SGER GeneBeans: A Modular System That Makes Genomic-Scale Analysis Accessible to Biologists

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Biologists now have access to vast amounts of DNA sequence and annotation data, but do not yet have tool sets that make it easy for a novice to ask biological questions about these large sequence data sets. An environment with a visual user interface for constructing series of queries and analyses without the need for the user to see the underlying computer code will be created. The system will use Enterprise JavaBeans (EJBs) to import sequence data from a variety of sources and store it in a relational database. Other EJBs will handle workflow, query the database, and analyze results. The EJB modules will be designed to make their results available to other modules. The system will be extensible in that it will be easy to add new modules that employ the appropriate interfaces. This system will allow users to ask questions about frequency, correlation, and significance, queries typical of data mining methods, without writing new programs. The prototype of our system will be tested both for undergraduate classroom use at a historically black university, NCA&T, and for research on genome structure in plant DNA sequences. New kinds of search algorithms and statistical analyses, which will be easily integrated into our modular system, will be designed involving the interdisciplinary training of a biology graduate student.