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ncats / translator-workflows

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Exploring Colaboratory For Notebook Sharing #59

Closed MarkDWilliams closed 5 years ago

MarkDWilliams commented 5 years ago

I've been exploring ways for us to share editable and executable notebooks with people without the need for them to spin up their own Jupyter environment and Colaboratory from Google seems to fit the bill. I've already uploaded a few notebooks to test, and ones which are self-contained (requiring only publicly available packages) seem to work fine, but there are some issues with notebooks that import code found elsewhere in the GitHub repo. I wanted to get people's thoughts on using Colaboratory and any ideas for resolving issues with intra-repo dependencies. I've included links to a few notebooks below. These seem to work fine: https://colab.research.google.com/github/ncats/translator-workflows/blob/master/greengamma/workflow1/module3/module/module3_ROBOKOP.ipynb https://colab.research.google.com/github/ncats/translator-workflows/blob/master/xray/WF1_2.1.ipynb#scrollTo=sN-Jj1USgHh7 This one has issues with dependencies: https://colab.research.google.com/github/NCATS-Tangerine/mvp-module-library/blob/master/WF2_FA_human.ipynb

cmungall commented 5 years ago

There is also https://mybinder.org/

It won't necessarily run on the existing notebooks in this repo as it requires either a requirements.txt or a Dockerfile. But in theory the dependencies are more under our control here

MarkDWilliams commented 5 years ago

Binder instance can be found here https://mybinder.org/v2/gh/ncats/translator-workflows/master

cmungall commented 5 years ago

ccing @diatomsRcool as I think she was working on this too

diatomsRcool commented 5 years ago

Yes. That's it.