Neocortical models in the Open Source Brain repository

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### 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](http://www.opensourcebrain.org/projects/osb/wiki/Meetings).

See also the page on [[Priorities]].

### Cell models

#### Individual cell models

##### Generic cortical pyramidal cell

[Pyramidal cells review](http://www.nature.com/nrn/journal/v9/n3/full/nrn2286.html) by Nelson Spruston

project:pospischiletal2008 (single compartment, conductance based; Regular Spiking (RS) neurons & Intrinsically Bursting (IB) neurons)

project:acnet2 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.

project:piriformcortexvanier

##### Layer 2/3 Pyramidal cell

project:thalamocortical (Fast Regular Bursting & Regular Spiking)

##### Layer 4 Spiny Stellate cell

project:thalamocortical

##### Layer 5 Pyramidal cell

project:mainenetalpyramidalcell:

project:rothmanetalkoleetalpyrcell

project:thalamocortical (Intrinsically bursting & Regular Spiking)

project:l5bpyrcellhayetal2011

There is a \*dedicated page on modelling L5 cells [here](/projects/l5pyramidalcellmodels/wiki*).

##### Layer 6 Pyramidal cell

project:thalamocortical

##### Interneurons

project:thalamocortical (Superficial & Deep Basket, Axo-axonic & LTS interneurons)

project:acnet2 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.

project:pospischiletal2008 (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](http://www.ncbi.nlm.nih.gov/pubmed/18568015) for nomenclature of features of GABAergic interneurons of the cerebral cortex.

[Channelpedia](http://channelpedia.epfl.ch/ionchannels) For ion channel names.

### Network models

#### Abstract cortical networks

project:izhikevichmodel

project:vogelsetal2011

project:destexhe\_jcns\_2009

project:brunel2000

#### Detailed network models

project:thalamocortical

project:acnet2

See the page on [[Modelling the thalamocortical loop]]