GeneLinkerô stores all of its dataset, experiment, gene, gene list, and annotation data in a database on the local file system under the GeneLinkerô directory (PPSI) in a folder named Repository. GeneLinkerô currently supports a MySQL, DB2, or Oracle database. The MySQL source code is provided on the GeneLinkerô CDROM in the MySQLSrc directory.
The default database used by GeneLinkerô is MySQL. If you are using this database, you are not required to install, configure, or maintain the database in any way. When GeneLinkerô is started, it will start the database, and when GeneLinkerô 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 GeneLinkerô computer and create a valid account for GeneLinkerô to use. You will have to start and stop the database manually. See Setting Up a DB2 GeneLinkerô Database for details of the DB2 setup process. See Setting Up an Oracle GeneLinkerô Database for details of the Oracle setup process.
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:
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:
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.
The GeneLinkerô database should not be tweaked or configured outside of GeneLinkerô.
It is recommended that you do not use the GeneLinkerô database with any other application or data. Doing so could result in an unusable, corrupted database.
The GeneLinkerô 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.
Setting Up a DB2 GeneLinkerô Database
Setting Up an Oracle GeneLinkerô Database