Document Type thesis Author Name Boyd, Joseph Email Address boydjr7 at gmail.com URN etd-050114-072807 Title BioBridge: Bringing Data Exploration to Biologists Degree MS Department Computer Science Advisors Matt Ward, Advisor Sam Politz, Reader Elizabeth Ryder, Department Head Keywords visualization omics data information visualization interactive visualization exploratory visualization biology Date of Presentation/Defense 2014-05-01 Availability unrestricted
Since the completion of the Human Genome Project in 2003, biologists have become exceptionally good at producing data. Indeed, biological data has experienced a sustained exponential growth rate, putting effective and thorough analysis beyond the reach of many biologists. This thesis presents BioBridge, an interactive visualization tool developed to bring intuitive data exploration to biologists. BioBridge is designed to work on omics style tabular data in general and thus has broad applicability.
This work describes the design and evaluation of BioBridge's Entity View primary visualization as well the accompanying user interface. The Entity View visualization arranges glyphs representing biological entities (e.g. genes, proteins, metabolites) along with related text mining results to provide biological context. Throughout development the goal has been to maximize accessibility and usability for biologists who are not computationally inclined. Evaluations were done with three informal case studies, one of a metabolome dataset and two of microarray datasets.
BioBridge is a proof of concept that there is an underexploited niche in the data analysis ecosystem for tools that prioritize accessibility and usability. The use case studies, while anecdotal, are very encouraging. These studies indicate that BioBridge is well suited for the task of data exploration. With further development, BioBridge could become more flexible and usable as additional use case datasets are explored and more feedback is gathered.
Files BioBridge_demo.zip jboyd.pdf README.txt
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