23 Apr 2021

Plankton Genomics: Multidisciplinary data mining to assess plankton distributions

With this webinar, we are concluding the series of introductions to the five Blue-Cloud real-life demonstrators. Experts from the partners involved will provide the most relevant details about the technical and conceptual issues that are being tackled thanks to the Blue-Cloud framework.

We are introducing "Plankton Genomics" on 23 April 2021 at 14:00 CEST, the demonstrator led by the European Bioinformatics Institute (EMBL-EBI) and created by the Faculty of Sciences at Sorbonne University, with contributions from Flanders Marine Institute (VLIZ). Data from leading infrastructures such as the European Nucleotide Archive (ENA) and EcoTaxa is employed in this demonstrator.

The aim of the plankton genomic demonstrator is to showcase a deep assessment of plankton distributions by mining data across biomolecular, imaging and environmental domains. It will draw on the outputs of initiatives such as Tara Oceans and will focus on two key objectives:

  • Notebook 1 - Species and functions discovery:
    • Discovery of as yet undescribed biodiversity from genetic and morphological signals from the characterisation of their geographical distributions, co-occurrences/exclusions and correlation with environmental contexts.
  • Notebook 2 - Biodiversity and ecology:
    • Exploration of genetic and morphological markers of plankton diversity and abundance, in particular the new ones discovered above, to predict their spatiotemporal distribution and serve as high-resolution EOVs for biological processes.

Discover the Plankton Genomics demonstrator


Draft Agenda

  • 14:00 - Introduction, Blue-Cloud vision and mission by Sara Pittonet Gaiarin (Trust-IT Services)
  • 14:05 - Introduction to the Plankton genomics demonstrator - Tara Oceans and the use its data in the Blue Cloud by Stéphane Pesant (EMBL-EBI)
  • 14:10 - 1st Notebook - Discovery of known and unknown genetic entities by Pavla Debeljak (Sorbonne Université)
  • 14:35 - 2nd Notebook - Next steps: extrapolation to unsampled parts of the ocean by Jean-Olivier Irisson (Sorbonne Université)
  • 14:45 - Questions & Answers


Sara Pittonet Gaiarin (Trust-IT Services), Senior Project Manager and Coordinator of the Blue-Cloud initiative

Pavla Debeljak (Sorbonne Université) is a postdoctoral researcher at the Muséum d’Histoire Naturelle, Paris. She holds Master’s degrees in Ecology and Science & Technology Studies from the University of Vienna, Austria and a Ph.D in Environmental Science from Sorbonne Université, France. In the Blue-Cloud project she contributes to the first part of the plankton genomics demonstrator, identifying “bona fide” functional and taxonomical unknowns in the Tara Oceans planktonic dataset. Her scientific background spans both academia and industry in the fields of microbial ecology. Her research interests include the deep ocean, carbon cycling, microplastics and the Southern Ocean.

Jean-Olivier Irisson (Sorbonne Université) is a computational ecologist who uses machine learning methods to study the dynamics and distribution of plankton in the world's ocean. He coordinates the participation of Sorbonne Université in the Blue Cloud project. He is particularly involved in the integration of the EcoTaxa plankton imaging platform into the Blue Cloud. He contributes to the second part of the plankton genomics demonstrator, that will use the unknown but coherent genetic entities extracted from the Tara Oceans dataset and map their potential distribution at global scale, to guide further research and help understanding their role.

Stéphane Pesant (European Molecular Biology Laboratory) is a senior curator for marine biological data at the European Bioinformatics Institute in Cambridge, UK. He holds a PhD in oceanography at Laval University (Québec, Canada) and trained as science-policy advisor at Fisheries & Oceans Canada. His scientific background is in plankton ecology, primary production and carbon fluxes, and he has extensive field work experience at sea, notably in the Arctic and Southern Ocean, and globally as part of expeditions on board the research sailboat Tara. Over the last decade, he lead open science and data integration activities for several European networks of excellence, research projects and data infrastructures. In the Blue-Cloud project he contributes to the coordination of plankton genomics demonstrator and data services from European research infrastructures Elixir and EuroBioImaging.

Event Type: 
Blue-Cloud Event