rtRBA: R. toruloides Resource Balance Analysis Model

Mooney, E.J., Suthers, P.F., Schroeder, W.L., Dinh, H.V., Li, X., Shen, Y., Xiao, T., Call, C.M., Baron, H., Subramanian, A.M., Weilandt, D.R., Keber, F.C., Wühr, M., Rabinowitz, J.D., Maranas, C.D. August 12, 2025. “rtRBA: R. toruloides Resource Balance Analysis Model.” GitHub.

This repository provides resources and model files for the genome-scale resource balance analysis (RBA) model rtRBA. Eric J. Mooney and Costas D. Maranas

Additional info is present in the publication for this model.

Program and packages requirements for the provided software implementation: Python 3 (plus packages: cobra, pandas, numpy, matplotlib, jupyter, scikit-learn, cplex (compiled from installed CPLEX linear programming solver), and all automatically-installed associated dependencies to those already listed) and GAMS with (“built-in”) Soplex solver. (Tested on Python 3.6 and GAMS 39.1.0. Python package installation could be done through “pip” and could take up to 1 hour) gsm_custom_functions.py contains many useful functions, and may be easier to use if you move it into your $PYTHONPATH directory.”

GitHub:  Python scripts, model resources