Petri Net Based Metabolic Network Parameters Fitting with GPU Acceleration
✍ Scribed by Jun Gao; Ruixin Zhu; Qi Liu; Zhiwei Cao
- Book ID
- 102097971
- Publisher
- John Wiley and Sons
- Year
- 2011
- Tongue
- English
- Weight
- 275 KB
- Volume
- 29
- Category
- Article
- ISSN
- 0256-7660
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✦ Synopsis
Abstract
Classical Petri net has been applied into biological analysis, especially as a qualitative model for biochemical pathways analysis, but lack of the ability for quantitative kinetic simulations. In our study, we presented an integration work of the qualitative model–Petri nets with the quantitative approach‐ordinary differential equations (ODEs) for the modeling and analysis of metabolic networks. As an application of our study, the computational modeling of arachidonic acid (AA) biochemical network was provided. A Petri net was set up to present the constraint‐based dynamic simulations on AA metabolic network combined with the validated ODEs model. Furthermore, Graphics Processing Unit (GPU) was adopted to accelerate the calculation of kinetic parameters unavailable from experiments. Our results have indicated that the proposed simulation method was practicable and useful with GPU acceleration, and provides new clues for the large‐scale qualitative and quantitative models of biochemical networks.