Development of Bioinformatics Infrastructure for Genomics Research

Nicola Mulder 1, * Ezekiel Adebiyi 2, 3 Marion Adebiyi 2, 3 Seun Adeyemi 4, 3 Azza Ahmed 5 Rehab Ahmed 5 Bola Akanle 4, 3 Mohamed Alibi 6 Don Armstrong 7 Shaun Aron 8 Efejiro Ashano 3, 9 Shakuntala Baichoo 10 Alia Benkahla 6 David Brown 11 Emile Chimusa 1, 12 Faisal Fadlelmola 13, 5 Dare Falola 3 Segun Fatumo 9 Kais Ghedira 6 Amel Ghouila 14 Scott Hazelhurst 8 Itunuoluwa Isewon 2, 3 Segun Jung 15 Samar Kassim 16 Jonathan Kayondo 17 Mamana Mbiyavanga 12 Ayton Meintjes 1 Somia Mohammed 5 Abayomi Mosaku 3 Ahmed Moussa 18 Mustafa Muhammd 5 Zahra Mungloo-Dilmohamud 10 Oyekanmi Nashiru 9 Trust Odia 3 Adaobi Okafor 3 Olaleye Oladipo 19, 3 Victor Osamor 4, 3 Jellili Oyelade 4, 3 Khalid Sadki 20 Samson Salifu 21 Jumoke Soyemi 22 Sumir Panji 12 Fouzia Radouani 23 Oussama Souiai 6 Özlem Tastan Bishop 11 Consortium H3abionet
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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Submitted on : Monday, January 28, 2019 - 4:08:14 PM
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Nicola Mulder, Ezekiel Adebiyi, Marion Adebiyi, Seun Adeyemi, Azza Ahmed, et al.. Development of Bioinformatics Infrastructure for Genomics Research. Global Heart, World Heart Federation, 2017, 12 (2), pp.91-98. ⟨10.1016/j.gheart.2017.01.005⟩. ⟨pasteur-01996885⟩

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