Project

A significant portion of your grade in this class is dedicated to a term project. This project will give you experience:

This project will be unlike many other projects you have had in that you will continually adopt the perspective of the biologist and their needs for the purpose of creating innovative technology.

Project Overview

Your overall goal in this project is to partner with a researcher in biomedical sciences, understand the problem that they are trying to solve, and the data they have generated or have access to so that you can devise a new or improved bioinformatics method that better meets their needs. When done well, you may find you create something truly innovative and of real value to biological researchers.

The project deliverables are as follows:

  1. Project proposal. In the first deliverable, you will choose a biologist to work with, meet with them to understand the problem are attempting to solve, and present a formulation of this problem. You will choose your project group. Groups of 4 to 5 students will be allowed. A list of biomedical researchers and a brief summary of their resarch area will be provided. Your group will rank the researchers according to their preference and provide that ranking to the instructor. Groups will be assigned to a biomedical researcher on a first-come-first-serve basis. If no preference is given then the instructor will do the selection for the group. The project proposal will be formatted using the Journal of Bioinformatics template and be approximately four pages. The proposal must describe the following: (1) the biological problem, (2) the bioinformatics formulation or approach to solving the problem, (3) the data provided by the researcher, and lastly, (4) a brief literature review.
  2. Project presentation. In the second deliverable, your group will present the problem and solution to the biological problem studied. The presentations will occur in the last weeks of the course. The presentation must be split equally among all the group members. The presentation must demo the website and software in order to illustrate typical use of the software. Your biomedical researchers will be invited to your presentation.
  3. Project Website. Websites are good for many purposes in bioinformatics. They give access to the code, sample data, development updates and relevant research papers. Their primary use is to allow prospective users (researchers in biology and biomedical science) to view and download your code. Keep this in mind when developing your website; there are many features that you can add to your site but only implement those that assist in helping users understand and run your code. At the minimum your group's project website should contain the following: concise explanation of your problem, group members name, course title and number (CIS 6930, University of Florida: Bioinformatic Algorithms), instructor's name (Dr. Christina Boucher), code and/or executables, instructions on how to install and run your code, sample data (possibly simulated), and paper. I should be able to download, install, and run your code with minimal assistance.
  4. Research Paper. For the final deliverable, you will submit a research paper via email to the instructor. This is worth the greatest part of your grade so make sure you spend a significant amount of time on it. You will submit a 10 to 12 page paper in Journal of Bioinformatics format. Use the latex class file provided by the journal and do not alter the latex class file at all. Your paper should have the following sections: abstract, introduction, related work, methods, results including an explanation of the data, discussion, and conclusion.

Project Deliverables

Below is a list of the project deliverables. Everything should be submitted via email to the instructor with the group members and biomedical research partner(s) cc-ed, unless specified.