EBRAINS - Cellular Level Simulation

Interactive Workflows and Use Cases

The EBRAINS Cellular Level Simulation Interactive Workflows and Use Cases is part of the EBRAINS Research Infrastructure ecosystem. It aims at providing scientists with powerful tools to reconstruct and simulate scaffold models of brain and brain tissue in a data-driven fashion.

A tight co-design loop between science and engineering ensures the required substantial technical and scientific innovations. As a result, the unique functionality of the platform allows novel questions to be addressed, which could previously not be researched.

• Getting started
  • Working with Collabs and Jupyter Notebook
  • Workflows and Use Case Organization
    • User experience
    • Use Case maturity
    • HPC access
    • Video Tutorials
    • Service Account
    • Neuroscience Gateway (NSG)
  • Service Accessibility
• HPC Status Monitor
  • HPC system status
  • HPC system status: user’s details
• Online Use Cases
  • Trace Analysis
    • Neuro Feature Extraction
    • Synaptic events fitting
      • Synaptic events fitting - Config
      • Synaptic events fitting - Analysis
    • Synaptic events fitting with user model
      • Synaptic events fitting with a user model - Config
      • Synaptic events fitting with user model - Analysis
    • Synaptic events fitting with user data
      • Synaptic events fitting with user data - Config
      • Synaptic events fitting with user data - Analysis
  • Morphology Analysis
    • Morphology Analysis
      • Preview
      • Instructions
    • Morphology Visualization
  • Single Cell Building
    • Overview
      • Hippocampal neurons
        • morph.json
        • features.json
        • protocols.json
        • parameters.json
    • Hippocampus
      • Hodgkin-Huxley Neuron Builder
      • Rebuild an existing single hippocampal cell model
        • Rebuild Single HippoCell - Config
        • BuildOwn Single HippoCell - NSG Job Manager
        • BuildOwn Single HippoCell - Analysis
      • Build your own single hippocampal cell model using HBP data
        • BuildOwn Single HippoCell - Config
        • BuildOwn Single HippoCell - NSG Job Manager
        • BuildOwn Single HippoCell - Analysis
    • Cerebellum
      • Mono compartmental Cerebellar Granule cell optimization
      • Multi compartmental Cerebellar Granule cell optimization
      • Custom Axon Cerebellar Granule cell simulation
      • Simulation and validation of a mouse Purkinje cell multicompartmental model
  • Single Cell In Silico Experiments
    • Single cell in silico experiments under current clamp
  • Small Circuit In Silico Experiments
    • In silico experiments of a small circuit extracted from large scale detailed network models
      • Usage
    • Configure and run a simplified cortical circuit with the CxSystem2 simulation framework
  • Brain area circuit in silico experiments
    • Hippocampus
      • Rat hippocampus CA1
        • Run Simulations
        • View Simulations
        • Simulation Details
      • Configure and run a hippocampus microcircuit