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).


h2. Conversion to NeuroML
We have converted are currently converting the [original model](http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=151825) original model 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) .

h3. *NeuroConstruct* project
h4. Ion 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.

h4. 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*.
h3. Idiosyncrasies in the conversion
h4. 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) .
h4. Inhomogeneous parameters over the dendritic tree
p=. 
The original *neuron* version results in piecewise linear interpolation of the distribution over each section.
Compare the *neuroConstuct* generated code
\<pre\>
//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
}

</pre>
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))