CNS*2020 Online

 CNS*2020 Tutorial code and comments
NetPyNE Slides
Video Presentation

Salvador Dura-Bernal, Robert A McDougal, William W Lytton 

T2: Understanding brain function requires characterizing the interactions occurring across many temporal and spatial scales. Mechanistic multiscale modeling aims to organize and explore these interactions. In this way, multiscale models provide insights into how changes at molecular and cellular levels, caused by development, learning, brain disease, drugs, or other factors, affect the dynamics of local networks and of brain areas. Large neuroscience data-gathering projects throughout the world (e.g. US BRAIN, EU HBP, Allen Institute) are making use of multiscale modeling, including the NEURON ecosystem, to better understand the vast amounts of information being gathered using many different techniques at different scales.

This tutorial will introduce multiscale modeling using two NIH-funded tools: the NEURON simulator [1], including the Reaction-Diffusion (RxD) module [2,3], and the NetPyNE tool [4]. The tutorial will include 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 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 combining all three tools that links intracellular molecular dynamics with network spiking activity and local field potentials. Basic familiarity with Python is recommended. No prior knowledge of NEURON or NetPyNE is required, however, participants are encouraged to download and install each of these packages prior to the tutorial.

TUTORIAL WEBSITE

Tools:

• NEURON: neuron.yale.edu/
• RxD: neuron.yale.edu/neuron/docs/reaction-diffusion
• NetPyNE: netpyne.org

Schedule (NY time):

10am - 1pm: NEURON and RxD
1pm - 4pm: NetPyNE (GUI and coding)

See website for detailed schedule: TUTORIAL WEBSITE

References:

1. Lytton WW, Seidenstein AH, Dura-Bernal S, McDougal RA, Schürmann F, Hines ML. Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON. Neural Comput. 28, 2063–2090, 2016.
2. McDougal R, Hines M, Lytton W. (2013) Reaction-diffusion in the NEURON simulator. Front. Neuroinform. 7, 28. 10.3389/fninf.2013.00028
3. Newton AJH, McDougal RA, Hines ML and Lytton WW (2018) Using NEURON for Reaction-Diffusion Modeling of Extracellular Dynamics. Front. Neuroinform. 12, 41. 10.3389/fninf.2018.00041
4. Dura-Bernal S, Suter B, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal R, Hines M, Shepherd GMG, Lytton WW. (2019) NetPyNE: a tool for data-driven multiscale modeling of brain circuits. eLife 2019;8:e44494