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Choosing a GoMiner Database Implementation

GoMiner supports MySQL database engines with 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.

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.

GoMiner™ is a development of the Genomics and Bioinformatics Group, Developmental Therapeutics Branch (DTB), Developmental Therapeutics Program (DTP), Center for Cancer Research (CCR), National Cancer Institute (NCI). 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.

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