cabsel/deltafba

DeltaFBA is a set of MATLAB functions that employs constraint-based modeling, in combination with differential gene expression data, to evaluate changes in the intracellular flux distribution between two conditions.

ΔFBA

ΔFBA is a set of MATLAB functions that employs constraint-based modeling, in combination with differential gene expression data, to evaluate changes in the intracellular flux distribution between two conditions.

Prerequisites

• MATLAB R2018 or greater
• COBRA Toolbox (Installation and setup)
• Gurobi Optimizer (Instructions)

License

Redistribution and use in source and binary forms, with or without modification, are permitted provided agreeing to the Simplified BSD Style License (see more).

License (RTF, 2 KB)

References

Sudharshan Ravi and Rudiyanto Gunawan, ΔFBA: Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data, bioRxiv, 427188, 2021. Abstract

Acknowledgement

This work is supported by funding from Swiss National Science Foundation and the University at Buffalo’s Center for Computational Research for computational support.

deltafba's Issues

Prod_Mets.R

There are two issues I would like to highlight:

1: Line 53and 162: test = as.matrix(S[allIdx,])

If allIdx only has only one value, the matrix will become a vector and mess up the computation. drop=FALSE should be added to prevent this.

2: When computing the flux sums, I am curious as to why the individual fluxes are not multiplied by the respective stoichiometric coefficients before being summed?