_toc.yml

# Table of contents

format: jb-book
root: intro 
parts:

  - caption: Course Materials
    numbered: False
    chapters:
    - file: Course_Materials/BMB961-003_Syllabus
      title: Syllabus
    - file: Course_Materials/BMB961-003_Schedule
      title: Course Schedule
    - file: Course_Materials/SoftwareSetupGuide
      title: Software Setup Guide
    - url: https://github.com/ADicksonLab/ml4md-jb/raw/main/Course_Materials/Final_project_description.pdf
      title: Final Project Description
 
  - caption: Week 01
    numbered: False
    chapters:
    - file: Week-01/W1_Lecture_Welcome.ipynb
    - file: Week-01/W1_Lab_Python_Refresher.ipynb
    - url: https://github.com/ADicksonLab/ml4md-jb/raw/main/Course_Materials/learn_python.zip
      title: LearnPython.zip
    - url: https://github.com/ADicksonLab/ml4md-jb/blob/8bc6b5d18b4f72c40ad50704cb6507c58f7f595c/Course_Materials/BMB_Community_Standards.pdf
      title: BMB_Community_Standards.pdf
    - url: https://raw.githubusercontent.com/ADicksonLab/ml4md-jb/main/Week-01/sEH_nowater.pdb
      title: sEH_nowater.pdb
    - url: https://github.com/ADicksonLab/ml4md-jb/raw/main/Week-01/sEH_unbinding.dcd
      title: sEH_unbinding.dcd

  - caption: Week 02
    numbered: False
    chapters:
    - file: Week-02/W2_Lecture_MLBasics.ipynb
    - file: Week-02/W2_Lab_MLBasics.ipynb
    - url: https://github.com/ADicksonLab/ml4md-jb/raw/main/Week-02/apple.vacuum.dat
      title: apple.vacuum.dat
    - url: https://github.com/ADicksonLab/ml4md-jb/raw/main/Week-02/apple.vacuum.highres.dat
      title: apple.vacuum.highres.dat
    - url: https://github.com/ADicksonLab/ml4md-jb/raw/main/Week-02/apple.leaf.air.highres.dat
      title: apple.leaf.air.highres.dat

  - caption: Week 03
    numbered: False
    chapters:
    - file: Week-03/W3_Lecture_NNArchitectures.ipynb
    - file: Week-03/W3_Lab_ConvNetworks.ipynb
    - url: https://github.com/ADicksonLab/ml4md-jb/raw/main/Week-03/aq15_pdbs.tgz
      title: aq15_pdbs.tgz
    - url: https://github.com/ADicksonLab/ml4md-jb/raw/main/Week-03/aq15.rgyr.dat
      title: aq15.rgyr.dat
    - url: https://github.com/ADicksonLab/ml4md-jb/raw/main/Week-03/aq15.pb.dat
      title: aq15.pb.dat
    - url: https://github.com/ADicksonLab/ml4md-jb/raw/main/Week-03/aq15.gb.dat
      title: aq15.gb.dat
    - url: https://github.com/ADicksonLab/ml4md-jb/raw/main/Week-03/aq15.sasa.dat
      title: aq15.sasa.dat

  - caption: Week 04
    numbered: False
    chapters:
    - file: Week-04/W4_Lecture_GenerativeModels.ipynb
    - file: Week-04/W4_Lab_GenerateMolecularConformations.ipynb

  - caption: Week 05
    numbered: False
    chapters:
    - file: Week-05/W5_Lecture-ProteinStructurePrediction.ipynb
    - file: Week-05/W5_Lab_StructurePrediction.ipynb
    - url: https://github.com/ADicksonLab/ml4md-jb/raw/main/Week-05/work7efy.zip
      title: work7efy.zip

  - caption: Week 06
    numbered: False
    chapters:
    - file: Week-06/W6_Lecture_MD-Concepts1.ipynb
    - file: Week-06/W6_Lab_Single-Particle-Langevin-Dynamics.ipynb

  - caption: Week 07
    numbered: False
    chapters:
    - file: Week-07/W7_Lecture_MD-Concepts2.ipynb
    - file: Week-07/W7_Lab_Liquid-Argon-Simulation.ipynb
    - url: https://github.com/ADicksonLab/ml4md-jb/blob/main/Week-07/traj_pos_T50.npy?raw=true
      title: traj_pos_T50.npy
    - url: https://github.com/ADicksonLab/ml4md-jb/blob/main/Week-07/traj_vel_T50.npy?raw=true
      title: traj_vel_T50.npy
    - url: https://github.com/ADicksonLab/ml4md-jb/blob/main/Week-07/traj_pos_T80.npy?raw=true
      title: traj_pos_T80.npy
    - url: https://github.com/ADicksonLab/ml4md-jb/blob/main/Week-07/traj_pos_T120.npy?raw=true
      title: traj_pos_T120.npy
    - url: https://github.com/ADicksonLab/ml4md-jb/blob/main/Week-07/traj_pos_T200.npy?raw=true
      title: traj_pos_T200.npy

  - caption: Week 08
    numbered: False
    chapters:
    - file: Week-08/W8_Lecture-Biomolecular-Simulation-1.ipynb
    - url: https://raw.githubusercontent.com/ADicksonLab/ml4md-jb/main/Week-08/input.pdb
      title: input.pdb
    - url: https://raw.githubusercontent.com/ADicksonLab/ml4md-jb/main/Week-08/water.pdb
      title: water.pdb
    - file: Week-08/W8_Lab-Angiotensin-Simulation.ipynb
    - url: https://raw.githubusercontent.com/ADicksonLab/ml4md-jb/main/Week-08/angiotensin.pdb
      title: angiotensin.pdb
    - file: Week-08/software.md

  - caption: Week 09
    numbered: False
    chapters:
    - file: Week-09/W9_Lecture-MarkovStateModels.ipynb
    - file: Week-09/W9_Lab-SimulationAnalysis.ipynb

  - caption: Week 10
    numbered: False
    chapters:
    - file: Week-10/W10_Lecture_FFConcepts.ipynb
    - file: Week-10/W10_Lab-MLFF_ANI.ipynb

  - caption: Week 11
    numbered: False
    chapters:
    - file: Week-11/W11_Final-Project-Demo-1-CHARMM-GUI.ipynb
    - file: Week-11/CHARMM_GUI_COLAB.ipynb
    - file: Week-11/CHARMM_GUI_HPCC.ipynb
    - file: Week-11/W11_Final-Project-Demo-2-ANI-ASE.ipynb