Accession
No. | Name | Source /
Entry Date | Species /
Tissue | Cell Compartment | Methodology /
Model Implementation |
| 57 | Chemotaxis | Bray et al. Mol.Biol.Cell (1993) 4(5): 469-482. ( peer-reviewed publication ) /
2003-06-10 00:00:00 | E. Coli /
- | Cell membrane + cytosol | Qualitative /
Mathematically equivalent |
| 58 | EGFR_MAPK | Bhalla US. Biophys J. (2004) 87(2):745-53. ( peer-reviewed publication ) /
2004-01-14 00:00:00 | Generic mammalian /
Neuronal | Synapse | Qualitative /
Exact GENESIS implementation |
| 59 | AMPAR_traff_
model0 | Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
2005-07-19 00:00:00 | General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density | Quantitative match to experiments /
Exact GENESIS implementation |
| 60 | AMPAR_traff_
model1 | Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
2005-07-19 00:00:00 | General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density | Quantitative match to experiments /
Exact GENESIS implementation |
| 61 | simple_AMPAR_
traff_model2 | Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
2005-07-19 00:00:00 | General Mammalian /
Neuronal | Postsynaptic Density, Synaptic Spine | Illustrative /
Exact GENESIS implementation |
| 62 | CaMKII_noPKA_
model3 | Hayer A, Bhalla US PLoS PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
2005-07-19 00:00:00 | General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| 63 | CaMKII_model3 | Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
2005-07-19 00:00:00 | General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| 64 | AMPAR_CaMKII_
strong_coupling | Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
2005-07-19 00:00:00 | General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| 65 | AMPAR_CaMKII_
weak_coupling | Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
2005-07-21 00:00:00 | General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| 66 | Jak-Stat_
Pathway | Yamada S et al. FEBS Letters 2003 Jan 16;534(1-3):190-6. ( Peer-reviewed publication ) /
2006-02-13 00:00:00 | mouse /
Liver | Cytosol, Nucleus | Quantitative match to experiments /
Exact GENESIS implementation |
| 67 | SOCS1_knockout | Yamada S et al. FEBS Letters 2003 Jan 16;534(1-3):190-6. ( Peer-reviewed publication ) /
2006-02-13 00:00:00 | mouse /
Liver | Nucleus , cytoplasm | Quantitative match to experiments /
Exact GENESIS implementation |
| 68 | Repressilator | Elowitz MB, Leibler S., Nature. 2000 Jan 20;403(6767):335-8. ( Peer-reviewed publication ) /
2006-02-13 00:00:00 | E. Coli /
E.coli Expression, Transposon, Lambda phage | Cytosol | Qualitative /
Exact GENESIS implementation |
| 69 | Quorum_
repressilator | Garcia-Ojalvo J, Elowitz MB, Strogatz SH. Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):10955-60.. ( Peer-reviewed publication ) /
2006-02-14 00:00:00 | E. Coli /
E.coli Expression, Transposon Tn10, Lambda phage Expression | Cytosol, Extracellular | Qualitative /
Exact GENESIS implementation |
| 70 | RanGTPase | Gorlich D et al EMBO J. 2003 Mar 3;22(5):1088-100. ( Peer-reviewed publication ) /
2006-05-12 00:00:00 | Eukaryotic system /
HeLa Cells | Cytosol, Nucleus | Qualitative /
Exact GENESIS implementation |
| 71 | RasGTPase | Phillips RA et al Biochemistry. 2003 Apr 8;42(13):3956-65. ( Peer-reviewed publication ) /
2006-05-12 00:00:00 | General Mammalian /
E.coli Expression system | Cytosol | Qualitative /
Exact GENESIS implementation |
| 72 | L-Arginine | Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51. ( Peer-reviewed publication ) /
2006-08-07 00:00:00 | Human /
Kidney cell expressing the rat brain nNOS | Cytosol | Quantitative match to experiments /
Exact GENESIS implementation |
| 73 | HomoArginine | Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51. ( Peer-reviewed publication ) /
2006-08-07 00:00:00 | human /
Kidney cell expressing the rat brain nNOS | Cytosol | Quantitative match to experiments /
Exact GENESIS implementation |
| 74 | NMArginine | Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51. ( Peer-reviewed publication ) /
2006-08-07 00:00:00 | human /
Kidney cell expressing the rat brain nNOS | Cytosol | Quantitative match to experiments /
Exact GENESIS implementation |
| 76 | Ajay_Bhalla_
2004_PKM_Tuning | Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. ( Peer-reviewed publication ) /
2006-12-12 00:00:00 | Rat /
Hippocampal CA1 | Dendrite | Semi -Quantitative match to experiments /
Exact GENESIS implementation |
| 77 | Ajay_Bhalla_
2004_PKM_MKP3_
Tuning | Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80 ( Peer-reviewed publication ) /
2006-12-12 00:00:00 | Rat /
Hippocampal CA1 | Dendrite | Semi-Quantitative match to experiments /
Exact GENESIS implementation |
| 75 | NOHArginine | Abu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51. ( Peer-reviewed publication ) /
2006-08-07 00:00:00 | human /
Kidney cell expressing the rat brain nNOS | Cytosol | Quantitative match to experiments /
Exact GENESIS implementation |
| 78 | Ajay_Bhalla_
2004_Feedback_
Tuning | Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. ( Peer-reviewed publication ) /
2006-12-12 00:00:00 | Rat /
Hippocampal CA1 | Dendrites | Semi-Quantitative match to experiments /
Exact GENESIS implementation |
| 79 | Ajay_Bhalla_
2007_Bistable | Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
2006-12-08 00:00:00 | Rat /
Hippocampal CA1 | Dendrite | Semi-Quantitative match to experiments /
Exact GENESIS implementation |
| 80 | Ajay_Bhalla_
2007_PKM | Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
2006-12-08 00:00:00 | Rat /
Hippocampal CA1 | Dendrite | Semi-Quantitative match to experiments /
Exact GENESIS implementation |
| 81 | Ajay_bhalla_
2007_ReacDiff1_
1e-12 | Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
2006-12-08 00:00:00 | Rat /
Hippocampal CA1 | Dendrite | Semi-Quantitative match to experiments /
Exact GENESIS implementation |
| 82 | Ajay_Bhalla_
2007_ReacDiff1_
1e-13 | Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
2006-12-08 00:00:00 | Rat /
Hippocampal CA1 | Dendrite | Semi-Quantitative match to experiments /
Exact GENESIS implementation |
| 83 | Ajay_Bhalla_
2007_ReacDiff2 | Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
2006-12-08 00:00:00 | Rat /
Hippocampal CA1 | Dendrite | Semi-Quantitative match to experiments /
Exact GENESIS implementation |
| 84 | Ajay_Bhalla_
2007_ReacDiff3 | Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
2006-12-08 00:00:00 | Rat /
Hippocampal CA1 | Dendrite | Semi-Quantitative match to experiments /
Exact GENESIS 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 /
- | Nucleus | Quantitative match to experiments /
Approximate implementation |
| 86 | BDNF_Receptor | Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) /
2009-02-12 00:00:00 | General Mammalian /
NIH 3T3 Expression | Surface, Cytosol | Qualitative /
Exact GENESIS implementation |
| 87 | AKT | Jain 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 | Qualitative /
Exact GENESIS implementation |
| 88 | S6K | Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) /
2009-02-12 00:00:00 | General Mammalian /
HEK293 cells | Surface, Cytosol | Qualitative /
Exact GENESIS implementation |
| 89 | 4EBP | Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) /
2009-02-12 00:00:00 | General Mammalian /
E.coli Expression | Surface, Cytosol | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| 90 | CaMKIII | Jain 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, Nucleus | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation,Approximate implementation |
| 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, Cytosol | Quantitative match to experiments, Hypothetical /
Exact GENESIS implementation |
| 93 | CaMKIV_submodel | Peer-reviewed publication /
2014-06-10 00:00:00 | General Mammalian /
Neuronal | Cytosol, Nucleus | Quantitative match to experiments /
Exact GENESIS implementation |
| 94 | mRNA synthesis | Peer-reviewed publication,Book /
2014-06-10 00:00:00 | General Mammalian/Neuronal /
Neuronal | Surface,Cytosol, Nucleus | Quantitative match to experiments,Approximate implementation,Qualitative,Qualitative /
Approximate implementation |
| 95 | Differential syn
thesis of mRNA | Peer-reviewed publication,Book /
2014-06-10 00:00:00 | General Mammalian/Neuronal /
Neuronal | Surface,Cytosol, Nucleus | Quantitative match to experiments,Approximate implementation,Qualitative,Qualitative /
Approximate implementation |
| 96 | BCM | Bhalla PLoS Comput Biol 2021 (peer reviewed publication) /
2022-05-19 00:00:00 | General Mammalian /
Neuronal | Cell membrane/cytosol | Qualitative /
Reduced ODE model |
| 97 | exc | Bhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
2022-09-30 15:13:55 | Generic /
| cytosol | Fit to elementary ODE model /
HillTau implementation |
arrow indicates that ordering is done according to ascending or descending order.