Czapanskiy Max F, Beltran Roxanne S
Hopkins Marine Station, Stanford University, Pacific Grove, CA, United States.
Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States.
Front Physiol. 2022 Jul 8;13:917976. doi: 10.3389/fphys.2022.917976. eCollection 2022.
What new questions could ecophysiologists answer if physio-logging research was fully reproducible? We argue that (computational hurdles resulting from prioritizing short-term goals over long-term sustainability) stemming from insufficient (field-wide tools, standards, and norms for analyzing and sharing data) trapped physio-logging in a scientific silo. This debt stifles comparative biological analyses and impedes interdisciplinary research. Although physio-loggers (e.g., heart rate monitors and accelerometers) opened new avenues of research, the explosion of complex datasets exceeded ecophysiology's informatics capacity. Like many other scientific fields facing a deluge of complex data, ecophysiologists now struggle to share their data and tools. Adapting to this new era requires a change in mindset, from "data as a noun" (e.g., traits, counts) to "data as a sentence", where measurements (nouns) are associate with transformations (verbs), parameters (adverbs), and metadata (adjectives). Computational reproducibility provides a framework for capturing the entire sentence. Though usually framed in terms of scientific integrity, reproducibility offers immediate benefits by promoting collaboration between individuals, groups, and entire fields. Rather than a tax on our productivity that benefits some nebulous greater good, reproducibility can accelerate the pace of discovery by removing obstacles and inviting a greater diversity of perspectives to advance science and society. In this article, we 1) describe the computational challenges facing physio-logging scientists and connect them to the concepts of and , 2) demonstrate how other scientific fields overcame similar challenges by embracing computational reproducibility, and 3) present a framework to promote computational reproducibility in physio-logging, and bio-logging more generally.
如果生理记录研究能够完全可重复,生态生理学家可以回答哪些新问题?我们认为,由于(将短期目标置于长期可持续性之上所带来的计算障碍)源于(缺乏用于分析和共享数据的全领域工具、标准和规范),生理记录被困在了一个科学孤岛中。这种困境抑制了比较生物学分析,阻碍了跨学科研究。尽管生理记录设备(如心率监测器和加速度计)开辟了新的研究途径,但复杂数据集的爆炸式增长超出了生态生理学的信息学能力。与许多面临复杂数据洪流的其他科学领域一样,生态生理学家现在难以共享他们的数据和工具。适应这个新时代需要思维方式的转变,从“将数据视为名词”(如特征、计数)转变为“将数据视为句子”,其中测量(名词)与转换(动词)、参数(副词)和元数据(形容词)相关联。计算可重复性提供了一个捕捉整个句子的框架。虽然通常是从科学诚信的角度来阐述,但可重复性通过促进个人、团体和整个领域之间的合作带来了直接好处。可重复性不是对我们生产力的一种征税,以惠及某种模糊的更大利益,而是可以通过消除障碍并引入更多样化的观点来加速发现的步伐,从而推动科学和社会的发展。在本文中,我们1)描述生理记录科学家面临的计算挑战,并将它们与[具体概念1]和[具体概念2]的概念联系起来,2)展示其他科学领域如何通过接受计算可重复性克服类似挑战,3)提出一个在生理记录以及更广泛的生物记录中促进计算可重复性的框架。