added dangling enz and reac, missing parameterchange entry,readout->unitquantity= ratio, readout->useRatio->true

Author: hrani

FindSim-Bhalla1999_fig2B.tsv

@@ -1,67 +1,68 @@
-Experiment metadata		
-transcriber	Nisha Ann Viswan	
-organization	National Centre for Biological Sciences	
-emailId	nishaav@ncbs.res.in	
-exptSource	Paper	
-citationId	PMID: 7657647	
-authors	Teng KK et al.	
-journal	J Biol Chem. 1995	
-		
-		
-		
-Experiment context		
-species	Rat	
-cell-types	Pheochromocytoma cell line (PC12)	
-temperature (Celsius)		
-Include pathway	EGFR,Sos,PLCg,PKC,Ras,MAPK	
-details	Fig 9A	
-notes	Simulation MAPK activity using calicum.	
-		
-Stimuli		
-timeUnits	sec	
-quantityUnits	mM	
-molecules	EGF	
-field	conc	
-Data		
-Time	Value	
-0	1.00E-04	
-		
-		
-Readouts		
-readoutType	Time-Series	
-timeUnits	sec	
-quantityUnits	nM	
-useRatio	FALSE	
-useXlog	FALSE	
-useYlog	FALSE	
-ratioReferenceTime	0	
-ratioReferenceEntity	MAPK_p,MAPK/MAPK_p_p	
-molecules	MAPK_p,MAPK/MAPK_p_p	
-experimentalReadout	conc	
-useSum	FALSE	
-useNormalization	FALSE	
-Data		
-Time	Value	stderr
-0	0.02	0
-300	1	0
-1800	0.12	0
-3600	0.1	0
-7200	0.08	0
-		
-		
-Model mapping		
-modelSource	Local path	
-fileName		
-citationId		
-citation		
-authors		
-modelSubset	kinetics/EGFR,kinetics/Sos,Ras,kinetics/MAPK,kinetics/Ca,PI3K_activation,PKC,Phosphatase,kinetics/CaM	
-stimulusMolecules	EGF	
-readoutMolecules	MAPK_p,MAPK/MAPK_p_p	
-referenceMolecule	MAPK_p,MAPK/MAPK_p_p	
-scoringFormula	abs((expt-sim)/(expt+sim+1e-9))	
-itemstodelete	PP2A,CaMKIII_bind_CaM_Ca4,phosph_AC2,GEF_Gprot_bg,bg_act_GEF,MEK_phospho,CaM(Ca)n_CaNAB/func,MEKp_phospho,mGluR_barr2_Raf_scaffolding	
-solver	Runge kutta method (gsl)	
-notes	Fig2B	
-parameterChange		
-Object	parameter	Value
+Experiment metadata		
+transcriber	Nisha Ann Viswan	
+organization	National Centre for Biological Sciences	
+emailId	nishaav@ncbs.res.in	
+exptSource	Paper	
+citationId	PMID: 7657647	
+authors	Teng KK et al.	
+journal	J Biol Chem. 1995	
+		
+		
+		
+Experiment context		
+species	Rat	
+cell-types	Pheochromocytoma cell line (PC12)	
+temperature (Celsius)		
+Include pathway	EGFR,Sos,PLCg,PKC,Ras,MAPK	
+details	Fig 9A	
+notes	Simulation MAPK activity using calicum.	
+		
+Stimuli		
+timeUnits	sec	
+quantityUnits	mM	
+molecules	EGF	
+field	conc	
+Data		
+Time	Value	
+0	0.0001	
+		
+		
+Readouts		
+readoutType	Time-Series	
+timeUnits	sec	
+quantityUnits	ratio	
+useRatio	True	
+useXlog	FALSE	
+useYlog	FALSE	
+ratioReferenceTime	300	
+ratioReferenceEntity	MAPK_p,MAPK/MAPK_p_p	
+molecules	MAPK_p,MAPK/MAPK_p_p	
+experimentalReadout	conc	
+useSum	FALSE	
+useNormalization	FALSE	
+Data		
+Time	Value	stderr
+0	0.02	0
+300	1	0
+1800	0.12	0
+3600	0.1	0
+7200	0.08	0
+		
+		
+Model mapping		
+modelSource	Local path	
+fileName		
+citationId		
+citation		
+authors		
+modelSubset	kinetics/EGFR,kinetics/Sos,Ras,kinetics/MAPK,kinetics/Ca,PI3K_activation,PKC,Phosphatase,kinetics/CaM	
+stimulusMolecules	EGF	
+readoutMolecules	MAPK_p+MAPK/MAPK_p_p	
+referenceMolecule	MAPK_p+MAPK/MAPK_p_p	
+scoringFormula	abs((expt-sim)/(expt+sim+1e-9))	
+itemstodelete	PP2A,CaMKIII_bind_CaM_Ca4,phosph_AC2,GEF_Gprot_bg,bg_act_GEF,MEK_phospho,CaM(Ca)n_CaNAB/func,MEKp_phospho,mGluR_barr2_Raf_scaffolding,cluster_phospho_S6K,MAPK_4E_BP_p_p,MAPK_4E_BP_phospho,MAPK_p_p/MAPK_p_p,Ca.PLC_g_phospho,dephosph_inhib1,dephosph_PP1_I_p,dephosph_inhib1_noCaM[0]	
+solver	Runge kutta method (gsl)	
+notes	Fig2B	
+parameterChange		
+Object	parameter	Value
+EGFR/EGF	concInit	0.0001