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Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases.
Database: The Journal of Biological Databases and Curation ( IF 5.8 ) Pub Date : 2020-07-04 , DOI: 10.1093/database/baaa032
Shawna Spoor 1 , Connor Wytko 1 , Brian Soto 1 , Ming Chen 2 , Abdullah Almsaeed 2 , Bradford Condon 2 , Nic Herndon 3 , Heidi Hough 1 , Sook Jung 1 , Meg Staton 2 , Jill Wegrzyn 4 , Dorrie Main 1 , F Alex Feltus 5 , Stephen P Ficklin 1
Affiliation  

Online biological databases housing genomics, genetic and breeding data can be constructed using the Tripal toolkit. Tripal is an open-source, internationally developed framework that implements FAIR data principles and is meant to ease the burden of constructing such websites for research communities. Use of a common, open framework improves the sustainability and manageability of such as site. Site developers can create extensions for their site and in turn share those extensions with others. One challenge that community databases often face is the need to provide tools for their users that analyze increasingly larger datasets using multiple software tools strung together in a scientific workflow on complicated computational resources. The Tripal Galaxy module, a ‘plug-in’ for Tripal, meets this need through integration of Tripal with the Galaxy Project workflow management system. Site developers can create workflows appropriate to the needs of their community using Galaxy and then share those for execution on their Tripal sites via automatically constructed, but configurable, web forms or using an application programming interface to power web-based analytical applications. The Tripal Galaxy module helps reduce duplication of effort by allowing site developers to spend time constructing workflows and building their applications rather than rebuilding infrastructure for job management of multi-step applications.

中文翻译:

Tripal和Galaxy:支持社区生物数据库的可重复科学工作流程。

可以使用Tripal工具包构建包含基因组,遗传和育种数据的在线生物数据库。Tripal是国际上开源的框架,其实施FAIR数据原则,旨在减轻为研究社区构建此类网站的负担。使用通用的开放框架可提高此类站点的可持续性和可管理性。网站开发人员可以为其网站创建扩展,然后与他人共享这些扩展。社区数据库通常面临的一个挑战是需要为用户提供工具,这些工具需要使用在复杂的计算资源上科学工作流中串在一起的多个软件工具来分析越来越大的数据集。Tripal Galaxy模块是Tripal的“插件”,通过将Tripal与Galaxy Project工作流管理系统集成在一起,满足了这一需求。站点开发人员可以使用Galaxy创建适合其社区需求的工作流,然后通过自动构建但可配置的Web表单或使用应用程序编程接口来为基于Web的分析应用程序提供动力,从而在其Tripal站点上共享这些工作流。Tripal Galaxy模块允许站点开发人员花费时间来构建工作流和构建其应用程序,而不是为多步应用程序的作业管理重建基础结构,从而帮助减少工作重复。但可配置的Web表单,或使用应用程序编程接口来驱动基于Web的分析应用程序。Tripal Galaxy模块允许站点开发人员花费时间来构建工作流和构建其应用程序,而不是为多步应用程序的作业管理重建基础结构,从而帮助减少工作重复。但可配置的Web表单,或使用应用程序编程接口来驱动基于Web的分析应用程序。Tripal Galaxy模块允许站点开发人员花费时间来构建工作流和构建其应用程序,而不是为多步应用程序的作业管理重建基础结构,从而帮助减少工作重复。
更新日期:2020-07-08
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