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Setup

Software

First things first you'll need an integrated development environment or IDE to start coding. We recomend VS code for coding in python and really anything other than R. Use the following link to install VS code:

VS Code Installation

Additionally, you'll need Anaconda for managing packages, use the following link to install Anaconda:

Anaconda Installation

Extensions

Once both are installed you'll need to install some extensions in VS code. We will be working with Jupyter notebooks so we need to install the Jupyter extension:

  1. Click Extensions
  2. Type Jupyter in the search bar and download the Jupyter extension

Project Setup

Now let's set up a space for us to work in. We will start by creating a virtual environment:

  1. Click Open Folder
  2. Create a folder and name it deep_learning
  3. Go inside the deep learning folder cd deep_learning
  4. Create 3 folders inside deep_learning:
  5. mkdir data
  6. mkdir scripts
  7. mkdir results

To download the data we will use:

  1. Go into the data folder: cd data
  2. curl --output gbm_cptac_2021.tar.gz https://cbioportal-datahub.s3.amazonaws.com/gbm_cptac_2021.tar.gz
  3. Extract the contents: tar -zxvf

Now to set up the virtual environment:

  1. Go to View > Terminal
  2. In terminal enter: conda create -n dl python=3.12 pytorch torchvision plotly
  3. Then enter y
  4. Then at the top of VS code select "Select Kernel"
  5. Select "dl"

Now Let's Start Coding!