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. 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.
Web page: http://tinyurl.com/digisalFunding details:
The foundations for the Digital Salmon knowledge base will be laid by the DigiSal project, Research Council of Norway (RCN) grant number 248792. It is part of Digital Life, the RCN's large-scale programme dedicated to systems biology.
- People (37)
- Projects (3)
- Institutions (6)
- Investigations (0+8)
- Studies (0+14)
- Assays (0+37)
- Data files (3+55)
- Models (0+2)
- SOPs (0+11)
- Publications (6)
- Presentations (2+15)
- Events (0+3)
I am the Data and Model Manager for the Digital Salmon and the GenoSysFat projects. We are building a knowledge base of salmon physiology in the form of mathematical models interlinked with omics data, for applications in aquaculture, ecology and management. My duties entail managing and standardizing the data formats, protocols, and annotations generated related to these data; serving as our point of contact with the FAIRDOM initiative for findable, accessible, interoperable and reusable data,
Software Engineer and Architect working within the FAIRDOM team.
Leading the development of SEEK and RightField.
Institutions: University of Wageningen
Assistant professor at Wageningen University & Research
Institutions: Norwegian University of Life Sciences
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
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
Salmon farmed on modern feeds contains less of the healthy, long-chain fatty acids (EPA and DHA) than before. Up until the turn of the millennium, farmed salmon were fed fish oil as a replacement for their omega-3 rich natural prey. However, fish oil is now a scarce resource, and more than half of the fat in modern feeds comes from plant oils that are inexpensive, but devoid of long-chain omega-3 fatty acids. How can we increase the omega-3 content of salmon on sustainable feeds?
One option is
This is a sandbox where DigiSal members can learn to use the SEEK.
Tutorial document: http://tinyurl.com/seek-ds17
The SEEK is a web interface to a database of research "assets" organised in a hierarchical "ISA structure" (investigation-study-assay) .
These are further organised into projects and programmes.
* Programme = Overarching research theme (The Digital Salmon)
* Project = Research grant (DigiSal, GenoSysFat)
* Investigation = a particular biological process, phenomenon or thing
Combined taxonomy table of abundance of OTUs (Operational Taxonomy Units) in both freshwater and saltwater samples from 16S V3-V4 Illumina sequencing of gut microbiota. Primers used for sequencing are given in https://fairdomhub.org/sops/270
The OTUs are presented in number of counts per sample (n=349). Each row represent one sample.
Contributor: Inga Leena Angell
Author: Edgar R. C.
Date Published: 18th Aug 2013
Journal: Nat Methods
PubMed ID: 23955772
Citation: Nat Methods. 2013 Oct;10(10):996-8. doi: 10.1038/nmeth.2604. Epub 2013 Aug 18.
Author: Edgar R. C.
Date Published: 12th Aug 2010
PubMed ID: 20709691
Citation: Bioinformatics. 2010 Oct 1;26(19):2460-1. doi: 10.1093/bioinformatics/btq461. Epub 2010 Aug 12.
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.
Author: Bekaert M.
Date Published: 14th Nov 2012
Journal: PLoS One
PubMed ID: 23166792
Citation: PLoS One. 2012;7(11):e49903. doi: 10.1371/journal.pone.0049903. Epub 2012 Nov 14.