I am trying to replicate the NEURON model described in this paper:
A cell model study of calcium influx mechanism regulated by calcium dependent potassium channels in Purkinje cell dendrites
Koji Chono, Hiroshi Takagi, Shozo Koyama, Hideo Suzuki, Etsuro Ito
However, I just cannot do it. I have contacted the prinipal author, Etsuro Ito but he seems to be unreachable. Replication should be elementry because this model is just a variant of the following NEURON model  has same equations, but just with different parameter values:
http://senselab.med.yale.edu/senselab/m ... odel=17664
Maybe I am just making mistakes in my coding. Has anyone else tried this? Would be so, so grateful to anyone that might be able to help.
purkinje cell
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Re: purkinje cell
What exactly is the manifestation of this failure to replicate?mikey wrote:I am trying to replicate the NEURON model described in this paper:
. . .
However, I just cannot do it.
Try one or more of the other authors.I have contacted the prinipal author
Typographical errors are common. Check the journal for notices of errata. Check themodel is just a variant of the following NEURON model  has same equations, but just with different parameter values
authors' own WWW sites to see if they mention errata or have made the code available.
If the only differences are numeric values of parameters, what coding is necessary?Maybe I am just making mistakes in my coding.
Q) What exactly is the manifestation of this failure to replicate?
A) My replicated model does not produce the same voltagetime relationships as depicted in the figures of the model. Using same stimulation protocal as paper.
Q) I have contacted the prinipal author Try one or more of the other authors.
A) I have tried to get contact details for them but alas...cannot. Also, the authors are Japanese and I think perhaps as you go along the authors  the chances of speaking english become less.
Q) Typographical errors are common. Check the journal for notices of errata.
A) Will do.
Q) Check the authors' own WWW sites to see if they mention errata or have made the code available.
A) Sadly not.
Q) Maybe I am just making mistakes in my coding.
If the only differences are numeric values of parameters, what coding is necessary?
A) True. No coding going on. Maybe I am making mistakes in my alteration of parameter values. But I think not  as it is a simple task and I have double checked a few times now.
A) My replicated model does not produce the same voltagetime relationships as depicted in the figures of the model. Using same stimulation protocal as paper.
Q) I have contacted the prinipal author Try one or more of the other authors.
A) I have tried to get contact details for them but alas...cannot. Also, the authors are Japanese and I think perhaps as you go along the authors  the chances of speaking english become less.
Q) Typographical errors are common. Check the journal for notices of errata.
A) Will do.
Q) Check the authors' own WWW sites to see if they mention errata or have made the code available.
A) Sadly not.
Q) Maybe I am just making mistakes in my coding.
If the only differences are numeric values of parameters, what coding is necessary?
A) True. No coding going on. Maybe I am making mistakes in my alteration of parameter values. But I think not  as it is a simple task and I have double checked a few times now.
One problem is that the equations are listed in the paper as:
m
alpha = A/B+exp((v+C)/(D))
beta = E/F+exp((v+C)/(D))
h
alpha = A/B+exp((v+G)/(H))
beta = E/F+exp((v+G)/(H))
I think this must be a mistake because I think it should be:
m
alpha = A/B+exp((v+C)/(D))
beta = E/F+exp((v+G)/(H))
h
alpha = A/B+exp((v+C)/(D))
beta = E/F+exp((v+G)/(H))
I have coded it up as I think it should be. Because Im thinking that the equations as they are in the paper must be wrong
m
alpha = A/B+exp((v+C)/(D))
beta = E/F+exp((v+C)/(D))
h
alpha = A/B+exp((v+G)/(H))
beta = E/F+exp((v+G)/(H))
I think this must be a mistake because I think it should be:
m
alpha = A/B+exp((v+C)/(D))
beta = E/F+exp((v+G)/(H))
h
alpha = A/B+exp((v+C)/(D))
beta = E/F+exp((v+G)/(H))
I have coded it up as I think it should be. Because Im thinking that the equations as they are in the paper must be wrong