Topics in Computational Biology

Abstract Due Date: April 19

Final Writeup Due Date: May 25

Semester Project

Recall that the semester project will be a writeup of a specific problem area and possible directions for future research. Each project will obviously cover a distinct topic, but because our class is so diverse, I expect that the focus of each writeup will be different since as well. One of the purposes of this project is to explore how your experience and background can be used to make progress on an interesting problem area in computational biology. A general outline for the structure of the writeup could be:

1. Introduction to Problem Area(s) and Biological Motivation
   • Where does this problem area lie? What is the information we are typically given?
   • What is the biological motivation for the studying the problem?
   • What are the implications of solving this problem or solving it more accurately/more efficiently?
2. Existing Approaches
   • How do biologists solve the problem?
   • What, if any, are the existing computational models for the problem?
   • Is the solution quality/performance of current methods satisfactory?
3. Extensions and Improvements
   • Can we make the problem more realistic? Will the problem still be solvable?
   • Have others proposed similar ideas? If so, where did they fail or succeed?
   • Can we improve existing algorithms? What are desirable properties of any algorithm for the given problem?
   • What are potential pitfalls to solving your proposed problem, or using your proposed solution?

Remember that this is a course in computational biology, so the theme of your writeup should be the computational models and goals for a given biological problem area. You should be mathematically precise, when possible, in your statement of the problems and goals. At a high level, your writeup should answer the question: How can the work in this problem area be improved using computational models or methods? Accordingly, please be rigorous about citations to previous work; your bibliography should contain references to original work, not just the survey papers used in your presentations.

Please submit an abstract of your semester project (this can be a short, one paragraph summary following the outline above) by 5pm, April 19. Your final writeup should be 8-12 pages, and typeset in 1.5 spacing, 12 point font, with 1.25 inch margins. The writeup must be emailed to me in PDF format on or before 5pm, May 25.

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