BioBayes: A software package for Bayesian inference in systems biology
BioBayes: A software package for Bayesian inference in systems biology
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DOI：
10.1093/bioinformatics/btn338
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发表时间：
2008-09-01
期刊：
影响因子：
5.8
通讯作者：
Girolami, Mark
中科院分区：
文献类型：
--
作者：
Vyshemirsky, Vladislav;Girolami, Mark
动机：在生化系统的数学模型中有几个层次的不确定性。动力学参数的值、模型的一般结构以及不能直接观察到的生物化学物种的行为往往存在一定程度的不确定性。贝叶斯推理方法为这些不确定条件下的建模和预测提供了一致的框架。我们提出了一个软件包应用贝叶斯推理方法的问题，在系统生物学。结果：本文描述的是一个软件包BioBayes，它提供了一个框架，用于贝叶斯参数估计和证据模型排序，而不是使用常微分方程定义的生化系统模型。该包是可扩展的，允许开发人员包含其他模块。目前还没有其他类似的软件包提供此功能。
Motivation: There are several levels of uncertainty involved in the mathematical modelling of biochemical systems. There often may be a degree of uncertainty about the values of kinetic parameters, about the general structure of the model and about the behaviour of biochemical species which cannot be observed directly. The methods of Bayesian inference provide a consistent framework for modelling and predicting in these uncertain conditions. We present a software package for applying the Bayesian inferential methodology to problems in systems biology.Results: Described herein is a software package, BioBayes, which provides a framework for Bayesian parameter estimation and evidential model ranking over models of biochemical systems defined using ordinary differential equations. The package is extensible allowing additional modules to be included by developers. There are no other such packages available which provide this functionality.