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Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience.
Ahmed, Azza E; Mpangase, Phelelani T; Panji, Sumir; Baichoo, Shakuntala; Souilmi, Yassine; Fadlelmola, Faisal M; Alghali, Mustafa; Aron, Shaun; Bendou, Hocine; De Beste, Eugene; Mbiyavanga, Mamana; Souiai, Oussema; Yi, Long; Zermeno, Jennie; Armstrong, Don; O'Connor, Brian D; Mainzer, Liudmila Sergeevna; Crusoe, Michael R; Meintjes, Ayton; Van Heusden, Peter; Botha, Gerrit; Joubert, Fourie; Jongeneel, C Victor; Hazelhurst, Scott; Mulder, Nicola.
Afiliación
  • Ahmed AE; Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan.
  • Mpangase PT; Department of Electrical and Electronic Engineering, Faculty of Engineering, University of Khartoum, Khartoum, Sudan.
  • Panji S; Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
  • Baichoo S; Computational Biology Division, Integrative Medical Biosciences, University of Cape Town, Cape Town, South Africa.
  • Souilmi Y; Department of Digital Technologies, University of Mauritius, Reduit, Mauritius.
  • Fadlelmola FM; Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia.
  • Alghali M; Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan.
  • Aron S; Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan.
  • Bendou H; Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
  • De Beste E; South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa.
  • Mbiyavanga M; South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa.
  • Souiai O; Computational Biology Division, Integrative Medical Biosciences, University of Cape Town, Cape Town, South Africa.
  • Yi L; Institut Pasteur De Tunis and Institut Superieur des Technologies Médicales de Tunis, University Tunis Al Manar, Tunis, Tunisia.
  • Zermeno J; South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa.
  • Armstrong D; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • O'Connor BD; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Mainzer LS; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
  • Crusoe MR; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Meintjes A; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Van Heusden P; Common Workflow Language Project, Vilnius, Lithuania.
  • Botha G; Computational Biology Division, Integrative Medical Biosciences, University of Cape Town, Cape Town, South Africa.
  • Joubert F; South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa.
  • Jongeneel CV; Computational Biology Division, Integrative Medical Biosciences, University of Cape Town, Cape Town, South Africa.
  • Hazelhurst S; Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
  • Mulder N; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
AAS Open Res ; 1: 9, 2018.
Article en En | MEDLINE | ID: mdl-32382696
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 compute environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. To address this need, in 2016 H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Hackathon, with the purpose of building key genomics 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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: AAS Open Res Año: 2018 Tipo del documento: Article País de afiliación: Sudán
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: AAS Open Res Año: 2018 Tipo del documento: Article País de afiliación: Sudán