The Wisconsin
Package Interface (SeqLab, formerly WPI) is a windowing environment layered on top of the command
line interface which you used with GCG in the past. In contrast to personal computer windowing
systems, which use Microsoft Windows or the Macintosh Finder to display windows, SeqLab uses
the so-called X-Windows system to send data
from the host computer to your display. Therefore, you need an X-Windows display, such as an
X-terminal, an X-server running on a microcomputer, or a workstation that runs X-Windows, if
you want to use SeqLab . You may have used X-Windows already to display GCG graphics on the screen.
As in the GCG command line version, SeqLab graphics can
be produced on various output devices such as printers, plotters and the screen.
SeqLab is neither a replacement for GCG, nor does it offer computational programs which are
not available in the GCG command line version other than its unique editing facilities
. SeqLab adds the convenience of window-oriented software usage, to launch, administer
and manipulate sequence and sequence-related data. Specifically, the edit mode of
SeqLab allows a very convenient multi-sequence editing and also implements viewing of features
in sequences if retrieved from the data bases. The normal operation of SeqLab does not
change or alter the way how results are produced by the GCG package.
IMPORTANT NOTE: To run SeqLab, your PC or Mac must be connected to the campus network
and run sufficiently fast. A colour screen
of at least 16 inch and high resolution is recommended. Personal computers running X-Windows
are known to require well more than 16 MByte of RAM (32 MByte recommended in Windows 3.1/Windows
95, and 64 MByte in Windows NT).
It will be important to note that version 9.x of the GCG package has the editing software
built-in that demands the use of X-Windows . If you used WPI only rarely before,
you might need SeqLab very much more in the future. Refer to the
SeqLab section for details on this very important feature of the GCG package. The windows
described below - Main List , and Output as well as Job
Manager - are supplemented by an additional mode called Edit mode which
allows to perform the same operations but while displaying sequences simultaneously. If you have
eventually used Steve
Smith's GDE program, you will recognise that SeqLab's edit mode is very similar
because it is derived from this system.
Briefly, you may use the "SeqLab edit mode" system to edit, cut, paste, select and manipulate
sequences, fragments of sequences and groups thereof. The use of color allows you to discriminate
amino acid properties, similarity information or strand orientation. If sequences are retrieved
from the database, Seqlab has a schematic feature display modus which displays recognized features
schematically. Results from multiple sequence alignments may be obtained after selecting regions
with the mouse, and pasted back to the editor after completion of the alignment. This special
mode is explained later in the
section on multiole sequence alignments .
In contrast to the GCG command line interface, SeqLab
allows you to define and store the set of sequences you want to work with. I.e., you no longer
need to remember which sequence files are of current interest. SeqLab will collect sequence files
for you when you 'add' them to the list. If you start SeqLab for the very first time, this list
is empty. The pull-down of the menu 'Sequence' allows you to 'Add' sequences to the list from
either
'Adding' sequences to the "main list window" neither alters
sequences nor changes their location. The purpose of 'adding' sequences to the list is just to
register the sequences within the SeqLab interface to utilise them more easily.
With the GCG
command line version, you type the name of a program, feed it with parameters, and wait for the
completion of the program. In contrast, SeqLab allows you to continue to work while another program
is running in the background. This is different from the 'batch' option. The programs are executed
like the ones you started by typing the command. In a way, SeqLab does the command typing for
you. There are several types of output: The results may be viewed or processed according to their character, e.g., a graphics file
can be plotted as a figure, and a list of file names can be added to the "main list window".
The "output
manager window" allows you to trigger these actions, including deletion and other file handling
commands.
Instead of waiting for a result, SeqLab allows
you to continue to work while another program is running in the background. The "job manager
window" lists the execution status of all the jobs that you have started. Programs running in
the background may generate output, in particular if they do not run as expected. Error messages
are displayed in the "job manager window".
SeqLab
allows you to have more than one window open. Instead of sequentially opening and closing all
the windows, you should try to keep at least the "main list window" and the "output manager window"
open simultaneously. If your screen is too small, try to work with minimised or iconized windows.
Given the proper configuration of the environment
, it is sufficient to type
% seqlab &
(The "&" is a symbol that lets you continue to use
this session for command-line input as it executes the program before this symbol in the "background".)
SeqLab can be configured in a sophisticated fashion. In contrast to the GCG command line interface,
SeqLab uses so-called "sets" of sequences which hold additional data such as start/end and other
information.
If you plan to use SeqLab in parallel to the GCG command line interface, it is important
to remember two important items:
================================= Begin Exercise 1
A small WPI exercise: Run a 'fasta' search of a database sequence against the SWISSPROT
database.
Proceed as follows: ================================= End Exercise 1
Small Computer Screens and SeqLab
If you feel that the screen of your personal computer is too small, you can either configure
your X-Windows server program to display scroll bars or start SeqLab with smaller characters
(recommended) to get a smaller window size. The latter can be done by typing
% seqlab -small
SeqLab Timing
The option to run jobs in the background may affect the timing of your session. WPI itself will
time out if you do not work for an extended period of time, i.e., you need to restart SeqLab
after returning from lunch or similar elongated pauses. At some sites system managers have configured
a time out for idle sessions on the entire computer system. If you did not save your current
list in the "main list window", this list will be lost if your session times out. Therefore,
better save your working list occasionally.
[next page] , or [overview] , or [table of contents] Purpose of SeqLab
The SeqLab Multiple Sequence Editor (SeqLab "edit mode")
SeqLab Details: The Concept of "Lists"
More SeqLab Details: The Concept of an "Output Manager"
Even more SeqLab Details: The Concept of a "Job Manager"
Interaction of SeqLab Windows
Starting SeqLab
SeqLab and the User
JAMF source file: session.jam
Next file in HTML:
'Setup of the GCG Plotting Environment '