Revision 77c446f0b39d67228621d4ba217d5369dee75ad4 authored by Vissarion Fisikopoulos on 07 December 2020, 15:42:37 UTC, committed by GitHub on 07 December 2020, 15:42:37 UTC
1 parent 95f86eb
README.md
This is a branch of **VolEsti** 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)*.
Authors: Apostolos Chalkis, Vissarion Fisikopoulos, Elias Tsigaridas, Haris Zafeiropoulos.
---
![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.
### 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 in folder `root/R-proj`)
2. `Rmosek` first complete the (a) [mosek installation guide](https://docs.mosek.com/9.2/install/installation.html) and then proceed to (b) [Rmosek installation guide](https://docs.mosek.com/9.2/rmosek/install-interface.html)
3. `pracma`
4. `Matrix`
5. `R.matlab`
### Installation
To install volesti of the current branch, in folder `/root/R-proj` run the following command in `R`:
```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`.
![histogram](doc/histograms/acetate_kinase.png)
Computing file changes ...