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

Azza E Ahmed ,Liudmila Sergeevna Mainzer,Ayton Meintjes,Sumir Panji,Hocine Bendou,Mamana Mbiyavanga,Fourie Joubert,Long Yi,Yassine Souilmi,Nicola Mulder,Michael R Crusoe,Peter Van Heusden,Don Armstrong,Gerrit Botha,Mustafa Alghali,Oussema Souiai,Phelelani T Mpangase,C Victor Jongeneel,Faisal M Fadlelmola,Eugene De Beste,Jennie Zermeno,Shaun Aron,Scott Hazelhurst,Shakuntala Baichoo,Brian D O’connor

doi:10.12688/aasopenres.12847.2

Abstract

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 computing environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. Building on the network's Standard Operating Procedures (SOPs) for common genomic analyses, H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Hackathon in 2016, with the purpose of translating those SOPs into 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.

Highlights

As an inherently interdisciplinary science, bioinformatics depends upon complementary expertise from biomedical scientists, statisticians and computer scientists[1]
It was decided that development and testing of the pipelines should occur on a single machine, with the ability to be ported to a cluster or an High-Performance Computing (HPC) environment, and tested and deployed on cloud-based platforms (Amazon, Microsoft Azure, EGI FedCloud, IBM Bluemix, and the new African Research Cloud initiative)
The communication and management tools used for this hackathon (Table 2) were important as these tools facilitated interaction between and across team members and enabled the participants to continue to work in a structured manner once back at their respective institutions, despite time zones differences

Summary

METHOD ARTICLE

Africa: The H3ABioNet cloud computing experience [version 2; peer review: 2 approved, 1 approved with reservations]. Mpangase3*, Sumir Panji[4], Shakuntala Baichoo 5, Yassine Souilmi 6, Faisal M. Fadlelmola 1, Mustafa Alghali[1], Shaun Aron[3], Hocine Bendou 7, Eugene De Beste[7], Mamana Mbiyavanga[4], Oussema Souiai 8, Long Yi7, Jennie Zermeno[9], Don Armstrong[9], Brian D. O'Connor[10], Liudmila Sergeevna Mainzer[9,11], Michael R. Crusoe 12, Ayton Meintjes 4, Peter Van Heusden 7, Gerrit Botha[4], Fourie Joubert[13], C. Victor Jongeneel 9, Scott Hazelhurst 3,14, Nicola Mulder 4.

Introduction

Discussion

Summary and impression