GeneLinker™ Database

Overview

GeneLinker™ stores all of its dataset, experiment, gene, gene list, and annotation data in a database on the local file system under the GeneLinker™ directory (PPSI) in a folder named Repository. GeneLinker™ currently supports a MySQL, DB2, or Oracle database. The MySQL source code is provided on the GeneLinker™ CDROM in the MySQLSrc directory.

MySQL

The default database used by GeneLinker™ is MySQL. If you are using this database, you are not required to install, configure, or maintain the database in any way. When GeneLinker™ is started, it will start the database, and when GeneLinker™ is shut down, it will shut down the database.

DB2 and Oracle

If you choose to use a DB2 or Oracle database, then you will have to install DB2 or Oracle on the GeneLinker™ computer and create a valid account for GeneLinker™ to use. You will have to start and stop the database manually. See Setting Up a DB2 GeneLinker™ Database for details of the DB2 setup process. See Setting Up an Oracle GeneLinker™ Database for details of the Oracle setup process.

Multiple Databases

Sometimes users may wish to maintain separate databases for different projects. GeneLinker supports this capability by setting the following values in the GeneLinker.conf preferences file:

mmc.genelinker.repository.database_name#
mmc.genelinker.repository.database_username#
mmc.genelinker.repository.database_password#
mmc.genelinker.repository.database_description#
mmc.genelinker.repository.location#
mmc.genelinker.repository.type#

where "#" is an integer value that starts at 1 for the first additional database and increases to 2, 3, and so on for each added database. The default database preference does not have any numerical suffix.

For example, the default values that are set during installation are:

mmc.genelinker.repository.database_name=localhost\:27331@GeneLinker
mmc.genelinker.repository.database_username=GeneLinker
mmc.genelinker.repository.database_password=mmc1337
mmc.genelinker.repository.database_description=GeneLinker Default
mmc.genelinker.repository.location=C\:\\Program Files\\MMC\\GeneLinker Platinum\\Repository
mmc.genelinker.repository.type=1303

And a typical altnerative database on the same machine is:

mmc.genelinker.repository.database_name1=localhost\:3306@GeneLinker
mmc.genelinker.repository.database_username1=GL_USER
mmc.genelinker.repository.location1=C\:\\mysql\\GLDATA
mmc.genelinker.repository.database_password1=test
mmc.genelinker.repository.database_description1=mySQL 4.0 Test Database
mmc.genelinker.repository.type1=1303

There are several things to note about these specifications. A specification must include all six pieces of information or it will not show up in the list of databases. In fact, the first incomplete specification encountered will terminate the search for further database values--if you expect to see several databases listed but some are missing, it is likely that one of the specifications has some information left out.

As well as the usual database connection information, two GeneLinker-specific pieces of information are required by these specifications: the location of the repository files and the type of the database.

The location of the repository files is the location used for binary data that are stored externally to the database tables. This location is also used for the lock file that ensures only one user is connected at any given time.

The database type must be one of:

1303 = mySQL
1305 = Oracle
1306 = DB2

Different databases may, of course, have different types.

Finally, the default database for a user is given by the key:

mmc.genelinker.repository.default=mySQL 4.0 Database

and may be set by selecting the "Make default" checkbox in the database selection dialog that is presented on application startup.

Note that if only one database is present in the preferences file then GeneLinker will use it without asking the user to select it.

Notes

The GeneLinker™ database should not be tweaked or configured outside of GeneLinker™.
It is recommended that you do not use the GeneLinker™ database with any other application or data. Doing so could result in an unusable, corrupted database.
The GeneLinker™ uninstall procedure has an option to keep or remove the database.
As an example, a typical file size would be approximately 0.5 Megabytes for a dataset consisting of 1000 genes by 100 samples.