Flux balance analysis (FBA) has emerged as a popular tool for analysing genome-scale metabolic networks. Its key benefit lies in the minimal experimental data needed to make quantitative predictions about biological behaviour. However, one of FBA’s primary disadvantages is that it predicts a range of possible flux solutions, rather than a single output.
Last year, Vangelis Simeonidis and I described an algorithm for extracting a unique solution that is representative of the set of possible fluxes. A number of people have asked for an implementation, and their (and so I suppose the FBA community’s) overwhelming software of choice is the COBRA toolbox (COnstraint-Based Reconstruction and Analysis) for MATLAB.
So, following popular opinion, here’s a two-step process to reproducing the results in Table 1 of our paper:
- Install COBRA
- Extract uniqueFBA.zip and run the script “example.m”
Please contact me with any bugs.
Smallbone, K., & Simeonidis, E. (2009). Flux balance analysis: A geometric perspective Journal of Theoretical Biology, 258 (2), 311-315 DOI: 10.1016/j.jtbi.2009.01.027