Team Coders Project

TeamCoders is a new project developed from a partnership between Health and Bioscience IDEAS and UCL Clinician Coders. Unlike a hackathon, the goal of this event is to create an inclusive, team building project involving code and biomedical research, bringing people from different background and coding skill levels to work together and quickly increase their coding skill.

Disease Progression Modelling with the Event Based Models

Learning objectives

By the end of the project, attendees will be able to:

  1. Understand the importance of medical imaging in extracting quantitative measures about the disease process in Alzheimer’s disease and other related forms of dementia
  2. Practice standard data cleaning and visualization techniques to interrogate and investigate the input data before analysis.
  3. Learn how to implement the Event Based Model with an application to reproduce findings from a seminal paper.
  4. Further knowledge of the model’s outputs and utilize them for predicting future outcomes

Prerequisites

Please see the Requirements page for the required software skills.

Please note that this course will be using the Python programming language. If you are interested in attending this course or going through its content, then we would recommend you have a basic familiarity with a scientific programming language, preferable Python or R. Understanding source code revision control using Git/Github is optional if your team prefers to collaborate in this manner.

We have provided a directory of Additional Resources in the repository. This material is optional, but we think it will probably be helpful for the course if you are not already familiar with these topics. It covers:

  • Basic overview of Python and Jupyter Notebooks
  • Working with git and GitHub
  • How imaging biomarkers for Alzheimer’s disease are extracted from MRI and PET scans.

If you have experience with R and not Python, don’t worry! Here are some helpful resources that you should look at before attending:

Format

Team Coders events are currently organised as virtual, online events. They will have a few initial kickoff sessions followed by teams working independently for the next couple of days, followed by a final recap session at the end of the week. The project will run for two weeks total.

Week 1

Day 1 (Expected time: 2 hours (3 hours max))

The first day will involve introductions, so that facilitators and participants can get to know each other a bit better, which will make interactions within the team and with the facilitators easier. Then there will be introductory lectures that will provide the background and concepts that will be explored as part of this project:

  • Imaging biomarkers in Alzheimer’s disease
  • An overview of the Event Based Model

Day 2 (Expected time: 2 hours (3 horus max))

The next day will be a more interactive, hands-on session. We will create the teams and then make sure everyone has their environments set up properly. Then we will start with the facilitator demonstrating the basic elements of the first task, which involves data cleaning and wrangling. This session is based on a demonstration notebook, which will be provided to the teams so that they can go through the individual steps themselves and what code was used for each of these steps. Once they have gone through this notebook, the teams will proceed to the project notebook. This will cover the same elements as the demonstration notebook, but it will only consist of some general instructions on what needs to be done, followed by a set of empty Python cells that the teams must complete. The project notebooks will build upon each other, so that the output from the first project notebook will be used as an input for the task in Week 2.

Days 3-4

Teams will work together using the information they learned from the lectures and the information provided in the demonstration notebook to solve the challenge set up in the project notebook. If needed, teams can arrange sessions with one of the facilitators, where they can discuss anything that is unclear to them or if they are stuck on a particular part of the task.

Day 5 (Expected time: 1 hour (2 hours max))

This will be an online recap session, where all teams will discuss the progress they made on the first task notebook, what they found easy, what they found difficult, and any additional things that they tried out.

Week 2

Day 6 (Expected time: 1 hour (2 hours max))

We will go through the second demonstration notebook, which is all about the Event Based Model. If time, we will also go over how the imaging measures in the spreadsheets that you are using are measured from MRI and PET images.

Days 7-9

Teams will work together on the project notebook to replicate the results from the original EBM paper by Alexandra Young and colleagues. Time permitting, they will try to do additional tasks around this dataset. Again, teams are free to request sessions with the facilitators to help them solve the task.

Day 10 (Expected time: 1 hour (2 hours max))

This will be a final recap session where each team will present their work, what they learned on the project, and how they think it will help with their future research.