parameter dictionary?

[carolinafernandezp]

Hello,

I'm interested in understanding what the different parameters in the .param files that get created mean (especially those that cannot be directly changed through the GUI). I believe there are a total of 255 parameters. For example:

• L5Pyr_soma_gkbar_hh2: 0.06
• L5Pyr_soma_gnabar_hh2: 0.32
• L5Pyr_soma_el_hh2: -65.0

Is there a dictionary of some sort that will tell me what these different parameters mean and their units?

Thank you

[rythorpe]

Sadly, no. Most of the parameters in .param files are poorly documented and ambiguous. For the very reason you bring up, we've been trying to discourage use of .param files in hnn-core. To answer your question about those specific parameters though,

• L5Pyr_soma_gkbar_hh2 is the maximal conductance of the Hodgkin-Huxley potassium current in L5 pyramidal cell soma compartments (microsiemens, uS)
• L5Pyr_soma_gnabar_hh2 is the same, except for sodium (microsiemens, uS)
• L5Pyr_soma_el_hh2 is the reversal potential for the leak current (I believe these are in millivolts, mV)

[jasmainak]

Take a look at this:

from hnn_core import jones_2009_model

net = jones_2009_model()

print(net.cell_types)
print(net.cell_types['L2_pyramidal'].sections)  # geometry of the cell compartments
print(net.cell_types['L2_pyramidal'].sections['apical_trunk'].mechs)  # mechanisms in a compartment and their parameters

Then to get what the parameters are actually doing, you have to look at the mod files. For e.g., if you look at hh2.mod you can see the equations and what the variables mean. @carolinafernandezp if you are familiar with git, I think starting a document that describes this would be great.