AAtDB release 1-2

Mike Cherry 726-5955 CHERRY at FRODO.MGH.HARVARD.EDU
Wed Oct 28 14:55:32 EST 1992


AAtDB 1-2 is now Available:

The second release of the Arabidopsis genome database, AAtDB, is now
available.

AAtDB, An Arabidopsis thaliana Data Base, uses the ACEDB genome
database software written by Richard Durbin (MCR-LMB, UK) and Jean
Thierry-Mieg (CNRS, France). The ACeDB software allows the user to
browse information by simply pointing and clicking with the
workstation mouse.  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 below.  The bibliographic reference list from
AAtDB 1-2 is also being made available in several formats.

Whats New:

Updated information contained in AAtDB release 1-2:

  - Unified Genetic Map. Including the Goodman, Meyerowitz, and Scolnik
    molecular markers and the visible genetic markers collected by
    Koornneef.
  - Addition of the Scolnik mapping data and updates of the Meyerowitz
    F2 data. Note that marker survey results are still being tabulated
    and will be included in the 1-3 release.
  - Strain catalog including all strains and clones available from the
    Nottingham Stock Centre and the ABRC at Ohio State University. The
    Kranz collection is now available from Nottingham.  The Feldmann
    T-DNA lines and the Scolnik RI lines are now available from both
    stock centers. The Strain Class has also been enhanced by the
    addition of a new Phenotype Class.
  - Bibliographic citations. Many duplicates were detected in the 1-1
    release.  Approximately 300 new references have also been added
    bringing the total number to over 2,800.
  - Updated list of Arabidopsis researchers.  Thanks to those that
    replied before October 15th.  Currently there is information on over
    600 researchers worldwide.
  - Arabidopsis DNA sequences from GenBank and EMBL as of October 15th.
    Currently there are 410 DNA sequences, an increase of 97.
  - BLASTX searchs were repeated the week of October 11th on all
    Arabidopsis DNA sequences against the NCBI non-redundant protein
    sequence database.
  - AAtDB 1-2 uses the new ACEDB 1.8 software.  There are several new
    features including a table editor to easily create tables of
    information.  The graphical sequence display window has also been
    enhanced. Several of the AAtDB Classes have been modified to
    include new types of information.
  - Minor updates and corrections are included for most parts of the
    database.

Availability:

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. A Macintosh version is
currently in beta testing phase.

A printed manual "An Introduction to ACeDB: For AAtDB, An Arabidopsis
thaliana database" is available on request from the MGH group.  While
this manual is not required to use the database many people have found
it very useful as a beginning tutorial for the ACEDB software. 

Bibliographic Information:

All references present in AAtDB 1-2 are available via anonymous ftp
from weeds.mgh.harvard.edu in Refer and Macintosh EndNote format. The
Refer format can be used by many reference database programs. The
Macintosh EndNote library is available as a BinHex 4.0 encoded
self-extracting StuffIt archive. The EndNote library requires 2.1 Mb
of hard disk space.  Both files are available in the aatdb directory.
The refer format file is called refer_aatdb_1-2.txt and the EndNote
containing file is called endnote_aatdb_1-2.hqx. If you convert this
list to other formats we would be happy to make it available.

Retreiving the Updated AAtDB:

Due to the large number of changes included in the AAtDB 1-2 release
we are not using the ACEDB update mechanism. Rather you must
completely replace your previous binary database file as directed
below. The size of the binary database file has not increased
eventhough there is a lot of new information. This was accomplished
partly by reducing the number of BLASTX similarities included in
release 1-2. A higher scoring cutoff was used.

The database binaries and update files are available via Internet ftp
transfer. You only need the AAtDB binaries for Sun, DECstation, and
SGI.  For NeXT workstations you must retrieve the ACEDB binaries from
ncbi.nlm.nih.gov and the update file. All the AAtDB binary and update
files are available via anonymous ftp from either weeds.mgh.harvard.edu
(directory aatdb) or ncbi.nlm.nih.gov (directory repository/aatdb).

Be sure to use binary mode to transfer all the files ending in ".Z".

If you do not have access to the Internet please send us a message. We
will try to get you a copy of the database via a tape. However use of
the network is recommended.

  Sun Microsystems SPARCstations:

Retrieve the file bin.at-sparc_1-2.tar.Z via anonymous ftp from
weeds.mgh.harvard.edu. Be sure to use binary mode to transfer this
file.  You will also need the INSTALL file, but it has not changed
from the 1-1 release. To extract the new version simply issue the
command:

      % source INSTALL


  Digital Equipment DECstations:

Retrieve the file bin.at-ultrix_1-2.tar.Z via anonymous ftp from
weeds.mgh.harvard.edu. Be sure to use binary mode to transfer this
file.  You will also need the INSTALL file, but it has not changed
from the 1-1 release. To extract the new version simply issue the
command:

      % source INSTALL


  Silicon Graphics IRIS:

Retrieve the file bin.at-sgi_1-2.tar.Z via anonymous ftp from
weeds.mgh.harvard.edu. Be sure to use binary mode to transfer this
file.  You will also need the INSTALL file, but it has not changed
from the 1-1 release. To extract the new version simply issue the
command:

      % source INSTALL


  NeXT:

Retrieve the file bin.next.1_8.tar.Z via anonymous ftp from
ncbi.nlm.nih.gov, this file is located in the repository/acedb
directory. Retrieve the file update.at_1-2.tar.Z via anonymous ftp from
repository/aatdb. You will also need the INSTALL file, but it has not changed
from the 1-1 release. To extract the new update files simply issue the
command:

      % source INSTALL

Now remove the database/ACEDB.wrm file. This will cause the ACEDB
software to prompt you to reinitialize the database. Then start AAtDB
with this command "aatdb". Once reinitialized you should add the
update files by first selecting "Write Access" then "Add Update".  See
the installation documentation for more details. Note this will add a
1-1 update that has zero objects. Also the software will prompt you to
increase the size of the database the suggested size is 25,000 blocks
for the binary database file.


WAIS and Gopher access:

AAtDB 1-2 information is also available via the Internet computer
network using either the WAIS or Gopher software. WAIS and Gopher
software is available for most types of computers. For Unix, Next, and
Macintosh WAIS clients use anonymous ftp to think.com, look in the
directory called "wais". For DOS, SunView and VMS WAIS clients use
anonymous ftp to samba.oit.unc.edu, look in the directory "pub/wais".
For IBM RS6000 WAIS client use anonymous ftp to ans.net, look in the
"pub/wais" directory. For Gopher clients use anonymous ftp to
boombox.micro.umn.edu, look in the "pub/gopher" directory.

Here is the specific information on the AAtDB servers:

WAIS:

(:source
   :version              3
   :ip-name              "weeds.mgh.harvard.edu"
   :ip-address           "132.183.190.21"
   :tcp-port             210
   :database-name        "AAtDB"
   :cost                 0.00
   :cost-unit            :free
   :maintainer           "curator at frodo.mgh.harvard.edu"
)


Gopher:

Name=Arabidopsis Research Companion
Type=1
Port=70
Host=weeds.mgh.harvard.edu

For More Information or to Ask Questions:
Contact Mike Cherry or Sam Cartinhour at FAX number 617-726-6893 or
via electronic mail at curator at frodo.mgh.harvard.edu.

Sam Cartinhour, J. Michael Cherry and Howard M. Goodman
Department of Molecular Biology, Massachusetts General Hospital
Department of Genetics, Harvard Medical School




More information about the Arab-gen mailing list