The CS 394C final project

You have at least two options for your final project. One is to do a project that involves software development, either to produce a new method and study it, or to compare existing methods. The other main option is to do a survey paper on some topic related to the research discussed in the course (for example, some aspect of phylogenetic analysis and multiple sequence alignment). Of these two basic categories, the survey paper is much easier, but the first category is much more fun!

Research Project

If you want to do a project that involves developing a new method or testing existing methods, please come see me early in the semester. I will help you learn how these studies are done, and we'll begin the planning for this kind of work early.

There are journals that you can consider submitting a research paper to, including PLoS Currents, Tree of Life. The advantage of PLoS Currents is that the requirements for acceptance do not focus on perceived impact (where reviewers can disagree substantially). It is not required that you submit your research paper to a journal, however! Some examples of research projects that you might consider doing:

Some projects that would require more substantial programming include

Survey Paper

Writing a good survey paper is not trivial. You will need to understand the papers you are reading and have some insights into the different contributions made by different papers. The quality of your writing is very important, and you should think of this as something that you would be willing to submit to a journal in the form that you submit it for a grade. That means, among other things, no typos, no grammatical mistakes, a proper bibliography (with full bibliographical information), and thoughtful exposition. Also hand in hardcopy of the main papers you reference. Be careful, of course, not to include any text from any other paper, unless you put quotes around it and properly attribute it.

When you write a survey paper, you need to specifically identify the question you are interested in, and why it is interesting and important. You should explain controversies (if any), the leading approaches, and the evidence in favor or against each approach. You need, as always, to really be critical - not necessarily just accepting what the authors say, but pointing out limitations of their approach. Examples of possible topics for a survey paper include: