DC_dFBA

Supporting codes of the paper: Nonlinear programming reformulation of dynamic flux balance analysis models.

The paper describes a nonlinear programming formulation for solving dynamic Flux Balance Analysis models. The methodology consists of incorporating a KKT reformulation of a parsimonious FBA problem and applying a collocation technique to the ODE system. Please refer to the paper for further information.

Case studies:

The files here are organized by the case studies solved on the paper with different metabolic networks models:

1. E. coli core
2. E. coli iJR904
3. E. coli iJO1366
4. S. cerevisiae iND750
5. Yeast 8.3

Scripts:

• main.jl: main file that defines all the parameters and initial conditions for the problem.
• pFBA_KKT_flux.jl: solves the DC_dFBA optimization problem in JuMP.
• plotar.jl: creates figures in PDF from the output.

Julia and packages versions:

• julia 1.5.3
• JuMP v0.21.4
• Ipopt v0.7.0
• HSL MA27