Peter Rose

Add modin-ray package for osx-64 to conda-forge

1

Mac osx-64 is a common development platform. While modin-dask is available for osx-64, modin-ray is not.

See issue: https://github.com/rcsb/mmtf-python/issues/28 I looked at the entity information in the MMTF files and indeed for example in 1o2f the third entity is missing (3 non-polymer syn 'PHOSPHITE ION' )....

Jupyter Lab: neo4jupyter.init_notebook_mode() -> Javascript Error: require is not defined

7

neo4jupyter (v 0.1.2) doesn't seem to work in Jupyter Lab: import neo4jupyter neo4jupyter.init_notebook_mode() Javascript Error: require is not defined

[Feature request] Use GISAID deep link URLs in metadata.tsv

6

Use GISAID deep links as URLs as described here: https://www.gisaid.org/help/publish-with-gisaid-references/

We need to refactor the code that processes variants to re-instate the update process.

Download for MX COVID-19 confirmed cases and deaths fails

5

The URls to download the Mexican confirmed cases and death give a 404 error (see: https://github.com/covid-19-net/covid-19-community/blob/master/notebooks/dataprep/02d-GOBMXCases.ipynb). We need to find out if there is a different way to download these...

The plot "Cummulative {pathogen} structures by release date" should use a unique color for each type of protein. notebooks/analyses/Coronavirus3DStructures.ipynb

Use log scale to display number of strains per country in : https://github.com/covid-19-net/covid-19-community/blob/master/notebooks/analyses/StrainB.1.1.7.ipynb

IndexError: list index out of range when running: https://hub.aws-uswest2-binder.pangeo.io/user/pwrose/lab/tree/3-mmtf-pyspark/6-Output.ipynb