9.2. Getting Started

9.2.1. Software Requirements

Jemboss is a graphical user interface for EMBOSS and EMBASSY. So, instead of learning specific syntax for command line use, the Jemboss window can be used to enter sequence information and click on relevant parameters to analyze nucleic and protein sequence data.

Jemboss is written in Java and so the computer that it runs on must support java. Java version 1.3 or higher should be used and is generally installed on most computers bought since 2006. If this is not the case, Java can be downloaded for free from http://www.java.com (use the optional test first to determine whether the computer is already equipped with java). Java Webstart (JWS), which is required to run the client/server Jemboss (Section 9.2.6, “Remote Installation”), is now bundled together with this download and will be installed on the computer at the same time.

9.2.2. Microsoft Desktop

Jemboss can be installed as a standalone (Section 9.2.5, “Local Installation”) version, or run as a remote client/server (Section 9.2.6, “Remote Installation”).

9.2.3. Apple Macintosh

Jemboss can be installed as a standalone version using the additional installation instructions (Section 9.2.5, “Local Installation”). Java Web Start must be installed in order to run a remote client/server (Section 9.2.6, “Remote Installation”).

9.2.4. Unix Platform

Jemboss can be installed as a standalone (Section 9.2.5, “Local Installation”) version, or run as a remote client/server (Section 9.2.6, “Remote Installation”) using Java Web Start.

9.2.5. Local Installation

A local Installation of Jemboss is one that is installed on the desktop computer. All files will be saved on this computer only and there is no option for remote file sharing. Commonly called a "standalone" version, instructions for installing it can be found in the EMBOSS Administrators Guide. If you install the mEMBOSS package for Windows then Jemboss is installed automatically and a shortcut icon will appear on the desktop at the installation stage. A jemboss.properties file is created on installation of the Jemboss software. It holds details of the default home (Section 9.3.2, “Home Directory”) and working (Section 9.3.3, “Working Directory”) directories. A file called .jembossFavorites holds the information for the Favourites list (Section 9.7.2, “Programme Selection”).

Additional installation instructions for MacOSX may be found in the EMBOSS Administrators Guide.

If there is already a Jemboss icon on the desktop machine, there is an easy check to determine whether it is a local or remote installation. Double click on the icon to open the Jemboss window. Select the File menu at the top left. If the menu options contain only Saved Results and Exit, then it is a standalone version.

If there is already a standalone version on the desktop, and a new version is to be installed, the old one must be cleanly uninstalled and the jemboss.properties file deleted (use the desktop search facility to locate this file if necessary).

9.2.6. Remote Installation

A remote (client/server) Installation is set up on a server at some location other than the desktop machine and the Jemboss window is created via a web page launch option. Many institutions offer this service for their students and staff and a username and password is generally required.

  • Access the remote Jemboss launch page by typing the appropriate URL into a web browser. Click the red Launch Jemboss link on the webpage and hit the Run button on the security warning page which appears. The Jemboss window will appear on the desktop computer. Enter your username and password to get started.

The initial launch of a new Jemboss version will be slightly longer than subsequent launches as new data must be downloaded to the local computer.

The local machine now plays host to a number of very small files. jemboss.properties contains information on the location of the home directory (Section 9.3.2, “Home Directory”); .jembossClientKeystore contains information that allows the client to connect with the remote server and .jembossFavorites (Section 9.7.2, “Programme Selection”) stores the list of favourite programs. Everything else is created and stored on the remote machine.

A remote server must be set up under a Unix/Linux operating system and instructions are available in the EMBOSS Administrators Guide.

9.2.7. Jemboss Session

Once a Jemboss Window is launched, either through a web page or from a desktop icon, a Jemboss session is started. This session then continues until the Jemboss window is closed. All session-specific information is then lost.

9.2.8. Session-specific Information

Jemboss stores a number of results (Section 9.6.4, “Current Sessions Results) and customisation information (Section 9.7, “Customisation”) as session-specific data. Session results are accessible whilst the current session is running and serve to provide a short and recent overview of analyses. Customisation information can be used as a default for a particular session or can be saved over several sessions.

9.2.9. The Jemboss Windows Main Jemboss Window

The main Jemboss window opens upon launch and consists of three panes, only two of which are immediately visible.

The left hand pane contains all the analysis programs, either listed individually or grouped into categories (Section 9.4.1, “Programme Selection”). The Keyword Search at the bottom of the pane allows all programs to be searched using AND and OR logic.

  • Click on the arrows at the top of the pane divider to hide and re-display the pane.

The central pane will contain the analysis interface for each selected program.

  • Click on the Information group category in the top half of the left hand pane and select the WhichDB program. In the central pane, type bgal_ecoli into the Input Section field and hit GO. The program returns with the USA information (Section 6.6, “The Uniform Sequence Address (USA)”) for the Escherichia coli bgal protein.

The third pane is the local file manager (Section 9.3.1, “Local File Management”) and may be opened and closed using the double arrow button on the bottom right of the central pane.

None of the Jemboss windows close automatically, so they should be closed once they have been finished with otherwise the screen will become cluttered. They can be closed using the File/Exit option or the red cross in the upper right hand corner of the window. File Managers

There are two file management windows. The local file manager (Section 9.3.1, “Local File Management”) opens in the main Jemboss Window (see above) and for remote installations (Section 9.2.6, “Remote Installation”) there is a remote file manager (Section 9.3.14, “Remote File management”) available in a separate pane. Results Managers

There are three results managers; the Job Manager (Section 9.6.3, “Job Manager), the Current Sessions Results (Section 9.6.4, “Current Sessions Results) and the Results Manager (Section, “Results Manager). They consist of two panes. The left hand pane contains a list of results, the right hand pane contains details of the analysis run. Results in these managers can be displayed individually or deleted both singly and in batches. Text Editors

The Text Editor window allows text to be entered and deleted, edits to be undone and re-done and the text and background colour, font and size to be altered. With the exception of any textual addition or deletions, there is no save option for any changes beyond the life of the window. The Text Editor windows are produced for: Saved Results (Section, “Saved Results Window”), Edit Notes (Section, “Edit Notes”), Local File (Section, “Local Results”) and Remote File (Section, “Results in remote file manager”).

9.2.10. Settings

Accessed using the Preferences menu on the top bar of the Jemboss main window, settings reports the information required by the Jemboss application in the Client Properties tab.

The settings window will remain attached to the Jemboss window, preventing all further function until it is closed.

9.2.11. Proxies

The Proxy is an intermediary between the local computer and any remote machines it may need to access. It is required for any non-direct Internet connection. Proxies are set by the command line on installation and information on them can be retrieved using the main Jemboss Preferences menu and the Settings option.

For the Jemboss standalone version (Section 9.2.5, “Local Installation”), the browser proxy is usually set at installation time and is the intermediary used to connect to any web server. In larger institutions, this proxy is likely to be the same as the one used for Internet browser windows. Personal computers rarely require a proxy.

For the Jemboss client/server version only (Section 9.2.6, “Remote Installation”), the browser proxy acts as the intermediary in the same way as for the standalone version, and the Proxy acts as an intermediary for the Jemboss client to access the remote Jemboss server.

9.2.12. Servers

For the Jemboss client/server version only (Section 9.2.6, “Remote Installation”). The server information contains the URL which hosts the remote Jemboss server and from where the application is launched.