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Bioreactor Modeling and Simulation (ChE-320)

Welcome to the repository for the Bioreactor Modeling and Simulation course (ChE-320) at EPFL. This course focuses on the principles of algorithmic design and analysis of biochemical reactors, with applications in the pharmaceutical, biotech, and chemical industries.

Course Overview

The course covers:

  • Enzyme and Microbial Kinetics: Understanding the rates of enzymatic reactions and microbial growth.
  • Bioreactor Design and Simulation:
    • Batch Reactors
    • Continuous Reactors
    • Fed-Batch Reactors
  • Chemical Engineering Design Principles:
    • Mass and Energy Balances
    • Mass Transfer
    • Process Control

Learning Objectives

By the end of this course, students will be able to:

  • Comprehend enzymatic reaction kinetics.
  • Evaluate tools and techniques for bioprocess design.
  • Apply programming tools for modeling enzymatic and microbial phenomena.
  • Analyze biochemical processes.
  • Visualize modeling results effectively.
  • Design and model bioreactors.

Programming Languages

While the course has traditionally utilized MATLAB for modeling and simulation tasks, we now strongly encourage the use of Python. Python offers several advantages:

  • Open-Source: Freely available and widely used in both academia and industry.
  • Extensive Libraries: Rich ecosystem of scientific libraries such as NumPy, SciPy, and Pandas.
  • Community Support: Large and active community for troubleshooting and collaboration.

Students are welcome to use the Integrated Development Environment (IDE) of their choice. Additionally, EPFL provides Noto, a centralized JupyterLab platform that allows users to run Jupyter Notebooks online without any local installation. Noto supports multiple programming languages, including Python, and is accessible to all EPFL members with their Gaspar credentials.

Course Structure

  • Lectures: 1 hour per week
  • Projects: 3 hours per week in groups of three

Assessment

The course includes five projects throughout the semester, each containing 2 to 3 problems to be solved using MATLAB or Python. Grading is based on:

  • Exercises: 4/6
  • Code Format and Clarity of Presentation: 2/6
  • Bonus: +0.5/6

Resources

  • Primary Textbooks:

    • Biological Reaction Engineering: Dynamic Modeling Fundamentals with Simulation Examples by I. J. Dunn et al.
    • Biochemical Engineering Fundamentals by J. E. Bailey and D. F. Ollis

  • Programming Tools:

    • Python: Recommended for its versatility and extensive libraries.
    • MATLAB: Available for those with existing proficiency.

Repository Contents

This repository includes:

  • Exercises Correction: jupyter notebooks consisting in the correction of the exercises.

Getting Started

  1. Clone the Repository: 
    git clone https://github.com/EPFL-CHE-320/bioreactor-modeling-simulation.git
  2. Navigate to the Directory: 
    cd bioreactor-modeling-simulation
  3. Set Up Your Programming Environment:
    • Python:
      • Use the IDE of your choice (e.g., PyCharm, VSCode, JupyterLab).
      • Alternatively, access Jupyter Notebooks online via EPFL's Noto platform:
        • Navigate to noto.epfl.ch and log in with your Gaspar credentials.
        • Clone the repository within Noto to access the course materials.
    • MATLAB:
      • Ensure MATLAB is installed on your system.
      • Add the repository folder to your MATLAB path.

License

This project is licensed under the Apache License 2.0. See the LICENSE file for details.

Contact

For questions or further information, please contact: