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

Index of group ./specifications/python

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importing and processing of a model in python

1. Import and export of a model in python

Startup command : bin/genesis-g3

(No model has been loaded for the following set of commands.)

1.1. Is startup successful ?

1. Expected output

Welcome to the GENESIS 3 shell

1.2. Can we find a python based model in the model library?

1. Executed command

sh cat /usr/local/neurospaces/models/library/channels/hodgkin-huxley/k.npy

2. Expected output

#! /usr/bin/env python

print "import\n"

import Neurospaces

print "initialize\n"

nmc = Neurospaces.getModelContainer()

print "construct\n"

c = nmc.Channel("/k")

gka = nmc.GateKinetic("/k/a")

gka.parameter("HH_AB_Add_Num", -600.0 )
gka.parameter("HH_AB_Mult", -10000 )
gka.parameter("HH_AB_Factor_Flag", -1.0 )
gka.parameter("HH_AB_Add_Den", -1.0 )
gka.parameter("HH_AB_Offset_E", 60e-3 )
gka.parameter("HH_AB_Div_E", -10.0e-3 )

gkb = nmc.GateKinetic("/k/b")

gkb.parameter("HH_AB_Add_Num", 125.0 )
gkb.parameter("HH_AB_Mult", 0.0 )
gkb.parameter("HH_AB_Factor_Flag", -1.0 )
gkb.parameter("HH_AB_Add_Den", 0.0 )
gkb.parameter("HH_AB_Offset_E", 70e-3 )
gkb.parameter("HH_AB_Div_E", 80e-3 )

1.3. Can we load a npy model ?

1. Executed command	npy_load channels/hodgkin-huxley/k.npy
2. Expected output

1.4. Can we export the model to an NDF file ?

1. Executed command

ndf_save /** STDOUT

2. Expected output

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

NEUROSPACES NDF

PRIVATE_MODELS
  GATE_KINETIC "a_2_2"
    PARAMETERS
      PARAMETER ( HH_AB_Div_E = -0.01 ),
      PARAMETER ( HH_AB_Offset_E = 0.06 ),
      PARAMETER ( HH_AB_Add_Den = -1 ),
      PARAMETER ( HH_AB_Factor_Flag = -1 ),
      PARAMETER ( HH_AB_Mult = -10000 ),
      PARAMETER ( HH_AB_Add_Num = -600 ),
    END PARAMETERS
  END GATE_KINETIC
  CHILD "a_2_2" "a_inserted_2"
  END CHILD
  GATE_KINETIC "b_3_3"
    PARAMETERS
      PARAMETER ( HH_AB_Div_E = 0.08 ),
      PARAMETER ( HH_AB_Offset_E = 0.07 ),
      PARAMETER ( HH_AB_Add_Den = 0 ),
      PARAMETER ( HH_AB_Factor_Flag = -1 ),
      PARAMETER ( HH_AB_Mult = 0 ),
      PARAMETER ( HH_AB_Add_Num = 125 ),
    END PARAMETERS
  END GATE_KINETIC
  CHILD "b_3_3" "b_inserted_3"
  END CHILD
  CHANNEL "k_1_1"
    BINDABLES
      INPUT Vm,
      OUTPUT G,
      OUTPUT I,
    END BINDABLES
    PARAMETERS
      PARAMETER ( POWER = 4 ),
    END PARAMETERS
    CHILD "a_2_2" "a"
    END CHILD
    CHILD "b_3_3" "b"
    END CHILD
  END CHANNEL
  CHILD "k_1_1" "k_inserted_1"
  END CHILD
END PRIVATE_MODELS
PUBLIC_MODELS
  CHILD "k_1_1" "k"
  END CHILD
END PUBLIC_MODELS