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. 2023 Oct 10:2023:6638714.
doi: 10.1155/2023/6638714. eCollection 2023.

PHINDaccess Hackathons for COVID-19 and Host-Pathogen Interaction: Lessons Learned and Recommendations for Low- and Middle-Income Countries

Kais Ghedira  1 , Hamza Dallali  2 , Monia Ardhaoui  3   4 , Zied Bouslema  5   6 , Yosr Hamdi  2 , Salma Feki Ben-Salah  7 , Hanen Chelbi  8 , Chiraz Atri  9 , Melek Chaouch  1 , Naira Dekhil  10 , Afef Rais  9 , Saifeddine Azouz  11 , Manel Gharbi  12 , Fatma Guerfali  9 , Chaima Hkimi  1 , Selim Kamoun  1 , Ayoub Ksouri  13 , Imen Moumni  14 , Houyem Ouragini  14 , Raghda Bsibes  15 , Zeineb Afifi  15 , Khouloud Youssfi  16 , Hichem Ben Hassine  16 , Najet Hadhri  15 , Helmi Mardassi  10 , Houcemeddine Othman  17   18   19 , Oussema Khamessi  20   21
Affiliations

PHINDaccess Hackathons for COVID-19 and Host-Pathogen Interaction: Lessons Learned and Recommendations for Low- and Middle-Income Countries

Kais Ghedira et al. Biomed Res Int. .

Abstract

Hackathons are collaborative events that bring together diverse groups to solve predefined challenges. The COVID-19 pandemic caused by SARS-CoV-2 has emphasized the need for portable and reproducible genomics analysis pipelines to study the genetic susceptibility of the human host and investigate human-SARS-CoV-2 protein interactions. To build and strengthen institutional capacities in OMICS data analysis applied to host-pathogen interaction (HPI), the PHINDaccess project organized two hackathons in 2020 and 2021. These hackathons are aimed at developing bioinformatics pipelines related to the SARS-CoV-2 viral genome, its phylodynamic transmission, and the identification of human genome host variants, with a focus on addressing global health challenges, particularly in low- and middle-income countries (LMIC). This paper outlines the preparation, proceedings, and lessons learned from these hackathons, including the challenges faced by participants and our recommendations based on our experience for organizing hackathons in LMIC and beyond.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Detailed participants' involvement in the hackathon. The hackathon involved 16 participants from the Institut Pasteur de Tunis. They have been organized in five complementary working groups or “teams.”
Figure 2
Figure 2
Main hackathon goals and components, including communication platforms.
Figure 3
Figure 3
A timeline of the hackathons' planning activities.
Figure 4
Figure 4
Example of a workflow for WES data analysis pipeline.
Figure 5
Figure 5
The hackathons as seen by participants.
See this image and copyright information in PMC

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