Choosing a GoMiner Database

GoMiner now supports two different database engines (MySQL and Derby) with various choices for implementations and deployment configurations. This page is intended to help you choose the right implementation. These options are available if you are using the original GoMiner interface, which we sometimes call Classic or GUI GoMiner, or if you are using the command-line interface. The Getting Started page can help you determine whether you want to use one of these or High-Throughput GoMiner.

Using MySQL with the database on discover.nci.nih.gov

This is the default configuration when you first download GoMiner. It is the easiest to use, because you don't have to make any configuration changes to get started. However, this configuration has the worst performance of the options listed here. This configuration is suitable if you are just evaluating GoMiner, or if you have small data sets. For datasets of substantial size, the performance limitations of this configuration start to become a significant obstacle. This option is limited to whatever version of the GO database that we currently have published.

How to use this option

Use the following database setting, to use this option.

On the database selection panel, there is a drop down box for Choose data adapter. Select: MySQL. You can skip this step if you are using the command-line interface.
Database Driver: com.mysql.jdbc.Driver
Database URL: jdbc:mysql://discover.nci.nih.gov:1521/GEEVS?autoReconnect=true
Username: deploy
Password: selectonly

Using Derby with a database on your machine

GoMiner now includes a built-in database engine, called Derby. All you need to do is download and unzip the Derby/GoMiner package. This option is easier than using MySQL locally, because you do not need to install a separate database engine. It is much faster than using our database instance on discover.nci.nih.gov, but it is not as fast as using MySQL locally. We provide a build of the Derby data that is in sync with our current build on discover.nci.nih.gov, but we don't provide the same set of tools for you to customize the build. There is not a ready collection of other GO database builds in the Derby format. If you do not have very detailed database requirements or build control, then this can be an easy option.

How to use this option

For most situations, there are just four steps.

Download the Derby/GoMiner package. The file is about 3 GB uncompressed, and may take several hours to download, depending on your bandwidth.
Unzip the downloaded file. It will take about 9 GB of diskspace uncompressed.
This zip archive includes a copy of the gominer.jar. Use this jar file to run GoMiner.
- Note: This is the same jar file that we usually distribute. It is included here as a convenience to maintain the relative location of GoMiner and the data, and so you don't need to change the Database URL in the next step.
On the database selection panel, there is a drop down box for Choose data adapter. Select: Derby.

Advanced configuration

If you move the data folder to a different location, you will need to adjust the JDBC URL. Otherwise the other settings should remain unchanged.

Database Driver: org.apache.derby.jdbc.EmbeddedDriver
Database URL: jdbc:derby:LOCATION WHERE YOU EXPANDED THE DATABASE FILE. The path can be relative to the working directory from which you launch GoMiner, or an absolute directory. E.g. jdbc:derby:/Users/barry/goMinerDerbyDB, jdbc:derby:D:\goMinerDerbyDB, jdbc:derby:goMinerDerbyDB.
Username: Leave this blank if you are using the GUI, use NONE if you are using the command-line interface
Password: Leave this blank if you are using the GUI, use NONE if you are using the command-line interface

Using MySQL with the database on your machine

This is the fastest and most flexible configuration, but it is also the most complex to set up. It is most useful if you are using GoMiner heavily, or if you want to customize your database, or use GoMiner with past builds from GO.

How to use this option

Use the following database setting, to use this option.

Follow these instructions.

We would like to hear from you. You can reach the team via email.

GoMiner was originally developed jointly by the Genomics and Bioinformatics Group (GBG) of LMP, NCI, NIH and the Medical Informatics and Bioimaging group of BME, Georgia Tech/Emory University. It is now maintained and under continuing development by GBG.

Notice and Disclaimer