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2019 Toronto Health Hack (4-5 October 2019)

Documentation

Talks/Slides

Getting started

The datasets are hosted on Google Cloud, which requires a Gmail account to manage permissions.

  1. Create a Gmail account, if you don't already have one. It will be used to manage your access to the resources.
  2. Give your gmail address to the session hosts.

Databases on BigQuery

BigQuery is a database system that makes it easy to explore data with Structured Query Language ("SQL").

  1. Open BigQuery.

  2. At the top of the console, select tdothealthhack-team as the project. This indicates the account used for billing.

  3. "Pin" a project to the resources menu to view available datasets. In the Resources menu on the left, click "Add data", "Pin a project", then add the following project names: physionet-data and tdothealthhack-data.

  4. You should be able preview the data available on these projects using the graphical interface.

  5. Now try running a query. For example, try counting the number of rows in the demo eICU patient table:

    SELECT count(*)
    FROM `physionet-data.eicu_crd_demo.patient` 

Executable notebooks on Colab

Several tutorials are provided below. Requirements for these notebooks are: (1) you have a Gmail account and (2) your Gmail address has been added to the appropriate Google Group by the workshop hosts.

R Markdown

Datasets can also be queried directly from R. You should be able to run the following RMarkdown notebook in a local version of RStudio: https://github.com/MIT-LCP/2019_toronto_health_hack/blob/master/tutorials/mimic-iii/mimic-iii-los.Rmd