Systematic Identification of Meaningful Metabolic Enzyme Regulation (SIMMER)

This repository contains scripts and data that can be used to reproduce the flux inference and kinetic model fitting results of Hackett 2016.

To install this repository as a local package run the following R code:


Vignettes are available that reproduce the flux inference and reaction equation fitting:

browseVignettes(package = "simmer")

Estimating metabolism-wide fluxes from boundary fluxes using quadratic programming

Integrating boundary fluxes with the yeast metabolic reconstruction in order to estimate metabolic fluxes. This script makes use of the Gurobi optimizer and R package which are freely available for academic use.

Fitting experimental data to reaction forms using MCMC and NNLS

Bayesian approach to fitting reaction equations to measured fluxes.

shackett/simmer documentation built on May 29, 2019, 8:06 p.m.