UK Biobank Visualisation

TL;DR for markers

We are not allowed to distribute the dataset, please head to the live version: https://biobank.hatout.dev/ to play with the app.

A web interface to visualise and explore UK Biobank.

Background

UK Biobank is a large-scale population study collecting clinically relevant data from 500,000 participants, including health, demographics, lifestyle and genetics. The resulting database is used to detect early biomarkers of diseases such as cancer, strokes, diabetes, heart conditions, arthritis, osteoporosis, eye disorders, depression and forms of dementia in a middle aged (40-60 years old) population.

Unfortunately, the ability to leverage this dataset for biomedical research is hindered by the fact that it is not made available in a user-friendly format. This explorer is an early attempt at bridging the gap between raw data and biomedical insights.

This project was realised as part of the third-year software engineering project at Imperial College London, under the supervision of Dr. Ben Glocker (@bglocker) and Stefan Winzeck.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See Deployment for notes on how to deploy the project on a live system.

Prerequisites

Runtimes

The project uses Python >= 3.8.x and Node >= v14.x.x.

Installing Python

Installing Node

$ python --version  # 2.7.16 ❌ - beware of the default MacOS installation of Python
$ python3 --version # 3.9.0  ✅
$ node --version # 14.1.0    ✅

Depedency Management

Depedencies are managed using pipenv and yarn.

$ pip/pip3 install --user pipenv
$ pipenv --version # pipenv, version 2020.x.x ✅

Installing yarn

$ yarn --version # 1.22.4 ✅

Deployment

The easiest way to deploy a production-like version of the explorer is using docker-compose. Put your dataset in dataset/ukbb-dataset.csv and simply run:

$ docker-compose up

Built With

Dash Plotly - The web framework used

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Authors

Rayan Hatout - GitHub | Twitter | LinkedIn
Richard Xiong -
Thomas Coste - LinkedIn
Archibald Fraikin -
Lydia He -
Karol Ciszek -

See also the list of contributors who participated in this project.

License

This project is licensed under the MIT License - see the LICENSE.md file for details

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