Changelog

Version 1.0

Initial Release

The first public release of the Neulite project.

Updates

bionetlite v1.0.1

  • Added automatic environment setup for tutorials

    • bionetlite can be run directly without pre-running BMTK tutorials

    • Required data files (SWC, JSON, etc.) are automatically downloaded on first run

    • Tutorial-specific simulation parameters are automatically configured

  • Fixed parameter order bug in connection.csv

  • Improved edge filtering

Neulite Kernel v1.0.1

  • Performance improvement through software pipelining of solve_matrix()

  • Changed synaptic current processing to implicit method

  • Fixed bit-shift processing order for delay

Enables large-scale biophysical neuron simulation on the supercomputer Fugaku.

Key Achievements

Large-Scale Simulation Results

  • Achieved simulation of whole mouse cortex model containing 9 million neurons and 260 billion synapses

  • Optimized for execution on Fugaku

bionetlite

Network Construction Tool:

  • NeuliteBuilder class extending BMTK’s NetworkBuilder

  • Existing BMTK code can be used with only import statement changes

  • Support for biophysical neuron models

  • Support for exp2syn synapse model

  • Automatic preprocessing of morphology files (SWC) - Conversion to Perisomatic model - Conversion to zero-based indexing - Sorting by depth-first search (DFS)

  • Automatic conversion of ion channel configuration (JSON→CSV)

  • Support for MPI parallel execution

Neulite

High-Performance Simulator:

  • Lightweight kernel implemented in C

  • Specialized in Perisomatic model from Allen Cell Types Database

  • Support for constant current input

  • Runs on a wide range of environments from Raspberry Pi to Fugaku

Generated Files

  • SONATA format (BMTK compatible)

  • Neulite format - <network_name>_population.csv - Neuron population definition - <src>_<trg>_connection.csv - Detailed synapse connection information - Processed SWC files - Ion channel configuration CSV - config.h - Simulation configuration header

Documentation

  • Project Overview

  • Detailed explanation of bionetlite and Neulite

  • Setup Guide

  • 4 tutorials - Tutorial 01: Single cell simulation - Tutorial 02: Understanding spike input - Tutorial 03: Single population - Tutorial 04: Multiple populations

  • User Guide - Basic usage - Configuration files - Parallel execution

  • Architecture - System overview - Design and implementation (including BMTK and BioNet background)

  • API Reference - NeuliteBuilder API - File format specification

  • Advanced Topics - Allen V1 model examples - Specifications and limitations

  • FAQ

Supported Environments

  • Linux (recommended)

  • macOS

  • Python 3.7 or higher

  • MPI environment (for parallel execution)

Known Limitations

Supported Models:

  • Only biophysical models supported (point neuron, virtual neuron not supported)

  • Only Perisomatic model supported

Supported Synapses:

  • Only exp2syn supported

Input Methods:

  • Only constant current input supported

  • Spike input and Virtual cell input not supported

Others:

  • Delay values support only int type (decimals are rounded)

  • Synapse connection positions are randomly determined at network construction time (different from bionet)

Future Plans

  • Addition of spike input functionality (implementation on Neulite side)

  • Support for new synapse models

  • Continuous performance improvement

  • Documentation expansion

  • Addition of tutorials