/ten-rules-jupyter

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

Primary LanguageJupyter NotebookMIT LicenseMIT

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

Build Status GitHub License

This repository is a supplement to

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

Tweets

Twitter Tweets

and its preprint

"Ten Simple Rules for Reproducible Research in Jupyter Notebook"

Tweets

Twitter Tweets

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.

Rule 9: Design Your Notebooks to Be Read, Run, and Explored. The nbviewer links below provide a non-interactive preview of notebooks and Binder 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.

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

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.

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 Binder Binder HTML
1-SimulateTree.ipynb Binder Binder HTML
2-SimulateSequences.ipynb Binder Binder 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.

Vice

Follow these step to run Jupyter Lab on VICE

Contact Us

If you encounter any problems with this repository, please report them here.