Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience.
Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience.
复制标题
DOI：
10.12688/aasopenres.12847.1
复制
发表时间：
2018-01-01
影响因子：
--
通讯作者：
Mulder, Nicola
中科院分区：
文献类型：
--
作者：
Ahmed, Azza E;Mpangase, Phelelani T;Mulder, Nicola
全球和非洲对便携式和可重复使用的基因组分析管道的需求正在增长，特别是随着非洲人类健康和遗传联盟(H3Africa)等合作项目的增长。泛非H3非洲生物信息学网络(H3ABioNet)认识到，需要适应不同计算环境的可移植、可重复使用的管道，需要培养工作流程语言和集装箱化技术方面的专门知识。为满足这一需求，H3ABioNet于2016年安排了其首个云计算和可复制工作流黑客马拉松，目的是构建能够在异质计算环境中运行的关键基因组分析管道，并满足H3Africa研究项目的需求。本文介绍了这次黑客马拉松的筹备情况，并反思了它对培养非洲研究人员的技术和科学专长的影响所吸取的经验教训。开发的工作流程在GitHub存储库中公开可用，并作为容器图像存放在quay.io上。
The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines adapted to heterogeneous compute environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. To address this need, in 2016 H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Hackathon, with the purpose of building key genomics analysis pipelines able to run on heterogeneous computing environments and meeting the needs of H3Africa research projects. This paper describes the preparations for this hackathon and reflects upon the lessons learned about its impact on building the technical and scientific expertise of African researchers. The workflows developed were made publicly available in GitHub repositories and deposited as container images on quay.io.