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每日翻译20190713

已有 435 次阅读 2019-7-13 07:21 |个人分类:翻译作品|系统分类:科研笔记| BEAUti, 设置模型, 灵活性

#编者信息

熊荣川

明湖实验室

xiongrongchuan@126.com

http://blog.sciencenet.cn/u/Bearjazz

User Interface

One area of signifcant improvement since   the last release publication is in the analysis construction and model specifcation   tool called Bayesian Evolutionary Analysis Utility (BEAUti). This acts as the   graphical user interface (GUI) for BEAST and allows the user to import data, select   models, choose prior distributions on individual parameters, and specify the   settings for the MCMC sampler (fg. 1). Although the BEAST model specifcation   format (a standard XML format structured text file) allows for great   flexibility in the construction of complex evolutionary models, the   constraints of a GUI unavoidably restrict the scope of the researcher to a   prespecifed set of models and combinations, hiding many advanced inference   models. Working directly within the BEAST XML input format, on the other   hand, represents a high barrier to the accessibility of BEAST and incurs   significant risk of inadvertent errors being introduced into the model. We   have concentrated development efforts on BEAUti to provide greater flexibility   in model specifcation while still maintaining the benefts of a visual,   table-based representation of the model, and automatic generation of BEAST   XML fles. Improvements to BEAUti provide support for multiple data partitions   in a joint analysis and the input of fossil calibration and trait   information.  

 

用户界面

自上次发布以来,有一个显著改进的地方是分析建构和模型特化工具Bayesian Evolutional Analysis UtilityBEAUti)。它充当BEAST的图形用户界面(GUI),允许用户导入数据、选择模型、选择单个参数的先验分布,并指定MCMC采样器的设置(图1)。虽然BEAST模型设定格式(一种标准的XML结构化格式文本文件)允许在构建复杂的进化模型时具有很大的灵活性,但是图形用户界面的约束不可避免地将研究者的范围限制为预先指定的一组模型和组合,隐藏许多高级推断模型。另一方面,直接在BEAST XML输入格式中操作意味着对BEAST的可访问性存在较高的障碍,并且会导致在模型中引入意外错误的重大风险。我们将开发工作集中在BEAUti上,以便在模型设定中提供更大的灵活性,同时仍然保持模型的可视化、基于表单呈现模型以及BEAST XML文件自动生成的好处。Beauti的改进为联合分析中的多个数据分区、化石校准以及特征信息的输入提供了支持。

Drummond A J , Suchard M A , Xie D , et al.   Bayesian Phylogenetics with BEAUti and the BEAST 1.7[J]. Molecular Biology   and Evolution, 2012, 29(8):1969-1973.




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