A new strategy for assessing sensitivities in biochemical models

Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences

Volumn 366, Issue 1880, 2008, Pages 3619-3631

  Sahle, Sven ^a   Mendes, Pedro ^b,c   Hoops, Stefan ^c   Kummer, Ursula ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

^c VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

Optimization; Robustness; Sensitivity analysis

Indexed keywords

COMPUTER NETWORKS; PLANNING; STRATEGIC PLANNING; THREE TERM CONTROL SYSTEMS;

INTEGRAL PART; OPTIMIZATION; PARAMETER SPACES; ROBUSTNESS;

SENSITIVITY ANALYSIS;

ALGORITHM; ANIMAL; ARTICLE; BIOCHEMISTRY; BIOLOGICAL MODEL; COMPUTER; COMPUTER PROGRAM; DRUG DESIGN; DRUG SCREENING; GLYCOLYSIS; HUMAN; METABOLISM; METHODOLOGY; REPRODUCIBILITY; SKELETAL MUSCLE; SYSTEMS BIOLOGY; THEORETICAL MODEL;

ALGORITHMS; ANIMALS; BIOCHEMISTRY; COMPUTERS; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; GLYCOLYSIS; HUMANS; MODELS, GENETIC; MODELS, THEORETICAL; MUSCLE, SKELETAL; REPRODUCIBILITY OF RESULTS; SOFTWARE; SYSTEMS BIOLOGY;

EID: 51049105974     PISSN: 1364503X     EISSN: None     Source Type: Journal    
DOI: 10.1098/rsta.2008.0108     Document Type: Article

References (22)

1. Bentele, M., Lavrik, I., Ulrich, M., Stösser, S., Heermann, D. W., Kalthoff, H., Krammer, P. H. & Eils, R. 2004 Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis. J. Cell Biol. 166, 839-851. (doi:10.1083/jcb.200404158)
2. Beyer, H.-G. 2001 The theory of evolution strategies. Berlin, Germany: Springer.
3. Butcher, E. C. 2005 Can cell systems biology rescue drug discovery? Nat. Rev. Drug Discov. 4, 461-467. (doi:10.1038/nrd1754)
4. Campolongo, F., Saltelli, A. & Tarantela, S. 2000 Sensitivity analysis as an ingredient of modeling. Stat. Sci. 15, 377-395. (doi:10.1214/ss/1009213004)
5. Cascante, M., Boros, L. G., Comin-Anduix, B., de Atauri, P., Centelle, J. J. & Lee, P. W. N. 2002 Metabolic control analysis in drug discovery and disease. Nat. Biotechnol. 20, 243-249. (doi:10.1038/nbt0302-243)
6. Corana, A., Marchesi, M., Martini, C. & Ridella, S. 1987 Minimizing multimodal functions of continuous variables with thesimulated annealin algorithm. ACM Trans. Math. Software 13, 262-280. (doi:10.1145/29380.29864)
7. Eberhart, R. C. & Kennedy, J. 1995 A new optimizer using particle swarm theory. In Proc. of the 6th Int. Symp. on Micromachine and Human Science, Nagoya, Japan, pp. 39-43.
8. Heinrich, R. & Rapoport, T. A. 1974 A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem. 42, 89-95. (doi:10.1111/j.1432-1033.1974.tb03318.x)
9. Heinrich, R. & Schuster, S. 1996 The regulation of cellular systems. Berlin, Germany: Springer.
10. Hoops, S. et al. 2006 COPASI - a COmplex PAthway Simulator. Bioinformatics 22, 3067-3074. (doi:10.1093/bioinformatics/bt1485)
11. Hucka, M. et al. 2003 The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531. (doi:10.1093/bioinformatics/btg015)
12. Kacser, H. & Burns, J. A. 1973 The control of flux. Symp. Soc. Exp. Biol. 27, 65-104.
13. Kirkpatrick, S., Gelatt Jr, C. D. & Vecchi, M. P. 1983 Optimization by simulated annealing. Science 220, 671-680. (doi:10.1126/ science.220.4598.671)
14. Lambeth, M. J. & Kushmerick, M. J. 2002 A computational model for glycogenosis in skeletal muscle. Ann. Biomed. Eng. 30, 808-827. (doi:10.1114/1.1492813)
15. Le Novère, N. et al. 2006 BIOMODELS database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34, D689-D691. (doi:10.1093/nar/gkj092)
16. Ludtke, N., Panzeri, S., Brown, M., Broomhead, D. S., Knowles, J., Montemurro, M. A. & Kell, D. B. 2008 Information-theoretic sensitivity analysis: a general method for credit assignment in complex networks. J. R. Soc. Interface 5, 223-235. (doi:10.1098/rsif.2007.1079)
17. Mendes, P. & Kell, D. B. 1998 Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14, 869-883. (doi:10.1093/bioinformatics/14.10.869)
18. Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N. & Teller, A. H. 1953 Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087-1092. (doi:10.1063/1.1699114)
19. Mitchell, M. 1995 An introduction to genetic algorithms. Boston, MA: MIT Press.
20. Stephanopoulos, G. & Vallino, J. J. 1991 Network rigidity and metabolic engineering in metabolite overproduction. Science 252, 1675-1681. (doi:10.1126/science.1904627)
21. Van Riel, N. A. 2006 Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments. Brief Bioinform. 7, 364-374. (doi:10.1093/bib/bbl040)
22. Wolpert, D. H. & Macready, W. G. 1997 No free lunch theorems for optimization. IEEE Trans. Evol. Comp. 1, 67-82. (doi:10.1109/4235.585893)