Partners | The Digital Salmon

DigiSal

The Digital Salmon will be an ensemble of mathematical descriptions of salmon physiology, combining mathematics, high-dimensional data analysis, computer science and measurement technology with genomics and experimental biology into a concerted whole.

Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges.

Spearheading this endeavour is the project DigiSal, funded by the Digital Life initiative of the Research Council of Norway.

The original vision was laid out in a January 2013 book chapter by Omholt, Gjuvsland & Vik: The Digital Salmon – Key to both More Science and More Profit. Pages 81-112 in Grue & Almås (ed.) Food from the Ocean – Norway’s Opportunities. Oslo, Norway: Novus, 2013.

 

FAIRDOM supports DigiSal in making their data and models findable, accessible, interoperable and reusable. Efficient organization among experiments, measurements, bioinformatics, statistics, and modelling is crucial for the success of the interdisciplinary systems biology approach in DigiSal. To formalize the interface between theory and experiments, models and data produced will be annotated with the same ontologies. Such labelling and cross-referencing is already in place for many -omics databases, whereas for mathematical models we are involved in the ongoing development of ontologies and standardization. A central data management platform based on The SEEK will integrate consortium data in a secure environment, with defined and documented standardised file formats to support the process of data acquisition, handling, storage and managing. The platform will be integrated with the salmon genome web resource SalmoBase, developed at NMBU as part of Elixir Norway (ESFRI project). The salmon genome was published in Nature on 18 April 2016, a crucial enabling step for the Digital Salmon.

The current data management process for Digital Salmon was presented at FAIRDOM’s first user meeting in Barcelona. You can view the presentation on the FAIRDOMHub https://fairdomhub.org/presentations/305

The DigiSal consortium is:

Host: Norwegian University of Life Sciences (systems biology, genomics, salmon gut microbiota)

Partners:

  1. Norwegian University of Science and Technology (metabolomics, systems biology)
  2. University of Bergen (regulatory annotation of salmon genome)
  3. University of Tromsø (metagenomics)
  4. Institute of marine research (gene editing)
  5. AquaGen, salmon breeding company (salmon families, genotypic & phenotypic data)
  6. Wageningen University and Research Centre, NL (metabolic reaction network modeling)
  7. University of Stirling, UK (genetics of fat metabolism in salmon)
  8. EWOS, feed producer (feed composition expertise