PeTTSy: a computational tool for perturbation analysis of complex systems biology models.
PeTTSy: a computational tool for perturbation analysis of complex systems biology models.
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DOI：
10.1186/s12859-016-0972-2
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发表时间：
2016-03-10
影响因子：
3
通讯作者：
Rand DA
中科院分区：
文献类型：
--
作者：
Domijan M;Brown PE;Shulgin BV;Rand DA
在过去的十年中，灵敏度分析技术已被证明是非常有用的分析复杂和高维系统生物学模型。然而，许多目前可用的工具箱要么使用参数采样，集中在一组有限的模型观测值的利益，研究优化的目标函数，或没有处理多个同时的模型参数的变化，其中的变化可以是永久的或暂时的。在这里，我们介绍了我们的新的，免费下载的工具箱，PeTTSy（扰动理论系统）。PeTTSy是MATLAB的一个软件包，它实现了一系列用于大型复杂常微分方程（ODE）模型的扰动理论和灵敏度分析的技术。PeTTSy是一个综合的建模框架，引入了许多新方法，并完全解决了振荡系统的分析问题。它检查模型的敏感性分析参数的扰动，扰动的时间，强度，长度和整体形状可以由用户控制。这可以在系统全局设置中完成，即，用户可以确定要扰动多少参数、扰动多少参数以及扰动多长时间。PeTTSy还为用户提供了探索参数扰动对许多不同类型输出的影响的能力：周期，相位（峰值的时间）和模型解决方案。PeTTSy可用于各种数学模型，包括自由运行和强迫振荡器以及信号系统。为了能够使用Fisher信息矩阵进行实验优化，它有效地允许联合收割机组合模型的多个变体（即，具有多个实验条件的模型），以便确定新实验的值。它在分析涉及许多变量和参数的大型复杂模型时特别有用。PeTTSy是一个用于分析监管和信号系统的大型复杂模型的综合工具。它允许在各种环境条件下模拟和分析模型，并对复杂的组合实验进行实验优化。凭借其独特的工具集，它为当前的灵敏度分析工具箱库提供了宝贵的补充。我们相信这个软件将对更广泛的生物学、系统生物学和建模社区有很大的用处。本文的在线版本（doi：10.1186/s12859-016-0972-2）包含补充材料，可供授权用户使用。
Over the last decade sensitivity analysis techniques have been shown to be very useful to analyse complex and high dimensional Systems Biology models. However, many of the currently available toolboxes have either used parameter sampling, been focused on a restricted set of model observables of interest, studied optimisation of a objective function, or have not dealt with multiple simultaneous model parameter changes where the changes can be permanent or temporary. Here we introduce our new, freely downloadable toolbox, PeTTSy (Perturbation Theory Toolbox for Systems). PeTTSy is a package for MATLAB which implements a wide array of techniques for the perturbation theory and sensitivity analysis of large and complex ordinary differential equation (ODE) based models. PeTTSy is a comprehensive modelling framework that introduces a number of new approaches and that fully addresses analysis of oscillatory systems. It examines sensitivity analysis of the models to perturbations of parameters, where the perturbation timing, strength, length and overall shape can be controlled by the user. This can be done in a system-global setting, namely, the user can determine how many parameters to perturb, by how much and for how long. PeTTSy also offers the user the ability to explore the effect of the parameter perturbations on many different types of outputs: period, phase (timing of peak) and model solutions. PeTTSy can be employed on a wide range of mathematical models including free-running and forced oscillators and signalling systems. To enable experimental optimisation using the Fisher Information Matrix it efficiently allows one to combine multiple variants of a model (i.e. a model with multiple experimental conditions) in order to determine the value of new experiments. It is especially useful in the analysis of large and complex models involving many variables and parameters. PeTTSy is a comprehensive tool for analysing large and complex models of regulatory and signalling systems. It allows for simulation and analysis of models under a variety of environmental conditions and for experimental optimisation of complex combined experiments. With its unique set of tools it makes a valuable addition to the current library of sensitivity analysis toolboxes. We believe that this software will be of great use to the wider biological, systems biology and modelling communities. The online version of this article (doi:10.1186/s12859-016-0972-2) contains supplementary material, which is available to authorized users.