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Accession
No.		NameSource /
Entry Date		Species /
Tissue		Cell CompartmentMethodology /
Model Implementation
103gainBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
 2022-09-30 22:14:44		Generic /
cytosolFit to elementary ODE model /
HillTau implementation
99convBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
 2022-09-30 17:54:52		Generic /
cytosolFit to elementary ODE model /
HillTau implementation
98exc2ndOrderBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
 2022-09-30 17:52:22		Generic /
cytosolFit to elementary ODE model /
HillTau implementation
100inhBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
 2022-09-30 22:08:48		Generic /
cytosolFit to elementary ODE model /
HillTau implementation
101
  • exc_tau_
    baseline
    		• Bhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
     2022-09-30 22:10:56    		Generic /
    		cytosolFit to elementary ODE model /
    HillTau implementation
    102modifierBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
     2022-09-30 22:13:03    		Generic /
    		cytosolFit to elementary ODE model /
    HillTau implementation
    97excBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
     2022-09-30 15:13:55    		Generic /
    		cytosolFit to elementary ODE model /
    HillTau implementation
    104fb_inhibBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
     2022-09-30 22:16:21    		Generic /
    		cytosolAbstract phenomenological model /
    HillTau implementation
    106bistableBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
     2022-09-30 22:20:03    		Generic /
    		cytosolAbstract phenomenological model /
    HillTau implementation
    107bcmBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
     2022-09-30 23:36:25    		Generic /
    		SynapseFit to ODE model and experiments /
    HillTau implementation
    108bcm_bistableBhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
     2022-09-30 23:49:58    		Generic /
    		cytosolAbstract phenomenological model /
    HillTau implementation
    111oscBhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
     2022-10-01 00:05:03    		Generic /
    		cytosolAbstract phenomenological model /
    HillTau implementation
    112conv2ndOrderBhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
     2022-10-01 00:07:32    		Generic /
    		cytosolFit to elementary ODE model /
    HillTau implementation
    46
  • MAPK_Asthagiri_
    enz_fb
    		• Asthagiri AR and Lauffenburger DA. Biotechnol Prog. (2001) 17(2):227-39. ( peer-reviewed publication ). /
     2003-02-22 00:00:00    		Chinese hamster (Cricetulus griseus); mammalian /
    Ovary - CHO cell line    		 Surface + cytosolQualitative /
    Approximate implementation
    45
  • MAPK_Asthagiri_
    adapt_fb
    		• Asthagiri AR and Lauffenburger DA. Biotechnol Prog. (2001) 17(2):227-39. ( peer-reviewed publication ). /
     2003-02-22 00:00:00    		Chinese hamster (Cricetulus griseus); mammalian /
    Ovary - CHO cell line    		 Surface, cytosolQuantitative match to experiments, Qualitative /
    Mathematically equivalent
    91
  • Protein_
    synthesis
    		• Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) /
     2009-02-12 00:00:00    		General Mammalian /
    -    		Cell membrane, CytosolQuantitative match to experiments, Hypothetical /
    Exact GENESIS implementation
    57ChemotaxisBray et al. Mol.Biol.Cell (1993) 4(5): 469-482. ( peer-reviewed publication ) /
     2003-06-10 00:00:00    		E. Coli /
    -    		Cell membrane + cytosolQualitative /
    Mathematically equivalent
    55ChemotaxisBray et al. Mol.Biol.Cell (1993) 4(5): 469-482. ( peer-reviewed publication ) /
     2003-06-10 00:00:00    		E. Coli /
    -    		Cell membrane + cytosolQuantitative match to experiments /
    Mathematically equivalent
    29Kierzek_LacZKierzek AM. et al. J Biol Chem. (2001) 276(11):8165-72. ( peer-reviewed publication ) /
     2002-01-28 00:00:00    		E. Coli /
    -    		InternalQualitative /
    Approximate implementation
    36luciferaseL. Yu. Brovko et al 1994, Biochemistry (Moscow) 59(2):195-201, 1994 ( peer-reviewed publication ). /
     2002-12-12 00:00:00    		E. Coli /
    -    		CytosolQualitative /
    Approximate implementation
    85
  • Mammalian_cell_
    cycle
    		• Novak B,Tyson JJ. J Theor Biol. 2004 Oct 21;230(4):563-79. ( Peer-reviewed publication ) /
     2006-12-21 00:00:00    		General Mammalian /
    -    		NucleusQuantitative match to experiments /
    Approximate implementation
    114syn_CaMKIIIBhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
     2022-10-01 00:12:23    		Rodent /
    Brain    		SynapseQuantitative fit to experiments /
    HillTau implementation
    90CaMKIIIJain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) /
     2009-02-12 00:00:00    		General Mammalian /
    Brain    		Surface, Cytosol, NucleusQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation,Approximate implementation
    87AKTJain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) /
     2009-02-12 00:00:00    		General Mammalian /
    Brain    		Surface, CytosolQualitative /
    Exact GENESIS implementation
    1fig2_egfrBhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication ) /
     2001-11-07 00:00:00    		Generic mammalian /
    Brain    		Surface - NucleusQuantitative match to experiments, Hypothetical /
    Exact GENESIS implementation
    113
  • syn_prot_
    minimal
    		• Bhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
     2022-10-01 00:09:57    		Rodent /
    Brain    		SynapseReduced quantitative fit to experiments /
    HillTau implementation
    110aut6Bhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
     2022-10-01 00:02:13    		Rodent /
    Brain    		SynapseQuantitative fit to experiments /
    HillTau implementation
    109
  • syn_prot_
    composite
    		• Bhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
     2022-09-30 23:58:38    		Rodent /
    Brain    		SynapseQuantitative fit to experiments /
    HillTau implementation
    32
  • Osc_Ca_
    IP3metabolism
    		•  Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication ) /
     2002-04-03 00:00:00    		Generic mammalian /
    Brain - Neuronal    		CytosolQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    23
  • NonOsc_Ca_
    IP3metabolism
    		•  Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication ) /
     2002-01-07 00:00:00    		Generic mammalian /
    Brain - Neuronal    		CytosolQuantitative match to experiments, Qualitative /
    Approximate implementation
    50
  • MAPK_network_
    2003
    		• Bhalla US Biophys J. 2004 Aug;87(2):745-53. ( peer-reviewed publication ) /
     2003-04-28 00:00:00    		Generic mammalian /
    Brain - Neuronal    		SynapseQualitative /
    Exact GENESIS implementation
    49CaMKII_2003Bhalla US. Biophys J. 2004 Aug;87(2):733-44. ( peer-reviewed publication ). /
     2003-04-28 00:00:00    		Generic mammalian /
    Brain - Neuronal    		SynapseQualitative /
    Exact GENESIS implementation
    24
  • Osc_Ca_
    IP3metabolism
    		•  Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication ) /
     2002-01-08 00:00:00    		Generic mammalian /
    Brain - Neuronal    		CytosolQuantitative match to experiments, Qualitative /
    Approximate implementation
    26PKC_turnoverIn-house  /
     2002-01-22 00:00:00    		Generic mammalian /
    Brain - Neuronal    		Cell membrane +CytosolQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    25cAMP_pathwayBhalla US Methods Enzymol. 2002;345:3-23). ( peer-reviewed publication ) /
     2002-01-12 00:00:00    		Generic mammalian /
    Brain - Neuronal    		Cell membrane + CytosolQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    31
  • NonOsc_Ca_
    IP3metabolism
    		•  Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication ) /
     2002-04-03 00:00:00    		Generic mammalian /
    Brain - Neuronal    		CytosolQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    33CaMKIIWilliam R. Holmes J Comput Neurosci. (2000) 8(1):65-85 ( peer-reviewed publication ) /
     2002-08-21 00:00:00    		Generic mammalian /
    Brain - Neuronal    		SynapseQualitative /
    Approximate implementation
    20
  • NOS_Phosph_
    regulation
    		• In-house /
     2001-12-25 00:00:00    		rat; Mammalian /
    Brain - Neuronal; expressed in E.coli    		CytosolQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    13PLCbeta1In-house  /
     2001-11-12 00:00:00    		Bovine; Mammalian /
    Brain - Neuronal; expressed in E.coli    		Cell MembraneQualitative /
    Exact GENESIS implementation
    37SERCA Mahaney JE. et al. Biophys J. (2000) 78(3) 1306-23. ( peer-reviewed publication ) /
     2002-12-31 00:00:00    		Canine /
    Cardiac; expressed in Baculovirus infected Sf21(Spodoptera frugiperda) insect cells.    		MicrosomesQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation