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Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience
Azza E Ahmed1,2, Phelelani T Mpangase3, Sumir Panji4
1Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan.
AAS Open Research
|May 12, 2020
Summary
African researchers enhanced genomics analysis skills through a cloud computing hackathon. This initiative translated standard operating procedures into portable, reproducible bioinformatics pipelines, boosting research capacity.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- Growing global and African demand for portable, reproducible genomics analysis pipelines.
- Need for technical expertise in workflow languages and containerization for collaborative projects like H3Africa.
- Pan-African Bioinformatics Network (H3ABioNet) identified challenges in heterogeneous computing environments.
Purpose of the Study:
- Translate Standard Operating Procedures (SOPs) into adaptable analysis pipelines.
- Enable pipelines to run across diverse computing environments for H3Africa projects.
- Foster technical and scientific expertise among African researchers.
Main Methods:
- Organized the first Cloud Computing and Reproducible Workflows Hackathon in 2016.
- Leveraged existing H3ABioNet SOPs for common genomic analyses.
- Developed portable workflows and containerized them for accessibility.
Main Results:
- Successfully translated SOPs into executable analysis pipelines.
- Workflows made publicly available on GitHub and Quay.io.
- Enhanced technical and scientific capacity of participating African researchers.
Conclusions:
- Hackathon effectively addressed the need for reproducible genomics workflows in Africa.
- Publicly available resources facilitate broader adoption and collaboration.
- Capacity building is crucial for advancing genomics research on the continent.
