![logo](doc/logo/volesti_logo.jpg)

**VolEsti** is a `C++` library for volume approximation and sampling of convex bodies (*e.g.* polytopes) with an `R` and limited `python` interface. **VolEsti** is part of the [GeomScale](https://geomscale.github.io) project.

This is a development branch that contains the supplementary code for the submission of the paper "Geometric algorithms for sampling the flux space of metabolic networks" at the 37th International Symposium on Computational Geometry 2021 (SoCG 21).

###  Dependencies

To run the code you need R 3.6.3 and you have to install the following R packages:  

1. `volesti` dependencies (see the DESCRIPTION file)  
2. `Rmosek` (a) [mosek installation guide](https://docs.mosek.com/9.2/install/installation.html) and (b) [Rmosek installation guide](https://docs.mosek.com/9.2/rmosek/install-interface.html)  
3. `pracma`
4. `Matrix`

###  Installation

To install volesti of the current branch, in folder `/root/R-proj` run:  
```r
Rcpp::compileAttributes()  
devtools::install()  
library(volesti)  
```

### Sample steady states

First you have to download the mat file of the model you wish to sample from [Bigg](http://bigg.ucsd.edu/models) or the Recon2D_v04, Recon_d_301 from [VMH](https://www.vmh.life/) and save it to the folder `root/R-proj/metabolic_mat_files`.  

Then follow the script `root/R-proj/example.R`. In that script we sample from the simplest model of the Escherichia Coli (the mat file is already saved in `root/R-proj/metabolic_mat_files`).  

If you execute it you shall get the following histogram that approximates the flux distribution of the reaction `Acetate kinase`.  

![histograms](doc/histograms/acetate_kinase.png)