Overview

System Architecture

bionetlite and Neulite are systems that leverage BMTK’s modular design.

Overall Picture

../_images/763493463-bmtk.png

BMTK is divided into the following three main components:

  • Builder: Network construction

  • Simulator: Simulation execution

  • Analyzer: Result analysis

bionetlite extends the Builder module, and Neulite functions as a new Simulator.

Interfaces Based on Level of Detail

BMTK provides multiple interfaces to support models with different levels of detail:

  • bionet: Biophysical network (NEURON)

  • bionetlite: Biophysical network (Neulite) ← This project

  • pointnet: Point neuron network (NEST)

  • filternet: Filter network (LGN Model)

  • popnet: Population statistics network (DiPDE)

Positioning of bionetlite

bionetlite handles biophysical networks like bionet, but differs in the following points:

  • Target simulator: NEURON → Neulite

  • Output format: SONATA format + Neulite-specific CSV format

  • Connection location determination: Simulator runtime → Network construction time

Design Philosophy

Separation of Network Construction and Simulation

Following BMTK’s design philosophy, bionetlite has the following advantages:

  1. Improved error handling: Detect network construction errors before simulation

  2. Reproducibility: Run the same simulation multiple times with the same network files

  3. Flexibility: Network files can be manually edited and validated

Lightweight Implementation

Following the design principle of Neulite kernel lightweight implementation, bionetlite performs the following processing:

  • Preprocessing consolidation: Execute morphology file and ion channel configuration preprocessing at build time

  • Simple file format: Easy to read and write with CSV format

  • Explicit data structure: Eliminates the need for complex processing on the simulator side

Next Steps