updated Azure ML how to guide and README

Author: zbyosufzai

README.md

@@ -86,10 +86,10 @@ After completing this prerequisite learning path, you should be able to:
  _Here are some Azure prerequisites you should make sure are completed before starting the modules. These will give you the necessary cloud computing skills to run the training modules such as launching a VM, cloning modules from GitHub, and more. If anything looks unfamiliar, follow the link to view documentation on that subject. After reading the documentation in the links below, complete the simple tasks described in the steps below as a knowledge check on what you just learned. Complete each step in order to learn the key skills you need to complete the learning modules in the next section!_
    - STEP 1: [Create a Resource Group](https://learn.microsoft.com/en-us/azure/azure-resource-manager/management/manage-resource-groups-portal)
    - STEP 2: [Navigate to Azure ML and Launch a Notebook](https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateAzureMLNotebooks.md)
-   - STEP 3: [Change your Notebook Kernel](https://learn.microsoft.com/en-us/azure/machine-learning/how-to-run-jupyter-notebooks?view=azureml-api-2#add-new-kernels)
+   - STEP 3: [Change/Add your Notebook Kernel](https://learn.microsoft.com/en-us/azure/machine-learning/how-to-run-jupyter-notebooks?view=azureml-api-2#add-new-kernels)
    - STEP 4: [Launch Azure Batch](https://learn.microsoft.com/en-us/azure/batch/quick-create-portal) and submit a test job
    - STEP 5: [Set budget alerts](https://learn.microsoft.com/en-us/azure/cost-management-billing/costs/tutorial-acm-create-budgets?tabs=psbudget) for 25%, 50%, and 75%.
-   - STEP 6:  Clone this GitHub repository into an Azure ML notebook using [the command line](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) or the [user interface](https://learn.microsoft.com/en-us/azure/machine-learning/concept-train-model-git-integration?view=azureml-api-2).
+   - STEP 6:  Clone this GitHub repository into an Azure ML notebook using [the command line](https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateAzureMLNotebooks.md). To learn more about GitHub cloning, check out the link [here](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository).
    - STEP 7: Review how to [open a GitHub issue](https://docs.github.com/en/issues/tracking-your-work-with-issues/creating-an-issue). If you have a question or a suggested enhancement, feel free to open an issue for this repository or for the module you are having trouble with. You can also email us at `CloudLab@nih.gov`.
 
 After completing this prerequisite learning path, you should be able to:

docs/HowToCreateAzureMLNotebooks.md

@@ -23,22 +23,54 @@ This guide will show you how to create a notebook in Azure Machine Learning Stud
   ![](../images/images_for_creating_Azure_ML_notebooks/5.png)
 
 
-6. Finally, give a unique compute name, select your **virtual machine size**, and click **Review + Create**.
+6. Finally, give a unique compute name, select your **Compute Instance**, and click **Review + Create**.
 
   ![](../images/images_for_creating_Azure_ML_notebooks/6.png)
 
-7. To clone an appropriate repository from GitHub.com, click **Terminal**.
+## Azure Notebooks UI vs. JupyterLab
+You have two options to interact with the notebook files: using the Azure Notebooks UI setting or the JupyterLab setting. The steps below will highlight how to clone a GitHub repo and run Jupyter files in each setting.
+
+**Option 1: Azure Notebooks UI**
+1. To clone an appropriate repository from GitHub.com, click **Terminal**.
 
  ![](../images/images_for_creating_Azure_ML_notebooks/7.png)
 
-8. Run `git clone ...`
+2. Run `git clone ...`, follow up with the URL of the GitHub repo you would like to clone (example: `git clone https://github.com/NIGMS/NIGMS-Sandbox.git`). Hit enter.
 
  ![](../images/images_for_creating_Azure_ML_notebooks/8.png)
 
-9. This will download the repository directory to your notebook.
+3. This will download the repository directory to your notebook.
 
  ![](../images/images_for_creating_Azure_ML_notebooks/9.png)
 
- 10. Finally, choose an appropriate Jupyter kernel.
+4. Now you should see your files listed under the **Files** tab. Click the file to open them and verify that it is running by navigating to **Compute**. Ensure there is a green dot next to your instance name and that the status displays **"Running.".**
+
+ ![](../images/images_for_creating_Azure_ML_notebooks/select_compute.png)
+ 
+
+5. Choose an appropriate Jupyter kernel (e.g., R, Python, etc.).
+
+![](../images/images_for_creating_Azure_ML_notebooks/kernel.png)
+
+6. Click the play button next to each cell to run the code or markdown cell.
+
+
+**Option 2: JupyterLab**
+
+1. After you have created your instance, navigate to **Compute** in the left side menu.
+2. Select your instance name.
+3. Confirm that your instance is running; if it's not, click the **Start** button.
+4. Click **JupyterLab**.
+   
+![](../images/images_for_creating_Azure_ML_notebooks/start_open_jl.png)
+
+5. Click **Terminal** in the launcher and run `git clone ...`, follow up with the URL of the GitHub repo you would like to clone (example: `git clone https://github.com/NIGMS/NIGMS-Sandbox.git`). Hit enter.
+
+![](../images/images_for_creating_Azure_ML_notebooks/launcher.png)
+
+6. Double-click to open files located in the left side bar.
+
+7. Select your kernel (default is Python).
+![](../images/images_for_creating_Azure_ML_notebooks/jl_kernel.png)
 
- ![](../images/images_for_creating_Azure_ML_notebooks/10.png)
+8. Select a cell and click the play button at the top to run the code or markdown cell.