Development of Bioinformatics Infrastructure for Genomics Research

Mulder, Nicola and Adebiyi, Ezekiel and Adebiyi, Marion and Adeyemi, S. and Ahmed, A. and Ahmed, R. and Akanle, B. and Alibi, M. and Armstrong, D. L. and Aron, S. and Ashanoz, E and Baichoo, S and Benkahla, A and Brown, D.K and Chimusa, E. and Fadlelmolak, F.M. and Falola, O. and Fatumo, S. and Ghedira, Kais and Ghouila, Amel and Hazelhurst, S. and Isewon, Itunuoluwa and Jung, S. and Kassim, S.K. and Kayondo, J.K. and Mbiyavanga, M. and Meintjes, A. and Mohammed, S. and Mosaku, Abayomi and Moussa, A. and Muhammd, M. and Mungloo-Dilmohamud, Z. and Nashiru, Oyekanmi and Odia, Trust and Sadki, K. and Salifu, S.P. and Soyemi, Jumoke and Panji, Sumir and Radouani, F. and Souiai, O. (2017) Development of Bioinformatics Infrastructure for Genomics Research. Global Heart (Gheart), 12 (2). pp. 91-98.

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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.

Item Type:	Article
Subjects:	Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Divisions:	Faculty of Engineering, Science and Mathematics > School of Electronics and Computer Science
Depositing User:	Unnamed user with email [email protected]
Date Deposited:	28 Apr 2020 15:55
Last Modified:	30 Apr 2020 20:39
URI:	http://eprints.federalpolyilaro.edu.ng/id/eprint/11

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