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Chapter 5: Compartments

Activity happens within the Compartments of the Cells.
KeywordValueDescription
COMPARTMENT
N/A
Indicates the start of a Compartment defintion section
TYPE
name(string)
The name used to refer to this compartment
SEED
value(integer)
The number used to seed the random nuber generator for the compartment
SPIKESHAPE
name(string)
The name of the spike shape to use in the compartment when it reaches threshold.
SPIKE_HALFWIDTH
mean(real)
stdev(real)
Deprecated. A compartment formerly could only become active if it had a halfwidth along with a spikeshape and threshold. The halfwidth parameter is no longer used by NCS.
TAU_MEMBRANE
mean(real)
stdev(real)
This value is used along with R_MEMBRANE to calculate the capacitance of the compartment.
( Capacitance = TAU_MEMBRANE / R_MEMBRANE )
R_MEMBRANE
mean(real)
stdev(real)
This value is used along with TAU_MEMBRANE to calculate the capacitance of the compartment.
( Capacitance = TAU_MEMBRANE / R_MEMBRANE )
If R_MEMBRANE = 0, then Capacitance is 0.0
THRESHOLD
mean(real)
stdev(real)
When the compartment's membrane voltage reaches the threshold, it begins a spike shape
LEAK_REVERSAL
mean(real)
stdev(real)
When a compartment updates its membrane voltage and there is no voltage clamp, a current leak must be calculated
Current Leak = LEAK_CONDUCTANCE * ( previous membrance voltage - LEAK_REVERSAL )
LEAK_CONDUCTANCE
mean(real)
stdev(real)
When a compartment updates its membrane voltage and there is no voltage clamp, a current leak must be calculated
Current Leak = LEAK_CONDUCTANCE * ( previous membrance voltage - LEAK_REVERSAL )
VMREST
mean(real)
stdev(real)
The voltage of a compartment will start at vmrest
CA_INTERNAL
mean(real)
stdev(real)
The compartment will start with the initial CA_INTERNAL specified
CA_EXTERNAL
mean(real)
stdev(real)
The compartment will start with the initial CA_EXTERNAL specified
CA_SPIKE_INCREMENT
meanreal)
stdev(real)
When a compartment reaches threshold, CA_INTERNAL will be increased by the CA_SPIKE_INCREMENT
CA_TAU
mean(real)
stdev(real)
Used to calculate the Calcium persistance of the compartment
Calcium persistance = 1.0 - dt / CA_TAU
where dt is related to the value os FSV specified in the Brain
dt = 1 / FSV
if FSV is 0, dt = 0
if CA_TAU is 0, Calcium persistence = 1.0
if Calcium persistence is less than 0 or greater than 1, it will be adjusted to those bounds

Calcium persistance affects the CA_INTERNAL
CA_INTERNAL = calcium persistance * CA_INTERNAL
CHANNEL
name(string)
The name of a channel which will be used by this compartment
END_COMPARTMENT
N/A
Indicates the end of a compartment definition section

Example

COMPARTMENT
        TYPE                    Soma-cNAC
        SEED                    999999
        SPIKESHAPE              AP_Hoff
        SPIKE_HALFWIDTH         10              0
        TAU_MEMBRANE            0.015           0.0
        R_MEMBRANE              200             0.0
        THRESHOLD               -40             0.0
        LEAK_REVERSAL           0.0             0.0
        LEAK_CONDUCTANCE        0.0             0.0
        VMREST                  -65             0.0
        CA_INTERNAL             5.0             0.0
        CA_EXTERNAL             0.0             0.0
        CA_SPIKE_INCREMENT      100             0.0
        CA_TAU                  0.07            0.0
        CHANNEL			a
END_COMPARTMENT
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Last updated Friday 6/15/2007