Extending the RAST Server to Support Reconstruction and Modeling of Cellular Networks

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Hope College is awarded a grant to extend the Rapid Annotation using Subsystem Technology (RAST) genome annotation server to support reconstruction and modeling of cellular networks. The RAST server (online at http://rast.nmpdr.org), is a genome annotation service that produces high-quality annotations of bacterial and archaeal genomes, along with a detailed metabolic reconstruction. This grant supports the development of software tools to enable three types of analyses that will be integrated into the RAST server: (1) generation and refinement of genome-scale metabolic reaction networks; (2) genome-based prediction of transcriptional regulons; and (3) analysis of gene expression microarray data and regulatory network prediction. A major challenge facing the bioinformatics community in view of the ever increasing pace of genome sequencing and generation of large-scale genome-based data sets is to provide tools that enable rapid, high-quality genome annotations and support efficient, integrated data analyses. The extended RAST server will provide a broad user community with an integrated suite of tools that enables sophisticated analyses of genomic and high throughput transcription data to be accomplished more efficiently than would be possible using disparate tools in different locations with different interfaces. This project will provide undergraduate students in biology and computer science with hands-on experience in interdisciplinary research that will prepare them for graduate work or other scientific activity, and will draw on Hope College's existing collaborations with area community colleges and the local public school system to provide research opportunities to students from underrepresented groups in the sciences. The project will be carried out in collaboration with the Fellowship for Interpretation of Genomes, and Burnham Institute for Medical Research.