NeuroSim Platform

Large-Scale Human Brain Mapping & Molecular-Level Neural Simulation

A production-grade, HPC-ready platform for multi-scale brain simulation
Inspired by the Blue Brain Project — engineered for the next generation of computational neuroscience

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Platform Overview

NeuroSim is a complete, modular platform for:

• Molecular-level ion channel and membrane dynamics
• Single-neuron electrophysiology (Hodgkin–Huxley and beyond)
• Microcircuit and network-scale simulation
• Brain data ingestion, reconstruction, and connectomics
• HPC-distributed parallel simulation (MPI + CUDA)
• ML-assisted parameter optimization and pattern discovery
• Interactive 3D visualization and analysis

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Architecture Summary

┌─────────────────────────────────────────────────────────────────────┐
│                        NeuroSim Platform                            │
├─────────────┬──────────────┬──────────────┬────────────────────────┤
│  Data Layer │  Simulation  │  HPC Layer   │   API / Visualization  │
│             │    Engine    │              │                        │
│ - Ingestion │ - Molecular  │ - MPI Dist.  │ - REST API Gateway     │
│ - Morphology│ - HH Models  │ - CUDA GPU   │ - 3D Neuron Viewer     │
│ - Connectome│ - Synaptic   │ - Scheduler  │ - Circuit Explorer     │
│ - Graph DB  │ - Network    │ - Checkpoints│ - Activity Heatmaps    │
│ - SWC/H5    │ - Multi-scale│ - Fault Tol. │ - Spike Analysis       │
└─────────────┴──────────────┴──────────────┴────────────────────────┘

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structure of the repository

neurosim/
├── README.md
├── cpp/                        # Performance-critical C++/CUDA core
│   ├── src/
│   │   ├── simulation_engine.cpp
│   │   ├── hodgkin_huxley.cpp
│   │   ├── synapse_model.cpp
│   │   ├── neurotransmitter.cpp
│   │   └── network_solver.cpp
│   ├── include/
│   │   ├── neurosim.h
│   │   ├── ion_channel.h
│   │   └── synapse.h
│   ├── kernels/
│   │   ├── hh_cuda.cu
│   │   ├── synapse_cuda.cu
│   │   └── diffusion_cuda.cu
│   └── mpi/
│       ├── distributed_sim.cpp
│       └── partition_manager.cpp
├── python/
│   ├── neurosim/               # Core Python library
│   │   ├── models/             # Biological models
│   │   ├── simulation/         # Simulation orchestration
│   │   ├── reconstruction/     # Morphology reconstruction
│   │   └── analysis/           # Post-processing & analysis
│   ├── api/                    # FastAPI REST services
│   ├── ml/                     # ML integration modules
│   ├── visualization/          # Visualization pipeline
│   ├── pipeline/               # Data pipelines
│   └── data/                   # Data access layer
├── services/                   # Microservices
│   ├── ingestion/
│   ├── reconstruction/
│   ├── scheduler/
│   └── gateway/
├── configs/                    # Simulation configurations
├── tests/                      # Test suite
├── docker/                     # Container definitions
├── infrastructure/             # IaC (Terraform, Kubernetes)
├── ci/                         # CI/CD pipelines
├── docs/                       # Documentation
└── scripts/                    # Utility scripts

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Quick Start

# Clone and set up environment
git clone https://github.com/your-org/neurosim
cd neurosim
pip install -e ".[dev]"

# Build C++ core
cmake -B build -DCMAKE_BUILD_TYPE=Release -DENABLE_CUDA=ON -DENABLE_MPI=ON
cmake --build build -j$(nproc)

# Run a single-neuron simulation
python -m neurosim.cli simulate --config configs/single_neuron_hh.yaml

# Run a microcircuit simulation on HPC
mpirun -np 64 python -m neurosim.cli simulate --config configs/l5_microcircuit.yaml

# Launch visualization dashboard
python -m neurosim.visualization.dashboard

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Scientific Standards

• Hodgkin–Huxley (1952) membrane dynamics
• NEURON-compatible morphology (SWC format)
• Allen Brain Atlas dataset integration
• BBP Blue Brain Cell Atlas connectivity
• SONATA network format support
• NeuroML2 model interchange
• HDF5/NWB data standards

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License

Apache 2.0 — See LICENSE for details