Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network

C Victor Jongeneel^{1

2}, Ovokeraye Achinike-Oduaran³, Ezekiel Adebiyi^{4

5}, Marion Adebiyi^{4

5}, Seun Adeyemi^{5

6}, Bola Akanle^{5

6}, Shaun Aron³, Efejiro Ashano^{5

7}, Hocine Bendou⁸, Gerrit Botha⁸, Emile Chimusa^{8

9}, Ananyo Choudhury³, Ravikiran Donthu¹, Jenny Drnevich¹, Oluwadamila Falola⁵, Christopher J Fields¹, Scott Hazelhurst^{3

10}, Liesl Hendry³, Itunuoluwa Isewon^{4

5}, Radhika S Khetani¹, Judit Kumuthini⁹, Magambo Phillip Kimuda¹¹, Lerato Magosi¹², Liudmila Sergeevna Mainzer^{1

2}, Suresh Maslamoney⁸, Mamana Mbiyavanga^{8

9}, Ayton Meintjes⁸, Danny Mugutso⁸, Phelelani Mpangase³, Richard Munthali³, Victoria Nembaware⁸, Andrew Ndhlovu³, Trust Odia⁵, Adaobi Okafor⁵, Olaleye Oladipo^{5

6}, Sumir Panji⁸, Venesa Pillay³, Gloria Rendon^{1

2}, Dhriti Sengupta³, Nicola Mulder⁸

Affiliations

¹ High-Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
² Institute for Genomic Biology and National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
³ Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
⁴ Department of Computer and Information Sciences, Covenant University, Ota, Nigeria.
⁵ Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria.
⁶ Directorate, Center for System and Information Service, Covenant University, Ota, Nigeria.
⁷ National Biotechnology Development Agency (NABDA), Federal Ministry of Science and Technology (FMST), Abuja, Nigeria.
⁸ Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa.
⁹ Centre for Proteomic and Genomic Research, Cape Town, South Africa.
¹⁰ School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.
¹¹ Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa.
¹² Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.

PMID: 28570565
PMCID: PMC5453403
DOI: 10.1371/journal.pcbi.1005419

Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network

C Victor Jongeneel et al. PLoS Comput Biol. 2017.

. 2017 Jun 1;13(6):e1005419.

doi: 10.1371/journal.pcbi.1005419. eCollection 2017 Jun.

Authors

Affiliations

¹ High-Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
² Institute for Genomic Biology and National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
³ Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
⁴ Department of Computer and Information Sciences, Covenant University, Ota, Nigeria.
⁵ Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria.
⁶ Directorate, Center for System and Information Service, Covenant University, Ota, Nigeria.
⁷ National Biotechnology Development Agency (NABDA), Federal Ministry of Science and Technology (FMST), Abuja, Nigeria.
⁸ Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa.
⁹ Centre for Proteomic and Genomic Research, Cape Town, South Africa.
¹⁰ School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.
¹¹ Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa.
¹² Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.

PMID: 28570565
PMCID: PMC5453403
DOI: 10.1371/journal.pcbi.1005419

Abstract

The H3ABioNet pan-African bioinformatics network, which is funded to support the Human Heredity and Health in Africa (H3Africa) program, has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Africa research groups. We describe a framework for the assessment of computational genomics analysis skills, which includes standard operating procedures, training and test datasets, and a process for administering the exercise. We present the experiences of 3 research groups that have taken the exercise and the impact on their ability to manage complex projects. Finally, we discuss the reasons why many H3ABioNet nodes have declined so far to participate and potential strategies to encourage them to do so.

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Conflict of interest statement

The authors have declared that no competing interests exist.

References

1. Rotimi C, Abayomi A, Abimiku A, Adabayeri VM, Adebamowo C, et al. Research capacity. Enabling the genomic revolution in Africa. Science. 2014;344(6190):1346–8. 10.1126/science.1251546 . - DOI - PMC - PubMed
1. Mulder NJ, Adebiyi E, Alami R, Benkahla A, Brandful J, Doumbia S, et al. H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa. Genome Res. 2016;26(2):271–7. 10.1101/gr.196295.115 . - DOI - PMC - PubMed
1. Chimusa ER, Mbiyavanga M, Masilela V, Kumuthini J. "Broadband" Bioinformatics Skills Transfer with the Knowledge Transfer Programme (KTP): Educational Model for Upliftment and Sustainable Development. PLoS Comput Biol. 2015;11(11):e1004512 10.1371/journal.pcbi.1004512 . - DOI - PMC - PubMed

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Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network

Affiliations

Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network

Authors

Affiliations

Abstract

Conflict of interest statement

References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources