CS/BioE 589AGB final projects and presentations

There are two types of final projects you can do: a survey paper or a research paper. If you do a survey paper, you will do this by yourself, but if you do a research paper then you can do this with someone else. When the final project involves two people, each person must be equally involved in the project, and be able to answer questions about the project. You have a lot of freedom in what you do, and can pick something on your own. However, this document should help you think of things you might want to do. The class presentation you do (between March 31 and April 14) needs to be closely connected to your final project. Therefore, you should have a pretty clear plan for the final project when you pick the paper for your class presentation. While you are thinking about the general area for a final project, you might look at this.

Research Project

If you want to do a research project, please come see me to discuss the possible projects. Datasets for studying methods can be obtained at my old lab webpage, as well as from other projects. Here are some simple examples of research projects:

Biological dataset analysis

The projects in this category involve using a biological dataset (possibly one that has already been published and studied) and analyzing it using a number of different pipelines, in order to understand how method choice impacts discovery.

Exploring methods on simulated data

With biological datasets, one rarely really knows the true phylogeny or multiple sequence alignment, and so evaluating the impact of method choice on final biological discovery is complicated. If you wish, therefore, you can use simulated datasets to explore performance of methods. Many papers provide links to published simulated datasets that you can use. Examples of questions you might address on simulated data include:

New method development

Multiple sequence alignment

Gene tree estimation



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: