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Index of group ./specifications/purkinje

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EDS purkinje cell model simplification and simulations

1. Simplification tests for the purkinje cell model with parameterized channels
2. Running the purkinje cell soma by itself, active channels, current injections
3. Running the purkinje cell main dendrite, active channels, current injections
4. Running the full purkinje cell, active channels, current injections
5. Running the full purkinje cell, active channels, complex spike

1. Simplification tests for the purkinje cell model with parameterized channels

Startup command : src/ns-sli ..//tests/scripts/PurkM9_model/purkinje_simplifying.g

Comments, Preparation, Reparation

1. Comment for this test definition
This test was derived from the model-container purkinje.t

1.1. Can the morphology be read ?

1. Expected output 
tests/scripts/PurkM9_model/Purk2M9.p read: 1600 compartments

1.2. What is the capacitance of the soma ?

1. Executed command
printparameter /Purkinje/soma CM
2. Expected output 
value = 0.0164

1.3. What is the capacitance of the first main segment ?

1. Executed command
printparameter /Purkinje/main[0] CM
2. Expected output 
value = 0.0164

1.4. What is the membrane resistance of the soma ?

1. Executed command
printparameter /Purkinje/soma RM
2. Expected output 
value = 1

1.5. What is the membrane resistance of the first main segment ?

1. Executed command
printparameter /Purkinje/main[0] RM
2. Expected output 
value = 3

1.6. What is the axial resistance of the soma ?

1. Executed command
printparameter /Purkinje/soma RA
2. Expected output 
value = 2.5

1.7. What is the axial resistance of the first main segment ?

1. Executed command
printparameter /Purkinje/main[0] RA
2. Expected output 
value = 2.5

1.8. What is the length of the first main segment ?

1. Executed command
printparameter /Purkinje/main[0] LENGTH
2. Expected output 
= 1.44697e-05

1.9. What is the length of the second main segment ?

1. Executed command
printparameter /Purkinje/main[1] LENGTH
2. Expected output 
= 2.35003e-05

1.10. What is the length of the first spiny dendrite ?

1. Executed command
printparameter /Purkinje/b0s01[0] LENGTH
2. Expected output 
= 6.16021e-06

1.11. What is the length of the second spiny dendrite ?

1. Executed command
printparameter /Purkinje/b0s01[1] LENGTH
2. Expected output 
= 2.22e-06

1.12. What is the length of one of the spinyd dendrites (the longest one) ?

1. Executed command
printparameter /Purkinje/b3s37[17] LENGTH
2. Expected output 
= 3.09897e-05

1.13. What is the somatopetal distance of the soma ?

1. Executed command
printparameter /Purkinje/soma SOMATOPETAL_DISTANCE
2. Expected output 
= 0

1.14. What is the somatopetal distance of the first main segment ?

1. Executed command
printparameter /Purkinje/main[0] SOMATOPETAL_DISTANCE
2. Expected output 
= 1.44697e-05

1.15. What is the somatopetal distance of the second main segment ?

1. Executed command
printparameter /Purkinje/main[1] SOMATOPETAL_DISTANCE
2. Expected output 
= 3.797e-05

1.16. What is the somatopetal distance of a spiny dendrite ?

1. Executed command
printparameter /Purkinje/b0s01[0] SOMATOPETAL_DISTANCE
2. Expected output 
= 4.41302e-05

1.17. What is the somatopetal distance of a spiny dendrite ?

1. Executed command
printparameter /Purkinje/b0s01[1] SOMATOPETAL_DISTANCE
2. Expected output 
= 4.63502e-05

1.18. What is the total dendritic length of the purkinje cell ?

1. Executed command
printparameter /Purkinje TOTALLENGTH
2. Expected output 
value = 0.0120441
3. Comment
the spines algorithm was not used, this values is without spines

1.19. What is the total surface of the purkinje cell ?

1. Executed command
printparameter /Purkinje TOTALSURFACE
2. Expected output 
value = 2.60908e-07
3. Comment
even without spines, this value is very different from the value in table 2 of the Rapp paper, this is due to shrinkage correction, yet there is an unexplained anomaly in the difference for surface and volume.  This value changed from value = 2.61092e-07 to 2.60908e-07 after float to double accommodations in the model-container.

1.20. What is the total volume of the purkinje cell ?

1. Executed command
printparameter /Purkinje TOTALVOLUME
2. Expected output 
value = 5.37774e-14
3. Comment
the spines algorithm was not used, this values is without spines (even without spines, this value is very different from the value in table 2 of the Rapp paper, this is due to shrinkage correction, yet there is an unexplained anomaly in the difference for surface and volume.)

1.21. Does the main dendrite of the purkinje cell have a well-defined calcium dependent potassium conductance ?

1. Executed command
printparameter /Purkinje/b0s01[1]/KC G_MAX
2. Expected output 
value = 799.999

1.22. Is conductance scaling done correctly ?

1. Executed command
printparameterscaled /Purkinje/b0s01[1]/KC G_MAX
2. Expected output 
1.27212e-08

1.23. Does the main dendrite of the purkinje cell have a well-defined calcium dependent potassium conductance (2) ?

1. Executed command
printparameter /Purkinje/b0s01[1]/KC Erev
2. Expected output 
value = -0.085

1.24. What are the forestspace IDs for the segment b0s01[1] ?

1. Executed command
serialMapping /Purkinje Purkinje/b0s01[1]
2. Expected output 
Traversal serial ID = 2623
Principal serial ID = 2623 of 56137 Principal successors
3. Comment
note the differences when using G2 tabchans, G3 ns-sli and plain G3

1.25. Can we assign a solver to the purkinje cell ?

1. Executed command
solverset /Purkinje purk_solver
2. Expected output 







1.26. Can we reduce the model ?





1. Executed command
reduce




2. Expected output 







1.27. After reducing, what is the capacitance of the soma ?





1. Executed command
printparameter /Purkinje/soma CM




2. Expected output 
value = 0.0164








1.28. After reducing, what is the capacitance of the first main segment ?





1. Executed command
printparameter /Purkinje/main[0] CM




2. Expected output 
value = 0.0164








1.29. After reducing, what is the membrane resistance of the soma ?





1. Executed command
printparameter /Purkinje/soma RM




2. Expected output 
value = 1








1.30. After reducing, what is the membrane resistance of the first main segment ?





1. Executed command
printparameter /Purkinje/main[0] RM




2. Expected output 
value = 3








1.31. After reducing, what is the axial resistance of the soma ?





1. Executed command
printparameter /Purkinje/soma RA




2. Expected output 
value = 2.5








1.32. After reducing, what is the axial resistance of the first main segment ?





1. Executed command
printparameter /Purkinje/main[0] RA




2. Expected output 
value = 2.5








1.33. After reducing, what is the length of the first main segment ?





1. Executed command
printparameter /Purkinje/main[0] LENGTH




2. Expected output 
= 1.44697e-05







1.34. After reducing, what is the length of the second main segment ?





1. Executed command
printparameter /Purkinje/main[1] LENGTH




2. Expected output 
= 2.35003e-05







1.35. After reducing, what is the length of the first spiny dendrite ?





1. Executed command
printparameter /Purkinje/b0s01[0] LENGTH




2. Expected output 
= 6.16021e-06







1.36. After reducing, what is the length of the second spiny dendrite ?





1. Executed command
printparameter /Purkinje/b0s01[1] LENGTH




2. Expected output 
= 2.22e-06







1.37. After reducing, what is the length of one of the spinyd dendrites (the longest one) ?





1. Executed command
printparameter /Purkinje/b3s37[17] LENGTH




2. Expected output 
= 3.09897e-05







1.38. After reducing, what is the somatopetal distance of the soma ?





1. Executed command
printparameter /Purkinje/soma SOMATOPETAL_DISTANCE




2. Expected output 
= 0







1.39. After reducing, what is the somatopetal distance of the first main segment ?





1. Executed command
printparameter /Purkinje/main[0] SOMATOPETAL_DISTANCE




2. Expected output 
= 1.44697e-05







1.40. After reducing, what is the somatopetal distance of the second main segment ?





1. Executed command
printparameter /Purkinje/main[1] SOMATOPETAL_DISTANCE




2. Expected output 
= 3.797e-05







1.41. After reducing, what is the somatopetal distance of a spiny dendrite ?





1. Executed command
printparameter /Purkinje/b0s01[0] SOMATOPETAL_DISTANCE




2. Expected output 
= 4.41302e-05







1.42. After reducing, what is the somatopetal distance of a spiny dendrite ?





1. Executed command
printparameter /Purkinje/b0s01[1] SOMATOPETAL_DISTANCE




2. Expected output 
= 4.63502e-05







1.43. After reducing, what is the total dendritic length of the purkinje cell ?





1. Executed command
printparameter /Purkinje TOTALLENGTH




2. Expected output 
value = 0.0120441





3. Comment
the spines algorithm was not used, this values is without spines







1.44. After reducing, what is the total surface of the purkinje cell ?





1. Executed command
printparameter /Purkinje TOTALSURFACE




2. Expected output 
value = 2.60908e-07




3. Comment
even without spines, this value is very different from the value in table 2 of the Rapp paper, this is due to shrinkage correction, yet there is an unexplained anomaly in the difference for surface and volume.  This value changed from value = 2.61092e-07 to 2.60908e-07 after float to double accommodations in the model-container.







1.45. After reducing, what is the total volume of the purkinje cell ?





1. Executed command
printparameter /Purkinje TOTALVOLUME




2. Expected output 
value = 5.37774e-14




3. Comment
the spines algorithm was not used, this values is without spines (even without spines, this value is very different from the value in table 2 of the Rapp paper, this is due to shrinkage correction, yet there is an unexplained anomaly in the difference for surface and volume.)







1.46. After reducing, does the main dendrite of the purkinje cell have a well-defined calcium dependent potassium conductance ?





1. Executed command
printparameter /Purkinje/b0s01[1]/KC G_MAX




2. Expected output 
value = 799.999







1.47. After reducing, is conductance scaling done correctly ?





1. Executed command
printparameterscaled /Purkinje/b0s01[1]/KC G_MAX




2. Expected output 
1.27212e-08







1.48. After reducing, does the main dendrite of the purkinje cell have a well-defined calcium dependent potassium conductance (2) ?





1. Executed command
printparameter /Purkinje/b0s01[1]/KC Erev




2. Expected output 
value = -0.085







1.49. After reducing, what are the forestspace IDs for the segment b0s01[1] ?





1. Executed command
serialMapping /Purkinje Purkinje/b0s01[1]




2. Expected output 
Traversal serial ID = 2623
Principal serial ID = 2623 of 56137 Principal successors





3. Comment
note the differences when using G2 tabchans, G3 ns-sli and plain G3







1.50. After reducing, can we assign a solver to the purkinje cell ?





1. Executed command
solverset /Purkinje purk_solver




2. Expected output 







2. Running the purkinje cell soma by itself, active channels, current injections
Startup command : src/ns-sli ..//tests/scripts/PurkM9_model/ACTIVE-soma1.g
Comments, Preparation, Reparation





1. Preparation needed before the commands below : 
Create the results directory




2. And repared afterwards using : 
Remove the generated output files in the results directory







2.1. Can the morphology be read ?





1. Expected output 
tests/scripts/PurkM9_model/Purk2M9_soma.p read: 1 compartments







2.2. Are the prototype library and the cell correctly constructed ?





1. Executed command
expand /**




2. Expected output 

- /proto
- /output
- /library
- /library/Purk_NaF
- /library/Purk_NaF/HH_activation
- /library/Purk_NaF/HH_activation/A
- /library/Purk_NaF/HH_activation/B
- /library/Purk_NaF/HH_inactivation
- /library/Purk_NaF/HH_inactivation/A
- /library/Purk_NaF/HH_inactivation/B
- /library/Purk_NaP
- /library/Purk_NaP/HH_activation
- /library/Purk_NaP/HH_activation/A
- /library/Purk_NaP/HH_activation/B
- /library/Purk_CaP
- /library/Purk_CaP/HH_activation
- /library/Purk_CaP/HH_activation/A
- /library/Purk_CaP/HH_activation/B
- /library/Purk_CaP/HH_inactivation
- /library/Purk_CaP/HH_inactivation/A
- /library/Purk_CaP/HH_inactivation/B
- /library/Purk_CaT
- /library/Purk_CaT/HH_activation
- /library/Purk_CaT/HH_activation/A
- /library/Purk_CaT/HH_activation/B
- /library/Purk_CaT/HH_inactivation
- /library/Purk_CaT/HH_inactivation/A
- /library/Purk_CaT/HH_inactivation/B
- /library/Purk_KA
- /library/Purk_KA/HH_activation
- /library/Purk_KA/HH_activation/A
- /library/Purk_KA/HH_activation/B
- /library/Purk_KA/HH_inactivation
- /library/Purk_KA/HH_inactivation/A
- /library/Purk_KA/HH_inactivation/B
- /library/Purk_KC
- /library/Purk_KC/HH_activation
- /library/Purk_KC/HH_activation/A
- /library/Purk_KC/HH_activation/B
- /library/Purk_KC/HH_concentration
- /library/Purk_KC/HH_concentration/A
- /library/Purk_KC/HH_concentration/B
- /library/Purk_K2
- /library/Purk_K2/HH_activation
- /library/Purk_K2/HH_activation/A
- /library/Purk_K2/HH_activation/B
- /library/Purk_K2/HH_concentration
- /library/Purk_K2/HH_concentration/A
- /library/Purk_K2/HH_concentration/B
- /library/Purk_Kdr
- /library/Purk_Kdr/HH_activation
- /library/Purk_Kdr/HH_activation/A
- /library/Purk_Kdr/HH_activation/B
- /library/Purk_Kdr/HH_inactivation
- /library/Purk_Kdr/HH_inactivation/A
- /library/Purk_Kdr/HH_inactivation/B
- /library/Purk_KM
- /library/Purk_KM/HH_activation
- /library/Purk_KM/HH_activation/A
- /library/Purk_KM/HH_activation/B
- /library/Purk_h1
- /library/Purk_h1/HH_activation
- /library/Purk_h1/HH_activation/A
- /library/Purk_h1/HH_activation/B
- /library/Purk_h2
- /library/Purk_h2/HH_activation
- /library/Purk_h2/HH_activation/A
- /library/Purk_h2/HH_activation/B
- /library/Purk_soma
- /library/Purk_soma/NaF
- /library/Purk_soma/NaF/HH_activation
- /library/Purk_soma/NaF/HH_activation/A
- /library/Purk_soma/NaF/HH_activation/B
- /library/Purk_soma/NaF/HH_inactivation
- /library/Purk_soma/NaF/HH_inactivation/A
- /library/Purk_soma/NaF/HH_inactivation/B
- /library/Purk_soma/NaP
- /library/Purk_soma/NaP/HH_activation
- /library/Purk_soma/NaP/HH_activation/A
- /library/Purk_soma/NaP/HH_activation/B
- /library/Purk_soma/CaT
- /library/Purk_soma/CaT/HH_activation
- /library/Purk_soma/CaT/HH_activation/A
- /library/Purk_soma/CaT/HH_activation/B
- /library/Purk_soma/CaT/HH_inactivation
- /library/Purk_soma/CaT/HH_inactivation/A
- /library/Purk_soma/CaT/HH_inactivation/B
- /library/Purk_soma/KA
- /library/Purk_soma/KA/HH_activation
- /library/Purk_soma/KA/HH_activation/A
- /library/Purk_soma/KA/HH_activation/B
- /library/Purk_soma/KA/HH_inactivation
- /library/Purk_soma/KA/HH_inactivation/A
- /library/Purk_soma/KA/HH_inactivation/B
- /library/Purk_soma/Kdr
- /library/Purk_soma/Kdr/HH_activation
- /library/Purk_soma/Kdr/HH_activation/A
- /library/Purk_soma/Kdr/HH_activation/B
- /library/Purk_soma/Kdr/HH_inactivation
- /library/Purk_soma/Kdr/HH_inactivation/A
- /library/Purk_soma/Kdr/HH_inactivation/B
- /library/Purk_soma/KM
- /library/Purk_soma/KM/HH_activation
- /library/Purk_soma/KM/HH_activation/A
- /library/Purk_soma/KM/HH_activation/B
- /library/Purk_soma/h1
- /library/Purk_soma/h1/HH_activation
- /library/Purk_soma/h1/HH_activation/A
- /library/Purk_soma/h1/HH_activation/B
- /library/Purk_soma/h2
- /library/Purk_soma/h2/HH_activation
- /library/Purk_soma/h2/HH_activation/A
- /library/Purk_soma/h2/HH_activation/B
- /library/Purk_soma/Ca_pool
- /library/Purk_maind
- /library/Purk_maind/CaT
- /library/Purk_maind/CaT/HH_activation
- /library/Purk_maind/CaT/HH_activation/A
- /library/Purk_maind/CaT/HH_activation/B
- /library/Purk_maind/CaT/HH_inactivation
- /library/Purk_maind/CaT/HH_inactivation/A
- /library/Purk_maind/CaT/HH_inactivation/B
- /library/Purk_maind/KA
- /library/Purk_maind/KA/HH_activation
- /library/Purk_maind/KA/HH_activation/A
- /library/Purk_maind/KA/HH_activation/B
- /library/Purk_maind/KA/HH_inactivation
- /library/Purk_maind/KA/HH_inactivation/A
- /library/Purk_maind/KA/HH_inactivation/B
- /library/Purk_maind/Kdr
- /library/Purk_maind/Kdr/HH_activation
- /library/Purk_maind/Kdr/HH_activation/A
- /library/Purk_maind/Kdr/HH_activation/B
- /library/Purk_maind/Kdr/HH_inactivation
- /library/Purk_maind/Kdr/HH_inactivation/A
- /library/Purk_maind/Kdr/HH_inactivation/B
- /library/Purk_maind/KM
- /library/Purk_maind/KM/HH_activation
- /library/Purk_maind/KM/HH_activation/A
- /library/Purk_maind/KM/HH_activation/B
- /library/Purk_maind/CaP
- /library/Purk_maind/CaP/HH_activation
- /library/Purk_maind/CaP/HH_activation/A
- /library/Purk_maind/CaP/HH_activation/B
- /library/Purk_maind/CaP/HH_inactivation
- /library/Purk_maind/CaP/HH_inactivation/A
- /library/Purk_maind/CaP/HH_inactivation/B
- /library/Purk_maind/KC
- /library/Purk_maind/KC/HH_activation
- /library/Purk_maind/KC/HH_activation/A
- /library/Purk_maind/KC/HH_activation/B
- /library/Purk_maind/KC/HH_concentration
- /library/Purk_maind/KC/HH_concentration/A
- /library/Purk_maind/KC/HH_concentration/B
- /library/Purk_maind/K2
- /library/Purk_maind/K2/HH_activation
- /library/Purk_maind/K2/HH_activation/A
- /library/Purk_maind/K2/HH_activation/B
- /library/Purk_maind/K2/HH_concentration
- /library/Purk_maind/K2/HH_concentration/A
- /library/Purk_maind/K2/HH_concentration/B
- /library/Purk_maind/Ca_pool
- /library/Purk_maind/Ca_nernst
- /library/Purk_axon
- /library/Purk_thickd
- /library/Purk_thickd/CaT
- /library/Purk_thickd/CaT/HH_activation
- /library/Purk_thickd/CaT/HH_activation/A
- /library/Purk_thickd/CaT/HH_activation/B
- /library/Purk_thickd/CaT/HH_inactivation
- /library/Purk_thickd/CaT/HH_inactivation/A
- /library/Purk_thickd/CaT/HH_inactivation/B
- /library/Purk_thickd/CaP
- /library/Purk_thickd/CaP/HH_activation
- /library/Purk_thickd/CaP/HH_activation/A
- /library/Purk_thickd/CaP/HH_activation/B
- /library/Purk_thickd/CaP/HH_inactivation
- /library/Purk_thickd/CaP/HH_inactivation/A
- /library/Purk_thickd/CaP/HH_inactivation/B
- /library/Purk_thickd/KM
- /library/Purk_thickd/KM/HH_activation
- /library/Purk_thickd/KM/HH_activation/A
- /library/Purk_thickd/KM/HH_activation/B
- /library/Purk_thickd/KC
- /library/Purk_thickd/KC/HH_activation
- /library/Purk_thickd/KC/HH_activation/A
- /library/Purk_thickd/KC/HH_activation/B
- /library/Purk_thickd/KC/HH_concentration
- /library/Purk_thickd/KC/HH_concentration/A
- /library/Purk_thickd/KC/HH_concentration/B
- /library/Purk_thickd/K2
- /library/Purk_thickd/K2/HH_activation
- /library/Purk_thickd/K2/HH_activation/A
- /library/Purk_thickd/K2/HH_activation/B
- /library/Purk_thickd/K2/HH_concentration
- /library/Purk_thickd/K2/HH_concentration/A
- /library/Purk_thickd/K2/HH_concentration/B
- /library/Purk_thickd/Ca_pool
- /library/Purk_thickd/Ca_nernst
- /library/Purk_spinyd
- /library/Purk_spinyd/CaT
- /library/Purk_spinyd/CaT/HH_activation
- /library/Purk_spinyd/CaT/HH_activation/A
- /library/Purk_spinyd/CaT/HH_activation/B
- /library/Purk_spinyd/CaT/HH_inactivation
- /library/Purk_spinyd/CaT/HH_inactivation/A
- /library/Purk_spinyd/CaT/HH_inactivation/B
- /library/Purk_spinyd/CaP
- /library/Purk_spinyd/CaP/HH_activation
- /library/Purk_spinyd/CaP/HH_activation/A
- /library/Purk_spinyd/CaP/HH_activation/B
- /library/Purk_spinyd/CaP/HH_inactivation
- /library/Purk_spinyd/CaP/HH_inactivation/A
- /library/Purk_spinyd/CaP/HH_inactivation/B
- /library/Purk_spinyd/KM
- /library/Purk_spinyd/KM/HH_activation
- /library/Purk_spinyd/KM/HH_activation/A
- /library/Purk_spinyd/KM/HH_activation/B
- /library/Purk_spinyd/KC
- /library/Purk_spinyd/KC/HH_activation
- /library/Purk_spinyd/KC/HH_activation/A
- /library/Purk_spinyd/KC/HH_activation/B
- /library/Purk_spinyd/KC/HH_concentration
- /library/Purk_spinyd/KC/HH_concentration/A
- /library/Purk_spinyd/KC/HH_concentration/B
- /library/Purk_spinyd/K2
- /library/Purk_spinyd/K2/HH_activation
- /library/Purk_spinyd/K2/HH_activation/A
- /library/Purk_spinyd/K2/HH_activation/B
- /library/Purk_spinyd/K2/HH_concentration
- /library/Purk_spinyd/K2/HH_concentration/A
- /library/Purk_spinyd/K2/HH_concentration/B
- /library/Purk_spinyd/Ca_pool
- /library/Purk_spinyd/Ca_nernst
- /Purkinje
- /Purkinje/soma
- /Purkinje/soma/NaF
- /Purkinje/soma/NaF/HH_activation
- /Purkinje/soma/NaF/HH_activation/A
- /Purkinje/soma/NaF/HH_activation/B
- /Purkinje/soma/NaF/HH_inactivation
- /Purkinje/soma/NaF/HH_inactivation/A
- /Purkinje/soma/NaF/HH_inactivation/B
- /Purkinje/soma/NaP
- /Purkinje/soma/NaP/HH_activation
- /Purkinje/soma/NaP/HH_activation/A
- /Purkinje/soma/NaP/HH_activation/B
- /Purkinje/soma/CaT
- /Purkinje/soma/CaT/HH_activation
- /Purkinje/soma/CaT/HH_activation/A
- /Purkinje/soma/CaT/HH_activation/B
- /Purkinje/soma/CaT/HH_inactivation
- /Purkinje/soma/CaT/HH_inactivation/A
- /Purkinje/soma/CaT/HH_inactivation/B
- /Purkinje/soma/KA
- /Purkinje/soma/KA/HH_activation
- /Purkinje/soma/KA/HH_activation/A
- /Purkinje/soma/KA/HH_activation/B
- /Purkinje/soma/KA/HH_inactivation
- /Purkinje/soma/KA/HH_inactivation/A
- /Purkinje/soma/KA/HH_inactivation/B
- /Purkinje/soma/Kdr
- /Purkinje/soma/Kdr/HH_activation
- /Purkinje/soma/Kdr/HH_activation/A
- /Purkinje/soma/Kdr/HH_activation/B
- /Purkinje/soma/Kdr/HH_inactivation
- /Purkinje/soma/Kdr/HH_inactivation/A
- /Purkinje/soma/Kdr/HH_inactivation/B
- /Purkinje/soma/KM
- /Purkinje/soma/KM/HH_activation
- /Purkinje/soma/KM/HH_activation/A
- /Purkinje/soma/KM/HH_activation/B
- /Purkinje/soma/h1
- /Purkinje/soma/h1/HH_activation
- /Purkinje/soma/h1/HH_activation/A
- /Purkinje/soma/h1/HH_activation/B
- /Purkinje/soma/h2
- /Purkinje/soma/h2/HH_activation
- /Purkinje/soma/h2/HH_activation/A
- /Purkinje/soma/h2/HH_activation/B
- /Purkinje/soma/Ca_pool








2.3. Quit the model-container querymachine.





1. Executed command
quit




2. Expected output 







2.4. Can we wait for a second and get back to the genesis prompt ?





1. Expected output 
genesis







2.5. Is the model correctly compiled by heccer ?





1. Executed command
call /neurospaces_integrator NSINTEGRATOR_DUMP




2. Expected output 
Heccer (pcName) : (/Purkinje)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0)
Heccer (dStep) : (2e-05)
Compartment (mc.iType) : (1)
Tables (iTabulatedGateCount) : (12)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -2.23189e-10 0 218562 1.00061
00001 :: INITIALIZECHANNEL 0.045 0.000209239
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 3 (nil)							 0.00784064
00004 :: CONCEPTGATE 1 1 (nil)							 0.263978
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: INITIALIZECHANNEL 0.045 2.78986e-08
00007 :: LOADVOLTAGETABLE
00008 :: CONCEPTGATE 2 3 (nil)							 0.0452931
00009 :: UPDATECOMPARTMENTCURRENT
00010 :: INITIALIZECHANNEL 0.137526 1.39493e-08
00011 :: LOADVOLTAGETABLE
00012 :: CONCEPTGATE 3 1 (nil)							 0.0389187
00013 :: CONCEPTGATE 4 1 (nil)							 0.0826021
00014 :: UPDATECOMPARTMENTCURRENT
00015 :: REGISTERCHANNELCURRENT
00016 :: FLUXPOOL							 0
00017 :: INITIALIZECHANNEL -0.085 4.18479e-07
00018 :: LOADVOLTAGETABLE
00019 :: CONCEPTGATE 5 4 (nil)							 0.0832441
00020 :: CONCEPTGATE 6 1 (nil)							 0.749501
00021 :: UPDATECOMPARTMENTCURRENT
00022 :: INITIALIZECHANNEL -0.085 1.67391e-05
00023 :: LOADVOLTAGETABLE
00024 :: CONCEPTGATE 7 2 (nil)							 0.0045016
00025 :: CONCEPTGATE 8 1 (nil)							 0.999979
00026 :: UPDATECOMPARTMENTCURRENT
00027 :: INITIALIZECHANNEL -0.085 1.11594e-09
00028 :: LOADVOLTAGETABLE
00029 :: CONCEPTGATE 9 1 (nil)							 0.0354084
00030 :: UPDATECOMPARTMENTCURRENT
00031 :: INITIALIZECHANNEL -0.03 8.36957e-09
00032 :: LOADVOLTAGETABLE
00033 :: CONCEPTGATE 10 1 (nil)							 0.0961851
00034 :: UPDATECOMPARTMENTCURRENT
00035 :: INITIALIZECHANNEL -0.03 8.36957e-09
00036 :: LOADVOLTAGETABLE
00037 :: CONCEPTGATE 11 1 (nil)							 0.0240463
00038 :: UPDATECOMPARTMENTCURRENT
00039 :: EXPONENTIALDECAY 188248 4e-05 1.1
			 (0) (nil) (nil) (nil)							 4e-05
00040 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00061)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.068)








2.6. Can we do 2000 simulation steps ?





1. Executed command
step 2000




2. Expected output 







2.7. Quit the simulator.





1. Executed command
quit




2. Expected output 







2.8. Is the generated output correct ?





1. Expected output 
application_output_file: ..//results/PurkM9_soma_only_0.03nA
expected_output_file: ..//tests/specifications/strings/PurkM9_soma_only_0.03nA.g2





2. Comment
The output file used for the test was generated using Genesis 2.2.1, and the first line removed, and selected white space removed.







3. Running the purkinje cell main dendrite, active channels, current injections
Startup command : src/ns-sli ..//tests/scripts/PurkM9_model/ACTIVE-main1.g
Comments, Preparation, Reparation





1. Preparation needed before the commands below : 
Create the results directory




2. And repared afterwards using : 
Remove the generated output files in the results directory







3.1. Can the morphology be read ?





1. Expected output 
tests/scripts/PurkM9_model/Purk2M9_main1.p read: 10 compartments







3.2. Is the cell constructed correctly ?





1. Executed command
expand /Purkinje/*




2. Expected output 

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








3.3. Quit the model-container querymachine.





1. Executed command
quit




2. Expected output 







3.4. Do we see the simulation time after the simulation has finished ?





1. Expected output 
time = 0.040000 ; step = 2000







3.5. Quit the simulator.





1. Executed command
quit




2. Expected output 







3.6. Is the generated output correct ?





1. Expected output 
application_output_file: ..//results/PurkM9_main1_only_-0.1nA
expected_output_file: ..//tests/specifications/strings/PurkM9_main1_only_-0.1nA





2. Comment
The output file generated using Genesis 2.2.1 is not used for this test.







4. Running the full purkinje cell, active channels, current injections
Startup command : src/ns-sli ..//tests/scripts/PurkM9_model/CURRENT9.g
Comments, Preparation, Reparation





1. Comment for this test definition
This test uses the original scripts of the Purkinje cell model




2. Preparation needed before the commands below : 
Create the results directory




3. And repared afterwards using : 
Remove the generated output files in the results directory







4.1. Can the morphology be read ?





1. Expected output 
tests/scripts/PurkM9_model/Purk2M9.p read: 1600 compartments







4.2. Do we have all the segments?





1. Executed command
segmentcount /Purkinje




2. Expected output 
Number of segments : 1600








4.3. Wat is the unscaled capacitance of the segments in the library ?





1. Executed command
printparameter /library/** CM




2. Expected output 
/library/Purk_soma->CM = 0.0164
/library/Purk_maind->CM = 0.0164
/library/Purk_axon->CM = 0.0164
/library/Purk_thickd->CM = 0.0164
/library/Purk_spinyd->CM = 0.0164








4.4. What is the unscaled membrane resistance of the segments in the library ?





1. Executed command
printparameter /library/** RM




2. Expected output 
/library/Purk_soma->RM = 1
/library/Purk_maind->RM = 3
/library/Purk_axon->RM = 3
/library/Purk_thickd->RM = 3
/library/Purk_spinyd->RM = 3








4.5. What is the unscaled conductance of the membrane channels in the library ?





1. Executed command
printparameter /library/** G_MAX




2. Expected output 
/library/Purk_NaF->G_MAX = 1
/library/Purk_NaP->G_MAX = 1
/library/Purk_CaP->G_MAX = 1
/library/Purk_CaT->G_MAX = 1
/library/Purk_KA->G_MAX = 1
/library/Purk_KC->G_MAX = 1
/library/Purk_K2->G_MAX = 1
/library/Purk_Kdr->G_MAX = 1
/library/Purk_KM->G_MAX = 1
/library/Purk_h1->G_MAX = 1
/library/Purk_h2->G_MAX = 1
/library/Purk_soma/NaF->G_MAX = 74999.9
/library/Purk_soma/NaP->G_MAX = 9.99999
/library/Purk_soma/CaT->G_MAX = 5
/library/Purk_soma/KA->G_MAX = 150
/library/Purk_soma/Kdr->G_MAX = 5999.99
/library/Purk_soma/KM->G_MAX = 0.4
/library/Purk_soma/h1->G_MAX = 3
/library/Purk_soma/h2->G_MAX = 3
/library/Purk_maind/CaT->G_MAX = 5
/library/Purk_maind/KA->G_MAX = 20
/library/Purk_maind/Kdr->G_MAX = 599.999
/library/Purk_maind/KM->G_MAX = 0.0999999
/library/Purk_maind/CaP->G_MAX = 45
/library/Purk_maind/KC->G_MAX = 799.999
/library/Purk_maind/K2->G_MAX = 3.9
/library/Purk_thickd/CaT->G_MAX = 5
/library/Purk_thickd/CaP->G_MAX = 45
/library/Purk_thickd/KM->G_MAX = 0.13
/library/Purk_thickd/KC->G_MAX = 799.999
/library/Purk_thickd/K2->G_MAX = 3.9
/library/Purk_spinyd/CaT->G_MAX = 5
/library/Purk_spinyd/CaP->G_MAX = 45
/library/Purk_spinyd/KM->G_MAX = 0.13
/library/Purk_spinyd/KC->G_MAX = 799.999
/library/Purk_spinyd/K2->G_MAX = 3.9





3. Comment
Some of these values should be rounded







4.6. What are the parameters of one of the segments in the reconstructed morphology ?





1. Executed command
export no ndf STDOUT /Purkinje/b3s46[0]




2. Expected output 
#!neurospacesparse
// -*- NEUROSPACES -*-

NEUROSPACES NDF

IMPORT
END IMPORT

PRIVATE_MODELS
END PRIVATE_MODELS

PUBLIC_MODELS
  ALIAS "Purk_thickd" "b3s46[0]"
    PARAMETERS
      PARAMETER ( ELEAK = -0.08 ),
      PARAMETER ( Vm_init = -0.068 ),
      PARAMETER ( RM = 3 ),
      PARAMETER ( CM = 0.0164 ),
      PARAMETER ( SURFACE = 8.70133e-11 ),
      PARAMETER ( rel_Z = 6.669e-06 ),
      PARAMETER ( rel_Y = 0 ),
      PARAMETER ( rel_X = 2.223e-06 ),
      PARAMETER ( LENGTH = 7.02974e-06 ),
      PARAMETER ( DIA = 3.94e-06 ),
      PARAMETER ( RA = 2.5 ),
      PARAMETER ( PARENT = ../br3[16] ),
    END PARAMETERS
  END ALIAS
END PUBLIC_MODELS








4.7. Quit the model-container querymachine.





1. Executed command
quit




2. Expected output 







4.8. Do we see the simulation time after the simulation has finished ?





1. Expected output 
time = 0.500060 ; step = 25003







4.9. Is the generated output correct ?





1. Expected output 
application_output_file: ..//results/PurkM9_soma_1.5nA
expected_output_file: ..//tests/specifications/strings/PurkM9_soma_1.5nA.g3-double





2. Comment
The output file generated using Genesis 2.2.1 is not used for this test.







5. Running the full purkinje cell, active channels, complex spike
Startup command : src/ns-sli ..//tests/scripts/PurkM9_model/CLIMB9.g
Comments, Preparation, Reparation





1. Comment for this test definition
This test uses the original scripts of the Purkinje cell model




2. Preparation needed before the commands below : 
Create the results directory




3. And repared afterwards using : 
Remove the generated output files in the results directory







5.1. Can the morphology be read ?





1. Expected output 
tests/scripts/PurkM9_model/Purk2M9.p read: 1600 compartments







5.2. Do we see the simulation time after the simulation has finished ?





1. Expected output 
time = 0.301160 ; step = 15058







5.3. Is the generated output correct ?





1. Expected output 
application_output_file: ..//results/PurkM9_CS
expected_output_file: ..//tests/specifications/strings/PurkM9_CS.g3-double





2. Comment
The output file generated using Genesis 2.2.1 is not used for this test.