Crate kair[−][src]
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
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 |