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 | 10.30-12:00 | | | - Dataset retrieval, processing and analysis | | | | - Course Project | | +------------+------------------------------------------------+-------------+ | 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 <https://www.anaconda.com/distribution/#download-section>_ and afterwards run, depending on if you have or not a GPU compatible with CUDA <https://docs.nvidia.com/deploy/cuda-compatibility/index.html>_ either:

.. code:: bash

conda install tensorflow-gpu

or

.. code:: bash

conda install tensorflow

Installing TensorFlow from Anaconda will make sure that you will also have the Correct CUDNN drivers <https://docs.nvidia.com/deeplearning/sdk/cudnn-install/index.html>_.

Then you can clone the repository to your own desktop by using git <https://git-scm.com/>_:

.. code:: bash

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

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

.. code:: bash

pip install -r requirements.txt

To test if your installation works properly you can launch a Jupiter notebook server <https://jupyter.org/>_ by running:

.. code:: bash

jupyter notebook

And then run the notebook available in the notebooks directory <https://github.com/LucaCappelletti94/bioinformatics_practice/blob/master/Notebooks/Testing%20that%20everything%20works.ipynb>_ 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? <https://www.youtube.com/watch?v=aircAruvnKk&t=1s>`_
- `Gradient Descent <https://www.youtube.com/watch?v=IHZwWFHWa-w>`_
- `Backpropagation - high-level <https://www.youtube.com/watch?v=Ilg3gGewQ5U>`_
- `Backpropagation - low-level <https://www.youtube.com/watch?v=tIeHLnjs5U8>`_

Tesla

The presentation of how they cracked autonomous driving at Tesla:

• Tesla: autopilot day <https://www.youtube.com/watch?v=Ucp0TTmvqOE>_

Welch labs

A small video playlist on neural networks:

- `Neural networks demystified <https://www.youtube.com/watch?v=bxe2T-V8XRs>`_

Kurzgesagt

The rise of automation:

• The Rise of the Machines – Why Automation is Different this Time <https://www.youtube.com/watch?v=WSKi8HfcxEk&t=27s>_

CGP Grey

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

- `Humans need not apply <https://www.youtube.com/watch?v=7Pq-S557XQU>`_

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 <https://www.youtube.com/watch?v=sXY6-wLesYY>_
• More background on HELAS3, focusing on the origin <https://www.youtube.com/watch?v=22lGbAVWhro>_
• What is gene regulation? (In bacteria) <https://www.youtube.com/watch?v=h_1QLdtF8d0>_