BioBind Practical - Jemboss File Manager

>Practical

This practical is designed to familiarise you with the File Manager. The practical should be attempted on the Jemboss interface incorporated into your BioBind software. Indented orange text denotes an action to be performed using the interface. Longer, black text explains that action. Should you have completed the relevant section of the practical and have further questions, please do not hesitate to contact us.

Open the file manager by clicking once on the double arrows, BioBind File Open

, at the bottom right hand corner of the Jemboss window.

This displays all the files in your local home directory and is the folder that Jemboss recognises as your "home" when you log in to your computer. It can be customised to represent a more appropriate folder for your bioinformatics analyses.

Highlight the name of the folder at the top of the file manager (the "top" directory) with a single click on the left hand mouse button. The highlighted folder name will be shaded purple.

Click once with the right hand mouse button to bring up the file management menu. Move the mouse down to the option New Folder and select it by clicking once on it with the left hand mouse button. Type your choice of folder name into the textbox that apppears. For the purposes of this practical, the folder name choice will be Demo.

Hit the OK button to see your new folder appear in the File Manager.

There are no restrictions on the number of letters and digits you can type into the New Folder box, although if the name is too long, then it may not be easily readable in the File Manager.

If this is the directory where you wish to store most of your files, it can be configured to appear automatically everytime you save your data. This data will also be immediately available on opening the File Manager.

Select the Preferences menu on the toolbar at the top of the Jemboss window and open the Advanced Options.

The lower section of the resulting window concerns the Local Home Directory. A box below shows the path (or "address") of this directory as it exists on your computer. It is this address that controls the top directory that appears in the File Manager and can be customised to display any specified directory on the computer.

Continue the path shown in the box by adding a back slash (\) on windows or a forward slash (/) on Linux and then the name of your chosen directory.

Hit the Set button and the new folder will automatically appear at the top of the list in the file manager.

Check the Save between Jemboss Sessions box and this will ensure that the Demo directory always appears as the top directory in the file manager when it is opened.

As the new directory is a sub-directory of the top - and therefore default - directory, the new directory name can just be added to the path. Were the directory elsewhere on the computer, then the path may have to be partially or wholly deleted and the new path typed into the box.

Individual directories can be created for several distinct projects, and the default directory altered to accomodate the relevant analysis.

To repeat the process, or to return to the default directory, revisit the Advanced Options in the Preferences menu and hit the Reset button. This will reset the local home directory path to its original setup.