[Ecell-cvs] SF.net SVN: ecell:[3882] ecell3/trunk/doc/samples

[<mor...@us...>]

Revision: 3882
          http://ecell.svn.sourceforge.net/ecell/?rev=3882&view=rev
Author:   moriyoshi
Date:     2010-12-28 08:40:14 +0000 (Tue, 28 Dec 2010)

Log Message:
-----------
* Update samples.

Modified Paths:
--------------
    ecell3/trunk/doc/samples/Drosophila/Drosophila-python.em
    ecell3/trunk/doc/samples/LTD/LTD.em

Modified: ecell3/trunk/doc/samples/Drosophila/Drosophila-python.em
===================================================================
--- ecell3/trunk/doc/samples/Drosophila/Drosophila-python.em	2010-12-28 08:37:54 UTC (rev 3881)
+++ ecell3/trunk/doc/samples/Drosophila/Drosophila-python.em	2010-12-28 08:40:14 UTC (rev 3882)
@@ -61,7 +61,7 @@
 	{
 		IsContinuous	1;
 		InitializeMethod "vs = 0.76; KI = 1;";
-		FireMethod "self.setFlux( (vs*KI) / (KI + (C0.MolarConc * C0.MolarConc * C0.MolarConc) ) * self.getSuperSystem().SizeN_A )";
+		FireMethod "self.Flux = ( (vs*KI) / (KI + (C0.variable.MolarConc * C0.variable.MolarConc * C0.variable.MolarConc) ) * self.superSystem.SizeN_A )";
 
 		VariableReferenceList	[ P0 Variable:.:M 1 ] [ C0 Variable:.:Pn ];
 	}
@@ -70,7 +70,7 @@
 	{
 		IsContinuous	1;
 		InitializeMethod "vm = 0.65; Km = 0.5;";
-		FireMethod "self.setFlux( (vm * S0.MolarConc) / ( Km + S0.MolarConc) * self.getSuperSystem().SizeN_A )";
+		FireMethod "self.Flux = ( (vm * S0.variable.MolarConc) / ( Km + S0.variable.MolarConc) * self.superSystem.SizeN_A )";
 
 		VariableReferenceList	[ S0 Variable:.:M -1 ];
 	}
@@ -79,7 +79,7 @@
 	{
 		IsContinuous	1;
 		InitializeMethod "Ks = 0.38;";
-		FireMethod "self.setFlux( (Ks * C0.MolarConc) * self.getSuperSystem().SizeN_A )";
+		FireMethod "self.Flux = ( (Ks * C0.variable.MolarConc) * self.superSystem.SizeN_A )";
 
 		VariableReferenceList	[ P0 Variable:.:P0 1 ] [ C0 Variable:.:M 0 ];
 	}
@@ -88,7 +88,7 @@
 	{
 		IsContinuous	1;
 		InitializeMethod "V1 = 3.2; K1 = 2;";
-		FireMethod "self.setFlux( ( V1 * S0.MolarConc) / (K1 + S0.MolarConc) * self.getSuperSystem().SizeN_A )";
+		FireMethod "self.Flux = ( ( V1 * S0.variable.MolarConc) / (K1 + S0.variable.MolarConc) * self.superSystem.SizeN_A )";
 
 		VariableReferenceList	[ P0 Variable:.:P1 1 ] [ S0 Variable:.:P0 -1 ];
 	}
@@ -97,7 +97,7 @@
 	{
 		IsContinuous	1;
 		InitializeMethod "V2 = 1.58; K2 = 2;";
-		FireMethod "self.setFlux( (V2 * S0.MolarConc) / (K2 + S0.MolarConc) * self.getSuperSystem().SizeN_A )";
+		FireMethod "self.Flux = ( (V2 * S0.variable.MolarConc) / (K2 + S0.variable.MolarConc) * self.superSystem.SizeN_A )";
 
 		VariableReferenceList	[ P0 Variable:.:P0 1 ] [ S0 Variable:.:P1 -1 ];
 	}
@@ -106,7 +106,7 @@
 	{
 		IsContinuous	1;
 		InitializeMethod "V3 = 5; K3 = 2;";
-		FireMethod "self.setFlux( ( V3 * S0.MolarConc) / (K3 + S0.MolarConc) * self.getSuperSystem().SizeN_A )";
+		FireMethod "self.Flux = ( ( V3 * S0.variable.MolarConc) / (K3 + S0.variable.MolarConc) * self.superSystem.SizeN_A )";
 
 		VariableReferenceList	[ P0 Variable:.:P2 1 ] [ S0 Variable:.:P1 -1];
 	}
@@ -115,7 +115,7 @@
 	{
 		IsContinuous	1;
 		InitializeMethod "V4 = 2.5; K4 = 2;";
-		FireMethod "self.setFlux( (V4 * S0.MolarConc) / (K4 + S0.MolarConc) * self.getSuperSystem().SizeN_A )";
+		FireMethod "self.Flux = ( (V4 * S0.variable.MolarConc) / (K4 + S0.variable.MolarConc) * self.superSystem.SizeN_A )";
 
 		VariableReferenceList	[ P0 Variable:.:P1 1 ] [ S0 Variable:.:P2 -1 ];
 	}
@@ -124,7 +124,7 @@
 	{
 		IsContinuous	1;
 		InitializeMethod "k1 = 1.9;";
-		FireMethod "self.setFlux( ( k1 * S0.MolarConc) * self.getSuperSystem().SizeN_A )";
+		FireMethod "self.Flux = ( ( k1 * S0.variable.MolarConc) * self.superSystem.SizeN_A )";
 
 		VariableReferenceList	[ P0 Variable:.:Pn 1 ] [ S0 Variable:.:P2 -1 ];
 	}
@@ -133,7 +133,7 @@
 	{
 		IsContinuous	1;
 		InitializeMethod "k2 = 1.3;";
-		FireMethod "self.setFlux( (k2 * S0.MolarConc) * self.getSuperSystem().SizeN_A )";
+		FireMethod "self.Flux = ( (k2 * S0.variable.MolarConc) * self.superSystem.SizeN_A )";
 
 		VariableReferenceList	[ P0 Variable:.:P2 1 ] [ S0 Variable:.:Pn -1 ];
 	}
@@ -142,7 +142,7 @@
 	{
 		IsContinuous	1;
 		InitializeMethod "vd = 0.95; Kd = 0.2;";
-		FireMethod "self.setFlux( ( vd * S0.MolarConc) / (Kd + S0.MolarConc) * self.getSuperSystem().SizeN_A )";
+		FireMethod "self.Flux = ( ( vd * S0.variable.MolarConc) / (Kd + S0.variable.MolarConc) * self.superSystem.SizeN_A )";
 
 		VariableReferenceList	[ S0 Variable:.:P2 -1 ];
 	}	

Modified: ecell3/trunk/doc/samples/LTD/LTD.em
===================================================================
--- ecell3/trunk/doc/samples/LTD/LTD.em	2010-12-28 08:37:54 UTC (rev 3881)
+++ ecell3/trunk/doc/samples/LTD/LTD.em	2010-12-28 08:40:14 UTC (rev 3882)
@@ -1072,7 +1072,7 @@
 		Name	PKC_PKC_active;
 		StepperID PASSIVE_1;
 
-		FireMethod "P0.Value = R0.Value + R1.Value + R2.Value + R3.Value";	
+		FireMethod "P0.variable.Value = R0.variable.Value + R1.variable.Value + R2.variable.Value + R3.variable.Value";	
 		VariableReferenceList	[ R0 :.:Ca_DAG_PKC 0 ] 
 					[ R1 :.:DAG_AA_PKC 0 ] 
 					[ R2 :.:AA_PKC 0 ] 
@@ -1085,7 +1085,7 @@
 		Name	MAPact;
 		StepperID PASSIVE_1;	
 
-		FireMethod "P0.Value = R0.Value + R1.Value";
+		FireMethod "P0.variable.Value = R0.variable.Value + R1.variable.Value";
 
 		VariableReferenceList	[ R0 :.:MAPK_P 0 ] 
 					[ R1 :.:MAPK_PP 0 ]


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