Wiki » History » Version 5
Boris Marin, 30 Apr 2014 14:58
1 | 1 | Boris Marin | L5 Pyramidal Neuron Almog and Korngreen (2014) |
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2 | 1 | Boris Marin | ============================================== |
3 | 1 | Boris Marin | |
4 | 1 | Boris Marin | Model description |
5 | 1 | Boris Marin | ----------------- |
6 | 1 | Boris Marin | |
7 | 4 | Boris Marin | 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). |
8 | 1 | Boris Marin | The relevant *neuron* files can be downloaded from [modelDB](http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=151825). |
9 | 1 | Boris Marin | h2. Conversion to NeuroML |
10 | 5 | Boris Marin | 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. |
11 | 5 | Boris Marin | 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) . |
12 | 5 | Boris Marin | |
13 | 4 | Boris Marin | h3. *NeuroConstruct* project |
14 | 4 | Boris Marin | h4. Ion Mechanisms |
15 | 4 | Boris Marin | 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. |
16 | 1 | Boris Marin | |
17 | 1 | Boris Marin | h4. Morphology |
18 | 1 | Boris Marin | 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*. |
19 | 1 | Boris Marin | h3. Idiosyncrasies in the conversion |
20 | 5 | Boris Marin | h4. General issues |
21 | 5 | Boris Marin | General comments/difficulties that occurred during the conversion are logged on the github repo as [issues](https://github.com/OpenSourceBrain/korngreen-pyramidal/issues) . |
22 | 4 | Boris Marin | h4. Inhomogeneous parameters over the dendritic tree |
23 | 4 | Boris Marin | p=. ![]({width: 80%}gih_comparison.png) |
24 | 4 | Boris Marin | The original *neuron* version results in piecewise linear interpolation of the distribution over each section. |
25 | 4 | Boris Marin | Compare the *neuroConstuct* generated code |
26 | 4 | Boris Marin | \<pre\> |
27 | 4 | Boris Marin | //neuroconstruct generated |
28 | 4 | Boris Marin | objref PathLengthApicalDends |
29 | 4 | Boris Marin | PathLengthApicalDends = new SubsetDomainIterator |
30 | 4 | Boris Marin | PathLengthApicalDends.update { |
31 | 4 | Boris Marin | x = PathLengthApicalDends.x |
32 | 4 | Boris Marin | p = PathLengthApicalDends.p |
33 | 4 | Boris Marin | gmax\_iA = 100000.0** (2.82824E-4 + (0.0033165 \* exp(((–1) \* 0.0117721) \* p))) // 100000.0 to convert from nc to NEURON units |
34 | 4 | Boris Marin | } |
35 | 3 | Boris Marin | |
36 | 4 | Boris Marin | </pre> |
37 | 4 | Boris Marin | With the original *.hoc* specification |
38 | 4 | Boris Marin | |
39 | 4 | Boris Marin | gbar_iA(0:1) = (gka_start+gka_beta*exp(gka_alpha*dist1)):(gka_start+gka_beta*exp(gka_alpha*dist2)) |