CNS*2023 Leipzig

Room
Handel 

Organizers
Robert A McDougal, Yale University, USA
Hermann Cuntz, Ernst Strüngmann Institute (ESI) for Neuroscience, Germany
Salvador Dura-Bernal, SUNY Downstate, USA
William W Lytton, SUNY Downstate, USA

Description
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. We will use NEURON through Python for single-cell simulations 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 specifications that facilitate 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 developments and new features in NEURON and NetPyNE. Basic familiarity (e.g. loops, functions, variables, if statements) 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.

Schedule

• 9:00 - 9:15 - Bill Lytton - Overview: Implementing the Conceptual Model
• 9:15 - 10:10 - Robert McDougal - NEURON scripting basics
• 10:10 - 10:40 - coffee break
• 10:40 - 11:10 - Robert McDougal - Finding and reusing model components
• 11:10 - 11:30 - Robert McDougal and Thomas Künzel - NEURON Toolbox for MATLAB
• 11:30 - 12:10 - Hermann Cuntz - Morphologies and the TREES Toolbox
• 12:10 - 14:00 - lunch break
• 14:00 - 14:45 - Adam Newton - Reaction-Diffusion
• 14:45 - 15:30 - Salvador Dura-Bernal - NetPyNE intro and GUI -- slides
• 15:30 - 16:00 - coffee break

• 16:00 - 17:20 - Salvador Dura-Bernal - NetPyNE scripting

Colab notebooks

• Python intro for NEURON
• Shared colab we'll build together
• Example: current clamp showing propagating wave over space
• Example: loading morphology
• Example: parameter sweeps and temperature
• Example: mod files
• Example: synaptic input and recording spike times
• Example: voltage clamp
• Example: non-pulse current clamp
• Example: integrate and fire cell
• Example: ModelView
• Example: saving a video of a cell spiking

Software Tools

• NEURON
• NetPyNE 
• TREES toolbox 
• MATLAB