Ten Simple Rules for Writing and Sharing Computational Analyses in Jupyter Notebooks

This repository is a supplement to

"Ten Simple Rules for Writing and Sharing Computational Analyses in Jupyter Notebooks"

and its preprint

"Ten Simple Rules for Reproducible Research in Jupyter Notebook"

Explore the example notebooks below for an application of the Ten Simple Rules.

In addition, we have setup jupyter-guide to crowdsource more technical and in-depth tutorials and to keep up with the rapidly evolving Jupyter ecosystem. We encourage you to contribute and share your expertise.

Example 1

This example demonstrates a reproducible 4-step workflow for predicting a protein fold classification using a Machine Learning approach.

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Rule 9: Design Your Notebooks to Be Read, Run, and Explored. The nbviewer links below provide a non-interactive preview of notebooks and buttons launch Jupyter Notebook or Jupyter Lab in your web browser using the Binder (mybinder.org) server (may be slow!). (See the Binder website how to setup links to a Git repository.) The HTML links provide a permanent static record of the notebooks. All notebooks can also be launched directly from the links in the 0-Workflow.ipynb top-level notebook.

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Nbviewer	Jupyter Notebook	Jupyter Lab	HTML
0-Workflow.ipynb			HTML
1-CreateDataset.ipynb			HTML
2-CalculateFeatures.ipynb			HTML
3-FitModel.ipynb			HTML
4-Predict.ipynb			HTML

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Rule 8: Share and Explain Your Data. To enable reproducibility, we provide a example1/data directory with all data required to run the workflow. A description of the data with download location and download date is available.

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Example 2

This example demonstrates a reproducible 2-step workflow for simulating a phylogenetic tree and sequences.

Nbviewer	Jupyter Notebook	Jupyter Lab	HTML
0-Workflow.ipynb			HTML
1-SimulateTree.ipynb			HTML
2-SimulateSequences.ipynb			HTML

Runnning Jupyter Notebooks on CyVerse/VICE

The new VICE (Visual Interactive Computing Environment) in the CyVerse Discovery Environment enables users to run Jupyter Lab in a production environment. To use VICE, sign up for a free CyVerse account.

Follow these step to run Jupyter Lab on VICE

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