Rodeo: A Platform for Discovery and Analysis of Protein Network Motifs

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Harvard University is awarded a grant to build a new publicly available informatics tool, called Rodeo that will allow the integration of data relevant to deciphering protein-protein interaction networks and will provide a number of methods for analyzing such data, including graph-theoretic mathematics. Rodeo will allow the integration and analysis of several databases including a comprehensive set of orthologs from over 50 genomes, a new set of protein-protein (p-p) interaction data from humans together with over 70,000 p-p interactions from other organisms, a massive set of gene expression data from new experiments and experiments hosted by NCBI, and a database of almost 100,000 Expressed Sequence Tags from an organism (the acorn worm) that may hold the key for understanding the developmental complexity which evolved in modern day vertebrate animals. Rodeo will allow the interrogation of data not just from one organism, but across multiple organisms, providing a way to search for convergently evolved patterns a vital step to understanding process. Rodeo will also allow the visualization of motifs to literally 'see' patterns of network complexity. Rodeo will also be a valuable tool for education and research on protein-protein interaction motifs, and a general resource on the application of graph algorithms to complex questions in biology. Rodeo will be made accessible to not just advanced scientists interested in network structures of interactomes, but to any student of biology concerned with learning more about the complexity of the cell. Specifically a training program will be developed consisting of a 2-day training course on 'motif discovery' at Harvard Medical School that will be open to the international scientific community at no cost. This will be co-taught by the PI and senior personnel on the proposal, with introductory lectures on graph models and algorithms for biology, as well as hands-on training with Rodeo. Secondly, a virtual training via the Rodeo web portal will be created that will contain extensive documentation, as well as streaming video of our 'motif discovery' training seminars. Thirdly, Rodeo tutorials will be held at two of the major symposia on biocomputing, which will also be available through the Rodeo web portal. And last not least, Rodeo will be incorporated into the training curriculum for graduate students in the Department of Systems Biology at the Medical School.