Genesis 2 Backwards Compatibility Bridge

Index of group ./specifications/tools/simplifying

simplifying models using the model-container

1. Simplifying model parameters of a small model

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

1.1. Can we enter the querymachine ?

1. Executed command	call model_container NEUROSPACES_QUERY
2. Expected output

1.2. What does the model look like ?

1. Executed command

export no ndf STDOUT /hardcoded_neutral/**

2. Expected output

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

NEUROSPACES NDF

IMPORT
END IMPORT

PRIVATE_MODELS
END PRIVATE_MODELS

PUBLIC_MODELS
  GROUP "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 ),
            ), ),
      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 = 
            GENESIS2
              (
                  PARAMETER ( scale = 1 ),
                  PARAMETER ( value = 4.18479e-07 ),
              ), ),
          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_Tau = -0.012 ),
              PARAMETER ( HH_AB_Offset_E = 0.027 ),
              PARAMETER ( HH_AB_Add = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = -0 ),
              PARAMETER ( HH_AB_Scale = 1400 ),
            END PARAMETERS
          END GATE_KINETIC
          GATE_KINETIC "B"
            PARAMETERS
              PARAMETER ( HH_AB_Tau = 0.004 ),
              PARAMETER ( HH_AB_Offset_E = 0.03 ),
              PARAMETER ( HH_AB_Add = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = -0 ),
              PARAMETER ( HH_AB_Scale = 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_Tau = 0.008 ),
              PARAMETER ( HH_AB_Offset_E = 0.05 ),
              PARAMETER ( HH_AB_Add = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = -0 ),
              PARAMETER ( HH_AB_Scale = 17.5 ),
            END PARAMETERS
          END GATE_KINETIC
          GATE_KINETIC "B"
            PARAMETERS
              PARAMETER ( HH_AB_Tau = -0.01 ),
              PARAMETER ( HH_AB_Offset_E = 0.013 ),
              PARAMETER ( HH_AB_Add = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = -0 ),
              PARAMETER ( HH_AB_Scale = 1300 ),
            END PARAMETERS
          END GATE_KINETIC
        END HH_GATE
      END CHANNEL
    END SEGMENT
  END GROUP
END PUBLIC_MODELS

3. Comment

It may be that the HH_AB_Mult parameter has a minus sign, even if its value is zero, this is due to the specific implementation details of NSSetupAlpha().

1.3. Can we ask the model-container to reduce the model ?

1. Executed command	reduce
2. Expected output

1.4. Have reducible items been removed ?

1. Executed command

export no ndf STDOUT /hardcoded_neutral/**

2. Expected output

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

NEUROSPACES NDF

IMPORT
END IMPORT

PRIVATE_MODELS
END PRIVATE_MODELS

PUBLIC_MODELS
  GROUP "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_Tau = -0.012 ),
              PARAMETER ( HH_AB_Offset_E = 0.027 ),
              PARAMETER ( HH_AB_Add = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = -0 ),
              PARAMETER ( HH_AB_Scale = 1400 ),
            END PARAMETERS
          END GATE_KINETIC
          GATE_KINETIC "B"
            PARAMETERS
              PARAMETER ( HH_AB_Tau = 0.004 ),
              PARAMETER ( HH_AB_Offset_E = 0.03 ),
              PARAMETER ( HH_AB_Add = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = -0 ),
              PARAMETER ( HH_AB_Scale = 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_Tau = 0.008 ),
              PARAMETER ( HH_AB_Offset_E = 0.05 ),
              PARAMETER ( HH_AB_Add = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = -0 ),
              PARAMETER ( HH_AB_Scale = 17.5 ),
            END PARAMETERS
          END GATE_KINETIC
          GATE_KINETIC "B"
            PARAMETERS
              PARAMETER ( HH_AB_Tau = -0.01 ),
              PARAMETER ( HH_AB_Offset_E = 0.013 ),
              PARAMETER ( HH_AB_Add = 1 ),
              PARAMETER ( HH_AB_Factor_Flag = -1 ),
              PARAMETER ( HH_AB_Mult = -0 ),
              PARAMETER ( HH_AB_Scale = 1300 ),
            END PARAMETERS
          END GATE_KINETIC
        END HH_GATE
      END CHANNEL
    END SEGMENT
  END GROUP
END PUBLIC_MODELS

3. Comment

Note that for unknown reasons sometimes the HH_AB_Mult parameter has a minus sign, even if its value is zero