Skip to main content

AG2P Hackathon – Accelerating the Integration of the African Genotype–Phenotype Database

The AG2P Hackathon is an intensive, in-person, five-day collaborative workshop focused on accelerating the integration of the African Genotype–Phenotype Database (AG2P). The workshop brings together members of the three AG2P Working Groups—Data Curation, Database Development, and Genotype–Phenotype Correlations—to transform parallel project activities into an integrated and functional prototype.

The workshop will combine hands-on training, technical development, data curation and harmonization, database integration, and genotype–phenotype analytical activities. Participants will work with African clinical, phenotypic, and genomic datasets, with an initial focus on cardiovascular diseases (CVD) and cancer in addition to infectious and rare diseases. The workshop will also facilitate knowledge transfer, harmonization of workflows and documentation practices, and the development of a shared technical roadmap toward AG2P Version 1.0.

Keywords: African genomics; genotype–phenotype database; data curation; data harmonization; genomic data; phenotypic data; bioinformatics; database development; AI; machine learning; deep learning; genotype–phenotype correlations; precision medicine

Skill level of training:

Advanced

Language: English

Credential awarded: Certificate of participation / attendance

Type of training: In Person

Venue

Institut Pasteur de Tunis, Tunis, Tunisia

Date(s) of training: 12 October 2026 - 16 October 2026

Organisers:

Lyndon Zass (UCT), Sindi Lukhele (UCT), Maroua Boujemaa (IPT), Yosr Hamdi (IPT), Marwa Khediri (IPT), Rym Elfessi (IPT) and Nouha Miled (IPT)

Intended Audience:

AfriGen-D AG2P Project Members

Syllabus and Tools:

The hackathon will focus on three interconnected areas:

  • Data curation and harmonization: standardization and preparation of African clinical, phenotypic, and genomic datasets.
  • Database development and integration: validation of the AG2P schema, data mapping, ingestion, querying, and prototype testing.
  • Genotype–phenotype analysis: application and testing of AI/ML/DL approaches and variant effect prediction resources.

Prerequisites:

Participants should have a basic to intermediate understanding of at least one of the following areas: genomics/bioinformatics, clinical or phenotypic data management, database development, data science, or AI/ML. For technical sessions, familiarity with genomic datasets, structured data, databases, or computational analysis is recommended.

Learning outcomes:

  • Finalize data curation and harmonization for CVD and Cancer datasets.
  • Initiate data collection and curation of other diseases such as infectious and rare diseases.
  • Integrate curated African datasets into the AG2P database.
  • Validate and refine the database schema using real curated data.
  • Deploy and test genotype–phenotype correlation models.
  • Produce a functional integrated AG2P prototype.
  • Define a roadmap for Version 1.0, including publications and sustainability plans.

Limitations:

  • The workshop has a limited duration of five days and cannot address all disease areas and data types represented in African populations.
  • The availability and quality of datasets may vary across data sources.
  • AI/ML model development and validation will be constrained by the size, completeness, heterogeneity, and representativeness of available African datasets.

Programme:

  • Day 1 (Morning): Plenary alignment and technical onboarding for all WGs. (Afternoon): Begin first parallel breakout sessions.
  • Days 2–4 (Morning): WGs work in parallel in dedicated breakout rooms, making focused technical progress on their respective tasks.
  • Days 2–4 (Afternoon): All three WGs convene in plenary to present morning progress, address the day’s integration objectives, surface challenges, and collaboratively identify solutions.
  • Day 5 (Morning): Full cross-WG integration sprint — all groups work together on the unified prototype. (Afternoon): Demonstration, validation, roadmap definition, and closing.