PHINDaccess Hackathons for COVID-19 and Host-Pathogen Interaction: Lessons Learned and Recommendations for Low- and
Kais Ghedira1, Hamza Dallali2, Monia Ardhaoui3,4
1Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia.
Insights
Two hackathons developed bioinformatics pipelines for SARS-CoV-2 genomics and host-pathogen interactions (HPI), strengthening OMICS data analysis capacity, especially in low- and middle-income countries (LMIC). Lessons learned offer recommendations for future global health bioinformatics events.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- The COVID-19 pandemic highlighted the need for robust genomics analysis for host susceptibility and human-SARS-CoV-2 interactions.
- Developing portable and reproducible bioinformatics pipelines is crucial for studying host-pathogen interactions (HPI).
Purpose of the Study:
- To build and strengthen institutional capacities in OMICS data analysis for HPI research.
- To develop bioinformatics pipelines for SARS-CoV-2 genomics, phylodynamics, and host genetic variants.
- To address global health challenges, particularly in low- and middle-income countries (LMIC).
Main Methods:
- Organized two hackathons in 2020 and 2021 under the PHINDaccess project.
- Focused on collaborative development of bioinformatics pipelines for viral genomics and host-pathogen interactions.
- Documented preparation, proceedings, challenges, and lessons learned.
Main Results:
- Successfully initiated the development of bioinformatics pipelines for SARS-CoV-2 analysis.
- Fostered capacity building in OMICS data analysis within participating institutions.
- Identified key challenges and practical considerations for conducting hackathons in LMIC settings.
Conclusions:
- Hackathons are effective for collaborative development of bioinformatics tools for infectious disease research.
- Capacity building in bioinformatics is essential for LMIC to address global health threats.
- Experience provides valuable insights for organizing similar events in diverse settings.
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.
