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Ahmed AE, Mpangase PT, Panji S, et al. Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience. AAS Open Res. 2019;1:9doi: 10.12688/aasopenres.12847.2.
Ahmed, A. E., Mpangase, P. T., Panji, S., Baichoo, S., Souilmi, Y., Fadlelmola, F. M., Alghali, M., Aron, S., Bendou, H., De Beste, E., Mbiyavanga, M., Souiai, O., Yi, L., Zermeno, J., Armstrong, D., O'Connor, B. D., Mainzer, L. S., Crusoe, M. R., Meintjes, A., Van Heusden, P., Botha, G., Joubert, F., Jongeneel, C. V., Hazelhurst, S., & Mulder, N. (2018). Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience. AAS open research, 19. https://doi.org/10.12688/aasopenres.12847.2
Ahmed, Azza E, et al. "Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience." AAS open research vol. 1 (2018): 9. doi: https://doi.org/10.12688/aasopenres.12847.2
Ahmed AE, Mpangase PT, Panji S, Baichoo S, Souilmi Y, Fadlelmola FM, Alghali M, Aron S, Bendou H, De Beste E, Mbiyavanga M, Souiai O, Yi L, Zermeno J, Armstrong D, O'Connor BD, Mainzer LS, Crusoe MR, Meintjes A, Van Heusden P, Botha G, Joubert F, Jongeneel CV, Hazelhurst S, Mulder N. Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience. AAS Open Res. 2019 Aug 07;1:9. doi: 10.12688/aasopenres.12847.2. eCollection 2018. PMID: 32382696; PMCID: PMC7194140.
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AAS Open Res. 2019 Aug 07;1:9. doi: 10.12688/aasopenres.12847.2. eCollection 2018.

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

AAS open research

Azza E Ahmed, Phelelani T Mpangase, 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 Sergeevna Mainzer, Michael R Crusoe, Ayton Meintjes, Peter Van Heusden, Gerrit Botha, Fourie Joubert, C Victor Jongeneel, Scott Hazelhurst, Nicola Mulder

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.

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.

Copyright: © 2019 Ahmed AE et al.

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

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 the

References

  1. J Open Res Softw. 2016;4(1): - PubMed
  2. Glob Health Epidemiol Genom. 2016 Nov 22;1:e20 - PubMed
  3. Elife. 2015 Jul 23;4:e09944 - PubMed
  4. Pharmgenomics Pers Med. 2018 Apr 10;11:59-66 - PubMed
  5. F1000Res. 2017 Jan 18;6:52 - PubMed
  6. Science. 2014 Jun 20;344(6190):1346-8 - PubMed
  7. Genome Res. 2016 Feb;26(2):271-7 - PubMed
  8. Genome Biol. 2017 Nov 23;18(1):223 - PubMed
  9. PLoS Comput Biol. 2019 Apr 1;15(4):e1006671 - PubMed
  10. Nat Biotechnol. 2017 Apr 11;35(4):316-319 - PubMed
  11. BMC Bioinformatics. 2018 Nov 29;19(1):457 - PubMed
  12. BMC Bioinformatics. 2014;15 Suppl 14:S7 - PubMed
  13. Glob Heart. 2017 Jun;12(2):91-98 - PubMed
  14. PLoS Comput Biol. 2017 Jun 1;13(6):e1005419 - PubMed
  15. Sci Transl Med. 2016 Apr 6;8(333):333ps8 - PubMed

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