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Revision 96344048632acd7871b0a92ac903fc07575517f4 authored by TolisChal on 07 December 2020, 16:23:16 UTC, committed by TolisChal on 07 December 2020, 16:23:16 UTC
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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.  



**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`:  

### 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`.  

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