Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience

• DOI: 10.12688/aasopenres.12847.1
• Publication Date: 2018-04-18T09:10:07Z
• Authors: Azza E. Ahmed; Phelelani T. Mpan...; Sumir Panji; Shakuntala Baichoo; Yassine Souilmi; Faisal M. Fadlelmola; Mustafa Alghali; Shaun Aron; Hocine Bendou; Eugene De Beste; Mamana Mbiyavanga; Oussema Souiai; Long Yi; Jennie Zermeno; Don Armstrong; Brian D. O'Connor; Liudmila Sergeevn...; Michael R. Crusoe; Ayton Meintjes; Peter Van Heusden; Gerrit Botha; Fourie Joubert; C. Victor Jongeneel; Scott Hazelhurst; Nicola Mulder
• Keywords: 0303 health sciences; 03 medical and health sciences; Method Article; 3. Good health

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.