CSC 210

Final Project

Logistics:

You must first consider the first option, Your Choice, below. A preliminary proposal, of length of about a page, of your choice for a project is due on April 20, 2010. Along with your proposal, please turn in a copy of the main reference article/source you intend to use for your proposal. If would be preferable to submit your proposal before this due date, if you have it ready. We will provide feedback on your proposal and will let you know if your proposal is accepted. If your proposal is rejected, then you must do the second choice, Professor's Suggestion.
If you cannot come up with a suitable project idea, you must still submit a preliminary proposal, explaining your efforts in looking for a project idea. In this case you must complete one of the Option 2, Professor's Suggestion, as your final project.
You must turn in your final project to get a grade in the course. The Final Project Report is due at 4PM on May 11, 2010. You may submit your project assignments before the due dates, if you prefer.
Your project reports should resemble a formal report; an introduction should set the project in context, the body should include the details of your findings, a conclusion, and references should round out your report. An appropriate length for your report should be about 8-12 pages.
This is a project assignment, not just a homework problem. Do not be discouraged by the open-ended nature of the task. Use this oppotunity to showcase your imagination and skills.

Option 1: Your Choice

For this choice you are asked to construct a project of your own choosing. Talk to your professors (including us), TAs, consult books, journals, the library of equations in Phaser, etc. as possible sources. For example, you can find a model equation of your choice and simulate it on the computer to uncover a phenomenon; you can write code to implement some numerical algorithms. If you have access to some experimental data, you can try to fit the data to a dynamic model.

Option 2: Professor's Suggestion

Try to read parts of the original paper Deterministic Nonperiodic Flow by E. N. Lorenz, Journal of the Atmospheric Sciences, 1963; 20: 130-141.
These famous differential equations (25-27) of this paper are in the ODE library of PHASER.
Try to reproduce some of the computational experiments descibed in the paper and create similar illustrations. Interpret your computational findings in terms of fluid mechanics.
You should explore the three-dimensional plotting facilities of PHASER to visualize the solutions.
You should create a sequence of simulations as the parameter r is varied and explain the dynamical changes (bifurcations) that can occur.
You should consult other sources on this famous example.

Option 2: Professor's Suggestion

On the ncbi genome site, find a bacterial species with at least two chromosomes and download these two chromosomes. Then find another related species (in the same genus) and download one more chromosome from that one. Now compute the distribution of overlapping 4-mers (substrings of length 4) for each of these chromosomes, by counting the number of appearances of each 4-mer in each chromosome. Compute the correlation of the distributions using the sample Pearson's correlation coefficient. What do you observe? What happens if we vary the size of the k-mers (instead of 4 use another value)? How do these distributions correlate to a chromosome of another unrelated species from a different genus?

Option 2: Professor's Suggestion

Download a large chromosome (> 5Mb) of a bacterial species. Identify all open reading frames (ORFs) in this chromosome. Compare this number to the number of known genes in this chromosome. What are your observations? Did you discover any regions which could potentially indicate the existence of novel undiscovered genes?