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COS597A
Structural Bioinformatics
Fall 2005
Course Projects
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Description:
The course project is the main focus of this seminar. It 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 a structural 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.
Written Proposals (due Wed Oct 19):
A one-page written project proposal should be submitted for each project.
The proposals should include enough detail to convince a reader that you've
found a good problem, you understand how hard it is, you've mapped out
a plan for how to attack it, and you have an idea about which experiments
you might run to test the success of your implementation.
Following is a brief outline you might follow ...
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Goal
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Previous Work
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What related work has been done?
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Approach
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What approach are we going to try?
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Why do we think it will work well?
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Methodology
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What steps (task list) are required?
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Which of these steps is particularly hard?
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What to do if the hard steps don't work out?
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Metrics
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How will we know when we are done?
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How will we know whether we have succeeded?
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Summary
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What will we learn by doing this project?
Project Proposal Presentations (during class
on Wed Oct 19):
Each student (or team of students) will give a 5-10 minute talk to present his/her course
project proposal to the class (with slides
and/or other props). You should be sure to convince us that: 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 have a specific, detailed plan, and 5) you will know when
you are done. 5-10 minutes is a very short amount of time. So, please come
with a presentation that is concise and to-the-point. You probably
want to use around 6 slides following the outline above.
Project Progress Presentations (during class
on Wed Nov 16 and Wed Dec 14):
Each student (or team of students) will give a 5 minute talk reporting the
(partial) results of his/her course
project proposal to the class (with slides
and/or other props) and possibly lead a short discussion about how best to
proceed. Please focus the talk on the new progress and results, repeating
the project goals/approach only as necessary.
Project Final Presentations (Jan 2006):
Each student ( team of students) should give a short presentation describing their project. Your goal should be to describe
in 15 minutes what you have done and why it is interesting. If
appropriate, please give a live demo.
Final Written Reports (due Jan 2006):
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
Resources
The following resources may be useful to you when working on your project: