_toc.yml

# Table of contents
# Learn more at https://jupyterbook.org/customize/toc.html

format: jb-book
root: Readme

parts:
  - caption: Course Information
    chapters:
    - file: Syllabus.md
    - file: Schedule.md
    
  - caption: Assignments
    chapters:
    - file: assignments/00-assignments.md
      sections:
      - file: assignments/hw-01.ipynb
      - file: assignments/hw-02.ipynb
      
  - caption: Topical Materials
    numbered: true
    chapters:
    - file: notebooks/01.00-What-is-Process-Control
      sections:
      - file: notebooks/01.01-What-is-Feedback
      - file: notebooks/01.02-Elements-of-Feedback-Control
#      - file: notebooks/01.05-Assignment-1
      
    - file: notebooks/02.00-Process-Modeling
      sections:
      - file: notebooks/02.01-One-Compartment-Pharmacokinetics
      - file: notebooks/02.02-Properties-of-Scalar-First-Order-Linear-Systems
      - file: notebooks/02.03-First-Order-Model-for-a-Single-Heater
      - file: notebooks/02.04-Fitting-a-Model-to-Data
      - file: notebooks/02.05-Second-Order
      - file: notebooks/02.06-Fed-Batch-Bioreactor
      - file: notebooks/02.07-Exothermic-CSTR
      - file: notebooks/02.08-Hare-and-Lynx
      - file: notebooks/02.09-Study-Guide
      
    - file: notebooks/03.00-Feedback-Control
      sections:
      - file: notebooks/03.01-Case-Study-Thermal-Cycling-PCR
      - file: notebooks/03.02-Setpoints
      - file: notebooks/03.03-Setpoints-Thermal-Cycler
      - file: notebooks/03.04-Relay-Control
      - file: notebooks/03.05-Implementing-Controllers
      - file: notebooks/03.06-Proportional-Integral-Control
      - file: notebooks/03.07-Integral-Windup-and-Bumpless-Transfer
      - file: notebooks/03.08-Controller-Tuning

    - file: notebooks/04/04.00-Process-Analytics
      sections:
      - file: notebooks/04/04.01-Learning-Goals
      - file: notebooks/04/04.02-Process-Historians
      - file: notebooks/04/04.03-State-Estimation
      - file: notebooks/04/04.04-Lab-Assigment-State-Estimation
      - file: notebooks/04/04.05-Anomaly-Detection
      - file: notebooks/04/04.06-Lab-Assignment-Anomaly-Detection
      - file: notebooks/04/04.07-Observer-Synthesis-LMI
      - file: notebooks/04/04.08-Envrironmental-Application
      - file: notebooks/04/04.09-Study-Questions
  
    - file: notebooks/05/05.00-Optimization
      sections:
      - file: notebooks/05/05.01-Linear-Production-Model
      - file: notebooks/05/05.02-Linear-Blending-Problem
      - file: notebooks/05/05.03-Homework_2
      - file: notebooks/05/05.04-Gasoline-Blending
      - file: notebooks/05/05.05-Linear-Programming
      - file: notebooks/05/05.06-Design-of-a-Cold-Weather-Fuel
      - file: notebooks/05/05.99-Pyomo-Examples
      - file: CBE30338-EV-Example
      - file: notebooks/milk-pooling
  
    - file: notebooks/06.00-Predictive-Control
      sections:
      - file: notebooks/07.01-Simulation-and-Optimal-Control-in-Pharmacokinetics
      - file: notebooks/06.01-Static-Operability
      - file: notebooks/06.02-Simulation-and-Open-Loop-Optimal-Control
      - file: notebooks/06.03-Predictive-Control
      - file: notebooks/06.04-Implementing-Predictive-Control
      - file: notebooks/06.06a-gompertz-tumor-growth
      - file: notebooks/06.06-gompertz-model-project
      - file: notebooks/06.07-time-as-decision-variable

#    - file: notebooks/07.00-Discrete-Event-Systems
#      sections:
#      - file: notebooks/06.01a-Introduction-to-Simpy
#      - file: notebooks/07.02-Agent-Based-Models
#      - file: notebooks/07.03-Chemotaxis
#      - file: notebooks/07.04-Project-Batch-Chemical-Process
#      - file: notebooks/07.05-Queuing-Systems-and-Poisson-Processes

    - file: notebooks/08.00-Projects
      sections:
      - file: notebooks/08.01-Project-Ideas
    
    - file: notebooks/09.00-Bibliography

  - caption: Control Laboratory
    numbered: true
    chapters:
    - file: tclab/00.00-tclab.md
      sections:
      - file: tclab/00.01-setting-up-tclab.ipynb
      - file: tclab/00.02-troubleshooting-tclab
      - file: tclab/00.03-using-tclab
      
    - file: tclab/01.00-step-testing.md
      sections:
      - file: tclab/01.01-step-testing.ipynb
      - file: tclab/01.02-first-order-model-for-a-single-heater
   
    - file: tclab/02.00-Empirical-Model-Identification
      sections:
      - file: tclab/02.02-Fitting-Step-Test-Data-to-Empirical-Models
      
    - file: tclab/03.00-Estimating-Model-Parameters
      sections:
#      - file: tclab/03.05-Two-State-Model-for-a-Single-Heater
#      - file: tclab/03.04-Two-Input-Two-Output-Model
#      - file: tclab/03.06-Four-State-Model
#      - file: tclab/03.10-TCLab-Lab-2-Model-Indentification-Solutions
      - file: tclab/03.10-TCLab-Lab-2-Model-Indentification
#      - file: tclab/03.11-TCLab-Lab-2-Fitting
    
    - file: tclab/04.00-Feedback-Control
      sections:
      - file: tclab/04.01-Relay-Control
      - file: tclab/04.02-Lab-Assignment-Relay-Control
#      - file: tclab/04.03-PID_Control
#      - file: tclab/04.10-Lab-Assignment-PID-Control
#      - file: tclab/04.11-Lab-Assignment-PI-Control
      
    - file: tclab/05.00-State-Estimation
      sections:
      - file: tclab/05.01-Open-and-Closed-Loop-Estimation
      
    - file: tclab/06.00-Optimal-Control
    
    - file: tclab/07.00-Predictive-Control-and-Real-Time-Optimization
      sections:
      - file: tclab/07.01-Optimization-Control-and-Estimation-using-Pyomo
      - file: tclab/07.02-Optimization-Control-and-Estimation-using-Pyomo-With-Windows-ipopt
        
  - caption: Python Tutorials
    chapters:
    - file: python/A.00-Python-Tutorials
      sections:
      - file: python/A.05-Tidy-Data-and-Pandas
      - file: python/A.10-Coding-Controllers-with-Python-Generators
      - file: python/A.11-Modular-Approach-to-Simulation-using-Python-Generators
      - file: python/A.30-Animation-in-Jupyter-Notebooks