Neocortical models in the Open Source Brain repository¶

Introduction¶

It is in the scientific community’s interest to have a detailed model of the Thalamocortical loop. This will aid us in understanding the role of cortex in processing information. Although there are a few existing models addressing this question, they are not updated with the latest findings of the field, the model’s development stops with the publication of the results. Also, often such detailed models are abandoned due to lack of financial and human resources to maintain such projects. New projects are built up from the scratch - this wastes precious resources, and is like re-inventing the wheel. This project differs specifically in this respect - by making the project open, new findings are encouraged to be added, bugs will be acknowledged and subsequently corrected. As it is the community that develops the project, the findings are open to all - immediately. The central idea is to arrive at a consensus of existing good models of cells and network alike and to build upon them. This will happen with benchmarking, version control and testing.

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