Resources

Useful resources for those starting computational projects in the solab!

• • Python

    • Google colab

      • • Run python notebooks directly in your web-browser!

        • Alternatives:

          • Jupyter by mybinder.org

          • Anaconda - install on your own computer

• • • A Whirlwind Tour of Python by J. VanderPlas

      • Introduction to Basic Python

    • Python Data Science Handbook by J. VanderPlas

      • Introduction to Scientific libraries used in Python

• • Mathematics and Statistics

• • • 3Blue1Brown - series of animated youtube videos

    • Essence of linear algebra

    • Essence of calculus

    • Neural Networks

    • Differential Equations

    • Advanced topics

      • The Elements of Statistical Learning by T. Hastie, R. Tibshirani and J. Friedman

      • Machine Learning: a Probabilistic Perspective by K. Murphy

• • Neural networks

• • • Interactive examples - BEST WAY TO LEARN!

      • Playground (for classification/regression)

      • GAN Lab (generative models)

      • Anomagram (Autoencoder)

      • Distill (interactive publications)

    • Deep Learning with Python (not free, link to Amazon) by F. Chollet

      • BIG picture introduction to NN

      • Notebooks to go with the book.

    • Advanced topics

      • Deep Learning by I. Goodfellow, Y. Bengio and A. Courville

    • Reviews

    • Deep learning: new computational modeling techniques for genomics

    • A Survey of Deep Learning for Scientific Discovery

• • Proteins

• • • Coevolution - List of milestones

• • Papers on machine learning for proteins

  • Workshops (by Sergey Ovchinnikov)

• • • Abinitio structure prediction (2018)

    • Structure prediction w/ experimental data (2018)

    • Rosetta-Boston-Club (2019) - going from PSSM, MRF to VAE