Git can facilitate greater reproducibility and increased transparency in science
Git can facilitate greater reproducibility and increased transparency in science
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DOI：
10.1186/1751-0473-8-7
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发表时间：
2013-12-01
影响因子：
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通讯作者：
Ram, Karthik
中科院分区：
文献类型：
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作者：
Ram, Karthik
背景：可重复性是优秀科学的标志。保持科学报告的高度透明度不仅对于获得科学界的信任和信誉至关重要，而且对于促进新想法的发展也至关重要。共享与出版物相关的数据和计算机代码变得越来越普遍，部分原因是为了满足期刊的数据存储要求和资助者的要求。尽管透明度有所提高，但如果没有更完整的工作流程，仍然很难复制或建立大多数科学出版物的发现。调查结果：版本控制系统（VCS）长期以来一直用于维护软件行业的代码存储库，现在正在科学领域找到新的应用。 Git 就是这样一个开源 VCS，它提供了一个轻量级但强大的框架，非常适合管理全套研究成果，例如数据集、统计代码、图表、实验室笔记和手稿。对于个人研究人员来说，Git 提供了一种强大的方法来跟踪和比较版本、追溯错误、以结构化方式探索新方法，同时维护完整的审计跟踪。对于更大规模的协作工作，Git 和 Git 托管服务使每个人都可以异步工作并随时合并他们的贡献，同时保持完整的作者追踪。在本文中，我提供了 Git 的概述以及用例，重点介绍了如何利用该工具使科学更具可重复性和透明性、促进新的合作并支持新颖的用途。
Background: Reproducibility is the hallmark of good science. Maintaining a high degree of transparency in scientific reporting is essential not just for gaining trust and credibility within the scientific community but also for facilitating the development of new ideas. Sharing data and computer code associated with publications is becoming increasingly common, motivated partly in response to data deposition requirements from journals and mandates from funders. Despite this increase in transparency, it is still difficult to reproduce or build upon the findings of most scientific publications without access to a more complete workflow.Findings: Version control systems (VCS), which have long been used to maintain code repositories in the software industry, are now finding new applications in science. One such open source VCS, Git, provides a lightweight yet robust framework that is ideal for managing the full suite of research outputs such as datasets, statistical code, figures, lab notes, and manuscripts. For individual researchers, Git provides a powerful way to track and compare versions, retrace errors, explore new approaches in a structured manner, while maintaining a full audit trail. For larger collaborative efforts, Git and Git hosting services make it possible for everyone to work asynchronously and merge their contributions at any time, all the while maintaining a complete authorship trail. In this paper I provide an overview of Git along with use-cases that highlight how this tool can be leveraged to make science more reproducible and transparent, foster new collaborations, and support novel uses.