Building mechanistic multiscale models with NEURON, NetPyNE, and TREES

Course Information


15 July 2023


Leipzig, Germany


Robert McDougal, Salvador Dura-Bernal, William W Lytton, Herman Cuntz


must register for CNS 2023 tutorials


Brain interactions occur across many temporal and spatial scales. Massive neuroscience-databasing projects throughout the world provide data at all these scales, data that can only be “compiled” and understood using simulation. Mechanistic multiscale modeling provides insights into how changes at molecular, synaptic, morphological and network + areal scales; produced by development, learning, brain disease, or drugs; affect dynamics and brain function.

This tutorial will introduce multiscale modeling using: the NEURON 9.0 simulator, including the Reaction-Diffusion (RxD) module, and the NetPyNE tool. The tutorial will combine background, examples and hands on exercises covering the implementation of models at four key scales: (1) intracellular dynamics (e.g. calcium buffering, protein interactions), (2) single neuron electrophysiology (e.g. action potential propagation), (3) neurons in extracellular space (e.g. spreading depression), and (4) networks of neurons. For single cell simulations, we will use NEURON through Python and introduce the new NEURON toolbox for MATLAB*. We will discuss the role of morphology and demonstrate incorporating real morphology information from NeuroMorpho.Org and synthetic morphology from the TREES toolbox.

For network simulations, we will use NetPyNE, a high-level interface to NEURON supporting both programmatic and GUI specification that facilitates the development, parallel simulation, and analysis of biophysically detailed neuronal circuits. We conclude with an example that links intracellular molecular dynamics with network spiking activity and local field potentials. 

The tutorial incorporates recent substantial developments and new features in both NEURON and NetPyNE. Basic familiarity (e.g. loops, functions, variables, if) with Python or MATLAB is recommended. No advanced programming experience or prior knowledge of NEURON or NetPyNE is required.

* MATLAB is a registered trademark of The MathWorks, Inc.

Software links:

How to register

Register for CNS 2023 here:!/ and be sure to sign up for the tutorials.