Title of article
Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience
Author/Authors
Ahmed, Azza E. Centre for Bioinformatics and Systems Biology - Faculty of Science - University of Khartoum, Khartoum, Sudan , T. Mpangase, Phelelani Sydney Brenner Institute for Molecular Bioscience - University of the Witwatersrand, Johannesburg, South Africa , Panji, Sumir Computational Biology Division - Integrative Medical Biosciences - University of Cape Town, Cape Town, South Africa , Baichoo, Shakuntala Department of Digital Technologies - University of Mauritius, Reduit, Mauritius , Souilmi, Yassine Australian Centre for Ancient DNA - University of Adelaide, Adelaide, Australia , Fadlelmola, Faisal M. Centre for Bioinformatics and Systems Biology - Faculty of Science - University of Khartoum, Khartoum, Sudan , Alghali, Mustafa Centre for Bioinformatics and Systems Biology - Faculty of Science - University of Khartoum, Khartoum, Sudan , Aron, Shaun Sydney Brenner Institute for Molecular Bioscience - University of the Witwatersrand, Johannesburg, South Africa , Bendou, Hocine South African National Bioinformatics Institute - University of the Western Cape, Cape Town, South Africa , Beste, Eugene De South African National Bioinformatics Institute - University of the Western Cape, Cape Town, South Africa , Mbiyavanga, Mamana Computational Biology Division - Integrative Medical Biosciences - University of Cape Town, Cape Town, South Africa , Souiai, Oussema Institut Pasteur De Tunis and Institut Superieur des Technologies Médicales de Tunis - University Tunis Al Manar, Tunis, Tunisia , Yi ,Long South African National Bioinformatics Institute - University of the Western Cape, Cape Town, South Africa , Zermeno, Jennie Institute for Genomic Biology - University of Illinois at Urbana-Champaign, Urbana, IL, USA , Armstrong, Don Institute for Genomic Biology - University of Illinois at Urbana-Champaign, Urbana, IL, USA , D. O'Connor, Brian Genomics Institute - University of California - Santa Cruz, Santa Cruz, CA, USA , Mainzer, Liudmila Sergeevna Institute for Genomic Biology - University of Illinois at Urbana-Champaign, Urbana, IL, USA , Crusoe, Michael R. Common Workflow Language Project, Vilnius, Lithuania , Meintjes, Ayton Computational Biology Division - Integrative Medical Biosciences, University of Cape Town, Cape Town, South Africa , Heusden, Peter Van South African National Bioinformatics Institute - University of the Western Cape, Cape Town, South Africa , Botha, Gerrit Computational Biology Division - Integrative Medical Biosciences, University of Cape Town, Cape Town, South Africa , Joubert, Fourie Centre for Bioinformatics and Computational Biology - Department of Biochemistry - Genetics and Microbiology - University of Pretoria, Pretoria, South Africa , Jongeneel, C. Victor Institute for Genomic Biology - University of Illinois at Urbana-Champaign, Urbana, IL, USA , Hazelhurst, Scott Sydney Brenner Institute for Molecular Bioscience - University of the Witwatersrand, Johannesburg, South Africa
Pages
18
From page
1
To page
18
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.
Keywords
Bioinformatics , hackathon , workflow , reproducible , pipeline , capacity building
Journal title
AAS Open Research
Serial Year
2019
Record number
2612384
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