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Development of Bioinformatics Infrastructure for Genomics Research

Authors:

Nicola J. Mulder ,

Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, ZA
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Ezekiel Adebiyi,

Department of Computer and Information Sciences, Covenant University, Ota; Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, NG
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Marion Adebiyi,

Department of Computer and Information Sciences, Covenant University, Ota; Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, NG
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Seun Adeyemi,

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota; Center for System and Information Service, Covenant University, Ota, NG
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Azza Ahmed,

Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, SD
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Rehab Ahmed,

Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, SD
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Bola Akanle,

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota; Center for System and Information Service, Covenant University, Ota, NG
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Mohamed Alibi,

Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis, Tunis, TN
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Don L. Armstrong,

Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, US
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Shaun Aron,

Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, ZA
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Efejiro Ashano,

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota; H3Africa Bioinformatics Network (H3ABioNet) Node, National Biotechnology Development Agency (NABDA), Federal Ministry of Science and Technology (FMST), Abuja, NG
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Shakuntala Baichoo,

University of Mauritius, Moka, MU
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Alia Benkahla,

Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis, Tunis, TN
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David K. Brown,

Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, ZA
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Emile R. Chimusa,

Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town; Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, ZA
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Faisal M. Fadlelmola,

Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum; Future University of Sudan, Khartoum, SD
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Dare Falola,

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, NG
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Segun Fatumo,

H3Africa Bioinformatics Network (H3ABioNet) Node, National Biotechnology Development Agency (NABDA), Federal Ministry of Science and Technology (FMST), Abuja, NG
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Kais Ghedira,

Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis, Tunis, TN
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Amel Ghouila,

Institut Pasteur de Tunis, LR11IPT02, Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), Tunis-Belvédère, TN
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Scott Hazelhurst,

Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, ZA
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Itunuoluwa Isewon,

Department of Computer and Information Sciences, Covenant University, Ota; Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, NG
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Segun Jung,

Computation Institute, University of Chicago and Argonne National Laboratory, Chicago, IL, US
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Samar Kamal Kassim,

Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbaseya, Cairo, EG
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Jonathan K. Kayondo,

Uganda Virus Research Institute (UVRI), Entebbe, UG
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Mamana Mbiyavanga,

Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, ZA
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Ayton Meintjes,

Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, ZA
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Somia Mohammed,

Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, SD
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Abayomi Mosaku,

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, NG
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Ahmed Moussa,

LAbTIC Laboratory, ENSA, Abdelmalek Essaadi University, Tangier, MA
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Mustafa Muhammd,

Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, SD
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Zahra Mungloo-Dilmohamud,

University of Mauritius, Moka, MU
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Oyekanmi Nashiru,

H3Africa Bioinformatics Network (H3ABioNet) Node, National Biotechnology Development Agency (NABDA), Federal Ministry of Science and Technology (FMST), Abuja, NG
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Trust Odia,

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, NG
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Adaobi Okafor,

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota
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Olaleye Oladipo,

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota; Center for System and Information Service, Landmark University, Omu-Aran, NG
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Victor Osamor,

Department of Computer and Information Sciences, Covenant University, Ota; Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, NG
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Jellili Oyelade,

Department of Computer and Information Sciences, Covenant University, Ota; Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, NG
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Khalid Sadki,

School of Sciences, Mohammed V University of Rabat, Rabat, MA
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Samson Pandam Salifu,

Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi; Kumasi Centre for Collaborative Research, South End Asougya Road, KNUST Campus, Kumasi, GH
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Jumoke Soyemi,

Department of Computer Science, Ilaro Polytechnic, Ilaro, NG
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Sumir Panji,

Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, ZA
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Fouzia Radouani,

Chlamydiae and Mycoplasma Laboratory, Institut Pasteur du Maroc, Casablanca, MA
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Oussama Souiai,

Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis, Tunis, TN
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Özlem Tastan Bishop,

Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, ZA
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The H3ABioNet Consortium, as members of the H3Africa Consortium

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.

Highlights

  • H3ABioNet is building capacity to enable analysis of genomic data in Africa.
  • Infrastructure has been built for clinical and genomic data storage, management, and analysis.
  • New algorithms and pipelines for African genomic data analysis have been developed.
  • Data are being harmonized using ontologies to enable easy search and retrieval.
  • Genomics training is implemented using various online and face-to-face approaches.
How to Cite: Mulder NJ, Adebiyi E, Adebiyi M, Adeyemi S, Ahmed A, Ahmed R, et al.. Development of Bioinformatics Infrastructure for Genomics Research. Global Heart. 2017;12(2):91–8. DOI: http://doi.org/10.1016/j.gheart.2017.01.005
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Published on 01 Jun 2017.
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