// The contents of this file are the work of G. von Dassow and Kerry Kim
// 2004-2006.  The model encoded in this file should be treated
// like any other piece of original scientific data, and must not be used in the
// production of any publication without the express permission of its creators.

&Model

&width		1		// Just a single cell
&height		1
&numsides	6		// Use 6 since documentation of Ingeneue says its the safest

&Network	endocycle

&Nodes
	&e2f
		&Location		cyto
		&Color			red
		&Show			on
		&Scale			1.0
		&Type			RNA
		&XPos			-10000
		&YPos			-10000
	&ende2f
	&E2F
		&Location		cyto
		&Color			red
		&Show			on
		&Scale			1.0
		&Type			PROTEIN
		&XPos			-10000
		&YPos			-10000
	&endE2F
	&E2Fp
		&Location		cyto
		&Color			255	30	30	//Light red
		&Show			on
		&Scale			1.0
		&Type			PROTEIN
		&XPos			-10000
		&YPos			-10000	
	&endE2Fp
	&rbf
		&Location		cyto
		&Color 			green
		&Show 			on
		&Scale			1.0
		&Type			RNA
		&XPos			-10000
		&YPos			-10000
	&endrbf
	&RBF
		&Location		cyto
		&Color			green
		&Show			on
		&Scale			1.0
		&Type			PROTEIN
		&XPos			-10000
		&YPos			-10000
	&endRBF
	&RBFp
		&Location		cyto
		&Color			30	255	30 // Light green
		&Show			on
		&Scale			1.0
		&Type			PROTEIN
		&XPos			-10000
		&YPos			-10000
	&endRBFp
	&ER
		&Location		cyto
		&Color			yellow
		&Show			on
		&Scale			1.0
		&Type			COMPLEX
		&XPos			-10000
		&YPos			-10000
	&endER
	&ERp
		&Location		cyto
		&Color			255	255	30	// Light yellow
		&Show			on
		&Scale			1.0
		&Type			COMPLEX
		&XPos			-10000
		&YPos			-10000
	&endERp
	&cyce
		&Location		cyto
		&Color			blue
		&Show			on
		&Scale			1.0
		&Type			RNA
		&XPos			-10000
		&YPos			-10000
	&endcyce
	&CYCE
		&Location		cyto
		&Color			blue
		&Show			on
		&Scale			1.0
		&Type			PROTEIN
		&XPos			-10000
		&YPos			-10000
	&endCYCE
&endNodes

&Interactions
	&e2f
		&DecayAff				e2f	H_e2f
		&ConstantInputAff			C_e2f
	&ende2f
	&E2F
		&DecayAff				E2F	H_E2F
		&TlnAff					e2f	H_E2F
		&PhosphorylateA_Aff			E2F	CYCE	P_maxE	K_Ce	nu_Ce
		&Dimerize_AAff 				E2F	RBF	k_RE	r_max
		&CleaveB_Aff				ER	k_ER
		&CleaveB_Aff				ERp	k_ERp
	&endE2F
	&E2Fp
		&DecayAff				E2Fp	H_E2Fp
		&PhosphorylateB_Aff			E2F	CYCE	P_maxE	K_Ce	nu_Ce
	&endE2Fp
	&rbf
		&DecayAff				rbf	H_rbf
		&ConstantInputAff			C_rbf	
	&endrbf
	&RBF
		&DecayAff				RBF	H_RBF
		&TlnAff					rbf	H_RBF
		&PhosphorylateA_Aff			RBF	CYCE	P_maxR	K_Cr	nu_Cr
		&Dimerize_AAff 				E2F	RBF	k_RE 	r_max
		&CleaveB_Aff				ER	k_ER
		&DephosphorylateB_Aff			RBFp	D_maxR
	&endRBF
	&RBFp
		&PhosphorylateB_Aff			RBF	CYCE	P_maxR	K_Cr	nu_Cr
		&CleaveB_Aff				ERp	k_ERp
		&DephosphorylateA_Aff			RBFp	D_maxR
		&DecayAff				RBFp	H_RBF
	&endRBFp
	&ER
		&Dimerize_BAff 				E2F	RBF	k_RE	r_max
		&CleaveA_Aff				ER	k_ER
		&PhosphorylateA_Aff			ER	CYCE	P_maxR	K_Cr	nu_Cr
		&DephosphorylateB_Aff			ERp	D_maxR
		&DecayAff				ER	H_RBF
	&endER
	&ERp
		&CleaveA_Aff				ERp	k_ERp	
		&DecayAff				ERp	H_RBF
		&PhosphorylateB_Aff			ER	CYCE	P_maxR	K_Cr	nu_Cr
		&DephosphorylateA_Aff			ERp	D_maxR
	&endERp
	&cyce
		&DecayAff				cyce	H_cyce
		&TxnLeakyCyceAff			E2F	E2Fp	ER	H_cyce	base	K_Ec	K_Rc	nu_Ec	nu_Rc
	&endcyce
	&CYCE
		&DecayAff				CYCE	H_CYCE
		&TlnAff					cyce	H_CYCE	
	&endCYCE
&endInteractions
&ParameterValues
	&K_Ec		0.3		0.05	1	Logarithmic
	&K_Ce		0.4		0.05	1	Logarithmic
	&K_Rc		0.5		0.05	1	Logarithmic
	&K_Cr		0.4		0.05	1	Logarithmic
	&nu_Ec		4		1	8	Linear
	&nu_Ce		4		1	8	Linear
	&nu_Rc		1		1	8	Linear
	&nu_Cr		2		1	8	Linear
	&P_maxE		1		0.01	1	Logarithmic
	&P_maxR		1		0.01	1	Logarithmic
	&H_e2f		60		60	60	Linear
	&H_E2F		60		10	120	Logarithmic
	&H_E2Fp		5		2	60	Logarithmic
	&H_rbf		60		60	60	Linear
	&H_RBF		120		2	120	Logarithmic
	&H_cyce		20		2	120	Logarithmic
	&H_CYCE		20		2	60	Logarithmic
	&C_e2f		0.01666		0.01666	0.01666	Linear
	&C_rbf		0.01666		0.01666	0.01666	Linear
	&base		0.1		0.1	0.1	Linear
	&D_maxR		0.4		0.01	1	Logarithmic
	&k_RE		0.4		0.1	1	Logarithmic
	&k_ER		0.02		0.01	0.1	Logarithmic
	&k_ERp		0.4		0.1	1	Logarithmic
	&r_max		1		1	1	Logarithmic
&endParameterValues
&InitLevels
	&BackgroundLevel	e2f	0
	&BackgroundLevel	E2F	0
	&BackgroundLevel	E2Fp	0
	&BackgroundLevel	rbf	0
	&BackgroundLevel	RBF	0
	&BackgroundLevel	RBFp	0
	&BackgroundLevel	ER	0
	&BackgroundLevel	ERp	0
	&BackgroundLevel	cyce	0
	&BackgroundLevel	CYCE	0
&endInitLevels

&endNetwork