from Dave Matthews, updated 2/95
HOW TO ACCESS GRAINGENES, IN ALL ITS GUISES
USER INTERFACES TO GRAINGENES AND ASSOCIATED DATASETS
The GrainGenes database is currently available in five formats: ACEDB,
Gopher, World Wide Web (WWW), CD-ROM, and electronic mail. The ACEDB
interface supports the most powerful query strategies and provides
interactive graphical displays of the genetic maps. On the other hand, for
many people the Gopher and WWW formats are easier to access, as well as
easier to use.
In addition, the Gopher and WWW formats include not only the core
GrainGenes dataset but also an equally large amount of information that is
in free text format or in structures other than that of ACEDB. Many of
these additional datasets are searchable online, and some are also available
for downloading in their entirety. They include
Annual Wheat Newsletter, volumes 37 - 41
Catalogue of Gene Symbols for Wheat
Commercial Wheat Cultivars of the US, an electronic monograph by Ken Kephart
HMW-glutenin subunit data for 1500 wheat cultivars, from Bob Graybosch
Wheat performance evaluations, organized by Ken Kephart
Wheat quality evaluations, from Bob Graybosch
The Gopher/WWW version of the core GrainGenes dataset is also updated
more frequently than the official release of the ACEDB version. Thus if for
example the current release version is 1.4, the Gopher "Search the GrainGenes
database" item will be version 1.4+.
The CD-ROM and email interfaces provide subsets of the WWW and Gopher
functionality, respectively.
ACCESS METHODS
For sites that are well connected to the Internet, the Gopher and WWW
formats of GrainGenes are the easiest to access, requiring only
- a direct network connection from your personal computer to the Internet
(no password needed), or
- a modem connection to a Unix or other Internet host running Gopher or WWW
software.
The ACEDB format of GrainGenes provides its graphical, mouse-based user
interface via the X11 network protocol. ACEDB access requires
- a Unix machine running the ACEDB software, or
- a direct network connection (as opposed to a modem connection) to such a
machine, and X11 software for your personal computer.
GOPHER
Identical copies of the GrainGenes Gopher server are maintained at two
independent sites, one at Cornell University, Ithaca, NY, and the other at
the National Agricultural Library, Beltsville, MD. If one is unavailable,
due to unforeseen but over the long term inevitable circumstances, simply
switch to the other one:
host greengenes.cit.cornell.edu, port 70
host probe.nalusda.gov, port 7002
The NAL has also established a Gopher server that allows searching all
the USDA-supported plant genome databases: GrainGenes, AAtDB (Arabidopsis),
MaizeDB, Soybase, TreeGenes, RiceGenes and SolGenes (Solanaceae). This
Gopher server is listed in the GrainGenes Gopher menu "Other plant genome
Gophers", or it can be accessed directly at
host probe.nalusda.gov, port 70.
WORLD WIDE WEB
The World Wide Web is a kind of super-Gopher system, with all the
features of the Gopher and more. Hypertext links, live querying of ACEDB
databases, and interconnections between heterogeneous databases are among
its greatest strengths. Those who have direct access (TCP or SLIP) to the
Internet can connect to the WWW by using the "Netscape" or "Mosaic"
software, which can be obtained by anonymous ftp from ftp.mcom.com or
ftp.ncsa.uiuc.edu, respectively. Those who have lower-speed access via a
Unix host can use the Unix WWW client program "lynx".
The address (URL) for the GrainGenes WWW page is: http://wheat.pw.usda.gov/
graingenes.html. This page contains links to
- the GrainGenes Gopher and everything in it,
- "GrainGenes WWW", a hypertext version of the core GrainGenes dataset,
supporting nearly all of the query functions available in the the ACEDB
version,
- fully formatted, illustrated documents available nowhere else but in print,
such as CIMMYT's "Wheat diseases and pests",
- other WWW servers of interest to GrainFolk.
"GrainGenes WWW" is provided by the Agricultural Genome Information
Server at the National Agricultural Library. This server also purveys
WWW databases for many other species. It can be reached at
http://probe.nalusda.gov:8000.
ACEDB
Copies of the ACEDB version of GrainGenes, for running on a Unix host,
can be obtained from the National Agricultural Library's anonymous ftp
server, probe.nalusda.gov, in directory pub/graingenes.
Users who have no Unix machine but do have direct network access (TCP/IP
or SLIP) and X11 software for their personal computer may request a
GrainGenes ACEDB account by writing to Dave Matthews at the address below.
X11 software for Macintosh includes MacX (Apple Computer) and eXodus (White
Pine Software); for MS Windows there are eXceed/W (Hummingbird
Communications) and DESQview/X (Quarterdeck Office Systems) among others.
CD-ROM
The January 1995 release of the Plant Genome Database CD-ROM contains
not only GrainGenes but also databases for Arabidopsis, maize, soybeans,
forest trees, rice, Solanaceae, and Chlamydomonas. It provides a WWW-like
interface to the core databases using Mosaic, and runs on Windows,
Macintosh and Unix machines. To order it, contact
Plant Genome Data and Information Center
National Agricultural Library
4th Floor
10301 Baltimore Blvd.
Beltsville, MD 20705-1513
or send your request via email to pgenome@nalusda.gov.
EMAIL SEARCHING
The same database search mechanism that is available via Gopher can also
be accessed by electronic mail. For instructions send the message "help" (in
the body of the message, not the Subject line) to waismail@probe.nalusda.gov.
HELPLINE
The NAL has set up a helpline for assistance in accessing and using the
plant genome databases. Help is available either by electronic mail to
pgenome@nalusda.gov, or by telephone at 301-504-6613. GrainGenes-specific
questions should be directed to
Olin Anderson
oandersn@pw.usda.gov
or
Dave Matthews
matthews@greengenes.cit.cornell.edu
.