Version at time of journal publication:

FedBatchDesigner

A user-friendly web tool for modeling and optimizing growth-arrested fed-batch bioprocesses. FedBatchDesigner enables rapid exploration of the effect of feed rate and time of switching to the growth-arrested production phase on the TRY metrics (Titer, Rate, Yield) for both constant and exponential feeding strategies.

Features

• Interactive visualization of productivity–titer trade-offs
• Support for constant and exponential feeding strategies
• Pre-loaded parameters for common organisms (E. coli, S. cerevisiae)
• Case study examples including valine and mevalonic acid production in E. coli
• Export results and plots for further analysis
• No registration required, no data stored permanently

Run locally (requires conda)

git clone https://github.com/julibeg/FedBatchDesigner.git
cd FedBatchDesigner
conda env create -f env.yml -n fbd -y
conda activate fbd
shiny run FedBatchDesigner/app.py -b

Usage

1. Input basic process parameters and reactor constraints
2. Provide stage-specific physiological data for your host organism
3. Explore the TRY landscape through interactive visualizations
4. Export results as CSV files and plots as PNG images

Implementation details

Built with:

• Shiny for Python
• Plotly

Case studies

L-valine production

• Demonstrates optimization of a two-stage fed-batch process with microaerobic production
• Parameter fitting notebook: case-studies/valine/fit-parameters.ipynb

Ethanol production with enforced ATP wasting

• Demonstrates optimization of a two-stage fed-batch process with nitrogen starvation
• Parameter fitting notebook: case-studies/ethanol-atp-wasting/fit-parameters.ipynb

Mevalonic acid production

• Shows process design for sulfur-limited production
• Parameter fitting notebook: case-studies/mevalonate/fit-parameters.ipynb

Model assumptions

1. Single substrate limitation
2. Zero substrate concentration during feed phases
3. Constant stage-specific host characteristics
4. Linear relationship between product formation and growth rate ($\pi = \pi_0 + \mu \cdot \pi_1$)
5. Negligible product formation during batch phase
6. Growth determined by remaining substrate after maintenance and production
7. Complete growth arrest in production stage
8. Neglected volume changes from base addition/evaporation
9. TRY metrics based on feed phase only

License

This project is licensed under the MIT License - see the LICENSE file for details.