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

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Converting the file: ExtendNetSpec.xml

NeuroML Level 3 file

General notesA network of cells connected in NeuroML Level 3. Extra tags are included to give an idea how the standard can be extended. Note most NeuroML compliant applications will ignore this extra data, but will still be able to extract the essential physiological information.

Cell: CellA

NameCellA
Description
As described in the NeuroML file
Simple test cell, just 2 segments
Properties
Abstraction level = Reduced cell model
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 0.033 mS cm-2 on: all 

Parameter gmax_max has value 0.011 on: all 

Parameter gmax_min has value 0.055 on: all 

Channel Mechanism: Na_Channel_NMODL
An active membrane conductance

Conductance density (gmax) of 0.8 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

Synapse: VoltDepGapJunc

NameVoltDepGapJunc

Synaptic Mechanism Model: Electrical Synapse

The model underlying the synaptic mechanism

Conductance
The conductance of the electrical connection
1.0E-9

Populations:

NameCellGroupA
Cell Type CellA
3 Instances

0: (0, 0, 0)

1: (0, 10, 0)

2: (0, 20, 0)


NameCellGroupB
Cell Type CellA
2 Instances

0: (0, 100, 0)

1: (20, 100, 0)



Projections:

Units
Unit system used in synapse properties, etc. below
Physiological Units

Projection NetworkConnection
From: CellGroupA
To: CellGroupB
Synaptic properties

Type: VoltDepGapJunc

3 connection instance(s):

0: From segment 0 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 1

2: From segment 0 on source cell 3 to segment 1 on target cell 1




Time to transform file: 0.118 secs