Kiphynet:一个在线网络模拟工具,连接细胞动力学和生理运输
M Deepa Maheshvare1, Rohit Charaborty1, Subhraneel Haldar1
1Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, 560012, India.
Metabolomics : Official journal of the Metabolomic Society
|August 7, 2024
概括
KiPhyNet是一款新的网络应用程序,通过跨越多个规模的功能网络来模拟人类新陈代谢. 它允许在微血管网络中进行交互式模拟和可视化生化过程,用于生理研究.
科学领域:
- 生理学建模 生理学建模
- 系统生物学 系统生物学
- 计算生物学是一种计算生物学.
背景情况:
- 人类的新陈代谢依赖于复杂的功能网络,在多个尺度上运行.
- 在生理学建模中,将这些多层次网络连接到本地和全球动态是一个重大挑战.
研究的目的:
- 开发一个交互式Web应用程序,用于模拟和可视化3D微血管网络中的运输和反应.
- 促进用于生理学研究的多omics和血管成像数据的整合.
主要方法:
- 使用一个离散的基于图形的建模框架 (KiPhyNet) 来弥合多尺度的功能网络.
- 在Python中实现,使用MATLAB作为模拟器引擎,部署在Apache网络服务器上.
- 同化多组和血管成像数据,将结构变化与功能反应联系起来.
主要成果:
- 能够模拟向-分散运输,生化交换和代谢反应.
- 用户可以交互检查模拟结果,包括稳定状态速度/压力和动态度场.
- 输入参数包括网络拓,生物物理属性,边界条件和运动性质.
结论:
- KiPhyNet为多尺度微血管网络模型提供可访问,无障碍的时间过程实验模拟.
- 为推进生理学和新陈代谢研究提供一个离散的建模框架.
- 应用程序及其文档在网上免费提供.
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