-4

John Morris john.morris at FRODO.MGH.HARVARD.EDU
Tue Nov 15 17:58:14 EST 1994


AAtDB, An Arabidopsis thaliana Database

A new release of AAtDB is now available for Unix workstations. An updated
Macintosh version should be available shortly. The information is also
available through the Internet using the Gopher and WAIS software clients.
To get your own copy of the software for UNIX or Mac connect via ftp to
weeds.mgh.harvard.edu.  More details below.


This UNIX release of AAtDB runs using the ACEDB 3.0 software

Special features of this new release include:

*       The  updated Recombinant Inbred Chromosomal Maps from Claire Lister
and Caroline Dean which now contains 379 loci.

*       The updated Visibile Marker map from David Meinke and Maartin
Koornneef with 279 loci.

*       Sequence updates from GenBank including over 3700 new EST entries.

*       New bibliographic information from Agricola and Medline

*       Additional mapping information from a variety of Arabidopsis
research community members.
*       Subgroups in the Sequence class for easier acess of specific types
of sequence information. (If you set up your own version of AAtDB, be sure
to read the retrieval and installation note, in the FTP directory mentioned
below, in order to display the new subgroups.)

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

   Map                  31         Locus                 1839
   Allele             1238         Map_Population          26
   Author             5167         Motif                  343
   Clone             19163         Paper                 4031
   Contact            1347         Probe                  528
   DNA_Resource       2869         Sequence             23211
   Gene_Class          244             Sequence_EST      8858
   Gene_Product        732             Sequence_Homol   12152
   Germplasm_Resource 7299             Sequence_Genomic+ 2201
   Image               238         Source                  59
   Journal             391         2_point_data          3745


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. 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 3-4.

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. An update to the visible marker map including many embryo
defective loci from David Meinke, and RAPD maps from Scolnik et al. (1992)
PNAS.

-- 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, now maintained and entered for AAtDB by Mary Anderson at
the Nottingham Arabidopsis Stock Centre. Includes many new entries from the
Nottingham and Ohio State stock centers.

-- 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 (Sept 94)

-- 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
architectures

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 132.183.190.21).

 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
132.183.190.21), 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
approx imately140 Mb of disk space to load and install, approximately 100
Mb final.

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
Gopher this is in Arabidopsis Information/AAtDB FTP archive/MacAATDB.  On
the anonymous ftp server, the file is in /aatdb/MacAAtDB.  Double clicking
on the file should 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
information.

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 funded by the U.S. Department of Agriculture Plant
Genome Research Program through the National Agricultural Library. The
AAtDB project is staffed by members of the Department of Molecular Biology
at Massachusetts General Hospital and Harvard Medical School, Boston USA.
AAtDB is available without charge via Internet FTP transfer and remote
X-windows access.







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