Resources

Here you can find and download the computational tools we have developed for metabolic network analysis. If you encounter any issues, please do not hesitate to contact us. As always, suggestions and comments are greatly welcomed!

Software

MATLAB scripts and examples for efficient loopless optimization of genome-scale stochiometric models. This method supports Gurobi and CPLEX solvers 
MATLAB and OCTAVE scripts and examples for generating a uniform random sample from genome-scale stoichiometric models without unfeasible loops. Scripts have been recently updated and incorporate fast pre-processing using Fast-SNP 
MATLAB scripts and examples of the GRASP framework for building thermodynamically feasible models of cellular metabolism
MATLAB scripts and examples with an efficient sampling implementation of the Adaptive Direction Sampling algorithm for generating loopless flux samples
MATLAB scripts and examples for the application of different Kernels for SMC-ABC on the simplex

Models

Refined genome-scale metabolic network reconstruction ofB. longum subs. infantis
First genome-scale metabolic network reconstruction ofH. campaniensis
Kinetic model ensembles of beta-carotene production in recombinant yeast strains