Tom Pollard

Make Jupyter notebooks web executable

1

Binder (http://mybinder.org/) can be used to make notebooks web executable. Setting this up on the repository would allow people to participate in workshops without any installation requirements.

Histograms in Table 1

11

Not sure how easy this would be to implement, but making a note of this idea: https://twitter.com/DocEd/status/1572603047590916097 > why don’t we just have a little histogram for each variable in...

As discussed in https://github.com/MIT-LCP/mimic-code/issues/1410#event-7683954515, the following page mentions "mimic_core", which no longer exists: https://mimic.mit.edu/docs/gettingstarted/cloud/bigquery/ @SichengH please could you remove mimic_core from this page?

At some point, migrate these repo (+ issues etc) to the new WFDB organisation on GitHub, if you're good with this: https://github.com/wfdb (@bemoody accept your invitation and I will make...

@ikarosilva we have created an organisation on GitHub to bring together the various WFDB repos/implementations into one place, and also to track things like the (forthcoming) WFDB specification documents. As...

I'm not sure exactly when this happened, but BigQuery updated the project search tool so that `physionet-data` is no longer findable using our existing instructions. The new process for pinning...

Note to investigate [Advanced Scientific Data Format](https://en.wikipedia.org/wiki/Advanced_Scientific_Data_Format). See https://asdf.readthedocs.io/en/latest/asdf/features.html for documentation on the format. It seems like ASDF it might be an option for creating file packages that contain human...

Implement `to_ccdef()` function to output WFDB data to CCDEF/HDF5 Critical Care Data Format

1

This needs more thought/discussion, but I wanted to make a note before I forget. If possible it would be helpful if we could introduce a function that would allow WFDB...

https://physionet.org/rest/database-list/ is being deprecated

16

As discussed in https://github.com/MIT-LCP/physionet-build/pull/1697, we plan to deprecate the `database-list` API on PhysioNet, in favour of a new API served from: `/api/v1/`. If/when https://physionet.org/rest/database-list/ is deprecated, the following function will...

TypeError: Int64: converted = maybe_downcast_numeric(result, dtype, do_round)

3

When run in a Colab notebook (specifically https://github.com/MIT-LCP/hack-aotearoa/blob/main/03_summary_statistics.ipynb), the following chunk raises a data type error (related to Int64 formatted values). ``` from tableone import TableOne %%bigquery cohort SELECT p.unitadmitsource,...