Review

. 2017 Jun;12(2):91-98.

doi: 10.1016/j.gheart.2017.01.005. Epub 2017 Mar 13.

Development of Bioinformatics Infrastructure for Genomics Research

Nicola J Mulder¹, Ezekiel Adebiyi², Marion Adebiyi², Seun Adeyemi³, Azza Ahmed⁴, Rehab Ahmed⁴, Bola Akanle³, Mohamed Alibi⁵, Don L Armstrong⁶, Shaun Aron⁷, Efejiro Ashano⁸, Shakuntala Baichoo⁹, Alia Benkahla⁵, David K Brown¹⁰, Emile R Chimusa¹¹, Faisal M Fadlelmola¹², Dare Falola¹³, Segun Fatumo¹⁴, Kais Ghedira⁵, Amel Ghouila¹⁵, Scott Hazelhurst⁷, Itunuoluwa Isewon², Segun Jung¹⁶, Samar Kamal Kassim¹⁷, Jonathan K Kayondo¹⁸, Mamana Mbiyavanga¹⁹, Ayton Meintjes¹⁹, Somia Mohammed⁴, Abayomi Mosaku¹³, Ahmed Moussa²⁰, Mustafa Muhammd⁴, Zahra Mungloo-Dilmohamud⁹, Oyekanmi Nashiru¹⁴, Trust Odia¹³, Adaobi Okafor¹³, Olaleye Oladipo²¹, Victor Osamor², Jellili Oyelade², Khalid Sadki²², Samson Pandam Salifu²³, Jumoke Soyemi²⁴, Sumir Panji¹⁹, Fouzia Radouani²⁵, Oussama Souiai⁵, Özlem Tastan Bishop¹⁰; H3ABioNet Consortium, as members of the H3Africa Consortium

Affiliations

¹ Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa. Electronic address: Nicola.mulder@uct.ac.za.
² Department of Computer and Information Sciences, Covenant University, Ota, Nigeria; Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria.
³ Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria; Center for System and Information Service, Covenant University, Ota, Nigeria.
⁴ Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan.
⁵ Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis, Tunis, Tunisia.
⁶ Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
⁷ Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
⁸ Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria; H3Africa Bioinformatics Network (H3ABioNet) Node, National Biotechnology Development Agency (NABDA), Federal Ministry of Science and Technology (FMST), Abuja, Nigeria.
⁹ University of Mauritius, Moka, Mauritius.
¹⁰ Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa.
¹¹ Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
¹² Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan; Future University of Sudan, Khartoum, Sudan.
¹³ Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria.
¹⁴ H3Africa Bioinformatics Network (H3ABioNet) Node, National Biotechnology Development Agency (NABDA), Federal Ministry of Science and Technology (FMST), Abuja, Nigeria.
¹⁵ Institut Pasteur de Tunis, LR11IPT02, Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), Tunis-Belvédère, Tunisia.
¹⁶ Computation Institute, University of Chicago and Argonne National Laboratory, Chicago, IL, USA.
¹⁷ Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbaseya, Cairo, Egypt.
¹⁸ Uganda Virus Research Institute (UVRI), Entebbe, Uganda.
¹⁹ Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
²⁰ LAbTIC Laboratory, ENSA, Abdelmalek Essaadi University, Tangier, Morocco.
²¹ Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria; Center for System and Information Service, Landmark University, Omu-Aran, Nigeria.
²² School of Sciences, Mohammed V University of Rabat, Rabat, Morocco.
²³ Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana; Kumasi Centre for Collaborative Research, South End Asougya Road, KNUST Campus, Kumasi, Ghana.
²⁴ Department of Computer Science, Ilaro Polytechnic, Ilaro, Nigeria.
²⁵ Chlamydiae and Mycoplasma Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.

PMID: 28302555
PMCID: PMC5582980
DOI: 10.1016/j.gheart.2017.01.005

Review

Development of Bioinformatics Infrastructure for Genomics Research

Nicola J Mulder et al. Glob Heart. 2017 Jun.

. 2017 Jun;12(2):91-98.

doi: 10.1016/j.gheart.2017.01.005. Epub 2017 Mar 13.

Authors

Affiliations

¹ Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa. Electronic address: Nicola.mulder@uct.ac.za.
² Department of Computer and Information Sciences, Covenant University, Ota, Nigeria; Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria.
³ Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria; Center for System and Information Service, Covenant University, Ota, Nigeria.
⁴ Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan.
⁵ Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis, Tunis, Tunisia.
⁶ Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
⁷ Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
⁸ Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria; H3Africa Bioinformatics Network (H3ABioNet) Node, National Biotechnology Development Agency (NABDA), Federal Ministry of Science and Technology (FMST), Abuja, Nigeria.
⁹ University of Mauritius, Moka, Mauritius.
¹⁰ Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa.
¹¹ Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
¹² Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan; Future University of Sudan, Khartoum, Sudan.
¹³ Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria.
¹⁴ H3Africa Bioinformatics Network (H3ABioNet) Node, National Biotechnology Development Agency (NABDA), Federal Ministry of Science and Technology (FMST), Abuja, Nigeria.
¹⁵ Institut Pasteur de Tunis, LR11IPT02, Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), Tunis-Belvédère, Tunisia.
¹⁶ Computation Institute, University of Chicago and Argonne National Laboratory, Chicago, IL, USA.
¹⁷ Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbaseya, Cairo, Egypt.
¹⁸ Uganda Virus Research Institute (UVRI), Entebbe, Uganda.
¹⁹ Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
²⁰ LAbTIC Laboratory, ENSA, Abdelmalek Essaadi University, Tangier, Morocco.
²¹ Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria; Center for System and Information Service, Landmark University, Omu-Aran, Nigeria.
²² School of Sciences, Mohammed V University of Rabat, Rabat, Morocco.
²³ Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana; Kumasi Centre for Collaborative Research, South End Asougya Road, KNUST Campus, Kumasi, Ghana.
²⁴ Department of Computer Science, Ilaro Polytechnic, Ilaro, Nigeria.
²⁵ Chlamydiae and Mycoplasma Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.

PMID: 28302555
PMCID: PMC5582980
DOI: 10.1016/j.gheart.2017.01.005

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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Figures

**Figure 1**
H3Africa Participant recruitment Database Quick Report Section

See this image and copyright information in PMC

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Development of Bioinformatics Infrastructure for Genomics Research

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Development of Bioinformatics Infrastructure for Genomics Research

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