&Model

// This is a comment.
// The contents of this file are the work of G. von Dassow, E. Meir, E. M. Munro,
// and G. M. Odell, 1997-2000.  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.

&width		8			// width of the cell grid - should be a multiple of two
&height		2
&numsides	6			// number of sides of each cell - should always be six
&extent		100			// this is a relic.

&Network	spnet		// this name will be used by Ingeneue to label output files

&Genes					
// the "Genes" block defines basic properties of Nodes
	&en
		&Location	cyto		// this Node resides in the cytoplasm; the other option is "membrane"
		&Color		cyan		// color for display in Cell View
		&Show		on			// whether to show this Node in Cell View
		&Scale		1			// largely a placeholder for a future function - ignore
		&Type		rna			// the options are "rna", "protein", and "complex"
	&enden
	
	&EN
		&Location	cyto
		&Color		cyan
		&Show		on
		&Scale		1
		&Type		protein
	&endEN
	
	&wg
		&Location	cyto
		&Color		green
		&Show		on
		&Scale		1
		&Type		rna
	&endwg
	
	&IWG
		&Location	cyto
		&Color		green
		&Show		off
		&Scale		1
		&Type		protein
	&endIWG

	&EWG
		&Location	membrane
		&Color		green
		&Show		off
		&Scale		1
		&Type		protein
	&endEWG
	
	&ptc
		&Location	cyto
		&Color		magenta
		&Show		off
		&Scale		1
		&Type		rna
	&endptc
	
	&PTC
		&Location	membrane
		&Color		magenta
		&Show		off
		&Scale		1
		&Type		protein
	&endPTC
	
	&cid
		&Location	cyto
		&Color		pink
		&Show		off
		&Scale		1
		&Type		rna
	&endcid
	
	&CID	
		&Location	cyto
		&Color		pink
		&Show		on
		&Scale		1
		&Type		protein
	&endCID
	
	&CN
		&Location	cyto
		&Color		pink
		&Show		on
		&Scale		1
		&Type		protein
	&endCN
	
	&hh
		&Location	cyto
		&Color		red
		&Show		on
		&Scale		1
		&Type		rna
	&endhh
	
	&HH
		&Location	membrane
		&Color		red
		&Show		off
		&Scale		1
		&Type		protein
	&endHH
	
	&PH
		&Location	membrane
		&Color		magenta
		&Show		off
		&Scale		1
		&Type		complex
	&endPH
	
	&B
		&Location	cyto
		&Color		white
		&Show		off
		&Scale		1
		&Type		protein
	&endB
	
&endGenes

&Interactions			  
// the "Interactions" block defines the interactions in the network, which amounts
// to defining the differential equations governing each Node.  Each Node's equation
// is built from pieces called Affectors.  The declaration of each Affector includes
// the declaration of whatever parameters appear in that term.  Each Affector is a sort
// of template; the Affector declarations specify which Nodes or parameters belong in
// which "slots" in the Affector.
	&en
		&Txn2bAff CN EWG K_WGen nu_WGen H_en K_CNen nu_CNen
		&DecayAff en H_en
	&enden
	
	&EN						// For example, the equation for EN consists of two terms:
		&TlnAff en H_EN		// ... one for translation of EN as a function of en concentration
		&DecayAff EN H_EN	// ... and one for first-order decay of EN
	&endEN

	&wg
		&Txn4Aff CN IWG CID H_wg K_WGwg nu_WGwg alpha_wg K_CIDwg nu_CIDwg beta_wg K_CNwg nu_CNwg
		&DecayAff wg H_wg 
	&endwg
			
	&IWG
		&TlnAff wg H_IWG
		&EndoIAff IWG EWG Endo_WG
		&ExoIAff IWG EWG Exo_WG
		&DecayAff IWG H_IWG
	&endIWG

	&EWG
		&ExoEAff IWG EWG Exo_WG
		&EndoEAff IWG EWG Endo_WG
		&MxferOutAff EWG Mxfer_WG
		&MxferInAff EWG Mxfer_WG
		&LMxferEAff EWG LMxfer_WG
		&LMxferIAff EWG LMxfer_WG
		&DecayAff EWG H_EWG
	&endEWG

	&ptc
		&Txn2aAff CN CID K_CIDptc nu_CIDptc H_ptc K_CNptc nu_CNptc
		&DecayAff ptc H_ptc 
	&endptc

	&PTC
		&HeterodimerizeA_ECAff	PTC	HH	K_PTC_HH	maxHH
		&TlnAff ptc H_PTC 
		&LMxferEAff PTC LMxfer_PTC
		&LMxferIAff PTC LMxfer_PTC
		&DecayAff PTC H_PTC 
	&endPTC
			
	&cid
		&Txn2aAff EN B K_Bcid nu_Bcid H_cid K_ENcid nu_ENcid 
		&DecayAff cid H_cid 
	&endcid
			
	&CID
		&CleavageA_ICAff CID PTC K_PTCCID nu_PTCCID C_CID
		&TlnAff cid H_CID 
		&DecayAff CID H_CID 
	&endCID
			
	&CN
		&CleavageB_ICAff CID PTC K_PTCCID nu_PTCCID C_CID
		&DecayAff CN H_CN 
	&endCN
			
	&hh
		&Txn2aAff CN EN K_ENhh nu_ENhh H_hh K_CNhh nu_CNhh
		&DecayAff hh H_hh 
	&endhh
			
	&HH
		&HeterodimerizeA_ECAff	HH	PTC	K_PTC_HH	maxPTC
		&TlnAff hh H_HH 
		&LMxferEAff HH LMxfer_HH
		&LMxferIAff HH LMxfer_HH
		&DecayAff HH H_HH 
	&endHH
			
	&PH
		&HeterodimerizeB_ECAff	PTC	HH	K_PTC_HH	maxHH 
		&DecayAff PH H_PH 
	&endPH
			
	&B					// B is a dummy Node that causes basal transcription of cid.
		&Formula1Aff B
	&endB
	
&endInteractions

&ParameterValues
// Parameters are declared implicitly above, in the Affector declarations, but
// in this block they are endowed with values and ranges.  The specifiers "Logarithmic"
// or "Linear" refer to the distribution from which random values of these parameters
// are to be chosen, and also the scale on which they are to be plotted.
		&K_WGen		0.1	0.001	1.0	Logarithmic
		&K_CNen		0.1	0.001	1.0	Logarithmic
		&K_WGwg		0.1	0.001	1.0	Logarithmic
		&K_CIDwg	0.1	0.001	1.0	Logarithmic
		&K_CNwg		0.1	0.001	1.0	Logarithmic
		&K_CIDptc	0.1	0.001	1.0	Logarithmic
		&K_CNptc	0.1	0.001	1.0	Logarithmic
		&K_Bcid		0.1	0.001	1.0	Logarithmic
		&K_ENcid	0.1	0.001	1.0	Logarithmic
		&K_PTCCID	0.1	0.001	1.0	Logarithmic
		&K_ENhh		0.1	0.001	1.0	Logarithmic
		&K_CNhh		0.1	0.001	1.0	Logarithmic

		&K_PTC_HH	0.0001	0.00001	0.001	Logarithmic
		&maxPTC		1000	1000	1000000	Logarithmic
		&maxHH		1000	1000	1000000	Logarithmic

		&C_CID		0.1	0.01	1.0	Logarithmic

		&nu_WGen	1.0	1.0	10.0	Linear
		&nu_CNen	1.0	1.0	10.0	Linear
		&nu_WGwg	1.0	1.0	10.0	Linear
		&nu_CIDwg	1.0	1.0	10.0	Linear
		&nu_CNwg	1.0	1.0	10.0	Linear
		&nu_CIDptc	1.0	1.0	10.0	Linear
		&nu_CNptc	1.0	1.0	10.0	Linear
		&nu_Bcid	1.0	1.0	1.0		Linear
		&nu_ENcid	1.0	1.0	10.0	Linear
		&nu_PTCCID	1.0	1.0	10.0	Linear
		&nu_ENhh	1.0	1.0	10.0	Linear
		&nu_CNhh	1.0	1.0	10.0	Linear

		&H_en	7.0	5.0	100.0	Linear
		&H_EN	15.0	5.0	100.0	Linear
		&H_wg	7.0	5.0	100.0	Linear
		&H_IWG	15.0	5.0	100.0	Linear
		&H_EWG	15.0	5.0	100.0	Linear
		&H_ptc	7.0	5.0	100.0	Linear
		&H_PTC	15.0	5.0	100.0	Linear
		&H_cid	7.0	5.0	100.0	Linear
		&H_CID	15.0	5.0	100.0	Linear
		&H_CN	15.0	5.0	100.0	Linear
		&H_hh	7.0	5.0	100.0	Linear
		&H_HH	15.0	5.0	100.0	Linear
		&H_PH	15.0	5.0	100.0	Linear

		&alpha_wg	1.0	1.0	10.0	Logarithmic
		&beta_wg	1.0	1.0	10.0	Logarithmic

		&Endo_WG	0.001	0.001	1.0		Logarithmic
		&Exo_WG		0.1		0.01	10.0	Logarithmic
		&Mxfer_WG	0.001	0.001	1.0		Logarithmic
		&LMxfer_WG	0.1		0.001	1.0		Logarithmic
		&LMxfer_PTC	0.1		0.001	1.0		Logarithmic
		&LMxfer_HH	0.1		0.001	1.0		Logarithmic

&endParameterValues

&InitLevels
// Each Node needs some information about its initial concentration in every cell,
// even just to say that it is uniformly off everywhere, as the "BackgroundLevel"
// tags do for most Nodes.  The subsequent blocks impose an initial pattern, which
// in this case consists of spaced columns of expression of en, EN, wg, and IWG.
	&BackgroundLevel	en		0.0
	&BackgroundLevel	EN		0.0
	&BackgroundLevel	wg 		0.0
	&BackgroundLevel	IWG		0.0
	&BackgroundLevel	EWG		0.0
	&BackgroundLevel	ptc		0.0
	&BackgroundLevel	PTC		0.0
	&BackgroundLevel	cid		0.0
	&BackgroundLevel	CID		0.0
	&BackgroundLevel	CN		0.0
	&BackgroundLevel	hh		0.0
	&BackgroundLevel	HH		0.0
	&BackgroundLevel	PH		0.0
	&BackgroundLevel	B		0.4		// this makes the basal activator of cid transcription is ubiquitous and uniform; parameter control the level at which cid responds to it.
	
	&ColumnIC
		&Node	en
		&Value	1.0		// a value of 1.0 generally means "full on"
		&Column	2		// to match Java arrays, the cell grid is numbered from 0, thus "Column 2" refers to the third column in the grid.
	&endIC
	&ColumnIC
		&Node	EN
		&Value	1.0
		&Column	2
	&endIC
	&ColumnIC
		&Node	wg
		&Value	1.0
		&Column	1
	&endIC
	&ColumnIC
		&Node	IWG
		&Value	1.0
		&Column	1
	&endIC
	&ColumnIC
		&Node	en
		&Value	1.0
		&Column	6
	&endIC
	&ColumnIC
		&Node	EN
		&Value	1.0
		&Column	6
	&endIC
	&ColumnIC
		&Node	wg
		&Value	1.0
		&Column	5
	&endIC
	&ColumnIC
		&Node	IWG
		&Value	1.0
		&Column	5
	&endIC
	
&endInitLevels

&endNetwork