Through this project you will get hands-on experience, managing and analyzing real biomedical
datasets. The goal of the project is to give students the opportunity to tackle a large,
interesting problem, which may lead to a publication. There will be a variety of suggested
projects to choose from. You are free to select a specific topic for your project.
Students are expected to write a project proposal, a final report/paper on their projects
and present their work in class. The projects will be carried out in teams of 2.
Once you have selected a specific topic for your project, you should do some background reading
so that you are capable of describing, in some detail, exactly what you expect to accomplish.
Once you have read up on your topic, you will be ready to write your proposal.
In the proposal you should describe what you plan to do and how you plan to do it. You should
describe the problem that you will be considering, previous work on this problem by others,
how you plan to address it, what tools you will use, what you expect to produce as a result of
this work, and anything else that you think the instructor should know to evaluate your plans.
The proposal should be approximately 5-10 pages long, self-contained, describing clearly the
alternatives that you will be considering and the milestones. Please provide a plan of
activities and time estimates, per group member. The proposals will be evaluated by the
instructor. After approval of the choice of topic you should start working on your project.
Your final report is expected to be a detailed report, treating in depth the agreed topic.
It should be in the form of a paper. You should describe what you did, what results you obtained,
and what you have learned and/or can conclude from your work. It should include an introduction,
a survey, your contributions (methodology, assumptions, rationale, etc), your experimental
results from the analysis of the biomedical data at hand, problems for future research, a list
of references, a brief description of the developed modules, and a manual that should explain how to
run your programs. You should state the reasons why you took a specific approach. If possible you
should compare your approach with others and provide some explanation/justification of the
results you obtained. Careful packaging for distribution and a demonstration is also expected.
The project involves three parts that are graded: a proposal (15%), a final report (75%)
and a short presentation (10%). You should submit electronically all these parts to
The final report will be graded according to the following guidelines:
a description of the purpose of the project and motivation, justification for the proposed
solutions, a report on the methodology you applied [30 pts.]
code and documentation produced: a source program listing [20 pts], a user's manual for running the
programs  pts, your testing efforts to evaluate the performance of the methods, and to validate
their correctness and completeness [30 pts], a description of the limitations and the
possibilities for improvements [10 pts].
- Proposal: Oct. 4
- Final report: Dec. 1
- Short presentation: Dec. 6