Patricia Agudelo-Romero, Talya Conradie, Jose Antonio Caparros-Martin, David Jimmy Martino, Anthony Kicic, Stephen Michael Stick, Christopher Hakkaart, Abhinav Sharma
{"title":"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早期到中期职业研究人员的经验教训。","authors":"Patricia Agudelo-Romero, Talya Conradie, Jose Antonio Caparros-Martin, David Jimmy Martino, Anthony Kicic, Stephen Michael Stick, Christopher Hakkaart, Abhinav Sharma","doi":"10.3389/fbinf.2025.1610015","DOIUrl":null,"url":null,"abstract":"<p><p>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.</p>","PeriodicalId":73066,"journal":{"name":"Frontiers in bioinformatics","volume":"5 ","pages":"1610015"},"PeriodicalIF":3.9000,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12425987/pdf/","citationCount":"0","resultStr":"{\"title\":\"Advancing bioinformatics capacity through Nextflow and nf-core: lessons from an early-to mid-career researchers-focused program at The Kids Research Institute Australia.\",\"authors\":\"Patricia Agudelo-Romero, Talya Conradie, Jose Antonio Caparros-Martin, David Jimmy Martino, Anthony Kicic, Stephen Michael Stick, Christopher Hakkaart, Abhinav Sharma\",\"doi\":\"10.3389/fbinf.2025.1610015\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>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.</p>\",\"PeriodicalId\":73066,\"journal\":{\"name\":\"Frontiers in bioinformatics\",\"volume\":\"5 \",\"pages\":\"1610015\"},\"PeriodicalIF\":3.9000,\"publicationDate\":\"2025-08-29\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12425987/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Frontiers in bioinformatics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.3389/fbinf.2025.1610015\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q2\",\"JCRName\":\"MATHEMATICAL & COMPUTATIONAL BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Frontiers in bioinformatics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3389/fbinf.2025.1610015","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}
Advancing bioinformatics capacity through Nextflow and nf-core: lessons from an early-to mid-career researchers-focused program at The Kids Research Institute Australia.
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.