{"id":15662643,"url":"https://github.com/lucacappelletti94/bioinformatics_practice","last_synced_at":"2025-05-06T00:59:33.987Z","repository":{"id":51794181,"uuid":"241868886","full_name":"LucaCappelletti94/bioinformatics_practice","owner":"LucaCappelletti94","description":"The practice section of the UNIMI Bioinformatics course","archived":false,"fork":false,"pushed_at":"2022-04-21T08:01:37.000Z","size":532371,"stargazers_count":18,"open_issues_count":0,"forks_count":3,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-05-06T00:59:24.836Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LucaCappelletti94.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-02-20T11:37:42.000Z","updated_at":"2024-04-11T11:46:07.000Z","dependencies_parsed_at":"2022-08-17T14:55:29.707Z","dependency_job_id":null,"html_url":"https://github.com/LucaCappelletti94/bioinformatics_practice","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2Fbioinformatics_practice","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2Fbioinformatics_practice/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2Fbioinformatics_practice/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LucaCappelletti94%2Fbioinformatics_practice/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LucaCappelletti94","download_url":"https://codeload.github.com/LucaCappelletti94/bioinformatics_practice/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252601721,"owners_count":21774662,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-03T13:33:44.269Z","updated_at":"2025-05-06T00:59:33.948Z","avatar_url":"https://github.com/LucaCappelletti94.png","language":"Jupyter Notebook","readme":"Bioinformatic practice laboratory\n==========================================================================\nPractice section of the UNIMI Bioinformatics course (2022 edition)\n\nWhere and when\n---------------------------------------\nThe lessons will be on Zoom in the following dates:\n\n+------------+------------------------------------------------+-------------+\n| Date       | Topics                                         | Time        |\n+------------+------------------------------------------------+-------------+\n| 13/04/2022 | - Setting up your environment                  | 10.30-12:00 |\n|            | - Dataset retrieval, processing and analysis   |             |\n|            | - Course Project                               |             |\n+------------+------------------------------------------------+-------------+\n| 21/04/2022 | Feed-forward and Convolutional neural networks | 10.30-13:00 |\n+------------+------------------------------------------------+-------------+\n| 27/04/2022 | Multi-modal feed-forward neural networks       | 10.30-12:00 |\n+------------+------------------------------------------------+-------------+\n\nUsing your own laptop at the lessons\n---------------------------------------\nYou can surely use your own laptop at the lessons, BUT please do install the python3 version of `Anaconda \u003chttps://www.anaconda.com/distribution/#download-section\u003e`_ and afterwards run, depending on if you have or not a `GPU compatible with CUDA \u003chttps://docs.nvidia.com/deploy/cuda-compatibility/index.html\u003e`_ either:\n\n.. code:: bash\n\n  conda install tensorflow-gpu\n\nor \n\n.. code:: bash\n\n  conda install tensorflow\n\nInstalling TensorFlow from Anaconda will make sure that you will also have the `Correct CUDNN drivers \u003chttps://docs.nvidia.com/deeplearning/sdk/cudnn-install/index.html\u003e`_.\n\nThen you can clone the repository to your own desktop by using `git \u003chttps://git-scm.com/\u003e`_:\n\n.. code:: bash\n\n  git clone https://github.com/LucaCappelletti94/bioinformatics_practice\n\nFinally, to install the required python packages you can run from within the repository:\n\n.. code:: bash\n\n  pip install -r requirements.txt\n  \nTo test if your installation works properly you can launch a `Jupiter notebook server \u003chttps://jupyter.org/\u003e`_ by running:\n\n.. code:: bash\n\n  jupyter notebook\n  \nAnd then run the `notebook available in the notebooks directory \u003chttps://github.com/LucaCappelletti94/bioinformatics_practice/blob/master/Notebooks/Testing%20that%20everything%20works.ipynb\u003e`_ to see if everything works.\n\nExtras and supplementary material\n-----------------------------------------------\nFor those very interested in ML that cannot wait to learn more, you can check out these videos:\n\n3Blue1Brown\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nThis is a youtube channel with great animations which show what a neural network is:\n\n- `What is a neural network? \u003chttps://www.youtube.com/watch?v=aircAruvnKk\u0026t=1s\u003e`_\n- `Gradient Descent \u003chttps://www.youtube.com/watch?v=IHZwWFHWa-w\u003e`_\n- `Backpropagation - high-level \u003chttps://www.youtube.com/watch?v=Ilg3gGewQ5U\u003e`_\n- `Backpropagation - low-level \u003chttps://www.youtube.com/watch?v=tIeHLnjs5U8\u003e`_\n\nTesla\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nThe presentation of how they cracked autonomous driving at Tesla:\n\n- `Tesla: autopilot day \u003chttps://www.youtube.com/watch?v=Ucp0TTmvqOE\u003e`_\n\nWelch labs\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nA small video playlist on neural networks:\n\n- `Neural networks demystified \u003chttps://www.youtube.com/watch?v=bxe2T-V8XRs\u003e`_\n\nKurzgesagt\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nThe rise of automation:\n\n- `The Rise of the Machines – Why Automation is Different this Time \u003chttps://www.youtube.com/watch?v=WSKi8HfcxEk\u0026t=27s\u003e`_\n\nCGP Grey\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nA video showing how artificial intelligence will be taking our jobs way before it becomes sentient:\n\n- `Humans need not apply \u003chttps://www.youtube.com/watch?v=7Pq-S557XQU\u003e`_\n\nSome videos on biology\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nVideos on the topics of biology we touched upon during the lessons but we could not properly explore in the available time:\n\n- `An history of HELAS3 \u003chttps://www.youtube.com/watch?v=sXY6-wLesYY\u003e`_\n- `More background on HELAS3, focusing on the origin \u003chttps://www.youtube.com/watch?v=22lGbAVWhro\u003e`_\n- `What is gene regulation? (In bacteria) \u003chttps://www.youtube.com/watch?v=h_1QLdtF8d0\u003e`_\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flucacappelletti94%2Fbioinformatics_practice","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flucacappelletti94%2Fbioinformatics_practice","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flucacappelletti94%2Fbioinformatics_practice/lists"}