CAP5937 (Fall 2004): Term Project The goal of the term project is to introduce yourself to a new computational problem in biology. Procedure 1. Select a team of two students among your classmates. One member team is also acceptable. 2. Take an appointment with Ravi (if you need to) to discuss your topic, and help in understanding/choosing a topic. 3. Select a topic of research. Pick a list of 3-10 relevant papers from recent literature. Define the problem as clearly as you can. 4. The deadline for initial project proposal is due on September 29(W), 2004. Email the proposal to Dr. Mukherjee and Ravi. 5. You will be asked to submit detailed reviews of at least two papers from the list of papers that you have chosen. The first review will be due along with your final proposal. 6. Talk with the professor and the TA about your project proposal. Finalize your project proposal by taking into account comments from the professor. The deadline for final proposal is October 13 (W), 2004. 7. Submit your second literature review by October 27(W), 2004. 8. Work on your project. If your project needs an implementation, do the coding. If your project is a survey of a technology/problem, do the research. 9. Write an intermediate report (strictly less than 10 pages) stating your progress. It is due on November 15(M), 2004. 10. Prepare your final project report. The report should be in a format that is acceptable to journals and/or conference proceedings (Size is limited to 50 typed pages, excluding references but including diagrams and tables. The typical project report is expected to be around 30 pages long). If there are too many tables, include only summary of results and put additional tables and diagrams in the Appendix). Both members of the team should jointly pursue this effort. State explicitly what is your personal effort and what is the group effort. 11. Typical format of a report is as follows: Title, author(s), affiliation, email Abstract ( 150 words), key words Introduction and Motivation Background on the biological aspect of the problem Review and critique of earlier work A summary of your approach and major contributions Background terminology and definitions Theory behind your method Technical approach and algorithms Analysis of algorithms Experimental results Theoretical justification/discussion of your results Conclusions ReferencesAppendices 12. Final Report should be submitted by December 1(W), 2004. Submit all your materials (the project report, the source code, the executable file, all the data files, and all related files) electronically to [email protected] with a copy to [email protected]. You may wish to create your own website for the project and give us your link. 13. You will be required to give a final presentation in the class. The dates for the final presentation will be announced later. 14. You are encouraged to discuss with Dr. Mukherjee and Ravi. We will try to provide more references when you select your topic. Start as early as
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