Research Themes

The following is a list of the cell and network models from the cerebellum which are available in the OSB.

Cerebellum on NeuroLex

Cellular models

There are a number of detailed cell models from the cerebellum in the OSB.

Purkinje cell

De Schutter & Bower 1994 model: Purkinje Cell - De Schutter and Bower 1994

Purkinje cell on NeuroLex

Cerebellar nucleus neuron

Steuber & Jaeger’s (deep) cerebellar nucleus neuron model: Cerebellar Nucleus Neuron - Steuber et al. 2011

Cerebellar nucleus neuron on NeuroLex

Granule cell

See here for more information.

Cerebellar granule cell on NeuroLex

Golgi cell

Cerebellar Golgi Cell - Solinas et al. 2007
Granule Cell Layer - Maex and De Schutter 1998
Golgi Cell Network - Vervaeke et al 2010

Golgi cell on NeuroLex

Network models

Granule cell layer

Granule Cell Layer - Maex and De Schutter 1998
Cerebellar gain and timing - Yamazaki & Nagao 2012

Granule cell layer on NeuroLex

Golgi cell network

Golgi Cell Network - Vervaeke et al 2010

Golgi cell on NeuroLex

Towards community developed cerebellar granule cell models

This project was started following the 2013 OSB kickoff meeting. At that meeting it was decided that the development of individual cell models from the cerebellum would be a good test case for exploring the requirements on technical infrastructure and the social aspects of collaborative model development. Due to the many independent granule cell layer networks being developed by participants at the OSB meeting, the cerebellar granule cell was identified as a good first cell model to focus on.

This wiki is intended to help gather the following information/requirements:

  • What granule cell models are out there?
  • What electrophysiological properties do labs wish to reproduce in their models?
  • What experimental data is publicly available on the behaviour of the granule cell?
  • How well do existing models reproduce these behaviours?

Models of the cerebellar granule cell

Models currently available on OSB

Model Summary
Cerebellar Granule Cell - Maex De Schutter 1998 Single compartment, conductance based
Cerebellar Granule Cell - Solinas et al. 2010 Single compartment, conductance based
Granule Cell - Steuber, Saviane & Berends Single compartment, conductance based
Multicompartmental granule cell - Diwakar et al. 2009 Multcompartmental, conductance based
I&F granule cell model - Rothman & Piasini Integrate and fire model
Cerebellar gain and timing - Yamazaki & Nagao 2012 Integrate and fire cell in network model

Other known granule cell models

Links to entries on ModelDB or PubMed articles…

Simões de Souza F, De Schutter E (2011) Robustness effect of gap junctions between Golgi cells on cerebellar cortex oscillations Neural Systems & Circuits 1:7:1-19 (ModelDB, reuses Cerebellar Granule Cell - Solinas et al. 2010 ?)

Target electrophysiological properties of granule cells

To facilitate comparison between granule cell models it would be good to quantify certain properties of the cell activity which labs find in their experimental data and which should be reproduced in models. An initial list of properties is:

  • Resting Potential
  • Input Resistance
  • Reversal potential of Na
  • Reversal potential of K
  • AP max depolarisation
  • Firing rate at ?? Hz
  • Total cell capacitance
  • Soma radius
  • More…

Different species, drugs, experimental conditions will lead to different values for these between labs. Nevertheless, it would be good to get input from as many labs as possible.

D’Angelo lab

Species: …
Experimental setup summary: …
Resting potential: …

Silver lab

These figures are mainly based on data obtained by Jason Rothman for the paper: Synaptic depression enables neuronal gain control Nature 2009.

Species: Sprague-Dawley rats
Region: Cerebellar vermis
Method: Whole-cell recordings *
Full methods here.
AP threshold:
38mV to42 mV*
AP height (from threshold to peak): 72 mV
AHP depth (from threshold to AHP minimum) 21 mV
Time of AP threshold to time of AHP minimum: 0.9 ms


Publicly accessible data on granule cell behaviour

Links to electrophysiological data in public repositories

_(Wishful thinking I know…)_

NeuroElectro properties of granule cells

http://www.neuroelectro.org/neuron/21/

How well do existing models reproduce these behaviours?

Information on construction of tests for comparing model behaviour to experimental data

Much of this will be based on NeuroUnit/SciUnit and existing test scripts in neuroConstruct projects (e.g. here). What kinds of tests would constitute a good start, e.g. “Properties X, Y, and Z from dataset A should be matched to within 0.5 SD of their mean”?

The following is a list of the cell and network models from the basal ganglia which are available in the OSB.

Cellular models

Striatal Spiny Projection Neuron

Also known as Medium Spiny Neuron.

Model by Avrama Blackwell and colleagues: Striatal Spiny Projection Neuron - Blackwell

Hippocampal models in the Open Source Brain repository

Introduction

For an introduction to the hippocampus see the article here on Scholarpedia.

Cellular models

The following detailed cell models from the hippocampus are available in the OSB.

CA1 Pyramidal Cell - Migliore et al. 2005

Reduced CA3 model - Pinsky and Rinzel 1994

Network models

More…

Projects with L5 pyramidal cells currently in OSB


L5 Pyramidal Cell - Mainen et al. 1995

Layer 5b Pyramidal cell - Hay et al. 2011
L5 Pyramidal cell - Rothman et al. 2009

Synaptic integration in L5 Pyramidal cell - Larkum et al. 2009
L5 Pyramidal Neuron - Almog and Korngreen 2014
Thalamocortical network - Traub et al. 2005 (Intrinsically bursting & Regular Spiking)

These projects were be discussed in detail at the 2013 OSB Hackathon.

See also this project by Chaitanya Chintaluri : https://github.com/ccluri/L5Pyr

Resources available for model tuning & optimisation

(Under development. If you have experience with model optimisation, please help by editing this page on GitHub)

Background

Published reviews

De Schutter...
..

Example publications incorporating model optimisation

Drukmann…
Hay et al…
Korngreen…

Software packages for model tuning

Neurotune by Mike Vella
Neurofitter

Introduction

This page will be updated during the 2013 OSB Hackathon.

See also the page on [[Priorities]].

Cell models

Individual cell models

Generic cortical pyramidal cell

Pyramidal cells review by Nelson Spruston

Minimal HH models - Pospischil et al. 2008 (single compartment, conductance based; Regular Spiking (RS) neurons & Intrinsically Bursting (IB) neurons)
Primary Auditory Cortex network is a network model of the thalamorecipient layer (IV) of primary auditory cortex (AI), and consists of 2 populations, pyramidal cells and basket cell interneurons.
Piriform Cortex Pyramidal Neuron

Layer 2/3 Pyramidal cell

Thalamocortical network - Traub et al. 2005 (Fast Regular Bursting & Regular Spiking)

Layer 4 Spiny Stellate cell

Thalamocortical network - Traub et al. 2005

Layer 5 Pyramidal cell

L5 Pyramidal Cell - Mainen et al. 1995:
L5 Pyramidal cell - Rothman et al. 2009
Thalamocortical network - Traub et al. 2005 (Intrinsically bursting & Regular Spiking)
Layer 5b Pyramidal cell - Hay et al. 2011

There is a *dedicated page on modelling L5 cells here.

Layer 6 Pyramidal cell

Thalamocortical network - Traub et al. 2005

Interneurons

Thalamocortical network - Traub et al. 2005 (Superficial & Deep Basket, Axo-axonic & LTS interneurons)
Primary Auditory Cortex network is a network model of the thalamorecipient layer (IV) of primary auditory cortex (AI), and consists of 2 populations, pyramidal cells and basket cell interneurons.
Minimal HH models - Pospischil et al. 2008 (Fast Spiking (FS) neurons)

Channel Properties

Morphology

Nomenclature

It is important to have a consistent naming in the models of the cells and channels. Although these are not currently adopted, they are advised. A standard naming helps in making models interchangeable and easily testable. There is no consensus yet on naming of individual compartments in a cell model. [Discuss]

Petilla terminology for nomenclature of features of GABAergic interneurons of the cerebral cortex.

Channelpedia For ion channel names.

Network models

Abstract cortical networks

Izhikevich Spiking Neuron Model
Balanced network with inhibitory plasticity - Vogels et al. 2011
Self Sustained Network Activity - Destexhe 2009
Sparsely connected spiking neuron network - Brunel 2000

Detailed network models

Thalamocortical network - Traub et al. 2005
Primary Auditory Cortex network
See the page on [[Modelling the thalamocortical loop]]

C. elegans

The complete nervous system of C. elegans is being modelled by the OpenWorm Project.

OpenWorm C. elegans network model