Use individual neuron model from BlueBrain's nmc-portal

#1

The nmc-portal ( https://bbp.epfl.ch/nmc-portal/welcome ) provide models of individual neurons (in the NEURON simulation environment) .
A model package contains a morphology file, the ion channel descriptions, the synapse descriptions and templates to instantiate the cell. There is code to construct the model, distribute the ion channels and synapses on the morphology, generate a GUI, and inject current clamp and synaptic input into the model.

Learn and get help to use these models during this hackathon.

#2

Hi,

I have difficulties locating biophysical parameters of different morphological cell groups at NMC portal which were used in the Markram et al Cell 2015 paper. I am particularly interested on the inhibitory cells. Parameters include membrane capacitance (or size to calculate it), leak conductance, leak equilibrium potential, action potential threshold, etc.

yours,
Simo Vanni

#3

Hi,
Below you can see the configuration file of one of the interneuron models. Every block represents one parameter.
ChannelSuffix is the name of the channel in the Neuron MOD file.
ParameterName is the parameter that was fitted (mostly maximal conductance):

Parameter NaTa_t.axonal.gNaTa_tbar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix NaTa_t
CellSection axonal
ParameterName gNaTa_tbar
}
Numerical_Parameters
{
Min 0
Max 4
}
}

Parameter Nap_Et2.axonal.gNap_Et2bar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix Nap_Et2
CellSection axonal
ParameterName gNap_Et2bar
}
Numerical_Parameters
{
Min 0
Max 1e-6
}
}

Parameter Nap_Et2.basal.gNap_Et2bar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix Nap_Et2
CellSection basal
ParameterName gNap_Et2bar
}
Numerical_Parameters
{
Min 0
Max 1e-6
}
}

Parameter K_Pst.axonal.gK_Pstbar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix K_Pst
CellSection axonal
ParameterName gK_Pstbar
}
Numerical_Parameters
{
Min 0
Max 1
}
}

Parameter K_Tst.axonal.gK_Tstbar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix K_Tst
CellSection axonal
ParameterName gK_Tstbar
}
Numerical_Parameters
{
Min 0
Max 1e-1
}
}

Parameter SK_E2.axonal.gSK_E2bar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix SK_E2
CellSection axonal
ParameterName gSK_E2bar
}
Numerical_Parameters
{
Min 0
Max 1e-1
}
}

Parameter SKv3_1.axonal.gSKv3_1bar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix SKv3_1
CellSection axonal
ParameterName gSKv3_1bar
}
Numerical_Parameters
{
Min 0
Max 2
}
}

Parameter Ca.axonal.gCabar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix Ca
CellSection axonal
ParameterName gCabar
}
Numerical_Parameters
{
Min 0
Max 1e-3
}
}

Parameter Ca_LVAst.axonal.gCa_LVAstbar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix Ca_LVAst
CellSection axonal
ParameterName gCa_LVAstbar
}
Numerical_Parameters
{
Min 0
Max 1e-2
}
}

Parameter CaDynamics_E2.axonal.gamma
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix CaDynamics_E2
CellSection axonal
ParameterName gamma
}
Numerical_Parameters
{
Min 0.0005
Max 0.05
}
}

Parameter CaDynamics_E2.axonal.decay
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix CaDynamics_E2
CellSection axonal
ParameterName decay
}
Numerical_Parameters
{
Min 20
Max 1000
}
}

Parameter Leak.axonal.g_pas
{
String_Parameters
{

    Type  Channel_conductance
    ChannelSuffix   none
    CellSection axonal  
    ParameterName g_pas
}
Numerical_Parameters
{
    Min                 1e-6
    Max                 1e-4
}

}

Parameter Leak.axonal.e_pas
{
String_Parameters
{

    Type  Channel_conductance
    ChannelSuffix   none
    CellSection axonal  
    ParameterName e_pas
}
Numerical_Parameters
{
    Min                 -80
    Max                 -60
}

}

Parameter NaTs2_t.somatic.gNaTs2_tbar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix NaTs2_t
CellSection somatic
ParameterName gNaTs2_tbar
}
Numerical_Parameters
{
Min 0
Max 1
}
}

Parameter Nap_Et2.somatic.gNap_Et2bar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix Nap_Et2
CellSection somatic
ParameterName gNap_Et2bar
}
Numerical_Parameters
{
Min 0
Max 1e-6
}
}

Parameter SKv3_1.somatic.gSKv3_1bar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix SKv3_1
CellSection somatic
ParameterName gSKv3_1bar
}
Numerical_Parameters
{
Min 0
Max 1
}
}

Parameter K_Pst.somatic.gK_Pstbar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix K_Pst
CellSection somatic
ParameterName gK_Pstbar
}
Numerical_Parameters
{
Min 0
Max 1
}
}

Parameter K_Tst.somatic.gK_Tstbar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix K_Tst
CellSection somatic
ParameterName gK_Tstbar
}
Numerical_Parameters
{
Min 0
Max 1e-1
}
}

Parameter K_Tst.basal.gK_Tstbar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix K_Tst
CellSection basal
ParameterName gK_Tstbar
}
Numerical_Parameters
{
Min 0
Max 1e-2
}
}

Parameter NaTs2_t.basal.gNaTs2_tbar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix NaTs2_t
CellSection basal
ParameterName gNaTs2_tbar
}
Numerical_Parameters
{
Min 0
Max 0.01
}
}

Parameter SK_E2.somatic.gSK_E2bar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix SK_E2
CellSection somatic
ParameterName gSK_E2bar
}
Numerical_Parameters
{
Min 0
Max 1e-1
}
}

Parameter Ca.somatic.gCabar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix Ca
CellSection somatic
ParameterName gCabar
}
Numerical_Parameters
{
Min 0
Max 1e-3
}
}

Parameter Ca_LVAst.somatic.gCa_LVAstbar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix Ca_LVAst
CellSection somatic
ParameterName gCa_LVAstbar
}
Numerical_Parameters
{
Min 0
Max 1e-2
}
}

Parameter CaDynamics_E2.somatic.gamma
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix CaDynamics_E2
CellSection somatic
ParameterName gamma
}
Numerical_Parameters
{
Min 0.0005
Max 0.05
}
}

Parameter CaDynamics_E2.somatic.decay
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix CaDynamics_E2
CellSection somatic
ParameterName decay
}
Numerical_Parameters
{
Min 20
Max 1000
}
}

Parameter Leak.somatic.g_pas
{
String_Parameters
{

    Type  Channel_conductance
    ChannelSuffix   none
    CellSection somatic  
    ParameterName g_pas
}
Numerical_Parameters
{
    Min                 1e-6
    Max                 1e-4
}

}

Parameter Leak.somatic.e_pas
{
String_Parameters
{

    Type  Channel_conductance
    ChannelSuffix   none
    CellSection somatic  
    ParameterName e_pas
}
Numerical_Parameters
{
    Min                 -80
    Max                 -60
}

}

Parameter SKv3_1.basal.gSKv3_1bar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix SKv3_1
CellSection basal
ParameterName gSKv3_1bar
}
Numerical_Parameters
{
Min 0
Max 4e-2
}
}

Parameter Im.basal.gImbar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix Im
CellSection basal
ParameterName gImbar
}
Numerical_Parameters
{
Min 0
Max 1e-3
}
}

Parameter Im.axonal.gImbar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix Im
CellSection axonal
ParameterName gImbar
}
Numerical_Parameters
{
Min 0
Max 1e-3
}
}

Parameter Im.somatic.gImbar
{
String_Parameters
{
Type Channel_conductance
ChannelSuffix Im
CellSection somatic
ParameterName gImbar
}
Numerical_Parameters
{
Min 0
Max 1e-3
}
}

Parameter Ih.basal.gIhbar
{
String_Parameters
{

    Type  Channel_conductance
    ChannelSuffix   Ih
    CellSection basal
    ParameterName gIhbar
}
Numerical_Parameters
{
    Min                 0.0
    Max                 0.1
}

}

Parameter Leak.basal.g_pas
{
String_Parameters
{

    Type  Channel_conductance
    ChannelSuffix   none
    CellSection basal  
    ParameterName g_pas
}
Numerical_Parameters
{
    Min                 1e-6
    Max                 1e-4
}

}

Parameter Leak.basal.e_pas
{
String_Parameters
{

    Type  Channel_conductance
    ChannelSuffix   none
    CellSection basal  
    ParameterName e_pas
}
Numerical_Parameters
{
    Min                 -80
    Max                 -60
}

}