Open source tools for reproducible neuroscience research

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Open source tools for reproducible neuroscience research

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2015-11-06-IU

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Open source tools for reproducible neuroscience research

Ariel Rokem, University of Washington eScience Institute

Follow along at http://arokem.github.io/2015-11-06-IU/

"An article about a computational result is advertising, not scholarship. The actual scholarship is the full software environment code and data, that produced the result" Buckheit and Donoho (2005)
How can we make that a reality?

Python

The lingua franca of reproducible computational science

Open source

Easy to learn

Phenomenal ecosystem of open-source tools

The scipy & nipy ecosystem

The scipy & nipy ecosystem

The scipy & nipy ecosystem

The scipy & nipy ecosystem

The foundations of the eco system

numpy scipy

Data visualization

Matplotlib Bokeh mpld3

Statistics and Machine learning

Pandas X-Ray Statsmodels Scikit Learn

Image processing

Scikit image Open CV ...

High performance computing

Cython Dask Numba Spark

Interactive computing and reproducible research

Jupyter
In Matlab too!

And Neuroscience?

The NIPY community Thunder
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Open source tools for reproducible neuroscience research Ariel Rokem, University of Washington eScience Institute Follow along at http://arokem.github.io/2015-11-06-IU/