Merge branch 'development' into neuroml_updates

* development:
  fixed loading netParams in some scenarios (bug caused by srting functions pre-processing)
  improvements in netParams validation (API and some error messages)
  Raster plot colored by phase + bug fixes
  Update cell input functions in netpyne/cell/inputs.py and user reference (#781)
  docstring for Batch (#780)
  extracted conditions checking code to separate method
  Fixed loading point cell params from legacy models (iincl. ssue 607). Re-factored cell class detection in pop.py
  Change type of geom, mechs and synMechs to accept string functions expressions
  Add metadata for sub-cellular connectivity
  Revert "Merge branch 'development' of https://github.com/suny-downstate-medical-center/netpyne into development"

CHANGES.md

@@ -1,3 +1,21 @@
+# Version in development
+
+**New features**
+
+- Raster plot colored by phase
+
+- Examples based on the CA3 model using the 'colorbyPhase' option in the plotRaster
+
+**Bug fixes**
+
+- Fixed loading point cell params from legacy models (issue 607)
+
+- Fix voltage movie tutorial
+
+- Fix to automatically include netstims in the sim.allSimData object when plotRaster 'include' selects 'all'
+
+- Fixed loading netParams in some scenarios (bug caused by srting functions pre-processing)
+
 # Version 1.0.5
 
 **New features**

doc/source/user_documentation.rst

@@ -305,7 +305,7 @@ Currently, 'rhythmic', 'evoked', 'poisson' and 'gauss' spike pattern generators
 
 * **evoked** - creates the ongoing external inputs (rhythmic)
 
-    * **start** - time of first spike. if -1, uniform distribution between startMin and startMax (ms)
+    * **start** - time of first spike
 
     * **inc** - increase in time of first spike; from cfg.inc_evinput (ms)
 

examples/CA3model_RasterColoredbyPhase/index.npjson

@@ -0,0 +1,6 @@
+{
+    "mod_folder": "mod",
+    "simConfig": "src/cfg.py",
+    "python_run": "src/init.py",
+    "netParams": "src/netParams.py"
+}

examples/CA3model_RasterColoredbyPhase/mod/CA1ih.mod

@@ -0,0 +1,64 @@
+: $Id: CA1ih.mod,v 1.4 2010/12/13 21:35:47 samn Exp $ 
+TITLE Ih CA3
+
+UNITS {
+  (mA) = (milliamp)
+  (mV) = (millivolt)
+}
+
+NEURON {
+  SUFFIX hcurrent
+  NONSPECIFIC_CURRENT ih
+  RANGE g, e, v50, htau, hinf
+  RANGE gfactor
+}
+
+PARAMETER {
+  celsius	(degC)
+  g= 0.0001	(mho/cm2)
+  e= -30	(mV)
+  v50=-82	(mV)
+  gfactor = 1
+}
+
+STATE {
+  h
+}
+
+ASSIGNED {
+  ih	  (mA/cm2) 
+  hinf
+  htau    (ms)
+  v	  (mV)
+}
+
+PROCEDURE iassign () { ih=g*h*(v-e)*gfactor }
+
+BREAKPOINT {
+  SOLVE states METHOD cnexp
+  iassign()
+}
+
+DERIVATIVE states { 
+  rates(v)
+  h'= (hinf- h)/ htau
+}
+
+INITIAL { 
+  rates(v)
+  h = hinf
+  iassign()
+}
+
+PROCEDURE rates(v (mV)) {
+  UNITSOFF
+  : HCN1
+  :hinf = 1/(1+exp(0.151*(v-v50)))
+  :htau = exp((0.033*(v+75)))/(0.011*(1+exp(0.083*(v+75))))
+
+  : HCN2
+  hinf = 1/(1+exp((v-v50)/10.5))
+  htau = (1/(exp(-14.59-0.086*v)+exp(-1.87+0.0701*v))) 
+  UNITSON
+}
+

examples/CA3model_RasterColoredbyPhase/mod/CA1ika.mod

@@ -0,0 +1,85 @@
+: $Id: CA1ika.mod,v 1.2 2010/12/01 05:06:07 samn Exp $ 
+TITLE Ika CA1
+
+UNITS {
+  (mA) = (milliamp)
+  (mV) = (millivolt)
+}
+
+NEURON {
+  SUFFIX kacurrent
+  NONSPECIFIC_CURRENT ika, ikad
+  RANGE g, gd, e, ninf, ntau, ndinf, ndtau, linf, ltau
+}
+
+PARAMETER {
+  celsius	(degC)
+  g= 0.048	(mho/cm2)
+  gd= 0		(mho/cm2)
+  e= -90	(mV)
+}
+
+STATE {
+  n
+  nd : distal
+  l
+}
+
+ASSIGNED {
+  v	(mV)
+  ika	(mA/cm2) 
+  ikad	(mA/cm2)
+  ninf
+  ntau  (ms)
+  ndinf
+  ndtau (ms)
+  linf
+  ltau	(ms)
+}
+
+PROCEDURE iassign () {
+  ika=g*n*l*(v-e)
+  ikad=gd*nd*l*(v-e)
+}
+
+BREAKPOINT {
+  SOLVE states METHOD cnexp
+  iassign()
+}
+
+DERIVATIVE states { 
+  rates(v)
+  n'= (ninf- n)/ ntau
+  l'= (linf- l)/ ltau
+  nd'= (ndinf-nd)/ndtau
+}
+
+INITIAL { 
+  rates(v)
+  n = ninf
+  l = linf
+  iassign()
+}
+
+PROCEDURE rates(v (mV)) {
+  LOCAL  a, b
+  UNITSOFF
+  a = exp(-0.038*(1.5+1/(1+exp(v+40)/5))*(v-11))
+  b =	exp(-0.038*(0.825+1/(1+exp(v+40)/5))*(v-11))
+  ntau=4*b/(1+a)
+  if (ntau<0.1) {ntau=0.1}
+  ninf=1/(1+a)
+
+  a=exp(-0.038*(1.8+1/(1+exp(v+40)/5))*(v+1))
+  b=exp(-0.038*(0.7+1/(1+exp(v+40)/5))*(v+1))
+  ndtau=2*b/(1+a)
+  if (ndtau<0.1) {ndtau=0.1}
+  ndinf=1/(1+a)
+
+  a = exp(0.11*(v+56))
+  ltau=0.26*(v+50)
+  if (ltau<2) {ltau=2}
+  linf=1/(1+a)
+  UNITSON
+}
+

examples/CA3model_RasterColoredbyPhase/mod/CA1ikdr.mod

@@ -0,0 +1,60 @@
+: $Id: CA1ikdr.mod,v 1.2 2010/12/01 05:10:52 samn Exp $ 
+TITLE IKDR CA1
+
+UNITS {
+  (mA) = (milliamp)
+  (mV) = (millivolt)
+}
+
+NEURON {
+  SUFFIX kdrcurrent
+  NONSPECIFIC_CURRENT ik
+  RANGE g, e, ninf, ntau
+}
+
+PARAMETER {
+  celsius	(degC)
+  g = 0.010	(mho/cm2)
+  e = -90	(mV)
+}
+
+STATE {
+  n 
+}
+
+ASSIGNED {
+  v	  (mV)
+  ik	  (mA/cm2) 
+  ninf
+  ntau    (ms)
+}
+
+PROCEDURE iassign () { ik=g*n*(v-e) }
+
+BREAKPOINT {
+  SOLVE states METHOD cnexp
+  iassign()
+}
+
+DERIVATIVE states { 
+  rates(v)
+  n'= (ninf- n)/ ntau
+}
+
+INITIAL { 
+  rates(v)
+  n = ninf
+  iassign()
+}
+
+PROCEDURE rates(v (mV)) {
+  LOCAL  a, b
+  UNITSOFF
+  a = exp(-0.11*(v-13))
+  b = exp(-0.08*(v-13)) 	
+  ntau=50*b/(1+a)
+  if (ntau<2) {ntau=2}
+  ninf=1/(1+a)
+  UNITSON
+}
+

examples/CA3model_RasterColoredbyPhase/mod/CA1ina.mod

@@ -0,0 +1,89 @@
+: $Id: CA1ina.mod,v 1.4 2010/11/30 19:50:00 samn Exp $ 
+TITLE INa CA1
+
+UNITS {
+  (mA) = (milliamp)
+  (mV) = (millivolt)
+}
+
+NEURON {
+  SUFFIX nacurrent
+  NONSPECIFIC_CURRENT ina
+  RANGE g, e, vi, ki
+  RANGE minf,hinf,iinf,mtau,htau,itau : testing
+}
+
+PARAMETER {
+  : v	    (mV)
+  celsius	    (degC)
+  g = 0.032   (mho/cm2)
+  e = 55	    (mV)
+  vi = -60    (mV)
+  ki = 0.8
+}
+
+STATE {
+  m
+  h
+  I : i 
+}
+
+ASSIGNED {
+  i (mA/cm2)
+  ina	(mA/cm2) 
+  minf
+  mtau    (ms)
+  hinf
+  htau	(ms)
+  iinf
+  itau	(ms)
+  v	(mV) : testing
+}
+
+: PROCEDURE iassign () { ina=g*m*m*m*h*i*(v-e) }
+PROCEDURE iassign () { i=g*m*m*m*h*I*(v-e) ina=i}
+
+BREAKPOINT {
+  SOLVE states METHOD cnexp
+  iassign()
+}
+
+DERIVATIVE states { 
+  rates(v)
+  m' = (minf - m) / mtau
+  h' = (hinf - h) / htau
+  : i' = (iinf - i) / itau	    
+  I' = (iinf - I) / itau	    
+}
+
+INITIAL { 
+  rates(v)
+  h = hinf
+  m = minf
+  : i = iinf
+  I = iinf
+  iassign() : testing
+}
+
+
+PROCEDURE rates(v (mV)) {
+  LOCAL  a, b
+  UNITSOFF
+  a = 0.4*(v+30)/(1-exp(-(v+30)/7.2))
+  b = 0.124*(v+30)/(exp((v+30)/7.2)-1) 	
+  mtau=0.5/(a+b)
+  if (mtau<0.02) {mtau=0.02}
+  minf=a/(a+b)
+  a = 0.03*(v+45)/(1-exp(-(v+45)/1.5))
+  b = 0.01*(v+45)/(exp((v+45)/1.5)-1)
+  htau=0.5/(a+b)
+  if (htau<0.5) {htau=0.5}
+  hinf=1/(1+exp((v+50)/4))
+  a =	exp(0.45*(v+66))
+  b = exp(0.09*(v+66))
+  itau=3000*b/(1+a)
+  if (itau<10) {itau=10}
+  iinf=(1+ki*exp((v-vi)/2))/(1+exp((v-vi)/2))
+  UNITSON
+}
+