diff test-data/e_coli_growth.ftbl @ 0:9b03a930b08b draft

"planemo upload commit 8e69ff6919990050909511d8bdfb520c19a4af72"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/e_coli_growth.ftbl	Mon May 04 03:24:12 2020 -0400
@@ -0,0 +1,822 @@
+PROJECT
+	NAME	VERSION	FORMAT	DATE	COMMENT
+	Nissle.ftbl	1		100910	modele E coli Nissle WT avec voies centrales completes et voies biomasse
+	Nissle.ftbl	2		121025	growth fluxes+pooled penthoses
+	Nissle.ftbl	3		121123	concentration measurements
+
+NETWORK
+	FLUX_NAME	EDUCT_1	EDUCT_2	PRODUCT_1	PRODUCT_2
+
+// Glycolyse.
+// PPP
+// TCA
+// voies anaplerotiques: pepc. enz malique
+// voie glyoxylate
+// avec pool interne unique de CO2 provenant soit du metabolisme soit de l'exterieur (CO2upt laisse libre)
+// saisie differentielle des substrats marques
+
+
+// Uptake substrats
+
+	Glucupt_1	Gluc_1		Glc
+		#ABCDEF		#ABCDEF
+
+	Glucupt_U	Gluc_U		Glc
+		#ABCDEF		#ABCDEF
+
+	Glucupt	Glc		Glc6P
+		#ABCDEF		#ABCDEF
+
+	CO2upt	CO2_ext		CO2		// entree de CO2 non marque
+		#A		#A		// ce flux est a laisser libre
+
+//	FTHF0	FTHF_0		FTHF		// prise en charge de FTHF non marque
+//		#A		#A
+
+//	FTHF1	FTHF_1		FTHF		// prise en charge de FTHF marque
+//		#a		#a
+
+
+// Embden Meyerhof Parnas Pathway
+
+	pgi	Glc6P		Fru6P
+		#ABCDEF		#ABCDEF
+
+	pfk	Fru6P		FruBP
+		#ABCDEF		#ABCDEF
+
+	ald	FruBP		GA3P	GA3P
+		#ABCDEF		#CBA	#DEF
+
+//	tpi	DHAP		GA3P
+//		#ABC		#CBA
+
+	pgk	GA3P		PGA
+		#ABC		#ABC
+
+	eno	PGA		PEP
+		#ABC		#ABC
+
+	pyk	PEP		Pyr
+		#ABC		#ABC
+
+
+// Methylglyoxal Pathway
+
+//	mgs	DHAP		Pyr
+//		#ABC		#ABC
+
+
+// Pentose Phosphate Pathway
+
+	zwf	Glc6P		Gnt6P
+		#ABCDEF		#ABCDEF
+
+	gnd	Gnt6P		CO2 	Rub5P
+		#ABCDEF		#A	#BCDEF
+
+	rib	Rub5P		Rib5P
+		#ABCDE		#ABCDE
+
+	xul	Rub5P		Xul5P
+		#ABCDE		#ABCDE
+
+	edd	Gnt6P		Pyr	GA3P
+		#ABCDEF		#ABC	#DEF
+
+//	ta	GA3P	Sed7P	Ery4P	Fru6P
+//		#ABC	#abcdefg	#defg	#abcABC
+
+//	tk1	Rib5P	Rib5P	GA3P	Sed7P
+//		#ABCDE	#abcde	#CDE	#ABabcde
+
+//	tk2	Rib5P	Ery4P	GA3P	Fru6P
+//		#ABCDE	#abcd	#CDE	#ABabcd
+
+	HR1	GA3P	E2	Xul5P
+		#CDE	#AB	#ABCDE
+
+	HR2	Fru6P		Ery4P	E2
+		#ABCDEF		#CDEF	#AB
+
+	HR3	Fru6P		GA3P	E3
+		#ABCDEF		#DEF	#ABC
+
+	HR4	Sed7P		Rib5P	E2
+		#abABCDE		#ABCDE	#ab
+
+	HR5	Ery4P	E3	Sed7P
+		#ABCD	#abc	#abcABCD
+
+
+// Tricarboxylic Acid Cycle
+
+	pdh	Pyr		AcCoA	CO2
+		#ABC		#BC	#A
+
+	citsynth	AcCoA	OAA	Cit
+		#AB	#abcd	#dcbaBA
+
+	idh	Cit		AKG	CO2
+		#ABCDEF		#ABCEF	#D
+
+	akgdh	AKG		Suc	CO2
+		#ABCDE		#BCDE	#A
+
+	fum_a	Suc		Mal
+		#ABCD		#ABCD
+
+	fum_b	Suc		Mal
+		#ABCD		#DCBA
+
+	maldh	Mal		OAA
+		#ABCD		#ABCD
+
+
+// Glyoxylate Shunt
+
+//	gs1	Cit		GlyOx	Suc
+//		#ABCDEF		#AB	#DCEF
+
+//	gs2	GlyOx	AcCoA	OAA
+//		#AB	#ab	#ABba
+
+
+// Anaplerotic Reactions
+
+	ppc	PEP	CO2	OAA			// PEPcarboxylase
+		#ABC	#a	#ABCa
+
+//	mae	Mal		Pyr	CO2		// enzyme malique
+//		#ABCD		#ABC	#D
+
+//	pck	OAA		PEP	CO2		// PEP carboxykinase
+//		#ABCD		#ABC	#D
+
+
+// Biosynthetic Pathways
+
+	// Glucose-6-Phosphate Family
+
+	bs_glc6P	Glc6P		BM_Glc6P
+		#ABCDEF		#ABCDEF
+
+	// Fructose-6-Phosphate Family
+
+	bs_fru6P	Fru6P		BM_Fru6P
+		#ABCDEF		#ABCDEF
+
+	// Phosphoglycerate Family
+
+	bs_pga	PGA		BM_PGA
+		#ABC		#ABC
+
+//	bs_pga_aux	BM_PGA		PGA_Aux
+//		#ABC		#ABC
+
+//	bs_pga1	BM_PGA		Ser
+//		#ABC		#ABC
+
+//	bs_pga1_aux	Ser		Ser_Aux
+//		#ABC		#ABC
+
+//	bs_pga2	Ser		Cys
+//		#ABC		#ABC
+
+//	bs_pga2_aux	Cys		Cys_Aux
+//		#ABC		#ABC
+
+//	bs_pga3	Ser		Gly	FTHF
+//		#ABC		#AB	#C
+
+//	bs_pga3_aux	Gly		Gly_Aux
+//		#AB		#AB
+
+	// TrioseP Family
+
+	bs_DHAP	GA3P		Glp
+		#ABC		#ABC
+
+	// Pyruvate Family
+
+	bs_pyr	Pyr		BM_Pyr
+		#ABC		#ABC
+
+//	bs_pyr1	BM_Pyr		Ala
+//		#ABC		#ABC
+
+//	bs_pyr1_aux	Ala		Ala_Aux
+//		#ABC		#ABC
+
+//	bs_pyr2	BM_Pyr	BM_Pyr	AKV	CO2
+//		#ABC	#abc	#ABbcC	#a
+
+//	bs_pyr4	AKV		Val
+//		#ABCDE		#ABCDE
+
+//	bs_pyr4_aux	Val		Val_Aux
+//		#ABCDE		#ABCDE
+
+//	bs_pyr3	AKV	BM_AcCoA	Leu	CO2
+//		#ABCDE	#ab	#abBCDE	#A
+
+//	bs_pyr3_aux	Leu		Leu_Aux
+//		#ABCDEF		#ABCDEF
+
+	// Erythrose-4-Phosphate Family
+
+	bs_e4p	Ery4P		BM_Ery4P
+		#ABCD		#ABCD
+
+//	bs_e4p_aux	BM_Ery4P		Ery4P_aux
+//		#ABCD		#ABCD
+
+	// Ribose-5-Phosphate Family
+
+	bs_rib5P	Rib5P		BM_Rib5P
+		#ABCDE		#ABCDE
+
+//	bs_rib5P1	BM_Rib5P	FTHF	His
+//		#ABCDE	#a	#EDCBAa
+
+//	bs_rib5P1_aux	His		His_Aux
+//		#ABCDEF		#ABCDEF
+
+//	bs_rib5P2	BM_Rib5P		Ri5P_Aux
+//		#ABCDE		#ABCDE
+
+
+	// Aromatic Amino Acids
+
+	bs_pep	PEP		BM_PEP
+		#ABC		#ABC
+
+//	bs_pep1	BM_PEP	BM_Ery4P	DAHP
+//		#ABC	#abcd	#ABCabcd
+
+//	bs_pep2	BM_PEP	DAHP	Chor
+//		#ABC	#abcdefg	#ABCabcdefg
+
+//	bs_pep3a	Chor		Phe	CO2
+//		#ABCDEFGHIJ		#ABCEFGHIJ	#D
+
+//	bs_pep3b	Chor		Phe	CO2
+//		#ABCDEFGHIJ		#ABCEJIHGF	#D
+
+//	bs_pep3_aux	Phe		Phe_Aux
+//		#ABCEFGHIJ		#ABCEFGHIJ
+
+//	bs_pep4a	Chor		Tyr	CO2
+//		#ABCDEFGHIJ		#ABCEFGHIJ	#D
+
+//	bs_pep4b	Chor		Tyr	CO2
+//		#ABCDEFGHIJ		#ABCEJIHGF	#D
+
+//	bs_pep4_aux	Tyr		Tyr_Aux
+//		#ABCEFGHIJ		#ABCEFGHIJ
+
+//	bs_pep5	BM_PEP		PEP_Aux
+//		#ABC		#ABC
+
+//	bs_pep6	Chor	BM_Rib5P	Trp	PyrCO2
+//		#ABCDEFGHIJ	#abcde	#edcbaJEFGHI	#ABCD
+
+//	bs_pep6_aux	Trp		Trp_Aux
+//		#ABCDEFGHIJK		#ABCDEFGHIJK
+
+//	bs_pep7	PyrCO2		Pyr	CO2
+//		#ABCD		#ABC	#D
+
+	// Acetyl-CoA
+
+	bs_accoa	AcCoA		BM_AcCoA
+		#AB		#AB
+
+//	bs_accoa_aux	BM_AcCoA		AcCoA_Aux
+//		#AB		#AB
+
+	// Alpha-Ketoglutarate Family
+
+	bs_akg	AKG		BM_AKG
+		#ABCDE		#ABCDE
+
+//	bs_akg1	BM_AKG		Glu
+//		#ABCDE		#ABCDE
+
+//	bs_akg2	Glu		Pro
+//		#ABCDE		#ABCDE
+
+//	bs_akg3	Glu		Gln
+//		#ABCDE		#ABCDE
+
+//	bs_akg4	Glu	CO2	Arg
+//		#ABCDE	#a	#ABCDEa
+
+//	bs_akg4_aux	Arg		Arg_Aux
+//		#ABCDEF		#ABCDEF
+
+//	bs_akg2_aux	Pro		Pro_Aux
+//		#ABCDE		#ABCDE
+
+
+	// Oxaloacetate Family
+
+	bs_oaa	OAA		BM_OAA
+		#ABCD		#ABCD
+
+//	bs_oaa1	BM_OAA		Asp
+//		#ABCD		#ABCD
+
+//	bs_oaa1_aux	Asp		Asp_Aux
+//		#ABCD		#ABCD
+
+//	bs_oaa2	Thr	BM_Pyr	Ile	CO2
+//		#ABCD	#abc	#ABbCDc	#a
+
+//	bs_oaa2_aux	Ile		Ile_Aux
+//		#ABCDEF		#ABCDEF
+
+//	bs_oaa3a	BM_OAA	BM_Pyr	Lys	CO2
+//		#ABCD	#abc	#ABCDcb	#a
+
+//	bs_oaa3b	BM_OAA	BM_Pyr	Lys	CO2
+//		#ABCD	#abc	#abcDCB	#A
+
+//	bs_oaa3_aux	Lys		Lys_Aux
+//		#ABCDEF		#ABCDEF
+
+//	bs_oaa4	BM_OAA		OAA_Aux
+//		#ABCD		#ABCD
+
+//	bs_oaa5	BM_OAA		Thr
+//		#ABCD		#ABCD
+
+//	bs_oaa5_aux	Thr		Thr_Aux
+//		#ABCD		#ABCD
+
+//	bs_oaa6	BM_OAA	FTHF	Met
+//		#ABCD	#a	#ABCDa
+
+//	bs_oaa6_aux	Met		Met_Aux
+//		#ABCDE		#ABCDE
+
+//	bs_oaa7	BM_OAA		Asn
+//		#ABCD		#ABCD
+
+//	bs_oaa7_aux	Asn		Asn_Aux
+//		#ABCD		#ABCD
+
+
+// Extracellular fluxes
+
+	out_co2	CO2		CO2_out			// CO2 output
+		#A		#A
+
+	out_Ac	AcCoA		Acetate			// Acetate output
+		#AB		#AB
+
+//	out_FTHF	FTHF		FTHF_out
+//		#A		#A
+
+FLUXES
+	NET
+		NAME	FCD	VALUE(F/C)	ED_WEIGHT	LOW(F)	INC(F)	UP(F)
+
+	// INPUT
+		Glucupt_1	F	0.8128
+		Glucupt_U	D
+		Glucupt	D
+		CO2upt	C	0.77	// fixed arbitrary
+//		FTHF0	F	0.00224836
+//		FTHF1	F	0.001
+
+	// Glycolysis
+		pgi	F	0.1
+		pfk	D
+		ald	D
+//		tpi	D
+		pgk	D	0.1
+		eno	D
+		pyk	D	1.21144
+
+	// PPP + EDP
+		zwf	D	0.4
+		gnd	D
+		edd	F	0.1
+		rib	D
+		xul	D
+//		ta	D
+//		tk1	D
+//		tk2	D
+		HR1	D
+		HR2	D
+		HR3	D
+		HR4	D
+		HR5	D
+
+	// TCA
+		pdh	D
+		citsynth	D
+		idh	D
+		akgdh	D
+		fum_a	D
+		fum_b	D
+		maldh	D
+//		gs1	C	0
+//		gs2	D
+		ppc	D
+//		mae	D
+//		pck	D
+
+	// Biosynthetic pathways
+		bs_glc6P	C	0.0132	// sortie de G6P
+		bs_fru6P	C	0.0045	// sortie de F6P
+		bs_pga	C	0.0958	// sortie de PGA
+//		bs_pga_aux	D
+//		bs_pga1	D
+//		bs_pga1_aux	C	0.0132	// sortie de Ser
+//		bs_pga2	D
+//		bs_pga2_aux	C	0.0056	// sortie de Cys
+//		bs_pga3	D
+//		bs_pga3_aux	C	0.0373	// sortie de Gly
+		bs_DHAP	C	0.0083
+		bs_pyr	C	0.1818	// sortie de Pyr
+//		bs_pyr1	D
+//		bs_pyr1_aux	D		// sortie d'Ala
+//		bs_pyr2	D
+//		bs_pyr4	D
+//		bs_pyr4_aux	C	0.0258	// sortie de Val
+//		bs_pyr3	D
+//		bs_pyr3_aux	C	0.0275	// sortie de Leu
+		bs_e4p	C	0.0247	// sortie d'E4P
+		bs_rib5P	C	0.0576	// sortie de R5P
+//		bs_rib5P1	D
+//		bs_rib5P1_aux	C	0.0058	// sortie d'His
+//		bs_rib5P2	D
+		bs_pep	C	0.0461	// sortie de PEP
+//		bs_pep1	D
+//		bs_pep2	D
+//		bs_pep3a	D
+//		bs_pep3b	D
+//		bs_pep3_aux	C	0.0113	// sortie de Phe
+//		bs_pep4a	D
+//		bs_pep4b	D
+//		bs_pep4_aux	C	0.0084	// sortie de Tyr
+//		bs_pep5	C	0.0033	// sorties autres que ac. amines
+//		bs_pep6	D
+//		bs_pep6_aux	D
+//		bs_pep7	D
+		bs_accoa	C	0.1895	// sortie d'AcCoA
+//		bs_accoa_aux	D		// sortie d'AcCoA pour biomasse en dehors de synthese Leu
+		bs_akg	C	0.0692	// sortie d'AcCoA
+//		bs_akg1	D
+//		bs_akg2	D		// sortie de Pro
+//		bs_akg3	C	0.0160	// sortie de Gln
+//		bs_akg4	D
+//		bs_akg2_aux	C	0.013475
+//		bs_akg4_aux	D
+		bs_oaa	C	0.1146
+//		bs_oaa1	D
+//		bs_oaa1_aux	C	0.0147	// sortie d'Asp
+//		bs_oaa2	D
+//		bs_oaa2_aux	C	0.0177	// sortie d'Ile
+//		bs_oaa3a	D
+//		bs_oaa3b	D
+//		bs_oaa3_aux	C	0.0209	// sortie de Lys
+//		bs_oaa4	D
+//		bs_oaa5	D
+//		bs_oaa5_aux	C	0.0155	// sortie de Thr
+//		bs_oaa6	D
+//		bs_oaa6_aux	C	0.0094	// sortie de Met
+//		bs_oaa7	D
+//		bs_oaa7_aux	C	0.0147	// sortie d'Asn
+
+	// Extracellular fluxes
+
+		out_co2	D	0.1		// sortie de CO2
+		out_Ac	F	0.48		// sortie d'acetate
+//		out_FTHF	D		// sortie de FTHF
+
+
+	XCH
+		NAME	FCD	VALUE(F/C)	ED_WEIGHT	LOW(F)	INC(F)	UP(F)
+
+	// INPUT
+		Glucupt_1	D
+		Glucupt_U	D
+		Glucupt	C	0
+		CO2upt	D
+//		FTHF0	D
+//		FTHF1	D
+
+	// Glycolysis
+		pgi	F	0.4
+		pfk	F	0.01
+		ald	F	0.4
+//		tpi	F	0.5
+		pgk	F	0.99
+		eno	F	0.99
+		pyk	F	0.4
+
+	// PPP + EDP
+		zwf	C	0
+		gnd	C	0
+		edd	C	0
+		rib	C	0.99	// fixed arbitrary big
+		xul	F	0
+//		ta	F	0.35468
+//		tk1	F	0.0960538
+//		tk2	F	0.0521646
+		HR1	C	0.24	// fixed arbitrary
+		HR2	F	0.0151117
+		HR3	F	0.14
+		HR4	C	0.04	// fixed arbitrary
+		HR5	F	0.02
+
+	// TCA
+		pdh	C	0.01
+		citsynth	C	0
+		idh	C	0
+		akgdh	C	0
+		fum_a	C	0.01	// fixed arbitrary
+		fum_b	D
+//		maldh	F	0.99
+		maldh	C	0.42	// fixed arbitrary
+//		gs1	C	0
+//		gs2	C	0
+		ppc	F	0.2
+//		mae	C	0
+//		pck	C	0
+
+	// Biosynthetic pathways
+		bs_glc6P	D
+		bs_fru6P	D
+		bs_pga	D
+//		bs_pga_aux	D
+//		bs_pga1	C	0
+//		bs_pga1_aux	D
+//		bs_pga2	C	0
+//		bs_pga2_aux	D
+//		bs_pga3	C	0.00824415
+//		bs_pga3_aux	D
+		bs_DHAP	D
+		bs_pyr	D
+//		bs_pyr1	C	0
+//		bs_pyr1_aux	D
+//		bs_pyr2	C	0
+//		bs_pyr4	C	0
+//		bs_pyr4_aux	D
+//		bs_pyr3	C	0
+//		bs_pyr3_aux	D
+		bs_e4p	D	0
+//		bs_e4p_aux	D
+		bs_rib5P	D	0
+//		bs_rib5P1	C	0
+//		bs_rib5P1_aux	D
+//		bs_rib5P2	D
+		bs_accoa	D	0
+//		bs_accoa_aux	D
+		bs_pep	D	0
+//		bs_pep1	C	0
+//		bs_pep2	C	0
+//		bs_pep3a	C	0
+//		bs_pep3b	C	0
+//		bs_pep3_aux	D
+//		bs_pep4a	C	0
+//		bs_pep4b	C	0
+//		bs_pep4_aux	D
+//		bs_pep5	D
+//		bs_pep6	C	0
+//		bs_pep6_aux	D
+//		bs_pep7	C	0
+		bs_akg	D	0
+//		bs_akg1	C	0
+//		bs_akg2	C	0
+//		bs_akg3	D
+//		bs_akg4	C	0
+//		bs_akg4_aux	D
+//		bs_akg2_aux	D
+		bs_oaa	D	0
+//		bs_oaa1	C	0
+//		bs_oaa1_aux	D
+//		bs_oaa2	C	0
+//		bs_oaa2_aux	D
+//		bs_oaa3a	C	0
+//		bs_oaa3b	C	0
+//		bs_oaa3_aux	D
+//		bs_oaa4	D
+//		bs_oaa5	C	0
+//		bs_oaa5_aux	D
+//		bs_oaa6	C	0
+//		bs_oaa6_aux	D
+//		bs_oaa7	C	0
+//		bs_oaa7_aux	D
+
+		// Flux de sortie
+		out_co2	C	0	// sortie de CO2
+		out_Ac	C	0	// sortie d'acetate
+//		out_FTHF	D	// sortie de FTHF. a laisser libre pour ne pas imposer de contraintes sur FTHF
+
+EQUALITIES
+	NET
+		VALUE	FORMULA
+
+		0	fum_a-fum_b		// scrambling reaction
+		1	Glucupt_1+Glucupt_U
+//		0	bs_oaa3a-bs_oaa3b
+//		0	bs_pep3a-bs_pep3b
+//		0	bs_pep4a-bs_pep4b
+
+	XCH
+		VALUE	FORMULA
+
+		0	fum_a-fum_b
+
+INEQUALITIES
+	NET
+		VALUE	COMP	FORMULA
+//		1	<=	pyk
+		0	<=	edd
+		0	<=	gnd
+		0	<=	zwf
+		0	<=	ppc
+		0	<=	idh
+		0	<=	akgdh
+//		0	<=	mae
+
+	XCH
+		VALUE	COMP	FORMULA
+
+FLUX_MEASUREMENTS
+	FLUX_NAME	VALUE	DEVIATION
+	out_Ac	0.497	0.04
+
+LABEL_INPUT
+	META_NAME	ISOTOPOMER	VALUE
+
+	Gluc_U	#111111	0.952
+		#011111	0.008
+		#101111	0.008
+		#110111	0.008
+		#111011	0.008
+		#111101	0.008
+		#111110	0.008
+
+	Gluc_1	#100000	0.9465
+		#110000	0.0107
+		#101000	0.0107
+		#100100	0.0107
+		#100010	0.0107
+		#100001	0.0107
+
+	CO2_ext	#0	0.9893
+		#1	0.0107
+
+//	FTHF_0	#0	1
+//	FTHF_1	#1	1
+
+
+LABEL_MEASUREMENTS
+	META_NAME	CUM_GROUP	VALUE	DEVIATION	CUM_CONSTRAINTS
+
+	AcCoA	1	0.495	0.02	#00
+		2	0.303	0.02	#01	// CH3 specific enrichment
+		3	0.012	0.02	#10
+		4	0.190	0.02	#11
+
+PEAK_MEASUREMENTS
+
+	META_NAME	PEAK_NO	VALUE_S	VALUE_D-	VALUE_D+	VALUE_DD	VALUE_T	DEVIATION_S	DEVIATION_D-	DEVIATION_D+	DEVIATION_DD/T
+
+METAB_MEASUREMENTS
+	META_NAME	VALUE	DEVIATION
+	// source: p.millard 2010/12/03 Nissle_Glc_conc.xlsx sent by email
+	Suc	15.8893144279264*1.e-3/10.7	1.e-2
+	Mal	6.47828321758155*1.e-3/10.7	1.e-2
+	PEP	0.588638938013844*1.e-3/10.7	1.e-2
+	PGA	5.35922289028553*1.e-3/10.7	1.e-2
+	Cit	17.4452511107891*1.e-3/10.7	1.e-2
+	Gnt6P	1.54945619497337*1.e-3/10.7	1.e-2
+	FruBP	5.27278870110121*1.e-3/10.7	1.e-2
+	Fru6P	1.07071770798187*1.e-3/10.7	1.e-2
+	Glc6P	5.24845556085526*1.e-3/10.7	1.e-2
+	Rub5P+Rib5P+Xul5P	1.66034545348219*1.e-3/10.7	1.e-2
+
+MASS_SPECTROMETRY
+	META_NAME	FRAGMENT	WEIGHT	VALUE	DEVIATION
+	Mal	1,2,3,4	1	0.587391867374382	0.0493159626907812
+			2	0.216493214407424	0.0306546571894417
+			3	0.159494782909672	0.03
+			4	0.0366201353085213	0.03
+	PEP	1,2,3	0	0.462166666666667	0.01
+			1	0.340003333333333	0.01
+			2	0.0273166666666667	0.01
+			3	0.170513333333333	0.01
+	PGA	1,2,3	0	0.447066666666667	0.0180848260520618
+			1	0.34127	0.018075350619006
+			2	0.02441	0.01
+			3	0.187253333333333	0.01
+	Gnt6P	1,2,3,4,5,6	0	0.0195533333333333	0.01
+			1	0.72562	0.0120547874307264
+			2	0.0571233333333333	0.01
+			3	0.0135033333333333	0.01
+			4	0.01331	0.01
+			5	0.0131033333333333	0.01
+			6	0.157793333333333	0.01
+	Sed7P	1,2,3,4,5,6,7	0	0.272433333333333	0.0122309539012022
+			1	0.23752	0.01
+			2	0.180446666666667	0.01
+			3	0.12744	0.01
+			4	0.06321	0.01
+			5	0.0839233333333333	0.01
+			6	0.01751	0.01
+			7	0.0175266666666667	0.01
+	FruBP	1,2,3,4,5,6	0	0.0853733333333333	0.02
+			1	0.482283333333333	0.02
+			2	0.140086666666667	0.02
+			3	0.0953466666666667	0.02
+			4	0.09712	0.02
+			5	0.0120166666666667	0.02
+			6	0.0877666666666667	0.02
+	Rib5P+Xul5P+Rub5P	1,2,3,4,5	0	0.433956666666667	0.0115292555411585
+			1	0.215956666666667	0.01
+			2	0.09658	0.01
+			3	0.129033333333333	0.01
+			4	0.0272733333333333	0.01
+			5	0.0971933333333333	0.01
+	Glc6P	1,2,3,4,5,6	0	0.0167633333333333	0.01
+			1	0.716826666666667	0.01
+			2	0.0578233333333333	0.01
+			3	0.0122433333333333	0.01
+			4	0.01151	0.01
+			5	0.01089	0.01
+			6	0.173946666666667	0.01
+	Fru6P	1,2,3,4,5,6	0	0.04716	0.01
+			1	0.623343333333333	0.0106878170518274
+			2	0.0820266666666667	0.01
+			3	0.03604	0.01
+			4	0.0315766666666667	0.01
+			5	0.0149133333333333	0.01
+			6	0.164943333333333	0.0111688555068697
+
+	Cit	1,2,3,4,5,6	1	0.322208057034832	0.03
+			2	0.288291305558056	0.03
+			3	0.212855540659154	0.03
+			4	0.117626468347467	0.03
+			5	0.0484839619377435	0.03
+			6	0.0105346664627478	0.03
+
+OPTIONS
+	OPT_NAME	OPT_VALUE
+	MATLAB_FOR_FLUX_EQ_CONSTR_MATR	1
+	include_growth_flux	1
+	mu	0.8
+	optctrl_maxit	50
+	commandArgs	--TIMEIT
+	//optctrl_btdesc	0.1
+	posttreat_R	plot_smeas.R
+METABOLITE_POOLS
+	META_NAME	META_SIZE	// size is in units of metab_scale option defined before
+	// source: p.millard 2010/12/03 Nissle_Glc_conc.xlsx sent by email
+	//Fum	-2.47158569399681*1.e-3/10.7
+	Suc	-15.8893144279264*1.e-3/10.7
+	Mal	-6.47828321758155*1.e-3/10.7
+	PEP	-0.588638938013844*1.e-3/10.7
+	//Aco	-0.871035781090548*1.e-3/10.7
+	PGA	-5.35922289028553*1.e-3/10.7
+	Cit	-17.4452511107891*1.e-3/10.7
+	//1-3diPG	-7.31670971749174*1.e-3/10.7
+	Gnt6P	-1.54945619497337*1.e-3/10.7
+	//Sed7P	-11.5512490274248*1.e-3/10.7 conc
+	//PRPP	-2.74943425027474*1.e-3/10.7
+	//CMP	-0.433742769835568*1.e-3/10.7
+	//UMP	-4.69421895911195*1.e-3/10.7
+	//cAMP	-0.109838817225867*1.e-3/10.7
+	FruBP	-5.27278870110121*1.e-3/10.7
+	//AMP	-0.801372321192278*1.e-3/10.7
+	//GMP	-0.394103922207334*1.e-3/10.7
+	//dCDP	-4.41071909173208*1.e-3/10.7
+	//CDP	-0.204009683016196*1.e-3/10.7
+	//UDP	-0.528949008341637*1.e-3/10.7
+	//ADP	-2.0246124170601*1.e-3/10.7
+	//GDP	-1.02724694822302*1.e-3/10.7
+	//CTP	-1.39055711133101*1.e-3/10.7
+	//UTP	-1.73433655893259*1.e-3/10.7
+	//ATP	-6.32820169657847*1.e-3/10.7
+	//UDP-Glc	-9.93608536663137*1.e-3/10.7 conc
+	//ADP-Glc	-0*1.e-3/10.7
+	//GDP-Man	-5.52555199979534*1.e-3/10.7
+	//G1P	-72.1756241692542*1.e-3/10.7 conc
+	//F1P	-0.0942291270750201*1.e-3/10.7
+	Fru6P	-1.07071770798187*1.e-3/10.7
+	Glc6P	-5.24845556085526*1.e-3/10.7
+	//M6P	-0.642830603277483*1.e-3/10.7
+	//Rib1P	-0.0558080128279041*1.e-3/10.7
+	Rub5P	-1.66034545348219/3*1.e-3/10.7
+//	Rib5P	-1.66034545348219/3*1.e-3/10.7
+	Rib5P	1.e-7	// fixed arbitrary low
+	Xul5P	-4*1.66034545348219/3*1.e-3/10.7
+	//dADP	-5.86959266616353*1.e-3/10.7 conc
+	//dATP	-13.1542008577561*1.e-3/10.7 conc
+	//dTDP	-9.52423600696743*1.e-3/10.7 conc
+	//dTTP	-19.9757914243397*1.e-3/10.7 conc