Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa.

With more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design and analysis of microbiome studies and data. However, high-quality bioinformatics courses are often impeded by differences in computational environments...

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Main Authors: Verena Ras, Gerrit Botha, Shaun Aron, Katie Lennard, Imane Allali, Shantelle Claassen-Weitz, Kilaza Samson Mwaikono, Dane Kennedy, Jessica R Holmes, Gloria Rendon, Sumir Panji, Christopher J Fields, Nicola Mulder
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2021-02-01
Series:PLoS Computational Biology
Online Access:https://doi.org/10.1371/journal.pcbi.1008640
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spelling doaj-9bacf3fec9e341ab96d9da36cfaa71d42021-07-09T04:31:58ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582021-02-01172e100864010.1371/journal.pcbi.1008640Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa.Verena RasGerrit BothaShaun AronKatie LennardImane AllaliShantelle Claassen-WeitzKilaza Samson MwaikonoDane KennedyJessica R HolmesGloria RendonSumir PanjiChristopher J FieldsNicola MulderWith more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design and analysis of microbiome studies and data. However, high-quality bioinformatics courses are often impeded by differences in computational environments, complicated software stacks, numerous dependencies, and versions of bioinformatics tools along with a lack of local computational infrastructure and expertise. To address this, H3ABioNet developed a 16S rRNA Microbiome Intermediate Bioinformatics Training course, extending its remote classroom model. The course was developed alongside experienced microbiome researchers, bioinformaticians, and systems administrators, who identified key topics to address. Development of containerised workflows has previously been undertaken by H3ABioNet, and Singularity containers were used here to enable the deployment of a standard replicable software stack across different hosting sites. The pilot ran successfully in 2019 across 23 sites registered in 11 African countries, with more than 200 participants formally enrolled and 106 volunteer staff for onsite support. The pulling, running, and testing of the containers, software, and analyses on various clusters were performed prior to the start of the course by hosting classrooms. The containers allowed the replication of analyses and results across all participating classrooms running a cluster and remained available posttraining ensuring analyses could be repeated on real data. Participants thus received the opportunity to analyse their own data, while local staff were trained and supported by experienced experts, increasing local capacity for ongoing research support. This provides a model for delivering topic-specific bioinformatics courses across Africa and other remote/low-resourced regions which overcomes barriers such as inadequate infrastructures, geographical distance, and access to expertise and educational materials.https://doi.org/10.1371/journal.pcbi.1008640
collection DOAJ
language English
format Article
sources DOAJ
author Verena Ras
Gerrit Botha
Shaun Aron
Katie Lennard
Imane Allali
Shantelle Claassen-Weitz
Kilaza Samson Mwaikono
Dane Kennedy
Jessica R Holmes
Gloria Rendon
Sumir Panji
Christopher J Fields
Nicola Mulder
spellingShingle Verena Ras
Gerrit Botha
Shaun Aron
Katie Lennard
Imane Allali
Shantelle Claassen-Weitz
Kilaza Samson Mwaikono
Dane Kennedy
Jessica R Holmes
Gloria Rendon
Sumir Panji
Christopher J Fields
Nicola Mulder
Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa.
PLoS Computational Biology
author_facet Verena Ras
Gerrit Botha
Shaun Aron
Katie Lennard
Imane Allali
Shantelle Claassen-Weitz
Kilaza Samson Mwaikono
Dane Kennedy
Jessica R Holmes
Gloria Rendon
Sumir Panji
Christopher J Fields
Nicola Mulder
author_sort Verena Ras
title Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa.
title_short Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa.
title_full Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa.
title_fullStr Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa.
title_full_unstemmed Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa.
title_sort using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in africa.
publisher Public Library of Science (PLoS)
series PLoS Computational Biology
issn 1553-734X
1553-7358
publishDate 2021-02-01
description With more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design and analysis of microbiome studies and data. However, high-quality bioinformatics courses are often impeded by differences in computational environments, complicated software stacks, numerous dependencies, and versions of bioinformatics tools along with a lack of local computational infrastructure and expertise. To address this, H3ABioNet developed a 16S rRNA Microbiome Intermediate Bioinformatics Training course, extending its remote classroom model. The course was developed alongside experienced microbiome researchers, bioinformaticians, and systems administrators, who identified key topics to address. Development of containerised workflows has previously been undertaken by H3ABioNet, and Singularity containers were used here to enable the deployment of a standard replicable software stack across different hosting sites. The pilot ran successfully in 2019 across 23 sites registered in 11 African countries, with more than 200 participants formally enrolled and 106 volunteer staff for onsite support. The pulling, running, and testing of the containers, software, and analyses on various clusters were performed prior to the start of the course by hosting classrooms. The containers allowed the replication of analyses and results across all participating classrooms running a cluster and remained available posttraining ensuring analyses could be repeated on real data. Participants thus received the opportunity to analyse their own data, while local staff were trained and supported by experienced experts, increasing local capacity for ongoing research support. This provides a model for delivering topic-specific bioinformatics courses across Africa and other remote/low-resourced regions which overcomes barriers such as inadequate infrastructures, geographical distance, and access to expertise and educational materials.
url https://doi.org/10.1371/journal.pcbi.1008640
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