Student Guide - Educational Tool for Bioprocessing Simulations

Magnus Stefansson, MBA, Ph.D.
Rabb School of Continuing Studies, Division of Graduate Professional Studies, Brandeis University

🎓 Quick Start for Students

Getting Started

1. Access the simulator: https://bioprocessing-app.streamlit.app/
2. The app loads automatically in your web browser
3. Start with pre-configured scenarios before adjusting parameters

📊 Understanding the Modes

Batch Culture

• What it is: All nutrients added at the beginning, like a closed system
• Real example: Home brewing beer
• Key learning: Growth phases, substrate limitation

Fed-Batch Culture

• What it is: Adding nutrients during the process
• Real example: Industrial insulin production
• Key learning: Feeding strategies, productivity improvement

Repeated Fed-Batch

• What it is: Multiple cycles with partial harvest
• Real example: Yeast production for baking
• Key learning: Process efficiency, cycle optimization

Bleed-Perfusion

• What it is: Continuous feeding and harvesting
• Real example: Monoclonal antibody production
• Key learning: Steady-state operation, highest productivity

🔧 Using the Simulator

Step 1: Choose a Scenario

• Start with "Classical Batch Culture" for your first simulation
• Click on the scenario name in the sidebar
• Parameters will automatically load

Step 2: Run the Simulation

• Click "Run Simulation" or adjust any parameter
• Watch the real-time plot update
• Observe biomass (cells), substrate (food), and product formation

Step 3: Analyze Results

• Look at the productivity metrics below the graph
• Compare different scenarios using the overlay feature
• Export data for your lab report

📈 Reading the Results

The Graph Shows:

• Blue line: Biomass concentration (cell growth)
• Orange line: Substrate concentration (nutrient depletion)
• Green line: Product concentration (what you're making)

Key Metrics to Understand:

• Productivity (g/L/h): How fast you make product
• Total Product: How much you make overall
• Efficiency: How well you convert nutrients to product

🎯 Assignment Tips

When Assignment Mode is ON:

• Parameters are locked by your instructor
• Focus on understanding the results
• Answer the guided questions thoroughly
• Think about real-world applications

Common Assignment Questions:

1. Why does growth stop? (substrate depletion, toxicity)
2. Which mode is most productive? (compare metrics)
3. How would you optimize this process? (parameter effects)

🔍 Troubleshooting

If you see strange results:

• Check that Y_xp (product yield) > 0
• Make sure parameters are in realistic ranges
• Ask your instructor about biological feasibility

If the app is slow:

• Use fewer cycles in repeated fed-batch mode
• Close other browser tabs
• Refresh the page if needed

📚 Study Tips

Before Lab:

• Review the four bioprocessing modes
• Understand what each parameter means
• Read about real industrial examples

During Lab:

• Start with scenarios, then experiment
• Take screenshots of interesting results
• Note parameter values that work well

After Lab:

• Export your data for analysis
• Compare your results with classmates
• Think about scale-up challenges

📞 Questions or Support

For technical issues or questions about the simulator:

Dr. Magnus Stefansson
Email: mostinn@brandeis.edu
Rabb School of Continuing Studies, Division of Graduate Professional Studies, Brandeis University

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📚 For Educational Use Only - This tool is designed exclusively for academic learning and training purposes.
© 2025 Magnus Stefansson. All rights reserved.