def loadModels(filepath):
""" load models into moose if file, if moosepath itself it passes back the path and
delete solver if exist """
modelpath = '/'
loaded = False
if os.path.isfile(filepath):
fpath, filename = os.path.split(filepath)
# print " head and tail ",head, " ",tail
# modelpath = filename[filename.rfind('/'): filename.rfind('.')]
# print "modelpath ",modelpath
# ext = os.path.splitext(filename)[1]
# filename = filename.strip()
modelpath = '/' + filename[:filename.rfind('.')]
modeltype = mtypes.getType(filepath)
subtype = mtypes.getSubtype(filepath, modeltype)
if subtype == 'kkit' or modeltype == "cspace":
moose.loadModel(filepath, modelpath)
loaded = True
elif subtype == 'sbml':
#moose.mooseReadSBML(filename,modelpath)
#loaded = True
pass
else:
print("This file is not supported for mergering")
modelpath = moose.Shell('/')
elif moose.exists(filepath):
modelpath = filepath
loaded = True
return modelpath, loaded
def loadModels(filepath):
""" load models into moose if file, if moosepath itself it passes back the path and
delete solver if exist """
modelpath = '/'
loaded = False
if os.path.isfile(filepath) :
fpath, filename = os.path.split(filepath)
# print " head and tail ",head, " ",tail
# modelpath = filename[filename.rfind('/'): filename.rfind('.')]
# print "modelpath ",modelpath
# ext = os.path.splitext(filename)[1]
# filename = filename.strip()
modelpath = '/'+filename[:filename.rfind('.')]
modeltype = mtypes.getType(filepath)
subtype = mtypes.getSubtype(filepath, modeltype)
if subtype == 'kkit' or modeltype == "cspace":
moose.loadModel(filepath,modelpath)
loaded = True
elif subtype == 'sbml':
#moose.mooseReadSBML(filename,modelpath)
#loaded = True
pass
else:
print("This file is not supported for mergering")
modelpath = moose.Shell('/')
elif moose.exists(filepath):
modelpath = filepath
loaded = True
return modelpath,loaded
def main( runTime ):
try:
moose.delete('/acc92')
print("Deleted old model")
except Exception as e:
print("Could not clean. model not loaded yet")
moose.loadModel('acc92_caBuff.g',loadpath,'gsl')
ca = moose.element(loadpath+'/kinetics/Ca')
pr = moose.element(loadpath+'/kinetics/protein')
clockdt = moose.Clock('/clock').dts
moose.setClock(8, 0.1)#simdt
moose.setClock(18, 0.1)#plotdt
print clockdt
print " \t \t simdt ", moose.Clock('/clock').dts[8],"plotdt ",moose.Clock('/clock').dts[18]
ori = ca.concInit
tablepath = loadpath+'/kinetics/Ca'
tableele = moose.element(tablepath)
table = moose.Table2(tablepath+'.con')
x = moose.connect(table, 'requestOut', tablepath, 'getConc')
tablepath1 = loadpath+'/kinetics/protein'
tableele1 = moose.element(tablepath1)
table1 = moose.Table2(tablepath1+'.con')
x1 = moose.connect(table1, 'requestOut', tablepath1, 'getConc')
ca.concInit = ori
print("[INFO] Running for 4000 with Ca.conc %s " % ca.conc)
moose.start(4000)
ca.concInit = 5e-03
print("[INFO] Running for 20 with Ca.conc %s " % ca.conc)
moose.start(20)
ca.concInit = ori
moose.start( runTime ) #here give the interval time
ca.concInit = 5e-03
print("[INFO] Running for 20 with Ca.conc %s " % ca.conc)
moose.start(20)
ca.concInit = ori
print("[INFO] Running for 2000 with Ca.conc %s " % ca.conc)
moose.start(2000)
pylab.figure()
pylab.subplot(2, 1, 1)
t = numpy.linspace(0.0, moose.element("/clock").runTime, len(table.vector)) # sec
pylab.plot( t, table.vector, label="Ca Conc (interval- 8000s)" )
pylab.legend()
pylab.subplot(2, 1, 2)
t1 = numpy.linspace(0.0, moose.element("/clock").runTime, len(table1.vector)) # sec
pylab.plot( t1, table1.vector, label="Protein Conc (interval- 8000s)" )
pylab.legend()
pylab.savefig( os.path.join( dataDir, '%s_%s.png' % (table1.name, runTime) ) )
print('[INFO] Saving data to csv files in %s' % dataDir)
tabPath1 = os.path.join( dataDir, '%s_%s.csv' % (table.name, runTime))
numpy.savetxt(tabPath1, numpy.matrix([t, table.vector]).T, newline='\n')
tabPath2 = os.path.join( dataDir, '%s_%s.csv' % (table1.name, runTime) )
numpy.savetxt(tabPath2, numpy.matrix([t1, table1.vector]).T, newline='\n')
def __init__(self, *args):
QWidget.__init__(self, *args)
#c = moose.ZombiePool('/compartment')
c = moose.Compartment('/compartment')
moose.loadModel('../Demos/Genesis_files/reaction.g','/rec')
for l in moose.wildcardFind('/rec/##[TYPE=ZombiePool]'):
if( moose.element(l).path == '/rec/kinetics/Sub'):
c = moose.element(l)
tablemodel = ObjectFieldsModel(c,['Field','Value'],self) #my_array, self)
tableview = QTableView()
tableview.setModel(tablemodel)
#tableview.setShowGrid(False)
vh = tableview.verticalHeader()
vh.setVisible(False)
hh = tableview.horizontalHeader()
hh.setStretchLastSection(True)
tableview.setAlternatingRowColors(True)
#tableview.resizeColumnsToContents()
layout = QVBoxLayout(self)
layout.addWidget(tableview)
self.setLayout(layout)
def _loadElec( self, efile, elecname ):
if ( efile[ len( efile ) - 2:] == ".p" ):
self.elecid = moose.loadModel( efile, '/library/' + elecname)[0]
print self.elecid
elif ( efile[ len( efile ) - 4:] == ".swc" ):
self.elecid = moose.loadModel( efile, '/library/' + elecname)[0]
else:
nm = NeuroML()
print "in _loadElec, combineSegments = ", self.combineSegments
nm.readNeuroMLFromFile( efile, \
params = {'combineSegments': self.combineSegments, \
'createPotentialSynapses': True } )
if moose.exists( '/cells' ):
kids = moose.wildcardFind( '/cells/#' )
else:
kids = moose.wildcardFind( '/library/#[ISA=Neuron],/library/#[TYPE=Neutral]' )
if ( kids[0].name == 'spine' ):
kids = kids[1:]
assert( len( kids ) > 0 )
self.elecid = kids[0]
temp = moose.wildcardFind( self.elecid.path + '/#[ISA=CompartmentBase]' )
transformNMDAR( self.elecid.path )
kids = moose.wildcardFind( '/library/##[0]' )
for i in kids:
i.tick = -1
def _loadElec(self, efile, elecname):
if (efile[len(efile) - 2:] == ".p"):
self.elecid = moose.loadModel(efile, '/library/' + elecname)[0]
print(self.elecid)
elif (efile[len(efile) - 4:] == ".swc"):
self.elecid = moose.loadModel(efile, '/library/' + elecname)[0]
else:
nm = NeuroML()
print("in _loadElec, combineSegments = ", self.combineSegments)
nm.readNeuroMLFromFile( efile, \
params = {'combineSegments': self.combineSegments, \
'createPotentialSynapses': True } )
if moose.exists('/cells'):
kids = moose.wildcardFind('/cells/#')
else:
kids = moose.wildcardFind(
'/library/#[ISA=Neuron],/library/#[TYPE=Neutral]')
if (kids[0].name == 'spine'):
kids = kids[1:]
assert (len(kids) > 0)
self.elecid = kids[0]
temp = moose.wildcardFind(self.elecid.path +
'/#[ISA=CompartmentBase]')
transformNMDAR(self.elecid.path)
kids = moose.wildcardFind('/library/##[0]')
for i in kids:
i.tick = -1
def loadModels(filename):
""" load models into moose if file, if moosepath itself it passes back the path and
delete solver if exist """
modelpath = '/'
loaded = False
if os.path.isfile(filename):
modelpath = filename[filename.rfind('/'):filename.rfind('.')]
ext = os.path.splitext(filename)[1]
filename = filename.strip()
modeltype = mtypes.getType(filename)
subtype = mtypes.getSubtype(filename, modeltype)
if subtype == 'kkit' or modeltype == "cspace":
moose.loadModel(filename, modelpath)
loaded = True
elif subtype == 'sbml':
#moose.ReadSBML()
pass
else:
print("This file is not supported for mergering")
modelpath = moose.Shell('/')
elif moose.exists(filename):
modelpath = filename
loaded = True
## default is 'ee' solver while loading the model using moose.loadModel,
## yet deleteSolver is called just to be assured
if loaded:
deleteSolver(modelpath)
return modelpath, loaded
def createMultiCompCell(file_name,
container_name,
library_name,
comp_type,
channelSet,
condSet,
rateParams,
CaParams=None,
CaPoolParams=None,
HCNParams=None,
cell_RM=None,
cell_CM=None,
cell_RA=None,
cell_initVm=None,
cell_Em=None):
# Create the channel types and store them in a library to be used by each compartment
# in the model
createChanLib(library_name, channelSet, rateParams, CaParams, HCNParams)
# Load in the model in question
if file_name.endswith('.p'):
cell = moose.loadModel(file_name, container_name)
for comp in moose.wildcardFind(cell.path + '/' + '#[TYPE=' +
comp_type + ']'):
for chan_name, cond in condSet.items():
SA = np.pi * comp.length * comp.diameter
proto = moose.element(library_name + '/' + chan_name)
chan = moose.copy(proto, comp, chan_name)[0]
chan.Gbar = cond * SA
m = moose.connect(chan, 'channel', comp, 'channel')
# Add the calcium pool to each compartment in the cell if it has been specified
if (CaPoolParams != None):
add_calcium(library_name, cell, CaPoolParams, comp_type)
for key in channelSet.keys():
if ("Ca" in key):
connect_cal2chan(channelSet[key].name,
channelSet[key].chan_type, cell,
CaPoolParams.caName, comp_type)
else:
cell = moose.loadModel(file_name, container_name)
setCompParameters(cell, comp_type, cell_RM, cell_CM, cell_RA,
cell_initVm, cell_Em)
for comp in moose.wildcardFind(cell.path + '/' + '#[TYPE=' +
comp_type + ']'):
for chan_name, cond in condSet.items():
SA = np.pi * comp.length * comp.diameter
proto = moose.element(library_name + '/' + chan_name)
chan = moose.copy(proto, comp, chan_name)[0]
chan.Gbar = cond * SA
m = moose.connect(chan, 'channel', comp, 'channel')
# Add the calcium pool to each compartment in the cell if it has been specified
if (CaPoolParams != None):
add_calcium(library_name, cell, CaPoolParams, comp_type)
for key in channelSet.keys():
if ("Ca" in key):
connect_cal2chan(channelSet[key].name,
channelSet[key].chan_type, cell,
CaPoolParams.caName, comp_type)
return cell
def test_kkit():
"""
The script demonstates to convert Chemical (Genesis) file back to Genesis
file using moose
"""
moose.loadModel(os.path.join(cwd, '../data/reaction.g'), '/model')
written = moose.writeKkit('/model', 'testsave.g')
print(written)
def main():
"""This example illustrates loading a kinetic model defined in Genesis format
into Moose using loadModel function and using writeSBML function
one can save the model into SBML format. \n
Moose needs to be compiled with libsbml
"""
#This command loads the file into the path '/Kholodenko'
moose.loadModel('../genesis/Kholodenko.g','/Kholodenko')
#Writes model to xml file
moose.writeSBML('/Kholodenko','Kholodenko_tosbml.xml')
def main():
"""This example illustrates loading a kinetic model defined in Genesis format
into Moose using loadModel function and using writeSBML function
one can save the model into SBML format. \n
libsbml should be installed
"""
#This command loads the file into the path '/Kholodenko'
moose.loadModel('../genesis/Kholodenko.g', '/Kholodenko')
#Writes model to xml file
written = mooseWriteSBML('/Kholodenko', '../genesis/Kholodenko_tosbml.xml')
print(written)
def main():
"""This example illustrates loading a kinetic model defined in Genesis format
into Moose using loadModel function and using writeSBML function
one can save the model into SBML format. \n
libsbml should be installed
"""
#This command loads the file into the path '/Kholodenko'
moose.loadModel('../genesis/Kholodenko.g','/Kholodenko')
#Writes model to xml file
written = mooseWriteSBML('/Kholodenko','../genesis/Kholodenko_tosbml.xml')
print(written)
def main():
# Schedule the whole lot
moose.setClock( 4, 0.1 ) # for the computational objects
moose.setClock( 5, 0.1 ) # clock for the solver
moose.setClock( 8, 1.0 ) # for the plots
# The wildcard uses # for single level, and ## for recursive.
#compartment = makeModel()
moose.loadModel( '../Genesis_files/M1719.cspace', '/model', 'ee' )
compartment = moose.element( 'model/kinetics' )
compartment.name = 'compartment'
ksolve = moose.Ksolve( '/model/compartment/ksolve' )
stoich = moose.Stoich( '/model/compartment/stoich' )
stoich.compartment = compartment
stoich.ksolve = ksolve
#ksolve.stoich = stoich
stoich.path = "/model/compartment/##"
state = moose.SteadyState( '/model/compartment/state' )
moose.useClock( 5, '/model/compartment/ksolve', 'process' )
moose.useClock( 8, '/model/graphs/#', 'process' )
moose.reinit()
state.stoich = stoich
#state.showMatrices()
state.convergenceCriterion = 1e-7
moose.le( '/model/graphs' )
a = moose.element( '/model/compartment/a' )
b = moose.element( '/model/compartment/b' )
c = moose.element( '/model/compartment/c' )
for i in range( 0, 100 ):
getState( ksolve, state )
moose.start( 100.0 ) # Run the model for 100 seconds.
b = moose.element( '/model/compartment/b' )
c = moose.element( '/model/compartment/c' )
# move most molecules over to b
b.conc = b.conc + c.conc * 0.95
c.conc = c.conc * 0.05
moose.start( 100.0 ) # Run the model for 100 seconds.
# move most molecules back to a
c.conc = c.conc + b.conc * 0.95
b.conc = b.conc * 0.05
moose.start( 100.0 ) # Run the model for 100 seconds.
# Iterate through all plots, dump their contents to data.plot.
displayPlots()
quit()
def loadFile(filename, target, merge=True):
"""Try to load a model from specified `filename` under the element
`target`.
if `merge` is True, the contents are just loaded at target. If
false, everything is deleted from the parent of target unless the
parent is root.
Returns
-------
a dict containing at least these three entries:
modeltype: type of the loaded model.
subtype: subtype of the loaded model, None if no specific subtype
modelroot: root element of the model, None if could not be located - as is the case with Python scripts
"""
istext = True
with open(filename, 'rb') as infile:
istext = mtypes.istextfile(infile)
if not istext:
print 'Cannot handle any binary formats yet'
return None
parent, child = posixpath.split(target)
p = moose.Neutral(parent)
if not merge and p.path != '/':
for ch in p.children:
moose.delete(ch)
try:
modeltype = mtypes.getType(filename)
subtype = mtypes.getSubtype(filename, modeltype)
except KeyError:
raise FileLoadError('Do not know how to handle this filetype: %s' % (filename))
pwe = moose.getCwe()
if modeltype == 'genesis':
if subtype == 'kkit' or subtype == 'prototype':
model = moose.loadModel(filename, target)
else:
print 'Only kkit and prototype files can be loaded.'
elif modeltype == 'cspace':
model = moose.loadModel(filename, target)
elif modeltype == 'xml' and subtype == 'neuroml':
model = neuroml.loadNeuroML_L123(filename)
else:
raise FileLoadError('Do not know how to handle this filetype: %s' % (filename))
moose.setCwe(pwe) # The MOOSE loadModel changes the current working element to newly loaded model. We revert that behaviour
# TODO: check with Aditya how to specify the target for
# neuroml reader
return {'modeltype': modeltype,
'subtype': subtype,
'model': model}
def main():
"""Test main"""
model = moose.Neutral('/model')
moose.loadModel('../Demos/Genesis_files/Kholodenko.g', '/model/Kholodenko')
# tab = moose.element('/model/Kholodenko/graphs/conc1/MAPK_PP.Co')
# print tab
# for t in tab.children:
# print t
app = QtGui.QApplication(sys.argv)
mainwin = QtGui.QMainWindow()
mainwin.setWindowTitle('Model tree test')
wildcardWidget = SearchWidget()
mainwin.setCentralWidget(wildcardWidget)
mainwin.show()
sys.exit(app.exec_())
def main():
"""Test main"""
model = moose.Neutral('/model')
moose.loadModel('../Demos/Genesis_files/Kholodenko.g', '/model/Kholodenko')
# tab = moose.element('/model/Kholodenko/graphs/conc1/MAPK_PP.Co')
# print tab
# for t in tab.children:
# print t
app = QtGui.QApplication(sys.argv)
mainwin = QtGui.QMainWindow()
mainwin.setWindowTitle('Model tree test')
wildcardWidget = SearchWidget()
mainwin.setCentralWidget(wildcardWidget)
mainwin.show()
sys.exit(app.exec_())
def load_neuron_file(fileName, cellPath, RM, RA, CM):
cell = moose.loadModel(fileName, cellPath)
for child in cell[0].children:
for comp in child:
comp.RM = RM
comp.RA = RA
comp.CM = CM
def loadChem():
chem = moose.Neutral( '/model/chem' )
modelId = moose.loadModel(
os.path.join( scriptDir, '..', 'genesis', 'chanPhosphByCaMKII.g' )
, '/model/chem', 'gsl'
)
nmstoich = moose.element( '/model/chem/kinetics/stoich' )
def main():
"""Test main: load a model and display the tree for it"""
model = moose.Neutral('/model')
moose.loadModel('../Demos/Genesis_files/Kholodenko.g', '/model/Kholodenko')
# tab = moose.element('/model/Kholodenko/graphs/conc1/MAPK_PP.Co')
# print tab
# for t in tab.children:
# print t
app = QtGui.QApplication(sys.argv)
mainwin = QtGui.QMainWindow()
mainwin.setWindowTitle('Model tree test')
tree = MooseTreeWidget()
tree.recreateTree(root='/model/')
mainwin.setCentralWidget(tree)
mainwin.show()
sys.exit(app.exec_())
def main():
solver = "gsl"
mfile = '../../Genesis_files/Kholodenko.g'
runtime = 5000.0
if ( len( sys.argv ) >= 2 ):
solver = sys.argv[1]
modelId = moose.loadModel( mfile, 'model', solver )
dt = moose.element( '/clock' ).dt
moose.reinit()
moose.start( runtime )
# Display all plots.
img = mpimg.imread( 'Kholodenko_tut.png' )
fig = plt.figure( figsize=( 12, 10 ) )
png = fig.add_subplot( 211 )
imgplot = plt.imshow( img )
ax = fig.add_subplot( 212 )
x = moose.wildcardFind( '/model/#graphs/conc#/#' )
t = numpy.arange( 0, x[0].vector.size, 1 ) * dt
ax.plot( t, x[0].vector * 100, 'b-', label='Ras-MKKK * 100' )
ax.plot( t, x[1].vector, 'y-', label='MKKK-P' )
ax.plot( t, x[2].vector, 'm-', label='MKK-PP' )
ax.plot( t, x[3].vector, 'r-', label='MAPK-PP' )
plt.ylabel( 'Conc (mM)' )
plt.xlabel( 'Time (seconds)' )
pylab.legend()
pylab.show()
def make_prototype(passive=True):
path = '%s/rc19' % (library.path)
pfile = 'rc19.p'
try:
return moose.element(path)
except ValueError:
pass
if not passive:
make_na()
make_kv()
make_km()
make_kca()
make_cat()
make_cahva()
make_h()
try:
proto = moose.element(path)
except ValueError:
print('Loading model %s to %s' % (pfile, path))
proto = moose.loadModel(pfile, path,
'ee') # hsolve is not functional yet
for comp in proto[0].children:
comp.initVm = -75e-3
for chan in moose.wildcardFind('%s/##[ISA=HHChannel]'):
chan.Gbar *= tadj
return proto
def main(standalone=False):
mfile = os.path.join(os.path.dirname(__file__), 'OSC_diff_vols.g')
runtime = 4000.0
modelId = moose.loadModel(mfile, 'model', 'ee')
kin = moose.element('/model/kinetics')
compt1 = moose.element('/model/compartment_1')
compt1.x1 += kin.x1
compt1.x0 += kin.x1
fixXreacs.fixXreacs('/model')
#fixXreacs.restoreXreacs( '/model' )
#fixXreacs.fixXreacs( '/model' )
ks1 = moose.Ksolve('/model/kinetics/ksolve')
ds1 = moose.Dsolve('/model/kinetics/dsolve')
s1 = moose.Stoich('/model/kinetics/stoich')
s1.compartment = moose.element('/model/kinetics')
s1.ksolve = ks1
s1.dsolve = ds1
s1.path = '/model/kinetics/##'
ks2 = moose.Ksolve('/model/compartment_1/ksolve')
ds2 = moose.Dsolve('/model/compartment_1/dsolve')
s2 = moose.Stoich('/model/compartment_1/stoich')
s2.compartment = moose.element('/model/compartment_1')
s2.ksolve = ks2
s2.dsolve = ds2
s2.path = '/model/compartment_1/##'
ds2.buildMeshJunctions(ds1)
moose.reinit()
moose.start(runtime)
# I don't have an analytic way to assess oscillations
assert (countCrossings('/model/graphs/conc2/M.Co', 0.001) == 4)
moose.delete('/model')
def loadChem( neuroCompt, spineCompt, psdCompt ): # We need the compartments to come in with a volume of 1 to match the # original CubeMesh. assert( neuroCompt.volume == 1.0 ) assert( spineCompt.volume == 1.0 ) assert( psdCompt.volume == 1.0 ) assert( neuroCompt.mesh.num == 1 ) #print 'volume = ', neuroCompt.mesh[0].volume #assert( neuroCompt.mesh[0].volume == 1.0 ) #an unfortunate mismatch # So we'll have to resize the volumes of the current compartments to the # new ones. modelId = moose.loadModel( 'x_compt.g', '/model', 'ee' ) chem = moose.element( '/model/model' ) chem.name = 'chem' oldN = moose.element( '/model/chem/compartment_1' ) oldS = moose.element( '/model/chem/compartment_2' ) oldP = moose.element( '/model/chem/kinetics' ) oldN.volume = neuroCompt.mesh[0].volume oldS.volume = spineCompt.mesh[0].volume oldP.volume = psdCompt.mesh[0].volume moveCompt( '/model/chem/kinetics/DEND', oldN, neuroCompt ) moveCompt( '/model/chem/kinetics/SPINE', oldS, spineCompt ) moveCompt( '/model/chem/kinetics/PSD', oldP, psdCompt )
def create_neuron(model, ntype, ghkYN):
p_file = find_morph_file(model,ntype)
try:
cellproto=moose.loadModel(p_file, ntype)
except IOError:
print('could not load model from {!r}'.format(p_file))
raise
#######channels
Cond = model.Condset[ntype]
for comp in moose.wildcardFind('{}/#[TYPE=Compartment]'.format(ntype)):
#If we are using GHK, just create one GHK per compartment, connect it to comp
#calcium concentration is connected in a different function
if ghkYN:
ghkproto=moose.element('/library/ghk')
ghk=moose.copy(ghkproto,comp,'ghk')[0]
moose.connect(ghk,'channel',comp,'channel')
else:
ghk=[]
for channame in Cond.keys():
c = _util.distance_mapping(Cond[channame], comp)
if c > 0:
log.debug('Testing Cond If {} {}', channame, c)
calciumPermeable = model.Channels[channame].calciumPermeable
add_channel.addOneChan(channame, c, comp, ghkYN, ghk, calciumPermeable=calciumPermeable)
#Compensate for actual, experimentally estimated spine density.
#This gives a model that can be simulated with no explicit spines or
#any number of explicitly modeled spines up to the actual spine density:
spines.compensate_for_spines(model,comp,model.param_cond.NAME_SOMA)
return cellproto
def _loadElec( self, efile, elecname, combineSegments ):
library = moose.Neutral( '/library' )
if ( efile[ len( efile ) - 2:] == ".p" ):
self.elecid = moose.loadModel( efile, self.model.path + '/' + elecname )
else:
nm = NeuroML()
nm.readNeuroMLFromFile( efile, \
params = {'combineSegments': combineSegments, \
'createPotentialSynapses': True } )
if moose.exists( '/cells' ):
kids = moose.wildcardFind( '/cells/#' )
else:
kids = moose.wildcardFind( '/library/#[ISA=Neuron],/library/#[TYPE=Neutral]' )
if ( kids[0].name == 'spine' ):
kids = kids[1:]
assert( len( kids ) > 0 )
self.elecid = kids[0]
temp = moose.wildcardFind( self.elecid.path + '/#[ISA=CompartmentBase]' )
moose.move( self.elecid, self.model )
self.elecid.name = elecname
self._transformNMDAR( self.elecid.path )
kids = moose.wildcardFind( '/library/##[0]' )
for i in kids:
i.tick = -1
def test_symcomp_readcell():
model = moose.Neutral("/model")
cell = moose.loadModel("symcomp.p", "%s/cell" % (model.path))
pg = moose.PulseGen("/model/pulse")
pg.delay[0] = 10e-3
pg.width[0] = 20e-3
pg.level[0] = 1e-6
pg.delay[1] = 1e9
moose.connect(pg, "output", moose.element("/model/cell/d1"), "injectMsg")
data = moose.Neutral("/data")
tab_soma = moose.Table("%s/soma_Vm" % (data.path))
tab_d1 = moose.Table("%s/d1_Vm" % (data.path))
tab_d2 = moose.Table("%s/d2_Vm" % (data.path))
moose.connect(tab_soma, "requestOut", moose.element("/model/cell/soma"), "getVm")
moose.connect(tab_d1, "requestOut", moose.element("/model/cell/d1"), "getVm")
moose.connect(tab_d2, "requestOut", moose.element("/model/cell/d2"), "getVm")
moose.setClock(0, simdt)
moose.setClock(1, simdt)
moose.setClock(2, simdt)
moose.useClock(
0, "/model/##[ISA=Compartment]", "init"
) # This is allowed because SymCompartment is a subclass of Compartment
moose.useClock(1, "/model/##", "process")
moose.useClock(2, "/data/##[ISA=Table]", "process")
moose.reinit()
moose.start(simtime)
t = np.linspace(0, simtime, len(tab_soma.vector))
data_matrix = np.vstack((t, tab_soma.vector, tab_d1.vector, tab_d2.vector))
np.savetxt("symcompartment_readcell.txt", data_matrix.transpose())
pylab.plot(t, tab_soma.vector, label="Vm_soma")
pylab.plot(t, tab_d1.vector, label="Vm_d1")
pylab.plot(t, tab_d2.vector, label="Vm_d2")
pylab.show()
def conv(fname):
kfile = "./KKIT_MODELS/" + fname + ".g"
modelId = moose.loadModel("./KKIT_MODELS/" + fname + ".g", 'model',
'none')[0]
sfile = "./SBML_MODELS/" + fname + ".xml"
moose.mooseWriteSBML('/model', sfile)
moose.delete(modelId)
def _loadElec(self, efile, elecname, combineSegments):
library = moose.Neutral('/library')
if (efile[len(efile) - 2:] == ".p"):
self.elecid = moose.loadModel(efile,
self.model.path + '/' + elecname)
else:
nm = NeuroML()
nm.readNeuroMLFromFile( efile, \
params = {'combineSegments': combineSegments, \
'createPotentialSynapses': True } )
if moose.exists('/cells'):
kids = moose.wildcardFind('/cells/#')
else:
kids = moose.wildcardFind(
'/library/#[ISA=Neuron],/library/#[TYPE=Neutral]')
if (kids[0].name == 'spine'):
kids = kids[1:]
assert (len(kids) > 0)
self.elecid = kids[0]
temp = moose.wildcardFind(self.elecid.path +
'/#[ISA=CompartmentBase]')
moose.move(self.elecid, self.model)
self.elecid.name = elecname
self._transformNMDAR(self.elecid.path)
kids = moose.wildcardFind('/library/##[0]')
for i in kids:
i.tick = -1
def main():
#solver = "gsl" # Pick any of gsl, gssa, ee..
solver = "gssa" # Pick any of gsl, gssa, ee..
mfile = '../../Genesis_files/Repressillator.g'
runtime = 6000.0
if ( len( sys.argv ) >= 2 ):
solver = sys.argv[1]
modelId = moose.loadModel( mfile, 'model', solver )
# Increase volume so that the stochastic solver gssa
# gives an interesting output
compt = moose.element( '/model/kinetics' )
compt.volume = 1e-19
dt = moose.element( '/clock' ).dt
moose.reinit()
moose.start( runtime )
# Display all plots.
img = mpimg.imread( 'repressillatorOsc.png' )
fig = plt.figure( figsize=(12, 10 ) )
png = fig.add_subplot( 211 )
imgplot = plt.imshow( img )
ax = fig.add_subplot( 212 )
x = moose.wildcardFind( '/model/#graphs/conc#/#' )
plt.ylabel( 'Conc (mM)' )
plt.xlabel( 'Time (seconds)' )
for x in moose.wildcardFind( '/model/#graphs/conc#/#' ):
t = numpy.arange( 0, x.vector.size, 1 ) * dt
pylab.plot( t, x.vector, label=x.name )
pylab.legend()
pylab.show()
def loadAndRun(solver=True):
simtime = 500e-3
model = moose.loadModel('../data/h10.CNG.swc', '/cell')
comp = moose.element('/cell/apical_e_177_0')
soma = moose.element('/cell/soma')
for i in range(10):
moose.setClock(i, dt)
if solver:
solver = moose.HSolve('/cell/solver')
solver.target = soma.path
solver.dt = dt
stim = moose.PulseGen('/cell/stim')
stim.delay[0] = 50e-3
stim.delay[1] = 1e9
stim.level[0] = 1e-9
stim.width[0] = 2e-3
moose.connect(stim, 'output', comp, 'injectMsg')
tab = moose.Table('/cell/Vm')
moose.connect(tab, 'requestOut', comp, 'getVm')
tab_soma = moose.Table('/cell/Vm_soma')
moose.connect(tab_soma, 'requestOut', soma, 'getVm')
moose.reinit()
print('[INFO] Running for %s' % simtime)
moose.start(simtime )
vec = tab_soma.vector
moose.delete( '/cell' )
return vec
def runDoser( kkit, ht, plotPos, doseList, var = "Ca", title = "", BDNF = -1 ):
ax = plotBoilerplate( char[plotPos], plotPos, title, xlabel = "[{}] ($\mu$M)".format( var ), ylabel = "aS6K ($\mu$M)" )
ax.set_xscale( "log" )
modelId = moose.loadModel( kkit, 'model', 'gsl' )
tmoose = time.time()
if BDNF > 0.0:
moose.element( '/model/kinetics/BDNF' ).concInit = BDNF * 1e-3
x, y = doseRespMoose( var, doseList )
tmoose = time.time() - tmoose
ax.plot( x , y, label = "aS6K_vs_Ca_moose" )
mvec = np.array( y )
jsonDict = hillTau.loadHillTau( ht )
hillTau.scaleDict( jsonDict, hillTau.getQuantityScale( jsonDict ) )
model = hillTau.parseModel( jsonDict )
outputMolIndex = model.molInfo.get( "aS6K" ).index
doseMolIndex = model.molInfo.get( var ).index
if BDNF > 0.0:
model.conc[ model.molInfo.get( "BDNF" ).index ] = BDNF * 1e-3
model.concInit[ model.molInfo.get( "BDNF" ).index ] = BDNF * 1e-3
tht = time.time()
x, y = doseResp( model, doseMolIndex, outputMolIndex, doseList )
tht = time.time() - tht
ax.plot( x , y, label = "aS6K_vs_" + var )
ax.set_ylim( 0.0, 0.5 )
print( "dose_resp runtimes: t Moose = {:.2f}; t HillTau = {:.4f}: ".format( tmoose, tht) )
htvec = np.array( y )
dy = htvec - mvec
print( char[plotPos], ": Dose_resp normalized rms diff =", np.sqrt( np.mean( dy * dy )) / np.max( htvec ))
def create_comp_model(container_name, file_name, comp_RM=None, comp_CM=None, comp_RA=None, comp_ELEAK=None, comp_initVm=None):
'Create compartmental model from *.p file or a *.swc file.'
if file_name.endswith('.p'):
root_comp = moose.loadModel(file_name, container_name)
elif file_name.endswith('swc'):
assert comp_RM is not None, "comp_RM needs valid value."
assert comp_CM is not None, "comp_CM needs valid value."
assert comp_RA is not None, "comp_RA needs valid value."
assert comp_ELEAK is not None, "comp_ELEAK needs valid value."
assert comp_initVm is not None, "comp_initVm needs valid value."
root_comp = moose.loadModel(file_name, container_name)
for comp in moose.wildcardFind(root_comp.path+'/#[TYPE=Compartment]'):
set_comp_values(comp, comp_RM, comp_CM, comp_RA, comp_initVm, comp_ELEAK)
else:
raise "Invalid cell model file type."
return root_comp
def main():
"""
This example illustrates loading, and running a kinetic model
for a bistable positive feedback system, defined in kkit format.
This is based on Bhalla, Ram and Iyengar, Science 2002.
The core of this model is a positive feedback loop comprising of
the MAPK cascade, PLA2, and PKC. It receives PDGF and Ca2+ as
inputs.
This model is quite a large one and due to some stiffness in its
equations, it runs somewhat slowly.
The simulation illustrated here shows how the model starts out in
a state of low activity. It is induced to 'turn on' when a
a PDGF stimulus is given for 400 seconds.
After it has settled to the new 'on' state, model is made to
'turn off'
by setting the system calcium levels to zero for a while. This
is a somewhat unphysiological manipulation!
"""
solver = "gsl" # Pick any of gsl, gssa, ee..
#solver = "gssa" # Pick any of gsl, gssa, ee..
mfile = '../../Genesis_files/acc35.g'
runtime = 2000.0
if ( len( sys.argv ) == 2 ):
solver = sys.argv[1]
modelId = moose.loadModel( mfile, 'model', solver )
# Increase volume so that the stochastic solver gssa
# gives an interesting output
compt = moose.element( '/model/kinetics' )
compt.volume = 5e-19
moose.reinit()
moose.start( 500 )
moose.element( '/model/kinetics/PDGFR/PDGF' ).concInit = 0.0001
moose.start( 400 )
moose.element( '/model/kinetics/PDGFR/PDGF' ).concInit = 0.0
moose.start( 2000 )
moose.element( '/model/kinetics/Ca' ).concInit = 0.0
moose.start( 500 )
moose.element( '/model/kinetics/Ca' ).concInit = 0.00008
moose.start( 2000 )
# Display all plots.
img = mpimg.imread( 'mapkFB.png' )
fig = plt.figure( figsize=(12, 10 ) )
png = fig.add_subplot( 211 )
imgplot = plt.imshow( img )
ax = fig.add_subplot( 212 )
x = moose.wildcardFind( '/model/#graphs/conc#/#' )
t = numpy.arange( 0, x[0].vector.size, 1 ) * x[0].dt
ax.plot( t, x[0].vector, 'b-', label=x[0].name )
ax.plot( t, x[1].vector, 'c-', label=x[1].name )
ax.plot( t, x[2].vector, 'r-', label=x[2].name )
ax.plot( t, x[3].vector, 'm-', label=x[3].name )
plt.ylabel( 'Conc (mM)' )
plt.xlabel( 'Time (seconds)' )
pylab.legend()
pylab.show()
def loadChem():
chem = moose.Neutral( '/model/chem' )
modelId = moose.loadModel(
os.path.join( scriptDir, '..', 'genesis', 'chanPhosphByCaMKII.g' )
, '/model/chem', 'gsl'
)
nmstoich = moose.element( '/model/chem/kinetics/stoich' )
def main():
"""
This example illustrates loading and running a reaction system that
spans two volumes, that is, is in different compartments. It uses a
kkit model file. You can tell if it is working if you see nice
relaxation oscillations.
"""
# the kkit reader doesn't know how to do multicompt solver setup.
solver = "ee"
mfile = '../Genesis_files/OSC_diff_vols.g'
runtime = 3000.0
simDt = 1.0
modelId = moose.loadModel(mfile, 'model', solver)
#moose.delete( '/model/kinetics/A/Stot' )
compt0 = moose.element('/model/kinetics')
compt1 = moose.element('/model/compartment_1')
assert (deq(compt0.volume, 2e-20))
assert (deq(compt1.volume, 1e-20))
dy = compt0.dy
compt1.y1 += dy
compt1.y0 = dy
assert (deq(compt1.volume, 1e-20))
# We now have two cubes adjacent to each other. Compt0 has 2x vol.
# Compt1 touches it.
stoich0 = moose.Stoich('/model/kinetics/stoich')
stoich1 = moose.Stoich('/model/compartment_1/stoich')
ksolve0 = moose.Ksolve('/model/kinetics/ksolve')
ksolve1 = moose.Ksolve('/model/compartment_1/ksolve')
stoich0.compartment = compt0
stoich0.ksolve = ksolve0
stoich0.path = '/model/kinetics/##'
stoich1.compartment = compt1
stoich1.ksolve = ksolve1
stoich1.path = '/model/compartment_1/##'
#stoich0.buildXreacs( stoich1 )
print ksolve0.numLocalVoxels, ksolve0.numPools, stoich0.numAllPools
assert (ksolve0.numLocalVoxels == 1)
assert (ksolve0.numPools == 7)
assert (stoich0.numAllPools == 6)
print len(stoich0.proxyPools[stoich1]),
print len(stoich1.proxyPools[stoich0])
assert (len(stoich0.proxyPools[stoich1]) == 1)
assert (len(stoich1.proxyPools[stoich0]) == 1)
print ksolve1.numLocalVoxels, ksolve1.numPools, stoich1.numAllPools
assert (ksolve1.numLocalVoxels == 1)
assert (ksolve1.numPools == 6)
assert (stoich1.numAllPools == 5)
stoich0.buildXreacs(stoich1)
print moose.element('/model/kinetics/endo')
print moose.element('/model/compartment_1/exo')
moose.le('/model/compartment_1')
moose.reinit()
moose.start(runtime)
# Display all plots.
for x in moose.wildcardFind('/model/#graphs/conc#/#'):
t = numpy.arange(0, x.vector.size, 1) * simDt
pylab.plot(t, x.vector, label=x.name)
pylab.legend()
pylab.show()
def load_axon():
model = moose.loadModel("axon_passive.p", "/axon")
for x in model[0].children:
print x.path, x.class_
pulsegen = moose.PulseGen("/pulsegen")
pulsegen.delay[0] = simdt * 200 # The Axon.g in oldmoose flips the current every 20 pulses
pulsegen.width[0] = simdt * 200
pulsegen.level[0] = inject
moose.connect(pulsegen, "outputOut", moose.element("/axon/soma"), "injectMsg")
data = moose.Neutral("/data")
tab = moose.Table("%s/Vm100" % (data.path))
moose.connect(tab, "requestData", moose.ObjId("/axon/c100"), "get_Vm")
pulsetab = moose.Table("/data/inject")
moose.connect(pulsetab, "requestData", pulsegen, "get_output")
solver = moose.HSolve("/hsolve")
solver.dt = simdt
solver.target = model.path
return {
"model": model,
"Vm": tab,
"inject": pulsetab,
"soma": moose.element("/axon/soma"),
"pulse": pulsegen,
"solver": solver,
}
def read_prototype(celltype, cdict):
"""Read the cell prototype file for the specified class. The
channel properties are updated using values in cdict."""
filename = '%s/%s.p' % (config.modelSettings.protodir, celltype)
logger.debug('Reading prototype file %s' % (filename))
adjust_chanlib(cdict)
cellpath = '%s/%s' % (config.modelSettings.libpath, celltype)
if moose.exists(cellpath):
return moose.element(cellpath)
for handler in logger.handlers:
handler.flush()
proto = moose.loadModel(filename, cellpath)
# If prototype files do not have absolute compartment positions,
# set the compartment postions to origin. This will avoid
# incorrect assignemnt of position when the x/y/z values in
# prototype file is just to for setting the compartment length.
if not config.modelSettings.morph_has_postion:
for comp in moose.wildcardFind('%s/#[TYPE=Compartment]' % (proto.path)):
comp.x = 0.0
comp.y = 0.0
comp.z = 0.0
leveldict = read_keyvals('%s/%s.levels' % (config.modelSettings.protodir, celltype))
depths = read_keyvals('%s/%s.depths' % (config.modelSettings.protodir, celltype))
depthdict = {}
for level, depthset in list(depths.items()):
if len(depthset) != 1:
raise Exception('Depth set must have only one entry.')
depthdict[level] = depthset.pop()
assign_depths(proto, depthdict, leveldict)
config.logger.debug('Read %s with %d compartments' % (celltype, len(moose.wildcardFind('%s/#[TYPE=Compartment]' % (proto.path)))))
return proto
def runDoser(kkit, ht, plotPos, title=""):
ax = plotBoilerplate(char[plotPos],
plotPos,
title,
xlabel="[Ca] ($\mu$M)",
ylabel="[synAMPAR] ($\mu$M)")
ax.set_xscale("log")
ax.set_xlim(0.01, 10)
ax.set_ylim(0, 0.6)
modelId = moose.loadModel(kkit, 'model', 'gsl')
x, y = doseRespMoose()
ax.plot(x, y, label="Syn_vs_Ca_moose")
moosey = np.array(y)
jsonDict = hillTau.loadHillTau(ht)
hillTau.scaleDict(jsonDict, hillTau.getQuantityScale(jsonDict))
model = hillTau.parseModel(jsonDict)
outputMolIndex = model.molInfo.get("synAMPAR").index
CaMolIndex = model.molInfo.get("Ca").index
x, y = doseResp(model, CaMolIndex, outputMolIndex)
ax.plot(x, y, label="Syn_vs_Ca")
hty = np.array(y)
dy = moosey - hty
print("Dose-resp normalized rms diff =",
np.sqrt(np.mean(dy * dy)) / np.max(hty))
def main():
"""
This example illustrates loading, and running a kinetic model
for a bistable positive feedback system, defined in kkit format.
This is based on Bhalla, Ram and Iyengar, Science 2002.
The core of this model is a positive feedback loop comprising of
the MAPK cascade, PLA2, and PKC. It receives PDGF and Ca2+ as
inputs.
This model is quite a large one and due to some stiffness in its
equations, it runs somewhat slowly.
The simulation illustrated here shows how the model starts out in
a state of low activity. It is induced to 'turn on' when a
a PDGF stimulus is given for 400 seconds.
After it has settled to the new 'on' state, model is made to
'turn off'
by setting the system calcium levels to zero for a while. This
is a somewhat unphysiological manipulation!
"""
solver = "gsl" # Pick any of gsl, gssa, ee..
#solver = "gssa" # Pick any of gsl, gssa, ee..
mfile = '../../genesis/acc35.g'
runtime = 2000.0
if ( len( sys.argv ) == 2 ):
solver = sys.argv[1]
modelId = moose.loadModel( mfile, 'model', solver )
# Increase volume so that the stochastic solver gssa
# gives an interesting output
compt = moose.element( '/model/kinetics' )
compt.volume = 5e-19
moose.reinit()
moose.start( 500 )
moose.element( '/model/kinetics/PDGFR/PDGF' ).concInit = 0.0001
moose.start( 400 )
moose.element( '/model/kinetics/PDGFR/PDGF' ).concInit = 0.0
moose.start( 2000 )
moose.element( '/model/kinetics/Ca' ).concInit = 0.0
moose.start( 500 )
moose.element( '/model/kinetics/Ca' ).concInit = 0.00008
moose.start( 2000 )
# Display all plots.
img = mpimg.imread( 'mapkFB.png' )
fig = plt.figure( figsize=(12, 10 ) )
png = fig.add_subplot( 211 )
imgplot = plt.imshow( img )
ax = fig.add_subplot( 212 )
x = moose.wildcardFind( '/model/#graphs/conc#/#' )
t = numpy.arange( 0, x[0].vector.size, 1 ) * x[0].dt
ax.plot( t, x[0].vector, 'b-', label=x[0].name )
ax.plot( t, x[1].vector, 'c-', label=x[1].name )
ax.plot( t, x[2].vector, 'r-', label=x[2].name )
ax.plot( t, x[3].vector, 'm-', label=x[3].name )
plt.ylabel( 'Conc (mM)' )
plt.xlabel( 'Time (seconds)' )
pylab.legend()
pylab.show()
def main():
"""
This example illustrates loading and running a reaction system that
spans two volumes, that is, is in different compartments. It uses a
kkit model file. You can tell if it is working if you see nice
relaxation oscillations.
"""
# the kkit reader doesn't know how to do multicompt solver setup.
solver = "ee"
mfile = '../Genesis_files/OSC_diff_vols.g'
runtime = 3000.0
simDt = 1.0
modelId = moose.loadModel( mfile, 'model', solver )
#moose.delete( '/model/kinetics/A/Stot' )
compt0 = moose.element( '/model/kinetics' )
compt1 = moose.element( '/model/compartment_1' )
assert( deq( compt0.volume, 2e-20 ) )
assert( deq( compt1.volume, 1e-20 ) )
dy = compt0.dy
compt1.y1 += dy
compt1.y0 = dy
assert( deq( compt1.volume, 1e-20 ) )
# We now have two cubes adjacent to each other. Compt0 has 2x vol.
# Compt1 touches it.
stoich0 = moose.Stoich( '/model/kinetics/stoich' )
stoich1 = moose.Stoich( '/model/compartment_1/stoich' )
ksolve0 = moose.Ksolve( '/model/kinetics/ksolve' )
ksolve1 = moose.Ksolve( '/model/compartment_1/ksolve' )
stoich0.compartment = compt0
stoich0.ksolve = ksolve0
stoich0.path = '/model/kinetics/##'
stoich1.compartment = compt1
stoich1.ksolve = ksolve1
stoich1.path = '/model/compartment_1/##'
#stoich0.buildXreacs( stoich1 )
print ksolve0.numLocalVoxels, ksolve0.numPools, stoich0.numAllPools
assert( ksolve0.numLocalVoxels == 1 )
assert( ksolve0.numPools == 7 )
assert( stoich0.numAllPools == 6 )
print len( stoich0.proxyPools[stoich1] ),
print len( stoich1.proxyPools[stoich0] )
assert( len( stoich0.proxyPools[stoich1] ) == 1 )
assert( len( stoich1.proxyPools[stoich0] ) == 1 )
print ksolve1.numLocalVoxels, ksolve1.numPools, stoich1.numAllPools
assert( ksolve1.numLocalVoxels == 1 )
assert( ksolve1.numPools == 6 )
assert( stoich1.numAllPools == 5 )
stoich0.buildXreacs( stoich1 )
print moose.element( '/model/kinetics/endo' )
print moose.element( '/model/compartment_1/exo' )
moose.le( '/model/compartment_1' )
moose.reinit()
moose.start( runtime )
# Display all plots.
for x in moose.wildcardFind( '/model/#graphs/conc#/#' ):
t = numpy.arange( 0, x.vector.size, 1 ) * simDt
pylab.plot( t, x.vector, label=x.name )
pylab.legend()
pylab.show()
def loadAndRun(solver=True):
simtime = 500e-3
model = moose.loadModel('../data/h10.CNG.swc', '/cell')
comp = moose.element('/cell/apical_e_177_0')
soma = moose.element('/cell/soma')
for i in range(10):
moose.setClock(i, dt)
if solver:
solver = moose.HSolve('/cell/solver')
solver.target = soma.path
solver.dt = dt
stim = moose.PulseGen('/cell/stim')
stim.delay[0] = 50e-3
stim.delay[1] = 1e9
stim.level[0] = 1e-9
stim.width[0] = 2e-3
moose.connect(stim, 'output', comp, 'injectMsg')
tab = moose.Table('/cell/Vm')
moose.connect(tab, 'requestOut', comp, 'getVm')
tab_soma = moose.Table('/cell/Vm_soma')
moose.connect(tab_soma, 'requestOut', soma, 'getVm')
moose.reinit()
print('[INFO] Running for %s' % simtime)
moose.start(simtime )
vec = tab_soma.vector
moose.delete( '/cell' )
return vec
def main():
"""
This is a toy model of synaptic bidirectional plasticity. The model has
a small a bistable chemical switch, and a small set of reactions that
decode calcium input. One can turn the switch on with short high
calcium pulses (over 2 uM for about 10 sec). One can turn it back off
again using a long, lower calcium pulse (0.2 uM, 2000 sec).
"""
method = 'old_gssa' # This is the Gillespie Stoichastic Systems Algorithm
if (len(sys.argv) >= 2):
method = sys.argv[1]
if (method == "gsl"):
method = "old_gsl"
if (method == "gssa"):
method = "old_gssa"
# Load in the model and set up to use the specified method
modelId = moose.loadModel('./stargazin_synapse.g', 'model', method)
moose.start(1000.0) # Run the model for 1000 seconds.
Ca = moose.element('/model/kinetics/BULK/Ca')
applyInputPulseTrain(Ca, 'concInit', [(1000.0, 1.0e-3), (10.0, 0.08e-3),
(50.0, 1.0e-3), (10.0, 0.08e-3),
(1000.0, 0.2e-3), (2000.0, 0.08e-3)])
moose.start(2000.0)
displayPlots()
quit()
def read_prototype(celltype, cdict):
"""Read the cell prototype file for the specified class. The
channel properties are updated using values in cdict."""
filename = '%s/%s.p' % (config.modelSettings.protodir, celltype)
logger.debug('Reading prototype file %s' % (filename))
adjust_chanlib(cdict)
cellpath = '%s/%s' % (config.modelSettings.libpath, celltype)
if moose.exists(cellpath):
return moose.element(cellpath)
for handler in logger.handlers:
handler.flush()
proto = moose.loadModel(filename, cellpath)
# If prototype files do not have absolute compartment positions,
# set the compartment postions to origin. This will avoid
# incorrect assignemnt of position when the x/y/z values in
# prototype file is just to for setting the compartment length.
if not config.modelSettings.morph_has_postion:
for comp in moose.wildcardFind('%s/#[TYPE=Compartment]' % (proto.path)):
comp.x = 0.0
comp.y = 0.0
comp.z = 0.0
leveldict = read_keyvals('%s/%s.levels' % (config.modelSettings.protodir, celltype))
depths = read_keyvals('%s/%s.depths' % (config.modelSettings.protodir, celltype))
depthdict = {}
for level, depthset in list(depths.items()):
if len(depthset) != 1:
raise Exception('Depth set must have only one entry.')
depthdict[level] = depthset.pop()
assign_depths(proto, depthdict, leveldict)
config.logger.debug('Read %s with %d compartments' % (celltype, len(moose.wildcardFind('%s/#[TYPE=Compartment]' % (proto.path)))))
return proto
def main():
"""Test main: load a model and display the tree for it"""
model = moose.Neutral('/model')
moose.loadModel('../Demos/Genesis_files/Kholodenko.g', '/model/Kholodenko')
# tab = moose.element('/model/Kholodenko/graphs/conc1/MAPK_PP.Co')
# print tab
# for t in tab.children:
# print t
app = QtGui.QApplication(sys.argv)
mainwin = QtGui.QMainWindow()
mainwin.setWindowTitle('Model tree test')
tree = MooseTreeWidget()
tree.recreateTree(root='/model/Kholodenko')
mainwin.setCentralWidget(tree)
mainwin.show()
sys.exit(app.exec_())
def make_prototype(passive=True):
path = '%s/rc19' % (library.path)
pfile = 'rc19.p'
try:
return moose.element(path)
except ValueError:
pass
if not passive:
make_na()
make_kv()
make_km()
make_kca()
make_cat()
make_cahva()
make_h()
try:
proto = moose.element(path)
except ValueError:
print('Loading model %s to %s' % (pfile, path))
proto = moose.loadModel(pfile, path, 'ee') # hsolve is not functional yet
for comp in proto[0].children:
comp.initVm = -75e-3
for chan in moose.wildcardFind('%s/##[ISA=HHChannel]'):
chan.Gbar *= tadj
return proto
def main():
"""
This is a toy model of synaptic bidirectional plasticity. The model has
a small a bistable chemical switch, and a small set of reactions that
decode calcium input. One can turn the switch on with short high
calcium pulses (over 2 uM for about 10 sec). One can turn it back off
again using a long, lower calcium pulse (0.2 uM, 2000 sec).
"""
method = 'old_gssa' # This is the Gillespie Stoichastic Systems Algorithm
if ( len( sys.argv ) >= 2 ):
method = sys.argv[1]
if ( method == "gsl" ):
method = "old_gsl"
if ( method == "gssa" ):
method = "old_gssa"
# Load in the model and set up to use the specified method
modelId = moose.loadModel( './stargazin_synapse.g', 'model', method )
moose.start( 1000.0 ) # Run the model for 1000 seconds.
Ca = moose.element( '/model/kinetics/BULK/Ca' )
applyInputPulseTrain(Ca, 'concInit'
, [ (1000.0, 1.0e-3)
, (10.0, 0.08e-3)
, (50.0, 1.0e-3)
, (10.0, 0.08e-3)
, (1000.0, 0.2e-3)
, (2000.0, 0.08e-3)
]
)
moose.start(2000.0)
displayPlots()
quit()
def main():
# Schedule the whole lot
moose.setClock(4, 0.1) # for the computational objects
moose.setClock(5, 0.2) # clock for the solver
moose.setClock(8, 1.0) # for the plots
# The wildcard uses # for single level, and ## for recursive.
#compartment = makeModel()
moose.loadModel('../../genesis/M1719.g', '/model', 'ee')
compartment = moose.element('model/kinetics')
compartment.name = 'compartment'
ksolve = moose.Ksolve('/model/compartment/ksolve')
stoich = moose.Stoich('/model/compartment/stoich')
stoich.compartment = compartment
stoich.ksolve = ksolve
#ksolve.stoich = stoich
stoich.path = "/model/compartment/##"
state = moose.SteadyState('/model/compartment/state')
moose.useClock(5, '/model/compartment/ksolve', 'process')
moose.useClock(8, '/model/graphs/#', 'process')
moose.reinit()
state.stoich = stoich
#state.showMatrices()
state.convergenceCriterion = 1e-7
for i in range(0, 50):
getState(ksolve, state)
moose.start(100.0) # Run the model for 100 seconds.
b = moose.element('/model/compartment/b')
c = moose.element('/model/compartment/c')
# move most molecules over to b
b.conc = b.conc + c.conc * 0.95
c.conc = c.conc * 0.05
moose.start(100.0) # Run the model for 100 seconds.
# move most molecules back to a
c.conc = c.conc + b.conc * 0.95
b.conc = b.conc * 0.05
moose.start(100.0) # Run the model for 100 seconds.
# Iterate through all plots, dump their contents to data.plot.
displayPlots()
quit()
def main():
# Setup parameters for simulation and plotting
simdt = 1e-2
plotDt = 1
# Factors to change in the dose concentration in log scale
factorExponent = 10 ## Base: ten raised to some power.
factorBegin = -20
factorEnd = 21
factorStepsize = 1
factorScale = 10.0 ## To scale up or down the factors
# Load Model and set up the steady state solver.
# model = sys.argv[1] # To load model from a file.
model = './19085.cspace'
modelPath, modelName, modelType = parseModelName(model)
outputDir = modelPath
modelId = moose.loadModel(model, 'model', 'ee')
dosePath = '/model/kinetics/b/DabX' # The dose entity
ksolve, state = setupSteadyState(simdt, plotDt)
vol = moose.element('/model/kinetics').volume
iterInit = 100
solutionVector = []
factorArr = []
enz = moose.element(dosePath)
init = float(enz.kcat) # Dose parameter
# Change Dose here to .
for factor in range(factorBegin, factorEnd, factorStepsize):
scale = factorExponent**(factor / factorScale)
enz.kcat = init * scale
print("scale={:.3f}\tkcat={:.3f}".format(scale, enz.kcat))
for num in range(iterInit):
stateType, solStatus, a, vector = getState(ksolve, state, vol)
if solStatus == 0:
#solutionVector.append(vector[0]/sum(vector))
solutionVector.append(a)
factorArr.append(scale)
joint = np.array([factorArr, solutionVector])
joint = joint[:, joint[1, :].argsort()]
# Plot dose response. Remove NaN from the values else plotting will fail.
ax = plt.subplot()
# plt.semilogx was failing. not sure why. That is why this convoluted
# approach.
ax.plot(joint[0, :], joint[1, :], marker="o", label='concA')
ax.set_xscale('log')
plt.xlabel('Dose')
plt.ylabel('Response')
plt.suptitle('Dose-Reponse Curve for a bistable system')
plt.legend(loc=3)
#plt.savefig(outputDir + "/" + modelName +"_doseResponse" + ".png")
plt.show()
quit()
def main():
# Setup parameters for simulation and plotting
simdt= 1e-2
plotDt= 1
# Factors to change in the dose concentration in log scale
factorExponent = 10 ## Base: ten raised to some power.
factorBegin = -20
factorEnd = 21
factorStepsize = 1
factorScale = 10.0 ## To scale up or down the factors
# Load Model and set up the steady state solver.
# model = sys.argv[1] # To load model from a file.
model = './19085.cspace'
modelPath, modelName, modelType = parseModelName(model)
outputDir = modelPath
modelId = moose.loadModel(model, 'model', 'ee')
dosePath = '/model/kinetics/b/DabX' # The dose entity
ksolve, state = setupSteadyState( simdt, plotDt)
vol = moose.element( '/model/kinetics' ).volume
iterInit = 100
solutionVector = []
factorArr = []
enz = moose.element(dosePath)
init = float(enz.kcat) # Dose parameter
# Change Dose here to .
for factor in range(factorBegin, factorEnd, factorStepsize ):
scale = factorExponent ** (factor/factorScale)
enz.kcat = init * scale
print( "scale={:.3f}\tkcat={:.3f}".format( scale, enz.kcat) )
for num in range(iterInit):
stateType, solStatus, a, vector = getState( ksolve, state, vol)
if solStatus == 0:
#solutionVector.append(vector[0]/sum(vector))
solutionVector.append(a)
factorArr.append(scale)
joint = np.array([factorArr, solutionVector])
joint = joint[:,joint[1,:].argsort()]
# Plot dose response. Remove NaN from the values else plotting will fail.
ax = plt.subplot()
# plt.semilogx was failing. not sure why. That is why this convoluted
# approach.
ax.plot( joint[0,:], joint[1,:] , marker="o", label = 'concA')
ax.set_xscale( 'log' )
plt.xlabel('Dose')
plt.ylabel('Response')
plt.suptitle('Dose-Reponse Curve for a bistable system')
plt.legend(loc=3)
#plt.savefig(outputDir + "/" + modelName +"_doseResponse" + ".png")
plt.show()
quit()
def load_neuron_file(fileName, cellPath, Rm, Ra, Cm, initVm):
cell = moose.loadModel(fileName, cellPath)
for child in cell[0].children:
for comp in child:
comp.Rm = Rm
comp.Ra = Ra
comp.Cm = Cm
comp.initVm = initVm
def create_swc_model(root_name, file_name, RM, CM, RA, ELEAK, initVM):
if file_name.endswith('.swc'):
root_comp = moose.loadModel(file_name, root_name)
else:
raise ValueError("Please provide valid swc file as input.")
for comp in moose.wildcardFind(root_comp.path+'/#[TYPE=Compartment]'):
set_comp_values(comp, RM, CM, RA, initVM, ELEAK)
return root_comp
def main():
# The wildcard uses # for single level, and ## for recursive.
#compartment = makeModel()
moose.loadModel('../Genesis_files/M1719.cspace', '/model', 'ee')
compartment = moose.element('model/kinetics')
compartment.name = 'compartment'
ksolve = moose.Ksolve('/model/compartment/ksolve')
stoich = moose.Stoich('/model/compartment/stoich')
stoich.compartment = compartment
stoich.ksolve = ksolve
#ksolve.stoich = stoich
stoich.path = "/model/compartment/##"
state = moose.SteadyState('/model/compartment/state')
moose.reinit()
state.stoich = stoich
#state.showMatrices()
state.convergenceCriterion = 1e-7
moose.le('/model/graphs')
a = moose.element('/model/compartment/a')
b = moose.element('/model/compartment/b')
c = moose.element('/model/compartment/c')
for i in range(0, 100):
getState(ksolve, state)
moose.start(100.0) # Run the model for 100 seconds.
b = moose.element('/model/compartment/b')
c = moose.element('/model/compartment/c')
# move most molecules over to b
b.conc = b.conc + c.conc * 0.95
c.conc = c.conc * 0.05
moose.start(100.0) # Run the model for 100 seconds.
# move most molecules back to a
c.conc = c.conc + b.conc * 0.95
b.conc = b.conc * 0.05
moose.start(100.0) # Run the model for 100 seconds.
# Iterate through all plots, dump their contents to data.plot.
displayPlots()
quit()
def main():
"""
The script demonstates to convert Chemical (Genesis) file back to Genesis
file using moose
"""
model = moose.loadModel(os.path.join( cwd, '../genesis/reaction.g'), '/model')
written = moose.mooseWriteKkit('/model', 'testsave.g')
print( written )
def main():
"""
This example illustrates parameter tweaking. It uses a kinetic model
for a relaxation oscillator, defined in kkit format.
We use the gsl solver here.
The model looks like this::
_________
| |
V |
M-----Enzyme---->M* All in compartment A
|\ /| ^
| \___basal___/ |
| |
endo |
| exo
| _______ |
| | \ |
V V \ |
M-----Enzyme---->M* All in compartment B
\ /|
\___basal___/
The way it works: We set the run off for a few seconds with the original
model parameters. This version oscillates. Then we double the endo
and exo forward rates and run it further to show that the period becomes
nearly twice as fast. Then we restore endo and exo, and instead double
the initial amounts of M. We run it further again to see what happens.
This model takes several seconds to run.
"""
mfile = '../genesis/OSC_Cspace.g'
runtime = 4000.0
modelId = moose.loadModel( mfile, 'model', 'gsl' )
moose.reinit()
moose.start( runtime )
# Here begins the parameter tweaking.
# Now we double the rates of the endo and exo reactions.
endo = moose.element( '/model/kinetics/endo' )
endo.Kf *= 2.0
exo = moose.element( '/model/kinetics/exo' )
exo.Kf *= 2.0
moose.start( runtime ) # run it again
# Now we restore rates, but double the total amount of M.
endo.Kf /= 2.0
exo.Kf /= 2.0
M = moose.element( '/model/kinetics/A/M' )
M.conc += M.concInit # concInit was the starting concentration.
moose.start( runtime ) # run it again
# Now plot the whole lot.
for x in moose.wildcardFind( '/model/#graphs/conc#/#' ):
pylab.plot( x.vector, label=x.name )
pylab.legend()
pylab.show()
def makeModel(): makeChannelPrototypes() cellId = moose.loadModel( 'dotp.p', '/model', 'Neutral' ) moose.element( '/model/soma' ).inject = 1.7e-9 graphs = moose.Neutral( '/graphs' ) addPlot( '/model/soma', 'getVm', 'somaVm' ) addPlot( '/model/apical_14', 'getVm', 'midVm' ) addPlot( '/model/lat_15_2', 'getVm', 'latVm' ) addPlot( '/model/apical_19', 'getVm', 'tipVm' )
def main():
# Setup parameters for simulation and plotting
simdt= 1e-2
plotDt= 1
# Factors to change in the dose concentration in log scale
factorExponent = 10 ## Base: ten raised to some power.
factorBegin = -20
factorEnd = 21
factorStepsize = 1
factorScale = 10.0 ## To scale up or down the factors
# Load Model and set up the steady state solver.
# model = sys.argv[1] # To load model from a file.
model = './19085.cspace'
modelPath, modelName, modelType = parseModelName(model)
outputDir = modelPath
modelId = moose.loadModel(model, 'model', 'ee')
dosePath = '/model/kinetics/b/DabX' # The dose entity
ksolve, state = setupSteadyState( simdt, plotDt)
vol = moose.element( '/model/kinetics' ).volume
iterInit = 1000
solutionVector = []
factorArr = []
enz = moose.element(dosePath)
init = enz.kcat # Dose parameter
# Change Dose here to .
for factor in range(factorBegin, factorEnd, factorStepsize ):
scale = factorExponent ** (factor/factorScale)
enz.kcat = init * scale
print factor
for num in range(iterInit):
stateType, solStatus, vector = getState( ksolve, state, vol)
if solStatus == 0:
solutionVector.append(vector[0]/sum(vector))
factorArr.append(scale)
joint = np.array([factorArr, solutionVector])
joint = joint[:,joint[1,:].argsort()]
# Plot dose response.
fig0 = plt.figure()
pylab.semilogx(joint[0,:],joint[1,:],marker="o",label = 'concA')
pylab.xlabel('Dose')
pylab.ylabel('Response')
pylab.suptitle('Dose-Reponse Curve for a bistable system')
pylab.legend(loc=3)
plt.savefig(outputDir + "/" + modelName +"_doseResponse" + ".png")
plt.show()
plt.close(fig0)
quit()
def createMultiCompCell(file_name, container_name, library_name, comp_type, channelSet, condSet,
rateParams, CaParams = None, CaPoolParams = None, HCNParams = None,
cell_RM = None, cell_CM = None, cell_RA = None, cell_initVm = None,
cell_Em = None):
# Create the channel types and store them in a library to be used by each compartment
# in the model
createChanLib(library_name, channelSet, rateParams, CaParams, HCNParams)
# Load in the model in question
if file_name.endswith('.p'):
cell = moose.loadModel(file_name, container_name)
for comp in moose.wildcardFind(cell.path + '/' + '#[TYPE=' + comp_type + ']'):
for chan_name, cond in condSet.items():
SA = np.pi*comp.length*comp.diameter
proto = moose.element(library_name + '/' + chan_name)
chan = moose.copy(proto, comp, chan_name)[0]
chan.Gbar = cond*SA
m = moose.connect(chan, 'channel', comp, 'channel')
# Add the calcium pool to each compartment in the cell if it has been specified
if (CaPoolParams != None):
add_calcium(library_name, cell, CaPoolParams, comp_type)
for key in channelSet.keys():
if ("Ca" in key):
connect_cal2chan(channelSet[key].name, channelSet[key].chan_type, cell,
CaPoolParams.caName, comp_type)
else:
cell = moose.loadModel(file_name, container_name)
setCompParameters(cell, comp_type, cell_RM, cell_CM, cell_RA, cell_initVm, cell_Em)
for comp in moose.wildcardFind(cell.path + '/' + '#[TYPE=' + comp_type + ']'):
for chan_name, cond in condSet.items():
SA = np.pi*comp.length*comp.diameter
proto = moose.element(library_name + '/' + chan_name)
chan = moose.copy(proto, comp, chan_name)[0]
chan.Gbar = cond*SA
m = moose.connect(chan, 'channel', comp, 'channel')
# Add the calcium pool to each compartment in the cell if it has been specified
if (CaPoolParams != None):
add_calcium(library_name, cell, CaPoolParams, comp_type)
for key in channelSet.keys():
if ("Ca" in key):
connect_cal2chan(channelSet[key].name, channelSet[key].chan_type, cell,
CaPoolParams.caName, comp_type)
return cell