Plankton Genomics Virtual Lab
Led by the European Bioinformatics Institute and created by the Faculty of Sciences at Sorbonne University, with contribution from Flanders Marine Institute.
Plankton Genomics
The demonstrator “Plankton Genomics” is led by the European Bioinformatics Institute (EMBL-EBI) and created by the Faculty of Sciences at Sorbonne University, with contribution from Flanders Marine Institute (VLIZ).
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:
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.
The initial users of the plankton genomics demonstrator are, primarily, scientific researchers, including taxonomists, computational ecologists and bioinformaticians with extensive knowledge of the data collected during the Tara Oceans Expedition. In the short term, we expect an important uptake of the demonstrator by European initiatives such as the H2020 Blue Growth project AtlantECO, the Ocean Sampling Day initiative, and the Marine Genomic Observatories in close collaboration with EMBRC and ASSEMBLE Plus.
The end-users include a broad base of scientists in quest of the identification of unknown sequences in the oceanic environment, and also interested, for example in plankton biogeography, marine biogeochemistry, ecosystem health, and climate science.
Services
The plankton genomics demonstrator will consist of two Jupyter Notebook with R packages that allow users to
