Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa.
Department of Biodiversity and Conservation Biology, University of the Western Cape, Bellville, South Africa.
PLoS Comput Biol. 2021 Feb 25;17(2):e1008640. doi: 10.1371/journal.pcbi.1008640. eCollection 2021 Feb.
With more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design and analysis of microbiome studies and data. However, high-quality bioinformatics courses are often impeded by differences in computational environments, complicated software stacks, numerous dependencies, and versions of bioinformatics tools along with a lack of local computational infrastructure and expertise. To address this, H3ABioNet developed a 16S rRNA Microbiome Intermediate Bioinformatics Training course, extending its remote classroom model. The course was developed alongside experienced microbiome researchers, bioinformaticians, and systems administrators, who identified key topics to address. Development of containerised workflows has previously been undertaken by H3ABioNet, and Singularity containers were used here to enable the deployment of a standard replicable software stack across different hosting sites. The pilot ran successfully in 2019 across 23 sites registered in 11 African countries, with more than 200 participants formally enrolled and 106 volunteer staff for onsite support. The pulling, running, and testing of the containers, software, and analyses on various clusters were performed prior to the start of the course by hosting classrooms. The containers allowed the replication of analyses and results across all participating classrooms running a cluster and remained available posttraining ensuring analyses could be repeated on real data. Participants thus received the opportunity to analyse their own data, while local staff were trained and supported by experienced experts, increasing local capacity for ongoing research support. This provides a model for delivering topic-specific bioinformatics courses across Africa and other remote/low-resourced regions which overcomes barriers such as inadequate infrastructures, geographical distance, and access to expertise and educational materials.
随着越来越多的非洲本土研究团队开展微生物组研究，对微生物组研究和数据分析的设计和分析方面的知识和技能的需求也在不断增加。然而，高质量的生物信息学课程通常受到计算环境、复杂的软件堆栈、众多依赖项以及生物信息学工具版本的差异，以及缺乏本地计算基础设施和专业知识的阻碍。为了解决这个问题，H3ABioNet 开发了一个 16S rRNA 微生物组中级生物信息学培训课程，扩展了其远程课堂模式。该课程是由经验丰富的微生物组研究人员、生物信息学家和系统管理员共同开发的，他们确定了需要解决的关键主题。H3ABioNet 之前已经进行了容器化工作流程的开发，并在这里使用 Singularity 容器来实现跨不同托管站点部署标准可复制软件堆栈。该试点课程于 2019 年在 11 个非洲国家的 23 个注册站点成功运行，正式注册的学员超过 200 人，现场支持的志愿者工作人员超过 106 人。在课程开始之前，托管教室就已经对容器、软件和分析在各种集群上的拉取、运行和测试进行了操作。容器允许在运行集群的所有参与教室中复制分析和结果，并在培训后仍然可用，以确保可以在实际数据上重复分析。因此，学员有机会分析自己的数据，同时接受经验丰富的专家培训和支持，从而提高了当地持续研究支持的能力。这为在非洲和其他远程/资源匮乏地区提供特定主题的生物信息学课程提供了一个模式，克服了基础设施不足、地理位置、以及获取专业知识和教育材料等方面的障碍。
