Models | Home |
Arabidopsis thaliana Shoot Apical
Meristem
Jönsson H, Heisler M, Reddy GV, Agrawal V, Gor V, Shapiro BE, Mjolsness E, Meyerowitz EM (2005) "Modeling the organization of the Wuschel domain in the shoot apical meristem," Bioinformatics 21(S1): i232-i240 View Reference |
nb.zip |
|
|
Belousov-Zhabotinski Reaction (published models)
Prigogene L Lefever R (1968) Symmetry breaking instabilities in dissipative systems. II. J. Chem. Phys 48, 1695-1700. View Reference |
nb.zip CelleratorML |
Oregonator (FIeld-Noyes Model): Field RJ, Körös E, Noyes RM (1972) Oscillations in Chemical Systems. II. Thorough Analysis of Temporal Oscillations in the Bromate-Cerium-Malonic Acid System. JACS, 94(25):8649-8664. View Reference |
nb.zip |
|
|
ClO2-I-MA Oscillators
Lengyel, Rabai, Epstein. "Experimental and Modeling Study of Oscillations in the Chlorine Dioxide-Iodine-Malonic Acid Reaction." Journal of the Am. Chem. Soc. (1990) 112:9104-9110 |
nb.zip CelleratorML |
XML for Modification of Lengyel reduced model to avoid 5th order reaction (example included in nb file above) |
CelleratorML |
|
|
Circadian Rhythms (Published Models)
(1) Vilar JMG, Kueh HY, Barkai N, Leibler S, (2002) "Mechanisms of noise resistance in genetic oscillators," PNAS, 99(9):5988-5992. View Reference (2) Barkai N, Leibler S (2000) "Circadian clocks limited by noise," Nature, 403:267-268. View Reference |
nb.zip |
Leloup JC, Goldbeter A (1999) Chaos and birhythmicity in a mdoel for circadian oscillations of the PER and TIM proteins in Drosophila. J Theor Biol 198:445-459. View Reference |
nb.zip |
|
|
Dominoes & Clocks (Published Models)
Gonze D & Goldbeter A (2000) A model for a network of phosphorylation-dephosphorylation cycles displaying the dynamics of dominoes and clocks, J. Theor. Biol; 210:167-186. Murray AW & Kirschner MW (1989) Dominoes and clocks: the union of two views of the cell cycle, Science: 246:614-621. |
nb.zip |
|
|
G-Protein Activation (Textbook Example)
Based on figure 11.7 ,page 403 of G.Fain (1999) Molecular and Cellular Physiology of Neurons, Harvard University Press |
nb.zip |
|
|
Lineage Determination (Published Model)
Chickarmane V, Peterson C (2008) " A Computational Model for Understanding Stem Cell, Trophectoderm and Endoderm Lineage Determination." PLoS ONE 3(10): e3478. Journal web site. [doi/10.1371/journal.pone.0003478] |
nb |
|
|
MAP-Kinase Cascades (Published Models)
Kholodenko, Boris N. (2000) "Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades." Eur J Biochem 267:1583-8. View Reference |
nb.zip |
|
nb.zip |
(1) Levchenko, A., Bruck, J., Sternberg, P.W. (2000). Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. PNAS, 97(11):5818–5823. View Reference. (2) Shapiro, B, Leevchenko A., Mjolsness E. (2001) Automatic Equation Generation for Signal Transduction with Applications to MAP-Kinase, in Foundations of Systems Biology, Edited by H. Kitano, MIT Press. |
nb.zip |
|
|
Mass Action Reactions (Demonstration Moddel)
Illustration of simple mass action arrows in xCellerator. |
nb.zip |
|
|
Mass Action Oscillations (Published Moddel)
Alfred Lotka "Undamped Oscillations from the Law of Mass Action" Journal of the American Chemical Society 49:1595-1599 (1920). |
nb.zip CelleratorML |
|
|
Mitotic Oscillators (Published Models)
Goldbeter, A. A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase. (1991) PNAS, 88:9107-1101 (1991).View Reference |
nb.zip |
|
nb.zip |
|
nb.zip |
|
nb.zip |
|
|
NF-κβ (Nuclear Factor Kappa Beta)
Hoffmann A, Levchnko A, Scott M, Baltimore D (2002) Science, 298(5596):1241-1245. View Reference |
nb.zip |
|
|
Repressilator
Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature. 403:335-338. View Reference |
nb.zip |
|
|
Ring Oscillators (classroom demonstration models)
GRN Model |
nb.zip |
|
nb.zip CelleratorML |
|
nb.zip |
|
nb.zip |
|
nb.zip |
|
nb.zip |