Welcome to MyoGen Logo

The modular and extandable simulation toolkit for neurophysiology

Documentation Python 3.12+ Version

Installation • Documentation • Examples • How to Cite

Overview#

MyoGen is a modular and extensible neuromuscular simulation framework for generating physiologically grounded motor-unit activity, muscle force, and surface EMG signals.

It supports end-to-end modeling of the neuromuscular pathway, from descending neural drive and spinal motor neuron dynamics to muscle activation and bioelectric signal formation at the electrode level. MyoGen is designed for algorithm validation, hypothesis-driven research, and education, providing configurable building blocks that can be independently combined and extended.

Highlights#

🧬 Biophysically inspired neuron models — NEURON-based motor neurons with validated calcium dynamics and membrane properties

🎯 Everything is inspectable — Complete access to every motor unit, spike time, fiber location etc. for rigorous algorithm testing

⚡️ Vectorized & parallel — Multi-core CPU processing with NumPy/Numba vectorization for fast computation

🔬 End-to-end simulation — From motor unit recruitment to high-density surface EMG in a single framework

📊 Reproducible science — Deterministic random seeds and standardized Neo Block outputs for exact replication

📦 NWB export — Optional export to Neurodata Without Borders format for data sharing via DANDI

🧰 Comprehensive toolkit — Surface EMG, intramuscular EMG, force generation, and spinal network modeling

Installation#

Requires Python 3.12+ — Check your version with python --version

System Requirements#

Platform

Before Installing MyoGen

Windows

NEURON 8.2.6 - Download, run installer, select “Add to PATH”

Linux

sudo apt install libopenmpi-dev (Ubuntu/Debian) or sudo dnf install openmpi-devel (Fedora)

macOS

brew install open-mpi

[!CAUTION]

Windows Users: Prerequisites

You MUST install the following before installing MyoGen on Windows:

1. Visual C++ Build Tools

Download and install Visual C++ Build Tools.

During installation, select these components:

  • MSVC Build Tools for x64/x86 (Latest)

  • MSVC v143 – VS 2022 C++ x64/x86 build tools

  • Windows 11 SDK (latest)

  • C++ core desktop features

2. NEURON Simulator

  1. Download: NEURON 8.2.6 Installer

  2. Run the installer and select “Add to PATH” when prompted

  3. Restart your terminal (close and reopen)

  4. Then continue with the installation below

Step 1: Install uv (Package Manager)#

We use uv - a fast Python package manager. Install it first:

Windows (open PowerShell):

powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

Linux/macOS:

curl -LsSf https://astral.sh/uv/install.sh | sh

After installing, restart your terminal (close and reopen it).

Step 2: Create a New Project#

Open a terminal and navigate to where you want your project:

# Create a new folder for your project
mkdir my_emg_project
cd my_emg_project

# Initialize a Python project
uv init

# Add MyoGen to your project
uv add myogen

That’s it! MyoGen is now installed and ready to use.

Step 3: Verify Installation#

Create a test file to make sure everything works:

# Create a test script
uv run python -c "from myogen import simulator; print('MyoGen installed successfully!')"

If you see MyoGen installed successfully! - you’re all set!

Alternative: pip install#

If you prefer pip over uv:

pip install myogen

For Developers (From Source)#

git clone https://github.com/NsquaredLab/MyoGen.git
cd MyoGen
uv sync
uv run poe setup_myogen

Optional: GPU Acceleration#

For 5-10× faster convolutions (requires NVIDIA GPU):

uv add cupy-cuda12x

Documentation#

📖 Read the full documentation

  • User Guide — Working with simulation outputs

  • API Reference — Complete class documentation

  • Examples — Step-by-step tutorials from recruitment to EMG

How to Cite#

If you use MyoGen in your research, please cite:

@article{simpetru_molinari_2026_myogen,
  title   = {MyoGen: Unified Biophysical Modeling of Human Neuromotor Activity and Resulting Signals},
  author  = {S{\^i}mpetru, Raul C. and Molinari, Ricardo G. and Rohlf, Devon R. and
             Batichotti, Rebeka L. and Watanabe, Renato N. and
             Elias, Leonardo A. and Del Vecchio, Alessandro},
  journal = {bioRxiv},
  note    = {preprint},
  year    = {2026},
  doi     = {10.64898/2026.01.01.697284},
  url     = {https://www.biorxiv.org/content/10.64898/2026.01.01.697284}
}

Contributing#

Contributions welcome! See issues if you want to add a feature or fix a bug.

License#

MyoGen is AGPL licensed. See LICENSE for details.

Package Structure#

MyoGen/
├── myogen/              # Main package source code
│   ├── simulator/       # Core simulation functionality
│   │   ├── core/        # Core simulation components
│   │   │   ├── emg/     # EMG signal generation
│   │   │   ├── muscle/  # Muscle modeling
│   │   │   └── spike_train/ # Motor neuron simulation
│   │   └── ...
│   ├── utils/           # Utility functions and tools
│   │   ├── plotting/    # Visualization utilities
│   │   ├── currents.py  # Current generation
│   │   └── nmodl.py     # NMODL file handling
│   └── ...
├── examples/            # Example scripts and tutorials
├── docs/                # Documentation source
├── pyproject.toml       # Project metadata and dependencies
└── uv.lock              # Pinned versions of dependencies