Main Neurospaces logo neurospaces 0.1675 Thu, 27 Dec 2007 15:58:18 -0600 hugo

Index of group ./specifications/simple_purkinje

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simple simulations of purkinje cell models

1. Commands for a simple simulation of the purkinje cell model
2. Commands for an interactive simulation of the purkinje cell model

1. Commands for a simple simulation of the purkinje cell model

Startup command : bin/genesis-g3

(No model has been loaded for the following set of commands.)

1.1. Is startup successful ?

1. Expected output 
GENESIS 3 shell

1.2. Can we find the library ?

1. Executed command
library_show
2. Expected output 

ndf_library:
  .:
    - algorithm_data/
    - cells/
    - channels/
    - chemesis/
    - contours/
    - conversions/
    - descriptor.yml
    - event_data/
    - examples/
    - fibers/
    - gates/
    - legacy/
    - mappers/
    - morphologies/
    - networks/
    - pools/
    - populations/
    - projectionqueries/
    - projections/
    - pulsegen/
    - segments/
    - tests/
    - utilities/

1.3. Can we find the single neuron library ?

1. Executed command
library_show ndf cells
2. Expected output 

ndf_library:
  cells:
    - BDK5cell2-nolib.ndf
    - RScell-nolib.ndf
    - cell1.ndf
    - izhikevich.ndf
    - purkinje/
    - simplecell-nolib.ndf
    - stand_alone.ndf
    - traub91-nolib.ndf
    - traub94-nolib.ndf
    - traub95-nolib.ndf

1.4. Can we find the purkinje cell models in the single neuron library ?

1. Executed command
library_show ndf cells/purkinje
2. Expected output 

ndf_library:
  cells/purkinje:
    - edsjb1994.ndf
    - edsjb1994_dendrogram.ndf
    - edsjb1994_partitioned.ndf
    - edsjb1994_passive.ndf
    - edsjb1994_spinesurface.ndf

1.5. Can we load the standard purkinje cell model ?

1. Executed command
ndf_load cells/purkinje/edsjb1994.ndf
2. Expected output 







1.6. Can we find the root element of the model ?





1. Executed command
list_elements




2. Expected output 

- /Purkinje








1.7. Can we find the segments and spines algorithm instance inside the root element ?





1. Executed command
list_elements /Purkinje




2. Expected output 

- /Purkinje/SpinesNormal_13_1
- /Purkinje/segments








1.8. Can we load the version of the purkinje cell with the partitioned dendritic tree ?





1. Executed command
ndf_load cells/purkinje/edsjb1994_partitioned.ndf




2. Expected output 







1.9. Can we find the root element of the model (2) ?





1. Executed command
list_elements




2. Expected output 

- /Purkinje








1.10. Can we find the segments and spines algorithm instance inside the root element ?





1. Executed command
list_elements /Purkinje




2. Expected output 

- /Purkinje/SpinesNormal_13_1
- /Purkinje/segments








1.11. Can we find the segments in /Purkinje/segments ?





1. Executed command
list_elements /Purkinje/segments




2. Expected output 

- /Purkinje/segments/soma
- /Purkinje/segments/main
- /Purkinje/segments/branches
- /Purkinje/segments/branchlets








1.12. Can we switch to the soma as current working element ?





1. Executed command
ce /Purkinje/segments/soma




2. Expected output 







1.13. Is the soma now our current working element ?





1. Executed command
pwe




2. Expected output 
/Purkinje/segments/soma








1.14. Can we obtain the value of the CM parameter of the soma ?





1. Executed command
parameter_show . CM




2. Expected output 
value = 0.0164








1.15. Can we obtain the value of the parameters of the soma segment ?





1. Executed command
model_parameter_show




2. Expected output 
  -
    'parameter name': rel_X
    type: number
    value: 0
  -
    'parameter name': rel_Y
    type: number
    value: 0
  -
    'parameter name': rel_Z
    type: number
    value: 0
  -
    'parameter name': DIA
    type: number
    value: 2.98e-05
  -
    'parameter name': Vm_init
    type: number
    value: -0.068
  -
    'parameter name': RM
    type: number
    value: 1
  -
    'parameter name': RA
    type: number
    value: 2.5
  -
    'parameter name': CM
    type: number
    value: 0.0164
  -
    'parameter name': ELEAK
    type: number
    value: -0.08








1.16. Can we obtain the value of the parameters of the cat channel inside the soma segment ?





1. Executed command
model_parameter_show cat




2. Expected output 
  -
    'parameter name': G_MAX
    type: number
    value: 5
  -
    'parameter name': Erev
    type: function
    'function name': NERNST
    'function parameters':

      -
        'parameter name': Cin
        'field name': concen
        type: field
        value: ../ca_pool->concen
        'resolved value': /Purkinje/segments/soma/ca_pool->concen
      -
        'parameter name': Cout
        type: number
        value: 2.4
      -
        'parameter name': valency
        'field name': VAL
        type: field
        value: ../ca_pool->VAL
        'resolved value': /Purkinje/segments/soma/ca_pool->VAL
      -
        'parameter name': T
        type: number
        value: 37








1.17. Can we find the segments in /Purkinje/segments/main ?





1. Executed command
list_elements /Purkinje/segments/main




2. Expected output 

- /Purkinje/segments/main/main[0]
- /Purkinje/segments/main/main[1]
- /Purkinje/segments/main/main[2]
- /Purkinje/segments/main/main[3]
- /Purkinje/segments/main/main[4]
- /Purkinje/segments/main/main[5]
- /Purkinje/segments/main/main[6]
- /Purkinje/segments/main/main[7]
- /Purkinje/segments/main/main[8]








1.18. Can we find the segments in /Purkinje/segments/branches ?





1. Executed command
list_elements /Purkinje/segments/branches




2. Expected output 

- /Purkinje/segments/branches/br1
- /Purkinje/segments/branches/br2
- /Purkinje/segments/branches/br3








1.19. Can we find the segments in /Purkinje/segments/branchlets ?





1. Executed command
list_elements /Purkinje/segments/branchlets




2. Expected output 

- /Purkinje/segments/branchlets/b0s01
- /Purkinje/segments/branchlets/b0s02
- /Purkinje/segments/branchlets/b0s03
- /Purkinje/segments/branchlets/b0s04
- /Purkinje/segments/branchlets/b1s05
- /Purkinje/segments/branchlets/b1s06
- /Purkinje/segments/branchlets/b1s07
- /Purkinje/segments/branchlets/b1s08
- /Purkinje/segments/branchlets/b1s09
- /Purkinje/segments/branchlets/b1s10
- /Purkinje/segments/branchlets/b1s11
- /Purkinje/segments/branchlets/b1s12
- /Purkinje/segments/branchlets/b1s13
- /Purkinje/segments/branchlets/b1s14
- /Purkinje/segments/branchlets/b1s15
- /Purkinje/segments/branchlets/b1s16
- /Purkinje/segments/branchlets/b1s17
- /Purkinje/segments/branchlets/b1s18
- /Purkinje/segments/branchlets/b1s19
- /Purkinje/segments/branchlets/b1s20
- /Purkinje/segments/branchlets/b2s21
- /Purkinje/segments/branchlets/b2s22
- /Purkinje/segments/branchlets/b2s23
- /Purkinje/segments/branchlets/b2s24
- /Purkinje/segments/branchlets/b2s25
- /Purkinje/segments/branchlets/b2s26
- /Purkinje/segments/branchlets/b2s27
- /Purkinje/segments/branchlets/b2s28
- /Purkinje/segments/branchlets/b2s29
- /Purkinje/segments/branchlets/b2s30
- /Purkinje/segments/branchlets/b2s31
- /Purkinje/segments/branchlets/b2s32
- /Purkinje/segments/branchlets/b2s33
- /Purkinje/segments/branchlets/b2s34
- /Purkinje/segments/branchlets/b3s35
- /Purkinje/segments/branchlets/b3s36
- /Purkinje/segments/branchlets/b3s37
- /Purkinje/segments/branchlets/b3s38
- /Purkinje/segments/branchlets/b3s39
- /Purkinje/segments/branchlets/b3s40
- /Purkinje/segments/branchlets/b3s41
- /Purkinje/segments/branchlets/b3s42
- /Purkinje/segments/branchlets/b3s43
- /Purkinje/segments/branchlets/b3s44
- /Purkinje/segments/branchlets/b3s45
- /Purkinje/segments/branchlets/b3s46








1.20. Can we run the simulation ?





1. Executed command
run /Purkinje 0.001




2. Expected output 







1.21. Can we find the output file in the file system ?





1. Executed command
sh ls -l /tmp/




2. Expected output 
 output








1.22. Can we find the output ?





1. Executed command
sh cat /tmp/output




2. Expected output 

0.001 -0.0678441





3. Comment
only testing the last line of output







2. Commands for an interactive simulation of the purkinje cell model
Startup command : bin/genesis-g3
(No model has been loaded for the following set of commands.)
2.1. Is startup successful ?





1. Expected output 
GENESIS 3 shell







2.2. Can we load the version of the purkinje cell with the partitioned dendritic tree ?





1. Executed command
ndf_load cells/purkinje/edsjb1994_partitioned.ndf




2. Expected output 







2.3. Can we find the root element of the model (2) ?





1. Executed command
list_elements




2. Expected output 

- /Purkinje








2.4. Can we find the segments and spines algorithm instance inside the root element ?





1. Executed command
list_elements /Purkinje




2. Expected output 

- /Purkinje/SpinesNormal_13_1
- /Purkinje/segments








2.5. Can we run the simulation ?





1. Executed command
run /Purkinje 0.001




2. Expected output 







2.6. Can we find the output file in the file system ?





1. Executed command
sh ls -l /tmp/




2. Expected output 
 output








2.7. Can we find the output ?





1. Executed command
sh cat /tmp/output




2. Expected output 

0.001 -0.0678441





3. Comment
only testing the last line of output







2.8. Can we apply current injection into the soma ?





1. Executed command
runtime_parameter_add /Purkinje/segments/soma INJECT 2e-9




2. Expected output 







2.9. Can we continue the simulation ?





1. Executed command
run /Purkinje 0.001




2. Expected output 







2.10. Can we find the output ?





1. Executed command
sh cat /tmp/output




2. Expected output 

0.002 -0.0586612





3. Comment
only testing the last line of output