Transforming XML file: NeuroMLFiles/Examples/NetworkML/CompleteNetwork.xml using XSL file: NeuroMLFiles/Schemata/v1.8.1/Level3/NeuroML_Level3_v1.8.1_HTML.xsl

View original file before transform

Converting the file: CompleteNetwork.xml

NeuroML Level 3 file

General notesA 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

NameCellA
Description
As described in the NeuroML file
Test cell for showing how channels can be placed on a cell
Total number of segments2
Total number of cables2 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

Namepas
Description
As described in the ChannelML file
Simple example of a leak/passive conductance.
Current voltage relationshipohmic
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

NameDoubExpSynA

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:

NameCellGroupA
Cell Type CellA
3 Instances

0: (0, 0, 0)

1: (50, 0, 0)

2: (100, 0, 0)


NameCellGroupB
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

InputRandomInputLow
Random stimulation

Frequency: 20 s-1

Synaptic mechanism: DoubExpSynA

Target of stimulationCellGroupA
Cells receiving input:

Cell: 1

Cell: 2, segment 1


InputRandomInputHigh
Random stimulation

Frequency: 100 s-1

Synaptic mechanism: DoubExpSynA

Target of stimulationCellGroupA
Cells receiving input:

Cell: 0




Time to transform file: 0.115 secs