Project introduction

You will assemble into groups of 3 to 4 students. You will have choice around the type of project you would want to do. Projects can be of two broad types:

• Data analysis projects where you use publicly available data to answer a biological or biomedical question. You must state your question(s) clearly, explain why your data set(s) are appropriate for the question, perform data analysis and modeling as appropriate, and show that your results are robust and generalizable. Your analytic methods must be concordant with the study design used to collect the data. It is recommended that you use at least two datasets, one to develop your analytic workflow, and the rest to validate your results. There is flexibility around this depending on the question and analytic methods you plan using for the project.
• Review projects where you do a literature review around methods to answer partcular analytic questions applicable to the life sciences. This will involve developing a well-annotated bibliography, data analysis or in silico experiments to demonstrate the methods you are reviewing and highlight their properties, a clear discussion on the strengths and limitations of the methods for applications, and or code to implement the method, either as a well-annotated set of scripts forming a workflow, or a R/Python package.

In both cases, you will be expected to present your work in a short final presentation, and submit both a final report and a slide deck of no more than 10 slides to describe the work you have done. Reports may be in the form of Quarto documents/webpages/websites, and can incorporate WebAssembly technology (webR or pyodide) to add interactive elements, but no Shiny/Dash/Streamlit applications will be allowed. Slide decks must contain only static material and browser-based interactivity (Javascript/WebAssembly).

There will be a template repository provided, which sets up your projects in a particular standard structure. The projects should be completely reproducible, which means, among other things, that there can be no links to personal spaces that are not publicly accessible, no hard-coded paths and no “magic” numbers. What we will aim for is what is often called a “research compendium”.

Some suggested project topics are provided here, but this is meant to give you an idea of what we’re looking for; you don’t have to do any of these topics, and can choose any topic, as long as the instructor agrees with the scope and depth of your proposed project.

We do strongly suggest that you use a reference manager like Zotero, and create citations in your Quarto documents using it. There should be a reference.bib file in your project which holds all the references you might be using.