The present invention is a data query and analysis tool useful for identifying patterns in experimental data. The methods and systems of the current invention provide context for biological data, including metabolic, gene expression and proteomic data, by applying the data to a network representation of biological processes. In doing so, Nodewalker moves beyond the traditional linear pathway view of biology to a network view, and uses the network as a data integration tool to seamlessly merge disparate data streams.

 
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