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

Index of group ./specifications/purkinje

Index
Up

EDS purkinje cell model

1. Elementary tests for the purkinje cell model with genesis alike channels

2. Elementary tests for the purkinje cell model with parameterized channels

3. Elementary tests for the purkinje cell model with parameterized channels

1. Elementary tests for the purkinje cell model with genesis alike channels

Startup command : ./neurospacesparse -v 1 -q legacy/cells/purk2m9s.ndf

1.1. Is neurospaces startup successful ?

1. Part of expected output

./neurospacesparse: No errors for .+?/legacy/cells/purk2m9s.ndf.

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

1. Executed command	printparameter /Purkinje/segments/main[0] LENGTH
2. Part of expected output	value = 1.44697e-05

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

1. Executed command	printparameter /Purkinje/segments/main[1] LENGTH
2. Part of expected output	value = 2.35003e-05

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

1. Executed command	printparameter /Purkinje/segments/b0s01[0] LENGTH
2. Part of expected output	value = 6.16021e-06

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

1. Executed command	printparameter /Purkinje/segments/b0s01[1] LENGTH
2. Part of expected output	value = 2.22e-06

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

1. Executed command	printparameter /Purkinje/segments/b3s37[17] LENGTH
2. Part of expected output	value = 3.09897e-05

1.7. What is the length of the first spine neck ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck LENGTH
2. Part of expected output	value = 6.6e-07

1.8. What is the length of the first spine head ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head LENGTH
2. Part of expected output	value = 6.8036e-07

1.9. What is the somatopetal distance of the soma ?

1. Executed command	printparameter /Purkinje/segments/soma SOMATOPETAL_DISTANCE
2. Part of expected output	value = 0

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

1. Executed command	printparameter /Purkinje/segments/main[0] SOMATOPETAL_DISTANCE
2. Part of expected output	value = 1.44697e-05

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

1. Executed command	printparameter /Purkinje/segments/main[1] SOMATOPETAL_DISTANCE
2. Part of expected output	value = 3.797e-05

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

1. Executed command	printparameter /Purkinje/segments/b0s01[0] SOMATOPETAL_DISTANCE
2. Part of expected output	value = 4.41302e-05

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

1. Executed command	printparameter /Purkinje/segments/b0s01[1] SOMATOPETAL_DISTANCE
2. Part of expected output	value = 4.63502e-05

1.14. What is the somatopetal distance of the spine neck for the previous dendritic segment ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck SOMATOPETAL_DISTANCE
2. Part of expected output	value = 4.70102e-05

1.15. What is the somatopetal distance of the spine head for the previous dendritic segment ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head SOMATOPETAL_DISTANCE
2. Part of expected output	value = 4.76906e-05

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

1. Executed command

printparameter /Purkinje TOTALLENGTH

2. Part of expected output

value = 0.0140198

3. Comment

this value is close to the value in table 2 of the Rapp paper, when shrinkage correction is not applied and spines are not added, yet there is an unexplained anomaly in the difference for surface and volume.

1.17. What is the total dendritic length of all the segments the purkinje cell ?

1. Executed command	printparameter /Purkinje/segments TOTALLENGTH
2. Part of expected output	value = 0.0140198
3. Comment	See developer TODOs
4. This test is currently not executed	(disabled is 'See developer TODOs')

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

1. Executed command

printparameter /Purkinje TOTALSURFACE

2. Part of expected output

value = 2.61206e-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.

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

1. Executed command	printparameter /Purkinje/segments TOTALSURFACE
2. Part of expected output	value = 2.61206e-07
3. Comment	See developer TODOs
4. This test is currently not executed	(disabled is 'See developer TODOs')

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

1. Executed command

printparameter /Purkinje TOTALVOLUME

2. Part of expected output

value = 5.39527e-14

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.

1.21. What is the total volume of all the segments the purkinje cell ?

1. Executed command	printparameter /Purkinje/segments TOTALVOLUME
2. Part of expected output	value = 5.39527e-14
3. Comment	See developer TODOs
4. This test is currently not executed	(disabled is 'See developer TODOs')

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

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/KC G_MAX
2. Part of expected output	800

1.23. Is conductance scaling done correctly ?

1. Executed command	printparameterscaled /Purkinje/segments/b0s01[1]/KC G_MAX
2. Part of expected output	1.27212e-08

1.24. Can we find spines in the model purkinje cell ?

1. Executed command

expand /Purkinje/segments/b0s01[1]/Purkinje_spine_0/**

2. Part of expected output

/Purkinje/segments/b0s01[1]/Purkinje_spine_0
- /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck
- /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head
- /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head/par
- /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head/par/synapse
- /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head/par/exp2

1.25. What are the forestspace IDs for the spine neck ?

1. Executed command	serialMapping /Purkinje Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck
2. Part of expected output	Traversal serial ID = 1139 Principal serial ID = 1139 of 25525 Principal successors

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

1. Executed command	serialMapping /Purkinje Purkinje/segments/b0s01[1]
2. Part of expected output	Traversal serial ID = 1128 Principal serial ID = 1128 of 25525 Principal successors
3. Comment	note the differences when using G2 tabchans, G3 ns-sli and plain G3

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

1. Executed command	solverset /Purkinje purk_solver
2. Part of expected output

1.28. Can the solver for the spine neck be found, is it the one we just assigned to it ?

1. Executed command	resolvesolver /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck
2. Part of expected output	Solver = purk_solver, solver serial ID = 1139 Solver serial context for 1139 = /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck

2. Elementary tests for the purkinje cell model with parameterized channels

Startup command : ./neurospacesparse -v 1 -q cells/purkinje/edsjb1994.ndf

2.1. Is neurospaces startup successful ?

1. Part of expected output

./neurospacesparse: No errors for .+?/cells/purkinje/edsjb1994.ndf.

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

1. Executed command	printparameter /Purkinje/segments/main[0] LENGTH
2. Part of expected output	value = 1.44697e-05

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

1. Executed command	printparameter /Purkinje/segments/main[1] LENGTH
2. Part of expected output	value = 2.35003e-05

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

1. Executed command	printparameter /Purkinje/segments/b0s01[0] LENGTH
2. Part of expected output	value = 6.16021e-06

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

1. Executed command	printparameter /Purkinje/segments/b0s01[1] LENGTH
2. Part of expected output	value = 2.22e-06

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

1. Executed command	printparameter /Purkinje/segments/b3s37[17] LENGTH
2. Part of expected output	value = 3.09897e-05

2.7. What is the length of the first spine neck ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck LENGTH
2. Part of expected output	value = 6.6e-07

2.8. What is the length of the first spine head ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head LENGTH
2. Part of expected output	value = 6.8036e-07

2.9. What is the somatopetal distance of the soma ?

1. Executed command	printparameter /Purkinje/segments/soma SOMATOPETAL_DISTANCE
2. Part of expected output	value = 0

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

1. Executed command	printparameter /Purkinje/segments/main[0] SOMATOPETAL_DISTANCE
2. Part of expected output	value = 1.44697e-05

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

1. Executed command	printparameter /Purkinje/segments/main[1] SOMATOPETAL_DISTANCE
2. Part of expected output	value = 3.797e-05

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

1. Executed command	printparameter /Purkinje/segments/b0s01[0] SOMATOPETAL_DISTANCE
2. Part of expected output	value = 4.41302e-05

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

1. Executed command	printparameter /Purkinje/segments/b0s01[1] SOMATOPETAL_DISTANCE
2. Part of expected output	value = 4.63502e-05

2.14. What is the somatopetal distance of the spine neck for the previous dendritic segment ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck SOMATOPETAL_DISTANCE
2. Part of expected output	value = 4.70102e-05

2.15. What is the somatopetal distance of the spine head for the previous dendritic segment ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head SOMATOPETAL_DISTANCE
2. Part of expected output	value = 4.76906e-05

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

1. Executed command

printparameter /Purkinje TOTALLENGTH

2. Part of expected output

value = 0.0140198

3. Comment

this value is close to the value in table 2 of the Rapp paper, when shrinkage correction is not applied and spines are not added, yet there is an unexplained anomaly in the difference for surface and volume.

2.17. What is the total dendritic length of all the segments the purkinje cell ?

1. Executed command	printparameter /Purkinje/segments TOTALLENGTH
2. Part of expected output	value = 0.0140198
3. Comment	See developer TODOs
4. This test is currently not executed	(disabled is 'See developer TODOs')

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

1. Executed command

printparameter /Purkinje TOTALSURFACE

2. Part of expected output

value = 2.61206e-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.

2.19. What is the total surface of all the segments the purkinje cell ?

1. Executed command	printparameter /Purkinje/segments TOTALSURFACE
2. Part of expected output	value = 2.61206e-07
3. Comment	See developer TODOs
4. This test is currently not executed	(disabled is 'See developer TODOs')

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

1. Executed command

printparameter /Purkinje TOTALVOLUME

2. Part of expected output

value = 5.39527e-14

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.

2.21. What is the total volume of all the segments the purkinje cell ?

1. Executed command	printparameter /Purkinje/segments TOTALVOLUME
2. Part of expected output	value = 5.39527e-14
3. Comment	See developer TODOs
4. This test is currently not executed	(disabled is 'See developer TODOs')

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

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/kc G_MAX
2. Part of expected output	800

2.23. Is conductance scaling done correctly ?

1. Executed command	printparameterscaled /Purkinje/segments/b0s01[1]/kc G_MAX
2. Part of expected output	1.27212e-08

2.24. Can we find spines in the model purkinje cell ?

1. Executed command

expand /Purkinje/segments/b0s01[1]/Purkinje_spine_0/**

2. Part of expected output

/Purkinje/segments/b0s01[1]/Purkinje_spine_0
- /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck
- /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head
- /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head/par
- /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head/par/synapse
- /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head/par/exp2

2.25. What are the forestspace IDs for the spine neck ?

1. Executed command	serialMapping /Purkinje Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck
2. Part of expected output	Traversal serial ID = 3036 Principal serial ID = 3036 of 65622 Principal successors

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

1. Executed command	serialMapping /Purkinje Purkinje/segments/b0s01[1]
2. Part of expected output	Traversal serial ID = 3000 Principal serial ID = 3000 of 65622 Principal successors
3. Comment	note the differences when using G2 tabchans, G3 ns-sli and plain G3

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

1. Executed command	solverset /Purkinje purk_solver
2. Part of expected output

2.28. Can the solver for the spine neck be found, is it the one we just assigned to it ?

1. Executed command	resolvesolver /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck
2. Part of expected output	Solver = purk_solver, solver serial ID = 3036 Solver serial context for 3036 = /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck

3. Elementary tests for the purkinje cell model with parameterized channels

Startup command : ./neurospacesparse -v 1 -q cells/purkinje/edsjb1994_spinesurface.ndf

3.1. Is neurospaces startup successful ?

1. Part of expected output

./neurospacesparse: No errors for .+?/cells/purkinje/edsjb1994_spinesurface.ndf.

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

1. Executed command	printparameter /Purkinje/segments/main[0] LENGTH
2. Part of expected output	value = 1.44697e-05

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

1. Executed command	printparameter /Purkinje/segments/main[1] LENGTH
2. Part of expected output	value = 2.35003e-05

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

1. Executed command	printparameter /Purkinje/segments/b0s01[0] LENGTH
2. Part of expected output	value = 6.16021e-06

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

1. Executed command	printparameter /Purkinje/segments/b0s01[1] LENGTH
2. Part of expected output	value = 2.22e-06

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

1. Executed command	printparameter /Purkinje/segments/b3s37[17] LENGTH
2. Part of expected output	value = 3.09897e-05

3.7. What is the length of the first spine neck ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck LENGTH
2. Part of expected output	symbol not found

3.8. What is the length of the first spine head ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head LENGTH
2. Part of expected output	symbol not found

3.9. What is the somatopetal distance of the soma ?

1. Executed command	printparameter /Purkinje/segments/soma SOMATOPETAL_DISTANCE
2. Part of expected output	value = 0

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

1. Executed command	printparameter /Purkinje/segments/main[0] SOMATOPETAL_DISTANCE
2. Part of expected output	value = 1.44697e-05

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

1. Executed command	printparameter /Purkinje/segments/main[1] SOMATOPETAL_DISTANCE
2. Part of expected output	value = 3.797e-05

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

1. Executed command	printparameter /Purkinje/segments/b0s01[0] SOMATOPETAL_DISTANCE
2. Part of expected output	value = 4.41302e-05

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

1. Executed command	printparameter /Purkinje/segments/b0s01[1] SOMATOPETAL_DISTANCE
2. Part of expected output	value = 4.63502e-05

3.14. What is the somatopetal distance of the spine neck for the previous dendritic segment ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck SOMATOPETAL_DISTANCE
2. Part of expected output	symbol not found

3.15. What is the somatopetal distance of the spine head for the previous dendritic segment ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head SOMATOPETAL_DISTANCE
2. Part of expected output	symbol not found

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

1. Executed command

printparameter /Purkinje TOTALLENGTH

2. Part of expected output

value = 0.0120441

3. Comment

this value is close to the value in table 2 of the Rapp paper, when shrinkage correction is not applied and spines are not added, yet there is an unexplained anomaly in the difference for surface and volume.

3.17. What is the total dendritic length of all the segments the purkinje cell ?

1. Executed command	printparameter /Purkinje/segments TOTALLENGTH
2. Part of expected output	value = 0.0120441
3. Comment	See developer TODOs
4. This test is currently not executed	(disabled is 'See developer TODOs')

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

1. Executed command

printparameter /Purkinje TOTALSURFACE

2. Part of expected output

value = 2.61092e-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.

3.19. What is the total surface of all the segments the purkinje cell ?

1. Executed command	printparameter /Purkinje/segments TOTALSURFACE
2. Part of expected output	value = 2.61092e-07
3. Comment	See developer TODOs
4. This test is currently not executed	(disabled is 'See developer TODOs')

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

1. Executed command

printparameter /Purkinje TOTALVOLUME

2. Part of expected output

value = 5.37774e-14

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.

3.21. What is the total volume of all the segments the purkinje cell ?

1. Executed command	printparameter /Purkinje/segments TOTALVOLUME
2. Part of expected output	value = 5.37774e-14
3. Comment	See developer TODOs
4. This test is currently not executed	(disabled is 'See developer TODOs')

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

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/kc G_MAX
2. Part of expected output	800

3.23. Is conductance scaling done correctly ?

1. Executed command	printparameterscaled /Purkinje/segments/b0s01[1]/kc G_MAX
2. Part of expected output	1.27212e-08

3.24. Can we find spines in the model purkinje cell ?

1. Executed command	expand /Purkinje/segments/b0s01[1]/Purkinje_spine_0/**
2. Part of expected output

3.25. What are the forestspace IDs for the spine neck ?

1. Executed command	serialMapping /Purkinje Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck
2. Part of expected output	symbol not found

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

1. Executed command	serialMapping /Purkinje Purkinje/segments/b0s01[1]
2. Part of expected output	Traversal serial ID = 3000 Principal serial ID = 3000 of 56778 Principal successors
3. Comment	note the differences when using G2 tabchans, G3 ns-sli and plain G3

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

1. Executed command	solverset /Purkinje purk_solver
2. Part of expected output

3.28. Can the solver for the spine neck be found, is it the one we just assigned to it ?

1. Executed command	resolvesolver /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck
2. Part of expected output	symbol not found