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GWAS Diversity Monitor

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Introduction

This is a repository which holds an early prototype of the GWAS Diversity Monitor, currently maintained as part of the Leverhulme Centre for Demographic Science. The re-released dashboard can be found at:



The interactive plots in this version are written in Bokeh and were prototyped on Heroku. Grateful attributions regarding data are made to the EMBL-EBI GWAS Catalog. In summary, the dashboard visualizes a systematic interactive review of all GWAS published to date. It borrows a couple of functions from our Scientometric Review of all GWAS. This repo can be cloned and ran on-the-fly to generate a server on localhost as required. The dashboard and associated summary statistics check daily for updates from the Catalog and update with new releases (i.e. we used to run generate_date.py on a daily cron job and push to the master branch for Heroku to catch).

Prerequisites

As a pre-requisite to running the Bokeh sever, you will need a working Python 3 installation with all of the necessary dependencies detailed in requirements.txt (generated by pipreqs). We strongly recommend virtual environments and Anaconda.

Running the Code

This server is operating system independent (through the os module) and should work on Windows, Linux and OS X all the same. To run: clone this directory, cd into the directory, and then run bokeh serve gwasdiversitymonitor_app --show in a terminal to launch the server. In more detail, main.py generates the figures itself, and contains functions for each of the six plots which are then added to a Jinja2 template using curdoc().add_root(). The template is stored in templates/index.html, and contains html and css to build in additional content (pulling in things like funding templates) and bootstrap it. The generate_data.py script updates the html with summary statistics from gwasdiversitymonitor_app/data/summary/summary.json.

Versioning

This dashboard prototype was halted at Version 0.8.0, and wholly represents a prototype. Please note: although the library logs data updates, it could be that additional dictionary based classifications are required with regards to the /data/support/dict_replacer_broad.tsv file. Please raise an issue in the new page for the project.

License

This work is free. You can redistribute it and/or modify it under the terms of the MIT license, subject to the conditions imposed by the EMBL-EBI license. The dashboard comes without any warranty, to the extent permitted by applicable law.

Acknowledgements

We are grateful to comments on the source code and infrastructure from Ian Knowles, Yi Liu, Molly Przeworski, Ben Domingue, Sam Trejo and the Sociogenome group more generally.

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An early prototype of the GWAS Diversity Monitor, written in Bokeh

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