Setting up your system for the course

You need to have done the following setup on your laptop before the course starts. Given the prerequisites, you should typically be fine doing this by yourself, but if you run into unexpected problems, we will have a drop-in help session (date and time TBD). If you discover errors below, please let us know.

NB! If you don't have the permissions to install software on your laptop, you must ask your system administrator to either give you such permissions or install the software for you. This will require extra time so please plan for this!

0. Terminal setup

Unix, Linux and MacOSX already have a terminal app installed:
- on MacOSX, you can find it by searching for "Terminal" in the launch pad.
On Windows, you may use, e.g., PowerShell, cmd initially, then you will switch to using WSL2

1. Setting up Pixi and Git

Pixi is the package manager that we will use to setup the course environment, so that all necessary requirements are available to run the labs on your laptops.

Git is the version control tool that we will use to make sure that your course material is up to date.

Both tools are fundamental to run the labs within this workshop. So make sure you install them!

OS-specific installation instructions:

If you have Linux or MacOSX, you will simply install Pixi and Git. If you have Windows, there are a few extra steps to complete before you can install the tools, see below.

On Mac OS X

First, make sure you have Xcode and CommandLineTools installed and updated to latest version (in AppStore). If you have not already installed CommadLineTools, go to a terminal window and run:

xcode-select --install

To download the latest version of Pixi and install it, run:

curl -fsSL https://pixi.sh/install.sh | sh

Now restart your terminal or shell to make the installation take effect. You can check if pixi is working by running:

pixi --version

You should also check that git is installed on your system:

git --version

If you don’t have it installed already, the system will then prompt you to install it.

On Linux

Download and install the latest version of Pixi:

curl -fsSL https://pixi.sh/install.sh | sh

Now restart your terminal or shell to make the installation take effect. You can check if pixi is working by running:

pixi --version

You should also check if git is installed on your system:

git --version

If the previous command fails, you should install Git:

sudo apt-get install git

On Windows

Unfortunately, not all packages that we need are compatible with windows machines. The good news is that Windows 10 and newer offer native linux support via the Windows Subsystem for Linux (WSL2). This allows you to run linux/bash commands from within windows without needing a virtual machine or dual-boot setup (i.e. having 2 operating systems).

On Windows 10-11, install the WSL if you don’t have it. Follow the instructions here: https://learn.microsoft.com/en-us/windows/wsl/install

In most cases, you can simply open PowerShell as Administrator and run:

wsl --install

Restart your computer if prompted.

Once you have WSL installed, open your Linux terminal by either:

Searching for “Ubuntu” in the Start menu, or
Running wsl in PowerShell or cmd

The first time, you will be asked to create a username and password.

Inside WSL, install Pixi:

curl -fsSL https://pixi.sh/install.sh | sh

Then, install Git:

sudo apt-get install git

2. Clone the workshop git repository

At this point you should have git on your system, you can just run:

git clone https://github.com/NBISweden/workshop_NN_DL.git

If you don't have git on your system, you will need to install it (go back to step 1. in the guide or look up instructions here).

3. Initialize the Pixi environment

Once you have cloned the course's Git repository, change to the repository directory:

cd workshop_NN_DL/

Then, initialize the Pixi environment by running:

pixi shell

Pixi will automatically install the necessary packages and tools (it may take a few minutes). When done, your shell prompt should look more or less as follows:

(workshop_nn_dl) user@PC:~/workshop_NN_DL$

Notice how it says "workshop_nn_dl" in brackets? That means that you are within the workshop's environment, and all the necessary tools to run the labs are now available to you. Next, you can test the installation by running:

pixi run test

That should print the following output:

(workshop_nn_dl) user@PC:workshop_NN_DL$ pixi run test
✨ Pixi task (test in default): python -c 'import torch; print(torch.cuda.is_available())'
False

You can also try launching Jupyter Lab:

jupyter lab

Jupyter lab should open in your browser if everything was installed correctly. If that doesn't happen, something might have gone wrong. Reach up to us at the pre-course drop-in meeting and we will try to help you solve the issue.

Future uses

Whenever you want to activate the workshop environment, for example after you've shut down your computer, just go back to the workshop repository directory on your drive and run pixi:

user@PC:~$ cd /path/to/workshop_NN_DL/
user@PC:workshop_NN_DL$ pixi shell
(workshop_nn_dl) user@PC:workshop_NN_DL$

And the environment will be ready

Google account setup

Some of the exercises will be run on Google's colab server and you will therefore need a Google account to do these exercises.
If you don't already have a google account, you need to create such an account

Refresh yourself on Statistics and ML

You should refresh your memory about basic Statistics and Machine Learning, including the following subjects (includes links to lecture notes from the NBIS course, Introduction to Biostatistics and Machine Learning)

Differentiation
Vectors. and Matrices
Linear models (including Generalized Linear Models)
Cross validation

Python programming

During the course, you will learn to use the python module pytorch. However, to follow code in the lectures and exercises, you should familiarize/refresh yourself with basic Python syntax, maybe focusing on:

the overall Python coding syntax, esp. the role of indentations
how to print to screen
variables types, assignment to variables
lists, dictionaries, indexing and slicing
how to call functions
if-else clauses
for and while loops
how to import from library modules and call module functions
how to define your own functions

There are a plethora of Python tutorials accessible on the internet (you just have to google). We here give just a few suggestions and we suggest you pick out the pieces of interest in these:

Software Carpentry Python (part 1) -- self-paced tutorial
Software Carpentry (Python (part 2) -- self-paced tutorial
The official Python tutorial -- very complete coverage of Python; useful for looking up stuff
The NBIS Introduction to Python programming -- here you can follow recorded lectures