CSSB-2004 Cellerator MathSBML SBML

Supplementary Information for CSSB-2004

INTERNATIONAL SCHOOL ON
COMPUTATIONAL SCIENCES FOR COMPLEX SYSTEMS IN BIOLOGY

Rovereto (Tn), Italy, 17-24 April 2004

Bruce E. Shapiro, Ph.D.

bshapiro at caltech dot edu

Class Notes
Class Notes (different from slides): Download PDF file (approx 5 MB)
Powerpoint Slides: .sit or .zip (approx 7 MB)

Quicktime Movies

Coupled Simple Harmonic Oscillators
Uncoupled CMX Oscillators
Coupled CMX Oscillators - weak coupling
Coupled CMX Oscillators - stronger coupling
Activator-Inhibitor Model
Shoot Apical Meristem Growth Simulation

Examples (Mathematica Notebooks)

Due to space limitations only the compressed versions (.sit, .zip, .tgz) of the notebooks are available online.

References
Texts on Enzyme Kinetics
  1. Cornish-Bowden, Athel (1995) Fundamentals of Enzyme Kinetics, Portland Press, London
  2. Segel, Irwin (1993), Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems , Wiley.
  3. Segel, Lee A (1991) Biological Kinetics, Cambridge University Press.
  4. Cantor, Charles R and Schimmel, Paul R (1980) The Behavior of Biological Macromolecules, Biophysical Chemistry, Part III, W.H. Freeman.
Texts on Mathematical and Computational Biology and Physiology
  1. Britton, Nicholas F (2002) Essential Mathematical Biology, Springer.
  2. Edelstein-Keshet, Leah (1988) Mathematical Models Biology, McGraw Hill.
  3. Fall, Christopher P, Marland Eric S, Swagner John M, and Tyson John J (2002) Computational Cell Biology, Springer.
  4. Keener JP, Sneyd J (1998) Mathematical Physiology, Springer/
  5. Murray JD (2002) Mathematical Biology I: An Introduction, Springer.
  6. Murray JD (2003) Mathematical Biology II: Spatial Models and Biomedical Applications.
Collections on Systems Biology
  1. Bower H, Bolouri H (2001) Computational Modeling of Genetic and Biochemical Networks, MIT Press.
  2. Kitano, H (2001) Foundations of Systems Biology, MIT Press.
  3. Kumar, S, Bentley B (2003) On Growth, Form and Computers, Elsevier.
Journal Papers and other Citations in the Notes
  1. Brown GC, Hoek JB, Kholodenko BN (1997) Why do protein kinases have more than one level? Trends Biochem. Sci., 22:288.
  2. Cobb MH, Goldsmith EJ (1995) How MAP Kinases are Regulated. J. Biol. Chem. 270:14843-14846.
  3. Elowitz,M.B., and Leibler,S. (2000) A synthetic oscillatory network of transcriptional regulators. Nature, 403:335-338.
  4. Fain GL (1999) Molecular and Cellular Physiology of Neurons, Harvard University Press.
  5. Ferrel JE (1997) How response get more switch-like as you move down a protein kinase cascade. Trends Biochem. Sci., 22:288-289.
  6. Ferrell JE, Machleder EM (1998) The Biochemical Basis of an All-or-None Cell Fate Switch in Xenopus Oocytes. Science. 280:895-898.
  7. Field RJ, Noyes RM (1974) Oscillations in chemical systems. IV. Limit cycle behavior in a model of a real chemical reaction. J. Chem. Phys. 60:1877.
  8. Gibson MA, Bruck J (2000) Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys Chem. 104: 1876-1889.
  9. Gillespie DT (1977) Exact stochastic simulations of coupled chemical reactions. J. Phys. Chem. 81: 2340-2361.
  10. Goldbeter A. (1997) Biochemical oscillations and cellular rhythms: the molecular basis of periodic and chaotic behavior, Cambridge University Press.
  11. Goldbeter, A (1991) A minimal cascade model for the mitotic oscillator involving cyclinand cdc2 cascade. Proc. Natl. Acad. Sci., USA, 88:9107-9111.
  12. Hoffmann A, Levchenko A, Scott ML, Baltimore DA (2002) The I-kappa-B-NF-kappa-B signaling module: temporal control and selective gene activation. Science, 298:1241-1245.
  13. Huang CF, Ferrell JE (1996) Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc. Natl. Acad. Sci. USA. 93:10078-10083.
  14. Jönsson H, Shapiro BE, Meyerowitz EM, Mjolsness E (2003) Signalling in multicellular models of plant development. On Growth, Form, and Computers, ed. Kumar S, Bentley JP, Elsevier, pp. 156-161.
  15. Kholodenko, B. M. (2000) Negative feedback and ultrasensitivity can bring aboutoscillations in the mitogen-activated protein kinase cascades. Eur. J. Biochem. 267: 1583-1588.
  16. Kholodenko BN, Hoek JB, Westerhoff HV, Brown GC (1997) Quantification of information transfer via cellular signal transduction pathways. FEBS Letters. 414:430-434.
  17. Levchenko A, Bruck, J, Sternberg PW (2000). Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc. Natl. Acad. Sci. USA 97:5818­5823.
  18. Mjolsness E, Sharp DH, Reinitz J (1991) A connectionist model of development. J. Theor. Biol. 152:429-453.
  19. Rumelhart DE, McClellend JL (1986) Parallel distributed processing. MIT Press.
  20. Savageau, MA (2001) Design principle for elementary gene circuits: elements, methods, and examples. Chaos 11: 142-159.
  21. Savageau, MA and Voit EO (1987) Recasting nonlinear differential equations as S-systems: a canonical nonlinear form. Math. Biosci. 87:83-115.
  22. Shapiro BE, Levchenko A, Mjolsness E (2002) Automatic Model Generation for Signal Transduction with Applications to Map Kinase Pathways. Foundations of Systems Biology, ed. H Kitano MIT Press, pp. 145-162.
  23. Shapiro BE, Levchenko A, Meyerowitz E, Wold B, Mjolsness ED (2003) Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinformatics 19: 677-678.
  24. Sveiczer A, Csikasz-Nagy A, Gyorffy B, Tyson JJ, Novak JJ (2000) Modeling the fission yeast cell cycle: Quantized cycle times in wee12 cdc25D mutant cells, Proc. Natl. Acad. Sci. USA, 97:7865­7870
  25. Tocque B, Delumeau I, Parker F, Maruier F, Multon M-C, Schweighoffer F (1997) RAS-GTPAse Activating Protein (GAP): A Putative Effector for RAS. Cellular Signalling, 9(2):153-158.
  26. Tyson, J.J. (1991) Modeling the cell division cycle: cdc2 and cyclin interactions. Proc. Natl. Acad. Sci., USA, 88:7328-7332.