natal-core 0.1.2

Numba-Accelerated Toolkit for Analysis of Lifecycle-based population genetic dynamics

⚡️ NATAL Core

Numba-Accelerated Toolkit for Analysis of Lifecycles

NATAL Core is a forward-time population genetics simulation engine that supports configurable lifecycles of species. It supports age-structured and discrete-generation populations, sperm storage, genetic presets, hook-based interventions, and high-performance Numba kernels. NATAL Core is especially useful for modeling gene drive systems in insect populations, but its flexible architecture allows it to be applied to a wide range of population genetics scenarios.

NATAL Core is part of the NATAL project. The full project also includes NATAL Inferencer, a toolkit for parameter inference in population genetics models based on NATAL Core.

Key Features

• 🪲 Forward-time configurable population modeling (age-structured and discrete-generation).
• 🧬 Genetic architecture definition with chromosomes, loci, and alleles.
• 🚀 Numba-accelerated kernels for high performance.
• 🧩 Built-in genetic presets, especially for homing drives and toxin-antidote drives.
• 🪝 Hook system for custom interventions during simulation.
• 🔍 Observation and filtering utilities for downstream analysis.
• 🗺️ Spatial simulation support across multiple demes.

Installation

1. Create a virtual environment

It is strongly recommended to use a virtual environment to manage dependencies.

Choose one of the following commands. Python 3.12 is recommended, but any Python version >= 3.9 should work.

uv venv --python 3.12 .venv            # uv (recommended)
python -m venv .venv                   # venv (please ensure Python >= 3.9 is used)
conda create -n natal-env python=3.12  # conda

On Windows, you can run py -3.12 -m venv .venv to specify Python 3.12 as the interpreter for the virtual environment.

2. Activate the virtual environment

Linux / macOS:

source .venv/bin/activate    # uv / venv
conda activate natal-env     # conda

Windows:

.venv\Scripts\activate       # uv / venv
conda activate natal-env     # conda

3. Install NATAL Core

uv pip install natal-core
# or
pip install natal-core

A Minimal Example

import natal as nt
from natal.ui import launch

# 1. Define the genetics architecture of a species
sp = nt.Species.from_dict(
    name="TestSpecies",
    structure={
        "chr1": {"loc1": ["WT", "Dr", "R2", "R1"]}
    },
    gamete_labels=["default", "cas9_deposited"]
)

# 2. Define a drive using built-in presets
drive = nt.HomingDrive(
    name="TestHoming",
    drive_allele="Dr",
    cas9_allele="Dr",
    target_allele="WT",
    resistance_allele="R2",
    functional_resistance_allele="R1",
    drive_conversion_rate=0.95,
    late_germline_resistance_formation_rate=0.9,
    functional_resistance_ratio=0.001,
    embryo_resistance_formation_rate=0.0,
    viability_scaling=1.0,
    fecundity_scaling={"female": 0.0},
    fecundity_mode="recessive",
    cas9_deposition_glab="cas9_deposited"
)

# 3. Define a release event using hooks
@nt.hook(event="first", priority=0)
def release_drive_carriers():
    return [
        nt.Op.add(genotypes="WT|Dr", ages=1, sex="male", delta=500, when="tick == 10")
    ]

# 4. Build a panmictic population
pop = (nt.DiscreteGenerationPopulation
    .setup(
        species=sp,
        name="TestPop",
        stochastic=True
    )
    .initial_state(
        individual_count={
        "male": {"WT|WT": 50000}, "female": {"WT|WT": 50000}
        }
    )
    .reproduction(
        eggs_per_female=100
    )
    .competition(
        low_density_growth_rate=6.0,
        carrying_capacity=100000,
        juvenile_growth_mode="concave"
    )
    .presets(drive).hooks(release_drive_carriers).build())

# 5. Launch interactive WebUI and run simulation
launch(pop)

For more ready-to-run examples, see the demos directory in the GitHub repository.

Documentation and Links

• Documentation (English): https://natal-core.readthedocs.io/en/latest/
• 文档 (中文): https://natal-core.readthedocs.io/zh-cn/latest/
• GitHub repository: https://github.com/jyzhu-pointless/natal-core
• PyPI package: https://pypi.org/project/natal-core/

License

This project is licensed under the MIT License.