Study on the Dynamic Models of Systems Biology from the View of Engineering

Article Preview

Abstract:

From the view of engineering, based on expatiating the features of systems biology, the paper discusses the workflows and the research emphasis of systems biology. It also explains how to model and analyze the dynamic process of signal transmitting network for a biological system by an example. Based on the complexity and uncertainty of the mathematical model, the right methods are chosen to realize the effective estimation of state variables and model parameters for the biochemical pathway.

You might also be interested in these eBooks

Info:

Periodical:

Pages:

952-957

Citation:

Online since:

November 2012

Export:

Price:

Permissions CCC:

Permissions PLS:

Сopyright:

© 2012 Trans Tech Publications Ltd. All Rights Reserved

Share:

Citation:

[1] Wu jiarui. The Characteristics of Systems Biology. . In Chinese

Google Scholar

[2] Hood L. A personal view of molecular technology and how it has changed biology. J Proteome Res, 2002,1 (5) :399-409

DOI: 10.1021/pr020299f

Google Scholar

[3] Jiang Taijiao, Xue Yanhong, Xu Tao. Systems Biology:a New Field of Biological Science. Progress in Biochemistry and Biophysics, 2004,Vol.31, No.11: 958. In Chinese

Google Scholar

[4] Lei Jun, Gu Min-min. Systems biology-An engineering perspective. World Science, No.7,2007:7-10. In Chinese

Google Scholar

[5] Allen W. Cowley, Jr., Mingyu Liang. Physiology and genomics: toward systems biology. Acta Physiologica Sinica, Feb. 25, 2006, 58(1):1-4, www.actaps.com.cn

Google Scholar

[6] Hiroaki Kitano (editor). Foundations of Systems Biology, MIT Press; October 15, (2001)

Google Scholar

[7] Minna Allarakhia, Anthony Wensley. Systems biology: A disruptive biopharmaceutical research paradigm. Technological Forecasting and Social Change, 74, 2007:1643-1660

DOI: 10.1016/j.techfore.2006.07.012

Google Scholar

[8] Yang Yu-di, Zhou Lu-jia. Mathematical models in systems biology and their applications. Letters in biotechnology, Vol.17, No.6, 2006: 981-984. In Chinese

Google Scholar

[9] Ingalls, B. P..Metabolic Control Analysis from a control-theoretic perspective. Proceedings of the 45th IEEE Conference on Decision and Control, San Diego, December, 2006.

DOI: 10.1109/cdc.2006.377367

Google Scholar

[10] Ingalls, B. P. and Sauro, H.M.. Sensitivity Analysis of Stoichiometric Networks: An Extension of Metabolic Control Analysis to Non-equilibrium Journal of Theoretical Biology, 222, 2003: 23-36

DOI: 10.1016/s0022-5193(03)00011-0

Google Scholar

[11] Ana P. Teixeira, Nuno Carinhas, etc. Hybrid semi-parametric mathematical systems: Bridging the gap between systems biology and process engineering. Journal of Biotechnology, 132, 2007: 418-425

DOI: 10.1016/j.jbiotec.2007.08.020

Google Scholar

[12] Olaf Wolkenhauer. Systems biology: The reincarnation of systems theory applied in biology?. Briefings in Bioinformatics, Vol.2, No.3, 2001: 258-270

DOI: 10.1093/bib/2.3.258

Google Scholar

[13] N.A.W. van Riel, E.D. Sontag. Parameter estimation in models combining signal transduction and metabolic pathways: the dependent input approach. IEE Proc. Syst. Biol., Vol. 153, No.4, 2006: 263-274

DOI: 10.1049/ip-syb:20050076

Google Scholar

[14] Wayne Materi and David S. Wishart. Computational systems biology in drug discovery and development: methods and applications. Drug discovery today, Vol.12, No.7/8, 2007: 295-303

DOI: 10.1016/j.drudis.2007.02.013

Google Scholar

[15] K.–H. CHo*, O. Wolkenhauert. Analysis and modeling of signal transduction pathways in systems biology. Biochemical Society Transactions, Vol.31, 2003:1503-1509

DOI: 10.1042/bst0311503

Google Scholar

[16] F. He, L. Yeung and M. Brown, Discrete-Time Model Representation for Biochemical Pathway Systems. IAENG International Journal of Computer Science, 34:1, IJCS_34_1_15

Google Scholar

[17] Runge–Kutta methods. http://en.wikipedia.org/wiki/Runge_kutta

Google Scholar

[18] E. A. Wan and R. der Merwe. The Unscented Kalman Filter for Nonlinear Estimation. Adaptive Systems for Signal Processing, Communications, and Control Symposium 2000. AS-SPCC. Lake Louise, Alta., Canada, October, 2000: 153-158

DOI: 10.1109/asspcc.2000.882463

Google Scholar

[19] O. Wolkenhauer. Systems Biology: Dynamic Pathway Modeling. www.sbi.uni-rostock.de, December, 2006:62

Google Scholar

[20] S. J. Julier and J. K. Uhlmann, "A New Extension of the Kalman Filter to Nonlinear Systems," in Proc. of AeroSense: The 11th Int. Symp. on Aerospace/Defence Sensing, Simulation and Controls., (1997)

Google Scholar