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

Index of group ./specifications/parameters

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parameter calculations on existing models

1. Parameter calculations on dendrites of the standard Purkinje cell model

2. Parameter calculations on spines of the standard Purkinje cell model

3. Parameter function correctness

4. Parameter calculations on dendrites of the standard Purkinje cell model (2)

5. Parameter calculations on spines of the standard Purkinje cell model (2)

6. Parameter function correctness

7. Wildcarded parameter query

8. Thickness of EM contours and points

1. Parameter calculations on dendrites of the standard Purkinje cell model

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. Does the soma of the purkinje cell have a diameter ?

1. Executed command	printparameter /Purkinje/segments/soma DIA
2. Part of expected output	= 2.98e-05

1.3. Does the soma of the purkinje cell not have a length ?

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

1.4. Does the soma of the purkinje cell have a surface ?

1. Executed command	printparameter /Purkinje/segments/soma SURFACE
2. Part of expected output	= 2.78986e-09

1.5. Does the soma of the purkinje cell have a time constant ?

1. Executed command	printparameter /Purkinje/segments/soma TAU
2. Part of expected output	= 0.0164

1.6. Does the soma of the purkinje cell have a well-defined delayed rectifier potassium conductance ?

1. Executed command	printparameter /Purkinje/segments/soma/Kdr G_MAX
2. Part of expected output	= 6000

1.7. Has the conductance been scaled according to the surface ?

1. Executed command	printparameterscaled /Purkinje/segments/soma/Kdr G_MAX
2. Part of expected output	= 1.67392e-05

1.8. What is the diameter of one of the spiny dendrites ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1] DIA
2. Part of expected output	= 2.28e-06

1.9. What is the length of one of the spiny dendrites ?

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

1.10. What is the time constant of one of the spiny dendrites ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1] TAU
2. Part of expected output	= 0.0492

1.11. 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

1.12. 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. Parameter calculations on spines of the standard Purkinje cell model

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

2.1. Can we find spines attached to a spiny dendrite in the model purkinje cell ?

1. Executed command	serialID /Purkinje Purkinje/segments/b0s01[1]/Purkinje_spine_0/head/par
2. Part of expected output	= 1141

2.2. What is the length of the spiny dendrite ?

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

2.3. What is the diameter of the spiny dendrite ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1] DIA
2. Part of expected output	= 2.28e-06

2.4. What is the surface of the spiny dendrite (must be corrected for virtual spines) ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1] SURFACE
2. Part of expected output	= 5.29772e-11

2.5. What is the length of the spine neck ?

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

2.6. What is the diameter of the spine neck ?

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

2.7. What is the surface of the spine neck ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck SURFACE
2. Part of expected output	= 4.1469e-13

2.8. What is the length of the spine head ?

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

2.9. What is the diameter of the spine head ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head DIA
2. Part of expected output	= 4.286e-07

2.10. What is the surface of the spine head ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head SURFACE
2. Part of expected output	= 9.16096e-13

2.11. What is the capacitance of the spiny dendrite ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1] CM
2. Part of expected output	= 0.0164

2.12. What is the scaled capacitance of the spiny dendrite (includes spine surface for virtual spines) ?

1. Executed command	printparameterscaled /Purkinje/segments/b0s01[1] CM
2. Part of expected output	= 8.68826e-13

2.13. What is the membrane resistance of the spiny dendrite ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1] RM
2. Part of expected output	= 3 neurospaces

2.14. What is the scaled membrane resistance of the spiny dendrite (includes spine surface for virtual spines) ?

1. Executed command	printparameterscaled /Purkinje/segments/b0s01[1] RM
2. Part of expected output	= 5.66282e+10

2.15. What is the axial resistance of the spiny dendrite ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1] RA
2. Part of expected output	= 2.5 neurospaces

2.16. What is the scaled axial resistance of the spiny dendrite (does not includes spine parameters) ?

1. Executed command	printparameterscaled /Purkinje/segments/b0s01[1] RA
2. Part of expected output	= 1.35936e+06

3. Parameter function correctness

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

3.1. Can we find the input to a nernst function ?

1. Executed command	printparameterinput /Purkinje/segments/main[0]/CaT Erev Cin
2. Part of expected output	value = Ca_pool

4. Parameter calculations on dendrites of the standard Purkinje cell model (2)

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

4.1. Is neurospaces startup successful ?

1. Part of expected output

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

4.2. Does the soma of the purkinje cell have a diameter ?

1. Executed command	printparameter /Purkinje/segments/soma DIA
2. Part of expected output	= 2.98e-05

4.3. Does the soma of the purkinje cell not have a length ?

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

4.4. Does the soma of the purkinje cell have a surface ?

1. Executed command	printparameter /Purkinje/segments/soma SURFACE
2. Part of expected output	= 2.78986e-09

4.5. Does the soma of the purkinje cell have a time constant ?

1. Executed command	printparameter /Purkinje/segments/soma TAU
2. Part of expected output	= 0.0164

4.6. Does the soma of the purkinje cell have a well-defined delayed rectifier potassium conductance ?

1. Executed command	printparameter /Purkinje/segments/soma/kdr G_MAX
2. Part of expected output	= 6000

4.7. Has the conductance been scaled according to the surface ?

1. Executed command	printparameterscaled /Purkinje/segments/soma/kdr G_MAX
2. Part of expected output	= 1.67392e-05

4.8. What is the diameter of one of the spiny dendrites ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1] DIA
2. Part of expected output	= 2.28e-06

4.9. What is the length of one of the spiny dendrites ?

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

4.10. What is the time constant of one of the spiny dendrites ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1] TAU
2. Part of expected output	= 0.0492

4.11. 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

4.12. Is conductance scaling done correctly ?

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

5. Parameter calculations on spines of the standard Purkinje cell model (2)

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

5.1. Can we find spines attached to a spiny dendrite in the model purkinje cell ?

1. Executed command	serialID /Purkinje Purkinje/segments/b0s01[1]/Purkinje_spine_0/head/par
2. Part of expected output	= 3038

5.2. What is the length of the spiny dendrite ?

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

5.3. What is the diameter of the spiny dendrite ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1] DIA
2. Part of expected output	= 2.28e-06

5.4. What is the surface of the spiny dendrite (must be corrected for virtual spines) ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1] SURFACE
2. Part of expected output	= 5.29772e-11

5.5. What is the length of the spine neck ?

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

5.6. What is the diameter of the spine neck ?

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

5.7. What is the surface of the spine neck ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/neck SURFACE
2. Part of expected output	= 4.1469e-13

5.8. What is the length of the spine head ?

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

5.9. What is the diameter of the spine head ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head DIA
2. Part of expected output	= 4.286e-07

5.10. What is the surface of the spine head ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1]/Purkinje_spine_0/head SURFACE
2. Part of expected output	= 9.16096e-13

5.11. What is the capacitance of the spiny dendrite ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1] CM
2. Part of expected output	= 0.0164

5.12. What is the scaled capacitance of the spiny dendrite (includes spine surface for virtual spines) ?

1. Executed command	printparameterscaled /Purkinje/segments/b0s01[1] CM
2. Part of expected output	= 8.68826e-13

5.13. What is the membrane resistance of the spiny dendrite ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1] RM
2. Part of expected output	= 3 neurospaces

5.14. What is the scaled membrane resistance of the spiny dendrite (includes spine surface for virtual spines) ?

1. Executed command	printparameterscaled /Purkinje/segments/b0s01[1] RM
2. Part of expected output	= 5.66282e+10

5.15. What is the axial resistance of the spiny dendrite ?

1. Executed command	printparameter /Purkinje/segments/b0s01[1] RA
2. Part of expected output	= 2.5 neurospaces

5.16. What is the scaled axial resistance of the spiny dendrite (does not includes spine parameters) ?

1. Executed command	printparameterscaled /Purkinje/segments/b0s01[1] RA
2. Part of expected output	= 1.35936e+06

6. Parameter function correctness

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

6.1. Can we find the input to a nernst function ?

1. Executed command	printparameterinput /Purkinje/segments/main[0]/cat Erev Cin
2. Part of expected output	value = ca_pool

7. Wildcarded parameter query

Startup command : ./neurospacesparse -q legacy/cells/golgi.ndf

Comments, Preparation, Reparation

1. Comment for this test definition

this test is superseded by the same type of test in parameteroperations.t

7.1. Can we find all the reversal potentials ?

1. Executed command

printparameter /** Erev

2. Part of expected output

/Golgi/Golgi_soma/CaHVA-&gt;Erev = 0.138533
/Golgi/Golgi_soma/H-&gt;Erev = -0.042
/Golgi/Golgi_soma/InNa-&gt;Erev = 0.055
/Golgi/Golgi_soma/KA-&gt;Erev = -0.09
/Golgi/Golgi_soma/KDr-&gt;Erev = -0.09
/Golgi/Golgi_soma/Moczyd_KC-&gt;Erev = -0.09
/Golgi/Golgi_soma/mf_AMPA-&gt;Erev = 0
/Golgi/Golgi_soma/pf_AMPA-&gt;Erev = 0

8. Thickness of EM contours and points

Startup command : ./neurospacesparse -q contours/section1.ndf

8.1. What is the thickness of the first contour ?

1. Executed command	printparameter /section1/e0 THICKNESS
2. Part of expected output	= 7e-08

8.2. Is the thickness inherited by the contour points ?

1. Executed command	printparameter /section1/e0/e0_0 THICKNESS
2. Part of expected output	= 7e-08

8.3. Is the thickness inherited by the contour points (2) ?

1. Executed command	printparameter /section1/e0/e0_1 THICKNESS
2. Part of expected output	= 7e-08

8.4. Is the thickness inherited by the contour points (3) ?

1. Executed command	printparameter /section1/e0/e0_2 THICKNESS
2. Part of expected output	= 7e-08