example for jupyter + nglview (+ pandas?)

MDAnalysis / scipy_proceedings

SciPy conference proceedings: MDAnalysis paper

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example for jupyter + nglview (+ pandas?) #18

Closed orbeckst closed 8 years ago

orbeckst commented 8 years ago

@dotsdl (or someone else) can you provide a representative snapshot of a Jupyter notebook session that shows how one can "typically" work with MDAnalysis interactively? It would be nice to have something like

load trajectory
visualize with nglview
compute something (maybe using pandas)
plot with matplotlib (or pandas/seaborn)

I'd like to have

[ ] image of the notebook in the browser
[ ] python code that could be shown in the paper

kain88-de commented 8 years ago

http://www.mdanalysis.org/2016/03/14/nglview/

we could start from this and additionally compute the RMSD

kain88-de commented 8 years ago

We can publish the notebook as a gist and link to it in the paper

kain88-de commented 8 years ago

notebook-example

gist

I'm not sure how you want to include them exactly though but feel free to use them.

I'm not sure about the screenshot because it will be to small to recognize anything. Code example are fine though.

dotsdl commented 8 years ago

I can work on making this a working section in the paper. Fine with you, @kain88-de?

kain88-de commented 8 years ago

yeah sure. It is only a copy of your blog post anyway.

dotsdl commented 8 years ago

Cool. Working on it now.