节约细节:标准和数据可重用性。

IF 2.6 Q2 BIOCHEMICAL RESEARCH METHODS Synthetic biology (Oxford, England) Pub Date : 2023-01-01 DOI:10.1093/synbio/ysac030
Ana Delgado
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摘要

自合成生物学以部件为基础的方法诞生以来,可重用性一直是一个关键问题。从BioBrick™标准部件开始,多方努力旨在使生物更具可交换性。然而,随着时间的推移,零件和其他基于脱氧核糖核酸的数据的可重用性已被证明是具有挑战性的。通过一系列定性访谈和国际研讨会,本文探讨了可重用性在真实实验室实践中的挑战。它显示了一些特定的方式,即标准在获取对科学家能够重复使用生物部件和数据至关重要的各种上下文信息方面存在缺陷。我认为,特定实验室的研究人员会形成一种意识,即他们需要分享多少具体细节,以便其他人能够理解他们的数据,并可能重用这些数据。当选择特定的报告格式,重新描述数据以获得更深入的知识或要求额外的信息时,研究人员制定了“细节经济”。两个实验室在学科、认识论、技术和地理方面的距离越远,就需要获取更详细的信息,以便在不同环境中重复使用数据。在合成生物学中,计算科学和工程研究人员以及实验生物学家之间的学科距离反映在对标准的不同看法上:应该包括什么样的信息以实现可重用性,什么样的信息可以被标准捕获,以及它们如何服务于产生和传播知识。我认为,这种跨学科的紧张关系是制定合成生物学标准困难的核心所在。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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An economy of details: standards and data reusability.

Reusability has been a key issue since the origins of the parts-based approach to synthetic biology. Starting with the BioBrick™ standard part, multiple efforts have aimed to make biology more exchangeable. The reusability of parts and other deoxyribonucleic acid-based data has proven over time to be challenging, however. Drawing on a series of qualitative interviews and an international workshop, this article explores the challenges of reusability in real laboratory practice. It shows particular ways that standards are experienced as presenting shortcomings for capturing the kinds of contextual information crucial for scientists to be able to reuse biological parts and data. I argue that researchers in specific laboratories develop a sense of how much circumstantial detail they need to share for others to be able to make sense of their data and possibly reuse it. When choosing particular reporting formats, recharacterizing data to gain closer knowledge or requesting additional information, researchers enact an 'economy of details'. The farther apart two laboratories are in disciplinary, epistemological, technical and geographical terms, the more detailed information needs to be captured for data to be reusable across contexts. In synthetic biology, disciplinary distance between computing science and engineering researchers and experimentalist biologists is reflected in diverging views on standards: what kind of information should be included to enable reusability, what kind of information can be captured by standards at all and how they may serve to produce and circulate knowledge. I argue that such interdisciplinary tensions lie at the core of difficulties in setting standards in synthetic biology.

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