George Dimitriadis, Ella Svahn, Andrew F MacAskill, Athena Akrami
{"title":"Heron,一个知识图编辑器,用于直观地实现基于python的实验管道。","authors":"George Dimitriadis, Ella Svahn, Andrew F MacAskill, Athena Akrami","doi":"10.7554/eLife.91915","DOIUrl":null,"url":null,"abstract":"<p><p>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.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4000,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Heron, a Knowledge Graph editor for intuitive implementation of Python-based experimental pipelines.\",\"authors\":\"George Dimitriadis, Ella Svahn, Andrew F MacAskill, Athena Akrami\",\"doi\":\"10.7554/eLife.91915\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>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. 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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.</p>\",\"PeriodicalId\":11640,\"journal\":{\"name\":\"eLife\",\"volume\":\"13 \",\"pages\":\"\"},\"PeriodicalIF\":6.4000,\"publicationDate\":\"2025-07-16\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"eLife\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.7554/eLife.91915\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"eLife","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.7554/eLife.91915","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOLOGY","Score":null,"Total":0}
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.
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.