A cooperative strategy for parameter estimation in large scale systems biology models

BMC Systems Biology

Volumn 6, Issue , 2012, Pages

  Villaverde, Alejandro F ^a   Egea, Jose A ^b   Banga, Julio R ^a  

^a INSTITUTO DE INVESTIGACIONES MARINAS   (Spain)

^b TECHNICAL UNIVERSITY OF CARTAGENA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI;

CARBON;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CALIBRATION; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; METHODOLOGY; SYSTEMS BIOLOGY; TIME;

ALGORITHMS; CALIBRATION; CARBON; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, BIOLOGICAL; SYSTEMS BIOLOGY; TIME FACTORS; TRANSCRIPTION, GENETIC;

EID: 84862556212     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-75     Document Type: Article

References (39)

1. van Riel N. Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments. Briefings Bioinf 2006, 7(4):364.
2. Stelling J. Mathematical models in microbial systems biology. Curr Opin Microbiol 2004, 7(5):513-518. 10.1016/j.mib.2004.08.004, 15451507.
3. Terzer M, Maynard N, Covert M, Stelling J. Genome-scale metabolic networks. Wiley Interdisciplinary Rev: Syst Biol Med 2009, 1(3):285-297.
4. Banga J, Balsa-Canto E. Parameter estimation and optimal experimental design. Essays Biochem 2008, 45:195. 10.1042/BSE0450195, 18793133.
5. Jaqaman K, Danuser G. Linking data to models: data regression. Nat Rev Mol Cell Biol 2006, 7(11):813-819. 10.1038/nrm2030, 17006434.
6. Ashyraliyev M, Fomekong-Nanfack Y, Kaandorp J, Blom J. Systems biology: parameter estimation for biochemical models. FEBS J 2008, 276(4):886-902.
7. Balsa-Canto E, Alonso A, Banga JR. An iterative identification procedure for dynamic modeling of biochemical networks. BMC Syst Biol 2010, 4:11. 10.1186/1752-0509-4-11, 2838808, 20163703.
8. Jamshidi N, Palsson B. Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models. Biophys J 2010, 98(2):175-185. 10.1016/j.bpj.2009.09.064, 2808481, 20338839.
9. Liebermeister W, Klipp E. Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor Biol Med Modell 2006, 3:41.
10. Liebermeister W, Klipp E. Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data. Theor Biol Med Modell 2006, 3:42.
11. Liebermeister W, Uhlendorf J, Klipp E. Modular rate laws for enzymatic reactions: thermodynamics, elasticities, and implementation. Bioinformatics 2010, 26(12):1528-1534. 10.1093/bioinformatics/btq141, 20385728.
12. Tran L, Rizk M, Liao J. Ensemble modeling of metabolic networks. Biophys J 2008, 95(12):5606-5617. 10.1529/biophysj.108.135442, 2599852, 18820235.
13. Covert M, Knight E, Reed J, Herrgard M, Palsson B. Integrating high-throughput and computational data elucidates bacterial networks. Nature 2004, 429(6987):92-96. 10.1038/nature02456, 15129285.
14. Covert M, Xiao N, Chen T, Karr J. Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics 2008, 24(18):2044. 10.1093/bioinformatics/btn352, 18621757.
15. Lee JM, Gianchandani E, Eddy J, Papin J. Dynamic analysis of integrated signaling, metabolic, and regulatory networks. PLoS Comput Biol 2008, 4(5):e1000086. 10.1371/journal.pcbi.1000086, 2377155, 18483615.
16. Smallbone K, Simeonidis E, Broomhead D, Kell D. Something from nothing: bridging the gap between constraint-based and kinetic modelling. FEBS J 2007, 274(21):5576-5585. 10.1111/j.1742-4658.2007.06076.x, 17922843.
17. Smallbone K, Simeonidis E, Swainston N, Mendes P. Towards a genome-scale kinetic model of cellular metabolism. BMC Syst Biol 2010, 4:6. 10.1186/1752-0509-4-6, 2829494, 20109182.
18. Kotte O, Zaugg J, Heinemann M. Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Syst Biol 2010, 6:355. 2858440, 20212527.
19. Chen W, Schoeberl B, Jasper P, Niepel M, Nielsen U, Lauffenburger D, Sorger P. Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Mol Syst Biol 2009, 5:239. 2644173, 19156131.
20. Banga JR. Optimization in computational systems biology. BMC Syst Biol 2008, 2:47. 10.1186/1752-0509-2-47, 2435524, 18507829.
21. Jostins L, Jaeger J. Reverse engineering a gene network using an asynchronous parallel evolution strategy. BMC Syst Biol 2010, 4:17. 10.1186/1752-0509-4-17, 2850326, 20196855.
22. Rodriguez-Fernandez M, Egea J, Banga J. Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems. BMC Bioinf 2006, 7:483.
23. Egea JA, Rodríguez-Fernández M, Banga JR, Martí R. Scatter search for chemical and bio-process optimization. J Global Optimization 2007, 37(3):481-503.
24. Egea JA, Balsa-Canto E, García MSG, Banga JR. Dynamic optimization of nonlinear processes with an enhanced scatter search method. Ind & Eng Chem Res 2009, 48:4388-4401. 10.1021/ie801717t, 23195362.
25. Egea JA, Martí R, Banga JR. An evolutionary method for complex-process optimization. Comput Operations Res 2010, 37(2):315-324.
26. Glover F, Laguna M, Martí R. Fundamentals of scatter search and path relinking. Control and Cybernetics 2000, 39(3):653-684.
27. Beyer HG, Schwefel HP. Evolution strategies - a comprehensive introduction. Nat Comput 2002, 1:3-52.
28. Banga JR, Moles CG, Alonso AA. Global optimization of bioprocesses using stochastic and hybrid methods. Front Global Optimization 2003, 74:45-70.
29. De La Maza M, Yuret D. Dynamic hill climbing. AI EXPERT 1994, 9:26-26.
30. García-López F, Melián-Batista B, Moreno-Pérez JA, Moreno-Vega M. Parallelization of the scatter search for the p-median problem. Parallel Computing 2002, 29(5):575-589.
31. Vrugt JA, Robinson B. Improved evolutionary optimization from genetically adaptive multimethod search. Proc Natl Acad Sci USA 2007, 104(3):708-711. 10.1073/pnas.0610471104, 1766340, 17215363.
32. Crainic T, Toulouse M. Parallel strategies for meta-heuristics. Handb Metaheuristics 2010, 57:497-541.
33. Toulouse M, Crainic TG, Sansó B. Systemic behavior of cooperative search algorithms. Parallel Comput 2004, 30:57-79.
34. IEEE World Congress on Computational Intelligence (CEC@WCCI-2012) Competition on Large Scale Global Optimization. 2012, [http://staff.ustc.edu.cn/~ketang/cec2012/lsgo_competition.htm], IEEE World Congress on Computational Intelligence (CEC@WCCI-2012).
35. Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27. 10.1093/nar/28.1.27, 102409, 10592173.
36. Hindmarsh AC. LSODE and, LSODI, two new initial value ordinary differential equation solvers. ACM-SIGNUM Newsletter 1980, 15(4):10-11.
37. EBML-EBI BioModels Database. [http://www.ebi.ac.uk/biomodels-main/], EBML-EBI.
38. Yang Z, Tang K, Yao X. Large scale evolutionary optimization using cooperative coevolution. Inf Sci 2008, 178(15):2985-2999.
39. Yang Z, Tang K, Yao X. Multilevel cooperative coevolution for large scale optimization. Evolutionary Computation, 2008. CEC 2008.(IEEE World Congress on Computational Intelligence). 2008, 1663-1670. IEEE Congress on, IEEE.