This project, supporting interdisciplinary computational projects in bioinformatics and computational biology, computational genomics, and plant sciences, enables several research projects, including: -Assembly, validation, and annotation of the maize genome, -Large-scale Express Sequence Tag (EST) clustering with applications to gene identification, -Detection of functional and regulatory clusters of proteins through whole organism protein network analysis, and -Design and simulation of FPGA-based engines for computational genomics. Enabling solution of large-scale applications of current relevance, the infrastructure contributes to develop, demonstrate, and disseminate high performance computing techniques and comprehensive software systems capable of solving such applications. The team consists of researchers with expertise in parallel algorithms, architectures, high-performance software development, bioinformatics and computational biology, molecular biology, functional genomics, maize genetics, and protein structural biology. The instrumentation will be used to perform clustering of the largest-scale human and mouse EST collections, and perform EST-based gene discovery at unprecedented sale and speed. Whole organism protein systems biology studies will be used to uncover functional and regulatory clusters of proteins. Design simulation of FPGAs for computational genomics applications will enable other researchers to solve large-scale problems with modest size cluster equipped with FPGAs.
Broader Impact: The project contributes web-based community resources and/or infusion of new knowledge into existing web-based community resources. The instrumentation benefits research and educational activities in the areas addressed. Collaborative ties with New Mexico State University, a Hispanic serving doctoral extensive institution ensures involvement of underrepresented students. Iowa offers Women in Science and Engineering summer program for high school female students
