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:

```
install.packages("devtools")
devtools::install_github("shackett/simmer")
```

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

`browseVignettes(package = "simmer")`

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.

- Load files describing valid reactions, species (their composition) both from the core SBML model and supplemented manual annotations
- Load files describing boundary conditions, reaction reversibility and auxotrophies
- Setup matrices defining the stoichiometry of each reaction and how reactions will be constrained
- Calculate fluxes using quadratic programming (calculate_QP_fluxes)
- Flux uncertainty can be calculated using python script (python/qp_fba_clust.py)

Bayesian approach to fitting reaction equations to measured fluxes.

- Load reaction equations (with embedded omic data)
- Set run parameters (number of samples, sampling frequency and burn-in)
- Fit reaction equations (fit_reaction_equations)

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

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