Functional Genomics Data Pipeline
The FGDP began as a simple pipeline that handled routine preprocessing, statistical tests, and clustering of microarray data (Grant et al, PMID 12651736). In the first incarnation, the system was rather inflexible in the order in which analyses could be performed. We therefore created this second version under the auspices of an R21 award from the National Library of Medicine (LM008309). This version was designed to utilize application server technology to permit distributed analysis, to allow easy extension to multiple genomic data types, and to include hooks for integration of controlled vocabularies and ontologies. The links below include installation instructions, code, and JavaDoc documentation files that you can download. Below is simple diagram of the present classes, together with a sample of how an additional class for a new data type (proteomics) would be linked. Our goal was to continue development through a consortium in the areas of proteomics, flow cytometry, and genotype with integration through ontological and orthological linking. However, these plans are on hold due to our failure to obtain the necessary funding in the present NIH climate. Please feel free to utilize code provided here under the GNU Lesser Public License (GLPL). Please note that EJB and Application Servers require substantial expertise and experience to successfully deploy and maintain, so we do not recommend that those without EJB experience attempt to use this software, and we are unable to support it in any way.
