Skip to content

BMTool

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

license

Overview

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

Installation

# Basic installation
pip install bmtool

# For development installation
git clone https://github.com/cyneuro/bmtool.git
cd bmtool
python setup.py develop

Key Features

BMTool provides multiple modules to assist with different aspects of neural modeling:

  • Single Cell Module: Analyze and tune biophysical cell models
  • Synapses Module: Configure and tune synaptic connections
  • Connectors Module: Build complex network connectivity patterns
  • BMPlot Module: Visualize network connectivity and simulation results
  • Analysis Module: Process spike and report data from simulations
  • SLURM Module: Manage simulation workflows on HPC clusters
  • Graphs Module: Analyze network properties and connectivity patterns

Command Line Interface

BMTool provides a CLI for accessing functionality directly from the command line:

bmtool --help

See the CLI documentation for more details.