https://github.com/lucacappelletti94/bioinformatics_practice

The practice section of the UNIMI Bioinformatics course
https://github.com/lucacappelletti94/bioinformatics_practice

Last synced: 14 days ago
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The practice section of the UNIMI Bioinformatics course

• Host: GitHub
• URL: https://github.com/lucacappelletti94/bioinformatics_practice
• Owner: LucaCappelletti94
• Created: 2020-02-20T11:37:42.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2022-04-21T08:01:37.000Z (over 2 years ago)
• Last Synced: 2024-10-04T13:33:22.907Z (about 1 month ago)
• Language: Jupyter Notebook
• Homepage:
• Size: 508 MB
• Stars: 18
• Watchers: 3
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst

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README

        
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 `_ and afterwards run, depending on if you have or not a `GPU compatible with CUDA `_ 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 `_.

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

.. 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 `_ by running:

.. code:: bash

  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) `_