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

Azza E Ahmed^#^{1

2}, Phelelani T Mpangase^#³, Sumir Panji⁴, Shakuntala Baichoo⁵, Yassine Souilmi⁶, Faisal M Fadlelmola¹, Mustafa Alghali¹, Shaun Aron³, Hocine Bendou⁷, Eugene De Beste⁷, Mamana Mbiyavanga⁴, Oussema Souiai⁸, Long Yi⁷, Jennie Zermeno⁹, Don Armstrong⁹, Brian D O'Connor¹⁰, Liudmila Sergeevna Mainzer^{9

11}, Michael R Crusoe¹², Ayton Meintjes⁴, Peter Van Heusden⁷, Gerrit Botha⁴, Fourie Joubert¹³, C Victor Jongeneel⁹, Scott Hazelhurst^{3

14}, Nicola Mulder⁴

Affiliations

¹ Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan.
² Department of Electrical and Electronic Engineering, Faculty of Engineering, University of Khartoum, Khartoum, Sudan.
³ Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
⁴ Computational Biology Division, Integrative Medical Biosciences, University of Cape Town, Cape Town, South Africa.
⁵ Department of Digital Technologies, University of Mauritius, Reduit, Mauritius.
⁶ Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia.
⁷ South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa.
⁸ Institut Pasteur De Tunis and Institut Superieur des Technologies Médicales de Tunis, University Tunis Al Manar, Tunis, Tunisia.
⁹ Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
¹⁰ Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
¹¹ National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
¹² Common Workflow Language Project, Vilnius, Lithuania.
¹³ Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
¹⁴ School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.

^# Contributed equally.

PMID: 32382696
PMCID: PMC7194140
DOI: 10.12688/aasopenres.12847.2

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

Azza E Ahmed et al. AAS Open Res. 2019.

. 2019 Aug 7:1:9.

doi: 10.12688/aasopenres.12847.2. eCollection 2018.

Authors

Affiliations

¹ Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan.
² Department of Electrical and Electronic Engineering, Faculty of Engineering, University of Khartoum, Khartoum, Sudan.
³ Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
⁴ Computational Biology Division, Integrative Medical Biosciences, University of Cape Town, Cape Town, South Africa.
⁵ Department of Digital Technologies, University of Mauritius, Reduit, Mauritius.
⁶ Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia.
⁷ South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa.
⁸ Institut Pasteur De Tunis and Institut Superieur des Technologies Médicales de Tunis, University Tunis Al Manar, Tunis, Tunisia.
⁹ Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
¹⁰ Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
¹¹ National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
¹² Common Workflow Language Project, Vilnius, Lithuania.
¹³ Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
¹⁴ School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.

^# Contributed equally.

PMID: 32382696
PMCID: PMC7194140
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.

Keywords: Bioinformatics; capacity building; hackathon; pipeline; reproducible; workflow.

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Conflict of interest statement

Competing interests: MRC in his role as CWL Community Engineer, has had his salary supported in the past by grants from Seven Bridges Genomics, Inc to its employers. The other authors declare that they have no competing interests.

Figures

**Figure 1.. Planning and execution of the H3ABioNet Cloud computing hackathon.**
H3ABioNet developed SOPs for 5 analysis niches needed within H3Africa projects. 4 out of these were implemented as portable workflows as a result of the H3ABioNet 2016 Cloud Computing hackathon that brought together early career scientists, expert mentors and collaborators by utilizing many planning and communication platforms. (SOPs: Standard Operating Procedures).

See this image and copyright information in PMC

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Grants and funding

LinkOut - more resources

Full Text Sources