ReproPhylo: An Environment for Reproducible Phylogenomics.
ReproPhylo: An Environment for Reproducible Phylogenomics.
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DOI：
10.1371/journal.pcbi.1004447
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发表时间：
2015-09
影响因子：
4.3
通讯作者：
Lunt DH
中科院分区：
文献类型：
--
作者：
Szitenberg A;John M;Blaxter ML;Lunt DH
实验的可重复性是科学过程的关键，尤其是在数据丰富的领域，如基因组学，准确报告分析所必需的。我们提出了ReproPhylo，一个可重复的基因组分析环境，以确保实验的可重复性，促进大规模数据的处理，并协助方法实验。Reproductivity和瞬时可重复性内置于ReproPhylo系统中，不需要用户干预或配置，因为它将实验工作流存储为包含显式出处和环境信息的单个序列化Python对象。这种“单一文件”方法确保了跨分析迭代的起源持久性，并由版本控制程序Git自动管理更改。这个文件，沿着一个Git存储库，是程序的主要再现性输出。此外，ReproPhylo还生成了一份广泛的人类可读报告，并生成了一个全面的实验存档文件，这两个文件都适合与出版物一起提交。该系统有利于参数和数据的彻底实验探索。ReproPhylo是一个独立于平台的CC0 Python模块，可以作为Docker镜像或WinPython自给自足的软件包轻松安装，带有一个Windows Notebook GUI，或者作为Galaxy发行版中的精简版本。
The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system and does not require user intervention or configuration because it stores the experimental workflow as a single, serialized Python object containing explicit provenance and environment information. This ‘single file’ approach ensures the persistence of provenance across iterations of the analysis, with changes automatically managed by the version control program Git. This file, along with a Git repository, are the primary reproducibility outputs of the program. In addition, ReproPhylo produces an extensive human-readable report and generates a comprehensive experimental archive file, both of which are suitable for submission with publications. The system facilitates thorough experimental exploration of both parameters and data. ReproPhylo is a platform independent CC0 Python module and is easily installed as a Docker image or a WinPython self-sufficient package, with a Jupyter Notebook GUI, or as a slimmer version in a Galaxy distribution.