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Update README.md in AWS
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hadiparsianNIH authored Feb 6, 2025
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Expand Up @@ -17,9 +17,13 @@ Included here are several submodules or tutorials in the form of Jupyter noteboo

### Creating a notebook instance

Follow the steps highlighted [here](https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateAWSSagemakerNotebooks.md) to create a new notebook instance in AWS SageMaker. For this module you should select Linux 2 and Python 3 in the Environment. In the Notebook instance type tab, select ml.t3.2xlarge from the dropdown box and set volume size to 20 GB. It is **important to shut down** the kernel at the end of your work to avoid getting charged.
- Follow the steps highlighted [here](https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateAWSSagemakerNotebooks.md) to create a new notebook instance in Amazon SageMaker. Follow steps and be especially careful to enable idle shutdown as highlighted. For this module, in [step 4](https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateAWSSagemakerNotebooks.md) in the "Notebook instance type" tab, select ml.m5.xlarge from the dropdown box, and set volume size to 20 GB. Select conda_python3 kernel in [step 8](https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateAWSSagemakerNotebooks.md).

To use our module, open a new Terminal window from your new notebook instance and clone this repo using `git clone https://github.com/NIGMS/Fundamentals-of-Bioinformatics.git`. Navigate to the directory for this project. You will then see the notebooks in your environment.
- You will need to download the tutorial files from GitHub. The easiest way to do this would be to clone the repository from NIGMS into your Amazon SageMaker notebook. To clone this repository, use the Git symbole on left menu and then insert the link `https://github.com/NIGMS/Fundamentals-of-Bioinformatics.git` as it illustrated in [step 7](https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateAWSSagemakerNotebooks.md). Please make sure you only enter the link for the repository that you want to clone. There are other bioinformatics related learning modules available in the [NIGMS Repository](https://github.com/NIGMS). This will download our tutorial files into a folder called `Introduction-to-Data-Science-for-Biology`.

**IMPORTANT NOTE**

Make sure that after you are done with the module, close the tab that appeared when you clicked **OPEN JUPYTERLAB**, then check the box next to the name of the notebook you created in [step 3](https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateAWSSagemakerNotebooks.md). Then click on **STOP** at the top of the Workbench menu. Wait and make sure that the icon next to your notebook is grayed out.

## **Software Requirements**

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