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pwrose committed Jun 21, 2024
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Expand Up @@ -31,18 +31,17 @@ This example demonstrates a reproducible 4-step workflow for predicting a protei

---

**Rule 9: Design Your Notebooks to Be Read, Run, and Explored.** The nbviewer links below provide a non-interactive preview of notebooks and ![Binder](https://mybinder.org/badge_logo.svg) buttons launch
Jupyter Notebook or Jupyter Lab in your web browser using the Binder ([mybinder.org](https://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.
**Rule 9: Design Your Notebooks to Be Read, Run, and Explored.** The nbviewer links below provide a static preview of notebooks. Click on the `launch binder` buttons to launch Jupyter Lab in your web browser using the Binder ([mybinder.org](https://mybinder.org/)) server (may be slow!). 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](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/0-Workflow.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example1%2F0-Workflow.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F0-Workflow.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/0-Workflow.html) |
| [1-CreateDataset.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/1-CreateDataset.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example1%2F1-CreateDataset.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F1-CreateDataset.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/1-CreateDataset.html) |
| [2-CalculateFeatures.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/2-CalculateFeatures.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example1%2F2-CalculateFeatures.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F2-CalculateFeatures.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/2-CalculateFeatures.html) |
| [3-FitModel.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/3-FitModel.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example1%2F3-FitModel.ipynb) |[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F3-FitModel.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/3-FitModel.html) |
| [4-Predict.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/4-Predict.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example1%2F4-Predict.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F4-Predict.ipynb)| [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/4-Predict.html) |
| Nbviewer | Jupyter Lab | HTML |
| --- | --- | --- |
| [0-Workflow.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/0-Workflow.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F0-Workflow.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/0-Workflow.html) |
| [1-CreateDataset.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/1-CreateDataset.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F1-CreateDataset.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/1-CreateDataset.html) |
| [2-CalculateFeatures.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/2-CalculateFeatures.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F2-CalculateFeatures.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/2-CalculateFeatures.html) |
| [3-FitModel.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/3-FitModel.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F3-FitModel.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/3-FitModel.html) |
| [4-Predict.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example1/4-Predict.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example1%2F4-Predict.ipynb)| [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example1/4-Predict.html) |

---

Expand All @@ -54,18 +53,62 @@ Jupyter Notebook or Jupyter Lab in your web browser using the Binder ([mybinder.

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

| Nbviewer | Jupyter Notebook | Jupyter Lab | HTML |
| --- | -- | --- | --- |
| [0-Workflow.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example2/0-Workflow.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example2%2F0-Workflow.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example2%2F0-Workflow.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example2/0-Workflow.html) |
| [1-SimulateTree.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example2/1-SimulateTree.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example2%2F1-SimulateTree.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example2%2F1-SimulateTree.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example2/1-SimulateTree.html) |
| [2-SimulateSequences.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example2/2-SimulateSequences.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?filepath=example2%2F2-SimulateSequences.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example2%2F2-SimulateSequences.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example2/2-SimulateSequences.html) |
| Nbviewer | Jupyter Lab | HTML |
| --- | --- | --- |
| [0-Workflow.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example2/0-Workflow.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example2%2F0-Workflow.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example2/0-Workflow.html) |
| [1-SimulateTree.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example2/1-SimulateTree.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example2%2F1-SimulateTree.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example2/1-SimulateTree.html) |
| [2-SimulateSequences.ipynb](https://nbviewer.jupyter.org/github/jupyter-guide/ten-rules-jupyter/blob/master/example2/2-SimulateSequences.ipynb) | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jupyter-guide/ten-rules-jupyter/master?urlpath=lab/tree/example2%2F2-SimulateSequences.ipynb) | [HTML](https://rawgit.com/jupyter-guide/ten-rules-jupyter/master/example2/2-SimulateSequences.html) |

## Runnning Jupyter Notebooks on CyVerse/VICE
The new [VICE (Visual Interactive Computing Environment)](https://cyverse-visual-interactive-computing-environment.readthedocs-hosted.com/en/latest/index.html) in the [CyVerse Discovery Environment](https://www.cyverse.org/discovery%20environment) enables users to run Jupyter Lab in a production environment. To use VICE, sign up for a free [CyVerse account](https://www.cyverse.org/create-account).
---

## Run Jupyter Lab on a local Machine (Laptop, Desktop)
Prerequisites: Miniconda3 (light-weight, preferred) or Anaconda3 and Mamba

* Install [Miniconda3](https://docs.conda.io/en/latest/miniconda.html)
* Install Mamba: ```conda install mamba -n base -c conda-forge```
------

1. Clone this git repository

```
git clone https://github.com/jupyter-guide/ten-rules-jupyter.git
```

2. Change into the directory

```
cd ten-rules-jupyter
```

3. Create CONDA environment

```
mamba env create -f environment.yml
```
4. Activate the CONDA environment

```
conda activate ten-rules-jupyter
```
5. Launch Jupyter Lab

```
jupyter lab
```

6. Deactivate the CONDA environment

```
conda deactivate
```

------

[![Vice](vice/vice_badge.png)](https://de.cyverse.org/de/?type=apps&app-id=8ec235d8-f173-11e9-a56f-008cfa5ae621&system-id=de)
> To remove the CONDA environment, run ```conda env remove -n notebooks-sharing```
------

[Follow these step to run Jupyter Lab on VICE](https://cyverse-visual-interactive-computing-environment.readthedocs-hosted.com/en/latest/user_guide/quick-jupyter.html)
## Citation
Rule A, Birmingham A, Zuniga C, Altintas I, Huang SC, et al. (2019) Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. PLOS Computational Biology 15(7): e1007007. [https://doi.org/10.1371/journal.pcbi.1007007](https://doi.org/10.1371/journal.pcbi.1007007)

## Contact Us
If you encounter any problems with this repository, please report them [here](https://github.com/jupyter-guide/ten-rules-jupyter/issues).

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