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Cellerator Model Repository

Cellerator Feature Demonstrations

ModelDescriptionDownload
Examples Typical Cellerator Arrow Reactions View in html
example.nb.zip example.nb.sit example.nb.tgz
Full Demo Demonstration of All Major Features demo.nb.zip
demo.nb.sit
demo.nb.tgz
Signal Transduction Notebooks - Published Models
ModelReferenceDownload
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. Model Details
Cellerator
SBML
Lorenz Equations Lorenz EN (1963) Deterministic nonperiodic flow. Journal of the Atmospheric Sciences, 20:130-141 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MAPK Oscillations (Mass Action) unpublished; Inspired by Kholodenko (2000) and Levchenko (2000) Cellerator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. Model Details
Cellerator
SBML
Mitotic Oscillator (6-Variable) JJ Tyson (1991) Modeling the Cell Division Cycle: cdc2 and Cyclin Interactions. PNAS, 88(16): 7328-7332. Model Details
Cellerator
SBML
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. Model Details
Cellerator
SBML
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. Model Details
Cellerator
SBML
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. Model Details
Cellerator
SBML
Mitotic Oscillator (6-variable Model) B Novak (2001) "Addition of a G1 Enemy," from a lecture given at Caltech, 26 March 2001. Cellerator
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. Model Details
Cellerator
SBML (unvalidated)
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. zip |  sit |  tgz
Repressilator MB Elowitz MB and S Leibler (2000) A synthetic oscillatory network of transcriptional regulators.Nature.403 :335 - 338. Model Details
Cellerator
SBML
Signal Transduction Notebooks - Toy Models
ModelDescriptionDownload
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
ModelDescriptionDownload
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