Dynamical modeling and multi-experiment fitting with PottersWheel.
Dynamical modeling and multi-experiment fitting with PottersWheel.
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DOI：
10.1093/bioinformatics/btn350
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发表时间：
2008-09-15
期刊：
影响因子：
--
通讯作者：
Timmer J
中科院分区：
文献类型：
--
作者：
Maiwald T;Timmer J
动机：系统生物学的建模者需要一个灵活的框架，使他们能够轻松地创建新的动态模型，研究它们的属性，并同时拟合多个实验数据集。多实验拟合是一种估计参数值、检验给定模型有效性和区分竞争模型假设的有效方法。它需要高性能的常微分方程积分和鲁棒优化。结果如下：我们在这里提出了全面的建模框架Potters-Wheel（PW），包括新的功能，以满足这些要求，重点是逆问题，即基于数据的建模部分观察和噪声系统，如信号转导通路和代谢网络。PW被设计为MATLAB工具箱，包括许多用户界面。确定性和随机优化程序相结合，在对数参数空间允许强大的参数校准拟合。模型研究包括模型数据符合性的统计检验、模型判别、可识别性分析以及基于Hessian和蒙特-卡罗的参数置信限的计算。丰富的应用程序编程接口可在自己的MATLAB代码中进行自定义。在广泛的性能分析中，我们确定并显着改进了一个积分器优化器对，与MATLAB优化工具箱相比，它将实际基准模型的拟合时间缩短了3000倍以上。可用性：PottersWheel可在http://www.PottersWheel.de/免费供学术使用。该网站包含详细的文档和介绍性视频。自2005年以来，该程序已在Windows，Linux和Macintosh计算机上广泛使用，并且不需要特殊的MATLAB工具箱。联系方式：maiwald@fdm.uni-freiburg.de补充信息：补充数据可从生物信息学在线网站获得。
Motivation: Modelers in Systems Biology need a flexible framework that allows them to easily create new dynamic models, investigate their properties and fit several experimental datasets simultaneously. Multi-experiment-fitting is a powerful approach to estimate parameter values, to check the validity of a given model, and to discriminate competing model hypotheses. It requires high-performance integration of ordinary differential equations and robust optimization. Results: We here present the comprehensive modeling framework Potters-Wheel (PW) including novel functionalities to satisfy these requirements with strong emphasis on the inverse problem, i.e. data-based modeling of partially observed and noisy systems like signal transduction pathways and metabolic networks. PW is designed as a MATLAB toolbox and includes numerous user interfaces. Deterministic and stochastic optimization routines are combined by fitting in logarithmic parameter space allowing for robust parameter calibration. Model investigation includes statistical tests for model-data-compliance, model discrimination, identifiability analysis and calculation of Hessian- and Monte-Carlo-based parameter confidence limits. A rich application programming interface is available for customization within own MATLAB code. Within an extensive performance analysis, we identified and significantly improved an integrator–optimizer pair which decreases the fitting duration for a realistic benchmark model by a factor over 3000 compared to MATLAB with optimization toolbox. Availability: PottersWheel is freely available for academic usage at http://www.PottersWheel.de/. The website contains a detailed documentation and introductory videos. The program has been intensively used since 2005 on Windows, Linux and Macintosh computers and does not require special MATLAB toolboxes. Contact: maiwald@fdm.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online.
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影响因子：
3.1
作者：
Lagarias, JC;Reeds, JA;Wright, PE
通讯作者：
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