Bioinformatic practice laboratory

Practice section of the UNIMI Bioinformatics course (2022 edition)

Where and when

The lessons will be on Zoom in the following dates:

Date	Topics	Time
13/04/2022	Setting up your environment Dataset retrieval, processing and analysis Course Project	10.30-12:00
21/04/2022	Feed-forward and Convolutional neural networks	10.30-13:00
27/04/2022	Multi-modal feed-forward neural networks	10.30-12:00

Using your own laptop at the lessons

You can surely use your own laptop at the lessons, BUT please do install the python3 version of Anaconda and afterwards run, depending on if you have or not a GPU compatible with CUDA either:

conda install tensorflow-gpu

or

conda install tensorflow

Installing TensorFlow from Anaconda will make sure that you will also have the Correct CUDNN drivers.

Then you can clone the repository to your own desktop by using git:

git clone https://github.com/LucaCappelletti94/bioinformatics_practice

Finally, to install the required python packages you can run from within the repository:

pip install -r requirements.txt

To test if your installation works properly you can launch a Jupiter notebook server by running:

jupyter notebook

And then run the notebook available in the notebooks directory to see if everything works.

Extras and supplementary material

For those very interested in ML that cannot wait to learn more, you can check out these videos:

3Blue1Brown

This is a youtube channel with great animations which show what a neural network is:

• What is a neural network?
• Gradient Descent
• Backpropagation - high-level
• Backpropagation - low-level

Tesla

The presentation of how they cracked autonomous driving at Tesla:

• Tesla: autopilot day

Welch labs

A small video playlist on neural networks:

• Neural networks demystified

Kurzgesagt

The rise of automation:

• The Rise of the Machines – Why Automation is Different this Time

CGP Grey

A video showing how artificial intelligence will be taking our jobs way before it becomes sentient:

• Humans need not apply

Some videos on biology

Videos on the topics of biology we touched upon during the lessons but we could not properly explore in the available time:

• An history of HELAS3
• More background on HELAS3, focusing on the origin
• What is gene regulation? (In bacteria)