Introduction to the NEURON simulator Arnd Roth Wolfson

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Introduction to the NEURON simulator Arnd Roth Wolfson Institute for Biomedical Research University College

Introduction to the NEURON simulator Arnd Roth Wolfson Institute for Biomedical Research University College London

The optogenetics revolution Fuhrmann et al. , 2015

The optogenetics revolution Fuhrmann et al. , 2015

The optogenetics revolution Fuhrmann et al. , 2015

The optogenetics revolution Fuhrmann et al. , 2015

The connectomics revolution Helmstaedter et al. , 2013

The connectomics revolution Helmstaedter et al. , 2013

The connectomics revolution Helmstaedter et al. , 2013

The connectomics revolution Helmstaedter et al. , 2013

Deep artificial neural networks

Deep artificial neural networks

Deep artificial neural networks Mnih et al. , 2015

Deep artificial neural networks Mnih et al. , 2015

Neuroinformatics: sharing, organizing and accessing experimental data Allen Institute http: //alleninstitute. org Janelia Research

Neuroinformatics: sharing, organizing and accessing experimental data Allen Institute http: //alleninstitute. org Janelia Research Campus https: //senselab. med. yale. edu/modeldb/ Open Source Brain http: //www. openconnectomeproject. org/ Human Brain Project http: //www. humanbrainproject. eu/ INCF http: //opensourcebrain. org/

Single neuron and network simulators NEURON http: //www. neuron. yale. edu/neuron/ GENESIS https: //senselab.

Single neuron and network simulators NEURON http: //www. neuron. yale. edu/neuron/ GENESIS https: //senselab. med. yale. edu/modeldb/ MOOSE http: //neuromorpho. org/ PSICS http: //www. psics. org/ NEST http: //opensourcebrain. org/

Mel, 1994

Mel, 1994

How do neurons transform synaptic inputs into action potential output?

How do neurons transform synaptic inputs into action potential output?

What are the functional compartments in neurons?

What are the functional compartments in neurons?

The structure of NEURON Simulation engine Scripting language for running simulations: hoc, Python Mechanism

The structure of NEURON Simulation engine Scripting language for running simulations: hoc, Python Mechanism description language: NMODL Graphical user interface: Inter. Views Extensions and interoperability (Python, Neuro. ML)

Compartmentalization in NEURON “section” “segment”

Compartmentalization in NEURON “section” “segment”

Compartmentalization in NEURON v(0) v(0. 25) v(0. 75) v(1) nseg = 2

Compartmentalization in NEURON v(0) v(0. 25) v(0. 75) v(1) nseg = 2

A sample hoc script create cable access cable L = 10000 /* micron */

A sample hoc script create cable access cable L = 10000 /* micron */ diam = 1 /* micron */ nseg = 1001 insert pas g_pas = 1/20000 /* 1/(Ohm*cm^2) = Siemens/cm^2 */ e_pas = -65 /* m. V */ xopen("cable. ses")

Important built-in variables in hoc t dt /* ms */ L diam nseg /*

Important built-in variables in hoc t dt /* ms */ L diam nseg /* micron */ cm /* µF/cm^2 */ Ra /* Ω*cm */ g_pas /* S/cm^2 = 1/(Ω*cm^2) */ e_pas /* m. V */ celsius /* °C */

NEURON documentation http: //www. neuron. yale. edu/neuron/static/py_doc/index. html

NEURON documentation http: //www. neuron. yale. edu/neuron/static/py_doc/index. html

An example model Mainen & Sejnowski (1996): Model. DB https: //senselab. med. yale. edu/Mode

An example model Mainen & Sejnowski (1996): Model. DB https: //senselab. med. yale. edu/Mode l. DB/Show. Model. cshtml? model=24 88

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