Chapter 4: Getting Started

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Material and Methods

NOTE: The following instructions make use of software packages which are copyrighted or licensed by software providers and need to be purchased and installed separately. If you start the program package's environment, or review the program's output file, you will find the corresponding copyright and acknowledgement notices. It is of all user's interest that these notices are carefully read and kept in mind in order to grant honours to those who deserve it.

NOTE: The following instructions make use of databases which are usually placed in the public domain. The rate of updates is steadily increasing. Make sure that you always use the latest database version you can get hold of. Remember to check with your software manager what the latest database release or description was if you publish data referring to sequence databases.

NOTE: The programs and data are brought to you by people who work hard to get you the best quality and performance. These installations are not free of cost, even if you might not need to pay fees directly. It is required that you acknowledge these organisations properly in publications in order to ensure their future funding.

The standard environment in the past was a text terminal or screen on a suitable equipment (PC, etc.) which displayed text on an area of 80x24 characters. Depending on the properties of the equipment attached to the screen or the capabilities of the program, it may be impossible to visualise graphics on the screen. If you are afraid that this is the case, contact your system or site manager for details. The most common types of text screens are called vt100-type screens. Even if you run the Wisconsin Package Interface (WPI), a text window is advantageous to have.

If your screen behaves strangely ( "unknown terminal" or similar messages) refer to the section "Common Problems" in order to set the required parameters correctly.

NOTE: The following does not need to be configured if you use a text-oriented display.

If you use local area networks , it is possible to send windows across the (local) network. The procedure required to do this is called X-Windows and is explained in detail in the appendix.

You can run X-Windows graphics on a terminal or computer other than the host where the corresponding molecular biology programs have been started. To do this, you must tell the host you are logged in to send the graphics window to your terminal or computer, i.e., you must know the name or IP address of the terminal or computer where you want to display the graphics. The variable which the host needs to know is called DISPLAY:

% setenv DISPLAY host.domain.country:0

Example:

 

  
 % setenv DISPLAY biodos.embnet.unibas.ch:0
  

  

 

  
Cannot open display