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.

tcarver@hgmp.mrc.ac.uk