Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture (DigiSal)
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. Project DigiSal will lay the foundations for a Digital Salmon: 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.
DigiSal will focus on challenges of novel feedstuffs, collaborating with the Foods of Norway centre for research-based innovation at NBMU. Salmon are carnivores but today aquaculture provides more than half their fat and protein from plants, challenging the metabolic system and affecting fish health and nutritional value of salmon meat. The newly sequenced salmon genome and related resources will enable a tightly integrated theoretical-experimental study of mechanistic interactions among genetic and feed factors.
Project objective: Establish a systems biology framework for adapting salmon breeding and nutrition strategies to modern feedstuffs, blazing the trail for a Digital Salmon endeavour.
• Provide and validate a framework for a model-based account of genetic and environmental variation in salmon metabolism
• Unravelling the systemic role of gut microbiota in adapting to new feeds
• Provide and validate a theoretical framework for systematic identification of targets for steering EPA/DHA metabolism through concerted use of nutrition and genetics
• Provide the foundation for a Digital Salmon knowledge base enabling adaption of a transformative pre-emptive research and development strategy
DigiSal is part of the Digital Life project by the BIOTEK2021 biotechnology programme of the Research Council of Norway.
- People (37)
- Institutions (6)
- Investigations (0+7)
- Studies (0+9)
- Assays (0+33)
- Data files (0+48)
- SOPs (1+14)
- Publications (4)
- Presentations (4+18)
- Organisms (3)
- Events (2+1)
Software Engineer and Architect working within the FAIRDOM team.
Leading the development of SEEK and RightField.
Institutions: Wageningen University & Researchorcid.org/0000-0001-5845-146X
Assistant professor at Wageningen University & Research
Institutions: Norwegian University of Life Sciencesorcid.org/0000-0002-7778-4515
Systems biology for salmon farming is what I do. I lead the DigiSal project (http://tinyurl.com/digisal), whose full title is "Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture". DigiSal is part of Digital Life, the first call dedicated to systems biology by the Research Council of Norway. I'm also one of the lead modellers in GenoSysFat (http://tinyurl.com/genosysfat), working to improve the omega-3 content of salmon farmed on sustainable feeds by
Expertise: yeast, fungi, Metabolomics, Proteomics, Stoichiometric modelling, carbon metabolism, Systems Biology, dynamics and control of biological networks, coupling metabolome and environome, rapid sampling experiments, Biochemistry
Tools: parameter estimation, ODE, HPLC, GC and LC/MS analysis of metabolites, Mass spectrometry (LC-MS/MS), continuous cultivation, Enzyme assay, Material balance based modeling, stimulus response experiments, Chromatography, Fermentation, Matlab, Metabolomics, Biochemistry and protein analysis
I've become a SysMO DB PAL for MOSES project in 2007 being a post-doc in lab of Prof. Matthias Reuss at University of Stuttgart. In the MOSES project, our major efforts were in the experimental data acquisition for dynamic model of primary carbon and anaerobic energy metabolism in yeast. The model implements prediction of perturbations of two types: glucose pulse and temperature jump. We implement “stimulus-response” methodology for the unraveling the dynamic structure of the network and to
We have adapted the definitions of terms in [ISA best practice] and [programmes and projects]:
Programme = Overarching research theme (The Digital Salmon)
Project = Research grant (DigiSal, GenoSysFat)
Investigation = a particular biological process, phenomenon or thing
(typically corresponds to [plans for] one or more closely related papers)
Study = experiment whose design reflects a specific biological research question
Assay = standardized measurement or diagnostic experiment using a
Contributor: Jon Olav Vik
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Date Published: No date defined
Journal: Mol Ecol
PubMed ID: 29431879
Citation: Mol Ecol. 2018 Feb 12. doi: 10.1111/mec.14533.
Authors: Torgeir R. Hvidsten, Fabian Grammes, Arne Gjuvsland, Lien S.,Koop B. F.,Sandve S. R.,Miller J. R.,Kent M. P.,Nome T.,Leong J. S.,Minkley D. R.,Zimin A.,Grove H.,Walenz B.,Hermansen R. A.,von Schalburg K.,Rondeau E. B.,Di Genova A.,Samy J. K.,Olav Vik J.,Vigeland M. D.,Caler L.,Grimholt U.,Jentoft S.,Inge Vage D.,de Jong P.,Moen T.,Baranski M.,Palti Y.,Smith D. R.,Yorke J. A.,Nederbragt A. J.,Tooming-Klunderud A.,Jakobsen K. S.,Jiang X.,Fan D.,Hu Y.,Liberles D. A.,Vidal R.,Iturra P.,Jones S. J.,Jonassen I.,Maass A.,Omholt S. W.,Davidson W. S.
Date Published: 18th Apr 2016
PubMed ID: 27088604
Citation: Nature. 2016 Apr 18;533(7602):200-5. doi: 10.1038/nature17164.
Author: Brazma A.,Hingamp P.,Quackenbush J.,Sherlock G.,Spellman P.,Stoeckert C.,Aach J.,Ansorge W.,Ball C. A.,Causton H. C.,Gaasterland T.,Glenisson P.,Holstege F. C.,Kim I. F.,Markowitz V.,Matese J. C.,Parkinson H.,Robinson A.,Sarkans U.,Schulze-Kremer S.,Stewart J.,Taylor R.,Vilo J.,Vingron M.
Date Published: 1st Dec 2001
Journal: Nat Genet
PubMed ID: 11726920
Citation: Nat Genet. 2001 Dec;29(4):365-71.
Author: Caporaso J. G.,Kuczynski J.,Stombaugh J.,Bittinger K.,Bushman F. D.,Costello E. K.,Fierer N.,Pena A. G.,Goodrich J. K.,Gordon J. I.,Huttley G. A.,Kelley S. T.,Knights D.,Koenig J. E.,Ley R. E.,Lozupone C. A.,McDonald D.,Muegge B. D.,Pirrung M.,Reeder J.,Sevinsky J. R.,Turnbaugh P. J.,Walters W. A.,Widmann J.,Yatsunenko T.,Zaneveld J.,Knight R.
Date Published: 11th Apr 2010
Journal: Nat Methods
PubMed ID: 20383131
Citation: Nat Methods. 2010 May;7(5):335-6. doi: 10.1038/nmeth.f.303. Epub 2010 Apr 11.
How do you communicate a complex research endeavour in simple words and pictures using only two minutes? In my case that turned out to be scientifically impossible, but we managed to shave it down to three. This poster shows and tells how we went about it.
Creator: Jon Olav Vik
Contributor: Jon Olav Vik
Three-minute presentation of the Digital Salmon research programme. Explains the societal challenge of sustainable fish feed, how systems biology helps speed up the search for better solutions, and the grand aim to build a library of mathematical models of salmon physiology linked to omics data.
Creators: Jon Olav Vik, Tor Martin Austad, Kristine Løwe
Contributor: Jon Olav Vik
Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/8022
Synonyms: Parasalmo mykiss, Oncorhynchus nerka mykiss, Salmo mykiss
Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/8030
Abstracts and posters from DigiSal for Digital Life 2018.
Start Date: 20th Mar 2018
End Date: 21st Mar 2018
Event Website: https://digitallifenorway.org/arrangementer/digitallife-2018
Our 2018 DigiSal project meeting is held as a satellite meeting of Digital Life 2018 (https://digitallifenorway.org/arrangementer/digitallife-2018).
Most of DS18 will be spent on breakout sessions to work on upcoming publications. Task leaders will prepare:
* Abstracts to DLN18. (Deadline was 15 Feb.) Presenting DigiSal progress here rather than at DS18 frees up time for the paper preparation sessions.
* Identify two papers in preparation, which will be worked on at DS18: Title, first and
Start Date: 21st Mar 2018
End Date: 22nd Mar 2018
Event Website: Not specified