This repository contains the master's thesis project of Rosemary McCloskey. I am a student in the CIHR Strategic Training Program in Bioinformatics at the Univeristy of British Columbia in Vancouver, Canada. My supervisor is Dr. Art Poon, a scientist at the BC Centre for Excellence in HIV/AIDS, and an adjunct professor in the Department of Medicine, Univerisity of British Columbia.
This project is divided into several folders, described below. Each of them contains a README with further details.
The programs and simulations in this project have quite a few external dependencies. To make this easier to manage, this folder contains a script to download and compile all the necessary programs and libraries. It has been tested on a couple of Linux systems. Realistically, it's not going to work on every system out of the box, but it should at least give you an idea of what to install.
Presentations, papers, etc.
Source code I have written for the project.
Papers I've read, and some notes about them. This isn't every paper I've read for this project, because realistically I often get lazy and don't bother writing notes. A lot of the notes are very sparse too, only a bullet point or two.
Reference manuals for software. I like having offline documentation. There is a Makefile which will download the most recent verison of everything.
This is the biggest section. Contains all the computational experiments.