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札: 一个工作流执行服务,鼓励在生物信息学中重复使用各种语言的工作流

Hirotaka Suetake¹, Tomoya Tanjo², Manabu Ishii³

¹Department of Creative Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo, Tokyo, Japan.

|July 29, 2024

概括

生物医学研究人员面临着各种工作流系统的挑战. 札为执行数据分析工作流提供了一个统一的平台,简化了对共享计算工具的访问.

科学领域:

生物医学信息学生物医学信息学
计算生物学计算生物学
基因组学就是基因组学.

背景情况:

生物医学数据分析中对高效计算的需求推动了工作流系统的采用.
工作流系统提高了研究人员的生产力,特别是在高通量DNA测序中,需要可扩展的计算.
虽然工作流系统提高了可移植性和共享性,但各种系统的扩散使研究工作碎片化.

研究的目的:

开发一个统一的解决方案来执行各种数据分析工作流程.
为了应对学习和使用多个不同的工作流系统的挑战.
为访问和运行共享计算工作流提供标准化界面.

主要方法:

开发了Sapporo,这是一款由API和基于浏览器的客户端组成的双组件应用程序.
该API遵循来自全球基因组学和健康联盟的工作流执行服务API标准.
实现了对四种主要工作流语言的支持:通用工作流语言,工作流描述语言,Snakemake和Nextflow.

主要成果:

札为工作流执行提供了一个统一的层,抽象了系统特定的差异.
该应用程序的API可为工作流运行提供标准化请求.
目前的实现成功地支持跨多种流行的工作流语言的执行.

结论:

札简化了生物医学研究中共享数据分析工作流程的利用.
它的可扩展和可扩展设计支持更广泛的研究社区访问有价值的计算资源.
这种统一的方法减轻了现有工作流系统多样性所带来的挑战.

关键词:

开放科学是一个开放的科学.工作流的工作流.工作流执行服务的工作流执行服务.工作流程语言的工作流程语言

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