David Wyde

Date of Award

2011

Document Type

Thesis

Degree Name

Bachelors

Department

Natural Sciences

First Advisor

Hart, Chris

Keywords

Software, Notebook, Genomics

Area of Concentration

Computer Science

Abstract

Data analysis is a central aspect of modern computational science. The scientific method emphasizes reproducibility of results, but intermediate steps in analytical processes are not always recorded and published. To verify or extend an existing experiment requires knowledge of each step in the original analysis. For data-centric disciplines like genomics, a complete �analysis pipeline� is the computational equivalent of a formal lab protocol. We have created a software project, called Poolside, that aims to help scientists programmatically analyze data in a reproducible way. Poolside is an open source web application with tools for computation and visualization. All of Poolside's features are accessible from a web browser. Its users don't need to download additional software. Poolside allows users to write and run code in the Python and Ruby programming languages. Poolside stores data persistently, and also has features for data visualization. It is intended to act as a �computational notebook�. Poolside is still in development; however, it already has some useful capabilities, and it provides a platform with which more sophisticated tools can be built.

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