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COS597A
Structural Bioinformatics
Fall 2007
Course Projects
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Description:
The course projects are the main focus of this seminar. They should be a
credible investigation of a research problem in structural bioinformatics.
Generally speaking, projects should propose a method for solving a specific
problem and then evaluate how well the method performs on an interesting data
set. Sample topics include analysis/characterization of X in a large
structural data set, prediction of X for a given structure, simulation of X for
a sequence or structure, and so on ... where X is a structural feature of a
molecule. Students are encouraged to perform the course project in
multidisciplinary teams -- for example, with one student from computer science
and another student from chemistry or molecular biology -- however, students may
work individually, if they wish.
Progress Reports (during class on Oct 25 and Dec 17):
Each student (or team of students) will give a 10-15 minute talk to present
his/her course projects to the class (with slides and/or other props).
You should have made significant progress by this point so that you can show
interesting, but not-yet-final, results. During your presentation,
you should try to hit as many of these points as possible: 1) you
are addressing an important problem, 2) you understand various approaches
to the problem, 3) you have found an interesting approach to attack the
problem, 4) you are able to implement the steps necessary to solve the problem,
4) you have an interesting data set to work with, and 5) you have a way to evaluate the
success of your method. You may also want to lead a discussion about your
project so that you can get ideas about how to proceed from the group.
Final Reports (due Nov 15 and Jan 2008):
Each student (or team of students) should submit written final report following
the same style/outline as a journal submission. It should contain descriptions of the goals
of your project, a review of related work, detailed descriptions of what you did
and why, and an analysis of your results. Following is a brief outline you might follow
...
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Introduction
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Goal
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What did we try to do?
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Who would benefit?
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Previous Work
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What related work have other people done?
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When do previous approaches fail/succeed?
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Approach
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What approach did we try?
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Under what circumstances do we think it should work well?
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Why do we think it should work well under those circumstances?
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Methodology
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What pieces had to be implemented to execute my approach?
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For each piece ...
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Were there several possible implementations?
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If there were several possibilities, what were the advantages/disadvantages
of each?
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Which implementation(s) did we do? Why?
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What did we implement? <== Include detailed descriptions
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What didn't we implement? Why not?
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Results
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How did we measure success?
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What experiments did we execute?
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Provide quantitative results.
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What do my results indicate?
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Discussion
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Overall, is the approach we took promising?
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What different approach or variant of this approach is better?
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What follow-up work should be done next?
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What did we learn by doing this project?
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Conclusion
Each student (or team of students) will give a 10-15 presentation describing
the final results of his/her project around Jan 15, 2008.
Resources
The following resources may be useful to you when working on your project: