Jemboss File Manager
Keywords: java, biology, bioinformatics, EMBOSS, GUI, Jemboss, computational biology, sequence analysis, interface

Jemboss is developed by the EMBOSS team and is a graphical interface to the European Molecular Biology Open Software Suite, EMBOSS. Jemboss incorporates the 200+ applications of both the EMBOSS and EMBASSY packages.

## Quick Start Guide

On the left of the main Jemboss window are the program menus. Programs are grouped by their type of analyses and these groups form the menu names. Programs can be sub-divided into further categories and then the program name with a short description of the program is given. Alternatively if the name of the program known the quickest method is to select it using the 'GoTo' field and the alphabetical scroll list.

The central pane in the Jemboss window displays the program parameters. 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. There are also popup tooltips for the parameters that appear if the mouse is held over the parameter text.

Advanced options may be selected from the form if an advanced options button appears next to the 'GO' button. 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 to monitor the status of batch processes. These are those EMBOSS applications that are computationally intensive. Instead of waiting for the results these processes are submitted as batch, which frees the interface for other analyses to be carried out. The middle button at the bottom of the Jemboss window 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 Jemboss will wait for the results to be returned to the screen.

This product includes code licensed from RSA Data Security.