bmtool 0.8.2.1

BMTool

bmtool

A comprehensive toolkit for developing computational neuroscience models with NEURON and BMTK

Documentation | Installation | Features | Contributing

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Overview

BMTool is a collection of utilities designed to streamline the development, analysis, and execution of large-scale neural network models using NEURON and the Brain Modeling Toolkit (BMTK). Whether you're building single-cell models, developing synaptic mechanisms, or running parameter sweeps on HPC clusters, BMTool provides the tools you need.

Features

Single Cell Modeling

• Analyze passive membrane properties
• Current injection protocols and voltage responses
• F-I curve generation and analysis
• Impedance profile calculations

Synapse Development

• Synaptic property tuning and validation
• Gap junction modeling and analysis
• Visualization of synaptic responses
• Parameter optimization tools

Network Construction

• Custom connectors for complex network models
• Distance-dependent connection probabilities
• Connection matrix visualization
• Network statistics and validation

Visualization

• Network position plotting (2D/3D)
• Connection matrices and weight distributions
• Raster plots and spike train analysis
• LFP and ECP visualization
• Power spectral density analysis

SLURM Cluster Management

• YAML-based simulation configuration
• Automated parameter sweeps (value-based and percentage-based)
• Multi-environment support for different HPC devices
• Job monitoring and status tracking
• Microsoft Teams webhook notifications

Analysis Tools

• Spike rate and population activity analysis
• Phase locking and spike-phase timing
• Oscillation detection with FOOOF
• Power spectral analysis
• Batch processing capabilities

Installation

Install the latest stable release from PyPI:

pip install bmtool

For development installation, see the Contributing Guide.

Documentation

Comprehensive documentation with examples and tutorials is available at:

https://cyneuro.github.io/bmtool/

Key Documentation Sections

• SLURM Module - Run simulations on HPC clusters
• Analysis Workflows - Process simulation results
• Network Building - Construct neural networks
• Single Cell Tools - Analyze individual neurons
• API Reference - Complete API documentation

Contributing

We welcome contributions from the community! To get started:

1. Read the Contributing Guide for setup instructions
2. Check out open issues or propose new features
3. Follow our code style guidelines using Ruff and pre-commit hooks

See CONTRIBUTING.md for detailed information on development setup, code standards, and the pull request process.

Requirements

• Python 3.8+
• NEURON 8.2.4
• BMTK
• See setup.py for complete dependency list

License

BMTool is released under the MIT License.

Support

For questions, bug reports, or feature requests:

• 📖 Check the documentation
• 🐛 Open an issue
• 💬 Contact: [e-mail]

Acknowledgments

Developed by the Neural Engineering Laboratory at the University of Missouri.