Cellerator Feature Demonstrations |
| Model | Description | Download |
| Examples |
Typical Cellerator Arrow Reactions |
View in html
example.nb.zip
example.nb.sit
example.nb.tgz
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| Full Demo |
Demonstration of All Major Features |
demo.nb.zip
demo.nb.sit
demo.nb.tgz
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| Signal Transduction Notebooks - Published Models |
| Model | Reference | Download |
| Belousov-Zhabotinskii Reaction |
R.J.Field and R.M.Noyes,J.Chem.Phys.60,1877 (1974); R.J.Field, E.Koros,R.M.Noyes,JACS 94,8649 (1972).
J.D. Murray, "Mathematical Biology" (1989) page 181. |
Model Details
Cellerator
SBML |
| Circadian Oscillator |
J-C.Leloup and A.Goldbeter (1999) Chaos and birhythmicity in a model for circadian oscillations
of the PER and TIM proteins in Drosophila. |
Model Details
Cellerator
SBML |
| Circadian Oscillator |
Vilar et al (2002) Mechanisms of Noise Resistance in Genetic Oscillators. PNAS, 99(9): 5988. |
Model Details
Cellerator
SBML |
| Glycolysis |
Sel'kov, in Keener & Sneyd (1998) Mathematical Physiology, page 18 |
Cellerator |
| G Protein Activation |
Textbook Example, e.g., G.L.Fain, Molecular and Cellular Physiology of Neurons (1999), Harvard Univ. Press, pp. 402ff. |
Cellerator
Picture
SBML Details
zipped-SBML
screen-SBML |
| IP3 Calcium Channels |
GWD Young and J Keizer (1992) A Single-Pool Inositol 1,4,5-Trisphosphate-Receptor-Based Model for Agonist-Stimulated Oscillations in Ca2+ Concentration. PNAS, 89(20):9895.
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Model Details
Cellerator
SBML |
| Lorenz Equations |
Lorenz EN (1963) Deterministic nonperiodic flow. Journal of the Atmospheric Sciences, 20:130-141
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Model Details
Cellerator
SBML |
| MAPK in Solution |
A Levchenko et al (2000) Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. PNAS, 97(11): 5818-5823. |
Model Details
Cellerator
SBML |
| MAPK on Scaffold |
A Levchenko et al (2000) Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. PNAS, 97(11): 5818-5823. |
Model Details
Cellerator
SBML |
| MAPK Oscillations (Michaelis-Menten) |
Kholodenko, Boris N. Eur J Biochem 267:1583-8 (2000) "Negative feedback and ultrasensitivity can bring about oscillations in the
mitogen-activated protein kinase cascades." |
Cellerator
Simulation |
| MAPK Oscillations (Mass Action) |
unpublished; Inspired by Kholodenko (2000) and Levchenko (2000) |
Cellerator
Simulation |
| Mitotic Oscillator (2-Variable) |
R Norel and Z Agur (1991) A model for the adjustment of the mitotic clock by cyclin and MPF levels. Science, 251:1076. |
Cellerator |
| Mitotic Oscillator (2-Variable) |
JJ Tyson (1991) Modeling the Cell Division Cycle: cdc2 and Cyclin Interactions. PNAS, 88(16): 7328-7332.
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Model Details
Cellerator
SBML
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| Mitotic Oscillator (6-Variable) |
JJ Tyson (1991) Modeling the Cell Division Cycle: cdc2 and Cyclin Interactions. PNAS, 88(16): 7328-7332.
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Model Details
Cellerator
SBML
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| Mitotic Oscillator (3-Variable) |
A Goldbeter (1991) A Minimal Cascade Model for the Mitotic Oscillator Involving Cyclin and cdc2 Kinase. PNAS, 88(20): 9107-9111.
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Model Details
Cellerator
SBML
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| Mitotic Oscillator (Goldbeter plus Inhibitor) |
TS Gardner et al (1998) A theory for controlling cell cycle dynamics using a reversibly binding inhibitor. PNAS, 95(24): 14190-14195.
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Model Details
Cellerator
SBML
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| Mitotic Oscillator (Fission Yeast, 13 Variable) |
B Novak and JJ Tyson (1997) Modeling the control of DNA replication in fission yeast. PNAS, 94(17): 9147-9152.
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Model Details
Cellerator
SBML
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| Mitotic Oscillator (6-variable Model) |
B Novak (2001) "Addition of a G1 Enemy," from a lecture given at Caltech, 26 March 2001.
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Cellerator
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| NFkB (Nuclear Factor Kappa Beta) |
Hoffmann A,Levchenko A,Scott ML,Baltimore D (2002) The I-kappa-Beta-NF-kappa-Beta signaling module: temporal control and selective gen activation.Science, 298:1241.
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Model Details
Cellerator
SBML (unvalidated)
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| Phosphorylation Cascades |
D Gonze and A Goldbeter (2001) A Model for a Network of Phosphorylation - dephosphorylation Cycles Displaying the Dynamics of Dominoes and Clocks.
Journal of Theoretical Biology, 210(2): 167-186.
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zip |
sit |
tgz
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| Repressilator |
MB Elowitz MB and S Leibler (2000) A synthetic oscillatory network of transcriptional regulators.Nature.403 :335 - 338.
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Model Details
Cellerator
SBML
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| Signal Transduction Notebooks - Toy Models |
| Model | Description | Download |
| Ring Oscillator |
Oscillations using enzymatic cascades. |
Cellerator |
| Ring Oscillator |
Oscillations using allosteric binding model (MWC). |
Cellerator |
| Ring Oscillator |
Oscillations using sigmoidal transcriptional activation (GRN). |
Cellerator |
| Multicellular Systems |
| Model | Description | Download |
| 6-Cell system |
Using Norel & Agur Minimal Mitotic Oscillator in each cell |
Cellerator |
| 6-Cell system |
Using Tyson 1991 6-variable Mitotic Oscillator in each cell |
Cellerator |
