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

Index of group ./specifications/parameteroperations

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parameter operations

1. Wildcarded parameter query for various parameter types

2. Retrieving parameters of various types

3. Conceptual level parameter operations

4. Finding parameter names, purkinje cell

5. Finding parameter names, small network

1. Wildcarded parameter query for various parameter types

Startup command : ./neurospacesparse -q -R legacy/networks/networksmall.ndf

1.1. Can we find all the reversal potentials of the soma ?

1. Executed command

printparameter /CerebellarCortex/Golgis/0/Golgi_soma/** Erev

2. Part of expected output

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

1.2. Can we find all the prototypes for the algorithms ?

1. Executed command	printparameter /** PROTOTYPE
2. Part of expected output	/CerebellarCortex/MossyFibers/MossyGrid->PROTOTYPE = "MossyFiber" /CerebellarCortex/Granules/GranuleGrid->PROTOTYPE = "Granule_cell" /CerebellarCortex/Golgis/GolgiGrid->PROTOTYPE = "Golgi_cell"
3. Comment	this requires a full implementation of alien types, see developer TODOs
4. This test is currently not executed	(disabled is 'this requires a full implementation of alien types, see developer TODOs')

1.3. Can we find the prototypes for the algorithms ?

1. Executed command	printparameter /CerebellarCortex/**/GolgiGrid PROTOTYPE
2. Part of expected output	/CerebellarCortex/Golgis/GolgiGrid->PROTOTYPE = "Golgi_cell"

2. Retrieving parameters of various types

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

2.1. Can we find a numeric parameter, segment CM ?

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

2.2. Can we scale a parameter, segment CM ?

1. Executed command	printparameterscaled /Purkinje/segments/soma CM
2. Part of expected output	scaled value = 4.57537e-11

2.3. Can we resolve a symbolic parameter, pool LENGTH ?

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

2.4. Can we resolve a string parameter, spines instance PROTOTYPE ?

1. Executed command	printparameter /Purkinje/SpinesNormal_13_1 PROTOTYPE
2. Part of expected output	value = "Purkinje_spine"

2.5. Can we find extended information for an Erev function parameter ?

1. Executed command

printparameterinfo /Purkinje/segments/soma/cat Erev

2. Part of expected output


'parameter name': Erev
type: function
'function name': NERNST
'function parameters':

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

2.6. Can we print all parameters on a given symbol?

1. Executed command

printparametertraversal /Purkinje/segments/soma/cat

2. Part of expected output


'parameter name': Erev
type: function
'function name': NERNST
'function parameters':

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

2.7. Can we find extended information for a segment's parameters ?

1. Executed command

symbolparameters /Purkinje/segments/main[2]

2. Part of expected output

  -
    'parameter name': Z
    type: number
    value: 3.8022e-05
  -
    'parameter name': Y
    type: number
    value: 1.1682e-05
  -
    'parameter name': X
    type: number
    value: 1.5649e-05
  -
    'parameter name': PARENT
    type: symbolic
    value: ../main[1]
  -
    'parameter name': rel_X
    type: number
    value: 1.666e-06
  -
    'parameter name': rel_Y
    type: number
    value: 1.111e-06
  -
    'parameter name': rel_Z
    type: number
    value: 6.666e-06
  -
    'parameter name': DIA
    type: number
    value: 8.5e-06
  -
    'parameter name': Vm_init
    type: number
    value: -0.068
  -
    'parameter name': RM
    type: number
    value: 3
  -
    'parameter name': RA
    type: number
    value: 2.5
  -
    'parameter name': CM
    type: number
    value: 0.0164
  -
    'parameter name': ELEAK
    type: number
    value: -0.08

2.8. Can we find extended information for a channel's parameters ?

1. Executed command

symbolparameters /Purkinje/segments/main[2]/cat

2. Part of 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-&gt;concen
        'resolved value': /Purkinje/segments/main[2]/ca_pool-&gt;concen
      -
        'parameter name': Cout
        type: number
        value: 2.4
      -
        'parameter name': valency
        'field name': VAL
        type: field
        value: ../ca_pool-&gt;VAL
        'resolved value': /Purkinje/segments/main[2]/ca_pool-&gt;VAL
      -
        'parameter name': T
        type: number
        value: 37

3. Conceptual level parameter operations

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

3.1. Can we find the endogenous firing frequency for the stellate cells ?

1. Executed command	printparameter /Purkinje/segments/br1[7]/stellate1 FREQUENCY
2. Part of expected output	parameter not found in symbol

3.2. Can we find the endogenous firing frequency for the stellate cells ?

1. Executed command	printparameter /Purkinje/segments/br1[7]/stellate2 FREQUENCY
2. Part of expected output	parameter not found in symbol

3.3. Set the endogenous firing frequency at the most conceptual level.

1. Executed command	setparameterconcept thickd::gaba::/Purk_GABA FREQUENCY number 30
2. Part of expected output	neurospaces

3.4. Is the conceptual setting propagated to the expanded representation ?

1. Executed command	printparameter /Purkinje/segments/br1[7]/stellate1 FREQUENCY
2. Part of expected output	= 30

3.5. Is the conceptual setting propagated to the expanded representation ?

1. Executed command	printparameter /Purkinje/segments/br1[7]/stellate2 FREQUENCY
2. Part of expected output	= 30

3.6. Is the conceptual setting propagated to the expanded representation ?

1. Executed command	printparameter /Purkinje/segments/b0s02[17]/stellate FREQUENCY
2. Part of expected output	= 30

3.7. Set the endogenous firing frequency at an intermediate conceptual level.

1. Executed command	setparameterconcept thickd::/thickd/stellate1 FREQUENCY number 40
2. Part of expected output	neurospaces

3.8. Is the conceptual setting propagated to the expanded representation ?

1. Executed command	printparameter /Purkinje/segments/br1[7]/stellate1 FREQUENCY
2. Part of expected output	= 40

3.9. Is the conceptual setting propagated to the expanded representation (should not) ?

1. Executed command	printparameter /Purkinje/segments/br1[7]/stellate2 FREQUENCY
2. Part of expected output	= 30

3.10. Is the conceptual setting propagated to the expanded representation (should not) ?

1. Executed command	printparameter /Purkinje/segments/b0s02[17]/stellate FREQUENCY
2. Part of expected output	= 30

4. Finding parameter names, purkinje cell

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

4.1. Can we find all the parameters of the purkinje cell ?

1. Executed command

printparameterset /Purkinje/**

2. Part of expected output

Parameter (BASE)
Parameter (Base)
Parameter (CHANNEL_TYPE)
Parameter (CM)
Parameter (DIA)
Parameter (DeNominatorOffset)
Parameter (ELEAK)
Parameter (Erev)
Parameter (FREQUENCY)
Parameter (G_MAX)
Parameter (HH_AB_Add_Den)
Parameter (HH_AB_Add_Num)
Parameter (HH_AB_Div_E)
Parameter (HH_AB_Factor_Flag)
Parameter (HH_AB_Mult)
Parameter (HH_AB_Offset_E)
Parameter (HighTarget)
Parameter (LENGTH)
Parameter (LowTarget)
Parameter (MembraneDependence)
Parameter (MembraneDependenceOffset)
Parameter (MembraneOffset)
Parameter (Multiplier)
Parameter (Nominator)
Parameter (PARENT)
Parameter (POWER)
Parameter (RA)
Parameter (RM)
Parameter (SURFACE)
Parameter (TAU)
Parameter (TAU1)
Parameter (TAU2)
Parameter (THICK)
Parameter (Tau)
Parameter (TauDenormalizer)
Parameter (Threshold)
Parameter (VAL)
Parameter (Vm_init)
Parameter (X)
Parameter (Y)
Parameter (Z)
Parameter (concen_init)
Parameter (dDeNominatorOffset)
Parameter (dFirstInitActivation)
Parameter (dFirstSteadyState)
Parameter (dMembraneOffset)
Parameter (dMembraneOffset1)
Parameter (dMembraneOffset2)
Parameter (dMultiplier)
Parameter (dMultiplier1)
Parameter (dMultiplier2)
Parameter (dNominator)
Parameter (dSecondInitActivation)
Parameter (dSecondSteadyState)
Parameter (dTauDenormalizer)
Parameter (dTauDenormalizer1)
Parameter (dTauDenormalizer2)
Parameter (delay)
Parameter (iFirstPower)
Parameter (iSecondPower)
Parameter (rel_X)
Parameter (rel_Y)
Parameter (rel_Z)
Parameter (state_init)
Parameter (weight)

5. Finding parameter names, small network

Startup command : ./neurospacesparse -q -R legacy/networks/networksmall.ndf

5.1. Can we find all the parameters in the network ?

1. Executed command

printparameterset /CerebellarCortex/**

2. Part of expected output

Parameter (BASE)
Parameter (BETA)
Parameter (CM)
Parameter (DIA)
Parameter (ELEAK)
Parameter (Erev)
Parameter (G_MAX)
Parameter (LENGTH)
Parameter (MAXIMUM)
Parameter (MINIMUM)
Parameter (NORMALIZE)
Parameter (RA)
Parameter (RATE)
Parameter (REFRACTORY)
Parameter (RM)
Parameter (SOURCE)
Parameter (TARGET)
Parameter (TAU)
Parameter (TAU1)
Parameter (TAU2)
Parameter (THICK)
Parameter (THRESHOLD)
Parameter (VAL)
Parameter (Vm_init)
Parameter (X)
Parameter (Xindex)
Parameter (Xpower)
Parameter (Y)
Parameter (Ypower)
Parameter (Z)
Parameter (Zpower)
Parameter (concen_init)
Parameter (delay)
Parameter (weight)

5.2. Can we find the parameters of the mossy fibers ?

1. Executed command

printparameterset /CerebellarCortex/MossyFibers/**

2. Part of expected output

Parameter (LENGTH)
Parameter (MAXIMUM)
Parameter (MINIMUM)
Parameter (RATE)
Parameter (REFRACTORY)
Parameter (THRESHOLD)
Parameter (X)
Parameter (Y)
Parameter (Z)

5.3. Can we find the parameters of one mossy fibers ?

1. Executed command	printparameterset /CerebellarCortex/MossyFibers/1
2. Part of expected output	Parameter (RATE) Parameter (REFRACTORY) Parameter (X) Parameter (Y) Parameter (Z)