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:
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 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.
The plankton genomics demonstrator will consist of two Jupyter Notebook with R packages that allow users to
Obtain lists of unknown taxonomies and functions,
Correlate these unknowns with environmental parameters,
Model the biogeography of unknowns using environmental climatologies from Copernicus,
The "Plankton Genomics: Multidisciplinary data mining to assess plankton distributions" webinar took place on 23 April 2021. It welcomed more than 70 participants and gave the opportunity to learn more about the Blue-Cloud Plankton Genomics demonstrator.
Read the highlights and watch the webinar recording!
The second interview in our series with representatives of Blue-Cloud data infrastructures is with Guy Cochrane from EMBL-EBI. Let's discover how the European Nucleotide Archive is contributing to Blue-Cloud's activities.
The first interview with a representative of data infrastructures involved in Blue-Cloud saw Jean-Olivier Irisson from Sorbonne Université offer an overview of the fascinating world of EcoTaxa, a web application dedicated to the visual exploration and the taxonomic annotation of images showcasing planktonic biodiversity.
Get to know the Blue-Cloud demonstrator “Plankton Genomics” led by EMBL-EBI, in collaboration with VLIZ and the Faculty of Sciences at Sorbonne University. How will it change the landscape for this area of marine research?