Machine Learning for Molecular Dynamics

BMB 961 Sec 003 - Spring 2022

This is the course content repository for instructors. Content on the main branch is rendered and distributed to a JupyterBook hosted here: https://adicksonlab.github.io/ml4md-jb.

List of instructors:

Alex Dickson
[email protected]
Associate Professor, Dept of Biochemistry & Molecular Biology and Dept of Computational Mathematics, Science & Engineering

Michael Feig
[email protected]
Professor, Dept of Biochemistry & Molecular Biology

To contribute content:

Clone this git repository to your computer:
git clone [email protected]:ADicksonLab/ml4md-jb.git
this will create a directory called ml4md-jb with all of the source files.

To be able to build and publish the html yourself then you I recommend creating a conda environment:
conda create -n jupyterbook
conda activate jupyterbook

and then installing these packages:
pip install jupyter-book
pip install ghp-import

jupyter-book commands begin with jb and are used to build the static html (in the _build folder). The ghp-import package commits the content of the _build folder to a special branch of the repo (gh_pages) that hosts the JupyterBook on the github.io site.

Adding content to the main branch:

To add a lesson, do the following on your terminal:

1. Make sure you are in the main branch:
   git checkout main
2. Make sure the branch is updated:
   git pull origin main
3. Copy the final versions of all of the files you need into that Day's folder (e.g. Day-02)
4. Update the _toc.yml file to uncomment out that day's notebooks and update the filenames if they have changed.
5. Add the notebooks and all of their dependent files and commit locally (don't forget _toc.yml!):
   git add Day-02/Day-02_Fidget_Spinners.ipynb Day-02/fidget_spinner.jpg _toc.yml
6. Commit your work locally:
   git commit -m 'day 2 content'
7. Push to the remote repository:
   git push origin main
8. Publish to the github.io site:
   jb build . (use --all flag to rebuild all pages when adding new entries)
   ghp-import -n -p -f _build/html
   or alternatively:
   ./build_and_deploy.sh

Making lecture slides from a Jupyter notebook

jupyter nbconvert Week-06/W6_Lecture_MD-Concepts1.ipynb --to slides --post serve