rust_sbml

Parser for the Systems Biology Markup Language (SBML):

• Standalone Rust library
• Python API

Getting started

Rust

Add it to your Cargo.toml with no default features to avoid all PyO3 nuisances.

[dependencies.rust_sbml]
version = "0.7.0"
default_features=false

For example,

use rust_sbml::Model;

let example=r#"<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
     <model timeUnits="second" extentUnits="mole" substanceUnits="mole">
     </model>
</sbml>"#;
let result = Model::parse(example);
println!("{:?}", result.unwrap());

See write_to_file.rs for an example on serializing to a file.

Python

It has only been tested on Linux.

Using pip

pip install rust_sbml

From source

Clone the repository.

git clone https://github.com/carrascomj/rust_sbml.git

You need maturin for building it.

python -m pip install maturin

• Build locally

  maturin build --release
  pip install .

• Build on virtualenv (no pip install required)

  # --release can be omitted to speed up compilation time
  maturin develop --release

Having it installed, you can use it as a normal Python package.

from rust_sbml import Model

sbml = Model("examples/EcoliCore.xml")
reaction = sbml.getListOfReactions()[0]
print(reaction.getListOfReactants())

Milestones

• getListOfSpecies() (id, name)
• getListOfCompartments() (id, name)
• getListOfReactions() (id, name)
  • .getListOfReactants() (id, name)
  • .getListOfProducts() (id, name)
• Capable of retrieving FBC bounds.
• Published to pypi
• Kinetic Laws, with naive mathml tailored for SBML.
• Metadata, with naive rdf tailored for SBML.
• Test suite with python calls.
• Test suite with libsbml comparison trough cobrapy.

License

Licensed under either of

• Apache License, Version 2.0, (LICENSE-APACHE or http://www.apache.org/licenses/LICENSE-2.0)
• MIT license (LICENSE-MIT or http://opensource.org/licenses/MIT)

at your option.

Contribution

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.

README.md is automatically generated on CI using cargo-readme. Please, modify README.tpl or lib.rs instead (check the github worflow for more details).