CSC 334: Topics in Computational Biology

Homework 6: Final project proposal

Due: Friday, Nov. 13, 11:59pm on Moodle

The goal of this assignment is to help you start working on your final project and assembling the different resources you want to use (literature, software, data, etc).

Submit your proposal (PDF for Word document) on Moodle, addressing the following points (unless you've already talked to me about doing a different type of project). It should be about a page long.

  • Motivation

    Why is this an interesting or relevant topic? You could talk about your personal motivation for this topic, or why it would be interesting to investigate in general.

  • Data

    What data will you use for this project? It could be real data or simulated data (if your ideal data is not available, simulated data is great alternative and I'm happy to talk more about that). Please be as specific as possible. If you are using real data, include a link to the data online. Here are a few databases to get started:

    1. NCBI: Over 14,000 different organisms (plants, animals, viruses, etc)

    2. 1000 genomes: More than 1000 humans genomes from around the world

    3. Neandertal genomes: Several ancient genomes, compared to human sequences
  • Software

    What software/methods will you use for the project? You can write your own method(s) or use existing software, but there should be some programming component. You could compare two existing methods, or compare your own method to an existing method. Even if you're planning to use existing software, there will likely be a significant programming component since you'll have to get the data in the right format, learn how to run the program, and interpret the results.

    If you are using any existing software, include a link.

  • Results

    What is the end goal of the project? It could be a specific type of figure or table, or the outcome of a comparison. In an ideal scenario, what might you be able to say about biology at the end of the project?

UPDATE: also include a list of references.