CADLIVE dynamic simulator: Direct link of biochemical networks to dynamic models
| Autor: | Rei Iwasaki, Yoshiyuki Sumida, Hiroyuki Kurata, Kouichi Masaki |
|---|---|
| Rok vydání: | 2005 |
| Předmět: |
Biochemical Phenomena
computer.internet_protocol Biology Biochemistry Models Biological Sensitivity and Specificity Feedback Software Escherichia coli Genetics Computer Simulation Representation (mathematics) Genetics (clinical) Simulation business.industry Process (computing) Gene Expression Regulation Bacterial Resources Expression (mathematics) Living systems Dynamic simulation Metabolism Genes Bacterial Feasibility Studies business computer Mathematics XML |
| Zdroj: | Genome Research. 15:590-600 |
| ISSN: | 1088-9051 |
| Popis: | We have developed the CADLIVE (Computer-Aided Design of LIVing systEms) Simulator that provided a rule-based automatic way to convert biochemical network maps into dynamic models, which enables simulating their dynamics without going through all of the reactions down to the details of exact kinetic parameters. The simulator supports the biochemical reaction maps that are generated by the previously developed GUI editor. Notice that the part of the GUI editor had been previously published, but, as yet, not the simulator. To directly link biochemical network maps to dynamic simulation, we have created the strategy of three layers and two stages with the efficient conversion rules in an XML representation. This strategy divides a molecular network into three layers, i.e., gene, protein, and metabolic layers, and partitions the conversion process into two stages. Once a biochemical map is provided, CADLIVE automatically builds a mathematical model, thereby facilitating one to simulate and analyze it. In order to demonstrate the feasibility of CADLIVE, we analyzed the Escherichia coli nitrogen-assimilation system (64 equations with 64 variables) that consists of multiple and complicated negative and positive feedback loops. CADLIVE predicted that the glnK gene is responsible for hysteresis or reversibility of nitrogen-related (Ntr) gene expression with respect to the ammonia concentration, supporting the experimental observation of the runaway expression of the Ntr genes. |
| Databáze: | OpenAIRE |
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