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.

toml [dependencies.rust_sbml] version = "0.3.0" default_features=false

For example,

```rust use rust_sbml::Model;

let example=r#" "#; let result = Model::parse(example); println!("{:?}", result.unwrap()); ```

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

Python

It has only been tested on Linux.

Using pip

shell pip install rust_sbml

From source

Clone the repository. shell git clone https://github.com/carrascomj/rust_sbml.git You need maturin for building it. shell python -m pip install maturin * Build locally shell maturin build --release pip install . * Build on virtualenv (no pip install required) shell # --release can be omitted to speed up compilation time maturin develop --release

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

```python from rust_sbml import Model

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

Milestones

• [x] getListOfSpecies() (id, name)
• [x] getListOfCompartments() (id, name)
• [x] getListOfReactions() (id, name)
  • [x] .getListOfReactants() (id, name)
  • [x] .getListOfProducts() (id, name)
• [x] Capable of retrieving FBC bounds.
• [x] Published to pypi
• [ ] Kinetic Laws.
• [ ] Metadata.
• [x] Test suite with python calls.
• [x] 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).