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

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Converting the file: MossyCellBiophys.xml

NeuroML Level 3 file

General notesExample of NeuroML file containing single Dentate Mossy Cell

Cell: MossyCell

NameMossyCell
Description
As described in the NeuroML file
An abstracted Mossy Cell morphology from Santhakumar et al 2005 including biophysical parameters
Authors
Translators of the model to NeuroML:
   Padraig Gleeson  (UCL)  p.gleeson - at - ucl.ac.uk
Referenced publicationSanthakumar, V., Aradi, I., and Soltesz, I. (2005). Role of mossy fiber sprouting and mossy cell loss in hyperexcitability: a network model of the dentate gyrus incorporating cell types and axonal topography. J Neurophysiol 93, 437-453. Pubmed
Reference in NeuronDB Dentate Gyrus Mossy cell
Total number of segments17
Total number of cables17 with 1 soma cable(s), 16 dendritic cable(s) and 0 axonal cable(s)
Cable details soma (id:0), number of segments in cable: 1
  This cable is present in groups: all  soma_group  

mcdend1_0 (id:1), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  pdend  

mcdend1_1 (id:2), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  ddend3seg  

mcdend1_2 (id:3), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  ddend3seg  mdend  

mcdend1_3 (id:4), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  ddend1seg  ddend3seg  

mcdend2_0 (id:5), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  pdend  

mcdend2_1 (id:6), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  ddend3seg  

mcdend2_2 (id:7), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  ddend3seg  mdend  

mcdend2_3 (id:8), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  ddend1seg  ddend3seg  

mcdend3_0 (id:9), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  pdend  

mcdend3_1 (id:10), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  ddend3seg  

mcdend3_2 (id:11), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  ddend3seg  mdend  

mcdend3_3 (id:12), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  ddend1seg  ddend3seg  

mcdend4_0 (id:13), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  pdend  

mcdend4_1 (id:14), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  ddend3seg  

mcdend4_2 (id:15), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  ddend3seg  mdend  

mcdend4_3 (id:16), number of segments in cable: 1
  This cable is present in groups: all  dendrite_group  ddend1seg  ddend3seg  

Biophysical properties of cell: MossyCell

Unit system of biophysical entities
This can be either SI Units or Physiological Units
Physiological Units
Channel Mechanism: borgka
An active membrane conductance

Conductance density (gmax) of 0.01 mS cm-2 on: all 

Channel Mechanism: Kf
An active membrane conductance

Conductance density (gmax) of 0.5 mS cm-2 on: pdend 

Channel Mechanism: hyperde3
An active membrane conductance

Conductance density (gmax) of 0.0050 mS cm-2 on: all 

Channel Mechanism: MossyLeakCond
An active membrane conductance

Conductance density (gmax) of 0.044 mS cm-2 on: dendrite_group 

Channel Mechanism: ccanl
An active membrane conductance

Conductance density (gmax) of 100000.0 mS cm-2 on: all 

Channel Mechanism: nca
An active membrane conductance

Conductance density (gmax) of 0.08 mS cm-2 on: all 

Channel Mechanism: lca
An active membrane conductance

Conductance density (gmax) of 0.6 mS cm-2 on: all 

Channel Mechanism: Nat
An active membrane conductance

Conductance density (gmax) of 120.0 mS cm-2 on: soma_group 

Channel Mechanism: MossyLeakCond
An active membrane conductance
This is a Passive Conductance and so conductance density (gmax) and reversal potential (e) should be sufficient parameters to specify the mechanism fully.

Conductance density (gmax) of 0.011 mS cm-2 on: soma_group 

Channel Mechanism: gskch
An active membrane conductance

Conductance density (gmax) of 16.0 mS cm-2 on: all 

Channel Mechanism: cagk
An active membrane conductance

Conductance density (gmax) of 16.5 mS cm-2 on: all 

Channel Mechanism: Nat
An active membrane conductance

Conductance density (gmax) of 120.0 mS cm-2 on: pdend 

Channel Mechanism: Kf
An active membrane conductance

Conductance density (gmax) of 0.5 mS cm-2 on: soma_group 

Specific Capacitance
This is the capacitance per unit area of the membrane

Specific Capacitance of 0.6 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 

Initial Membrane Potential
This quantity is often required for computational simulations and specifies the potential difference across the membrane at the start of the simulation.

Initial Membrane Potential -60.0 mV on: all 






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