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Application Build: 246 Database Build: 2008-04 | ![]() |
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Overview | Database Options | Installing MySQL Locally | Enhancement Algorithm |
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.
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.
Use the following database setting, to use this option.
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.
For most situations, there are just four steps.
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.
Use the following database setting, to use this option.
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.