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

Index of group ./specifications/reducing

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reducing model parameters

1. Reducing model parameters in a simple cell model

2. Reducing model parameters in a single compartment model with one channel

1. Reducing model parameters in a simple cell model

Startup command : ./neurospacesparse -q -v 1 tests/cells/reducing.ndf

1.1. Is neurospaces startup successful ?

1. Part of expected output

./neurospacesparse: No errors for .+?/tests/cells/reducing.ndf.

1.2. Do we find reducable items in the model (such as GENESIS2 and undefined parameters) ?

1. Executed command

export no ndf STDOUT /**

2. Part of expected output

#!neurospacesparse
// -*- NEUROSPACES -*-

NEUROSPACES NDF

IMPORT
END IMPORT

PRIVATE_MODELS
END PRIVATE_MODELS

PUBLIC_MODELS
  CELL "hardcoded_neutral"
    SEGMENT "c"
      BINDINGS
        INPUT ka-&gt;I,
      END BINDINGS
      PARAMETERS
        PARAMETER ( LENGTH = 0 ),
        PARAMETER ( DIA = 2.98e-05 ),
        PARAMETER ( RM = 
          GENESIS2
            (
                PARAMETER ( scale = 1 ),
                PARAMETER ( value = 3.58441e+08 ),
            ), ),
        PARAMETER ( RA = 
          GENESIS2
            (
                PARAMETER ( scale = 1 ),
                PARAMETER ( value = 360502 ),
            ), ),
        PARAMETER ( Vm_init = -0.068 ),
        PARAMETER ( ELEAK = -0.08 ),
        PARAMETER ( CM = 
          GENESIS2
            (
                PARAMETER ( scale = 1 ),
                PARAMETER ( value = 4.57537e-11 ),
            ), ),
        PARAMETER ( SURFACE = 2.78986e-09 ),
      END PARAMETERS
      CHANNEL "ka"
        BINDABLES
          INPUT Vm,
          OUTPUT G,
          OUTPUT I,
        END BINDABLES
        BINDINGS
          INPUT ..-&gt;Vm,
        END BINDINGS
        PARAMETERS
          PARAMETER ( CHANNEL_TYPE = "ChannelActInact" ),
          PARAMETER ( G_MAX = 150 ),
          PARAMETER ( Erev = -0.085 ),
        END PARAMETERS
        HH_GATE "HH_activation"
          PARAMETERS
            PARAMETER ( HH_NUMBER_OF_TABLE_ENTRIES = 1.79769e+308 ),
            PARAMETER ( state_init = 0.0837136 ),
            PARAMETER ( POWER = 4 ),
          END PARAMETERS
          GATE_KINETIC "A"
            PARAMETERS
              PARAMETER ( HH_AB_Div_E = -0.012 ),
              PARAMETER ( HH_AB_Offset_E = 0.027 ),
              PARAMETER ( HH_AB_Add_Den = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = 0 ),
              PARAMETER ( HH_AB_Add_Num = 1400 ),
            END PARAMETERS
          END GATE_KINETIC
          GATE_KINETIC "B"
            PARAMETERS
              PARAMETER ( HH_AB_Div_E = 0.004 ),
              PARAMETER ( HH_AB_Offset_E = 0.03 ),
              PARAMETER ( HH_AB_Add_Den = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = 0 ),
              PARAMETER ( HH_AB_Add_Num = 490 ),
            END PARAMETERS
          END GATE_KINETIC
        END HH_GATE
        HH_GATE "HH_inactivation"
          PARAMETERS
            PARAMETER ( HH_NUMBER_OF_TABLE_ENTRIES = 1.79769e+308 ),
            PARAMETER ( state_init = 0.747485 ),
            PARAMETER ( POWER = 1 ),
          END PARAMETERS
          GATE_KINETIC "A"
            PARAMETERS
              PARAMETER ( HH_AB_Div_E = 0.008 ),
              PARAMETER ( HH_AB_Offset_E = 0.05 ),
              PARAMETER ( HH_AB_Add_Den = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = 0 ),
              PARAMETER ( HH_AB_Add_Num = 17.5 ),
            END PARAMETERS
          END GATE_KINETIC
          GATE_KINETIC "B"
            PARAMETERS
              PARAMETER ( HH_AB_Div_E = -0.01 ),
              PARAMETER ( HH_AB_Offset_E = 0.013 ),
              PARAMETER ( HH_AB_Add_Den = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = 0 ),
              PARAMETER ( HH_AB_Add_Num = 1300 ),
            END PARAMETERS
          END GATE_KINETIC
        END HH_GATE
      END CHANNEL
    END SEGMENT
  END CELL
END PUBLIC_MODELS

1.3. Can we reduce the model ?

1. Executed command	reduce
2. Part of expected output

1.4. Do we find the reduced items in the model (removed GENESIS2 and undefined parameters) ?

1. Executed command

export no ndf STDOUT /**

2. Part of expected output

#!neurospacesparse
// -*- NEUROSPACES -*-

NEUROSPACES NDF

IMPORT
END IMPORT

PRIVATE_MODELS
END PRIVATE_MODELS

PUBLIC_MODELS
  CELL "hardcoded_neutral"
    SEGMENT "c"
      BINDINGS
        INPUT ka-&gt;I,
      END BINDINGS
      PARAMETERS
        PARAMETER ( RA = 2.5 ),
        PARAMETER ( RM = 1 ),
        PARAMETER ( CM = 0.0164 ),
        PARAMETER ( DIA = 2.98e-05 ),
        PARAMETER ( Vm_init = -0.068 ),
        PARAMETER ( ELEAK = -0.08 ),
      END PARAMETERS
      CHANNEL "ka"
        BINDABLES
          INPUT Vm,
          OUTPUT G,
          OUTPUT I,
        END BINDABLES
        BINDINGS
          INPUT ..-&gt;Vm,
        END BINDINGS
        PARAMETERS
          PARAMETER ( G_MAX = 150 ),
          PARAMETER ( Erev = -0.085 ),
        END PARAMETERS
        HH_GATE "HH_activation"
          PARAMETERS
            PARAMETER ( state_init = 0.0837136 ),
            PARAMETER ( POWER = 4 ),
          END PARAMETERS
          GATE_KINETIC "A"
            PARAMETERS
              PARAMETER ( HH_AB_Div_E = -0.012 ),
              PARAMETER ( HH_AB_Offset_E = 0.027 ),
              PARAMETER ( HH_AB_Add_Den = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = 0 ),
              PARAMETER ( HH_AB_Add_Num = 1400 ),
            END PARAMETERS
          END GATE_KINETIC
          GATE_KINETIC "B"
            PARAMETERS
              PARAMETER ( HH_AB_Div_E = 0.004 ),
              PARAMETER ( HH_AB_Offset_E = 0.03 ),
              PARAMETER ( HH_AB_Add_Den = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = 0 ),
              PARAMETER ( HH_AB_Add_Num = 490 ),
            END PARAMETERS
          END GATE_KINETIC
        END HH_GATE
        HH_GATE "HH_inactivation"
          PARAMETERS
            PARAMETER ( state_init = 0.747485 ),
            PARAMETER ( POWER = 1 ),
          END PARAMETERS
          GATE_KINETIC "A"
            PARAMETERS
              PARAMETER ( HH_AB_Div_E = 0.008 ),
              PARAMETER ( HH_AB_Offset_E = 0.05 ),
              PARAMETER ( HH_AB_Add_Den = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = 0 ),
              PARAMETER ( HH_AB_Add_Num = 17.5 ),
            END PARAMETERS
          END GATE_KINETIC
          GATE_KINETIC "B"
            PARAMETERS
              PARAMETER ( HH_AB_Div_E = -0.01 ),
              PARAMETER ( HH_AB_Offset_E = 0.013 ),
              PARAMETER ( HH_AB_Add_Den = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = 0 ),
              PARAMETER ( HH_AB_Add_Num = 1300 ),
            END PARAMETERS
          END GATE_KINETIC
        END HH_GATE
      END CHANNEL
    END SEGMENT
  END CELL
END PUBLIC_MODELS

2. Reducing model parameters in a single compartment model with one channel

This command definition is currently disabled (disabled is 'todo')

Startup command : ./neurospacesparse -q -v 1 tests/cells/singlea_naf.ndf

2.1. Is neurospaces startup successful ?

1. Part of expected output	./neurospacesparse: No errors for .+?/tests/cells/singlea_naf.ndf.
2. This test is currently not executed	(disabled is 'todo')

2.2. Do we find reducable items in the model (such as CHANNEL_TYPE) ?

1. Executed command

export no ndf STDOUT /**

2. Part of expected output

#!neurospacesparse
// -*- NEUROSPACES -*-

NEUROSPACES NDF

IMPORT
    FILE "soma" "tests/segments/soma.ndf"
    FILE "gate1" "gates/naf_activation.ndf"
    FILE "gate2" "gates/naf_inactivation.ndf"
END IMPORT

PRIVATE_MODELS
  ALIAS "gate1::/naf_activation" "naf_gate_activation"
  END ALIAS
  ALIAS "gate2::/naf_inactivation" "naf_gate_inactivation"
  END ALIAS
  CHANNEL "NaF"
    BINDABLES
      INPUT Vm,
      OUTPUT G,
      OUTPUT I,
    END BINDABLES
    PARAMETERS
      PARAMETER ( CHANNEL_TYPE = "ChannelActInact" ),
      PARAMETER ( G_MAX = 75000 ),
      PARAMETER ( Erev = 0.045 ),
    END PARAMETERS
    CHILD "naf_gate_activation" "naf_gate_activation"
    END CHILD
    CHILD "naf_gate_inactivation" "naf_gate_inactivation"
    END CHILD
  END CHANNEL
  SEGMENT "soma2"
    BINDABLES
      OUTPUT Vm,
    END BINDABLES
    BINDINGS
      INPUT NaF-&gt;I,
    END BINDINGS
    PARAMETERS
      PARAMETER ( Vm_init = -0.028 ),
      PARAMETER ( RM = 1 ),
      PARAMETER ( RA = 2.5 ),
      PARAMETER ( CM = 0.0164 ),
      PARAMETER ( ELEAK = -0.08 ),
    END PARAMETERS
    CHILD "NaF" "NaF"
      BINDINGS
        INPUT ..-&gt;Vm,
      END BINDINGS
    END CHILD
  END SEGMENT
END PRIVATE_MODELS

PUBLIC_MODELS
  CELL "singlea_naf"
    SEGMENT_GROUP "segments"
      CHILD "soma2" "soma"
        PARAMETERS
          PARAMETER ( rel_X = 0 ),
          PARAMETER ( rel_Y = 0 ),
          PARAMETER ( rel_Z = 0 ),
          PARAMETER ( DIA = 2.98e-05 ),
        END PARAMETERS
      END CHILD
    END SEGMENT_GROUP
  END CELL
END PUBLIC_MODELS

3. This test is currently not executed

(disabled is 'todo')

2.3. Can we reduce the model (2) ?

1. Executed command	reduce
2. Part of expected output
3. This test is currently not executed	(disabled is 'todo')

2.4. Do we find the reduced items in the model (removed CHANNEL_TYPE and correct parameter structure) ?

1. Executed command

export no ndf STDOUT /**

2. Part of expected output

#!neurospacesparse
// -*- NEUROSPACES -*-

NEUROSPACES NDF

IMPORT
    FILE "soma" "tests/segments/soma.ndf"
    FILE "gate1" "gates/naf_activation.ndf"
    FILE "gate2" "gates/naf_inactivation.ndf"
END IMPORT

PRIVATE_MODELS
  ALIAS "gate1::/naf_activation" "naf_gate_activation"
  END ALIAS
  ALIAS "gate2::/naf_inactivation" "naf_gate_inactivation"
  END ALIAS
  CHANNEL "NaF"
    BINDABLES
      INPUT Vm,
      OUTPUT G,
      OUTPUT I,
    END BINDABLES
    PARAMETERS
      PARAMETER ( G_MAX = 75000 ),
      PARAMETER ( Erev = 0.045 ),
    END PARAMETERS
    CHILD "naf_gate_activation" "naf_gate_activation"
    END CHILD
    CHILD "naf_gate_inactivation" "naf_gate_inactivation"
    END CHILD
  END CHANNEL
  SEGMENT "soma2"
    BINDABLES
      OUTPUT Vm,
    END BINDABLES
    BINDINGS
      INPUT NaF-&gt;I,
    END BINDINGS
    PARAMETERS
      PARAMETER ( Vm_init = -0.028 ),
      PARAMETER ( RM = 1 ),
      PARAMETER ( RA = 2.5 ),
      PARAMETER ( CM = 0.0164 ),
      PARAMETER ( ELEAK = -0.08 ),
    END PARAMETERS
    CHILD "NaF" "NaF"
      BINDINGS
        INPUT ..-&gt;Vm,
      END BINDINGS
    END CHILD
  END SEGMENT
END PRIVATE_MODELS

PUBLIC_MODELS
  CELL "singlea_naf"
    SEGMENT_GROUP "segments"
      CHILD "soma2" "soma"
        PARAMETERS
          PARAMETER ( rel_X = 0 ),
          PARAMETER ( rel_Y = 0 ),
          PARAMETER ( rel_Z = 0 ),
          PARAMETER ( DIA = 2.98e-05 ),
        END PARAMETERS
      END CHILD
    END SEGMENT_GROUP
  END CELL
END PUBLIC_MODELS

3. This test is currently not executed

(disabled is 'todo')