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. 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

...

The aim of this investigation is to understand molecular mechanisms of PUFA biosynthesis and regulation in order to enable the sustainable use of vegetable oils in aquafeeds as current sources of fish oils are unable to meet increasing demands for omega-3 PUFAs. By generating gene knockouts, we would like to study the genes that are crucial for multi-tissue synthesis of PUFA synthesis in vivo.

By generating CRISPR-mediated elovl2 knockout, we are planning to study the crucial role of elovl2 for multi-tissue synthesis of 22:6n-3 in vivo. Endogenously synthesized PUFAs are important for transcriptional regulation of lipogenic genes in Atlantic salmon. This study demonstrates key roles of elovl2 at two penultimate steps of PUFA synthesis in vivo and suggests Srebp-1 as a main regulator of endogenous PUFA synthesis in Atlantic salmon.

Differential expression analysis (using R package edgeR) on liver gene expression between salmon with all four fads2 genes knockout, only fads2d6b & fads2d6c knockout and wildtype. All salmon was given either a low-PUFA diet or a high-PUFA diet

Total lipids are extracted from tissues of white muscle, liver and whole brain from three fish per dietary treatment.

The three different CRISPR target sites within the elovl2 gene (T1-3) were characterised by Sanger sequencing, sequencing on average 8 clones per individual.

RNAseq is utilised to validate the SnpEff annotation predictions for aberrant splicing. For this purpose the percentage exon retention for exons 4, 6 and 7 are calculated using RNAseq data.

Stranded RNAseq libraries were prepared from 1µg total RNA from liver tissue using TruSeq Stranded mRNA library preparation kit (Illumina, San Diego, USA) using double unique indices (#20022371), according to the manufacturer's instruction (Part 15031057 Rev.E). Libraries were sequenced at the Norwegian Sequencing Centre (NSC). All libraries were pooled, and the same pool was sequenced on 4 flow cell lanes on a HiSeq 3000 machine (Illumina), generating 100bp single-end reads.

RNA sequencing files

...

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files.

Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

We have adapted the definitions of terms in [ISA best practice][1] and [programmes and projects][2]:

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

...

1. Digital biotechnology

2. The value chain

3. Examples

4. Tools and funding

5. Data sharing

https://www.dnvgl.com/ocean-space/index.html

Björgólfur Hávarðsson is Innovation Manager in the NCE Seafood Innovation Cluster, Norway. He leads AquaCloud, a sea-louse forecast system that streams data from 3000 netcages to provide individually tailored precautionary recommendations to its participants. What do the participants contribute, and what do they get out? What are their motivations, and how was the collaboration organised?

Look to medicine: Computer models enter clinical practice.

The genotype x environment --> phenotype map.

The Digital Life Norway network and researcher projects.

The Digital Salmon: a library of models and data.

The merits of mathematical modelling.

Commoditizing models and data.

Goals for the workshop:

• Participants' input!

• Is there support for a Digital Salmon knowledge base?

-- Moral commitment from industry, academia, funders.

-- Some form of consortium, reponsible for next workshop.

...

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.

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.

My graduation project presentation given on 22 of June at the Hanze University of Applied Sciences Groningen in The Netherlands.

Improve project deployment by letting your team focus on code quality instead of fixes problems. Spend more time on new features and let your project progress getting tested automatically.

The first Digital Salmon industry workshop raised awareness of the Digital Salmon vision and engaged major industry players in discussions on data sharing and reuse, guidelines and best practices for private-public collaboration. The workshop was a success, and a Digital Salmon working group was formed, comprising industry, academia and funding bodies. Its first task is to develop a white paper to be presented to the industry in summer of 2020.

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

...

Abstracts and posters from DigiSal for Digital Life 2018.

Detailed programme with organizers' notes.