Methods for Simulating the Dynamics of Complex Biological Processes

Methods in Cell Biology

Volumn 84, Issue , 2008, Pages 807-842

  Schilstra, Maria J ^a   Martin, Stephen R ^b   Keating, Sarah M ^a  

^a UNIVERSITY OF HERTFORDSHIRE   (United Kingdom)

^b NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; KINETICS; MICROTUBULE; REVIEW; STATISTICS; TIME;

ALGORITHMS; COMPUTER SIMULATION; KINETICS; MICROTUBULES; MODELS, BIOLOGICAL; STOCHASTIC PROCESSES; TIME FACTORS;

EID: 35448944695     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0091-679X(07)84025-8     Document Type: Review

References (63)

1. Andrews S.S., and Bray D. Stochastic simulation of chemical reactions with spatial resolution and single molecule detail. Phys. Biol. 1 (2004) 137-151
2. Atkins P.W. "Physical Chemistry." (1994), Oxford University Press, Oxford, UK
3. Bayley P.M., Schilstra M.J., and Martin S.R. A simple formulation of microtubule dynamics: Quantitative implications of the dynamic instability of microtubule populations in vivo and in vitro. J. Cell Sci. 93 (1989) 241-254
4. Bornstein B.J. "LibSBML": SBML, The Systems Biology Markup Language (2006). http://www.sbml.org/software/libsbml/
5. Bortz A.B., Kalos M.H., and Lebowitz J.L. A new algorithm for Monte Carlo simulation of Ising spin systems. J. Comput. Phys. 17 (1975) 10-18
6. Brylawski B.P., and Caplow M. Rate for nucleotide release from tubulin. J. Biol. Chem. 258 (1983) 760-763
7. CellML. "The CellML Project: Overview-Portal." (2006). http://www.cellml.org
8. CellML Model Repository. "Model Repository--Portal." (2006). http://www.cellml.org/models
9. Chen Y.-D., and Hill T.L. Monte Carlo study of the GTP cap in a five-start helix model of a microtubule. Proc. Natl. Acad. Sci. USA 82 (1985) 1131-1135
10. Cornish-Bowden A. "Fundamentals of Enzyme Kinetics." (1995), Portland Press, London
11. Cornish-Bowden A. "Fundamentals of Enzyme Kinetics." (2001), Portland Press, London, UK
12. Cuellar A.A., Lloyd C.M., Nielsen P.F., Bullivant D.P., Nickerson D.P., and Hunter P.J. An overview of CellML 1.1, a biological model description language. Simulation 79 (2003) 740-747
13. Duke T.A.J. Molecular model of muscle contraction. Proc. Natl. Acad. Sci. USA 96 (1999) 2770-2775
14. Dynasim A.B. "Dymola.". Dynasim (2006). http://www.dynasim.se
15. Ellner S.R., and Guckenheimer J. "Dynamic Models in Biology." (2006), Princeton University Press, Princeton, NJ
16. Engelborghs Y., and Eccleston J. Fluorescence stopped-flow study of the binding of S6-GTP to tubulin. FEBS Lett. 141 (1982) 78-81
17. Ermentrout B. "Simulating, Analyzing, and Animating Dynamical Systems: A Guide to XPPAUT for Researchers and Students." (2002), SIAM, Philadelphia, PA
18. Fell D. "Understanding the Control of Metabolism." (1997), Portland Press, London
19. Funahashi A., Tanimura N., Morohashi M., and Kitano H. CellDesigner: A process diagram editor for gene-regulatory and biochemical networks. Biosilico 1 (2003) 159-162
20. Gear C.W. "Numerical Initial Value Problems in Ordinary Differential Equations." (1971), Prentice-Hall, Englewood Cliffs, NJ
21. Gibson M.A., and Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. A. 104 (2000) 1876-1889
22. Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 (1977) 2340-2361
23. Gillespie D.T. Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115 (2001) 1716-1733
24. Gilman A., and Arkin A.P. Genetic "code": Representations and dynamical models of genetic components and networks. Annu. Rev. Genom. Hum. Genet. 3 (2002) 341-369
25. Ginkel M., Kremling A., Nutsch T., Rehner R., and Gilles E.D. Modular modeling of cellular systems with ProMoT/Diva. Bioinformatics 19 (2003) 1169-1176
26. Goryanin I., Hodgman T., and Selkov E. Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics 15 (1999) 749-758
27. Hindmarsh A.C., Brown P.N., Grant K.E., Lee S.L., Serban R., Shumaker D.E., and Woodward C.S. SUNDIALS: Suite of nonlinear and differential/algebraic equation solvers. ACM Trans. Math. Software 31 (2005) 363-396
28. Horio T., and Hotani H. Visualization of the dynamic instability of individual microtubules by dark-field microscopy. Nature 321 (1986) 605
29. Hucka M., Finney A., Sauro H.M., Bolouri H., Doyle J.C., Kitano H., the rest of the SBML Forum, Arkin A.P., Bornstein B.J., Bray D., Cornish-Bowden A., Cuellar A.A., Dronov S., et al. The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19 (2003) 524-531
30. Hucka M., Finney A., Bornstein B., Keating S.M., Shapiro B.E., Matthews J., Kovitz B., Schilstra M.J., Funahashi A., Doyle J.C., and Kitano H. Evolving a lingua franca and associated software infrastructure for computational systems biology: The systems biology markup language (SBML) project. Syst. Biol. 1 (2004) 41-53
31. Janulevicius A., van Pelt J., and van Ooyen A. Compartment volume influences microtubule dynamic instability: A model study. Biophys. J. 90 (2006) 788-798
32. Keating S.M., Bornstein B.J., Finney A., and Hucka M. SBMLToolbox: An SBML toolbox for MATLAB users. Bioinformatics 22 10 (2006) 1275-1277 doi:10.1093/bioinformatics/btl111
33. Kitano H., Funahashi A., Matsuoka Y., and Oda K. Using process diagrams for the graphical representation of biological networks. Nat. Biotechnol. 23 (2005) 961-966
34. Kruse K., and Elf J. Kinetics in Spatially Extended Systems. In: Szalasi Z., Stelling J., and Periwal V. (Eds). "Systems Modeling in Cellular Biology" (2006), MIT Press, Cambridge, MA 177-198
35. Le Novere N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., and Hucka M. BioModels database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucl. Acids Res. 34 (2006) D689-D691
36. Lloyd C.M., Halstead M.D.B., and Nielsen P.F. CellML: Its future, present and past. Prog. Biophys. Mol. Biol. 85 (2004) 433-450
37. Macey R.I., and Oster G.F. "Berkeley Madonna." (2001). http://www.berkeleymadonna.com
38. Markevich N.I., Hoek J.B., and Kholodenko B.N. Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J. Cell Biol. 164 (2004) 353-359
39. Martin S.R., Schilstra M.J., and Bayley P.M. Dynamic instability of microtubules: Monte-Carlo simulation and application to different types of microtubule lattice. Biophys. J. 65 (1993) 578-596
40. Mendes P. Biochemistry by numbers: Simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22 (1997) 361-363
41. Mendes P., and Kummer U. "COPASI." (2006). http://www.copasi.org/tiki-index.php
42. Meyers J., Craig J., and Odde D.J. Potential for control of signaling pathways via cell size and shape. Curr. Biol. 16 (2006) 1685-1693
43. ModelKinetix. "ModelMaker." (2006). http://www.modelkinetix.com/modelmaker/index.htm
44. Olivier B.G., Rohwer J.M., and Hofmeyr J.-H.S. Modelling cellular systems with PySCeS. Bioinformatics 21 (2005) 560-561
45. Press W.H., Flannery B.P., Teukolsky B.P., and Vetterling W.T. "Numerical Recipes: The Art of Scientific Computing. Fortran Version." (1989), Cambridge University Press, Cambridge, UK
46. Ramsey S., Orrell D., and Bolouri H. Dizzy: Stochastic simulation of large-scale genetic regulatory networks. J. Bioinform. Comput. Biol. 3 (2005) 415-436
47. Rumbaugh J., Blaha M., Premerlani W., Eddy F., and Lorensen W. "Object-Oriented Modelling and Design." (1991), Prentice-Hall, London
48. Sauro H.M. In: Hofmeyr J.-H.S., Rohwer J.M., and Snoep J.L. (Eds). "Animating the Cellular Map. 9th International BioThermoKinetics Meeting" (2000), Stellenbosch University Press, Stellenbosch, South Africa 221-228
49. SBML. "SBML.org-The home site for the Systems Biology Markup Language." (2006). http://sbml.org
50. Schilstra M.J., and Martin S.R. An elastically tethered viscous load imposes a regular gait on the motion of myosin-V. Simulation of the effect of transient force relaxation on a stochastic process. J. R. Soc. Interf. 3 (2006) 153-165
51. Schmidt H., and Jirstrand M. Systems biology toolbox for MATLAB: A computational platform for research in systems biology. Bioinformatics 22 (2006) 514-515
52. Segel I.H. "Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems." (1975), John Wiley & Sons Inc., USA
53. Shapiro B.E., Hucka M., Finney A., and Doyle J.C. MathSBML: A package for manipulating SBML-based biological models. Bioinformatics 20 (2004) 2829-2831
54. Slepchenko B.M., Schaff J., Macara I.G., and Loew L.M. Quantitative cell biology with the virtual cell. Trends Cell Biol. 13 (2003) 570-576
55. Swade D. When money flowed like water Inc. Magazine September 1995 (1995). http://pf.inc.com/magazine/19950915/2624.html
56. In: Szalasi Z., Stelling J., and Periwal V. (Eds). "Systems Modeling in Cellular Biology." (2006), MIT Press, Cambridge, MA
57. Takahashi K., Ishikawa N., Sadamoto Y., Ohta S., Shiozawa A., Miyoshi F., Naito Y., Nakayama Y., and Tomita M. E-Cell 2: Multi-platform E-cell simulation system. Bioinformatics 19 (2003) 1727-1729
58. VanBuren V., Cassimeris L., and Odde D.J. Mechanochemical model of microtubule structure and self-assembly kinetics. Biophys. J. 89 (2005) 2911-2926
59. Weisstein E. "Mathworld". Wolfram Research (2006). http://mathworld.wolfram.com/
60. Wikipedia Contributors. "Wikipedia." Wikipedia, The Free Encyclopedia (2006). http://en.wikipedia.org
61. Wilkinson D.J. "Stochastic Modelling for Systems Biology." (2006), Chapman & Hall/CRC, London
62. Zeigler B.P., Praehofer H., and Kim T.G. "Theory of Modelling and Simulation: Integrating Discrete Event and Continuous Complex Dynamic Systems." (2000), Academic Press, San Diego
63. Zewail A. In: Grenthe I. (Ed). "Nobel Lectures, Chemistry 1996-2000" (2003), World Scientific Publishing Co., Singapore 274-367