This BioCompanion copy is a demo version .
This section is intended for the interested researcher who is new to the field, and wants to
get familiar with the startup procedures to run molecular biology computing programs. This session
assumes that you have access to a computer and work in a networked environment to access this
computer remotely.
NOTE:
The following instructions make use of software packages which
are copyrighted or licensed by software providers and need to be purchased and installed separately.
If you start the program package's environment, or review the program's
output file, you will find the corresponding copyright and acknowledgement notices. It is of
all user's interest that these notices are carefully read and kept in mind in order to grant
honours to those who deserve it.
NOTE:
The following instructions make use of databases which are usually
placed in the public domain. The rate of updates is steadily increasing. Make sure that you always
use the latest database version you can get hold of. Remember to check with your software manager
what the latest database release or description was if you publish data referring to sequence
databases.
NOTE: The programs and data are brought to you by people who work hard to get you the best quality
and performance. These installations are not free of cost, even if you might not need to pay
fees directly. It is required that you acknowledge these organisations properly in publications
in order to ensure their future existence.
The standard environment in the past was a text terminal or screen
on a suitable equipment (PC, etc.) which displayed text on an area of
80x24 characters.
Do you have a text-only screen or can it run line-mode graphics only?
Depending on the properties of the equipment attached to the screen or the capabilities of
the program, it may be impossible to visualise graphics on the screen . If you
are afraid that this is the case, contact your system or site manager for details. If you do
not know whether this is the case, ask your colleagues or try the graphics test output from the
GCG package as described below.
On personal computers, you use to have a screen which displays graphics, windows, buttons etc.
as generated on your own computer. Depending on the capabilities and resolutions of your system,
this might be on a 9 inch black and white or a 21 inch colour monitor. Frequently, we use terminal
emulators which open a window on the PC or Mac screen that behaves as if it were a terminal,
i.e. the functionality of a screen connected to the remote computer is emulated (or
pretended) to be the same as a terminal. Terminals in the 80's did not have a mouse or a graphics
computer interface. Therefore, the mouse will not operate even if you run a terminal emulator
on the PC which does have a mouse. This is because the functionality of such an input device
is not part of the terminal principle.
Graphics as you know it from the PC or Mac are also unknown in the terminal principle, as images
are computed locally, whereas the terminal is a program which runs already, and takes text commands
from the remote system to display the result as text. The only images you may expect are special
commands which cause single lines rather than text to be displayed. Eventually, text and graphics
in this mode will be shown in up to four or eight colours, very much like the plotter outputs
you might have seen from measuring computers in the laboratory.
The most common types of text screens are called vt100-type screens. Even
if you run the #seqlab SeqLab
(formerly, WPI) product from GCG, a text window is advantageous to have. Depending on your local
setup, it might even be essential to log in via a text terminal first in order to launch the
X-Windows system (see below).
If your screen behaves strangely ( "unknown terminal" or similar
messages) refer to the section "Common Problems"
in order to set the required parameters correctly.
NOTE: The following does not need to be configured if you use a text-oriented or line-mode-graphics
display. If you do not know what this means, read this
section carefully.
In order to achieve a more user-friendly usage of remote computers, a system has been designed
which enables the remote computer to generate a window (like your PC does it) but send this window
across the network in order to display this window on your PC or Mac screen.
This is far from trivial as your PC or Mac used to display only locally created windows so far.
However, you might decide to go for this route and launch a program which is permanently listening
on the network whether a remote computer wants to send a window to your computer which must be
displayed. This system is called X-Windows. The prerequisite for the local desktop to be able
to display these windows, therefore, is From these prerequisites it is obvious that a sufficient local compute and display setup must
be provided before X-Windows can be used as a standard setup. A major drawback of the method
is that the windows as they come in via the wire will most frequently not have the look
and feel as the locally generated windows. This affects the shape and layout of windows,
scroll bars, boxes and menus.
It is suggested that you run a powerful, high-end PC with a reasonably sized monitor
(17 inch at least) before thinking of using X-Windows. The alternative were a second
screen on the desktop which acts as a X-Windows terminal . This is a device
which is only used for display of remote images and, therefore, does not run any of the local
desktop applications you are used to. Cost/benefit evaluations should be performed carefully
before purchasing such a device.
Recommendation:
The Wisconsin Package Interface (which used to be the ancestor
of SeqLab ), and Seqlab itself are programs
that need X-Windows and may benefit your working performance positively in a molecular biology
environment. Starting with GCG version 9 (1996/7), it is required to run X-Windows if you want
to benefit from the multiple sequence features as provided in SeqLab.
As mentioned above, if you use local area networks
, it is possible to send windows across the (local) network. To use the X-Windows system, your
program which listens on the network for incoming windows (the so-called X Server )
must be running on the local PC or Mac. If this is not the case, start it and maintain it running
during all time which you want to use X-Windows.
The main benefit of X-Windows is that you (the researcher) will have a nice user interface available
locally rather than on the remote host where the corresponding molecular biology
programs have been started. To actually receive the windows, you must tell the host you are logged
in to send the graphics window to your terminal or computer, i.e.,
you must know the name or IP address of the terminal or computer where you want to display the
graphics. Depending on your set-up, this data might have been communicated automatically at the
time you started your session, or you need to define this manually.
The variable which the host needs to know (and frequently does so automatically) is called DISPLAY:
% setenv DISPLAY host.domain.country:0
Example:
SECURITY ADVICE: Do not allow anybody to send windows to your screen. Potential security risks
of unintended data exposure have been exploited in the past which strongly suggest that you authorise
only these hosts for access which are required.
[next page] , or [overview] , or [table of contents] Standard Environment
Material and Methods
Setup of the Text Screen
X-Windows principle
Usage of X Windows
% setenv DISPLAY biodos.embnet.unibas.ch:0
Refer to the description above for prerequisites
of this configuration when using personal computers.
Depending on your setup, X-Windows applies
a security procedure which restricts the sending of windows around the world. Therefore, you
must "allow" your terminal or computer to display the window on your screen (as described in
section "Common Technical Problems" ). If this is not
the case, the error message is
Cannot open display
Refer to the section "Configuration Problems"
to escape from this situation.
JAMF source file: session.jam
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'Standard Programs'