Yang Jin

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) [1]. 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 ...

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

This is the fatty acid profile data from the freshwater portion of the feed switch trial. eg: D0_MA_M_6 (Day 0, MA- Marine oil, L-liver, fish number 6)

Fatty acid Systematic Name C14:0 Myristic acid myristin-syre C16:0 Palmitic acid palmitin-syre C16:1n7 Palmitoleic palmitolein-syre C17:0 C17:1 C18:0 stearic acid stearin-syre 18:1n9c oleic acid olje-syre C18:2n6c linoleic acid linolsyre C20:1 eicosenoic acid C18:3n3 linolenic acid linolensyre C20:2 eicosadienoic C22:1 cetoleic acid cetolein-syre ...

This is the fatty acid profile data from the seawater portion of the feed switch trial. eg: D0_MA_M_6 (Day 0, MA- Marine oil, Muscle, fish number 6)

Fatty acid Systematic Name C14:0 Myristic acid myristin-syre C16:0 Palmitic acid palmitin-syre C16:1n7 Palmitoleic palmitolein-syre C17:0 C17:1 C18:0 stearic acid stearin-syre 18:1n9c oleic acid olje-syre C18:2n6c linoleic acid linolsyre C20:1 eicosenoic acid C18:3n3 linolenic acid linolensyre C20:2 eicosadienoic C22:1 cetoleic acid cetolein-syre ...

A file which combine previous metabolomics samples ID to new sample ID file (https://fairdomhub.org/data_files/1330)

Information for salmon genes, including transcript length used for calculating transcrip per million (TPM) value

A list of interesting lipid genes

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

Atlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and rearing conditions for growth and feed efficiency. Marine feed ingredients must be replaced to meet global demand, with challenges for fish health and sustainability. Metabolic models can address this by connecting genomes to metabolism, which converts nutrients in the feed to energy and biomass, but such models are currently not available for major aquaculture species ...