Dynamic community-level metabolic modeling for fermentation kinetics and metabolic interactions of the yogurt starter culture based on metagenomic analysis

• helper functions are in /workflow/functions.py

1. Metagenomic analysis(scripts not in this repo)
2. Genome scale metabolic model reconstruction
3. Model refinement
4. Model evaluation
5. Dynamic simulation

1. MetaWRAP: https://github.com/bxlab/metaWRAP
2. CarveMe: https://github.com/cdanielmachado/carveme
3. COBRApy: https://github.com/opencobra/cobrapy
4. Seaborn statistical data visualization:https://seaborn.pydata.org/index.html

Qiu, S., Zeng, H., Yang, Z., Hung, W., Wang, B., Yang, A. (2023). Dynamic metagenome‐scale metabolic modeling of a yogurt bacterial community. Biotechnology and Bioengineering. https://doi.org/10.1002/bit.28492