Systems biology informatics manager for the Digital Salmon - Ref. 15/03842

Organization
Norwegian University of Life Sciences
Job Location
1430 Ås
Norway
Salary
NOK 482800-559600 per year
Benefits

NMBU offers:

  • The national node for digital production biology within Digital Life Norway, with great opportunities for cross-disciplinary theoretical-experimental, applied research.
  • Beautiful surroundings just outside Oslo.
  • A sociable and inclusive work environment.
  • Various welfare schemes.
Job Description

Job Description *

The Department of Animal and Aquacultural Sciences seeks a bioinformatician with skills in ontological annotation, semantic interoperability and knowledge management (Researcher, 3 years with possibility of extension). The successful candidate will be central in establishing a knowledge base for the systems biology of farmed salmon, and will work within the Centre for Integrative Genetics (CIGENE).

Research project

The project “Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture (DigiSal)” is part of Digital Life Norway, the first call dedicated to systems biology by the Research Council of Norway. Effective management of data and model resources is key in this endeavour, and DigiSal will initiate The Digital Salmon: a knowledge base of salmon genetics and physiology, interfacing closely with complementary databases, repositories, and research infrastructures such as ELIXIR. It will eventually encompass a coherent digital and mathematical representation of the salmon body, which can be adjusted to represent individuals with different genetic make-ups, populations, disease states, feeding regimes, or other scenarios of interest. A separate, but related part of the salmon knowledge base will address the metagenomics of the microbiota of the salmon gut. The use of standard formats and ontological annotation enables new knowledge to automatically connect to that which already exists, aiding discoverability and reuse of knowledge. This knowledge base will enable aquaculture industry to quickly address emerging challenges, quickly reanalysing existing data and identifying knowledge gaps to rapidly acquire required new data.

Main tasks

The successful applicant will help design the architecture of the Digital Salmon knowledge base, in close interaction with the researchers that will contribute to and benefit from the knowledge base, and with partners that provide technical solutions. The latter include FAIRDOM, who provide the SEEK commons as part of their knowledge management platform (http://fairdomhub.org), and will work with the DigiSal team to assist with adaptations required to support DigiSal Project; the ELIXIR node at NMBU, with focuses primarily on the salmon genome; the ELIXIR node for marine metagenomics in Tromsø; and the Digital Life Norway network. Users include bioinformaticians and wet-lab researchers who generate various omics data and microscopy images, and systems biologists who develop physiological models, in particular constraint-based models of salmon metabolism.

 

Further tasks include:

  • Training project participants in use of The SEEK for a) extracting and analyzing information and b) entering new information
  • Annotating resources for semantic interoperability: a) resources generated in DigiSal b) from literature etc
  • Assisting researchers in establishing best practice structuring of data using community standards.
Requirements

Academic qualifications

Minimum requirements

  • PhD in relevant field of informatics, bioinformatics or systems biology.
  • Experience with semantic web standard technologies (e.g. RDF, OWL, SPARQL).
  • Experience with semantic annotation.
  • Familiarity with knowledge management in cross-disciplinary biology research projects.

Additional preferred requirements

  • Familiarity with relevant European research infrastructures and data or model repositories.
  • Basic understanding of mathematical modelling in biology.
  • Experience in web development.
  • Experience in software development.

 

Desired personal qualities

The systems biology informatics manager will be central in integrating data and models to facilitate transdisciplinary research for salmon production. Thus, the following personal characteristics are important:

  • Excellent ability to synthesize information: Collect user requirements, prioritize them, and propose practical solutions.
  • Excellent English skills
  • Ability to communicate well with biological researchers to identify users’ needs and promote effective use of the SEEK system.
  • Willingness to spend shorter stays at collaborating institutions
  • Ability for independent work displaying initiative, creative and careful thought
How to Apply

Email enquiries welcome: Jon Olav Vik, [email protected]

Full announcement with link to application form: http://tinyurl.com/digisal-informatics-manager

Please note that it's okay to upload a CV as a pdf attachment, saving the hassle of entering the information piecemeal into the electronic application system.

About Our Organization

The Norwegian University of Life Sciences (NMBU) has 1700 employees and 5100 students, and is currently located on two campuses – Ås, about 30 km south of Oslo, and Adamstuen in Oslo. NMBU does basic and applied research addressing global challenges regarding energy and climate change, the environment, health, food safety, technology and renewable solutions, use and conservation of land and natural resources, and development of the bio-economy.

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