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

Version: 1, Uploaded by: Administrator, Date Uploaded: 25 November 2022

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Reference (Identifier)

GS-00643

Title

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

Broad Theme Classification

2. Engineering and Technology

Second Level Classification

2.11 Other Engineering and Technologies

Country Specific Sectors

27. Artificial Intelligence/ Machine Learning

Author Name

Mr. Azza E. Ahmed

Institution

University of Khartoum

Co-Author 1 Name

Phelelani T. Mpangase

Co-Author 2 Name

Sumir Panji

Co-Author 3 Name

Dr. Shakuntala Baichoo

Co-Author 3 Institution

University of Mauritius

Co-Author 4 Name

Yassine Souilmi

Co-Author 5 Name

Faisal M. Fadlelmola

Co-Author 6 Name

Mustafa Alghali

Co-Author 7 Name

Shaun Aron

Co-Author 8 Name

Hocine Bendou

Co-Author 9 Name

Eugene De Beste

Co-Author 10 Name

Mamana Mbiyavanga

Co-Author 11 Name

Oussema Souiai

Co-Author 12 Name

Long Yi

Co-Author 13 Name

Jennie Zermeno

Co-Author 14 Name

Don Armstrong

Co-Author 15 Name

Brian D. O'Connor

Co-Author 16 Name

Liudmila Sergeevna Mainzer

Co-Author 17 Name

Michael R. Crusoe

Co-Author 18 Name

Ayton Meintjes

Co-Author 19 Name

Peter Van Heusden

Co-Author 20 Name

Gerrit Botha

Co-Author 21 Name

Fourie Joubert

Co-Author 22 Name

C. Victor Jongeneel

Co-Author 23 Name

Scott Hazelhurst

Co-Author 24 Name

Nicola Mulder

Page Range

1-17

Date Published

7 August 2019

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

Language

English

Publisher

African Academy of Sciences

Content Classification

Journal Article

Note/Remarks

Source: Google Scholar

Date Uploaded

25 November 2022

Size

File Format

Hyperlink

Journal

AAS Open Research

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

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

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