and development of Web-based bio-simulator for analyzing metabolic pathways
Recently we have implemented an efficient, user-friendly web-based gbiosimulatorh named BEST-KIT (Biochemical Engineering System analyzing Tool-KIT) for analyzing a large scale nonlinear reaction network such as metabolic pathways.The main module of BEST-KIT named gMassAction++h can be used now ( URL: http://www.best-kit.org/ ). This module can easily be used by even those who are unfamiliar with computer technology and with computer programming, and have several remarkable properties; (1)It is developed in Java and Java applet, and client user can use it from ganyh platform machine through web browser. (2) With the gmouseh, the users can easily design and update an arbitrary reaction scheme (nonlinear system) in the editing window (working area) through an efficient GUI even if the number of reaction components is relatively large. (3) After the scheme has been edited, cumbersome simultaneous nonlinear differential equations can be automatically produced without writing troublesome equations. (4)In this module, mathematical modeling is represented by using mass action law (mass balance) and approximate velocity functions related to enzyme kinetics under the steady state conditions, furthermore users can construct a reaction scheme in which both were intermingled. (5) This module form a gclient-server systemh, whereby, heavy numerical calculation of the constructed scheme, which might require long cpu-time on the client machine, can be carried out on the server machine (virtual cpu-server having a high-performance cpu-capability) through the Internet, and the results are sent back in graphic form to the client. (6)In gMassAction++h, by using a parameter-fitting module, we can estimate unknown kinetic parameters based on the observed time-course data. The estimation is executed by using nonlinear numerical optimization techniques such as a modified Powell method(MP) or genetic algorithm(GA) or hybrid method(GA + MP).
Recently we have implemented an efficient, user-friendly web-based gbiosimulatorh named BEST-KIT (Biochemical Engineering System analyzing Tool-KIT) for analyzing a large scale nonlinear reaction network such as metabolic pathways.The main module of BEST-KIT named gMassAction++h can be used now ( URL: http://www.best-kit.org/ ). This module can easily be used by even those who are unfamiliar with computer technology and with computer programming, and have several remarkable properties; (1)It is developed in Java and Java applet, and client user can use it from ganyh platform machine through web browser. (2) With the gmouseh, the users can easily design and update an arbitrary reaction scheme (nonlinear system) in the editing window (working area) through an efficient GUI even if the number of reaction components is relatively large. (3) After the scheme has been edited, cumbersome simultaneous nonlinear differential equations can be automatically produced without writing troublesome equations. (4)In this module, mathematical modeling is represented by using mass action law (mass balance) and approximate velocity functions related to enzyme kinetics under the steady state conditions, furthermore users can construct a reaction scheme in which both were intermingled. (5) This module form a gclient-server systemh, whereby, heavy numerical calculation of the constructed scheme, which might require long cpu-time on the client machine, can be carried out on the server machine (virtual cpu-server having a high-performance cpu-capability) through the Internet, and the results are sent back in graphic form to the client. (6)In gMassAction++h, by using a parameter-fitting module, we can estimate unknown kinetic parameters based on the observed time-course data. The estimation is executed by using nonlinear numerical optimization techniques such as a modified Powell method(MP) or genetic algorithm(GA) or hybrid method(GA + MP).
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