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High-Throughput GoMiner is not a replacement for GoMiner, but a companion to it. In fact, the original GoMiner is one component of High-Throughput GoMiner. The following picture describes the relationship between the two. High-Throughput GoMiner uses the command line interface of the original GoMiner to incorporate it into the high-throughput processing stream.
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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.