来自生物医学出版物的木星笔记本的计算可复制性
Sheeba Samuel1,2, Daniel Mietchen3,4,5
1Heinz-Nixdorf Chair for Distributed Information Systems, Friedrich Schiller University Jena, Jena 07743, Germany.
GigaScience
|January 11, 2024
概括
在生物医学研究中,木星笔记本的计算可重现性很低. 在10,388个Reran笔记本中,只有1,203个成功运行,其中许多产生了不同的结果,突出了改善工作流程的需要.
科学领域:
- 计算生物学 计算生物学
- 生物信息学是一种生物信息学.
- 科学复制性 科学复制性
背景情况:
- Jupyter笔记本被广泛用于记录和共享生物医学研究中的计算工作流程.
- 评估这些笔记本电脑在规模上的计算可重复性对于科学完整性至关重要,但尚未得到广泛研究.
- 这项研究重点关注与生物医学出版物相关的Jupyter笔记本的可复制性.
研究的目的:
- 评估与生物医学出版物相关的Jupyter笔记本的计算可重现性.
- 确定影响笔记本复制性的因素,并探索共同的挑战.
- 为改善科学研究中的Jupyter相关工作流提供见解.
主要方法:
- 使用自动化工作流来分析PubMed Central索引出版物的Jupyter笔记本.
- 笔记本是通过文本挖掘识别的,位于GitHub上,并在受控环境中重新运行.
- 通过检查成功执行并将结果与原始输出进行比较来评估可重复性.
主要成果:
- 在重新运行的具有声明依赖性的 10,388 个 Python Jupyter 笔记本中,只有 1,203 个没有错误地执行.
- 在成功执行的笔记本中,879个产生了相同的结果,而324个与原始相比产生了不同的结果.
- 许多笔记本电脑在执行或依赖性安装过程中遇到了错误.
结论:
- 在生物医学出版物中Jupyter笔记本的计算可复制性是一个重大挑战.
- 确定了影响可复制性的常见问题和做法.
- 讨论了改进Jupyter笔记本工作流程的建议,以提高科学可重复性.
关键词:
在 GitHub 上,我们可以找到 GitHub.朱皮特笔记本 朱皮特笔记本在PubMed中央公众医院.在这里,Python是Python.计算可复制性的计算可复制性依赖性衰退,依赖性的衰退.工作流程文件工作流程文件.更多相关视频
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