Changeset 726 for trunk/src/moose/cells.py

Timestamp:

03/11/10 15:24:33 (2 years ago)

Author:

apdavison

Message:

Resumed implementation of the moose module. HH_cond_exp2.py example runs and gives the same results with moose as with neuron (nest is different - need to figure out why).

Files:

• trunk/src/moose/cells.py (modified) (3 diffs)

trunk/src/moose/cells.py

@@ -1 @@
-from pyNN import common, cells
+import moose
+from pyNN import standardmodels, cells
+
+mV = 1e-3
+ms = 1e-3
+nA = 1e-9
+
+class SingleCompHH(moose.Neutral):
+    
+    def __init__(self, path, GbarNa=0.0, GbarK=0.0, GLeak=0.0, Cm=1.0,
+                 ENa=40*mV, EK=-90*mV, VLeak=-65*mV, Voff=-63*mV, ESynE=0*mV,
+                 ESynI=-70*mV, tauE=2*ms, tauI=5*ms, inject=0*nA, initVm=-65*mV):
+        moose.Neutral.__init__(self, path)
+        self.comp = moose.Compartment("compartment", self)
+        print "compartment is at %s" % self.comp.path
+        print locals()
+        self.comp.initVm = initVm
+        self.comp.Rm = 1/GLeak
+        self.comp.Cm = Cm
+        self.comp.Em = VLeak
+        self.comp.inject = inject
+        self.na = moose.HHChannel("na", self.comp)
+        self.na.Ek = ENa
+        self.na.Gbar = GbarNa
+        self.na.Xpower = 3
+        self.na.Ypower = 1
+        self.na.setupAlpha("X", 3.2e5 * (13*mV+Voff), -3.2e5, -1, -(13*mV+Voff), -4*mV, # alpha
+                               -2.8e5 * (40*mV+Voff),  2.8e5, -1, -(40*mV+Voff), 5*mV)  # beta
+        self.na.setupAlpha("Y", 128,                   0,      0, -(17*mV+Voff), 18*mV, # alpha
+                                4.0e3,                 0,      1, -(40*mV+Voff), -5*mV) # beta
+
+        self.k = moose.HHChannel("k", self.comp)
+        self.k.Ek = EK
+        self.k.Gbar = GbarK
+        self.k.Xpower = 4
+        self.k.setupAlpha("X", 3.2e4 * (15*mV+Voff), -3.2e4, -1, -(15*mV+Voff), -5*mV,
+                               500,                  0,       0, -(10*mV+Voff),  40*mV)
+
+        #self.synE = moose.SynChan("excitatory", self.comp)
+        #self.synE.Ek = ESynE
+        #self.synE.tau1 = 1e-6
+        #self.synE.tau2 = tauE
+        #self.synE.Gbar = 1e-9
+        #self.synI = moose.SynChan("inhibitory", self.comp)
+        #self.synI.Ek = ESynI
+        #self.synI.tau1 = 1e-6
+        #self.synI.tau2 = tauI
+        #self.synI.Gbar = 1e-9
+    
+        #self.comp.connect("channel", self.synE, "channel")
+        #self.comp.connect("channel", self.synI, "channel")
+        self.comp.connect("channel", self.na, "channel")
+        self.comp.connect("channel", self.k , "channel")
+        
+        self.comp.useClock(0)
+        self.comp.useClock(1, "init")
+
+    def record_v(self):
+        self.vmTable = moose.Table("Vm", self)
+        self.vmTable.stepMode = 3
+        self.vmTable.connect("inputRequest", self.comp, "Vm")
+        self.vmTable.useClock(2)
+        print "vmTable is at %s" % self.vmTable.path
+        #moose.PyMooseBase.getContext().useClock(0, self.comp.path+"/##")
+
+#a = SingleCompHH("/comp", 1e-9, 1e-9, 1e-9, 1e-12, -0.06, 0.08, -0.06, 0.001, 0.05, -0.05, 1e-2, 2e-2, 1e-9, -0.06)
+#print "Successfully setup SingleCompHH"
+
+
 
 class HH_cond_exp(cells.HH_cond_exp):
     """Single compartment cell with an Na channel and a K channel"""
-    translations = common.build_translations(
+    translations = standardmodels.build_translations(
         ('gbar_Na',    'GbarNa', 1e-9),   
         ('gbar_K',     'GbarK', 1e-9),    
@@ -11 +79 @@
         ('e_rev_Na',   'ENa', 1e-3),
         ('e_rev_K',    'EK', 1e-3), 
-        ('e_rev_leak', 'Vleak', 1e-3),
+        ('e_rev_leak', 'VLeak', 1e-3),
         ('e_rev_E',    'ESynE', 1e-3),
         ('e_rev_I',    'ESynI', 1e-3),
@@ -19 +87 @@
         ('v_init',     'initVm', 1e-3),
     )
-    moose_name = "SingleCompHH"
+    model = SingleCompHH