Webinar: Test the Virtual Labs - Plankton Genomics

After our successful Hackathon, which welcomed more than 30 teams from all around the world, we have launched a new webinar series to invite the entire marine research community to test the Blue-Cloud Virtual Labs.

The Plankton Genomics Virtual Lab is led by the European Bioinformatics Institute (EMBL-EBI) and created by the Faculty of Sciences at Sorbonne University.

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: Exploring genetic data & identifying clusters containing unknown genes

   

  •  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: Mapping the geographic distribution of plankton functional gene clusters using habitat prediction models

   

  •  Exploration of genetic and morphological markers of plankton diversity and abundance, in particular the new ones discovered above, to predict their spatio-temporal distribution and serve as high-resolution EOVs for biological processes.

Agenda

• 11:00 - Sara Pittonet Gaiarin, Trust-IT Services, Blue-Cloud Project Coordinator - Blue-Cloud introduction - Download slides
• 11:05 - Eric Pelletier, Genoscope, CEA - Genes and functions
• 11:15 - Jean-Olivier Irisson, Laboratoire d'Océanographie de Villefranche, Sorbonne Université - Habitat modeling - Download slides
• 11:25 - Alexandre Schickele, Laboratoire d'Océanographie de Villefranche, Sorbonne Université - Plankton Genomics Virtual Lab - Download slides
• 11:45 - Q&A

Who attended

Representatives from key organisations in marine research and policy, including UNESCO, the European Commission, CNR, CNRS, OGS, ISPRA, IFREMER.

Services developed

• Identification of genetic data and clusters containing unknown genes: A service to enable the discovery of the unknown marine plankton genes (from annotation files) of the Tara Ocean expedition dataset and the building of gene clusters by similarities of sequences and larger metabolic pathways.
• Geographical map of plankton functional gene clusters' distribution: A service to map the geographical distribution of plankton functional gene clusters using habitat models, considering the previous result as input data and proposes tools. It is based on a machine learning method, to explore the relationship between the abundance of plankton genes and the environmental context.

Test the Virtual Lab