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|Title: ||Development of Bioinformatics Infrastructure for Genomics Research in H3Africa|
|Authors: ||The H3ABioNet
Mulder, Nicola J.
Armstrong, Don L.
Brown, David K.
Chimusa, Emile R.
Fadlelmola, Faisal M.
Salifu, Samson Pandam
Bishop, Özlem Tastan
|Issue Date: ||Mar-2017|
|Publisher: ||Global Heart|
|Citation: ||Global Heart, March-2017, http://dx.doi.org/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
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
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.|
|Description: ||An article published by Global Heart, March-2017, http://dx.doi.org/10.1016/ j.gheart.2017.01.005|
|Appears in Collections:||College of Science|
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