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 understanding the interplay between nutrition and genetics ("feeding and breeding").
My broad background in quantitative biology ranges from ecology to climate effects to cardiac modelling. For five years I worked on causally cohesive genotype-phenotype modelling and the analysis and comparison of virtual physiology models. I have also worked within the Infrastructure for Systems Biology Europe (ISBE), laying the foundations for "modelling as a service" to academia and industry.
GenoSysFat (Norwegian University of Life Sciences) ; DigiSal (Norwegian University of Life Sciences) ; FAIRDOM user meeting (Norwegian University of Life Sciences) ; SEEK tutorial for DigiSal (Norwegian University of Life Sciences) ; Systems toxicology of Atlantic cod (Norwegian University of Life Sciences)
- Projects (5)
- Institutions (1)
- Investigations (0+7)
- Studies (0+10)
- Assays (0+35)
- Data files (3+52)
- Models (0+2)
- SOPs (1+7)
- Publications (5)
- Presentations (3+6)
- Events (2+3)
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
Good data and model management improves the longevity and impact of your interdisciplinary research. FAIRDOM offers software and expertise to support you in better managing your interdisciplinary life-science projects, particularly in systems and synthetic biology. If you have never heard of data and model management, or are curious about it, or you are an expert keen to exchange ideas, our user meeting is the place for you!
At the meeting you will:
- Learn why data and model management is
Organisms: Homo sapiens
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
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
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. Raw data are available in the Sequence Read Archive database under accession number SRP119730 (https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP119730).
Investigations: 1 hidden item
Studies: 1 hidden item
Assays: 1 hidden item
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.
Date Published: 15th Jan 2018
Journal: Appl Environ Microbiol
Citation: Appl Environ Microbiol 84(2) : e01974-17
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.
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
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