CADLIVE optimizer: web-based parameter estimation for dynamic models

Source Code for Biology and Medicine

Hiroyuki Kurata¹  Shogo Takagi¹  Shinpei Tonami¹  Yuki Kato¹  Kazuhiro Maeda¹  Kentaro Inoue¹ 

[1] Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan

关键词: Dynamic model;    Genetic algorithm;    Optimization;    Simulator;   

Others  :  806193
DOI  :  10.1186/1751-0473-7-9

 received in 2012-04-25, accepted in 2012-08-15,  发布年份 2012

【 摘 要 】

Computer simulation has been an important technique to capture the dynamics of biochemical networks. In most networks, however, few kinetic parameters have been measured in vivo because of experimental complexity. We develop a kinetic parameter estimation system, named the CADLIVE Optimizer, which comprises genetic algorithms-based solvers with a graphical user interface. This optimizer is integrated into the CADLIVE Dynamic Simulator to attain efficient simulation for dynamic models.

【 授权许可】

   
2012 Inoue et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

【 参考文献 】

• [1]Mendes P, Kell D: Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 1998, 14:869-883.
• [2]Moles CG, Mendes P, Banga JR: Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res 2003, 13:2467-2474.
• [3]Vilela M, Chou IC, Vinga S, Vasconcelos AT, Voit EO, Almeida JS: Parameter optimization in S-system models. BMC Syst Biol 2008, 2:35. BioMed Central Full Text
• [4]Zi Z, Klipp E: SBML-PET: a Systems Biology Markup Language-based parameter estimation tool. Bioinformatics 2006, 22:2704-2705.
• [5]Ji X, Xu Y: libSRES: a C library for stochastic ranking evolution strategy for parameter estimation. Bioinformatics 2006, 22:124-126.
• [6]Liu X, Jiang J, Ajayi O, Gu X, Gilbert D, Sinnott R: BioNessie(G) - a Grid enabled biochemical networks simulation environment. Stud Health Technol Inform 2008, 138:147-157.
• [7]Balsa-Canto E, Banga JR: AMIGO, a toolbox for advanced model identification in systems biology using global optimization. Bioinformatics 2011, 27:2311-2313.
• [8]Kurata H, Inoue K, Maeda K, Masaki K, Shimokawa Y, Zhao Q: Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis. Nucleic Acids Res 2007, 35:e134.
• [9]Kurata H, Masaki K, Sumida Y, Iwasaki R: CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models. Genome Res 2005, 15:590-600.
• [10]Kurata H, Matoba N, Shimizu N: CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle. Nucleic Acids Res 2003, 31:4071-4084.
• [11]Inoue K, Tomeda S, Tonami S, Shimokawa Y, Ono M, Kurata H: CADLIVE Converter for constructing a biochemical network map. Biochem Eng J 2011, 54:200-206.
• [12]Maeda K, Kurata H: Quasi-multiparameter sensitivity measure for robustness analysis of complex biochemical networks. J Theor Biol 2011, 272:174-186.
• [13]Masaki K, Maeda K, Kurata H: Biological design principles of complex feedback modules in the E. coli ammonia assimilation system. Artificial life 2012, 18:53-90.