Jemboss is the new Graphical User Interface (GUI) to EMBOSS, designed to facilitate the use of programs. It is written in the programming language Java, enabling the interface to be used in both PC and UNIX environments. Unfortunately the older Mac platform does not support this GUI, and only Macs running MacOS X can run Jemboss.

The interface has been written in collaboration with the EMBOSS team. Jemboss was released as a beta release in January 2002 and has been in wide use since then, not least on many of the training courses. There have been substantial changes, and improvements in the functioning of the interface. If, however, you spot something that doesn't work, or you have any suggestions, please let us know on the web form.

A web launch tool (Java Web Start) must be installed on the client (i.e. user's computer) before Jemboss can be accessed, to allow this Java program to be downloaded and launched from the web. The client computer should already have Java 1.3 (or higher) installed. This will automatically be the case for most proprietary PCs and many UNIX systems.

Follow the links on the Jemboss home page  to the Java Web Start download that is required (i.e. for the PC, UNIX, Linux, or Mac OS X).

Launching the Interface

Goto the Jemboss home page. Click on Launch Jemboss to open the interface. It may take a few moments for the program to load when Jemboss is first launched. This is because the Jemboss client is downloaded to the local machine. After a short delay, in which a window requiring a username and password may appear, the Jemboss interface will be displayed. If Jemboss is being run remotely from the HGMP-RC, the username and password is a mandatory requirement for running applications. The interface may be downloaded and browsed, however, without logging in. If the "exit" button is pressed, the entire Jemboss launch will be terminated.

Subsequent launches will proceed much more quickly, as the relevant files will be stored on your computer. However, after each new Jemboss update, the lastest version will once again be downloaded to your machine, and the new files will replace the old ones.

On the left hand side of the interface, EMBOSS programs are grouped into menus based on program categories. Clicking on one menu with the mouse button will display sub menus and finally the EMBOSS applications. These programs are listed together with a short description, enabling the user to best choose the most useful program for the purpose. Programs are also listed in alphabetical order in a scroll menu also on the left hand side of the interface window. This window is linked to the Go To field just above it, in which the name of the required application may be typed. Programs are highlighted in the scroll menu on typing of the first unambiguous letter of their name. They may then be selected by clicking on them once with the left mouse button or pressing return.

The program form for the selected application appears in the main panel. The program name is shown in red at the top of the form, followed by the short description defining its function.

File Managers

File management in Jemboss allows the transfer of files between the local client machine and the remote (server) machine. The local file manager can be displayed on the right side of the main window and can be seen by clicking on the (red and blue) arrow icon at the bottom right hand corner of the window. Clicking on this will open the local file manager to display all files in the users local home directory. This local home directory is chosen by default when the program launches. For those who do not wish to work in this directory, it may be altered using the Preferences menu on the Jemboss tool bar. Select Advanced Options and type in the path for the desired directory. This path must then be set before the local home directory is altered. Currently this procedure is necessary for every new Jemboss session. Pressing the reset button at any time will revert the file manager back to the default directory.

The Local Home Directory path represents the location of your files on your computer. Thus they may be accessed using this information at any time without Jemboss.

All files and folders in the local directory are displayed vertically in alphabetical order, much as they would be in other file management applications. Folders may be opened by clicking either on them, or the magnifying glass icon to the left of them. A text file may be edited by double clicking with the left hand mouse button on the filename to display the contents. After editing, the file may be saved under the same, or a different filename.

If Jemboss is running as a client using a remote server, then remote files may also be accessed. This is achieved by using the File menu on the Jemboss tool bar and following it to the sub menu Local and Remote Files. If Jemboss is being used as a client run from the HGMP-RC, the remote file list appearing in the separate window will reflect all data in the HGMP-RC home directory. The default view for this file manager displays local files at the top, and remote files at the bottom. Your remote files may also be replaced by the contents of your scratch directory, if you are using Jemboss from the HGMP-RC.

By default, the local/remote file manager launches as a vertical split window. This may be altered to a horizontal split, if this view were preferred. Should the file manager be closed and then re-opened during a single Jemboss session,the manager will retain the preferred view.

Files may be transferred between file managers using the drag & drop technique. On transferring a file, a remote file must be placed on top of an existing file or folder in order for it to be saved onto the local disc, or vice versa.

A file management pop-up menu may be accessed by a single click on the right hand mouse button in either file manager. The file manager may be refreshed, and files renamed or deleted by selecting a file and then the appropriate option. A new folder may also be added to the existing data. In this case it is first necessary to highlight the directory in which you wish to create your new folder.

Running an Application

Sequences may be added to the program in a number of ways. They may be entered straight into the filename box using the EMBOSS convention Universal Sequence Address (USA). Files may be transferred from local or remote accounts by the drag & drop method: the relevant file is transferred into the filename box from either file manager; sequences may be pasted into the filename box by selecting the paste option. Sequence properties may also be entered using the Input Sequence Options menu. This latter option allows you to choose the database from which you would like to retrieve your sequence, but you must ensure that you TYPE the sequence identifier or accession number INTO THE SEQUENCE FILENAME BOX. The HGMP-RC has a vast resource of databases from which you can choose. If you are using Jemboss from an alternative remote server, different databases may be available to you.

If no sequence options are specified, EMBOSS will calculate them for the sequence provided. However, sequences in the formats raw and Intelligenetics must be specified, as the program cannot understand these formats initially.

Some programs have a LOAD SEQUENCE ATTRIBUTES button. This is required when the parameters, such as gap penalties and matrices, used by a program depend on the sequence given. Once the sequence is entered and this button is selected then only the parameters relevant to your sequence will be used. This may also affect some of the default parameters that are used. Where this option is available, it should be deployed for each sequence entered.

Those parameters which are not relevant to a particular analysis are greyed out. If you would prefer not to show the redundant (for that sequence) parameters, deselect Shade unused parameters from the Advanced Options menu of the Jemboss window Preferences option on the toolbar. This preferred view will remain throughout the Jemboss session, but must be reconfigured on every new Jemboss launch.

Different applications will have various options available on the program form. Select, or fill in these options as required. If an "Output Sequence Name" is entered, your output will automatically be saved onto the server, using that name. If you do not enter one, however, the file is automatically saved onto the HGMP-RC server using a default output name. Further parameters may be found in the Advanced Options section.

Hit the "Go" button to run an application. If you do not understand the significance of a parameter option, use the mouse over facility to see of there is extra help available. If this is the case, information will appear on screen in a purple box. Alternatively, click on the information icon at the bottom of the page, which will take you to the program documentation.

Job Manager

Programs are run, by default, as either a batch, or an interactive process. Interactive applications disable Jemboss whilst they are running, and the results, which should be achieved in a matter of seconds, will pop up on the screen. Batch mode is the default for jobs that are particularly computing intensive, and may take a while to run. In this instance, processes are logged for each session by the Job Manager, which is found on the bottom bar of the Jemboss window. The job status, i.e. whether it is running or has been completed, is displayed on the Job manager bar.

To view the results, the job manager window can be displayed by clicking on the bar. The left hand side of the window displays all batch jobs run in a single session, with the name of the application run, the time and date of the run. Applications may be highlighted, and, if the run is complete, the parameters used in the program will appear in the right hand pane of the window in command line style format. If the process is still running, the word "pending" will appear in this pane. Click on the Display button to view the results.

The job manager will refresh by default every 15 seconds. The frequency can be changed by altering the time limit in the Advanced Options sub-menu of the Jemboss Preferences menu to a minimum of 5 and a maximum of 60 seconds. Refreshing the job manager involves calls to the remote server, so if the network is poor, it may be a good idea to alter this automatic process to refresh after a longer period of time. The Job Manager also contains a refresh button on the toolbar, which allows the user to refresh the page manually.

Processes may be discarded from the Job Manager at the user's descretion, by highlighting the relevant application results, and using the Delete button, which will discard the process entirely. Several adjacent jobs may be deleted at once, by holding the shift key down and highlighting each job using the cursor keys or the mouse. If jobs are not directly over or below each other, then the control key should be used. On deleting more than one job simultaneoulsy, a warning mesage will pop up, detailing which processes have been selected. If this is correct, proceed by clicking on "yes". Clicking the "no" button will bring you back to the job manager window.

No jobs will appear in the job manager at the start of a new Jemboss session, although the results remain saved on the server. The job manager window can be closed at any time by using the File menu, clicking on the small cross in the right hand corner of the window, or using the shortcut CTL + E.

Results Window

The results of a program are displayed in a separate, tabbed window on the screen. If the job has run successfully, the results will be displayed in a tab with a default file name. This is usually the name of the first sequence on which the analysis has been run. A second tab is labelled cmd and contains all command line parameters used to communicate the specific requirements of the analysis to the EMBOSS program. This information may be useful should you wish to repeat an analysis at any time. Further tabs contain the contents of the input files. Should the program run not have been successful, a tab displaying an error message will appear in the window. If there is no error message, but there is no results tab, it is likely that something has gone wrong with the input files, and the application could not run.

All results are stored on the remote server and remain there until deleted by the user. The log of results is accessed by using the Saved Results on Server option under the File menu in the Jemboss window. The left pane of the resulting window details all applications run. Use the File menu to list the applications either in alphabetical order, or in the order in which they were run. On highlighting the name of an application, the command line parameters will appear in the right hand pane of the window. The results of the process may be displayed using the Display button at the bottom of the window or by double clicking on the program name. To delete results, highlight the program, or programs, you wish to discard and click on the Delete button at the bottom of the saved results window. This window may be closed at any time by using the File menu, clicking on the small cross in the right hand corner of the window, or using the shortcut CTL + E

Saving Results

Results are automatically saved to your specified Local Home Directory. If you have not specified a path for this, then it will be saved to the default directory. Alternatively, you may select your own filespace on the local computer in the save window. Type the filename into the appropriate field. Text files may be appended with any extension, but Jemboss graphics must be saved with the extension .png to allow them to be recognised later. Once you have saved a file, the local file manager with automaticaly update, to show your new file.

The Save window defaults to a display of files with the suffixes .fasta; .msf; .gcg; .embl; .swiss. Should your file have a different extension, it will not be displayed immediately, and you will need to alter the Files of Type menu to read "All Files".

Graphics files with the extension .png may be viewed both in the Jemboss interface and also in your web browser.

Sequence List

This window allows the user to store their commonly used sequences. A sequence file can be dragged from the file managers into this window or a database entry (e.g. sw:pax6_human) can simply be typed into the table. The files then can be dragged and dropped back into the program sequence fields in the main Jemboss window when required.

An EMBOSS list file contains "references" to sequences, for example the file could look like:

Selecting 'List' in the Sequence List table will automatically prepend the filename with '@' (indicating to EMBOSS that this is a list file) when it is dragged into a application sequence field.

If the 'Default' column is selected then this sequence will automatically be the input sequence used when an EMBOSS application is chosen.

The sequence length can be calculated by selecting the sequence and clicking on 'Calculate sequence attributes' under the 'Tools' menu. The sequence start and end positions will then be displayed.

Saving the sequence list, between Jemboss sessions, is not done automatically. Go to the tools menu and select 'Save Sequence List' if this table is to used in the next Jemboss session. This simply creates '.jembossSeqList' file in the user's home directory. This will then be loaded in (unless deleted from the file system) on the next Jemboss launch.

A sequence file can be opened by selecting the sequence in the table and opening it from the 'File' menu. Extra rows can be added to the table and sequences can be deleted from the 'Tools' menu.


Here are a couple of simple programs to familiarise you with Jemboss.