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Introduction to the simulation of structurally detailed large-scale neuronal networks

Tutorial at CNS 2019 in Barcelona.

Tutors: Alexander van Meegen, Dennis Terhorst

Schedule

PART I / Morning

  • Introduction (AvM & DT)

  • NEST Introduction (DT)

    • NEST background presentation
    • unsynchronized troubleshooting and Jupyter notebook examples
    • re-synchronized Brunel-Notebook presentation
  • Snakemake Introduction (AvM)

    • short presentation
    • unsynchronized Brunel-Workflow tasks
    • re-synchronized Brunel-Workflow solutions

PART II / Afternoon

  • Multi-area-networks Introduction

    • short motivation (AvM)
    • short HPC outlook (DT)
    • unsynchronized workflow / script building
    • additional: unsynchronized HPC
  • Advanced NEST & Outro (AvM & DT)

Installation

We recommend using a conda environment to get all necessary dependencies. After installing conda create a new environment and activate it:

conda env create -f environment.yml
conda activate CNS2019_NEST

If nest is not found in jupyter notebooks reinstall the correct python kernel for the notebooks:

python -m ipykernel install --prefix $CONDA_PREFIX

Acknowledgements

This tutorials extensively makes use of previous NEST tutorials by

  • Hannah Bos
  • David Dahmen
  • Moritz Deger
  • Jochen Martin Eppler
  • Espen Hagen
  • Abigail Morrison
  • Jannis Schuecker
  • Johanna Senk
  • Tom Tetzlaff
  • Sacha van Albada

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