Crate kair

Constraint-Based Reconstruction and Analysis. It uses the rust_sbml to read a SBML document and translates it into a LP formulation using lp_modeler

COBRA methods available

• Flux Balance Analysis.
• Flux Variablity Analysis.

Examples

Read and optimize e_coli_core model

use kair::{ModelLp, flux_analysis::fba};
use std::{str::FromStr, fs::File, io::{BufReader, prelude::*}};
use good_lp::default_solver;

let file = std::fs::File::open("examples/EcoliCore.xml").unwrap();
let mut buf_reader = BufReader::new(file);
let mut contents = String::new();
buf_reader.read_to_string(&mut contents).unwrap();
let mut model = ModelLp::from_str(&contents).unwrap();
for (name, val) in fba(&mut model, default_solver).unwrap().iter() {
    println!("{} = {}", name, val)
}

Additional links

• Github repository, open to PRs!
• rust_sbml: SBML parser in rust.
• cobrapy: fully featured COBRA package written in Python.

Re-exports

pub use flux_analysis::fba;

pub use model::ModelLp;

Modules

flux_analysis

COBRA methods that take an LpProblem and a Solver

model

Structs for the formulation of the LP problem from the SBML model