|
Converting the file: CompleteNetwork.xml
NeuroML Level 3 file
| General notes | A completely specified network in NeuroML Level 3. While this is useful for
exporting/importing/saving from an application, better practice might be to have the cell
definitions, the channel mechanisms, and network specification in separate files. |
Cell: CellA
| Name | CellA |
| Description |
| As described in the NeuroML file |
| Test cell for showing how channels can be placed on a cell |
| Total number of segments | 2 |
| Total number of cables | 2
with 1 soma cable(s),
1 dendritic cable(s)
and 0 axonal cable(s)
|
| Cable details |
SomaCable (id:0),
number of segments in cable: 1
This cable is present in groups: soma_group
DendriteCable (id:1),
number of segments in cable: 1
This cable is present in groups: dendrite_group
|
Biophysical properties of cell: CellA
| Unit system of biophysical entities |
| This can be either SI Units or Physiological Units |
| Physiological Units |
| Channel Mechanism: pas |
| An active membrane conductance |
|
Conductance density (gmax) of 0.0330033 mS cm-2 on: all
|
| Specific Capacitance |
| This is the capacitance per unit area of the membrane |
| Specific Capacitance of
1.0 uf/cm2 on: all
|
| Specific Axial Resistance |
| This is the specific cytoplasmic resistance along a dendrite/axon |
| Specific Axial Resistance of
0.1 Kohm cm on: all
|
Channel: pas
| Name | pas |
| Description |
| As described in the ChannelML file |
| Simple example of a leak/passive conductance. |
| Current voltage relationship | ohmic |
| Ion involved in channel |
| The ion which is actually flowing through the channel and its default reversal potential.
Note that the reversal potential will normally depend on the internal and external concentrations of the ion at the segment on which the channel is placed. |
| non_specific (default Enon_specific = -54.3)
|
| Default maximum conductance density |
| Note that the conductance density of the channel will be set when it is placed on the cell. |
| Gmax = 0.3 |
| Conductance expression |
| Expression giving the actual conductance as a function of time and voltage |
| Gnon_specific(v,t) = Gmax
|
| Current due to channel |
| Ionic current through the channel |
| Inon_specific(v,t) =
Gnon_specific(v,t) * (v - Enon_specific) |
Synapse: DoubExpSynA
| Name | DoubExpSynA |
|
Synaptic Mechanism Model: Double Exponential Synapse
The model underlying the synaptic mechanism
|
| Expression for conductance |
|
G(t) = max_conductance * A * ( e-t/decay_time - e-t/rise_time ) for t >= 0
|
| |
| where the normalisation factor is: |
|
A =
|
1
|
|
e-peak_time / decay_time - e -peak_time / rise_time
|
| and the time to reach max conductance is: |
|
peak_time =
|
(decay_time * rise_time)/(decay_time - rise_time) * ln(decay_time/rise_time)
|
| |
| Note that if rise_time = 0 this simplifies to a single exponential synapse: |
|
G(t) = max_conductance * e-t/decay_time for t >= 0
|
| |
| Note also if decay_time = rise_time = alpha_time, the waveform is for an alpha synapse with peak at alpha_time: |
|
G(t) = max_conductance * (t/alpha_time) * e( 1 - t/alpha_time) for t >= 0
|
|
| Maximum conductance |
| The peak conductance which the synapse will reach |
| 1.0E-5 |
| Rise time |
| Characteristic time (tau) over which the double exponential synaptic conductance rises |
| 1 |
| Decay time |
| Characteristic time (tau) over which the double exponential synaptic conductance decays |
| 2 |
| Reversal potential |
| The effective reversal potential for the ion flow through the synapse when the conductance is non zero |
| 0 |
Populations:
| Name | CellGroupA |
| Cell Type |
CellA
|
| 3 Instances | 0: (0, 0, 0)
1: (50, 0, 0)
2: (100, 0, 0)
|
| Name | CellGroupB |
| Cell Type |
CellA
|
| 2 Instances | 0: (0, 100, 0)
1: (50, 100, 0)
|
Projections:
| Units |
| Unit system used in synapse properties, etc. below |
| Physiological Units |
| Projection | NetworkConnection |
| From: |
CellGroupA |
| To: |
CellGroupB |
| Synaptic properties | Type:
DoubExpSynA
Delay: 5 ms (internal) Weight: 1 Threshold: -20 mV |
| 3 connection instance(s): |
0: From
segment 0 (fract along:
0.5) on
source cell 0
to
segment 1 on
target cell 1
1: From
segment 0 on
source cell 2
to
segment 0 on
target cell 0
2: From
segment 0 on
source cell 1
to
segment 1 on
target cell 1, delay: 10 ms (internal), weight: 0.5
|
Inputs:
| Units |
| Unit system used in synapse properties, etc. below |
| SI Units |
| Input | RandomInputLow |
| Random stimulation | Frequency: 20 s-1
Synaptic mechanism: DoubExpSynA |
| Target of stimulation | CellGroupA |
| Cells receiving input: |
Cell: 1
Cell: 2, segment 1
|
| Input | RandomInputHigh |
| Random stimulation | Frequency: 100 s-1
Synaptic mechanism: DoubExpSynA |
| Target of stimulation | CellGroupA |
| Cells receiving input: |
Cell: 0
|
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