Directed Study

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October 0, 00

Professor Horace McAllister

University College of the Cariboo

Box 010

Kamloops, B.C.

VC 5N

Dear Professor McAllister

Re "Directed Study" course proposal in area of computational biology

I enjoyed meeting with you last Friday and discussing the option of taking a "directed study" course under your supervision. Computational biology was the area of study that I was considering, and given your past research in Computer Science and Molecular Biology, I would like you to supervise me during this course. As per our discussion, I have created the following proposal for the "directed study" course that I would like to take.

Course Name and Department

• COMP 48 Directed Study Computational Biology

• Computer Science Department.

Course Description

This course will allow student's to develop and implement algorithms for selected problems in computational biology, including the simulation of the immune system and the determination of methods for inferring specific aspects of protein structure from protein sequence data. Students will work under the supervision of Professor Horace McAllister.

Prerequisites

• Admission to the 4th year of the BTACS degree program, or to the 4th year of the Computing Science Major program.

• 6 credits of first year Biology.

• credits of second year Biology.

Schedule

Students enrolled in "directed study" course must attend occasional class meetings where they will be advised about how to do independent work, how to prepare an oral presentation, how to write the final report, etc.

The student is expected to average at least 10-15 hours per week and to make regular progress reports to his/her faculty advisor. A written report must be submitted to the faculty advisor at the end of the semester.

The following is a proposed schedule for the class meetings

• Thursday, September 18

"Getting Started Meeting"

• Monday, October 15

"Beginning-of-the-Semester Project Proposals".

• Monday, November 17

"Progress report".

• Tuesday, December

"End-of-the-Semester Project Presentations"

• Monday, January 6

"Final Written Reports"

Methods of evaluation

1. Project Plan Proposal presentation 10%

. Progress Report 0%

. Project Presentations 5%

4. Final Written Report 45%

1. Project Plan Proposal presentation (5 minutes)

• Problem description What am I going to do? Why is it important?

• Approach Previous approaches, my approach.

• Methods Specifics steps, deliverables

• Summary

. Progress Report (approx. 50 words)

• Remind of proposal problem

• Report what has been done so far

• Give some preliminary results (if applicable)

• Discuss any difficulties

• Discuss what work is remaining

. Project Presentations

• Review problem description

• Describe your approach to problem

• Give details of your work

• Give important results

4. Final Written Report (approx. 1000 1500 words)

• Abstract

• Introduction What problems are you trying to solve?

• Previous Work Identify work done by others.

• Approach Describe approach to problem used and how it is different from other approaches.

• Methods How was the work done?

• Results

• Discussion What did you learn? What can be done now?

• Conclusion Summarize work done.

• References Cite using APA style.

Possible Topics

• Applications of protein structure determination

• Simulation of the immune system

• Prediction of protein function and protein-to-protein interactions

• Developing a visualization of biological datasets

Conclusion

This course will allow me to explore the practical applications of computers and computing science in the fields of biology. If you choose to accept this proposal, then this course should be made available during the winter semester (January to May) 004.

If you have any further questions about the course outline that I have proposed, or would like to discuss the details of the topics associated with this course, please give me a call at 555-44.

Sincerely

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