Visual model checking approach of high level Petri-net and its application to dynamic biological pathway model

高层Petri网可视化模型检验方法及其在动态生物通路模型中的应用

• 批准号: 20700265
• 负责人: NAGASAKI Masao
• 金额: $ 2.66万
• 依托单位: The University of Tokyo
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Young Scientists (B)
• 财政年份: 2008
• 资助国家: 日本
• 起止时间: 2008 至 2009
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20700265/
• 关键词: ペトリネット; オントロジー; 視覚的デバッグ; モデル検査; OWL; HFPNe; 細胞分化; ASTD

The pathway modeling and simulation architecture named (Hybrid Functional Petri net: HFPNe) has been developed and implemented. In this research, a model checking concept is introduced to the HFPNe. A simulation model of C. elegans cell fate determination is created using HFPNe and the reasonable rule of the cell fate determination is selected by using the model checking approach. Furthermore, an algorithm to extract the active sub-pathways from a given HFPNe model and the trajectory of these sub-pathways is developed. The applicability is demonstrated using the circadian clock simulation model with HFPNe.

开发并实现了混合功能Petri网（HybridFunctionalPetrinet：HFPNe）的通路建模与仿真体系结构。在这项研究中，模型检测的概念被引入到HFPNe。建立了C.利用HFPNe建立了线虫细胞命运判定模型，并利用模型检验方法选择了合理的细胞命运判定规则。此外，一个算法来提取活跃的子路径从一个给定的HFPNe模型和这些子路径的轨迹。使用HFPNe的生物钟模拟模型证明了其适用性。

项目成果

A computational platform for systems biology

系统生物学计算平台

• 发表时间: 2009
• 期刊: Cell Illustrator 4. 0 10
• 作者: Nagasaki;M.;Saito A.;Jeong E;Li C.;Kojima;K;Ikeda;E.;Miyano;S
• 通讯作者: S

Simulation-based model checking approach to cell fate pecification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension

基于仿真的模型检查方法，通过具有可扩展性的混合功能 Petri 网，对秀丽隐杆线虫外阴发育过程中的细胞命运进行指定

• 发表时间: 2009
• 期刊: BMC Systems Biology 3
• 作者: Li;C. *;Nagasaki;M. *;Ueno;K.;Miyano;S.
• 通讯作者: S.

Systematic reconstruction of TRANSPATH data into Cell System Markup Language

• DOI: 10.1186/1752-0509-2-53
• 发表时间: 2008-06-23
• 期刊: BMC SYSTEMS BIOLOGY
• 作者: Nagasaki, Masao;Saito, Ayumu;Miyano, Satoru
• 通讯作者: Miyano, Satoru

Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram.

• DOI: 10.1186/1752-0509-4-39
• 发表时间: 2010-04-01
• 期刊: BMC systems biology
• 作者: Li C;Nagasaki M;Saito A;Miyano S
• 通讯作者: Miyano S

Rule-based reasoning for system dynamics in cell systems

细胞系统中系统动力学的基于规则的推理

• 发表时间: 2008
• 期刊: Genome Informatics 20
• 作者: Jeong;E. Nagasaki;M.;MiYano;S.
• 通讯作者: S.