MySQL Database Installation

UltraScan supports an SQL database interface for managing the AUC data, such as experimental scans, buffer files, peptide files, investigator information, and so on. MySQL is an open source, very capable database engine available for all hardware platforms, and has been tested to perform well with UltraScan. Please follow these instructions to get MySQL properly initialized to work with UltraScan on your system:

Getting MySQL onto your computer:

  1. Most distributions of Unix come with MySQL and therefore MySQL can be installed using the respective package manager. For all other distributions, you can download a source distribution and compile it on your system. More information is available at

  2. After successfully installing MySQL you will need to start the program with the appropriate switches. The default start script does not allow for sufficiently large file transfers between UltraScan and MySQL, and a special option needs to be used to enable large file transfers. We have found the following command to work well for us:

    safe_mysqld --user=mysql -O key_buffer=16M -O \
    table_cache=128 -O sort_buffer=4M -O record_buffer=1M -O max_allowed_packet=24M &

  3. Now verify that MySQL is working properly by checking for the running mysql process on your machine.

  4. Next, use the MySQL command line client to set up permissions for the database. You start the client by typing as root at the commandline:

    systemprompt#:  mysql -u root

  5. This should open up the "mysql>" command shell. This is where you can enter the MySQL configuration commands:


  6. Assuming you wanted to create a database called "mydata" on your MySQL server, you would have to type in the following commands:

    mysql> CREATE DATABASE mydata
    mysql> quit

  7. Now that the database is created, you need to set access permissions for the users of the database. There are two ways to do that: First, you can assign permissions for each existing user that should have access authorization, or second, you can use a fictional user name everyone can use to connect to the database. In the latter method, only a single user has to be configured in MySQL for access permissions. Assuming you wanted to grant access rights to your "mydata" database to user "sqluser" with password "secret_word" on your computer, which happens to be named "", you would have to enter the following commands into the "mysql>" command shell:

    systemprompt#:  mysql -u root mydata
           BY 'secret_word' WITH GRANT OPTION;
    mysql> quit

    Repeat for each additional user for which you want to grant access. MySQL will not use the system password, "secret_word" in this case will go with the database, not the user name.

  8. If you want to make the database accessible outside of your system, you can grant access in the following way:

    systemprompt#:  mysql -u root mydata
           BY 'secret_word' WITH GRANT OPTION;
    mysql> quit

  9. Now you need to tell UltraScan about the new database. You have to do that in the Database Configuration Module, which is started from the File:Configuration:Database Preferences menu.

  10. Finally, you should run the Initialize Database Template command on your database to initialize the database tables. After initialization, MySQL should accept all new data via the UltraScan Database Interface.


Security Configuration Notes:

Please keep in mind the following security considerations:

www contact: Borries Demeler

This document is part of the UltraScan Software Documentation distribution.
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Last modified on January 12, 2003.