🧬 Rust SBML

A Rust crate providing a robust interface for reading and writing SBML (Systems Biology Markup Language) files. Built as an ergonomic wrapper around the libsbml C++ library with type-safe Rust abstractions.

🚀 Features

• Type-safe builder pattern API for SBML model creation
• Seamless serialization/deserialization of annotations using serde
• Bundled libsbml library - no external installation required
• Cross-platform support (macOS and Windows)
• Comprehensive error handling and type safety

📦 Installation

Currently available through Git:

cargo add --git https://github.com/EnzymeML/sbml-rs

System Requirements

• CMake: Required for building the bundled libsbml library
• Rust: 1.70 or higher (recommended)

Platform Support

✅ Tested and supported:

• macOS (arm64, x86_64)
• Windows (x86_64)
• Linux (x86_64)

Please note, due to ongoing development to support platforms, the crate is currently only available as a static library for Windows and Linux. MacOS is available as a dynamic library. We will update this section as we add more support.

💡 Usage

The crate follows SBML's hierarchical structure, with all operations flowing through the root SBMLDocument. We offer two API styles:

1. Builder pattern (recommended)
2. Traditional setter methods

Creating SBML Models

use sbml::prelude::*;

let doc = SBMLDocument::new(3, 2);

// Create a model
let model = doc.create_model("Model");

// Create a compartment
let compartment = model.build_compartment("cytosol")
    .name("Cytosol")
    .build();

// Create the glucose species with annotation
let glucose = model
    .build_species("glucose")
    .name("Glucose")
    .compartment(&compartment.id())
    .initial_amount(10.0)
    .boundary_condition(true)
    .annotation_serde(&glucose_annotation)?
    .build();

// Export to SBML XML
let sbml_string = doc.to_xml_string();

Type-Safe Annotations

Leverage Rust's type system for SBML annotations:

use sbml::prelude::*;

#[derive(Serialize, Deserialize, Debug)]
struct MyAnnotation {
    #[serde(rename = "@xmlns")]
    xmlns: String,
    key: String,
    value: i32,
}

// Create and attach annotation
let annotation = MyAnnotation {
    xmlns: "http://my.namespace.com".to_string(),
    key: "test".to_string(),
    value: 1,
};

let species = model.build_species("glucose")
    .name("Glucose")
    .compartment(&compartment.id())
    .initial_amount(10.0)
    .boundary_condition(true)
    .annotation_serde(&annotation)?
    .build();

// Read annotation
let retrieved: MyAnnotation = species.get_annotation_serde()?;

🛠️ Development

Code Quality

# Format code
cargo fmt

# Run linter
cargo clippy --all-targets --all-features

# Run tests
cargo test

🤝 Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

📚 Resources

• SBML Documentation
• libsbml Documentation

🙏 Acknowledgements

This crate is a Rust port of the libsbml library. Special thanks to the SBML team for their excellent work.

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

🚧 Roadmap

The following table shows the current implementation status of SBML objects in this crate:

SBML Object	Status
Model	⚠️ Partially
Compartment	✅ Implemented
Species	✅ Implemented
Parameter	✅ Implemented
Reaction	✅ Implemented
Rule	✅ Implemented
AssignmentRule	✅ Implemented
RateRule	✅ Implemented
UnitDefinition	✅ Implemented
Unit	✅ Implemented
KineticLaw	❌ Not yet implemented
SpeciesReference	✅ Implemented
ModifierSpeciesReference	✅ Implemented
InitialAssignment	❌ Not yet implemented
Event	❌ Not yet implemented
EventAssignment	❌ Not yet implemented
Trigger	❌ Not yet implemented
Delay	❌ Not yet implemented
Priority	❌ Not yet implemented
FunctionDefinition	❌ Not yet implemented
Constraint	❌ Not yet implemented
LocalParameter	❌ Not yet implemented
StoichiometryMath	❌ Not yet implemented
CompartmentType	❌ Not yet implemented
SpeciesType	❌ Not yet implemented
SBase	✅ Implemented
ListOf	✅ Implemented
ASTNode	❌ Not yet implemented
CVTerm	❌ Not yet implemented
Date	❌ Not yet implemented
ModelHistory	❌ Not yet implemented
ModelCreator	❌ Not yet implemented

Future development priorities:

1. Complete implementation of remaining SBML core objects
2. Improve error handling and validation
3. Add more examples and documentation
4. Performance optimizations