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