Online Companion to Wayne’s Poster for Retreat 2016

Links and resources for Jupyter Notebook and how to launch shareable active Jupyter Notebooks from a poster presented at Upstate Medical University’s Biomedical Sciences Retreat 2016. Poster entitled: Biomedical Science on Jupyter: Comprehensible and Reproducible Scientific Workflows with Shared, Active Jupyter Notebooks

Launch Demo Binder

Go to an example repository by clicking HERE.

Once there, click on the Binder button to launch the demo.

Give the notebook a minute to load and then press SHIFT+ENTER on your keyboard or press the play button in the toolbar several times to step through and run cells.

The cells that should run will have the In [ ] on the left and they will become filled with numbers when complete. Several will have viewable output.

Go back to the repository main page. Once there, click the blue text that says Decoding translation in the cloud and at....

This will open a rendering of the notebook, but you see all the In [ ] on the left have nothing between the brackets and none of the output cells are present.

This is a static rendering of the notebook. We cannot interact with it. If I had saved the completely run notebook, the output would be there but we still would not be able to interact with it. (And so it is useful, but not as useful as an active Jupyter Notebook.)

(A richer version of the static version of the notebook can be viewed here via the nbviewer that will render any Github-hosted Jupyter Notebook. Often this works better for notebooks that have fancy plots embedded that the default Github rendering doesn’t handle.)

This was a very simple notebook that has a good mix of the features as it was meant to touch casually on some molecular biology aspects while introducing the Jupyter Notebook system to some students that visited Upstate.

The repository hosting that Jupyter Notebook can be found here. To get the launch binder button to work I had to previously tell the Freeman Lab’s Binder system found at mybinder.org to build a binder from that repository at Github. That binder then becomes available for users to spin up notebooks on-demand, essentially instantaneously.

Basic Notebooks to Illustrate Use in the Lab

These links will take you to the Github page where you’ll see links to the static notebooks as well as Binder buttons to launch the notebooks as active notebooks using the Freeman Lab’s Binder system found at mybinder.org.

Click the Binder button at any of the following repositories for an active notebook:

Notable Notebooks

See the penultimate page of this online documentation for a list of example scientific Jupyter Notebooks, entitled A sampling of scientific notebooks & extensions.

To get there, the easiest way is to click here press or Next in the bottom right of each page three times to get to the page entitled References and Resources to Match Poster Sections.

See that page as well as for the list of example notebooks using the Github/Binder approach.