MOOSE script does not work

[dilawar]

MOOSE script does not work

[dilawar]

This is due to several changes made to MOOSE. The name of fields are standardized and changed; see the official documentation page (http://moose.ncbs.res.in/pymoose/index.html).

The working version of script having one passive soma and a current injection is following. The output should be like charging and discharging of RC circuit. Here I've changed the default values of RM and CM.

The moose.connect statements are changed to reflect the new naming scheme.

#!/usr/bin/env python

"""excercise.py: This is a simple excercise in moose. We just simulate a soma as
described by Subha on tutorial.

Last modified: Tue Feb 18, 2014  06:20PM

"""

__author__           = "Dilawar Singh"
__copyright__        = "Copyright 2013, NCBS Bangalore"
__credits__          = ["NCBS Bangalore", "Bhalla Lab"]
__license__          = "GPL"
__version__          = "1.0.0"
__maintainer__       = "Dilawar Singh"
__email__            = "[email protected]"
__status__           = "Development"


import moose

model = None
soma = None 
vmtab = None

def buildModel():
    global model 
    global soma
    model = moose.Neutral('/model')
    soma = moose.Compartment('/model/soma')
    soma.Em = -60e-3
    soma.Rm = 1e10
    soma.Cm = 1e-10
    return model

def stimulus():
    global soma
    global vmtab
    pulse = moose.PulseGen('/model/pulse')
    pulse.delay[0] = 50e-3
    pulse.width[0] = 100e-3
    pulse.level[0] = 1e-9
    pulse.delay[1] = 1e9
    vmtab = moose.Table('/soma_Vm')
    moose.connect(pulse, 'output', soma, 'injectMsg')
    moose.connect(vmtab, 'requestOut', soma , 'getVm')

def main():
    global vmtab
    buildModel()
    stimulus()
    moose.reinit()
    t = 500e-2
    moose.start(t)
    import pylab
    t = pylab.linspace(0, t, len(vmtab.vector))
    pylab.plot(t, vmtab.vector)
    pylab.savefig('soma_passive.png')

if __name__ == '__main__':
    main()

The output should be

[dilawar]

The working script can be found here https://raw.githubusercontent.com/BhallaLab/moose-examples/master/passive/passive_soma.py