_toc.yml

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

format: jb-book
root: intro
parts:
  - caption: Getting Started
    chapters: 
      - file: setup.md
      - file: ed_yong.md
  # - caption: Educational Resources
  - caption: Ecology
    chapters:
      - file: ecology/cavaliere_summary.md
  - caption: Mathematical Optimization
    chapters:
      - file: optimization/fundamentals.md
        sections:
          - file: optimization/core_concepts.md
          - file: optimization/convex_analysis.md
      - file: optimization/linear_programming.md
        sections:
          - file: optimization/graphical-solution.md
          - file: optimization/numerical_solution.md
          - file: optimization/code_solution.ipynb
          - file: optimization/duality.md
  - caption: Flux Balance Analysis
    chapters:
      - file: fba/what_is_fba.md
      - file: fba/fba-units.md
      - file: fba/fba_from_scratch.md
        sections:
          - file: fba/elementary_example.ipynb
          - file: fba/intermediate_example.ipynb
  # - caption: Creating, Reusing & Curating GEMs
  - caption: Necessary Software & Tools
    chapters:
      - file: software_and_tools/vivarium/Vivarium_intro.md
        sections:
          - file: software_and_tools/vivarium/Vivarium_interface_basics.ipynb
      - file: software_and_tools/cobra/cobra.mb
        sections:
          - file: software_and_tools/cobrapy.ipynb
  # - caption: Evaluating GEMs
  # - caption: Simulations