Update outdated example notebooks

.github/workflows/test.yml

@@ -55,6 +55,23 @@ jobs:
       uses: codecov/codecov-action@v3
       with:
         fail_ci_if_error: false
+
+  examples:
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.9"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip install tox-gh-actions
+    - name: Run tox
+      run: |
+        tox -e examples
+
   docs:
     runs-on: ubuntu-22.04
     steps:

.gitignore

@@ -21,3 +21,4 @@ bin
 *.ipynb_checkpoints
 lib
 fllog.txt
+*.DS_Store

examples/deap/GranuleCell1/GranuleCell1.py

@@ -63,7 +63,7 @@ def __init__(self, conductances):
 
 def steps(step_number, parameters):
 
-      # instantiate the class
+    # instantiate the class
     cell = GrCmono(parameters)
 
     # no table are in use from the mod files
@@ -130,8 +130,7 @@ def steps(step_number, parameters):
         stim3[0].dur = stimdata['stim2dur']
         stim3[0].amp = stimdata['stim2amp']
 
-        # Code to record everything.
-
+    # Code to record everything.
     time = h.Vector()
     time.record(h._ref_t)
 

examples/deap/GranuleCell1/GranuleCellDeap1-scoop.py

@@ -13,6 +13,7 @@
 import efel
 import numpy as np
 import GranuleCell1 as grcsteps
+import bluepyopt.deapext
 
 from scoop import futures
 
@@ -36,7 +37,6 @@
 from deap import base
 from deap import creator
 from deap import tools
-from deap import algorithms
 
 FEATURES = ['voltage_base',
             'Spikecount',
@@ -175,17 +175,15 @@ def uniform(lower_list, upper_list, dimensions):
 toolbox.register("mate", deap.tools.cxSimulatedBinaryBounded, eta=ETA, low=LOWER, up=UPPER)
 toolbox.register("mutate", deap.tools.mutPolynomialBounded, eta=ETA, low=LOWER, up=UPPER, indpb=0.1)
 toolbox.register("variate", deap.algorithms.varAnd)
-toolbox.register("select", plot_selector, selector=tools.selIBEA)
+toolbox.register("select", plot_selector, selector=bluepyopt.deapext.tools.selIBEA)
 toolbox.register("map", futures.map)
-# toolbox.register("select", tools.selIBEA)
-# toolbox.register("select", tools.selIBEA)
 
 def main():
     pop = toolbox.population(n=MU)
-    pop, logbook = algorithms.eaAlphaMuPlusLambda(pop, toolbox, MU,
-                                                  None, CXPB, 1 - CXPB,
-                                                  NGEN, verbose=False)
+    pop, logbook = bluepyopt.deapext.algorithms.eaAlphaMuPlusLambdaCheckpoint(pop, toolbox, MU,
+                                                   CXPB, 1 - CXPB,
+                                                  NGEN)
     return pop, logbook
 
 if __name__ == '__main__':
-    print main()
+    main()

examples/deap/deap_efel.py

@@ -39,7 +39,7 @@
 # The higher this value, the more spread
 ETA = 10.0
 
-# Seletor to use
+# Selector to use
 SELECTOR = "NSGA2"
 
 # Number of parameters
@@ -51,7 +51,7 @@
 
 # Create a fitness function
 # By default DEAP selector will try to optimise fitness values,
-# so we add a -1 weight value to minise
+# so we add a -1 weight value to minimise
 creator.create("Fitness", base.Fitness, weights=[-1.0] * 2)
 
 # Create an individual that consists of a list

examples/nmc-portal/mechanisms/Grc_kca.mod

@@ -0,0 +1,99 @@
+TITLE Cerebellum Granule Cell Model
+
+COMMENT
+	Reference: Theta-Frequency Bursting and Resonance in Cerebellar Granule Cells:Experimental
+	Evidence and Modeling of a Slow K+-Dependent Mechanism
+	Egidio D'Angelo,Thierry Nieus,Arianna Maffei,Simona Armano,Paola Rossi,Vanni Taglietti,
+	Andrea Fontana and Giovanni Naldi
+ENDCOMMENT
+
+NEURON { 
+	SUFFIX GrC_KCa 
+	USEION k READ ek WRITE ik 
+	USEION ca READ cai
+	RANGE gkbar, ik, ica, g, alpha_c, beta_c
+	RANGE Aalpha_c, Balpha_c, Kalpha_c
+	RANGE Abeta_c, Bbeta_c, Kbeta_c 
+	RANGE c_inf, tau_c 
+} 
+
+UNITS { 
+	(mA) = (milliamp) 
+	(mV) = (millivolt) 
+	(molar) = (1/liter)
+	(mM) = (millimolar)
+} 
+
+PARAMETER { 
+	Aalpha_c = 2.5 (/ms)
+	Balpha_c = 1.5e-3 (mM)
+
+	:Kalpha_c = -0.085 (/mV)
+	Kalpha_c =  -11.765 (mV)
+
+	Abeta_c = 1.5 (/ms)
+	Bbeta_c = 0.15e-3 (mM)
+
+	:Kbeta_c = -0.085 (/mV)
+	Kbeta_c = -11.765 (mV)
+
+	v (mV) 
+	cai (mM)
+	gkbar= 0.004 (mho/cm2) 
+	ek = -84.69 (mV) 
+	celsius = 30 (degC) 
+} 
+
+STATE { 
+	c 
+} 
+
+ASSIGNED { 
+	ik (mA/cm2) 
+	ica (mA/cm2)
+
+	c_inf 
+	tau_c (ms) 
+	g (mho/cm2) 
+	alpha_c (/ms) 
+	beta_c (/ms) 
+} 
+
+INITIAL { 
+	rate(v) 
+	c = c_inf 
+} 
+
+BREAKPOINT { 
+	SOLVE states METHOD derivimplicit 
+	g = gkbar*c 
+	ik = g*(v - ek) 
+	alpha_c = alp_c(v) 
+	beta_c = bet_c(v) 
+} 
+
+DERIVATIVE states { 
+	rate(v) 
+	c' =(c_inf - c)/tau_c 
+} 
+
+FUNCTION alp_c(v(mV))(/ms) { LOCAL Q10
+	Q10 = 3^((celsius-30(degC))/10(degC))
+	alp_c = Q10*Aalpha_c/(1+(Balpha_c*exp(v/Kalpha_c)/cai)) 
+} 
+
+FUNCTION bet_c(v(mV))(/ms) { LOCAL Q10
+	Q10 = 3^((celsius-30(degC))/10(degC))
+	bet_c = Q10*Abeta_c/(1+cai/(Bbeta_c*exp(v/Kbeta_c))) 
+} 
+
+PROCEDURE rate(v (mV)) {LOCAL a_c, b_c 
+	TABLE c_inf, tau_c 
+	DEPEND Aalpha_c, Balpha_c, Kalpha_c, 
+	       Abeta_c, Bbeta_c, Kbeta_c, celsius FROM -100 TO 100 WITH 200 
+	a_c = alp_c(v)  
+	b_c = bet_c(v) 
+	tau_c = 1/(a_c + b_c) 
+	c_inf = a_c/(a_c + b_c) 
+} 
+

examples/nmc-portal/mechanisms/Grc_lkg2.mod

@@ -0,0 +1,36 @@
+TITLE Cerebellum Granule Cell Model
+
+COMMENT
+	Reference: Theta-Frequency Bursting and Resonance in Cerebellar Granule Cells:Experimental
+	Evidence and Modeling of a Slow K+-Dependent Mechanism
+	Egidio D'Angelo,Thierry Nieus,Arianna Maffei,Simona Armano,Paola Rossi,Vanni Taglietti,
+	Andrea Fontana and Giovanni Naldi
+ENDCOMMENT
+
+NEURON { 
+	SUFFIX GrC_Lkg2 
+	NONSPECIFIC_CURRENT il
+	RANGE egaba, ggaba , i
+} 
+
+UNITS { 
+	(mA) = (milliamp) 
+	(mV) = (millivolt) 
+} 
+
+PARAMETER { 
+	v (mV) 
+	ggaba = 2.17e-5 (mho/cm2)
+	celsius = 30 (degC)
+	egaba = -65 (mV)
+} 
+
+ASSIGNED { 
+	il (mA/cm2) 
+	i (mA/cm2) 
+}
+
+BREAKPOINT { 
+	il = ggaba*(v - egaba) 
+	i =il
+} 

examples/nmc-portal/mechanisms/Grg_kv.mod

@@ -0,0 +1,97 @@
+TITLE Cerebellum Granule Cell Model
+
+COMMENT
+	Reference: Theta-Frequency Bursting and Resonance in Cerebellar Granule Cells:Experimental
+	Evidence and Modeling of a Slow K+-Dependent Mechanism
+	Egidio D'Angelo,Thierry Nieus,Arianna Maffei,Simona Armano,Paola Rossi,Vanni Taglietti,
+	Andrea Fontana and Giovanni Naldi
+ENDCOMMENT
+
+NEURON { 
+	SUFFIX GrG_KV 
+	USEION k READ ek WRITE ik 
+	RANGE gkbar, ik, g, alpha_n, beta_n 
+	RANGE Aalpha_n, Kalpha_n, V0alpha_n
+	RANGE Abeta_n, Kbeta_n, V0beta_n
+	RANGE n_inf, tau_n 
+} 
+
+UNITS { 
+	(mA) = (milliamp) 
+	(mV) = (millivolt) 
+} 
+
+PARAMETER { 
+	:Kbeta_n = -0.0125 (/mV)
+
+	Aalpha_n = -0.01 (/ms-mV)
+	Kalpha_n = -10 (mV)
+	V0alpha_n = -25 (mV)
+	Abeta_n = 0.125 (/ms)
+
+	Kbeta_n = -80 (mV)
+	V0beta_n = -35 (mV)
+	v (mV)  
+	gkbar= 0.003 (mho/cm2) 
+	ek = -84.69 (mV) 
+	celsius = 30 (degC) 
+} 
+
+STATE { 
+	n 
+} 
+
+ASSIGNED { 
+	ik (mA/cm2) 
+	n_inf 
+	tau_n (ms) 
+	g (mho/cm2) 
+	alpha_n (/ms) 
+	beta_n (/ms) 
+} 
+
+INITIAL { 
+	rate(v) 
+	n = n_inf 
+} 
+
+BREAKPOINT { 
+	SOLVE states METHOD derivimplicit 
+	g = gkbar*n*n*n*n 
+	ik = g*(v - ek) 
+	alpha_n = alp_n(v) 
+	beta_n = bet_n(v) 
+} 
+
+DERIVATIVE states { 
+	rate(v) 
+	n' =(n_inf - n)/tau_n 
+} 
+
+FUNCTION alp_n(v(mV))(/ms) { LOCAL Q10
+	Q10 = 3^((celsius-6.3(degC))/10(degC)) 
+	alp_n = Q10*Aalpha_n*linoid(v-V0alpha_n, Kalpha_n)
+} 
+
+FUNCTION bet_n(v(mV))(/ms) { LOCAL Q10
+	Q10 = 3^((celsius-6.3(degC))/10(degC)) 
+	bet_n = Q10*Abeta_n*exp((v-V0beta_n)/Kbeta_n) 
+} 
+
+PROCEDURE rate(v (mV)) {LOCAL a_n, b_n 
+	TABLE n_inf, tau_n 
+	DEPEND Aalpha_n, Kalpha_n, V0alpha_n, 
+               Abeta_n, Kbeta_n, V0beta_n, celsius FROM -100 TO 100 WITH 200 
+	a_n = alp_n(v)  
+	b_n = bet_n(v) 
+	tau_n = 1/(a_n + b_n) 
+	n_inf = a_n/(a_n + b_n) 
+} 
+
+FUNCTION linoid(x (mV),y (mV)) (mV) {
+        if (fabs(x/y) < 1e-6) {
+                linoid = y*(1 - x/y/2)
+        }else{
+                linoid = x/(exp(x/y) - 1)
+        }
+}