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Cited by 85Genetics, Bioinformatics, and Biomedical ResearchScientific Computing and Data ManagementResearch Data Management Practices

Development of Bioinformatics Infrastructure for Genomics Research

Open access
Mulder, Nicola J., Adebiyi, Ezekiel, Adebiyi, Marion, Adeyemi, Seun, Ahmed, Azza, Ahmed, Rehab, Akanle, Bola, Alibi, Mohamed +38 more·2017·Global Heart
DOI 10.1016/j.gheart.2017.01.005PMC PMC5582980
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Abstract

BACKGROUND: Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community. OBJECTIVES: H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis. METHODS AND RESULTS: Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for downstream interpretation of prioritized variants. To provide support for these and other bioinformatics queries, an online bioinformatics helpdesk backed by broad consortium expertise has been established. Further support is provided by means of various modes of bioinformatics training. CONCLUSIONS: For the past 4 years, the development of infrastructure support and human capacity through H3ABioNet, have significantly contributed to the establishment of African scientific networks, data analysis facilities, and training programs. Here, we describe the infrastructure and how it has affected genomics and bioinformatics research in Africa.

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  • H3ABioNet provides cost-effective examples for training local scientists in LMICs.

    “Frameworks such as the H3ABioNet, a pan-African bioinformatics network designed to build capacity to enable H3Africa researchers to analyze their data in Africa, provide cost-effective examples for training local scientists in LMICs75.”

    From Clinical use of current polygenic risk scores may exacerbate health disparities (2019) · cites this paper as [75]

    The Approach and implementation section describes H3ABioNet as a pan-African network building local capacity, and Genomics skills training describes its courses and other training for African scientists. Our copy does not establish that the training is cost-effective or assess it as a model across LMICs; the cited evidence is specific to Africa. Page numbers were not available in the indexed passages. (LLM, conf=0.86)

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Authors
Mulder, N. J., Adebiyi, E., Adebiyi, M., Adeyemi, S., Ahmed, A., Ahmed, R., Akanle, B., Alibi, M., Armstrong, D. L., Aron, S., Ashano, E., Baichoo, S., Benkahla, A., Brown, D. K., Chimusa, E. R., Fadlelmola, F. M., Falola, D., Fatumo, S., Ghedira, K., Ghouila, A., Hazelhurst, S., Isewon, I., Jung, S., Kassim, S. K., Kayondo, J. K., Mbiyavanga, M., Meintjes, A., Mohammed, S., Mosaku, A., Moussa, A., Muhammd, M., Mungloo-Dilmohamud, Z., Nashiru, O., Odia, T., Okafor, A., Oladipo, O., Osamor, V., Oyelade, J., Sadki, K., Salifu, S. P., Soyemi, J., Panji, S., Radouani, F., Souiai, O., Tastan Bishop, Ö., & Members of the HAfrica Consortium, T. H. C.
Affiliations
  • University of Cape Town (ZA)
  • Covenant University (NG)
  • University of Khartoum (SD)
  • Institut Pasteur de Tunis (TN)
  • University of Illinois Urbana-Champaign (US)
  • University of the Witwatersrand (ZA)
  • University of Mauritius (MU)
  • Rhodes University (ZA)
  • Federal Ministry of Innovation, Science and Technology (NG)
  • Argonne National Laboratory (US)
  • Ain Shams University (EG)
  • Uganda Virus Research Institute (UG)
  • Abdelmalek Essaâdi University (MA)
  • Mohammed V University (MA)
  • Kwame Nkrumah University of Science and Technology (GH)
  • Institut Pasteur du Maroc (MA)
Corresponding author
Mulder, Nicola J.
ORCID
Venue
Global Heart
Publisher
Ubiquity Press, Ltd.
Published
2017-06-01
Volume
12
Issue
2
Pages
91
ISSN
  • 2211-8160 (ISSN-L)
  • 2211-8179
DOI
10.1016/j.gheart.2017.01.005
PMC
PMC5582980
OpenAlex
W2595620420
Cited by
85
References
1
Citations by year
2026: 16 · 2025: 12 · 2024: 8 · 2023: 2 · 2022: 11 · 2021: 14 · 2020: 4 · 2019: 12 · 2018: 4 · 2017: 2
FWCI
0.56
Type
journal article
Language
en
Open access
Licence
Locations
  • Global Heart (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Covenant University Repository (Covenant University) (acceptedVersion)
  • Landmark University Repository (Landmark University) (acceptedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
  • HAL (submittedVersion)
Funders
National Human Genome Research Institute (U41HG006941)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
  • Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
  • Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
Keywords
H3ABioNet, H3Africa, bioinformatics infrastructure, capacity building, genomic data management, netmap, data harmonization, metadata search, galaxies, bioinformatics pipeline, Docker, variant prioritization, bioinformatics education, help desk
MeSH terms
Africa, Humans, Computational Biology, Genomics, Biomedical Research

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