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docs: Update README for running notebooks (#286) (#288)
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* Updated the python version from 3.7 to 3.10
* Provided description about running the notebook on VS Code
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Co-authored-by: Manish Kuniyal <[email protected]>
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korikuzma and manish0kuniyal authored Dec 6, 2023
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Expand Up @@ -104,7 +104,7 @@ Here are some things to try.

Once installed as described above, type

$ source venv/3.7/bin/activate
$ source venv/3.10/bin/activate
$ jupyter notebook --notebook-dir notebooks/

The following jupyter extensions are recommended but not required
Expand All @@ -113,6 +113,22 @@ The following jupyter extensions are recommended but not required
$ jupyter contrib nbextension install --user
$ jupyter nbextension enable toc2/main

## Running the Notebooks on the Terra platform

[Terra](https://terra.bio) is a cloud platform for biomedical research developed by the Broad Institute, Microsoft and Verily. The platform includes preconfigured environments that provide user-friendly access to various applications commonly used in bioinformatics, including Jupyter Notebooks.

We have created a public [`VRS-demo-notebooks`](https://app.terra.bio/#workspaces/terra-outreach/VRS-demo-notebooks) workspace in Terra that contains the demo notebooks along with instructions for running them with minimal setup. To get started, see either the [`VRS-demo-notebooks`](https://app.terra.bio/#workspaces/terra-outreach/VRS-demo-notebooks) workspace or the [`Terra.ipynb`](notebooks/Terra.ipynb) notebook in this repository.

## Running the Notebooks with VS Code

[VS Code](https://code.visualstudio.com/) is a code editor developed by Microsoft. It is lightweight, highly customizable, and supports a wide range of programming languages, with a robust extension system. You can download VS Code [here](https://code.visualstudio.com/Download).

**1. Open VS Code**: Launch Visual Studio Code.
**2. Install the Jupyter Extension**: Use Extensions view (Ctrl+Shift+X or ⌘+Shift+X) to install the [Jupyter extension](https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter).
**3. Open the Project in VS Code**: Navigate to your project folder and open it in VS Code.
**4. Select the Jupyter Kernel**: In a notebook, click `Select Kernel` at the top right. Select the option where the path is `venv/3.10/bin/python3`. See [here](https://code.visualstudio.com/docs/datascience/jupyter-kernel-management) for more information on managing Jupyter Kernels in VS Code.
**5. Run the Notebook**: After selecting the kernel you can now run the notebook.

# Development

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