

                            Jemboss 

Using the Interface

    The Jemboss window is split into three panes. On the left are the menus
and alphabetical scroll list, for selecting the emboss applications. The
menu splits the programs into group with the name of the program and a short
description of what the program does. If you are already familiar with the
names of the programs the scroll list (bottom left) may be quicker to use.

    The central pane in the Jemboss window displays the program parameters
that the user would be presented with if running EMBOSS from the command
line. The user will need to fill in this and has the opportunity to change
any default parameters. To obtain more information and help for an
application there is a "HELP" button at the bottom of each program form.
Next to this is a "GO" button which will set the application running.

     Jemboss has two separate file managers, a local one, located in the
right hand pane of the interface, and a remote (or server) file manager. The
local file manager can be opened using the arrow in the bottom right hand
corner of Jemboss. The remote file manager is displayed in a separate window
when selected from the "File" menu option. Both these can be used to
transfer files to the input field of an application, by dragging and
dropping them. Data may be displayed and edited by double clicking on a
file.

     Jemboss incorporates the 100+ applications of both the EMBOSS and
EMBASSY packages.  On initial program selection, the program form will
appear. An input file must be entered into the sequence filename box, or
pasted into the appropriate field. Various parameters may be selected from
the form. Advanced options may be selected from an additional form.
Parameter selections may be regulated according to the input sequence, with
unobtainable options shaded out, or omited from the form altogether.
Application output files appear in a separate window, and can be saved to
the local disk.

     Previous outputs may be accessed from their store on the server. The
command line  used to construct the analysis is displayed, and the output
data may be obtained, edited and saved. Unwanted analyses should be deleted
from this table.

    The job manager is used in the client server mode. It is found at the
bottom of the the EMBOSS program form. The middle button can be used to look
at all batch jobs submitted in a session. If a application is designated
batch then it will be sent to a batch queue. If a job is designated
interactive then it will be run interactively and the client will wait for
the results to be returned to the users screen.


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tcarver@hgmp.mrc.ac.uk

