Heron,一个知识图编辑器,用于直观地实现基于python的实验管道。

IF 6.4 1区 生物学 Q1 BIOLOGY
eLife Pub Date : 2025-07-16 DOI:10.7554/eLife.91915
George Dimitriadis, Ella Svahn, Andrew F MacAskill, Athena Akrami
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引用次数: 0

摘要

为了实现一个研究项目,实验者在硬件和软件上面临着相互冲突的设计和实现选择。这包括在实现的便利性(时间、专业知识和资源)与未来的灵活性、不透明(黑箱)组件的数量和可再现性之间进行平衡。为了解决这个问题,我们提出了Heron,一个基于python的平台,用于构建和运行实验和数据分析管道。Heron允许研究人员根据他们自己的思维模式来设计实验,以知识图的形式表示,这是一种反映实验逻辑流程的结构。这种方法加快了实施(以及随后的更新),同时最大限度地减少了黑箱组件,提高了透明度和可重复性。Heron支持软件和硬件组合的集成,否则过于复杂或昂贵,使其在具有大量相互关联组件的实验科学中特别有用,如机器人,神经科学,行为科学,物理,化学和环境科学。与纯可视化工具不同,Heron将完全控制(仪器和软件组合)和灵活性与高级编程和图形用户界面的易用性相结合。它假定Python的中级熟练程度,并提供了一个干净、模块化的代码库,鼓励文档和重用。通过消除难以进入的技术障碍,Heron使没有正式工程背景的研究人员能够构建复杂、可靠和可重复的实验装置——弥合了科学创造力和技术实施之间的差距。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Heron, a Knowledge Graph editor for intuitive implementation of Python-based experimental pipelines.

To realise a research project, experimenters face conflicting design and implementation choices across hardware and software. These include balancing ease of implementation - time, expertise, and resources - against future flexibility, the number of opaque (black box) components and reproducibility. To address this, we present Heron, a Python-based platform for constructing and running experimental and data analysis pipelines. Heron allows researchers to design experiments according to their own mental schemata, represented as a Knowledge Graph - a structure that mirrors the logical flow of an experiment. This approach speeds up implementation (and subsequent updates), while minimising black box components, increasing transparency and reproducibility. Heron supports the integration of software and hardware combinations that are otherwise too complex or costly, making it especially useful in experimental sciences with a large number of interconnected components such as robotics, neuroscience, behavioural sciences, physics, chemistry, and environmental sciences. Unlike visual-only tools, Heron combines full control (of instrument and software combinations) and flexibility with the ease of high-level programming and Graphical User Interfaces. It assumes intermediate Python proficiency and offers a clean, modular code base that encourages documentation and reuse. By removing inaccessible technical barriers, Heron enables researchers without formal engineering backgrounds to construct sophisticated, reliable and reproducible experimental setups - bridging the gap between scientific creativity and technical implementation.

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来源期刊
eLife
eLife BIOLOGY-
CiteScore
12.90
自引率
3.90%
发文量
3122
审稿时长
17 weeks
期刊介绍: eLife is a distinguished, not-for-profit, peer-reviewed open access scientific journal that specializes in the fields of biomedical and life sciences. eLife is known for its selective publication process, which includes a variety of article types such as: Research Articles: Detailed reports of original research findings. Short Reports: Concise presentations of significant findings that do not warrant a full-length research article. Tools and Resources: Descriptions of new tools, technologies, or resources that facilitate scientific research. Research Advances: Brief reports on significant scientific advancements that have immediate implications for the field. Scientific Correspondence: Short communications that comment on or provide additional information related to published articles. Review Articles: Comprehensive overviews of a specific topic or field within the life sciences.
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