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通过Nextflow和nf-core提升生物信息学能力:来自澳大利亚儿童研究所一个以早期至中期职业研究人员为重点的项目的经验教训。

Advancing bioinformatics capacity through Nextflow and nf-core: lessons from an early-to mid-career researchers-focused program at The Kids Research Institute Australia.

作者信息

Agudelo-Romero Patricia, Conradie Talya, Caparros-Martin Jose Antonio, Martino David Jimmy, Kicic Anthony, Stick Stephen Michael, Hakkaart Christopher, Sharma Abhinav

机构信息

Wal-Yan Respiratory Research Centre, The Kids Research Institute Australia, Perth, WA, Australia.

Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.

出版信息

Front Bioinform. 2025 Aug 29;5:1610015. doi: 10.3389/fbinf.2025.1610015. eCollection 2025.

Abstract

The increasing adoption of high-throughput "omics" technologies has heightened the demand for standardized, scalable, and reproducible bioinformatics workflows. Nextflow and nf-core provide a robust framework for researchers, particularly early- and mid-career researchers (EMCRs), to navigate complex data analysis. At The Kids Research Institute Australia, we implemented a structured approach to bioinformatics capacity building using these tools. This perspective presents nine practical rules derived from lessons learnt, which facilitated the successful adoption of Nextflow and nf-core, addressing implementation challenges, knowledge gaps, resource allocation, and community support. Our experience serves as a guide for institutions aiming to establish sustainable bioinformatics capabilities and empower EMCRs.

摘要

高通量“组学”技术的日益普及,增加了对标准化、可扩展且可重复的生物信息学工作流程的需求。Nextflow和nf-core为研究人员,尤其是早期和中期职业研究人员(EMCRs)提供了一个强大的框架,以应对复杂的数据分析。在澳大利亚儿童研究所,我们采用了一种结构化方法,利用这些工具进行生物信息学能力建设。本文观点提出了九条从经验教训中得出的实用规则,这些规则促进了Nextflow和nf-core的成功应用,解决了实施挑战、知识差距、资源分配和社区支持等问题。我们的经验可为旨在建立可持续生物信息学能力并增强EMCRs能力的机构提供指导。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4820/12425987/e5202ba11a53/fbinf-05-1610015-g001.jpg

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