/reproducible-biomodel-case-study

Reproducible case studies from BioModels

Primary LanguageJupyter NotebookMIT LicenseMIT

Reproducible case studies from BioModels

Set up

  • python -m venv rcs # Create a python virtual environment
  • source rcs/bin/activate # Activate the virtual environment
  • pip install -r requirements.txt # Install in the virtual environment
  • deactivate # Exit the virtual environment

Start a session

  • source rcs/bin/activate # Activate the virtual environment
  • jupyter lab # Start jupyter labs
  • Copy the URL shown in the terminal session into your web browser

Open a notebook

  • Use the left pane to select the notebook
  • Double click on the desired notebook
  • To run the notebook, use the Jupyter menu: kernel>Restart kernel and run all cells

End a session

  • deactivate # Exit the virtual environment

Building the book

  • rm -rf reproducible-biomodel-case-study/_build
  • jupyter-book build reproducible-biomodel-case-study