KAIr (COBRA Alternative In rust)

COnstraint-Based Reconstruction and Analysis (COBRA) methods enable the use of knowledge-based reconstructions of the metabolism of a particular organism to simulate its metabolic network.

kair provides the translation from a SBML (using rust_sbml) document to the most basic Linear Programming formulation of COBRA: Flux Balance Analysis (FBA). Being f(z) a function to optimize (historically, the biomass pseudoreaction or the ATPase), S and stoichimetry matrix; and v the flux vector representing the reactions in the reconstruction:

The FBA problem can then be optimized thanks to lp_modeler.

See What is flux balance analysis?, Orth et al., 2010 for a brief description of FBA.

Installation

Add kair it to your Cargo.toml:

[dependencies]
kair = "0.3.0"

Make sure you have installed the Cbc solver.

# Debian
sudo apt install coinor-cbc
# Arch
sudo pacman -S coin-or
# Mac OS
brew tap coin-or-tools/coinor && brew install coin-or-tools/coinor/cbc

Example

Some use statements to get started.

use kair::ModelLP;
use std::str::FromStr;

First, read the SBML document, we will be using the e_coli_core model.

let file_str = std::fs::read_to_string("examples/EcoliCore.xml").unwrap();
let model = ModelLP::from_str(&file_str).unwrap();

Having read the document, the LP problem is already formulated. We can print some information about it:

println!(
      "Model has {:?} constraints and {:?} variables",
      &model.constraints.len(),
      &model.variables.len()
  );

Output

Model has 144 constraints and 95 variables

Finally, we can optimize it and print the solution, which is just a HashMap of pairs variable name -> solution value.

for (name, val) in model.optimize().unwrap().iter() {
    println!("{} = {}", name, val)
}

Output

R_EX_co2_e_ = 22.809834
R_ATPM_ = 8.39
R_H2Ot_ = -29.175827
R_GLNS_ = 0.22346173
...
R_BIOMASS_Ecoli_core_w_GAM_ = 0.8739215
...
R_EX_pi_e_ = -3.214895
R_SUCOAS_ = -5.064376
R_PGL_ = 4.959985
R_TKT1_ = 1.4969838

To run this example, on the root of this repository, run

cargo run --example ecoli

kair 0.3.1

KAIr (COBRA Alternative In rust)

Installation

Example