Genomic data analysis pipeline. Bio-specimens for genomic experimentation are submitted to the Microarray and Genomic Shared Resource (MGSR) using the GNomEx LIMS. If derived from patients, the samples are first annotated using the Bio Sample Tracking database. The MGSR uses GNomEx to process the samples through microarray or next generation sequencing experiments and to distribute the raw data. Genomic analysis is performed on the raw data and uploaded into GNomEx's analysis project center. The GWrap GUI command line wrapper is available for local processing using the USeq and TiMAT2 analysis packages. Final genomic analysis (e.g. track data) is annotated, organized, and distributed to DAS/2-enabled genome applications such as IGB using GenoPub. Red boxes denote applications discussed in this paper, blue boxes represent related applications detailed elsewhere.