Worcester Polytechnic Institute Electronic Theses and Dissertations Collection

Title page for ETD etd-050114-072807

Document Typethesis
Author NameBoyd, Joseph
Email Address boydjr7 at gmail.com
TitleBioBridge: Bringing Data Exploration to Biologists
DepartmentComputer Science
  • Matt Ward, Advisor
  • Sam Politz, Reader
  • Elizabeth Ryder, Department Head
  • Keywords
  • visualization
  • omics data
  • information visualization
  • interactive visualization
  • exploratory visualization
  • biology
  • Date of Presentation/Defense2014-05-01
    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.

  • BioBridge_demo.zip
  • jboyd.pdf
  • README.txt

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