Known issues » History » Version 4
Version 3 (Padraig Gleeson, 30 Apr 2014 14:57) → Version 4/21 (Padraig Gleeson, 30 Apr 2014 14:57)
Known issues with Traub et al 2005.
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This is a quite complex and detailed model and as discussed in the [original paper](http://www.ncbi.nlm.nih.gov/pubmed/15525801?dopt=Abstract)
> Any model, even of a small bit of cortex, is subject to difficulties and hazards: limited data, large numbers of parameters, criticisms that models with complexity comparable to the modeled system cannot be scientifically useful, the expense and slowness of the necessary computations, and serious uncertainties as to how a complex model can be compared with experiment and shown to be predictive.
> The above difficulties and hazards are too real to be dismissed readily. In our opinion, the only way to proceed is through a state of denial that any of the difficulties need be fatal. The reader must then judge whether the results, preliminary as they must be, help our understanding.
Even the published Fortran version of this model was acknowledged to be incomplete. Each conversion of this model will deviate to a small or large extent from this version.
### Limitations of the conversion of the model to NEURON
It is useful to read the [notes on conversion of this model to NEURON from Fortran](http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=82894&file=\nrntraub\README) by Tom Morse and Michael Hines
An updated version of this model in NEURON is being worked on [here](https://github.com/hglabska/Thalamocortical/network)
### Limitations of the conversion of the model to MOOSE
TODO…
### Limitations of the conversion of the model to NeuroML
Important details of the process of conversion of the cell models to NeuroML, and matching cell behaviour across simulators is present in the [2010 NeuroML paper](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000815).
Issues:
**Initialization of ion channels**
**NMDA conductance wave form**
**Firing rate vs. injected current of cells**
Model can be exported to [(mostly valid) NeuroML 2](https://github.com/OpenSourceBrain/Thalamocortical/tree/master/neuroConstruct/generatedNeuroML2), but does not
-----------------------------------
This is a quite complex and detailed model and as discussed in the [original paper](http://www.ncbi.nlm.nih.gov/pubmed/15525801?dopt=Abstract)
> Any model, even of a small bit of cortex, is subject to difficulties and hazards: limited data, large numbers of parameters, criticisms that models with complexity comparable to the modeled system cannot be scientifically useful, the expense and slowness of the necessary computations, and serious uncertainties as to how a complex model can be compared with experiment and shown to be predictive.
> The above difficulties and hazards are too real to be dismissed readily. In our opinion, the only way to proceed is through a state of denial that any of the difficulties need be fatal. The reader must then judge whether the results, preliminary as they must be, help our understanding.
Even the published Fortran version of this model was acknowledged to be incomplete. Each conversion of this model will deviate to a small or large extent from this version.
### Limitations of the conversion of the model to NEURON
It is useful to read the [notes on conversion of this model to NEURON from Fortran](http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=82894&file=\nrntraub\README) by Tom Morse and Michael Hines
An updated version of this model in NEURON is being worked on [here](https://github.com/hglabska/Thalamocortical/network)
### Limitations of the conversion of the model to MOOSE
TODO…
### Limitations of the conversion of the model to NeuroML
Important details of the process of conversion of the cell models to NeuroML, and matching cell behaviour across simulators is present in the [2010 NeuroML paper](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000815).
Issues:
**Initialization of ion channels**
**NMDA conductance wave form**
**Firing rate vs. injected current of cells**
Model can be exported to [(mostly valid) NeuroML 2](https://github.com/OpenSourceBrain/Thalamocortical/tree/master/neuroConstruct/generatedNeuroML2), but does not