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 clients.
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, publisher.
-- 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 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 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: ftp://ftp.ebi.ac.uk/pub/databases/ace/aatdb ftp://ncbi.nlm.nih.gov/repository/aatdb/aatdb.3x ftp://weeds.mgh.harvard.edu/aatdb/aatdb.3x
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; ftp://ncbi.nlm.nih.gov/repository/aatdb/MacAAtDB ftp://weeds.mgh.harvard.edu/aatdb/MacAAtDB
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