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A major component of this course will involve a project. Information on the project can be found on this page.
The project will be involve reading and understanding one (or more) published research papers in the field of mathematical oncology. The project should focus on a specific biological problem studied (at least partially) from a mathematical perspective. That is, the paper should not be entirely experimental, but should have quantitative aspects. Topics can be chosen as you'd like, but should both (1) relate to cancer, and (2) be distinct from work directly covered in class. To make (2) more clear: you may investigate a topic discussed (such as optimal therapy, quiescence, data fitting, competition, etc.), but you should not work entirely from a paper explicitly discussed. You will be expected to submit a typed report, as well as give a short presentation on May 5th (the day of the scheduled Final Exam). You must work in groups of three or four fellow students, and all work will be submitted (and graded) as one. More explicit information on the individual components can be found below.
Topics can be selected as you like, but hopefully will reflect the interest of everyone in the group. The work does need to be based in mathematics, so that there is a substantive quantitative component. Note that you will be expected to reproduce major results from the work, so I suggest carefully considering the feasibility of this before making final selections. I will ask for prior approval on the topic and the primary paper (see Tentative Schedule below), so as to assess the level of difficulty, and to confirm there are aspects which I think are reasonably reproducible. For an idea of possible topics, see below. If your group would like further assistance in choosing a topic/paper, feel free to contact me.
You and your group will be expected to read, understand, and reproduce certain aspects of your chosen paper(s). To submit to me, you should include a basic summary of the work and the results. This should include an introduction discussing the biological problem, methods used (mathematical and experimental), and conclusions. You should also include a critique of the work, e.g. does it answer the question?, what assumptions are made and are they reasonable?, what could be improved upon?, etc. Essentially, I am asking you to rewrite the paper as you understand it, with a critique and possibly even future directions. Note that this should not be a verbatim reproduction, but rather a summary of your understanding in your own words. You should include mathematical calculations/derivations; specifically elaborating on details which may omitted (this is common in papers). You will also be expected to reproduce some figures via numerical calculations, and the entire document should be typed (I suggest LaTeX, but you may use anything you'd like). By mid-April, I will ask for progress reports, including figures and calculations which you will reproduce (see Tentative Schedule below); some results you may copy/paste directly (for example, any experimental data), as I don't expect you to rewrite the paper entirely. The final report will be due on May 5th. There is no explicit requirement on length, but I do expect the main aspects of the original paper to be included.
During the scheduled Final Exam period (May 5th), your group will be asked to give a short presentation to the rest of the class. It should be around ten to twenty minutes in length, and will most likely be given with slides (although you can give a "chalk talk" if you'd like, it may be hard with certain figures). Each member of the group should participate, and your goal will be summarize the work and your results/conclusions, as well as to motivate the problem biologically. You should be prepared to answer any questions I or others in the class may have.