bmtool

bmtool

A collection of modules to make developing Neuron and BMTK models easier.

In depth documentation and examples can be found here

Getting Started

Installation

pip install bmtool

For developers who will be pulling down additional updates to this repository regularly use the following instead.

git clone https://github.com/cyneuro/bmtool.git
cd bmtool
python setup.py develop

Then download updates (from this directory) with

git pull

BMTool provides several modules to simplify the development of computational neuroscience models with NEURON and the Brain Modeling Toolkit (BMTK). It offers functionality for:

• Single Cell Modeling: Analyze passive properties, current injection, FI curves, and impedance profiles
• Synapse Development: Tools for tuning synaptic properties and gap junctions
• Network Construction: Connectors for building complex network structures
• Visualization: Plot connection matrices, network positions, and more
• Simulation Management: Run simulations on SLURM clusters with parameter sweeps
• Analysis: Process simulation results efficiently

Development

Code Quality Tools

BMTool now uses modern Python code quality tools to maintain high standards:

• Ruff: A fast Python linter for code style and error checking
• Pyright: Static type checker to catch type-related bugs early

To install development dependencies in your conda environment:

# Activate your conda environment
conda activate bmtk

# Install development dependencies
pip install -e ".[dev]"

To run the tools:

# Run Ruff linter
ruff check bmtool/

# Run Ruff with auto-fix
ruff check --fix bmtool/

# Run Pyright type checker
pyright