Neulite
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Getting Started

  • Overview
    • About This Document
    • System Architecture
    • What is Bionetlite?
    • What is Neulite Kernel?
    • Usage Flow
    • Next Steps
  • What is Bionetlite?
    • Overview
    • Features
      • Reuse of Existing Code
    • Technical Details
      • Main Processing
    • Comparison of Output Files
    • Usage Example
      • Automatic Support for Data Standardization
    • Related Links
  • What is Neulite Kernel?
    • Overview
    • Features
      • Lightweight Design
      • High Portability
    • Technical Details
      • Design Philosophy
      • Target Neuron Model
    • Supported Environments
      • Recommended Environment
      • Achievements on Fugaku
    • Related Links
  • Getting Started
    • bionetlite Setup
      • Prerequisites
      • Setup Procedure
        • Step 1: Create Virtual Environment (Recommended)
        • Step 2: Install BMTK and NEURON
        • Step 3: Install Required Packages
        • Step 4: Clone the neulite Repository
        • Step 5: Place bionetlite
        • Step 6: Verification
      • Basic Usage
        • Changing the Import
        • Network Construction
        • Confirming Output Files
      • Optional Settings
      • Details of Dependent Packages
        • Major Dependent Packages of bionetlite
      • Next Steps
      • References
    • Building Neulite Kernel
      • Prerequisites
      • Build Procedure
        • Step 1: Clone the neulite Repository
        • Step 2: Navigate to Kernel Directory
        • Step 3: Build
        • Step 4: Execution
      • Verification of Build
      • Troubleshooting
        • Compilation Error
        • Executable not found
      • Next Steps

Tutorials

  • Tutorial 1: Steady-State Current Injection in a Single Cell
    • Overview
    • Changes from bionet to bionetlite
    • Code Example
    • Generated Files
      • <network_name>_population.csv
      • <src>_<trg>_connection.csv
      • Processed SWC File
    • Files Generated by Neulite
      • mcortex_population.csv
      • mcortex_mcortex_connection.csv
      • kernel/config.h
    • Building and Running the Neulite Kernel
      • Step 1: Deploy Kernel Sources
      • Step 2: Build the Kernel
      • Step 3: Place the Binary
      • Step 4: Run the Simulation
      • Simulation Result Files
    • Comparison of Execution Results with BMTK
    • Next Steps
  • Tutorial 2: Spike Input Simulation
    • Overview
    • Changes from BMTK to bionetlite
    • Code Example
    • Generated Files
      • mcortex_population.csv
    • Limitations
    • Next Steps
  • Tutorial 3: Single Population Network
    • Overview
    • Changes from BMTK to bionetlite
    • Generated Files
      • mcortex_population.csv
      • mcortex_mcortex_connection.csv
      • Specification
    • Next Steps
  • Tutorial 4: Network with Multiple Populations
    • Overview
    • Changes from BMTK to bionetlite
    • Generated Files
      • population.csv
      • connection.csv
    • Files Generated by Neulite
      • V1_population.csv
      • V1_V1_connection.csv
    • Building and Running the Neulite Kernel
      • Step 1: Deploy Kernel Sources
      • Step 2: Build the Kernel
      • Step 3: Place the Binary
      • Step 4: Run the Simulation
      • Simulation Result Files
    • About Mixing with LIF Models
    • Next Steps

User Guide

  • Basic Usage
    • Building Networks with bionetlite
      • Initializing NeuliteBuilder
        • Parameter Description
      • Adding Nodes
        • Supported Model Types
      • Adding Edges (Synaptic Connections)
        • Defining Basic Connections
        • Supported Synapse Models
      • Saving the Network
    • Execution Flow
      • Limitations
    • Next Steps
  • Configuration
    • Overview
    • Role of Configuration Files
    • Structure of config.json
      • Basic Execution Settings
      • Input Configuration (Current Injection)
      • Component Configuration
    • Automatic Generation of config.h
      • How to Use bionetlite
      • Generated config.h
      • Output Location
    • Advanced Usage
      • Using the simulation_config Parameter
      • Disabling config.h Generation
    • Compatibility with Existing BMTK config
    • Next Steps
  • Parallel Execution
    • About Parallel Execution
    • Basic Usage
    • No Code Changes Required
    • How Parallel Execution Works
    • Next Steps

Architecture

  • Overview
    • System Architecture
      • Overall Picture
    • Interfaces Based on Level of Detail
    • Positioning of bionetlite
    • Design Philosophy
      • Separation of Network Construction and Simulation
      • Lightweight Implementation
    • Next Steps
  • Design and Implementation
    • About BMTK
      • Modular Design
      • Data Standardization
    • About BioNet
      • BioNet Builder
      • BioNet Simulator
    • Design of bionetlite
      • NetworkBuilder Override
    • Processing Flow
    • Parallel Execution Support
    • Next Steps

API Reference

  • API Reference
    • Overview
    • NeuliteBuilder Class
      • Initialization
      • Main Methods
        • add_nodes()
        • add_edges()
        • build()
        • save_nodes()
        • save_edges()
      • Configuration Methods
        • set_config_path()
        • set_dir()
    • Basic Usage Example
    • Parallel Execution
    • Next Steps
  • File Formats
    • Overview
    • SONATA Format Files
    • Neulite Format Files
    • <network_name>_population.csv
      • Header
      • Columns
      • Example
    • <src>_<trg>_connection.csv
      • Header
      • Columns
      • Example
    • SWC File (Processed)
      • Processing Details
      • Format
    • Ion Channel Configuration CSV
      • Header
      • Meaning of Rows
      • Main Parameters
    • config.h
      • Generated Macros
      • Parameters
    • Directory Structure
    • Next Steps
  • Unit System Reference
    • User-Specified Units (BMTK/bionetlite)
      • Simulation Parameters
      • Current Injection Parameters
      • Synapse Parameters
      • Morphology and Ion Channel Files
    • Unit Conversions in Internal Processing
      • Unit System List
      • Other Parameters
      • Conversion from BMTK to NEURON
    • Developer Information
      • Conversion Implementation Locations
    • Reference Links

Advanced Topics

  • Allen V1 Model: Large-scale Network
    • Overview
    • Model Overview
      • Model Source
      • bionetlite Coverage
    • Code Examples
      • Modifying Existing BMTK Code
    • Parallel Execution
    • Generated Files
    • Verifying Results
    • Next Steps
      • Related Links
  • Specifications and Limitations
    • Supported Features
      • Neuron Models
      • Synapse Models
      • Input Methods
      • Morphology Models
        • What is the Perisomatic Model?
    • Detailed Limitations
      • 1. Neuron Model Limitations
        • Possible in bionet but not yet supported in bionetlite
      • 2. Input Method Limitations
      • 3. Synapse Model Limitations
      • 4. Synapse Connection Position Limitations
      • 5. Data Type Limitations
      • 6. Notes on Perisomatic Model
    • Summary of Support Status
    • Future Development
    • Next Steps

Others

  • Frequently Asked Questions (FAQ)
    • General Questions
      • What is bionetlite?
      • Why is bionetlite necessary?
      • What is the difference between bionet and bionetlite?
    • Installation and Environment
      • What Python version is required?
      • What operating systems are supported?
      • Can it run on supercomputers?
    • Usage
      • How to convert existing bionet code to bionetlite?
      • Can I use Point neuron or Virtual neuron?
      • Why can’t I use synapse models other than exp2syn?
      • Can I use spike input?
    • Parallel Execution
      • How to run in parallel?
    • Troubleshooting
      • “Module not found” error
      • Connection positions are different from bionet
      • Delay value accepts only integers
    • Related Resources
  • Publication
    • Key Papers
    • Paper Abstract
      • Key Achievements
      • Technical Contributions
  • How to Cite
    • BibTeX
    • Paper Information
  • Changelog
    • Version 1.0
      • Updates
      • Key Achievements
      • Supported Environments
      • Known Limitations
    • Future Plans
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