Evidence map›Paper›PMID 32382696›Full record

ArticleAAS open research2018

Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience.

Azza E Ahmed, Phelelani T Mpangase, Sumir Panji, Shakuntala Baichoo, Yassine Souilmi, Faisal M Fadlelmola, Mustafa Alghali, Shaun Aron, Hocine Bendou, Eugene De Beste and 15 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in AAS open research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. A community-based approach to image analysis of cells, tissues and tumors.Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society · 2022
    Review
  5. Article
  6. Article
  7. H3ABioNet genomic medicine and microbiome data portals hackathon proceedings.Database : the journal of biological databases and curation · 2021
    Article
  8. Article
  9. Article
  10. DissectingFrontiers in genetics · 2019
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

25 authors.

Azza E Ahmed *Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan.ORCID https://orcid.org/0000-0002-1358-8371
Phelelani T Mpangase *Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
Sumir PanjiComputational Biology Division, Integrative Medical Biosciences, University of Cape Town, Cape Town, South Africa.
Shakuntala BaichooDepartment of Digital Technologies, University of Mauritius, Reduit, Mauritius.ORCID https://orcid.org/0000-0002-9335-1939
Yassine SouilmiAustralian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia.ORCID https://orcid.org/0000-0001-7543-4864
Faisal M FadlelmolaCentre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan.ORCID https://orcid.org/0000-0001-8351-264X
Mustafa AlghaliCentre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan.
Shaun AronSydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
Hocine BendouSouth African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa.ORCID https://orcid.org/0000-0001-5371-6107
Eugene De BesteSouth African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa.
Mamana MbiyavangaComputational Biology Division, Integrative Medical Biosciences, University of Cape Town, Cape Town, South Africa.
Oussema SouiaiInstitut Pasteur De Tunis and Institut Superieur des Technologies Médicales de Tunis, University Tunis Al Manar, Tunis, Tunisia.ORCID https://orcid.org/0000-0003-2443-114X
Long YiSouth African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa.
Jennie ZermenoInstitute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Don ArmstrongInstitute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Brian D O'ConnorGenomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Liudmila Sergeevna MainzerInstitute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Michael R CrusoeCommon Workflow Language Project, Vilnius, Lithuania.ORCID https://orcid.org/0000-0002-2961-9670
Ayton MeintjesComputational Biology Division, Integrative Medical Biosciences, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0000-0001-5076-2941
Peter Van HeusdenSouth African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa.ORCID https://orcid.org/0000-0001-6553-5274
Gerrit BothaComputational Biology Division, Integrative Medical Biosciences, University of Cape Town, Cape Town, South Africa.
Fourie JoubertCentre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
C Victor JongeneelInstitute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.ORCID https://orcid.org/0000-0002-3922-1906
Scott HazelhurstSydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.ORCID https://orcid.org/0000-0002-0581-149X
Nicola MulderComputational Biology Division, Integrative Medical Biosciences, University of Cape Town, Cape Town, South Africa.ORCID https://orcid.org/0000-0003-4905-0941

Funding

H3ABioNet: a sustainable African Bioinformatics Network for H3AfricaU41HG006941 · NHGRI · UNIVERSITY OF CAPE TOWN · PI MULDER, NICOLA · 2012 to 2017
$14.8M
H3ABioNet: informatics solutions for H3AfricaU24HG006941 · NHGRI · UNIVERSITY OF CAPE TOWN · PI MULDER, NICOLA · 2017 to 2021
$12.9M
NHGRI NIH HHS U24 HG006941NHGRI NIH HHS U41 HG006941
6 · The paper itself

Abstract

The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines adapted to heterogeneous computing environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. Building on the network's Standard Operating Procedures (SOPs) for common genomic analyses, H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Hackathon in 2016, with the purpose of translating those SOPs into analysis pipelines able to run on heterogeneous computing environments and meeting the needs of H3Africa research projects. This paper describes the preparations for this hackathon and reflects upon the lessons learned about its impact on building the technical and scientific expertise of African researchers. The workflows developed were made publicly available in GitHub repositories and deposited as container images on Quay.io.

Indexed as

Bioinformaticscapacity buildinghackathonpipelinereproducibleworkflow

Identifiers

PMID32382696
PMCPMC7194140

What OpenQuestion holds

Textmetadata
LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.