This repository contains all the information and building scripts required to construct a ME-model for P. putida KT2440, iPpu1676-ME using coralME.

If you are using iPpu1676-ME, please cite Tibocha-Bonilla, J.D., Gandhi, V., Lieng, C. et al. Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida. npj Syst Biol Appl 11, 55 (2025). https://doi.org/10.1038/s41540-025-00521-1.

1. Clone repository
2. run pip install -r requirements.txt

1. Clone repository
2. docker build --file "./Dockerfile-Python3.10" . -t "pputidame"
3. docker run --detach -p 10000:8888 -v USER/PATH/TO/pputidame/:/opt/notebooks/ pputidame
4. In your browser, go to localhost:10000

Jupyter Notebooks contain the following analyses:

0. Reconstruction and constraining of the ME-model
1. Omics overview and analysis
2. Comparison of model predictions and omics
3. Final visualization of the comparison of model predictions and omics
4. Allocation observed in the omics data
5. Flux Variability Analysis of M- and ME-models
6. Analysis of intracellular phenotype (comparison with MFA)