Popping On-line With the Maize Genome Sybase Database
maryp at ligate
Thu Jan 6 16:46:46 EST 1994
THE MAIZE GENOME DATABASE IS AVAILABLE ON-LINE
MaizeDB, the full-capability relational Sybase database for maize
genome data, is now available for on-line access. MaizeDB is part of
the Plant Genome Database, which is under development at the National
Agricultural Library and which has the goal of encompassing information
on all plant species in a single database.
MaizeDB contains a broad array of information on maize genetics and
breeding, integrated in a relational structure using Sybase software.
Current categories of information include loci, alleles and other
variations, gene products, stocks, maps, probes, phenotypic traits,
references, and people. In the next few months we expect to add
information on pests and stresses and results of quantitative trait
Certain data which you may find interesting to explore:
Updated BNL and UMC maps.
Current lit, attached as we identify them.
Genbank numbers (attached to allele, locus, probe)
Addresses of persons for clones/probes, mail, phone, etc
(addresses are not necessarily current;
please be patient pending a systematic update).
Southern blot (gel) pattern, data
All interested users may access MaizeDB without charge. Our sole
condition is that you inform us if you see something in either the
content or format of the database that needs correction or
improvement. You may leave notes directly in the Sybase version of
MaizeDB (under the "/" at top left corner of database forms; see also
Hints and Tutorial) or contact us as indicated on the next page. We
know there will be some things, chaotic or cryptic to the "naive" user,
that we have lost the capacity to recognize because we have forgotten
the problems or have explained them away to each other. We
continuously upgrade "helps", and will incorporate suggestions from you
at any time, but especially need suggestions now, in the early phases
of accessibility. Is the first screen you see sufficiently clear? The
second? Are the "helps" intuitively comfortable? Do you find
information where you expect to?
Guests may search two data formats: gopher flat files or the Sybase
database, Maizedb. As a guest, both formats are accessible to you
whether you use Gopher or directly log into
teosinte.agron.missouri.edu, the machine where the data are stored. For
direct logins, USER NAME is 'guest', PASSWORD is 'corncob'. You may
mail yourself data retrieved by Gopher or Sybase searches.
DATA AVAILABLE TO GOPHER SEARCHING
The MaizeDB Gopher server is updated regularly from the underlying
Sybase database and allows RAPID, USER-FRIENDLY full text searches of
most portions of the data. The Gopher access lacks the robust query
and browsing capabilities of the full-featured database, but it is
sufficient for many purposes. If one searches for "ht1" under the Loci
category, for example, Gopher will respond with a list of "documents"
containing that character string; those documents can then be viewed
one by one. Guidelines on formulating searches in Gopher are contained
under the menu option "Gopher Information". Other menu choices include
links to other Plant Genome gophers and to other biology gophers.
A. TYPE OF COMPUTERS AND CONNECTIONS REQUIRED
You may access the data using a MacIntosh, a PC or a Unix computer but
you will need to be connected to the Internet. Intervening modem
connections will work, but do not support an X-windows (this is not the
same as Windows) display of the Sybase database. A major advantage of
X-Windows is that you will be able to use a mouse to navigate. You do
not need to use an X-Window, but may use keyboard commands. The
keyboard commands are relatively simple and may be obtained when you first login.
B. GOPHER: GOPHER AND SYBASE SEARCHES
You may access our gopher client by any of the below:
(a) login on teosinte.agron.missouri.edu as described below
(b) installing your own gopher (client) software
(c) connecting to some other gopher client. CAUTION: If you use gopher
software installed on a system with an IBM 3270 emulation (which many
university mainframe systems use), the Gopher "Guest Access" option to
the relational database will not function correctly.
GETTING GOPHER SOFTWARE
You will need the gopher client software. Software for Unix, MacIntosh,
and PC computers is available without cost by anonymous ftp (file
transfer protocol) from:
The software and help files are in the directory:
For anonymous ftp, the user name is "anonymous" and the password is
your email address: yourname at yourmachine.etc. Downloading the software
and installation is easiest if you have access to a campus computing
services desk, or a systems administrator or can get help from a
The program may be modified so that it automatically calls up the Maize
Genome Database gopher at "teosinte.agron.missouri.edu" or
"184.108.40.206". Otherwise, you will first connect to the University of
Minnesota gopher, and you will be able to access the Maize gopher from
the listing of gophers that are located in Missouri (USA).
C. DIRECT LOG IN: GOPHER AND SYBASE SEARCHES
(1) If using an X-window, you need to allow teosinte (the machine where
MaizeDB resides) to open a window on your machine:
- Unix: type xhost + teosinte.agron.missouri.edu
- MacIntosh, PC: set the xterm appropriately on your X-Windows software.
(2)Establish a telnet connection to: teosinte.agron.missouri.edu
There are several ways to do this, depending on your computer and
software. On Unix machines, at the prompt, type:
telnet teosinte.agron.missouri.edu If you have a MacIntosh or
PC you will find software helpful.
(3) Login as 'guest' and use password 'corncob'; if you are successful,
a list of options will appear as follows:
1- VT100 Version of MaizeDB
2- X-Windows Version of MaizeDB
3- MaizeDB Gopher (vt100)
4- Set Erase Character to ^H
5- Help for X-Windows
6- Help for Sybase
7- Mail Sybase Tutorial to Yourself
For relational (SYBASE) searches:
a. Choose selection #2 "X-Windows ..." if you have an X-Window
(this is not the same as Windows)
b. Choose selection #1 "VT100 Version of MaizeDB" if you are not
using an X-window OR if you are connected by an intervening modem.
Refer to the list of keyboard commands (Option #6, Help for
Sybase) for navigating in a vt100 emulation.
For GOPHER searches: choose selection #3 "MaizeDB Gopher (vt100)"
For guidelines on querying and navigating around MaizeDB, refer to option 7:
"Mail Sybase Tutorial to Yourself.
MaizeDB Development Team:
Ed Coe (ed at teosinte.agron.missouri.edu)
Denis Hancock(dhancock at teosinte.agron.missouri.edu)
Mary Berlyn(mary at fetalpig.biology.yale.edu)
Patrick Byrne (byrne at teosinte.agron.missouri.edu)
Georgia Davis (gdavis at teosinte.agron.missouri.edu)
Stan Letovsky (letovsky-stan at cs.yale.edu)
Mary Polacco (maryp at teosinte.agron.missouri.edu)
Marty Sachs (msachs at uiuc.edu)
Faxed information and queries may be sent to (314) 874-4063. If you
are unable to use the email addresses as given,
teosinte.agron.missouri.edu is also known as 220.127.116.11.
Phone contact for help: 314-882-1722 (Denis Hancock).
More information about the Gen-link