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
Neulite
Index
Index