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FitMultiCell:模拟和参数化多规模和多细胞过程的计算模型

Emad Alamoudi¹, Yannik Schälte^1,2,3, Robert Müller⁴

¹Life and Medical Sciences Institute, University of Bonn, Bonn 53113, Germany.

Bioinformatics (Oxford, England)

|November 10, 2023

概括

我们开发了FitMultiCell,这是一个开源管道,用于建模,模拟和参数化复杂的多尺度生物模型. 该工具解决了计算挑战,使系统生物学应用中多细胞过程的有效分析成为可能.

科学领域:

系统生物学系统生物学
计算生物学计算生物学
生物物理学的生物物理.

背景情况:

生物组织表现出复杂的动态,需要多尺度模型进行分析.
对这些模型的参数推理是计算密集的,阻碍了定量理解和预测.
像近似贝叶斯计算 (ABC) 这样的现有方法在复杂的模拟中面临可扩展性问题.

研究的目的:

介绍FitMultiCell,这是一个开源管道,用于高效建模,模拟和参数化多尺度模型.
为分析多细胞过程提供一个用户友好和可扩展的解决方案.
促进系统生物学中的定量理解和假设测试.

主要方法:

将Morpheus建模和模拟工具与pyABC统计推理工具集成.
开发一个模块化管道,以实现无工作流的执行.
实施高性能基础设施来处理计算要求高的问题.
引入一种新的标准来制定参数推理问题,以确保可重现性.

主要成果:

展示了FitMultiCell管道的计算效率和用户友好性.
展示了管道在各种生物问题上的广泛应用.
验证了管道处理整个工作流程的能力,从建模到参数化.
通过标准化的问题制定,确保可复制性和可重复使用性.

结论:

在多细胞系统中,FitMultiCell为多规模建模和参数化提供了可扩展和高效的解决方案.
管道显著受益于基于图像的系统生物学研究.
FitMultiCell增强了对复杂生物过程进行定量分析,预测和理解的能力.

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