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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...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7906323/ https://www.ncbi.nlm.nih.gov/pubmed/33630830 http://dx.doi.org/10.1371/journal.pcbi.1008640 |
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author | Ras, Verena Botha, Gerrit Aron, Shaun Lennard, Katie Allali, Imane Claassen-Weitz, Shantelle Mwaikono, Kilaza Samson Kennedy, Dane Holmes, Jessica R. Rendon, Gloria Panji, Sumir Fields, Christopher J Mulder, Nicola |
author_facet | Ras, Verena Botha, Gerrit Aron, Shaun Lennard, Katie Allali, Imane Claassen-Weitz, Shantelle Mwaikono, Kilaza Samson Kennedy, Dane Holmes, Jessica R. Rendon, Gloria Panji, Sumir Fields, Christopher J Mulder, Nicola |
author_sort | Ras, Verena |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-7906323 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-79063232021-03-03 Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa Ras, Verena Botha, Gerrit Aron, Shaun Lennard, Katie Allali, Imane Claassen-Weitz, Shantelle Mwaikono, Kilaza Samson Kennedy, Dane Holmes, Jessica R. Rendon, Gloria Panji, Sumir Fields, Christopher J Mulder, Nicola PLoS Comput Biol Education 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. Public Library of Science 2021-02-25 /pmc/articles/PMC7906323/ /pubmed/33630830 http://dx.doi.org/10.1371/journal.pcbi.1008640 Text en © 2021 Ras et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Education Ras, Verena Botha, Gerrit Aron, Shaun Lennard, Katie Allali, Imane Claassen-Weitz, Shantelle Mwaikono, Kilaza Samson Kennedy, Dane Holmes, Jessica R. Rendon, Gloria Panji, Sumir Fields, Christopher J Mulder, Nicola Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa |
title | 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_short | 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 |
topic | Education |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7906323/ https://www.ncbi.nlm.nih.gov/pubmed/33630830 http://dx.doi.org/10.1371/journal.pcbi.1008640 |
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