One Ocean, One Health: Multi-Omics Hackathon

Summary

The Hackathon will address simple, but challenging questions using a combination, or a comparison of environmental genomics, proteomics, metabolomics and phenomics (imaging) data from Mission Microbiomes AtlantECO. 

The Hackathon will consist of a series of online, self-paced learning modules about

1. the nature, potential and limitation of omics data;
2. accessing omics data programmatically; and
3. novel analysis approaches to combine and/or compare multi-omics data.   

Participants will meet in person for 5 days in the Azores (8-12 September) to work in small teams and hack the data and rise to the challenge.

Participants are strongly encouraged to join the AtlantECO Final Scientific Conference the following week in the Azores (15-19 September 2025) in order to present the Hackathon results.

The Hackathon is a good complement to AtlantECO’s Synergy Summer School on Complexity and emergence in marine ecosystems/seascape: theory, mechanisms and data, which takes place in Italy (June 30 - July 4 2025). The Summer School is not a prerequisite to the Hackathon, but you are encouraged to participate in both events.

Academic Mentors

• Genomics: Dr. Lois Maignien, Université de Bretagne Occidentale (UBO), France 
• Proteomics: Dr. Mak Saito, Woods Hole Oceanographic Institution (WHOI), USA
• Metabolomics: Dr. Georg Pohnert, Friedrich Schiller University Jena (FSU), Germany
• Phenomics (imaging): (TBC)
• Complex systems approach: Dr. Ferenc Jordan, Keynote Research Korlatolt Felelossegu Tarsasag (KNR), Hungary 
• Network analysis: Dr. Samuel Chaffron, Centre national de la recherche scientifique (CNRS), France

Data infrastructure Mentors

• Provenance metadata: Dr. Stéphane Pesant, European Bioinformatics Institute (EMBL-EBI), UK
• Genomics: ENA / MGnify trainer (tbc), European Bioinformatics Institute (EMBL-EBI), UK
• Proteomics: PRIDE trainer (tbc), European Bioinformatics Institute (EMBL-EBI), UK
• Metabolomics: Metabolights trainer (tbc), European Bioinformatics Institute (EMBL-EBI), UK
• Phenomics (imaging): BioImageArchive trainer (tbc), European Bioinformatics Institute (EMBL-EBI), UK
• Environmental context: Copernicus (tbc)

Draft Programme

Online (self paced) phase (June/August 2025)

• Module 1. The nature of ‘omics data
  • Background reading/recorded material x4 ‘omics data types
  • Recorded presentation (min 15 min) x4 ‘omics data types
  • Quiz
• Module 2. The power and limitations of ‘omics data
  • Background reading/recorded material x4 ‘omics data types
  • Recorded presentation (min 15 min) x4 ‘omics data types
  • Quiz
• Module 3. Accessing ‘omics data
  • Background reading/recorded material x4 ‘omics data types + environmental data + metadata
  • Recorded presentation (min 15 min) x4 ‘omics data types + environmental data + metadata
  • Quiz
• Module 4. Complex systems approaches and network analysis
  • Background reading/recorded material x3
  • Recorded presentation (min 15 min) x3
  • Quiz

Onsite Hackathon (8-12 September)

General programme of the in-person hackathon:

1. Monday (pm): Flash presentations by participants & discussion on the hackathon "challenges"
2. Tuesday (am)(pm): Teamwork, mentoring clinics & end-of-day debrief of progress
3. Wednesday (am)(pm): Teamwork, mentoring clinics & end-of-day debrief of progress
4. Thursday (am)(pm): Teamwork (work on presentation/pitch), presentation clinic & end-of-day presentation of pitches
5. Friday (am)(pm): Teamwork (finalising analyses & presentation/pitch)

The morning sessions are from 9:00 to 12h30. The afternoon sessions are from 14h00 to 18h00.