# L5 Pyramidal Neuron Almog and Korngreen (2014)

## Model description

This model originally appeared in **Almog M., Korngreen A.** *A Quantitative Description of Dendritic Conductances and Its Application to Dendritic Excitation in Layer 5 Pyramidal Neurons* [J Neurosci 34(1):1](http://www.jneurosci.org/content/34/1/182). The relevant *neuron* files can be downloaded from [modelDB](http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=151825).

## Conversion to NeuroML

We have converted the [original model](http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=151825) to NeuroML. Most *.mod* mechanisms can be mapped to [ChannelML](http://neuroml.org/NeuroMLValidator/Transform.jsp?localFile=NeuroMLFiles/Schemata/v1.8.1/Level2/ChannelML_v1.8.1.xsd&xslFile=NeuroMLFiles/Schemata/XSD_Readable.xsl) with exception of the Calcium mechanisms described in terms of the [GHK](http://en.wikipedia.org/wiki/GHK_flux_equation) formalism. These latter needed to be translated to [NeuroML2](http://www.neuroml.org/neuroml2.php), which supports arbitrary current laws.

The NeuroML version reproduces the results from the *bac6.ses* script bundled with the [modelDB](http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=151825) version, taking into account that some [issues](https://github.com/OpenSourceBrain/korngreen-pyramidal/issues). 

### *NeuroConstruct* project

#### Ionic Mechanisms

Both original and NeuroML versions of the ionic mechanisms were imported into a *neuroConstruct* project, with simulation configurations allowing the comparison of both implementations. Mechanisms were named according the following convention: the original *.mod* mechanisms were suffixed with *_nrn*, while the NeuroML mechanisms had no suffix.

#### Morphology

Cell [morphology](http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=151825&file=\Demo\cells\A140612.hoc) from the *modelDB* project was exported to NeuroML using *neuron*.

### Idiosyncrasies in the conversion

#### General issues

General comments/difficulties that occurred during the conversion are logged on the github repo as [issues](https://github.com/OpenSourceBrain/korngreen-pyramidal/issues).

#### Inhomogeneous parameters over the dendritic tree

![](gih_comparison.png)

The original *neuron* version results in piecewise linear interpolation of the distribution over each section. Compare the *neuroConstuct* generated code

     //neuroconstruct generated

     objref PathLengthApicalDends

     PathLengthApicalDends = new SubsetDomainIterator

     PathLengthApicalDends.update {

         x = PathLengthApicalDends.x

         p = PathLengthApicalDends.p

         gmax\_iA = 100000.0** (2.82824E-4 + (0.0033165 \* exp(((–1) \* 0.0117721) \* p))) // 100000.0 to convert from nc to NEURON units

     }

With the original *.hoc* specification

    gbar_iA(0:1) = (gka_start+gka_beta*exp(gka_alpha*dist1)):(gka_start+gka_beta*exp(gka_alpha*dist2))