Cerebellar purkinje cell (De Schutter and Bower 1994)

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Accession:7176
Tutorial simulation of a cerebellar Purkinje cell. This tutorial is based upon a GENESIS simulation of a cerebellar Purkinje cell, modeled and fine-tuned by Erik de Schutter. The tutorial assumes that you have a basic knowledge of the Purkinje cell and its synaptic inputs. It gives visual insight in how different properties as concentrations and channel conductances vary and interact within a real Purkinje cell.
Reference:
1 . De Schutter E, Bower JM (1994) An active membrane model of the cerebellar Purkinje cell. I. Simulation of current clamps in slice. J Neurophysiol 71:375-400 [PubMed]
2 . De Schutter E, Bower JM (1994) An active membrane model of the cerebellar Purkinje cell II. Simulation of synaptic responses. J Neurophysiol 71:401-19 [PubMed]
3 . Staub C, De Schutter E, Knöpfel T (1994) Voltage-imaging and simulation of effects of voltage- and agonist-activated conductances on soma-dendritic voltage coupling in cerebellar Purkinje cells. J Comput Neurosci 1:301-11 [PubMed]
4 . De Schutter E, Bower JM (1994) Simulated responses of cerebellar Purkinje cells are independent of the dendritic location of granule cell synaptic inputs. Proc Natl Acad Sci U S A 91:4736-40 [PubMed]
5 . De Schutter E (1998) Dendritic voltage and calcium-gated channels amplify the variability of postsynaptic responses in a Purkinje cell model. J Neurophysiol 80:504-19 [PubMed]
6 . Jaeger D, De Schutter E, Bower JM (1997) The role of synaptic and voltage-gated currents in the control of Purkinje cell spiking: a modeling study. J Neurosci 17:91-106 [PubMed]
7 . de Schutter E (1994) Modelling the cerebellar Purkinje cell: experiments in computo. Prog Brain Res 102:427-41 [PubMed]
8 . De Schutter E (1997) A new functional role for cerebellar long-term depression. Prog Brain Res 114:529-42 [PubMed]
9 . Steuber V, Mittmann W, Hoebeek FE, Silver RA, De Zeeuw CI, Häusser M, De Schutter E (2007) Cerebellar LTD and pattern recognition by Purkinje cells. Neuron 54:121-36 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s): Cerebellum Purkinje GABA cell;
Channel(s): I Na,p; I Na,t; I T low threshold; I p,q; I A; I K; I M; I K,Ca; I Sodium; I Calcium; I Potassium;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: GENESIS;
Model Concept(s): Activity Patterns; Dendritic Action Potentials; Active Dendrites; Detailed Neuronal Models; Tutorial/Teaching; Synaptic Integration;
Implementer(s): Cornelis, Hugo [hugo at bbf.uia.ac.be]; Airong, Dong [tard at fimmu.com];
Search NeuronDB for information about:  Cerebellum Purkinje GABA cell; I Na,p; I Na,t; I T low threshold; I p,q; I A; I K; I M; I K,Ca; I Sodium; I Calcium; I Potassium; 
prcs: Producing diffs from 0.58 to parpat-storage-film.3.
Index: 0.58/xgraph.g
--- 0.58/xgraph.g Mon, 24 Jul 2000 17:38:55 +0200 hugo (purkinje/20_xgraph.g 1.13.1.1.1.1.2.1.2.1 644)
+++ parpat-storage-film.3/xgraph.g Wed, 27 Sep 2000 11:39:30 +0200 hugo (purkinje/20_xgraph.g 1.13.1.1.1.1.2.1.2.1.1.1 640)
@@ -23,6 +23,11 @@
 
 // xgraph.g : xgraph functionality
 
+
+//v default color for plots
+
+int iDefaultPlotColor = 38
+
 int include_xgraph
 
 if ( {include_xgraph} == 0 )
@@ -49,7 +54,7 @@
 
 function XGraphPlotColor
 
-	//- get next available color
+	//- get next color
 
 	int color = {getfield /xgraphs/graph cNextColor}
 
@@ -79,7 +84,7 @@
 
 	//- modulo 64 to get a legal value
 
-	color = {color + 18} % 64
+	color = {color + 19} % 64
 
 	//- increment the color count
 
@@ -194,7 +199,7 @@
 
 function XGraphNextPlotMode(mode)
 
-str path
+str mode
 
 	//v result of function
 
@@ -1172,6 +1177,7 @@
 		xmax {runtime / 1000} \
 		ymin -0.1 \
 		ymax 0.05 \
+		bg white \
 		XUnits "t (sec)" 
 
 	//- add a button to clear the graph
@@ -1228,7 +1234,7 @@
 	//- add an initialized field for allocated colors
 
 	addfield /xgraphs/graph cNextColor -descr "next color to allocate"
-	setfield /xgraphs/graph cNextColor 1
+	setfield /xgraphs/graph cNextColor {iDefaultPlotColor}
 
 	//- set clock to use for graph
 
@@ -1481,6 +1487,12 @@
 	//- register next output mode
 
 	XGraphNextPlotMode {xcOutputValue}
+
+	// reset next plot color
+
+	//! don't do this, read the comments in XCellCBAddPlot why.
+
+	//setfield /xgraphs/graph cNextColor {iDefaultPlotColor}
 end
 
 
Index: 0.58/xcell.g
--- 0.58/xcell.g Thu, 30 Mar 2000 16:43:16 +0200 hugo (purkinje/21_xcell.g 1.1.1.6.1.5.2.6.1.1.2.1 644)
+++ parpat-storage-film.3/xcell.g Wed, 27 Sep 2000 11:39:30 +0200 hugo (purkinje/21_xcell.g 1.1.1.6.1.5.2.6.1.1.2.1.1.2 640)
@@ -117,6 +117,9 @@
 //////////////////////////////////////////////////////////////////////////////
 
 
+include movie.g
+
+
 //v bool to indicate first toggle for tabchannel has been created
 
 int bButtonsCreated = 0
@@ -129,6 +132,10 @@
 
 str strXCLibrary = "XCLib"
 
+//v movie handle for xcell widget
+
+str xcellMovieHandle = ""
+
 
 ///
 /// SH:	XCellElectrodeName
@@ -1964,13 +1971,46 @@
 		-offlabel "No Electrodes" \
 		-script "XCellSetupElectrodes <v>"
 
-	//- create label as seperator
+/*
+** original code from -r 0
+**
+*/
+/* 	//- create label as seperator */
+
+/* 	create xlabel /xcell/sep3 \ */
+/* 		-xgeom 70% \ */
+/* 		-ygeom 6:graph.top \ */
+/* 		-wgeom 30% \ */
+/* 		-title "" */
+
+	//- create button for film settings
 
-	create xlabel /xcell/sep3 \
+	create xbutton /xcell/filmSettings \
 		-xgeom 70% \
-		-ygeom 6:graph.top \
-		-wgeom 30% \
-		-title ""
+		-ygeom 4:graph.top \
+		-wgeom 20% \
+		-title "Settings" \
+		-script "echo Film settings"
+
+	//- create toggle to enable filming
+
+	create xtoggle /xcell/filmToggle \
+		-xgeom 0:filmSettings.right \
+		-ygeom 4:graph.top \
+		-wgeom 10% \
+		-title "Film" \
+		-script "XCellCBScheduleMovie <value>"
+
+	//- remove previous movie images
+
+	sh "rm 2>/dev/null -f /tmp/movies/*"
+
+	//- create movie elements
+
+	sh "mkdir 2>/dev/null /tmp/movies"
+
+	xcellMovieHandle \
+		= {MovieCreateElements /xcell/ /tmp/movies/purkinje 0 0}
 
 	//- create toggle to change normalized / absolute output
 
@@ -2177,6 +2217,10 @@
 	//! the field cNextColor should be considered private,
 	//! but read the comments below to understand why I had to
 	//! read it as if it is public.
+	//!
+	//! With this public read it becomes more difficult to decide if the
+	//! graph should do a reset (and skipping back to the default color)
+	//! Modularity with genesis scripts can be tough...
 
 	//- get allocated color
 
@@ -2210,6 +2254,66 @@
 
 			XCellAddElectrode {path} {electrode} {color}
 		end
+	end
+end
+
+
+///
+/// SH:	XCellCBScheduleMovie
+///
+/// PA:	movieHandle...:	movie handle to schedule
+///	bOn...........: 1 == schedule, 0 == do not schedule
+///
+/// DE:	Rechedule a movie handle
+///
+/// NO: It seems impossible to pass variable from Xodus script fields,
+///	hardcoded {{xcellMovieHandle}}
+///
+
+function XCellCBScheduleMovie(bOn)
+
+int bOn
+
+	//- if turn on
+
+	if ( {bOn} == 1 )
+
+		//- diag's
+
+		echo "Enabling movie "{{xcellMovieHandle}}
+
+		//- schedule
+
+		MovieSchedule \
+			{{xcellMovieHandle}} \
+			/tmp/movies/purkinje \
+			{getstat -step} \
+			10000000
+
+	//- else if turn off
+
+	elif ( {bOn} == 0 )
+
+		//- diag's
+
+		echo "Disabling movie "{{xcellMovieHandle}}
+
+		//- schedule
+
+		MovieSchedule \
+			{{xcellMovieHandle}} \
+			/tmp/movies/purkinje \
+			0 \
+			0
+
+	//- else
+
+	else
+
+		//- diag's
+
+		echo "XCellCBScheduleMovie : Wrong mode requested for movie"
+
 	end
 end
 
Index: 0.58/settings.g
--- 0.58/settings.g Wed, 05 Jan 2000 11:55:14 +0100 hugo (purkinje/23_settings.g 1.8.2.2.1.1.1.1.1.1 644)
+++ parpat-storage-film.3/settings.g Fri, 29 Sep 2000 20:06:06 +0200 hugo (purkinje/23_settings.g 1.8.2.2.1.1.1.1.1.1.2.2 640)
@@ -23,6 +23,12 @@
 
 // settings.g : control panel settings
 
+
+//v normal path for xcell script
+
+str cbXCell
+
+
 int include_settings
 
 if ( {include_settings} == 0 )
@@ -33,9 +39,13 @@
 include actions.g
 
 
-//v normal path for xcell script
+function SettingsPFStored
 
-str cbXCell
+end
+
+function SettingsPFNovel
+
+end
 
 
 ///
@@ -815,7 +825,7 @@
 
 	create xlabel nooffset \
 		-ygeom 3:pulse \
-		-title "Offset not available"
+		-title "Amplitude not available"
 
 	//- hide the offset dialog
 
@@ -825,7 +835,7 @@
 
 	create xlabel nowidth \
 		-ygeom 3:offset \
-		-title "Width not  available"
+		-title "Width not available"
 
 	//- hide the width dialog
 
@@ -1476,7 +1486,7 @@
 
 	str element
 
-	foreach element ( {el {cellpath}/##[][TYPE=synchan]} )
+	foreach element ( {el {cellpath}/##[][TYPE=channelC3]} )
 
 		//- for vitro mode
 
Index: 0.58/info.g
--- 0.58/info.g Fri, 29 Oct 1999 21:02:10 +0200 hugo (purkinje/28_info.g 1.4.2.1 644)
+++ parpat-storage-film.3/info.g Wed, 27 Sep 2000 11:39:30 +0200 hugo (purkinje/28_info.g 1.4.2.1.1.1 640)
@@ -125,7 +125,7 @@
 		-xgeom 200 \
 		-ygeom 330 \
 		-wgeom 450 \
-		-hgeom 200
+		-hgeom 230
 
 	//- make created form current element
 
Index: 0.58/credits.txt
--- 0.58/credits.txt Mon, 25 Jan 1999 16:30:02 +0100 hugo (purkinje/30_credits.tx 1.1 644)
+++ parpat-storage-film.3/credits.txt Sun, 11 Jul 1999 22:37:50 +0200 hugo (purkinje/30_credits.tx 1.1.1.2 640)
@@ -2,9 +2,9 @@
 Purkinje tutorial : credits
 ---------------------------
 
+Purkinje cell model. Erik De Schutter and Jim M. Bower
 functional ideas ... Erik De Schutter, erik@bbf.uia.ac.be
 genesis coding ..... Hugo Cornelis, hugo@bbf.uia.ac.be
+documentation ...... Hugo Cornelis, Erik De Schutter
 
-general feedback ... Reinoud Maex, Erik De Schutter
-
-
+general feedback ... Reinoud Maex, Volker Steuber
Index: 0.58/control.g
--- 0.58/control.g Mon, 24 Jul 2000 16:00:59 +0200 hugo (purkinje/31_control.g 1.14.1.1.2.1.1.1.1.1.1.1.1.2 664)
+++ parpat-storage-film.3/control.g Wed, 27 Sep 2000 11:39:30 +0200 hugo (purkinje/31_control.g 1.14.1.1.2.1.1.1.1.1.1.1.1.2.1.1 640)
@@ -181,10 +181,20 @@
 
 	int steps = time / 1000 / dt
 
-	//- give an informational message
-
 	echo "Running simulation for "{steps}" steps"
 
+	// prepare the input files
+
+	filecnt = {rand_int {filenum/2 - 75} {filenum/2 - 1}}
+        infile1 = (infile) @ (filecnt) @ ".dat"
+	echo stored PF pattern is {infile1}
+        setfield /infileStored nx {spinenum} ny 1 filename {infile1} leave_open 1
+        
+        filecnt = {rand_int {filenum/2} {filenum/2 + 74}}
+        infile1 = (infile) @ (filecnt) @ ".dat"
+	echo novel PF pattern is {infile1}
+        setfield /infileNovel nx {spinenum} ny 1 filename {infile1} leave_open 1
+
 	//- do the simulation steps
 
 	step {steps} -background
@@ -339,6 +349,18 @@
 
 		ActionClimbingStart {strength}
 
+	elif (action == 4)
+
+		echo "Presenting stored PF pattern"
+
+	        ActionPFPatternStart "/infileStored"
+
+	elif (action == 5)
+
+		echo "Presenting novel PF pattern"
+
+		ActionPFPatternStart "/infileNovel"
+
 	//- else we have an unkown action
 
 	else
@@ -640,7 +662,7 @@
 
 	create xdialog time \
 		-value {runtime} \
-		-title "time (msec) : " \
+		-title "Time (msec) : " \
 		-script "SetRunTime <v>"
 
 	//- create the time step dialog
@@ -756,18 +778,48 @@
 		-title "Settings" \
 		-script "SettingsIClamp"
 
+
+	create xbutton pfstored \
+		-wgeom 70% \
+		-title "Stored PF pattern" \
+		-script "ToggleAction 4"
+
+	//- create settings button
+
+	create xbutton PFStoredSettings \
+		-xgeom 0:last.right \
+		-ygeom 0:iClamp \
+		-wgeom 30% \
+		-title "Settings" \
+		-script "SettingsPFStored"
+
+
+	create xbutton pfnovel \
+		-wgeom 70% \
+		-title "Novel PF pattern" \
+		-script "ToggleAction 5"
+
+	//- create settings button
+
+	create xbutton PFNovelSettings \
+		-xgeom 0:last.right \
+		-ygeom 0:pfstored \
+		-wgeom 30% \
+		-title "Settings" \
+		-script "SettingsPFNovel"
+
 	//- create the parallel fiber button
 
 	create xbutton parallel \
 		-wgeom 70% \
-		-title "Activate parallel fibers" \
+		-title "Random synchr PFs" \
 		-script "ToggleAction 1"
 
 	//- create settings button
 
 	create xbutton parallelSettings \
 		-xgeom 0:last.right \
-		-ygeom 0:iClamp \
+		-ygeom 0:pfnovel \
 		-wgeom 30% \
 		-title "Settings" \
 		-script "SettingsParallel"
@@ -806,7 +858,7 @@
 
 	//- create information label
 
-	create xlabel info \
+/*	create xlabel info \
 		-title "Simulation information"
 
 	//- create help button
@@ -825,6 +877,7 @@
 		-wgeom 50% \
 		-title "Credits" \
 		-script "InfoCredits"
+*/
 
 	//- show the control panel
 
Index: 0.58/bounds.txt
--- 0.58/bounds.txt Thu, 18 Mar 1999 14:33:34 +0100 hugo (purkinje/34_bounds.txt 1.3 644)
+++ parpat-storage-film.3/bounds.txt Sun, 11 Jul 1999 20:24:33 +0200 hugo (purkinje/34_bounds.txt 1.4 640)
@@ -8,7 +8,7 @@
 ##
 ## (C) 1998-2002 BBF-UIA
 ##
-## see our site at http://bbf-www.uia.ac.be/ for more information regarding
+## see our site at http://www.bbf.uia.ac.be/ for more information regarding
 ## the Purkinje cell and genesis simulation software.
 ##
 ##
@@ -37,50 +37,46 @@
 # 6-9. Same as 2-5, normalized mode
 #
 #
-# 1	2	3	4	5	6	7	8	9
+# 1		2	3	4	5	6	7	8	9
 #
-_Vm	-0.09	0.02	-0.1	0.05	-0.09	0.02	-0.1	0.05
-Ca_pool_Ca	0	0.001	0	0.001	0	0.001	0	0.001
-# adapted to normalized mode
-CaP_Ik	5e-12	3e-11	0	1e-10	0.0025	0.0015	0	0.05
-# end
-CaT_Ik	4e-13	6e-13	0	1.3e-12	4e-13	6e-13	0	1.3e-12
-K2_Ik	-4e-11	-1e-13	-6e-11	0	-4e-11	-1e-13	-6e-11	0
-KA_Ik	-2e-11	0	-3e-10	0	-2e-11	0	-3e-10	0
-KC_Ik	-1e-11	-7e-11	-2e-10	0	-1e-11	-7e-11	-2e-10	0
-KM_Ik	-9e-13	0	-9e-12	0	-9e-13	0	-9e-12	0
-Kdr_Ik	-5e-10	0	-7e-10	0	-5e-10	0	-7e-10	0
-NaF_Ik	0	1.6e-09	0	7e-10	0	1.6e-09	0	7e-10
-NaP_Ik	2e-11	2e-10	0	4e-10	2e-11	2e-10	0	4e-10
-h1_Ik	2e-12	1e-11	0	6e-11	2e-12	1e-11	0	6e-11
-h2_Ik	6e-13	1.8e-12	0	1e-11	6e-13	1.8e-12	0	1e-11
-excitatory_Ik	0	2.8e-11	0	4e-11	0	2.8e-11	0	4e-11
-inhibitory_Ik	-6e-10	0	-1e-09	0	-6e-10	0	-1e-09	0
-CaP_Gk	1e-11	6e-11	0	2e-10	1e-11	6e-11	0	2e-10
-CaT_Gk	3.5e-12	4.8e-12	0	1e-11	3.5e-12	4.8e-12	0	1e-11
-K2_Gk	0	2e-10	0	3e-10	0	2e-10	0	3e-10
-KA_Gk	3e-09	1.5e-06	0	6e-09	3e-09	1.5e-06	0	6e-09
-KC_Gk	5e-11	3e-10	0	7e-10	5e-11	3e-10	0	7e-10
-KM_Gk	2e-12	1.4e-11	0	2.5e-10	2e-12	1.4e-11	0	2.5e-10
-Kdr_Gk	0	1e-09	0	2.5e-08	0	1e-09	0	2.5e-08
-NaF_Gk	2e-09	1.2e-08	0	3.5e-08	2e-09	1.2e-08	0	3.5e-08
-NaP_Gk	1e-10	2e-09	0	4e-09	1e-10	2e-09	0	4e-09
-h1_Gk	7.5e-11	4e-10	0	1.6e-09	7.5e-11	4e-10	0	1.6e-09
-h2_Gk	3e-11	6e-11	0	2e-10	3e-11	6e-11	0	2e-10
-# adapted to normalized mode
-excitatory_Gk	0	6e-10	0	1e-09	0	5e-09	0	8e-09
-inhibitory_Gk	0	3e-09	0	1e-08	0	1.5e-08	0	3e-08
-# end 
-CaP_Ek	0.117	0.127	0.07	0.14	0.117	0.127	0.07	0.14
-CaT_Ek	0.11	0.126	0.07	0.14	0.11	0.126	0.07	0.14
-K2_Ek	0	1	0	1	0	1	0	1
-KA_Ek	0	1	0	1	0	1	0	1
-KC_Ek	0	1	0	1	0	1	0	1
-KM_Ek	0	1	0	1	0	1	0	1
-Kdr_Ek	0	1	0	1	0	1	0	1
-NaF_Ek	0	1	0	1	0	1	0	1
-NaP_Ek	0	1	0	1	0	1	0	1
-h1_Ek	0	1	0	1	0	1	0	1
-h2_Ek	0	1	0	1	0	1	0	1
-excitatory_Ek	0	1	0	1	0	1	0	1
-inhibitory_Ek	0	1	0	1	0	1	0	1
+_Vm		-0.08	0.02	-0.1	0.05	-0.08	0.02	-0.1	0.05
+Ca_pool_Ca	0.0	0.005	0.0	0.010	0.0	0.005	0.0	0.010
+CaP_Ik		0.0	1e-10	0.0	6e-10	0.0	0.05	0.0	0.08
+CaT_Ik		0.0	1e-12	0.0	6e-11	0.0	0.003	0	0.004
+K2_Ik		-1e-11	0.0	-2e-11	0.0	-0.02	0.0	-0.04	0.0
+KA_Ik		-5e-12	0.0	-5e-10	0.0	-0.001	0.0	-0.004	0.0
+KC_Ik		-1e-11	0.0	-4e-10	0.0	-0.003	0.0	-0.005	0.0
+KM_Ik		-2e-13	0.0	-4e-13	0.0	-0.02	0.0	-0.03	0.0
+Kdr_Ik		-2e-11	0.0	-2e-8	0.0	-0.0005	0.0	-0.001	0.0
+NaF_Ik		0.0	1.6e-9	0.0	3e-7	0.0	0.0001	0.0	0.001
+NaP_Ik		0.0	2e-10	0.0	2e-9	0.0	0.02	0.0	0.07
+h1_Ik		0.0	2e-12	0.0	2e-11	-0.001	0.002	-0.004	0.004
+h2_Ik		0.0	1e-12	0.0	1e-11	-0.001	0.001	-0.002	0.002
+excitatory_Ik	0.0	2e-11	0.0	4e-11	0.0	3e-10	0.0	1e-9
+inhibitory_Ik	-6e-10	0.0	-1e-09	0.0	-3e-10	0.0	-5e-10	0.0
+CaP_Gk		0.0	2e-9	0.0	6e-9	0.0	0.5	0.0	1.0
+CaT_Gk		0.0	1e-10	0.0	4e-10	0.0	0.02	0.0	0.03
+K2_Gk		0.0	2e-10	0.0	1e-9	0.0	0.5	0.0	0.8
+KA_Gk		0.0	5e-11	0.0	7e-9	0.0	0.01	0.0	0.03
+KC_Gk		0.0	5e-10	0.0	5e-9	0.0	0.05	0.0	0.05
+KM_Gk		0.0	1e-11	0.0	5e-10	0.0	0.3	0.0	0.5
+Kdr_Gk		0.0	1e-9	0.0	3e-7	0.0	0.01	0.0	0.05
+NaF_Gk		0.0	1e-7	0.0	6e-6	0.0	0.01	0.0	0.03
+NaP_Gk		0.0	1e-8	0.0	3e-8	0.0	0.1	0.0	1.0
+h1_Gk		0.0	2e-10	0.0	1e-9	0.0	0.02	0.0	0.1
+h2_Gk		0.0	1e-10	0.0	5e10	0.0	0.005	0.0	0.01
+excitatory_Gk	0.0	5e-10	0.0	7e-10	0.0	5e-09	0.0	8e-09
+inhibitory_Gk	0.0	1e-09	0.0	1e-08	0.0	1e-08	0.0	2e-08
+CaP_Ek		0.10	0.14	0.07	0.14	0.10	0.14	0.07	0.14
+CaT_Ek		0.10	0.14	0.07	0.14	0.10	0.14	0.07	0.14
+K2_Ek		-0.09	1	-0.09	1	-0.09	1	-0.09	1
+KA_Ek		-0.09	-0.08	-0.09	-0.08	-0.09	-0.08	-0.09	-0.08
+KC_Ek		-0.09	-0.08	-0.09	-0.08	-0.09	-0.08	-0.09	-0.08
+KM_Ek		-0.09	-0.08	-0.09	-0.08	-0.09	-0.08	-0.09	-0.08
+Kdr_Ek		-0.09	-0.08	-0.09	-0.08	-0.09	-0.08	-0.09	-0.08
+NaF_Ek		0.04	0.05	0.04	0.05	0.04	0.05	0.04	0.05
+NaP_Ek		0.04	0.05	0.04	0.05	0.04	0.05	0.04	0.05
+h1_Ek		-0.04	-0.02	-0.04	-0.02	-0.04	-0.02	-0.04	-0.02
+h2_Ek		-0.04	-0.02	-0.04	-0.02	-0.04	-0.02	-0.04	-0.02
+excitatory_Ek	-0.01	0.01	-0.01	0.01	-0.01	0.01	-0.01	0.01
+inhibitory_Ek	-0.09	-0.07	-0.09	-0.07	-0.09	-0.07	-0.09	-0.07
Index: 0.58/actions.g
--- 0.58/actions.g Mon, 24 Jul 2000 16:00:59 +0200 hugo (purkinje/35_actions.g 1.13.1.1 644)
+++ parpat-storage-film.3/actions.g Fri, 29 Sep 2000 20:06:06 +0200 hugo (purkinje/35_actions.g 1.13.1.3 640)
@@ -23,6 +23,11 @@
 
 // actions.g : parallel fiber and climbing fiber actions
 
+
+include mapping.g
+
+int PFPatternSteps = 0
+
 int include_actions
 
 if ( {include_actions} == 0 )
@@ -30,8 +35,7 @@
 	include_actions = 1
 
 
-include mapping.g
-
+int PFPatternDelaySteps = bidelay / dt
 
 //v climbing step delay while climbing fiber is firing
 
@@ -42,6 +46,93 @@
 int climbingSynapse = 0
 
 
+function ActionPFPattern(inelement)
+
+str inelement
+
+    if (PFPatternSteps == 0)
+
+  	for (i = 0; {i <= spinenum - 1}; i = i + 1)
+	  setfield {cellpath}/par_presyn[{i}] z {getfield {inelement} val[{i}][{0}]}
+        end
+        PFPatternSteps = 1
+   
+    elif (PFPatternSteps == 1)
+	
+	for (i = 0; {i <= spinenum - 1}; i = i + 1)
+	  setfield {cellpath}/par_presyn[{i}] z 0
+        end
+        PFPatternSteps = 2
+
+    elif ((PFPatternSteps > 1) && (PFPatternSteps < PFPatternDelaySteps))
+
+	PFPatternSteps = PFPatternSteps + 1
+
+    elif (PFPatternSteps == PFPatternDelaySteps)
+	
+	setfield {cellpath}/bc_presyn z {biamp}
+	PFPatternSteps = PFPatternDelaySteps + 1
+
+    elif (PFPatternSteps > PFPatternDelaySteps)
+	
+	setfield {cellpath}/bc_presyn z 0
+	PFPatternSteps = 0
+	setfield /actions/pfpattern command ""
+
+    end
+
+end
+
+
+
+function ActionPFPatternInit(path)
+   
+str path
+
+    create script_out {path}pfpattern
+    setfield /actions/pfpattern command ""
+
+    // create {spinenum} presynaptic elements for synchronous PF input
+    // add messages to the AMPA receptors
+    for (i = 0; {i <= spinenum - 1}; i = i + 1)
+        create neutral {cellpath}/par_presyn[{i}]
+	disable {cellpath}/par_presyn[{i}]
+	setfield {cellpath}/par_presyn[{i}] z 0
+	addmsg {cellpath}/par_presyn[{i}] \
+               {cellpath}/spine[{i}]/head[{i}]/par ACTIVATION z
+    end
+
+    // create the basket cell presynaptic element
+    // add messages to GABA receptors
+    create neutral {cellpath}/bc_presyn
+    disable {cellpath}/bc_presyn
+    setfield {cellpath}/bc_presyn z 0
+    addmsg {cellpath}/bc_presyn {cellpath}/soma/basket ACTIVATION z
+    addmsg {cellpath}/bc_presyn {cellpath}/main[]/basket ACTIVATION z
+
+    // create the input elements
+    create disk_in /infileStored
+    create disk_in /infileNovel
+
+
+
+end
+
+
+
+function ActionPFPatternStart(inelement)
+
+str inelement
+
+    PFPatternSteps = 0
+
+    setfield /actions/pfpattern \
+             command "ActionPFPattern "{inelement}
+
+end
+
+
+
 ///
 /// SH:	ActionBasket
 ///
@@ -92,6 +183,7 @@
 end
 
 
+
 ///
 /// SH:	ActionBasketInit
 ///
@@ -149,7 +241,7 @@
 	//- set field in script object
 
 	setfield /actions/basket \
-		command "ActionBasket "{level / dt}
+		command "ActionBasket "{level}
 
 	// call reset on the script to avoid bugs
 
@@ -423,7 +515,7 @@
 	//- set field in script object
 
 	setfield /actions/climbing \
-		command "ActionClimbing "{strength / dt}
+		command "ActionClimbing "{strength}
 
 	// call reset on the script to avoid bugs
 
@@ -1359,7 +1451,7 @@
 		//- set field of script object
 
 		setfield /actions/parallel \
-			command "ActionParallelLocal "{branch}" "{level / dt}
+			command "ActionParallelLocal "{branch}" "{level}
 
 		// call reset on the script to avoid bugs
 
@@ -1414,7 +1506,7 @@
 		//- set field of script object
 
 		setfield /actions/parallel \
-			command "ActionParallelDistr "{number}" "{level / dt}
+			command "ActionParallelDistr "{number}" "{level}
 
 		// call reset on the script to get around some bugs
 
@@ -1452,6 +1544,10 @@
 	//- initialize synchronous parallel fiber
 
 	ActionParallelInit /actions/
+
+	ActionPFPatternInit /actions/
+	
+
 end
 
 
Index: 0.58/TUTORIAL.g
--- 0.58/TUTORIAL.g Tue, 04 Jan 2000 15:16:41 +0100 hugo (purkinje/36_TUTORIAL.g 1.1.1.3.1.6.3.1.1.1 640)
+++ parpat-storage-film.3/TUTORIAL.g Wed, 27 Sep 2000 11:39:30 +0200 hugo (purkinje/36_TUTORIAL.g 1.1.1.3.1.6.3.1.1.1.2.2 640)
@@ -1,4 +1,5 @@
 //genesis - Purkinje cell version M9 genesis2 master script
+// Copyright: Theoretical Neurobiology, Born-Bunge Foundation - UA, 1998-1999.
 //
 // $Id: purkinje-0.58-purkinje-parpat-storage-film.3.patch 1.2 Thu, 04 Apr 2002 11:55:56 +0200 hugo $
 //
@@ -22,14 +23,14 @@
 
 //- give header
 
-echo "-----------------------------------------------------------------"
+echo "-------------------------------------------------------------------------"
 echo
 echo "Purkinje tutorial, version " -n
 // $Format: "echo \"$ProjectVersion$ ($ProjectDate$)\""$
echo "Release1.3.2 (Thu, 04 Apr 2002 12:46:38 +0200)"
 echo "                       Simulation script"
 echo
-echo "-----------------------------------------------------------------"
+echo "-------------------------------------------------------------------------"
 
 //- include default definitions
 
@@ -263,6 +264,10 @@
 //- set clock for refresh elements
 
 setclock 10 {dt * 239}
+
+//- set clock for movie elements
+
+setclock 11 {dt * outputRate}
 
 //- set delay in steps for climbing fiber
 
Index: 0.58/README
--- 0.58/README Mon, 27 Dec 1999 19:02:49 +0100 hugo (purkinje/37_README 1.2.1.1 644)
+++ parpat-storage-film.3/README Wed, 27 Sep 2000 11:39:30 +0200 hugo (purkinje/37_README 1.2.1.1.1.1 640)
@@ -1,12 +1,12 @@
 $Id: purkinje-0.58-purkinje-parpat-storage-film.3.patch 1.2 Thu, 04 Apr 2002 11:55:56 +0200 hugo $
 
-README file for the Tutorial Simulation of a cerebellar Purkinje cell
+README file for the Tutorial simulation of a cerebellar Purkinje cell
 
 This tutorial is based upon a GENESIS simulation of a cerebellar Purkinje 
 cell, modeled and fine-tuned by Erik de Schutter. The tutorial assumes that
 you have a basic knowledge of the Purkinje cell and its synaptic inputs. It 
-gives visual insights in how different properties as concentrations and 
-channel conductances vary and interfere within a real Purkinje cell.
+gives visual insight in how different properties as concentrations and 
+channel conductances vary and interact within a real Purkinje cell.
 
 In order to run the simulation, you need the following : 
 
@@ -26,21 +26,32 @@
    right hand corner of your display.
 
 2) Change to the directory where the TUTORIAL.g script resides. If you are
-   reading this file, you will probably be in the wright directory.
+   reading this file, you should be in the correct directory.  The tutorial
+   will create some files in this directory, so you will need to have write
+   privileges.  If the tutorial is installed in a system directory for which
+   you do not have write permission, copy the tutorial files to a directory
+   in which you are allowed to create files.
+
+3) At the shell prompt, type "./TUTORIAL".  (This Unix shell script will
+   create any needed files and will start GENESIS using the TUTORIAL.g
+   script.  You do not need to start GENESIS yourself.)  After a long
+   initialization period, a window with a Purkinje cell and a control panel
+   will appear. To move on, click the 'Help' button in the control panel.
+   This will popup the on-line help window.  These instructions, which you
+   will need to read before running the tutorial, are contained in the file
+   "help.txt".
+
+Ambitious users can run this tutorial using different model setup files
+(all the files titled Purk_*, including the morphology file, can be
+changed).  Before you do so you need to reconfigure the simulation by 
+running "genesis makeconfig.g". After some diagnostic messages, you 
+should return to the shell prompt.
+
+For feedback write:
+Concepts and documentation: Erik de Schutter - erik@bbf.uia.ac.be
+Bugs:                       Hugo Cornelis - hugo@bbf.uia.ac.be
 
-3) Type at the shell prompt : "TUTORIAL".
+Consult our webpages at bbf-www.uia.ac.be for relevant publications and
+additional documentation concerning the model scripts.
 
-
-If you get an error message like this one :
-
-<Purk_chanload> line 65 <- <Purk_chanload> line 80 <- <TUTORIAL.g> line 142
-** Error -  can't read file 'Purk_NaF.tab': wrong version #50331648
-
-Then retry making a configuration file for the tutorial by typing at the UNIX 
-shell prompt "genesis makeconfig.g". Afterwards type "genesis TUTORIAL.g". 
-If this does not work, consult your system administrator or a person with
-knowledge of UNIX and the Genesis neural simulator.
-
-
-Erik de Schutter - erik@bbf.uia.ac.be
-Hugo Cornelis - hugo@bbf.uia.ac.be
+Copyright for all the scripts: Born-Bunge Foundation - UA 1998-1999.
Index: 0.58/Purk_syn.g
--- 0.58/Purk_syn.g Mon, 27 Dec 1999 18:17:48 +0100 hugo (purkinje/38_Purk_syn.g 1.3 644)
+++ parpat-storage-film.3/Purk_syn.g Fri, 29 Sep 2000 20:06:06 +0200 hugo (purkinje/38_Purk_syn.g 1.5 640)
@@ -10,8 +10,9 @@
 ** E. De Schutter and J.M. Bower: An active membrane model of the
 ** cerebellar Purkinje cell: II. Simulation of synaptic responses.
 ** Journal of Neurophysiology  71: 401-419 (1994).
-** http://bbf-www.uia.ac.be/TNB/TNB_pub7.html
+** http://www.bbf.uia.ac.be/TNB/TNB_pub7.html
 ** Consult this reference for sources of experimental data.
+** See http://www.bbf.uia.ac.be/models/PM9.shtml for general model info.
 */
 
 // CONSTANTS
@@ -44,14 +45,14 @@
 
 	/* asynchronously firing channel */
     if (!({exists GABA}))
-		create synchan GABA
+		create channelC3 GABA
     end
     setfield GABA Ek {E_GABA} tau1 {0.93e-3} tau2 {26.50e-3}  \
         gmax {G_GABA} frequency {0.0}
 
 	/* synchronously firing channel */
     if (!({exists GABA2}))
-		create synchan GABA2
+		create channelC2 GABA2
     end
     setfield GABA2 Ek {E_GABA} tau1 {0.93e-3} tau2 {26.50e-3}  \
         gmax {GB_GABA}
@@ -64,7 +65,7 @@
 
 	/* asynchronously firing channel */
     if (!({exists non_NMDA}))
-		create synchan non_NMDA
+		create channelC3 non_NMDA
     end
 
     setfield non_NMDA Ek {E_non_NMDA} tau1 {0.50e-3} tau2 {1.20e-3}  \
@@ -72,7 +73,7 @@
 
 	/* synchronously firing channel */
     if (!({exists non_NMDA2}))
-        create synchan non_NMDA2
+        create channelC2 non_NMDA2
     end
 
     setfield non_NMDA2 Ek {E_non_NMDA} tau1 {0.50e-3} tau2 {1.20e-3}
Index: 0.58/Purk_const.g
--- 0.58/Purk_const.g Mon, 27 Dec 1999 18:17:48 +0100 hugo (purkinje/39_Purk_const 1.3 644)
+++ parpat-storage-film.3/Purk_const.g Wed, 27 Sep 2000 11:39:30 +0200 hugo (purkinje/39_Purk_const 1.4 640)
@@ -14,9 +14,14 @@
 echo Using Purkinje 2M9 preferences. Crank Nicholson method.
 /* variables controlling hsolve integration */
 float dt = 2.0e-5
-int tab_xdivs = 149; int tab_xfills = 2999
+int tab_xdivs = 149
+int tab_xfills = 2999
+
 /* The model is quite sensitive to these values in NO_INTERP (caclmode=0) */
-float tab_xmin = -0.10; float tab_xmax = 0.05; float Ca_tab_max = 0.300
+float tab_xmin = -0.10
+float tab_xmax = 0.05
+float Ca_tab_max = 0.300
+
 // only used for proto channels
 float GNa = 1, GCa = 1, GK = 1, Gh = 1
 /* cable parameters */
Index: 0.58/Purk_cicomp.g
--- 0.58/Purk_cicomp.g Fri, 29 Oct 1999 21:02:10 +0200 hugo (purkinje/40_Purk_cicom 1.2 644)
+++ parpat-storage-film.3/Purk_cicomp.g Wed, 27 Sep 2000 11:39:30 +0200 hugo (purkinje/40_Purk_cicom 1.3 640)
@@ -13,12 +13,13 @@
 ** E. De Schutter and J.M. Bower: An active membrane model of the
 ** cerebellar Purkinje cell. I. Simulation of current clamps in slice.
 ** Journal of Neurophysiology  71: 375-400 (1994).
-** http://bbf-www.uia.ac.be/TNB/TNB_pub8.html
+** http://www.bbf.uia.ac.be/TNB/TNB_pub8.html
 ** E. De Schutter and J.M. Bower: An active membrane model of the
 ** cerebellar Purkinje cell: II. Simulation of synaptic responses.
 ** Journal of Neurophysiology  71: 401-419 (1994).
-** http://bbf-www.uia.ac.be/TNB/TNB_pub7.html
+** http://www.bbf.uia.ac.be/TNB/TNB_pub7.html
 ** Consult these references for sources of experimental data.
+** See http://www.bbf.uia.ac.be/models/PM9.shtml for general model info.
 */
 
 
Index: 0.58/Purk_chansave.g
--- 0.58/Purk_chansave.g Fri, 29 Oct 1999 21:02:10 +0200 hugo (purkinje/41_Purk_chans 1.2 644)
+++ parpat-storage-film.3/Purk_chansave.g Wed, 27 Sep 2000 11:39:30 +0200 hugo (purkinje/41_Purk_chans 1.3 640)
@@ -12,8 +12,9 @@
 ** E. De Schutter and J.M. Bower: An active membrane model of the
 ** cerebellar Purkinje cell. I. Simulation of current clamps in slice.
 ** Journal of Neurophysiology  71: 375-400 (1994).
-** http://bbf-www.uia.ac.be/TNB/TNB_pub8.html
+** http://www.bbf.uia.ac.be/TNB/TNB_pub8.html
 ** Consult this reference for sources of equations and experimental data.
+** See http://www.bbf.uia.ac.be/models/PM9.shtml for general model info.
 */
 
 
Index: 0.58/Purk_chanload.g
--- 0.58/Purk_chanload.g Fri, 29 Oct 1999 21:02:10 +0200 hugo (purkinje/42_Purk_chanl 1.2 644)
+++ parpat-storage-film.3/Purk_chanload.g Wed, 27 Sep 2000 11:39:30 +0200 hugo (purkinje/42_Purk_chanl 1.3 640)
@@ -13,8 +13,9 @@
 ** E. De Schutter and J.M. Bower: An active membrane model of the
 ** cerebellar Purkinje cell. I. Simulation of current clamps in slice.
 ** Journal of Neurophysiology  71: 375-400 (1994).
-** http://bbf-www.uia.ac.be/TNB/TNB_pub8.html
+** http://www.bbf.uia.ac.be/TNB/TNB_pub8.html
 ** Consult this reference for sources of equations and experimental data.
+** See http://www.bbf.uia.ac.be/models/PM9.shtml for general model info.
 */
 
 
@@ -126,7 +127,7 @@
     /* Equations from the literature */
     /* delayed rectifier type K current eq1
     ** Refs: Yamada (his equations are also for 22C) */
-    if (!{exists Purk_Kdr})
+    if (!{exists Purk_dr})
 	    create tabchannel Purk_Kdr
 	    setfield Purk_Kdr Ek {EK} Gbar {GK} Ik 0 Gk 0 Xpower 2  \
 		Ypower 1 Zpower 0
Index: 0.58/random.g
--- 0.58/random.g Thu, 04 Apr 2002 11:22:47 +0200 hugo ()
+++ parpat-storage-film.3/random.g Wed, 27 Sep 2000 11:06:49 +0200 hugo (purkinje/b/10_random.g 1.1 640)
@@ -0,0 +1,10 @@
+function rand_int(min, max)
+int min
+int max
+  
+  int randint = {round {rand {min} {max}}}
+
+  return randint
+
+end
+
Index: 0.58/XPATREC9A.g
--- 0.58/XPATREC9A.g Thu, 04 Apr 2002 11:22:47 +0200 hugo ()
+++ parpat-storage-film.3/XPATREC9A.g Fri, 29 Sep 2000 20:06:06 +0200 hugo (purkinje/b/11_XPATREC9A. 1.2 640)
@@ -0,0 +1,266 @@
+//genesis - Purkinje cell version M9 genesis2 master script
+
+// use the time to seed random number generator
+randseed
+
+// one spine for each of the 1474 spiny compts
+int spinenum = 1474
+int syncnum = 1000
+
+int filenum = 200
+int filecnt
+
+float bidelay = 0.001
+float biamp = 0.0
+
+float phertz = 28
+float ihertz = 1000
+
+int i, j, k, l
+float t
+str name, hstr
+include defaults
+include random
+
+str cellfile = "../patrecog/pfiles/Purk2M9s.p"
+str infile = "../patrecog/pfinput/PFeff_" @ (filenum) @ "_" @ (syncnum) @ "_"
+str infile1
+
+cellpath = "/Purkinje"
+
+include Purk_hficonst
+EREST_ACT = -0.055
+
+/* special scripts  to create the prototypes */
+include Purk_chanload
+//include Purk_chansave
+include Purk_cicomp 
+include Purk_syn 
+
+//- set default output rate
+
+int outputRate = 10
+
+//- set default chanmode for solver : normalized
+
+int iChanMode = 5
+
+//- set default mode : in vitro
+// changed to in vivo
+
+int iVVMode = 0
+
+//- set default for current : current clamp on
+// changed to off
+
+int iCurrentMode = 0
+
+//- speed of climbing fiber volley (in sec)
+
+float delay = 0.00020
+
+//- strength of climbing fiber synapses
+
+float strength = 1.0
+
+//- speed of climbing fiber volley (in steps == delay / dt)
+//- this variable is set later on when dt is defined in an other module
+
+int delaysteps = 0.00020 / 1
+
+//- include the utility module, it is needed by multiple others modules,
+//- but since I do not like multiple includes, I include it here.
+
+include utility.g
+
+//- include the config module
+
+include config.g
+
+//- default we do not update the config file
+
+int bUpdateConfig = 0
+
+include info.g
+include bounds.g
+include config.g
+include control.g
+include xgraph.g
+include xcell.g
+
+//- ensure that all elements are made in the library
+
+ce /library
+
+//- make prototypes of channels and synapses
+
+make_Purkinje_chans
+make_Purkinje_syns
+
+//- set the firing frequencies at the library level
+//- this forces the hsolve object to reserve space for these fields
+
+setfield /library/GABA frequency {ihertz}
+setfield /library/non_NMDA frequency {phertz}
+
+//- add fields to the library elements to respect the vivo / vitro mode
+
+addfield /library/GABA freqmode -description "frequency operation mode"
+addfield /library/non_NMDA freqmode -description "frequency operation mode"
+
+//- set the added fields to the current vivo/vitro mode
+
+setfield /library/GABA freqmode {iVVMode}
+setfield /library/non_NMDA freqmode {iVVMode}
+
+//- add fields to distinguish between inhibition and excitation
+
+addfield /library/GABA synmode -description "synaptic mode"
+addfield /library/non_NMDA synmode -description "synaptic mode"
+
+//- set field to "in" for inhibition
+
+setfield /library/GABA synmode "in"
+
+//- set field to "ex" for excitation
+
+setfield /library/non_NMDA synmode "ex"
+
+//- make prototypes of compartements and spines
+
+make_Purkinje_comps
+make_Purkinje_spines
+
+//- read cell data from .p file
+
+readcell {cellfile} {cellpath}
+
+//- read configuration file
+
+ConfigRead {cellfile} {cellpath}
+
+//- initialize actions
+
+ActionsInit
+
+//- initialize boundaries
+
+BoundsInit "bounds.txt"
+
+//- set simulation clocks
+for (i = 0; i <= 8; i = i + 1)
+	setclock {i} {dt}
+end
+
+//- set the output clock
+
+setclock 9 {dt * outputRate}
+
+//- set clock for refresh elements
+
+setclock 10 {dt * 239}
+
+
+//- set delay in steps for climbing fiber
+
+delaysteps = {delay / dt}
+
+//- setup the hines solver
+
+echo preparing hines solver {getdate}
+ce {cellpath}
+create hsolve solve
+
+//- We change to current element solve and then set the fields of the parent
+//- (solve) to get around a bug in the "." parsing of genesis
+
+ce solve
+
+setfield . \
+        path "../##[][TYPE=compartment]" \
+        comptmode 1 \
+        chanmode {iChanMode} \
+        calcmode 0
+
+/*
+setfield . \
+        path "../b#[][TYPE=compartment],../main[][TYPE=compartment]" \
+        comptmode 1 \
+        chanmode {iChanMode} \
+        calcmode 0
+*/
+
+
+//- create all info widgets
+
+InfoCreate
+
+//- create all settings widgets
+
+SettingsCreate
+
+//- setup the solver with all messages from the settings
+
+call /Purkinje/solve SETUP
+
+//- Use method to Crank-Nicolson
+
+setmethod 11
+
+//- go back to simulation element
+
+ce {cellpath}
+
+//- set colorscale
+
+xcolorscale rainbow3
+
+//- create the xcell widget
+
+XCellCreate
+
+//- create the graph widget
+
+XGraphCreate
+
+//- set default state
+
+XCellReset
+
+//- reset graph
+
+XGraphReset
+
+//- create the control panel
+
+ControlPanelCreate
+
+//- reset all elements
+
+reset
+
+//- to further initialize all elements (e.g. colors of xcell element)
+//- we do one step in the simulation and then a reset
+
+step 1
+
+//- update the firing frequencies for stellate and parallel fibers
+
+UpdateFrequencies
+
+//- reset all elements
+
+reset
+
+// switch to in vivo mode
+
+ToggleMode 1
+
+echo Purkinje cell equilibration...
+
+step 0.1 -time
+
+setfield /xgraphs/graph xmin 0.1
+xshow /xgraphs
+XCellCBAddPlot /Purkinje/soma
+
Index: 0.58/Purk_ticonst.g
--- 0.58/Purk_ticonst.g Thu, 04 Apr 2002 11:22:47 +0200 hugo ()
+++ parpat-storage-film.3/Purk_ticonst.g Wed, 27 Sep 2000 11:06:49 +0200 hugo (purkinje/b/12_Purk_ticon 1.1 640)
@@ -0,0 +1,75 @@
+//genesis  - Purkinje cell M9 genesis2.1 script
+/* Copyright E. De Schutter (Caltech and BBF-UIA) */
+
+/* This file defines important simulation parameters, including gmax
+** and Ek for all channels.  Everything uses SI units. */
+
+// version with tonic inhibition 
+// note that ihertz has to be set to 0 in the main script
+
+echo Using Purkinje 2M9 preferences. Crank Nicholson method.
+/* variables controlling hsolve integration */
+float dt = 2.0e-5
+int tab_xdivs = 149
+int tab_xfills = 2999
+
+/* The model is quite sensitive to these values in NO_INTERP (caclmode=0) */
+float tab_xmin = -0.10
+float tab_xmax = 0.05
+float Ca_tab_max = 0.300
+
+// only used for proto channels
+float GNa = 1, GCa = 1, GK = 1, Gh = 1
+/* cable parameters */
+float CM = 0.0164 		// *9 relative to passive
+float RMs = 1.000 		// /3.7 relative to passive comp
+float RMd = 3.0                 // standard value, no GABA channels on main dendrite and spines
+float RMtd = 0.8902            // tonic inhibition to thick dendrite
+float RMsd = 0.4323            // tonic inhibition to spiny dendrite
+float RA = 2.50
+/* preset constants */
+float ELEAK = -0.0800 		// Ek value used for the leak conductance
+float EREST_ACT = -0.0680 	// Vm value used for the RESET
+/* concentrations */
+float CCaO = 2.4000 		//external Ca as in normal slice Ringer
+float CCaI = 0.000040		//internal Ca in mM
+//diameter of Ca_shells
+float Shell_thick = 0.20e-6
+float CaTau = 0.00010	 	// Ca_concen tau
+/* Currents: Reversal potentials in V and max conductances S/m^2 */
+/* Codes: s=soma, m=main dendrite, t=thick dendrite, d=spiny dendrite */
+float ENa = 0.045
+float GNaFs = 75000.0
+float GNaPs = 10.0
+float ECa = 0.0125*{log {CCaO/CCaI}} // 0.135 V
+float GCaTs = 5.00
+float GCaTm = 5.00
+float GCaTt = 5.00
+float GCaTd = 5.00
+float GCaPm = 45.0
+float GCaPt = 45.0
+float GCaPd = 45.0
+float EK = -0.085
+float GKAs = 150.0
+float GKAm = 20.0
+float GKdrs = 6000.0
+float GKdrm = 600.0
+float GKMs = 0.400
+float GKMm = 0.100
+float GKMt = 0.130
+float GKMd = 0.130
+float GKCm = 800.0
+float GKCt = 800.0
+float GKCd = 800.0
+float GK2m = 3.90
+float GK2t = 3.90
+float GK2d = 3.90
+float Eh = -0.030
+float Ghs = 3.00
+/* synapses: */
+float E_GABA = -0.080
+float G_GABA = 0.0//70.0/dt
+float GB_GABA = 20.0/dt
+float E_non_NMDA = 0.000
+float G_par_syn = 750.0/dt
+float G_cli_syn = 150.0/dt
Index: 0.58/Purk_spiticomp.g
--- 0.58/Purk_spiticomp.g Thu, 04 Apr 2002 11:22:47 +0200 hugo ()
+++ parpat-storage-film.3/Purk_spiticomp.g Wed, 27 Sep 2000 11:06:49 +0200 hugo (purkinje/b/13_Purk_spiti 1.1 640)
@@ -0,0 +1,264 @@
+//genesis - Purkinje cell M9 genesis2.1 script
+/* Copyright E. De Schutter (Caltech and BBF-UIA) */
+
+/**********************************************************************
+** Sets up active membrane Purkinje cell compartment prototypes 
+**  and dendritic spine prototypes.
+** E. De Schutter, Caltech, 1991-1992
+** This version sets up a passive soma and active dendritic compartments 
+**  with stellate cell synapses.
+**********************************************************************/
+
+/* References:
+** E. De Schutter and J.M. Bower: An active membrane model of the
+** cerebellar Purkinje cell. I. Simulation of current clamps in slice.
+** Journal of Neurophysiology  71: 375-400 (1994).
+** http://www.bbf.uia.ac.be/TNB/TNB_pub8.html
+** E. De Schutter and J.M. Bower: An active membrane model of the
+** cerebellar Purkinje cell: II. Simulation of synaptic responses.
+** Journal of Neurophysiology  71: 401-419 (1994).
+** http://www.bbf.uia.ac.be/TNB/TNB_pub7.html
+** E. De Schutter and J.M. Bower: Simulated responses of cerebellar
+** Purkinje cells are independent of the dendritic location of granule 
+** cell synaptic inputs. Proceedings of the National Academy of Sciences 
+** USA 91: 4736-4740 (1994).
+** http://www.bbf.uia.ac.be/TNB/TNB_pub6.html
+** Consult these references for sources of experimental data.
+** See http://www.bbf.uia.ac.be/models/PM9.shtml for general model info.
+*/
+
+function make_Purkinje_comps
+/* separate function so we can have local variables */
+
+	float len, dia, surf, shell_vol, shell_dia
+	int i
+
+	echo making Purkinje compartment library...
+
+	/* make spherical soma prototype with sodium currents*/
+	len = 0.00e-6
+	dia = 20.0e-6
+	surf = dia*dia*{PI}
+	shell_dia = 2*{Shell_thick}
+	shell_vol = (3*dia*dia*shell_dia - 3*dia*shell_dia*shell_dia + shell_dia*shell_dia*shell_dia)*{PI}/6.0
+	if (!({exists Purk_soma}))
+		create compartment Purk_soma
+	end
+	setfield Purk_soma Cm {{CM}*surf} Ra {8.0*{RA}/(dia*{PI})}  \
+	    Em {ELEAK} initVm {EREST_ACT} Rm {{RMs}/surf} inject 0.0  \
+	    dia {dia} len {len}
+
+    /* make main dendrite prototype with fast Ca currents */
+    len = 200.00e-6
+    dia = 2.00e-6
+    surf = len*dia*{PI}
+    shell_vol = (2*dia*shell_dia - shell_dia*shell_dia)*len*{PI}/4.0
+    if (!({exists Purk_maind}))
+        create compartment Purk_maind
+    end
+    setfield Purk_maind Cm {{CM}*surf} Ra {4.0*{RA}*len/(dia*dia*{PI})}  \
+        Em {ELEAK} initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0  \
+        dia {dia} len {len}
+
+    if (!({exists Purk_thickd}))    // Lets copy before we add currents
+
+        copy Purk_maind Purk_thickd
+    end
+    if (!({exists Purk_spinyd}))    // Lets copy before we add currents
+
+        copy Purk_maind Purk_spinyd
+    end
+
+	copy Purk_CaT Purk_maind/CaT
+	addmsg Purk_maind Purk_maind/CaT VOLTAGE Vm
+	addmsg Purk_maind/CaT Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/CaT Gbar {{GCaTm}*surf}
+	copy Purk_KA Purk_maind/KA
+	addmsg Purk_maind Purk_maind/KA VOLTAGE Vm
+	addmsg Purk_maind/KA Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KA Gbar {{GKAm}*surf}
+	copy Purk_Kdr Purk_maind/Kdr
+	addmsg Purk_maind Purk_maind/Kdr VOLTAGE Vm
+	addmsg Purk_maind/Kdr Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/Kdr Gbar {{GKdrm}*surf}
+	copy Purk_KM Purk_maind/KM
+	addmsg Purk_maind Purk_maind/KM VOLTAGE Vm
+	addmsg Purk_maind/KM Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KM Gbar {{GKMm}*surf}
+	copy Purk_CaP Purk_maind/CaP
+	addmsg Purk_maind Purk_maind/CaP VOLTAGE Vm
+	addmsg Purk_maind/CaP Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/CaP Gbar {{GCaPm}*surf}
+	copy Purk_KC Purk_maind/KC
+	addmsg Purk_maind Purk_maind/KC VOLTAGE Vm
+	addmsg Purk_maind/KC Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KC Gbar {{GKCm}*surf}
+	copy Purk_K2 Purk_maind/K2
+	addmsg Purk_maind Purk_maind/K2 VOLTAGE Vm
+	addmsg Purk_maind/K2 Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/K2 Gbar {{GK2m}*surf}
+	create Ca_concen Purk_maind/Ca_pool
+	setfield Purk_maind/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_maind/CaT Purk_maind/Ca_pool I_Ca Ik
+	addmsg Purk_maind/CaP Purk_maind/Ca_pool I_Ca Ik
+	addmsg Purk_maind/Ca_pool Purk_maind/KC CONCEN Ca
+	addmsg Purk_maind/Ca_pool Purk_maind/K2 CONCEN Ca
+	create nernst Purk_maind/Ca_nernst
+	setfield Purk_maind/Ca_nernst Cin {CCaI} Cout {CCaO} valency {2} \
+	     scale {1.0} T {37}
+	addmsg Purk_maind/Ca_pool Purk_maind/Ca_nernst CIN Ca
+	addmsg Purk_maind/Ca_nernst Purk_maind/CaP EK E
+	addmsg Purk_maind/Ca_nernst Purk_maind/CaT EK E
+
+	/* make thick dendrite prototype with fast Ca current */
+	/* similar to main dendrite but has CaP and no Kdr */
+	/* passive prototype already copied from Purk_maind */
+	setfield Purk_thickd Cm {{CM}*surf} Ra {4.0*{RA}*len/(dia*dia*{PI})}  \
+          Em {ELEAK} initVm {EREST_ACT} Rm {{RMtd}/surf} inject 0.0  \
+          dia {dia} len {len}
+
+        copy Purk_CaT Purk_thickd/CaT
+	addmsg Purk_thickd Purk_thickd/CaT VOLTAGE Vm
+	addmsg Purk_thickd/CaT Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/CaT Gbar {{GCaTt}*surf}
+	copy Purk_CaP Purk_thickd/CaP
+	addmsg Purk_thickd Purk_thickd/CaP VOLTAGE Vm
+	addmsg Purk_thickd/CaP Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/CaP Gbar {{GCaPt}*surf}
+	copy Purk_KM Purk_thickd/KM
+	addmsg Purk_thickd Purk_thickd/KM VOLTAGE Vm
+	addmsg Purk_thickd/KM Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/KM Gbar {{GKMt}*surf}
+	copy Purk_KC Purk_thickd/KC
+	addmsg Purk_thickd Purk_thickd/KC VOLTAGE Vm
+	addmsg Purk_thickd/KC Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/KC Gbar {{GKCt}*surf}
+	copy Purk_K2 Purk_thickd/K2
+	addmsg Purk_thickd Purk_thickd/K2 VOLTAGE Vm
+	addmsg Purk_thickd/K2 Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/K2 Gbar {{GK2t}*surf}
+	create Ca_concen Purk_thickd/Ca_pool
+	setfield Purk_thickd/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_thickd/CaT Purk_thickd/Ca_pool I_Ca Ik
+	addmsg Purk_thickd/CaP Purk_thickd/Ca_pool I_Ca Ik
+	addmsg Purk_thickd/Ca_pool Purk_thickd/KC CONCEN Ca
+	addmsg Purk_thickd/Ca_pool Purk_thickd/K2 CONCEN Ca
+	create nernst Purk_thickd/Ca_nernst
+	setfield Purk_thickd/Ca_nernst Cin {CCaI} Cout {CCaO}  \
+	    valency {2} scale {1.0} T {37}
+	addmsg Purk_thickd/Ca_pool Purk_thickd/Ca_nernst CIN Ca
+	addmsg Purk_thickd/Ca_nernst Purk_thickd/CaP EK E
+	addmsg Purk_thickd/Ca_nernst Purk_thickd/CaT EK E
+	for (i=1; i<=2; i = i+1)
+	    copy GABA Purk_thickd/stell{i}
+	    setfield Purk_thickd/stell{i} gmax {{G_GABA}/5*surf}
+	    addmsg Purk_thickd/stell{i} Purk_thickd CHANNEL Gk Ek
+	    addmsg Purk_thickd  Purk_thickd/stell{i}  VOLTAGE Vm
+	end
+
+	/* make spiny dendrite prototype with high threshold Ca current  \
+	    */
+	/* passive prototype already copied from Purk_maind */
+	setfield Purk_spinyd Cm {{CM}*surf} Ra {4.0*{RA}*len/(dia*dia*{PI})}  \
+          Em {ELEAK} initVm {EREST_ACT} Rm {{RMsd}/surf} inject 0.0  \
+          dia {dia} len {len}
+
+        copy Purk_CaT Purk_spinyd/CaT
+	addmsg Purk_spinyd Purk_spinyd/CaT VOLTAGE Vm
+	addmsg Purk_spinyd/CaT Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/CaT Gbar {{GCaTd}*surf}
+	copy Purk_CaP Purk_spinyd/CaP
+	addmsg Purk_spinyd Purk_spinyd/CaP VOLTAGE Vm
+	addmsg Purk_spinyd/CaP Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/CaP Gbar {{GCaPd}*surf}
+	copy Purk_KM Purk_spinyd/KM
+	addmsg Purk_spinyd Purk_spinyd/KM VOLTAGE Vm
+	addmsg Purk_spinyd/KM Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/KM Gbar {{GKMd}*surf}
+	copy Purk_KC Purk_spinyd/KC
+	addmsg Purk_spinyd Purk_spinyd/KC VOLTAGE Vm
+	addmsg Purk_spinyd/KC Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/KC Gbar {{GKCd}*surf}
+	copy Purk_K2 Purk_spinyd/K2
+	addmsg Purk_spinyd Purk_spinyd/K2 VOLTAGE Vm
+	addmsg Purk_spinyd/K2 Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/K2 Gbar {{GK2d}*surf}
+	create Ca_concen Purk_spinyd/Ca_pool
+	setfield Purk_spinyd/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_spinyd/CaP Purk_spinyd/Ca_pool I_Ca Ik
+	addmsg Purk_spinyd/CaT Purk_spinyd/Ca_pool I_Ca Ik
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/KC CONCEN Ca
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/K2 CONCEN Ca
+	create nernst Purk_spinyd/Ca_nernst
+	setfield Purk_spinyd/Ca_nernst Cin {CCaI} Cout {CCaO}  \
+	    valency {2} scale {1.0} T {37}
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/Ca_nernst CIN Ca
+	addmsg Purk_spinyd/Ca_nernst Purk_spinyd/CaP EK E
+	addmsg Purk_spinyd/Ca_nernst Purk_spinyd/CaT EK E
+	copy GABA Purk_spinyd/stell
+	setfield Purk_spinyd/stell gmax {{G_GABA}*surf}
+	addmsg Purk_spinyd/stell Purk_spinyd CHANNEL Gk Ek
+	addmsg Purk_spinyd  Purk_spinyd/stell  VOLTAGE Vm
+end
+
+/*********************************************************************/
+function make_Purkinje_spines
+/* separate function so we can have local variables */
+/* one standard format, may be rescaled in attach_spines */
+/* Reference: Harris KM, Stevens JK: Dendritic spines of rat
+**  cerebellar Purkinje cells: serial electron microscopy with
+**  reference to their biophysical characteristics.  J Neurosci 8: p
+**  4455-4469, 1988. */
+
+	float len, dia, surf, vol
+
+    /* make spine with average length and diameter */
+	/* make spine neck */
+	len = 0.66e-6
+	dia = 0.20e-6
+	surf = len*dia*{PI}
+	vol = len*dia*dia*{PI}/4.0
+	if (!({exists Purk_spine}))
+		create compartment Purk_spine
+	end
+	setfield Purk_spine Cm {{CM}*surf}  \
+	    Ra {4.0*{RA}*len/(dia*dia*{PI})} Em {ELEAK}  \
+	    initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0 x {len} dia {dia} \
+		len {len}
+
+	/* make spine head */
+	len = 0.00e-6
+	// derived from average surface
+	dia = 0.54e-6
+	surf = dia*dia*{PI}
+	create compartment Purk_spine/head
+	setfield Purk_spine/head Cm {{CM}*surf} Ra {8.0*{RA}/(dia*{PI})} \
+	     Em {ELEAK} initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0  \
+	    x {dia} dia {dia} len {len}
+
+	/* make a combined prototype: neck+head */
+	addmsg Purk_spine/head Purk_spine RAXIAL Ra Vm
+	addmsg Purk_spine Purk_spine/head AXIAL Vm
+
+	copy Purk_spine Purk_spine2
+
+	/* put non-NMDA channel on combined prototype */
+	copy non_NMDA Purk_spine/head/par
+	setfield Purk_spine/head/par gmax {{G_par_syn}*surf}
+	addmsg  Purk_spine/head  Purk_spine/head/par	VOLTAGE Vm
+	addmsg Purk_spine/head/par Purk_spine/head CHANNEL Gk Ek
+
+	/* put non-NMDA channel on combined prototype */
+	copy non_NMDA2 Purk_spine2/head/par2
+	setfield Purk_spine2/head/par2 gmax {{G_par_syn}*surf}
+	addmsg  Purk_spine2/head  Purk_spine2/head/par2	VOLTAGE Vm
+	addmsg Purk_spine2/head/par2 Purk_spine2/head CHANNEL Gk Ek
+
+end
+/*********************************************************************/
Index: 0.58/Purk_spicomp.g
--- 0.58/Purk_spicomp.g Thu, 04 Apr 2002 11:22:47 +0200 hugo ()
+++ parpat-storage-film.3/Purk_spicomp.g Wed, 27 Sep 2000 11:06:49 +0200 hugo (purkinje/b/14_Purk_spico 1.1 640)
@@ -0,0 +1,256 @@
+//genesis - Purkinje cell M9 genesis2.1 script
+/* Copyright E. De Schutter (Caltech and BBF-UIA) */
+
+/**********************************************************************
+** Sets up active membrane Purkinje cell compartment prototypes 
+**  and dendritic spine prototypes.
+** E. De Schutter, Caltech, 1991-1992
+** This version sets up a passive soma and active dendritic compartments 
+**  with stellate cell synapses.
+**********************************************************************/
+
+/* References:
+** E. De Schutter and J.M. Bower: An active membrane model of the
+** cerebellar Purkinje cell. I. Simulation of current clamps in slice.
+** Journal of Neurophysiology  71: 375-400 (1994).
+** http://www.bbf.uia.ac.be/TNB/TNB_pub8.html
+** E. De Schutter and J.M. Bower: An active membrane model of the
+** cerebellar Purkinje cell: II. Simulation of synaptic responses.
+** Journal of Neurophysiology  71: 401-419 (1994).
+** http://www.bbf.uia.ac.be/TNB/TNB_pub7.html
+** E. De Schutter and J.M. Bower: Simulated responses of cerebellar
+** Purkinje cells are independent of the dendritic location of granule 
+** cell synaptic inputs. Proceedings of the National Academy of Sciences 
+** USA 91: 4736-4740 (1994).
+** http://www.bbf.uia.ac.be/TNB/TNB_pub6.html
+** Consult these references for sources of experimental data.
+** See http://www.bbf.uia.ac.be/models/PM9.shtml for general model info.
+*/
+
+function make_Purkinje_comps
+/* separate function so we can have local variables */
+
+	float len, dia, surf, shell_vol, shell_dia
+	int i
+
+	echo making Purkinje compartment library...
+
+	/* make spherical soma prototype with sodium currents*/
+	len = 0.00e-6
+	dia = 20.0e-6
+	surf = dia*dia*{PI}
+	shell_dia = 2*{Shell_thick}
+	shell_vol = (3*dia*dia*shell_dia - 3*dia*shell_dia*shell_dia + shell_dia*shell_dia*shell_dia)*{PI}/6.0
+	if (!({exists Purk_soma}))
+		create compartment Purk_soma
+	end
+	setfield Purk_soma Cm {{CM}*surf} Ra {8.0*{RA}/(dia*{PI})}  \
+	    Em {ELEAK} initVm {EREST_ACT} Rm {{RMs}/surf} inject 0.0  \
+	    dia {dia} len {len}
+
+    /* make main dendrite prototype with fast Ca currents */
+    len = 200.00e-6
+    dia = 2.00e-6
+    surf = len*dia*{PI}
+    shell_vol = (2*dia*shell_dia - shell_dia*shell_dia)*len*{PI}/4.0
+    if (!({exists Purk_maind}))
+        create compartment Purk_maind
+    end
+    setfield Purk_maind Cm {{CM}*surf} Ra {4.0*{RA}*len/(dia*dia*{PI})}  \
+        Em {ELEAK} initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0  \
+        dia {dia} len {len}
+
+    if (!({exists Purk_thickd}))    // Lets copy before we add currents
+
+        copy Purk_maind Purk_thickd
+    end
+    if (!({exists Purk_spinyd}))    // Lets copy before we add currents
+
+        copy Purk_maind Purk_spinyd
+    end
+
+	copy Purk_CaT Purk_maind/CaT
+	addmsg Purk_maind Purk_maind/CaT VOLTAGE Vm
+	addmsg Purk_maind/CaT Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/CaT Gbar {{GCaTm}*surf}
+	copy Purk_KA Purk_maind/KA
+	addmsg Purk_maind Purk_maind/KA VOLTAGE Vm
+	addmsg Purk_maind/KA Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KA Gbar {{GKAm}*surf}
+	copy Purk_Kdr Purk_maind/Kdr
+	addmsg Purk_maind Purk_maind/Kdr VOLTAGE Vm
+	addmsg Purk_maind/Kdr Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/Kdr Gbar {{GKdrm}*surf}
+	copy Purk_KM Purk_maind/KM
+	addmsg Purk_maind Purk_maind/KM VOLTAGE Vm
+	addmsg Purk_maind/KM Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KM Gbar {{GKMm}*surf}
+	copy Purk_CaP Purk_maind/CaP
+	addmsg Purk_maind Purk_maind/CaP VOLTAGE Vm
+	addmsg Purk_maind/CaP Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/CaP Gbar {{GCaPm}*surf}
+	copy Purk_KC Purk_maind/KC
+	addmsg Purk_maind Purk_maind/KC VOLTAGE Vm
+	addmsg Purk_maind/KC Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KC Gbar {{GKCm}*surf}
+	copy Purk_K2 Purk_maind/K2
+	addmsg Purk_maind Purk_maind/K2 VOLTAGE Vm
+	addmsg Purk_maind/K2 Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/K2 Gbar {{GK2m}*surf}
+	create Ca_concen Purk_maind/Ca_pool
+	setfield Purk_maind/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_maind/CaT Purk_maind/Ca_pool I_Ca Ik
+	addmsg Purk_maind/CaP Purk_maind/Ca_pool I_Ca Ik
+	addmsg Purk_maind/Ca_pool Purk_maind/KC CONCEN Ca
+	addmsg Purk_maind/Ca_pool Purk_maind/K2 CONCEN Ca
+	create nernst Purk_maind/Ca_nernst
+	setfield Purk_maind/Ca_nernst Cin {CCaI} Cout {CCaO} valency {2} \
+	     scale {1.0} T {37}
+	addmsg Purk_maind/Ca_pool Purk_maind/Ca_nernst CIN Ca
+	addmsg Purk_maind/Ca_nernst Purk_maind/CaP EK E
+	addmsg Purk_maind/Ca_nernst Purk_maind/CaT EK E
+
+	/* make thick dendrite prototype with fast Ca current */
+	/* similar to main dendrite but has CaP and no Kdr */
+	/* passive prototype already copied from Purk_maind */
+	copy Purk_CaT Purk_thickd/CaT
+	addmsg Purk_thickd Purk_thickd/CaT VOLTAGE Vm
+	addmsg Purk_thickd/CaT Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/CaT Gbar {{GCaTt}*surf}
+	copy Purk_CaP Purk_thickd/CaP
+	addmsg Purk_thickd Purk_thickd/CaP VOLTAGE Vm
+	addmsg Purk_thickd/CaP Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/CaP Gbar {{GCaPt}*surf}
+	copy Purk_KM Purk_thickd/KM
+	addmsg Purk_thickd Purk_thickd/KM VOLTAGE Vm
+	addmsg Purk_thickd/KM Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/KM Gbar {{GKMt}*surf}
+	copy Purk_KC Purk_thickd/KC
+	addmsg Purk_thickd Purk_thickd/KC VOLTAGE Vm
+	addmsg Purk_thickd/KC Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/KC Gbar {{GKCt}*surf}
+	copy Purk_K2 Purk_thickd/K2
+	addmsg Purk_thickd Purk_thickd/K2 VOLTAGE Vm
+	addmsg Purk_thickd/K2 Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/K2 Gbar {{GK2t}*surf}
+	create Ca_concen Purk_thickd/Ca_pool
+	setfield Purk_thickd/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_thickd/CaT Purk_thickd/Ca_pool I_Ca Ik
+	addmsg Purk_thickd/CaP Purk_thickd/Ca_pool I_Ca Ik
+	addmsg Purk_thickd/Ca_pool Purk_thickd/KC CONCEN Ca
+	addmsg Purk_thickd/Ca_pool Purk_thickd/K2 CONCEN Ca
+	create nernst Purk_thickd/Ca_nernst
+	setfield Purk_thickd/Ca_nernst Cin {CCaI} Cout {CCaO}  \
+	    valency {2} scale {1.0} T {37}
+	addmsg Purk_thickd/Ca_pool Purk_thickd/Ca_nernst CIN Ca
+	addmsg Purk_thickd/Ca_nernst Purk_thickd/CaP EK E
+	addmsg Purk_thickd/Ca_nernst Purk_thickd/CaT EK E
+	for (i=1; i<=2; i = i+1)
+	    copy GABA Purk_thickd/stell{i}
+	    setfield Purk_thickd/stell{i} gmax {{G_GABA}/5*surf}
+	    addmsg Purk_thickd/stell{i} Purk_thickd CHANNEL Gk Ek
+		addmsg Purk_thickd  Purk_thickd/stell{i}  VOLTAGE Vm
+	end
+
+	/* make spiny dendrite prototype with high threshold Ca current  \
+	    */
+	/* passive prototype already copied from Purk_maind */
+	copy Purk_CaT Purk_spinyd/CaT
+	addmsg Purk_spinyd Purk_spinyd/CaT VOLTAGE Vm
+	addmsg Purk_spinyd/CaT Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/CaT Gbar {{GCaTd}*surf}
+	copy Purk_CaP Purk_spinyd/CaP
+	addmsg Purk_spinyd Purk_spinyd/CaP VOLTAGE Vm
+	addmsg Purk_spinyd/CaP Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/CaP Gbar {{GCaPd}*surf}
+	copy Purk_KM Purk_spinyd/KM
+	addmsg Purk_spinyd Purk_spinyd/KM VOLTAGE Vm
+	addmsg Purk_spinyd/KM Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/KM Gbar {{GKMd}*surf}
+	copy Purk_KC Purk_spinyd/KC
+	addmsg Purk_spinyd Purk_spinyd/KC VOLTAGE Vm
+	addmsg Purk_spinyd/KC Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/KC Gbar {{GKCd}*surf}
+	copy Purk_K2 Purk_spinyd/K2
+	addmsg Purk_spinyd Purk_spinyd/K2 VOLTAGE Vm
+	addmsg Purk_spinyd/K2 Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/K2 Gbar {{GK2d}*surf}
+	create Ca_concen Purk_spinyd/Ca_pool
+	setfield Purk_spinyd/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_spinyd/CaP Purk_spinyd/Ca_pool I_Ca Ik
+	addmsg Purk_spinyd/CaT Purk_spinyd/Ca_pool I_Ca Ik
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/KC CONCEN Ca
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/K2 CONCEN Ca
+	create nernst Purk_spinyd/Ca_nernst
+	setfield Purk_spinyd/Ca_nernst Cin {CCaI} Cout {CCaO}  \
+	    valency {2} scale {1.0} T {37}
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/Ca_nernst CIN Ca
+	addmsg Purk_spinyd/Ca_nernst Purk_spinyd/CaP EK E
+	addmsg Purk_spinyd/Ca_nernst Purk_spinyd/CaT EK E
+	copy GABA Purk_spinyd/stell
+	setfield Purk_spinyd/stell gmax {{G_GABA}*surf}
+	addmsg Purk_spinyd/stell Purk_spinyd CHANNEL Gk Ek
+	addmsg Purk_spinyd  Purk_spinyd/stell  VOLTAGE Vm
+end
+
+/*********************************************************************/
+function make_Purkinje_spines
+/* separate function so we can have local variables */
+/* one standard format, may be rescaled in attach_spines */
+/* Reference: Harris KM, Stevens JK: Dendritic spines of rat
+**  cerebellar Purkinje cells: serial electron microscopy with
+**  reference to their biophysical characteristics.  J Neurosci 8: p
+**  4455-4469, 1988. */
+
+	float len, dia, surf, vol
+
+    /* make spine with average length and diameter */
+	/* make spine neck */
+	len = 0.66e-6
+	dia = 0.20e-6
+	surf = len*dia*{PI}
+	vol = len*dia*dia*{PI}/4.0
+	if (!({exists Purk_spine}))
+		create compartment Purk_spine
+	end
+	setfield Purk_spine Cm {{CM}*surf}  \
+	    Ra {4.0*{RA}*len/(dia*dia*{PI})} Em {ELEAK}  \
+	    initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0 x {len} dia {dia} \
+		len {len}
+
+	/* make spine head */
+	len = 0.00e-6
+	// derived from average surface
+	dia = 0.54e-6
+	surf = dia*dia*{PI}
+	create compartment Purk_spine/head
+	setfield Purk_spine/head Cm {{CM}*surf} Ra {8.0*{RA}/(dia*{PI})} \
+	     Em {ELEAK} initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0  \
+	    x {dia} dia {dia} len {len}
+
+	/* make a combined prototype: neck+head */
+	addmsg Purk_spine/head Purk_spine RAXIAL Ra Vm
+	addmsg Purk_spine Purk_spine/head AXIAL Vm
+
+	copy Purk_spine Purk_spine2
+
+	/* put non-NMDA channel on combined prototype */
+	copy non_NMDA Purk_spine/head/par
+	setfield Purk_spine/head/par gmax {{G_par_syn}*surf}
+	addmsg  Purk_spine/head  Purk_spine/head/par	VOLTAGE Vm
+	addmsg Purk_spine/head/par Purk_spine/head CHANNEL Gk Ek
+
+	/* put non-NMDA channel on combined prototype */
+	copy non_NMDA2 Purk_spine2/head/par2
+	setfield Purk_spine2/head/par2 gmax {{G_par_syn}*surf}
+	addmsg  Purk_spine2/head  Purk_spine2/head/par2	VOLTAGE Vm
+	addmsg Purk_spine2/head/par2 Purk_spine2/head CHANNEL Gk Ek
+
+end
+/*********************************************************************/
Index: 0.58/Purk_passconst.g
--- 0.58/Purk_passconst.g Thu, 04 Apr 2002 11:22:47 +0200 hugo ()
+++ parpat-storage-film.3/Purk_passconst.g Wed, 27 Sep 2000 11:06:49 +0200 hugo (purkinje/b/15_Purk_passc 1.1 640)
@@ -0,0 +1,70 @@
+//genesis  - Purkinje cell M9 genesis2.1 script
+/* Copyright E. De Schutter (Caltech and BBF-UIA) */
+
+/* This file defines important simulation parameters, including gmax
+** and Ek for all channels.  Everything uses SI units. */
+
+echo Using Purkinje 2M9 preferences. Crank Nicholson method.
+/* variables controlling hsolve integration */
+float dt = 2.0e-5
+int tab_xdivs = 149
+int tab_xfills = 2999
+
+/* The model is quite sensitive to these values in NO_INTERP (caclmode=0) */
+float tab_xmin = -0.10
+float tab_xmax = 0.05
+float Ca_tab_max = 0.300
+
+// only used for proto channels
+float GNa = 1, GCa = 1, GK = 1, Gh = 1
+/* cable parameters */
+float CM = 0.0164 		// *9 relative to passive
+float RMs = 1.000 		// /3.7 relative to passive comp
+float RMd = 3.0
+float RA = 2.50
+/* preset constants */
+float ELEAK = -0.0800 		// Ek value used for the leak conductance
+float EREST_ACT = -0.0680 	// Vm value used for the RESET
+/* concentrations */
+float CCaO = 2.4000 		//external Ca as in normal slice Ringer
+float CCaI = 0.000040		//internal Ca in mM
+//diameter of Ca_shells
+float Shell_thick = 0.20e-6
+float CaTau = 0.00010	 	// Ca_concen tau
+/* Currents: Reversal potentials in V and max conductances S/m^2 */
+/* Codes: s=soma, m=main dendrite, t=thick dendrite, d=spiny dendrite */
+float ENa = 0.045
+float GNaFs = 75000.0
+float GNaPs = 10.0
+float ECa = 0.0125*{log {CCaO/CCaI}} // 0.135 V
+float GCaTs = 5.00
+float GCaTm = 0//5.00
+float GCaTt = 0//5.00
+float GCaTd = 0//5.00
+float GCaPm = 0//45.0
+float GCaPt = 0//45.0
+float GCaPd = 0//45.0
+float EK = -0.085
+float GKAs = 150.0
+float GKAm = 0//20.0
+float GKdrs = 6000.0
+float GKdrm = 0//600.0
+float GKMs = 0.400
+float GKMm = 0//0.100
+float GKMt = 0//0.130
+float GKMd = 0//0.130
+float GKCm = 0//800.0
+float GKCt = 0//800.0
+float GKCd = 0//800.0
+float GK2m = 0//3.90
+float GK2t = 0//3.90
+float GK2d = 0//3.90
+float Eh = -0.030
+float Ghs = 3.00
+/* synapses: */
+float E_GABA = -0.080
+float G_GABA = 70.0/dt
+float GB_GABA = 20.0/dt
+float E_non_NMDA = 0.000
+float G_par_syn = 750.0/dt
+float G_cli_syn = 150.0/dt
Index: 0.58/Purk_iticomp.g
--- 0.58/Purk_iticomp.g Thu, 04 Apr 2002 11:22:47 +0200 hugo ()
+++ parpat-storage-film.3/Purk_iticomp.g Wed, 27 Sep 2000 11:06:49 +0200 hugo (purkinje/b/16_Purk_itico 1.1 640)
@@ -0,0 +1,296 @@
+//genesis - Purkinje cell M9 genesis2.1 script
+/* Copyright E. De Schutter (Caltech and BBF-UIA) */
+
+/**********************************************************************
+** Sets up active membrane Purkinje cell compartment prototypes 
+**  and dendritic spine prototypes.
+** E. De Schutter, Caltech, 1991-1992
+** This version sets up active compartments with stellate cell synapses.
+**********************************************************************/
+
+/* References:
+** E. De Schutter and J.M. Bower: An active membrane model of the
+** cerebellar Purkinje cell. I. Simulation of current clamps in slice.
+** Journal of Neurophysiology  71: 375-400 (1994).
+** http://www.bbf.uia.ac.be/TNB/TNB_pub8.html
+** E. De Schutter and J.M. Bower: An active membrane model of the
+** cerebellar Purkinje cell: II. Simulation of synaptic responses.
+** Journal of Neurophysiology  71: 401-419 (1994).
+** http://www.bbf.uia.ac.be/TNB/TNB_pub7.html
+** Consult these references for sources of experimental data.
+** See http://www.bbf.uia.ac.be/models/PM9.shtml for general model info.
+*/
+
+function make_Purkinje_comps
+/* separate function so we can have local variables */
+
+	float len, dia, surf, shell_vol, shell_dia
+	int i
+
+	echo making Purkinje compartment library...
+
+	/* make spherical soma prototype with sodium currents*/
+	len = 0.00e-6
+	dia = 20.0e-6
+	surf = dia*dia*{PI}
+	shell_dia = 2*{Shell_thick}
+	shell_vol = (3*dia*dia*shell_dia - 3*dia*shell_dia*shell_dia + shell_dia*shell_dia*shell_dia)*{PI}/6.0
+	if (!({exists Purk_soma}))
+		create compartment Purk_soma
+	end
+	setfield Purk_soma Cm {{CM}*surf} Ra {8.0*{RA}/(dia*{PI})}  \
+	    Em {ELEAK} initVm {EREST_ACT} Rm {{RMs}/surf} inject 0.0  \
+	    dia {dia} len {len}
+
+	copy Purk_NaF Purk_soma/NaF
+	addmsg Purk_soma Purk_soma/NaF VOLTAGE Vm
+	addmsg Purk_soma/NaF Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/NaF Gbar {{GNaFs}*surf}
+	copy Purk_NaP Purk_soma/NaP
+	addmsg Purk_soma Purk_soma/NaP VOLTAGE Vm
+	addmsg Purk_soma/NaP Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/NaP Gbar {{GNaPs}*surf}
+	copy Purk_CaT Purk_soma/CaT
+	addmsg Purk_soma Purk_soma/CaT VOLTAGE Vm
+	addmsg Purk_soma/CaT Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/CaT Gbar {{GCaTs}*surf}
+	copy Purk_KA Purk_soma/KA
+	addmsg Purk_soma Purk_soma/KA VOLTAGE Vm
+	addmsg Purk_soma/KA Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/KA Gbar {{GKAs}*surf}
+	copy Purk_Kdr Purk_soma/Kdr
+	addmsg Purk_soma Purk_soma/Kdr VOLTAGE Vm
+	addmsg Purk_soma/Kdr Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/Kdr Gbar {{GKdrs}*surf}
+	copy Purk_KM Purk_soma/KM
+	addmsg Purk_soma Purk_soma/KM VOLTAGE Vm
+	addmsg Purk_soma/KM Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/KM Gbar {{GKMs}*surf}
+	copy Purk_h1 Purk_soma/h1
+	addmsg Purk_soma Purk_soma/h1 VOLTAGE Vm
+	addmsg Purk_soma/h1 Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/h1 Gbar {{Ghs}*surf}
+	copy Purk_h2 Purk_soma/h2
+	addmsg Purk_soma Purk_soma/h2 VOLTAGE Vm
+	addmsg Purk_soma/h2 Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/h2 Gbar {{Ghs}*surf}
+	create Ca_concen Purk_soma/Ca_pool
+	setfield Purk_soma/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_soma/CaT Purk_soma/Ca_pool I_Ca Ik
+
+    /* make main dendrite prototype with fast Ca currents */
+    len = 200.00e-6
+    dia = 2.00e-6
+    surf = len*dia*{PI}
+    shell_vol = (2*dia*shell_dia - shell_dia*shell_dia)*len*{PI}/4.0
+    if (!({exists Purk_maind}))
+        create compartment Purk_maind
+    end
+    setfield Purk_maind Cm {{CM}*surf} Ra {4.0*{RA}*len/(dia*dia*{PI})}  \
+        Em {ELEAK} initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0  \
+        dia {dia} len {len}
+
+    if (!({exists Purk_thickd}))    // Lets copy before we add currents
+
+        copy Purk_maind Purk_thickd
+    end
+    if (!({exists Purk_spinyd}))    // Lets copy before we add currents
+
+        copy Purk_maind Purk_spinyd
+    end
+
+	copy Purk_CaT Purk_maind/CaT
+	addmsg Purk_maind Purk_maind/CaT VOLTAGE Vm
+	addmsg Purk_maind/CaT Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/CaT Gbar {{GCaTm}*surf}
+	copy Purk_KA Purk_maind/KA
+	addmsg Purk_maind Purk_maind/KA VOLTAGE Vm
+	addmsg Purk_maind/KA Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KA Gbar {{GKAm}*surf}
+	copy Purk_Kdr Purk_maind/Kdr
+	addmsg Purk_maind Purk_maind/Kdr VOLTAGE Vm
+	addmsg Purk_maind/Kdr Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/Kdr Gbar {{GKdrm}*surf}
+	copy Purk_KM Purk_maind/KM
+	addmsg Purk_maind Purk_maind/KM VOLTAGE Vm
+	addmsg Purk_maind/KM Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KM Gbar {{GKMm}*surf}
+	copy Purk_CaP Purk_maind/CaP
+	addmsg Purk_maind Purk_maind/CaP VOLTAGE Vm
+	addmsg Purk_maind/CaP Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/CaP Gbar {{GCaPm}*surf}
+	copy Purk_KC Purk_maind/KC
+	addmsg Purk_maind Purk_maind/KC VOLTAGE Vm
+	addmsg Purk_maind/KC Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KC Gbar {{GKCm}*surf}
+	copy Purk_K2 Purk_maind/K2
+	addmsg Purk_maind Purk_maind/K2 VOLTAGE Vm
+	addmsg Purk_maind/K2 Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/K2 Gbar {{GK2m}*surf}
+	create Ca_concen Purk_maind/Ca_pool
+	setfield Purk_maind/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_maind/CaT Purk_maind/Ca_pool I_Ca Ik
+	addmsg Purk_maind/CaP Purk_maind/Ca_pool I_Ca Ik
+	addmsg Purk_maind/Ca_pool Purk_maind/KC CONCEN Ca
+	addmsg Purk_maind/Ca_pool Purk_maind/K2 CONCEN Ca
+	create nernst Purk_maind/Ca_nernst
+	setfield Purk_maind/Ca_nernst Cin {CCaI} Cout {CCaO} valency {2} \
+	     scale {1.0} T {37}
+	addmsg Purk_maind/Ca_pool Purk_maind/Ca_nernst CIN Ca
+	addmsg Purk_maind/Ca_nernst Purk_maind/CaP EK E
+	addmsg Purk_maind/Ca_nernst Purk_maind/CaT EK E
+
+	/* make thick dendrite prototype with fast Ca current */
+	/* similar to main dendrite but has CaP and no Kdr */
+	/* passive prototype already copied from Purk_maind */
+	setfield Purk_thickd Cm {{CM}*surf} Ra {4.0*{RA}*len/(dia*dia*{PI})}  \
+          Em {ELEAK} initVm {EREST_ACT} Rm {{RMtd}/surf} inject 0.0  \
+          dia {dia} len {len}
+
+        copy Purk_CaT Purk_thickd/CaT
+	addmsg Purk_thickd Purk_thickd/CaT VOLTAGE Vm
+	addmsg Purk_thickd/CaT Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/CaT Gbar {{GCaTt}*surf}
+	copy Purk_CaP Purk_thickd/CaP
+	addmsg Purk_thickd Purk_thickd/CaP VOLTAGE Vm
+	addmsg Purk_thickd/CaP Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/CaP Gbar {{GCaPt}*surf}
+	copy Purk_KM Purk_thickd/KM
+	addmsg Purk_thickd Purk_thickd/KM VOLTAGE Vm
+	addmsg Purk_thickd/KM Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/KM Gbar {{GKMt}*surf}
+	copy Purk_KC Purk_thickd/KC
+	addmsg Purk_thickd Purk_thickd/KC VOLTAGE Vm
+	addmsg Purk_thickd/KC Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/KC Gbar {{GKCt}*surf}
+	copy Purk_K2 Purk_thickd/K2
+	addmsg Purk_thickd Purk_thickd/K2 VOLTAGE Vm
+	addmsg Purk_thickd/K2 Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/K2 Gbar {{GK2t}*surf}
+	create Ca_concen Purk_thickd/Ca_pool
+	setfield Purk_thickd/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_thickd/CaT Purk_thickd/Ca_pool I_Ca Ik
+	addmsg Purk_thickd/CaP Purk_thickd/Ca_pool I_Ca Ik
+	addmsg Purk_thickd/Ca_pool Purk_thickd/KC CONCEN Ca
+	addmsg Purk_thickd/Ca_pool Purk_thickd/K2 CONCEN Ca
+	create nernst Purk_thickd/Ca_nernst
+	setfield Purk_thickd/Ca_nernst Cin {CCaI} Cout {CCaO}  \
+	    valency {2} scale {1.0} T {37}
+	addmsg Purk_thickd/Ca_pool Purk_thickd/Ca_nernst CIN Ca
+	addmsg Purk_thickd/Ca_nernst Purk_thickd/CaP EK E
+	addmsg Purk_thickd/Ca_nernst Purk_thickd/CaT EK E
+	for (i=1; i<=2; i = i+1)
+	    copy GABA Purk_thickd/stell{i}
+	    setfield Purk_thickd/stell{i} gmax {{G_GABA}/5*surf}
+	    addmsg Purk_thickd/stell{i} Purk_thickd CHANNEL Gk Ek
+		addmsg Purk_thickd  Purk_thickd/stell{i}  VOLTAGE Vm
+	end
+
+	/* make spiny dendrite prototype with high threshold Ca current  \
+	    */
+	/* passive prototype already copied from Purk_maind */
+	setfield Purk_spinyd Cm {{CM}*surf} Ra {4.0*{RA}*len/(dia*dia*{PI})}  \
+          Em {ELEAK} initVm {EREST_ACT} Rm {{RMsd}/surf} inject 0.0  \
+          dia {dia} len {len}
+
+        copy Purk_CaT Purk_spinyd/CaT
+	addmsg Purk_spinyd Purk_spinyd/CaT VOLTAGE Vm
+	addmsg Purk_spinyd/CaT Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/CaT Gbar {{GCaTd}*surf}
+	copy Purk_CaP Purk_spinyd/CaP
+	addmsg Purk_spinyd Purk_spinyd/CaP VOLTAGE Vm
+	addmsg Purk_spinyd/CaP Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/CaP Gbar {{GCaPd}*surf}
+	copy Purk_KM Purk_spinyd/KM
+	addmsg Purk_spinyd Purk_spinyd/KM VOLTAGE Vm
+	addmsg Purk_spinyd/KM Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/KM Gbar {{GKMd}*surf}
+	copy Purk_KC Purk_spinyd/KC
+	addmsg Purk_spinyd Purk_spinyd/KC VOLTAGE Vm
+	addmsg Purk_spinyd/KC Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/KC Gbar {{GKCd}*surf}
+	copy Purk_K2 Purk_spinyd/K2
+	addmsg Purk_spinyd Purk_spinyd/K2 VOLTAGE Vm
+	addmsg Purk_spinyd/K2 Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/K2 Gbar {{GK2d}*surf}
+	create Ca_concen Purk_spinyd/Ca_pool
+	setfield Purk_spinyd/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_spinyd/CaP Purk_spinyd/Ca_pool I_Ca Ik
+	addmsg Purk_spinyd/CaT Purk_spinyd/Ca_pool I_Ca Ik
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/KC CONCEN Ca
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/K2 CONCEN Ca
+	create nernst Purk_spinyd/Ca_nernst
+	setfield Purk_spinyd/Ca_nernst Cin {CCaI} Cout {CCaO}  \
+	    valency {2} scale {1.0} T {37}
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/Ca_nernst CIN Ca
+	addmsg Purk_spinyd/Ca_nernst Purk_spinyd/CaP EK E
+	addmsg Purk_spinyd/Ca_nernst Purk_spinyd/CaT EK E
+	copy GABA Purk_spinyd/stell
+	setfield Purk_spinyd/stell gmax {{G_GABA}*surf}
+	addmsg Purk_spinyd/stell Purk_spinyd CHANNEL Gk Ek
+	addmsg Purk_spinyd  Purk_spinyd/stell  VOLTAGE Vm
+end
+
+/*********************************************************************/
+function make_Purkinje_spines
+/* separate function so we can have local variables */
+/* one standard format, may be rescaled in attach_spines */
+/* Reference: Harris KM, Stevens JK: Dendritic spines of rat
+**  cerebellar Purkinje cells: serial electron microscopy with
+**  reference to their biophysical characteristics.  J Neurosci 8: p
+**  4455-4469, 1988. */
+
+	float len, dia, surf, vol
+
+    /* make spine with average length and diameter */
+	/* make spine neck */
+	len = 0.66e-6
+	dia = 0.20e-6
+	surf = len*dia*{PI}
+	vol = len*dia*dia*{PI}/4.0
+	if (!({exists Purk_spine}))
+		create compartment Purk_spine
+	end
+	setfield Purk_spine Cm {{CM}*surf}  \
+	    Ra {4.0*{RA}*len/(dia*dia*{PI})} Em {ELEAK}  \
+	    initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0 x {len} dia {dia} \
+		len {len}
+
+	/* make spine head */
+	len = 0.00e-6
+	// derived from average surface
+	dia = 0.54e-6
+	surf = dia*dia*{PI}
+	create compartment Purk_spine/head
+	setfield Purk_spine/head Cm {{CM}*surf} Ra {8.0*{RA}/(dia*{PI})} \
+	     Em {ELEAK} initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0  \
+	    x {dia} dia {dia} len {len}
+
+	/* make a combined prototype: neck+head */
+	addmsg Purk_spine/head Purk_spine RAXIAL Ra Vm
+	addmsg Purk_spine Purk_spine/head AXIAL Vm
+
+	copy Purk_spine Purk_spine2
+
+	/* put non-NMDA channel on combined prototype */
+	copy non_NMDA Purk_spine/head/par
+	setfield Purk_spine/head/par gmax {{G_par_syn}*surf}
+	addmsg  Purk_spine/head  Purk_spine/head/par	VOLTAGE Vm
+	addmsg Purk_spine/head/par Purk_spine/head CHANNEL Gk Ek
+
+	/* put non-NMDA channel on combined prototype */
+	copy non_NMDA2 Purk_spine2/head/par2
+	setfield Purk_spine2/head/par2 gmax {{G_par_syn}*surf}
+	addmsg  Purk_spine2/head  Purk_spine2/head/par2	VOLTAGE Vm
+	addmsg Purk_spine2/head/par2 Purk_spine2/head CHANNEL Gk Ek
+
+end
+/*********************************************************************/
Index: 0.58/Purk_icomp.g
--- 0.58/Purk_icomp.g Thu, 04 Apr 2002 11:22:47 +0200 hugo ()
+++ parpat-storage-film.3/Purk_icomp.g Wed, 27 Sep 2000 11:06:49 +0200 hugo (purkinje/b/17_Purk_icomp 1.1 640)
@@ -0,0 +1,288 @@
+//genesis - Purkinje cell M9 genesis2.1 script
+/* Copyright E. De Schutter (Caltech and BBF-UIA) */
+
+/**********************************************************************
+** Sets up active membrane Purkinje cell compartment prototypes 
+**  and dendritic spine prototypes.
+** E. De Schutter, Caltech, 1991-1992
+** This version sets up active compartments with stellate cell synapses.
+**********************************************************************/
+
+/* References:
+** E. De Schutter and J.M. Bower: An active membrane model of the
+** cerebellar Purkinje cell. I. Simulation of current clamps in slice.
+** Journal of Neurophysiology  71: 375-400 (1994).
+** http://www.bbf.uia.ac.be/TNB/TNB_pub8.html
+** E. De Schutter and J.M. Bower: An active membrane model of the
+** cerebellar Purkinje cell: II. Simulation of synaptic responses.
+** Journal of Neurophysiology  71: 401-419 (1994).
+** http://www.bbf.uia.ac.be/TNB/TNB_pub7.html
+** Consult these references for sources of experimental data.
+** See http://www.bbf.uia.ac.be/models/PM9.shtml for general model info.
+*/
+
+function make_Purkinje_comps
+/* separate function so we can have local variables */
+
+	float len, dia, surf, shell_vol, shell_dia
+	int i
+
+	echo making Purkinje compartment library...
+
+	/* make spherical soma prototype with sodium currents*/
+	len = 0.00e-6
+	dia = 20.0e-6
+	surf = dia*dia*{PI}
+	shell_dia = 2*{Shell_thick}
+	shell_vol = (3*dia*dia*shell_dia - 3*dia*shell_dia*shell_dia + shell_dia*shell_dia*shell_dia)*{PI}/6.0
+	if (!({exists Purk_soma}))
+		create compartment Purk_soma
+	end
+	setfield Purk_soma Cm {{CM}*surf} Ra {8.0*{RA}/(dia*{PI})}  \
+	    Em {ELEAK} initVm {EREST_ACT} Rm {{RMs}/surf} inject 0.0  \
+	    dia {dia} len {len}
+
+	copy Purk_NaF Purk_soma/NaF
+	addmsg Purk_soma Purk_soma/NaF VOLTAGE Vm
+	addmsg Purk_soma/NaF Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/NaF Gbar {{GNaFs}*surf}
+	copy Purk_NaP Purk_soma/NaP
+	addmsg Purk_soma Purk_soma/NaP VOLTAGE Vm
+	addmsg Purk_soma/NaP Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/NaP Gbar {{GNaPs}*surf}
+	copy Purk_CaT Purk_soma/CaT
+	addmsg Purk_soma Purk_soma/CaT VOLTAGE Vm
+	addmsg Purk_soma/CaT Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/CaT Gbar {{GCaTs}*surf}
+	copy Purk_KA Purk_soma/KA
+	addmsg Purk_soma Purk_soma/KA VOLTAGE Vm
+	addmsg Purk_soma/KA Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/KA Gbar {{GKAs}*surf}
+	copy Purk_Kdr Purk_soma/Kdr
+	addmsg Purk_soma Purk_soma/Kdr VOLTAGE Vm
+	addmsg Purk_soma/Kdr Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/Kdr Gbar {{GKdrs}*surf}
+	copy Purk_KM Purk_soma/KM
+	addmsg Purk_soma Purk_soma/KM VOLTAGE Vm
+	addmsg Purk_soma/KM Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/KM Gbar {{GKMs}*surf}
+	copy Purk_h1 Purk_soma/h1
+	addmsg Purk_soma Purk_soma/h1 VOLTAGE Vm
+	addmsg Purk_soma/h1 Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/h1 Gbar {{Ghs}*surf}
+	copy Purk_h2 Purk_soma/h2
+	addmsg Purk_soma Purk_soma/h2 VOLTAGE Vm
+	addmsg Purk_soma/h2 Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/h2 Gbar {{Ghs}*surf}
+	create Ca_concen Purk_soma/Ca_pool
+	setfield Purk_soma/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_soma/CaT Purk_soma/Ca_pool I_Ca Ik
+
+    /* make main dendrite prototype with fast Ca currents */
+    len = 200.00e-6
+    dia = 2.00e-6
+    surf = len*dia*{PI}
+    shell_vol = (2*dia*shell_dia - shell_dia*shell_dia)*len*{PI}/4.0
+    if (!({exists Purk_maind}))
+        create compartment Purk_maind
+    end
+    setfield Purk_maind Cm {{CM}*surf} Ra {4.0*{RA}*len/(dia*dia*{PI})}  \
+        Em {ELEAK} initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0  \
+        dia {dia} len {len}
+
+    if (!({exists Purk_thickd}))    // Lets copy before we add currents
+
+        copy Purk_maind Purk_thickd
+    end
+    if (!({exists Purk_spinyd}))    // Lets copy before we add currents
+
+        copy Purk_maind Purk_spinyd
+    end
+
+	copy Purk_CaT Purk_maind/CaT
+	addmsg Purk_maind Purk_maind/CaT VOLTAGE Vm
+	addmsg Purk_maind/CaT Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/CaT Gbar {{GCaTm}*surf}
+	copy Purk_KA Purk_maind/KA
+	addmsg Purk_maind Purk_maind/KA VOLTAGE Vm
+	addmsg Purk_maind/KA Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KA Gbar {{GKAm}*surf}
+	copy Purk_Kdr Purk_maind/Kdr
+	addmsg Purk_maind Purk_maind/Kdr VOLTAGE Vm
+	addmsg Purk_maind/Kdr Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/Kdr Gbar {{GKdrm}*surf}
+	copy Purk_KM Purk_maind/KM
+	addmsg Purk_maind Purk_maind/KM VOLTAGE Vm
+	addmsg Purk_maind/KM Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KM Gbar {{GKMm}*surf}
+	copy Purk_CaP Purk_maind/CaP
+	addmsg Purk_maind Purk_maind/CaP VOLTAGE Vm
+	addmsg Purk_maind/CaP Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/CaP Gbar {{GCaPm}*surf}
+	copy Purk_KC Purk_maind/KC
+	addmsg Purk_maind Purk_maind/KC VOLTAGE Vm
+	addmsg Purk_maind/KC Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KC Gbar {{GKCm}*surf}
+	copy Purk_K2 Purk_maind/K2
+	addmsg Purk_maind Purk_maind/K2 VOLTAGE Vm
+	addmsg Purk_maind/K2 Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/K2 Gbar {{GK2m}*surf}
+	create Ca_concen Purk_maind/Ca_pool
+	setfield Purk_maind/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_maind/CaT Purk_maind/Ca_pool I_Ca Ik
+	addmsg Purk_maind/CaP Purk_maind/Ca_pool I_Ca Ik
+	addmsg Purk_maind/Ca_pool Purk_maind/KC CONCEN Ca
+	addmsg Purk_maind/Ca_pool Purk_maind/K2 CONCEN Ca
+	create nernst Purk_maind/Ca_nernst
+	setfield Purk_maind/Ca_nernst Cin {CCaI} Cout {CCaO} valency {2} \
+	     scale {1.0} T {37}
+	addmsg Purk_maind/Ca_pool Purk_maind/Ca_nernst CIN Ca
+	addmsg Purk_maind/Ca_nernst Purk_maind/CaP EK E
+	addmsg Purk_maind/Ca_nernst Purk_maind/CaT EK E
+
+	/* make thick dendrite prototype with fast Ca current */
+	/* similar to main dendrite but has CaP and no Kdr */
+	/* passive prototype already copied from Purk_maind */
+	copy Purk_CaT Purk_thickd/CaT
+	addmsg Purk_thickd Purk_thickd/CaT VOLTAGE Vm
+	addmsg Purk_thickd/CaT Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/CaT Gbar {{GCaTt}*surf}
+	copy Purk_CaP Purk_thickd/CaP
+	addmsg Purk_thickd Purk_thickd/CaP VOLTAGE Vm
+	addmsg Purk_thickd/CaP Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/CaP Gbar {{GCaPt}*surf}
+	copy Purk_KM Purk_thickd/KM
+	addmsg Purk_thickd Purk_thickd/KM VOLTAGE Vm
+	addmsg Purk_thickd/KM Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/KM Gbar {{GKMt}*surf}
+	copy Purk_KC Purk_thickd/KC
+	addmsg Purk_thickd Purk_thickd/KC VOLTAGE Vm
+	addmsg Purk_thickd/KC Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/KC Gbar {{GKCt}*surf}
+	copy Purk_K2 Purk_thickd/K2
+	addmsg Purk_thickd Purk_thickd/K2 VOLTAGE Vm
+	addmsg Purk_thickd/K2 Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/K2 Gbar {{GK2t}*surf}
+	create Ca_concen Purk_thickd/Ca_pool
+	setfield Purk_thickd/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_thickd/CaT Purk_thickd/Ca_pool I_Ca Ik
+	addmsg Purk_thickd/CaP Purk_thickd/Ca_pool I_Ca Ik
+	addmsg Purk_thickd/Ca_pool Purk_thickd/KC CONCEN Ca
+	addmsg Purk_thickd/Ca_pool Purk_thickd/K2 CONCEN Ca
+	create nernst Purk_thickd/Ca_nernst
+	setfield Purk_thickd/Ca_nernst Cin {CCaI} Cout {CCaO}  \
+	    valency {2} scale {1.0} T {37}
+	addmsg Purk_thickd/Ca_pool Purk_thickd/Ca_nernst CIN Ca
+	addmsg Purk_thickd/Ca_nernst Purk_thickd/CaP EK E
+	addmsg Purk_thickd/Ca_nernst Purk_thickd/CaT EK E
+	for (i=1; i<=2; i = i+1)
+	    copy GABA Purk_thickd/stell{i}
+	    setfield Purk_thickd/stell{i} gmax {{G_GABA}/5*surf}
+	    addmsg Purk_thickd/stell{i} Purk_thickd CHANNEL Gk Ek
+		addmsg Purk_thickd  Purk_thickd/stell{i}  VOLTAGE Vm
+	end
+
+	/* make spiny dendrite prototype with high threshold Ca current  \
+	    */
+	/* passive prototype already copied from Purk_maind */
+	copy Purk_CaT Purk_spinyd/CaT
+	addmsg Purk_spinyd Purk_spinyd/CaT VOLTAGE Vm
+	addmsg Purk_spinyd/CaT Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/CaT Gbar {{GCaTd}*surf}
+	copy Purk_CaP Purk_spinyd/CaP
+	addmsg Purk_spinyd Purk_spinyd/CaP VOLTAGE Vm
+	addmsg Purk_spinyd/CaP Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/CaP Gbar {{GCaPd}*surf}
+	copy Purk_KM Purk_spinyd/KM
+	addmsg Purk_spinyd Purk_spinyd/KM VOLTAGE Vm
+	addmsg Purk_spinyd/KM Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/KM Gbar {{GKMd}*surf}
+	copy Purk_KC Purk_spinyd/KC
+	addmsg Purk_spinyd Purk_spinyd/KC VOLTAGE Vm
+	addmsg Purk_spinyd/KC Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/KC Gbar {{GKCd}*surf}
+	copy Purk_K2 Purk_spinyd/K2
+	addmsg Purk_spinyd Purk_spinyd/K2 VOLTAGE Vm
+	addmsg Purk_spinyd/K2 Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/K2 Gbar {{GK2d}*surf}
+	create Ca_concen Purk_spinyd/Ca_pool
+	setfield Purk_spinyd/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_spinyd/CaP Purk_spinyd/Ca_pool I_Ca Ik
+	addmsg Purk_spinyd/CaT Purk_spinyd/Ca_pool I_Ca Ik
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/KC CONCEN Ca
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/K2 CONCEN Ca
+	create nernst Purk_spinyd/Ca_nernst
+	setfield Purk_spinyd/Ca_nernst Cin {CCaI} Cout {CCaO}  \
+	    valency {2} scale {1.0} T {37}
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/Ca_nernst CIN Ca
+	addmsg Purk_spinyd/Ca_nernst Purk_spinyd/CaP EK E
+	addmsg Purk_spinyd/Ca_nernst Purk_spinyd/CaT EK E
+	copy GABA Purk_spinyd/stell
+	setfield Purk_spinyd/stell gmax {{G_GABA}*surf}
+	addmsg Purk_spinyd/stell Purk_spinyd CHANNEL Gk Ek
+	addmsg Purk_spinyd  Purk_spinyd/stell  VOLTAGE Vm
+end
+
+/*********************************************************************/
+function make_Purkinje_spines
+/* separate function so we can have local variables */
+/* one standard format, may be rescaled in attach_spines */
+/* Reference: Harris KM, Stevens JK: Dendritic spines of rat
+**  cerebellar Purkinje cells: serial electron microscopy with
+**  reference to their biophysical characteristics.  J Neurosci 8: p
+**  4455-4469, 1988. */
+
+	float len, dia, surf, vol
+
+    /* make spine with average length and diameter */
+	/* make spine neck */
+	len = 0.66e-6
+	dia = 0.20e-6
+	surf = len*dia*{PI}
+	vol = len*dia*dia*{PI}/4.0
+	if (!({exists Purk_spine}))
+		create compartment Purk_spine
+	end
+	setfield Purk_spine Cm {{CM}*surf}  \
+	    Ra {4.0*{RA}*len/(dia*dia*{PI})} Em {ELEAK}  \
+	    initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0 x {len} dia {dia} \
+		len {len}
+
+	/* make spine head */
+	len = 0.00e-6
+	// derived from average surface
+	dia = 0.54e-6
+	surf = dia*dia*{PI}
+	create compartment Purk_spine/head
+	setfield Purk_spine/head Cm {{CM}*surf} Ra {8.0*{RA}/(dia*{PI})} \
+	     Em {ELEAK} initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0  \
+	    x {dia} dia {dia} len {len}
+
+	/* make a combined prototype: neck+head */
+	addmsg Purk_spine/head Purk_spine RAXIAL Ra Vm
+	addmsg Purk_spine Purk_spine/head AXIAL Vm
+
+	copy Purk_spine Purk_spine2
+
+	/* put non-NMDA channel on combined prototype */
+	copy non_NMDA Purk_spine/head/par
+	setfield Purk_spine/head/par gmax {{G_par_syn}*surf}
+	addmsg  Purk_spine/head  Purk_spine/head/par	VOLTAGE Vm
+	addmsg Purk_spine/head/par Purk_spine/head CHANNEL Gk Ek
+
+	/* put non-NMDA channel on combined prototype */
+	copy non_NMDA2 Purk_spine2/head/par2
+	setfield Purk_spine2/head/par2 gmax {{G_par_syn}*surf}
+	addmsg  Purk_spine2/head  Purk_spine2/head/par2	VOLTAGE Vm
+	addmsg Purk_spine2/head/par2 Purk_spine2/head CHANNEL Gk Ek
+
+end
+/*********************************************************************/
Index: 0.58/Purk_hfipassconst.g
--- 0.58/Purk_hfipassconst.g Thu, 04 Apr 2002 11:22:47 +0200 hugo ()
+++ parpat-storage-film.3/Purk_hfipassconst.g Wed, 27 Sep 2000 11:06:49 +0200 hugo (purkinje/b/18_Purk_hfipa 1.1 640)
@@ -0,0 +1,70 @@
+//genesis  - Purkinje cell M9 genesis2.1 script
+/* Copyright E. De Schutter (Caltech and BBF-UIA) */
+
+/* This file defines important simulation parameters, including gmax
+** and Ek for all channels.  Everything uses SI units. */
+
+echo Using Purkinje 2M9 preferences. Crank Nicholson method.
+/* variables controlling hsolve integration */
+float dt = 2.0e-5
+int tab_xdivs = 149
+int tab_xfills = 2999
+
+/* The model is quite sensitive to these values in NO_INTERP (caclmode=0) */
+float tab_xmin = -0.10
+float tab_xmax = 0.05
+float Ca_tab_max = 0.300
+
+// only used for proto channels
+float GNa = 1, GCa = 1, GK = 1, Gh = 1
+/* cable parameters */
+float CM = 0.0164 		// *9 relative to passive
+float RMs = 1.000 		// /3.7 relative to passive comp
+float RMd = 3.0
+float RA = 2.50
+/* preset constants */
+float ELEAK = -0.0800 		// Ek value used for the leak conductance
+float EREST_ACT = -0.0680 	// Vm value used for the RESET
+/* concentrations */
+float CCaO = 2.4000 		//external Ca as in normal slice Ringer
+float CCaI = 0.000040		//internal Ca in mM
+//diameter of Ca_shells
+float Shell_thick = 0.20e-6
+float CaTau = 0.00010	 	// Ca_concen tau
+/* Currents: Reversal potentials in V and max conductances S/m^2 */
+/* Codes: s=soma, m=main dendrite, t=thick dendrite, d=spiny dendrite */
+float ENa = 0.045
+float GNaFs = 75000.0
+float GNaPs = 10.0
+float ECa = 0.0125*{log {CCaO/CCaI}} // 0.135 V
+float GCaTs = 5.00
+float GCaTm = 0//5.00
+float GCaTt = 0//5.00
+float GCaTd = 0//5.00
+float GCaPm = 0//45.0
+float GCaPt = 0//45.0
+float GCaPd = 0//45.0
+float EK = -0.085
+float GKAs = 150.0
+float GKAm = 0//20.0
+float GKdrs = 6000.0
+float GKdrm = 0//600.0
+float GKMs = 0.400
+float GKMm = 0//0.100
+float GKMt = 0//0.130
+float GKMd = 0//0.130
+float GKCm = 0//800.0
+float GKCt = 0//800.0
+float GKCd = 0//800.0
+float GK2m = 0//3.90
+float GK2t = 0//3.90
+float GK2d = 0//3.90
+float Eh = -0.030
+float Ghs = 3.00
+/* synapses: */
+float E_GABA = -0.080
+float G_GABA = 70.0/(dt*1000)
+float GB_GABA = 20.0/dt
+float E_non_NMDA = 0.000
+float G_par_syn = 750.0/dt
+float G_cli_syn = 150.0/dt
Index: 0.58/Purk_hfihfeconst.g
--- 0.58/Purk_hfihfeconst.g Thu, 04 Apr 2002 11:22:47 +0200 hugo ()
+++ parpat-storage-film.3/Purk_hfihfeconst.g Wed, 27 Sep 2000 11:06:49 +0200 hugo (purkinje/b/19_Purk_hfihf 1.1 640)
@@ -0,0 +1,70 @@
+//genesis  - Purkinje cell M9 genesis2.1 script
+/* Copyright E. De Schutter (Caltech and BBF-UIA) */
+
+/* This file defines important simulation parameters, including gmax
+** and Ek for all channels.  Everything uses SI units. */
+
+echo Using Purkinje 2M9 preferences. Crank Nicholson method.
+/* variables controlling hsolve integration */
+float dt = 2.0e-5
+int tab_xdivs = 149
+int tab_xfills = 2999
+
+/* The model is quite sensitive to these values in NO_INTERP (caclmode=0) */
+float tab_xmin = -0.10
+float tab_xmax = 0.05
+float Ca_tab_max = 0.300
+
+// only used for proto channels
+float GNa = 1, GCa = 1, GK = 1, Gh = 1
+/* cable parameters */
+float CM = 0.0164 		// *9 relative to passive
+float RMs = 1.000 		// /3.7 relative to passive comp
+float RMd = 3.0
+float RA = 2.50
+/* preset constants */
+float ELEAK = -0.0800 		// Ek value used for the leak conductance
+float EREST_ACT = -0.0680 	// Vm value used for the RESET
+/* concentrations */
+float CCaO = 2.4000 		//external Ca as in normal slice Ringer
+float CCaI = 0.000040		//internal Ca in mM
+//diameter of Ca_shells
+float Shell_thick = 0.20e-6
+float CaTau = 0.00010	 	// Ca_concen tau
+/* Currents: Reversal potentials in V and max conductances S/m^2 */
+/* Codes: s=soma, m=main dendrite, t=thick dendrite, d=spiny dendrite */
+float ENa = 0.045
+float GNaFs = 75000.0
+float GNaPs = 10.0
+float ECa = 0.0125*{log {CCaO/CCaI}} // 0.135 V
+float GCaTs = 5.00
+float GCaTm = 5.00
+float GCaTt = 5.00
+float GCaTd = 5.00
+float GCaPm = 45.0
+float GCaPt = 45.0
+float GCaPd = 45.0
+float EK = -0.085
+float GKAs = 150.0
+float GKAm = 20.0
+float GKdrs = 6000.0
+float GKdrm = 600.0
+float GKMs = 0.400
+float GKMm = 0.100
+float GKMt = 0.130
+float GKMd = 0.130
+float GKCm = 800.0
+float GKCt = 800.0
+float GKCd = 800.0
+float GK2m = 3.90
+float GK2t = 3.90
+float GK2d = 3.90
+float Eh = -0.030
+float Ghs = 3.00
+/* synapses: */
+float E_GABA = -0.080
+float G_GABA = 70.0/(dt*1000)
+float GB_GABA = 20.0/dt
+float E_non_NMDA = 0.000
+float G_par_syn = 750.0/(dt*1000)
+float G_cli_syn = 150.0/dt
Index: 0.58/Purk_hficonst.g
--- 0.58/Purk_hficonst.g Thu, 04 Apr 2002 11:22:47 +0200 hugo ()
+++ parpat-storage-film.3/Purk_hficonst.g Wed, 27 Sep 2000 11:06:49 +0200 hugo (purkinje/b/20_Purk_hfico 1.1 640)
@@ -0,0 +1,70 @@
+//genesis  - Purkinje cell M9 genesis2.1 script
+/* Copyright E. De Schutter (Caltech and BBF-UIA) */
+
+/* This file defines important simulation parameters, including gmax
+** and Ek for all channels.  Everything uses SI units. */
+
+echo Using Purkinje 2M9 preferences. Crank Nicholson method.
+/* variables controlling hsolve integration */
+float dt = 2.0e-5
+int tab_xdivs = 149
+int tab_xfills = 2999
+
+/* The model is quite sensitive to these values in NO_INTERP (caclmode=0) */
+float tab_xmin = -0.10
+float tab_xmax = 0.05
+float Ca_tab_max = 0.300
+
+// only used for proto channels
+float GNa = 1, GCa = 1, GK = 1, Gh = 1
+/* cable parameters */
+float CM = 0.0164 		// *9 relative to passive
+float RMs = 1.000 		// /3.7 relative to passive comp
+float RMd = 3.0
+float RA = 2.50
+/* preset constants */
+float ELEAK = -0.0800 		// Ek value used for the leak conductance
+float EREST_ACT = -0.0680 	// Vm value used for the RESET
+/* concentrations */
+float CCaO = 2.4000 		//external Ca as in normal slice Ringer
+float CCaI = 0.000040		//internal Ca in mM
+//diameter of Ca_shells
+float Shell_thick = 0.20e-6
+float CaTau = 0.00010	 	// Ca_concen tau
+/* Currents: Reversal potentials in V and max conductances S/m^2 */
+/* Codes: s=soma, m=main dendrite, t=thick dendrite, d=spiny dendrite */
+float ENa = 0.045
+float GNaFs = 75000.0
+float GNaPs = 10.0
+float ECa = 0.0125*{log {CCaO/CCaI}} // 0.135 V
+float GCaTs = 5.00
+float GCaTm = 5.00
+float GCaTt = 5.00
+float GCaTd = 5.00
+float GCaPm = 45.0
+float GCaPt = 45.0
+float GCaPd = 45.0
+float EK = -0.085
+float GKAs = 150.0
+float GKAm = 20.0
+float GKdrs = 6000.0
+float GKdrm = 600.0
+float GKMs = 0.400
+float GKMm = 0.100
+float GKMt = 0.130
+float GKMd = 0.130
+float GKCm = 800.0
+float GKCt = 800.0
+float GKCd = 800.0
+float GK2m = 3.90
+float GK2t = 3.90
+float GK2d = 3.90
+float Eh = -0.030
+float Ghs = 3.00
+/* synapses: */
+float E_GABA = -0.080
+float G_GABA = 70.0/(dt*1000)
+float GB_GABA = 20.0/dt
+float E_non_NMDA = 0.000
+float G_par_syn = 750.0/dt
+float G_cli_syn = 150.0/dt
Index: 0.58/Purk_hfi2const.g
--- 0.58/Purk_hfi2const.g Thu, 04 Apr 2002 11:22:47 +0200 hugo ()
+++ parpat-storage-film.3/Purk_hfi2const.g Wed, 27 Sep 2000 11:06:49 +0200 hugo (purkinje/b/21_Purk_hfi2c 1.1 640)
@@ -0,0 +1,70 @@
+//genesis  - Purkinje cell M9 genesis2.1 script
+/* Copyright E. De Schutter (Caltech and BBF-UIA) */
+
+/* This file defines important simulation parameters, including gmax
+** and Ek for all channels.  Everything uses SI units. */
+
+echo Using Purkinje 2M9 preferences. Crank Nicholson method.
+/* variables controlling hsolve integration */
+float dt = 2.0e-5
+int tab_xdivs = 149
+int tab_xfills = 2999
+
+/* The model is quite sensitive to these values in NO_INTERP (caclmode=0) */
+float tab_xmin = -0.10
+float tab_xmax = 0.05
+float Ca_tab_max = 0.300
+
+// only used for proto channels
+float GNa = 1, GCa = 1, GK = 1, Gh = 1
+/* cable parameters */
+float CM = 0.0164 		// *9 relative to passive
+float RMs = 1.000 		// /3.7 relative to passive comp
+float RMd = 3.0
+float RA = 2.50
+/* preset constants */
+float ELEAK = -0.0800 		// Ek value used for the leak conductance
+float EREST_ACT = -0.0680 	// Vm value used for the RESET
+/* concentrations */
+float CCaO = 2.4000 		//external Ca as in normal slice Ringer
+float CCaI = 0.000040		//internal Ca in mM
+//diameter of Ca_shells
+float Shell_thick = 0.20e-6
+float CaTau = 0.00010	 	// Ca_concen tau
+/* Currents: Reversal potentials in V and max conductances S/m^2 */
+/* Codes: s=soma, m=main dendrite, t=thick dendrite, d=spiny dendrite */
+float ENa = 0.045
+float GNaFs = 75000.0
+float GNaPs = 10.0
+float ECa = 0.0125*{log {CCaO/CCaI}} // 0.135 V
+float GCaTs = 5.00
+float GCaTm = 5.00
+float GCaTt = 5.00
+float GCaTd = 5.00
+float GCaPm = 45.0
+float GCaPt = 45.0
+float GCaPd = 45.0
+float EK = -0.085
+float GKAs = 150.0
+float GKAm = 20.0
+float GKdrs = 6000.0
+float GKdrm = 600.0
+float GKMs = 0.400
+float GKMm = 0.100
+float GKMt = 0.130
+float GKMd = 0.130
+float GKCm = 800.0
+float GKCt = 800.0
+float GKCd = 800.0
+float GK2m = 3.90
+float GK2t = 3.90
+float GK2d = 3.90
+float Eh = -0.030
+float Ghs = 3.00
+/* synapses: */
+float E_GABA = -0.080
+float G_GABA = 70.0/(dt*4000)
+float GB_GABA = 20.0/dt
+float E_non_NMDA = 0.000
+float G_par_syn = 750.0/dt
+float G_cli_syn = 150.0/dt
Index: 0.58/Purk_bicomp.g
--- 0.58/Purk_bicomp.g Thu, 04 Apr 2002 11:22:47 +0200 hugo ()
+++ parpat-storage-film.3/Purk_bicomp.g Wed, 27 Sep 2000 11:06:49 +0200 hugo (purkinje/b/22_Purk_bicom 1.1 640)
@@ -0,0 +1,296 @@
+//genesis - Purkinje cell M9 genesis2.1 script
+/* Copyright E. De Schutter (Caltech and BBF-UIA) */
+
+/**********************************************************************
+** Sets up active membrane Purkinje cell compartment prototypes 
+**  and dendritic spine prototypes.
+** E. De Schutter, Caltech, 1991-1992
+** This version sets up active compartments with stellate cell synapses.
+**********************************************************************/
+
+/* References:
+** E. De Schutter and J.M. Bower: An active membrane model of the
+** cerebellar Purkinje cell. I. Simulation of current clamps in slice.
+** Journal of Neurophysiology  71: 375-400 (1994).
+** http://www.bbf.uia.ac.be/TNB/TNB_pub8.html
+** E. De Schutter and J.M. Bower: An active membrane model of the
+** cerebellar Purkinje cell: II. Simulation of synaptic responses.
+** Journal of Neurophysiology  71: 401-419 (1994).
+** http://www.bbf.uia.ac.be/TNB/TNB_pub7.html
+** Consult these references for sources of experimental data.
+** See http://www.bbf.uia.ac.be/models/PM9.shtml for general model info.
+*/
+
+function make_Purkinje_comps
+/* separate function so we can have local variables */
+
+	float len, dia, surf, shell_vol, shell_dia
+	int i
+
+	echo making Purkinje compartment library...
+
+	/* make spherical soma prototype with sodium currents*/
+	len = 0.00e-6
+	dia = 20.0e-6
+	surf = dia*dia*{PI}
+	shell_dia = 2*{Shell_thick}
+	shell_vol = (3*dia*dia*shell_dia - 3*dia*shell_dia*shell_dia + shell_dia*shell_dia*shell_dia)*{PI}/6.0
+	if (!({exists Purk_soma}))
+		create compartment Purk_soma
+	end
+	setfield Purk_soma Cm {{CM}*surf} Ra {8.0*{RA}/(dia*{PI})}  \
+	    Em {ELEAK} initVm {EREST_ACT} Rm {{RMs}/surf} inject 0.0  \
+	    dia {dia} len {len}
+
+	copy Purk_NaF Purk_soma/NaF
+	addmsg Purk_soma Purk_soma/NaF VOLTAGE Vm
+	addmsg Purk_soma/NaF Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/NaF Gbar {{GNaFs}*surf}
+	copy Purk_NaP Purk_soma/NaP
+	addmsg Purk_soma Purk_soma/NaP VOLTAGE Vm
+	addmsg Purk_soma/NaP Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/NaP Gbar {{GNaPs}*surf}
+	copy Purk_CaT Purk_soma/CaT
+	addmsg Purk_soma Purk_soma/CaT VOLTAGE Vm
+	addmsg Purk_soma/CaT Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/CaT Gbar {{GCaTs}*surf}
+	copy Purk_KA Purk_soma/KA
+	addmsg Purk_soma Purk_soma/KA VOLTAGE Vm
+	addmsg Purk_soma/KA Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/KA Gbar {{GKAs}*surf}
+	copy Purk_Kdr Purk_soma/Kdr
+	addmsg Purk_soma Purk_soma/Kdr VOLTAGE Vm
+	addmsg Purk_soma/Kdr Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/Kdr Gbar {{GKdrs}*surf}
+	copy Purk_KM Purk_soma/KM
+	addmsg Purk_soma Purk_soma/KM VOLTAGE Vm
+	addmsg Purk_soma/KM Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/KM Gbar {{GKMs}*surf}
+	copy Purk_h1 Purk_soma/h1
+	addmsg Purk_soma Purk_soma/h1 VOLTAGE Vm
+	addmsg Purk_soma/h1 Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/h1 Gbar {{Ghs}*surf}
+	copy Purk_h2 Purk_soma/h2
+	addmsg Purk_soma Purk_soma/h2 VOLTAGE Vm
+	addmsg Purk_soma/h2 Purk_soma CHANNEL Gk Ek
+	setfield Purk_soma/h2 Gbar {{Ghs}*surf}
+	create Ca_concen Purk_soma/Ca_pool
+	setfield Purk_soma/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_soma/CaT Purk_soma/Ca_pool I_Ca Ik
+	copy GABA2 Purk_soma/basket
+	setfield Purk_soma/basket gmax    {{GB_GABA}*surf}
+	addmsg Purk_soma/basket  Purk_soma  CHANNEL Gk  Ek
+	addmsg Purk_soma  Purk_soma/basket    VOLTAGE Vm
+
+    /* make main dendrite prototype with fast Ca currents */
+    len = 200.00e-6
+    dia = 2.00e-6
+    surf = len*dia*{PI}
+    shell_vol = (2*dia*shell_dia - shell_dia*shell_dia)*len*{PI}/4.0
+    if (!({exists Purk_maind}))
+        create compartment Purk_maind
+    end
+    setfield Purk_maind Cm {{CM}*surf} Ra {4.0*{RA}*len/(dia*dia*{PI})}  \
+        Em {ELEAK} initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0  \
+        dia {dia} len {len}
+
+    if (!({exists Purk_thickd}))    // Lets copy before we add currents
+
+        copy Purk_maind Purk_thickd
+    end
+    if (!({exists Purk_spinyd}))    // Lets copy before we add currents
+
+        copy Purk_maind Purk_spinyd
+    end
+
+	copy Purk_CaT Purk_maind/CaT
+	addmsg Purk_maind Purk_maind/CaT VOLTAGE Vm
+	addmsg Purk_maind/CaT Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/CaT Gbar {{GCaTm}*surf}
+	copy Purk_KA Purk_maind/KA
+	addmsg Purk_maind Purk_maind/KA VOLTAGE Vm
+	addmsg Purk_maind/KA Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KA Gbar {{GKAm}*surf}
+	copy Purk_Kdr Purk_maind/Kdr
+	addmsg Purk_maind Purk_maind/Kdr VOLTAGE Vm
+	addmsg Purk_maind/Kdr Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/Kdr Gbar {{GKdrm}*surf}
+	copy Purk_KM Purk_maind/KM
+	addmsg Purk_maind Purk_maind/KM VOLTAGE Vm
+	addmsg Purk_maind/KM Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KM Gbar {{GKMm}*surf}
+	copy Purk_CaP Purk_maind/CaP
+	addmsg Purk_maind Purk_maind/CaP VOLTAGE Vm
+	addmsg Purk_maind/CaP Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/CaP Gbar {{GCaPm}*surf}
+	copy Purk_KC Purk_maind/KC
+	addmsg Purk_maind Purk_maind/KC VOLTAGE Vm
+	addmsg Purk_maind/KC Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/KC Gbar {{GKCm}*surf}
+	copy Purk_K2 Purk_maind/K2
+	addmsg Purk_maind Purk_maind/K2 VOLTAGE Vm
+	addmsg Purk_maind/K2 Purk_maind CHANNEL Gk Ek
+	setfield Purk_maind/K2 Gbar {{GK2m}*surf}
+	create Ca_concen Purk_maind/Ca_pool
+	setfield Purk_maind/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_maind/CaT Purk_maind/Ca_pool I_Ca Ik
+	addmsg Purk_maind/CaP Purk_maind/Ca_pool I_Ca Ik
+	addmsg Purk_maind/Ca_pool Purk_maind/KC CONCEN Ca
+	addmsg Purk_maind/Ca_pool Purk_maind/K2 CONCEN Ca
+	create nernst Purk_maind/Ca_nernst
+	setfield Purk_maind/Ca_nernst Cin {CCaI} Cout {CCaO} valency {2} \
+	     scale {1.0} T {37}
+	addmsg Purk_maind/Ca_pool Purk_maind/Ca_nernst CIN Ca
+	addmsg Purk_maind/Ca_nernst Purk_maind/CaP EK E
+	addmsg Purk_maind/Ca_nernst Purk_maind/CaT EK E
+	copy GABA2 Purk_maind/basket
+	setfield Purk_maind/basket gmax    {{GB_GABA}*surf/2}
+	addmsg Purk_maind/basket  Purk_maind  CHANNEL Gk  Ek
+	addmsg Purk_maind  Purk_maind/basket    VOLTAGE Vm
+
+	/* make thick dendrite prototype with fast Ca current */
+	/* similar to main dendrite but has CaP and no Kdr */
+	/* passive prototype already copied from Purk_maind */
+	copy Purk_CaT Purk_thickd/CaT
+	addmsg Purk_thickd Purk_thickd/CaT VOLTAGE Vm
+	addmsg Purk_thickd/CaT Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/CaT Gbar {{GCaTt}*surf}
+	copy Purk_CaP Purk_thickd/CaP
+	addmsg Purk_thickd Purk_thickd/CaP VOLTAGE Vm
+	addmsg Purk_thickd/CaP Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/CaP Gbar {{GCaPt}*surf}
+	copy Purk_KM Purk_thickd/KM
+	addmsg Purk_thickd Purk_thickd/KM VOLTAGE Vm
+	addmsg Purk_thickd/KM Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/KM Gbar {{GKMt}*surf}
+	copy Purk_KC Purk_thickd/KC
+	addmsg Purk_thickd Purk_thickd/KC VOLTAGE Vm
+	addmsg Purk_thickd/KC Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/KC Gbar {{GKCt}*surf}
+	copy Purk_K2 Purk_thickd/K2
+	addmsg Purk_thickd Purk_thickd/K2 VOLTAGE Vm
+	addmsg Purk_thickd/K2 Purk_thickd CHANNEL Gk Ek
+	setfield Purk_thickd/K2 Gbar {{GK2t}*surf}
+	create Ca_concen Purk_thickd/Ca_pool
+	setfield Purk_thickd/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_thickd/CaT Purk_thickd/Ca_pool I_Ca Ik
+	addmsg Purk_thickd/CaP Purk_thickd/Ca_pool I_Ca Ik
+	addmsg Purk_thickd/Ca_pool Purk_thickd/KC CONCEN Ca
+	addmsg Purk_thickd/Ca_pool Purk_thickd/K2 CONCEN Ca
+	create nernst Purk_thickd/Ca_nernst
+	setfield Purk_thickd/Ca_nernst Cin {CCaI} Cout {CCaO}  \
+	    valency {2} scale {1.0} T {37}
+	addmsg Purk_thickd/Ca_pool Purk_thickd/Ca_nernst CIN Ca
+	addmsg Purk_thickd/Ca_nernst Purk_thickd/CaP EK E
+	addmsg Purk_thickd/Ca_nernst Purk_thickd/CaT EK E
+	for (i=1; i<=2; i = i+1)
+	    copy GABA Purk_thickd/stell{i}
+	    setfield Purk_thickd/stell{i} gmax {{G_GABA}/5*surf}
+	    addmsg Purk_thickd/stell{i} Purk_thickd CHANNEL Gk Ek
+		addmsg Purk_thickd  Purk_thickd/stell{i}  VOLTAGE Vm
+	end
+
+	/* make spiny dendrite prototype with high threshold Ca current  \
+	    */
+	/* passive prototype already copied from Purk_maind */
+	copy Purk_CaT Purk_spinyd/CaT
+	addmsg Purk_spinyd Purk_spinyd/CaT VOLTAGE Vm
+	addmsg Purk_spinyd/CaT Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/CaT Gbar {{GCaTd}*surf}
+	copy Purk_CaP Purk_spinyd/CaP
+	addmsg Purk_spinyd Purk_spinyd/CaP VOLTAGE Vm
+	addmsg Purk_spinyd/CaP Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/CaP Gbar {{GCaPd}*surf}
+	copy Purk_KM Purk_spinyd/KM
+	addmsg Purk_spinyd Purk_spinyd/KM VOLTAGE Vm
+	addmsg Purk_spinyd/KM Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/KM Gbar {{GKMd}*surf}
+	copy Purk_KC Purk_spinyd/KC
+	addmsg Purk_spinyd Purk_spinyd/KC VOLTAGE Vm
+	addmsg Purk_spinyd/KC Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/KC Gbar {{GKCd}*surf}
+	copy Purk_K2 Purk_spinyd/K2
+	addmsg Purk_spinyd Purk_spinyd/K2 VOLTAGE Vm
+	addmsg Purk_spinyd/K2 Purk_spinyd CHANNEL Gk Ek
+	setfield Purk_spinyd/K2 Gbar {{GK2d}*surf}
+	create Ca_concen Purk_spinyd/Ca_pool
+	setfield Purk_spinyd/Ca_pool tau {CaTau}  \
+	    B {1.0/(2.0*96494*shell_vol)} Ca_base {CCaI}  \
+	    thick {Shell_thick}
+	addmsg Purk_spinyd/CaP Purk_spinyd/Ca_pool I_Ca Ik
+	addmsg Purk_spinyd/CaT Purk_spinyd/Ca_pool I_Ca Ik
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/KC CONCEN Ca
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/K2 CONCEN Ca
+	create nernst Purk_spinyd/Ca_nernst
+	setfield Purk_spinyd/Ca_nernst Cin {CCaI} Cout {CCaO}  \
+	    valency {2} scale {1.0} T {37}
+	addmsg Purk_spinyd/Ca_pool Purk_spinyd/Ca_nernst CIN Ca
+	addmsg Purk_spinyd/Ca_nernst Purk_spinyd/CaP EK E
+	addmsg Purk_spinyd/Ca_nernst Purk_spinyd/CaT EK E
+	copy GABA Purk_spinyd/stell
+	setfield Purk_spinyd/stell gmax {{G_GABA}*surf}
+	addmsg Purk_spinyd/stell Purk_spinyd CHANNEL Gk Ek
+	addmsg Purk_spinyd  Purk_spinyd/stell  VOLTAGE Vm
+end
+
+/*********************************************************************/
+function make_Purkinje_spines
+/* separate function so we can have local variables */
+/* one standard format, may be rescaled in attach_spines */
+/* Reference: Harris KM, Stevens JK: Dendritic spines of rat
+**  cerebellar Purkinje cells: serial electron microscopy with
+**  reference to their biophysical characteristics.  J Neurosci 8: p
+**  4455-4469, 1988. */
+
+	float len, dia, surf, vol
+
+    /* make spine with average length and diameter */
+	/* make spine neck */
+	len = 0.66e-6
+	dia = 0.20e-6
+	surf = len*dia*{PI}
+	vol = len*dia*dia*{PI}/4.0
+	if (!({exists Purk_spine}))
+		create compartment Purk_spine
+	end
+	setfield Purk_spine Cm {{CM}*surf}  \
+	    Ra {4.0*{RA}*len/(dia*dia*{PI})} Em {ELEAK}  \
+	    initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0 x {len} dia {dia} \
+		len {len}
+
+	/* make spine head */
+	len = 0.00e-6
+	// derived from average surface
+	dia = 0.54e-6
+	surf = dia*dia*{PI}
+	create compartment Purk_spine/head
+	setfield Purk_spine/head Cm {{CM}*surf} Ra {8.0*{RA}/(dia*{PI})} \
+	     Em {ELEAK} initVm {EREST_ACT} Rm {{RMd}/surf} inject 0.0  \
+	    x {dia} dia {dia} len {len}
+
+	/* make a combined prototype: neck+head */
+	addmsg Purk_spine/head Purk_spine RAXIAL Ra Vm
+	addmsg Purk_spine Purk_spine/head AXIAL Vm
+
+	copy Purk_spine Purk_spine2
+
+	/* put non-NMDA channel on combined prototype */
+	copy non_NMDA Purk_spine/head/par
+	setfield Purk_spine/head/par gmax {{G_par_syn}*surf}
+	addmsg  Purk_spine/head  Purk_spine/head/par	VOLTAGE Vm
+	addmsg Purk_spine/head/par Purk_spine/head CHANNEL Gk Ek
+
+	/* put non-NMDA channel on combined prototype */
+	copy non_NMDA2 Purk_spine2/head/par2
+	setfield Purk_spine2/head/par2 gmax {{G_par_syn}*surf}
+	addmsg  Purk_spine2/head  Purk_spine2/head/par2	VOLTAGE Vm
+	addmsg Purk_spine2/head/par2 Purk_spine2/head CHANNEL Gk Ek
+
+end
+/*********************************************************************/
Index: 0.58/movie.g
--- 0.58/movie.g Thu, 04 Apr 2002 11:22:47 +0200 hugo ()
+++ parpat-storage-film.3/movie.g Fri, 29 Sep 2000 20:06:06 +0200 hugo (purkinje/b/8_movie.g 1.2 644)
@@ -0,0 +1,219 @@
+// genesis
+
+int include_movie
+
+if ( {include_movie} == 0 )
+
+	include_movie = 1
+
+
+int movie_static = 0
+
+
+///
+/// SH:	GIFMake
+///
+/// PA:	xwID....: window ID to create gif file for
+///	label...: label to prepend to the file name
+///	iBegin..: first step
+///	iEnd....: last step
+///
+/// DE:	Dump gif for window xwID, unique for ({label},{time})
+///	
+///
+
+function GIFMake(xwID,label,iBegin,iEnd)
+
+str xwID
+str label
+int iBegin
+int iEnd
+
+	//- get actual step
+
+//	echo {xwID} {label} {iBegin} {iEnd}
+
+	str actual = {getstat -step}
+
+ 	if (actual >= iBegin && actual < iEnd)
+
+/*
+		// dump gif file
+
+		xwd -silent -id {xwID} \
+		| xwdtopnm \
+		| ppmtogif >{label}.{actual}.gif
+*/
+
+		xdump /xcell {label}.{actual}.ppm
+ 	end
+end
+
+
+///
+/// SH:	MovieCreateElements
+///
+/// PA:	path...: parent xform for created elements (ending in '/')
+///	label..: prefix label for filenames
+///	iBegin.: first step
+///	iEnd...: last step
+///
+/// RE: Movie handle
+///
+/// DE:	Create elements for creating a movie of the given xform
+///	Created elements use clock 11
+///
+
+function MovieCreateElements(path,label,iBegin,iEnd)
+
+str path
+str label
+int iBegin
+int iEnd
+
+	//- give diagnostics
+
+	echo "Creating movie elements for "{path}" with label "{label}
+
+	//- create a movie handle
+
+	str movieHandle = { {path} @ "_movie" @ {movie_static} }
+
+	//- create script out
+
+	create script_out {movieHandle}
+
+	//- add and set path field
+
+	addfield {movieHandle} path -description "Path to take snapshots from"
+
+	setfield {movieHandle} \
+		path {path}
+
+	//- increment movie element count
+
+	movie_static = {movie_static} + 1
+
+	//- set clock
+
+	useclock {movieHandle} 11
+
+	//- set command to create an image at every time step
+
+/*
+** failure of lexical analyzer with this one
+**
+	setfield ^ \
+		command {"xwd -silent -id " \
+			 @ {getfield {path} xwID} \
+			 @ " | xwdtopnm | ppmtogif >" \
+			 @ {label} \
+			 @ ".{getstat -time}" \
+			 @ ".gif"}
+*/
+
+	setfield {movieHandle} \
+		command {"GIFMake " \
+			 @ {getfield {path} xwID} \
+			 @ " " \
+			 @ {label} \
+			 @ " " \
+			 @ {iBegin} \
+			 @ " " \
+			 @ {iEnd}}
+
+//	create script_out {path}sched
+
+//	useclock ^ 10
+
+//	setfield ^ command "echo Scheduled at {getstat -time}"
+
+	//- schedule elements
+
+	//call {path}_movie RESET
+
+	reset
+
+	//- return created movie handle 
+
+	return {movieHandle}
+end
+
+
+///
+/// SH:	MovieSchedule
+///
+/// PA:	handle.: movie handle to schedule
+///	label..: prefix label for filenames
+///	iBegin.: first step
+///	iEnd...: last step
+///
+/// DE:	Schedule a movie handle
+///
+///	first call MovieCreateElements on the given xform to init.
+///
+
+function MovieSchedule(handle,label,iBegin,iEnd)
+
+str handle
+str label
+int iBegin
+int iEnd
+
+	//- give diagnostics
+
+	echo "Scheduling movie elements for "{handle}" with label "{label}
+
+	//- set command to create an image at every time step
+
+/*
+** failure of lexical analyzer with this one
+**
+	setfield ^ \
+		command {"xwd -silent -id " \
+			 @ {getfield {path} xwID} \
+			 @ " | xwdtopnm | ppmtogif >" \
+			 @ {label} \
+			 @ ".{getstat -time}" \
+			 @ ".gif"}
+*/
+
+	//echo "Film for widget : "{getfield {handle} path}
+
+/*
+** script_out cannot handle added fields, {path} not available
+*/
+/* 	setfield {handle} \ */
+/* 		command {"GIFMake " \ */
+/* 			 @ {getfield {getfield {handle} path} xwID} \ */
+/* 			 @ " " \ */
+/* 			 @ {label} \ */
+/* 			 @ " " \ */
+/* 			 @ {iBegin} \ */
+/* 			 @ " " \ */
+/* 			 @ {iEnd}} */
+
+/*
+** hardcoded path
+*/
+
+	setfield {handle} \
+		command {"GIFMake " \
+			 @ {getfield "/xcell" xwID} \
+			 @ " " \
+			 @ {label} \
+			 @ " " \
+			 @ {iBegin} \
+			 @ " " \
+			 @ {iEnd}}
+
+	//- schedule elements
+
+	call {handle} RESET
+
+end
+
+
+end
+
+