Author Archives: community

Position available with Digital Salmon: Two researcher/postdoctoral positions – systems biology modelling (NMBU, Ås, Norway)

Application deadline: Saturday 2018-12-15.

Email enquiries welcome: Jon Olav Vik,  

The Norwegian University of Life Sciences has two vacant researcher or postdoc positions (up to two years) in systems biology of Atlantic salmon metabolism. These are part of the Digital Salmon, a transdisciplinary project using experimental omics data on metabolic reaction networks. Ideal for modellers seeking challenges and exposure to a world-class environment in integrative genetics and systems biology.

The Digital Salmon (2016-2020, 4 M€) is the national flagship project in digital production biology and part of the national consortium for biotechnology, Digital Life Norway. Its objective is to establish a systems biology framework for adapting salmon breeding and nutrition strategies to modern feedstuffs. The long-term goal is to accumulate a library of various models of life processes in the salmon body, to quickly construct suit-tailored computer simulations to compute effective use of resources, for food security, fish welfare and human health. Such a knowledge base will enable faster response to challenges such as climate change, diseases, or scarcity of feedstuffs.

Main tasks:

  • Develop and validate genome-scale and tissue-specific metabolic reconstructions for salmon

  • Use these models to interpret multi-omics data from experiments on omega-3 metabolism under fish- vs plant-based feed, freshwater vs seawater, and more.

  • Develop a test suite of metabolic function for automatic quality control, documentation and benchmarking of our models.

Three-minuted animated film about the project:

Full advertisement and online application form:

Application deadline: Saturday 2018-12-15. Email enquiries welcome: Jon Olav Vik,

A new version of SEEK is now available, version 1.7.0

A new version of SEEK is now available, version 1.7.0. Full details can
be found at

Highlights include

– Programme wide sharing permissions
Researchers can now apply the fine-grained sharing permissions of assets in SEEK to share with whole programmes. This offers our researchers further support in making data “as open as possible, as closed as necessary”.

– ISA graph improvements
The ISA graph has been modified to provide better visuals for larger ISA structures. In addition we also offer a list-style view of the ISA structure for those wanting to navigate their assets with a more traditional view. You can find screen shots, and further information in our documentation

– Changes to Sample Type visibility
A Sample Type now only become visible outside of a Project if it has public samples associated. This change has allowed us to open up Sample Type creation to all members of projects, where previously only project administrators were able to create sample types.

– Special support for for NCBI sample attribute types
Users can now select NCBI IDs as a special sample attribute. This allows automatic linking with Organisms registered in SEEK. This is part of our ongoing work to replace SEEK strains with a dedicated Sample Type.

– Linking Documents to Events, and vice versa.

There has also been quite a bit of back-end maintenance and tidying up.

The guide to upgrade is available at Note that with this
version Ruby 2.4 is required, using 2.2 or 2.3 will result in errors.

The fairdom/seek:1.7 docker image is also available, and upgrading for
Docker Compose can be found at the end of

We Are Providing Data Management Support for the Second ERACoBioTech Call.

FAIRDOM currently supports more than half of the projects from the first ERACoBioTech Call in their data management. We are offering our support services for the second  ERA CoBioTech call. We can work with you to draft your data management plan, and then provide software, training, and support throughout your project. We will be holding webinars on the following dates.

Webinar Dates and Times for Second ERACoBioTech Call

Monday 29th October 2018: 13:00 GMT / 14:00 CET
Wednesday 7th November 2018: 14:00 GMT / 15:00 CET
Tuesday 13th November 2018: 11:00 GMT / 12:00 CET

To register, please fill in the google form: Webinar Registration

For more information please visit:

Updates to the FAIRDOM software (SEEK v1.6.0)

A new version of SEEK is now available, and the FAIRDOMHub has been updated with the changes. 

Version 1.6.0

Release date: June 8th 2018

Integration with NeLS

We’ve been working with ELIXIR Norway to facilitate linking of SEEK with the ELIXIR Norwegian e-Infrastructure for Life Sciences (NeLS). This interlinking allows Norwegian life scientists the ability to store and compute Bioinformatics data in the NeLS portal, then link and share this data directly in SEEK. This is a leap forward for Norwegian life scientists in ensuring their data is FAIR.


Our JSON API can now support researchers in reading data from SEEK, as well as writing and submitting new entries. This allows all users programmatic access to data published in SEEK, as well as for publishing in SEEK. The current write support covers Datafiles, SOPs, Models, Investigation, Studies and Assays and linking them together. More details about the api can be found in the API Guide. The API will facilitate researchers in embedding SEEK within their day to day data workflows, ensuring better adherance to the FAIR principles.

Data Upload Workflow and Metadata Wizard

We’ve made some changes to the upload workflow that you will encounter when uploading DataFiles, and developed integrated support for templates that have RightField embedded metadata. Now, the dataFile is registered before additional metadata details are asked for. This allows any relevant metadata in the RightField tab of the DataFile to be read, extracted, and used to auto-populate the upload form where possible. The supported templates are now provided as part of the templates generated for Sample Types, but will soon be available more widely.

The Wizard for uploading DataFile metadata has also undergone a revamp, with it now being split into logical steps that can easily be stepped through.

You can find out more details here



Creating Assays from the DataFile

Ever got stuck when uploading a DataFile and wanting to link it to an Assay, but realising you haven’t created the Assay you want to link it to? Well, now Assays can be created and linked to the DataFile being submitted as part of the same process. This can either be manual or from the details provided within a template.

New Document Asset Type

Have you ever wanted to upload a deliverable, report, meeting minutes or other project management document in SEEK, but not felt there was a suitable asset type? We have now created support for a new Document asset type. This allows you to catalogue general documents that do not fit as other asset types.

Terms and Conditions

When you install and manage your own SEEK, it is important you are also able to provide your users with information about theTerms and Conditions that must be accepted as part of the registration process. This is now configurable by Admin of the SEEK installation.

Simplified DOI creation

We have simplified the interface for creating DOI’s for individual items. It is now clearer when looking at an individual item how to mint a DOI for that item.

There have also been many other bug fixes and small improvements. A full list of changes included in this release can be found in the SEEK Change Log.

Making FAIR data management easier for Norwegian life science researchers.

The new versions of the FAIRDOM/SEEK platform and the ELIXIR Norwegian e-Infrastructure for Life Sciences (NeLS) are now linked. This will provide SEEK and NeLS users with unprecedented opportunities for storing, sharing, and archiving of data in ways that comply with the FAIR principles.

FAIRDOM is committed to ensuring that FAIR data management is simple, practical, and fits in with researchers day-to-day work. As part of this we work with the community in ensuring that key platforms for our partners can integrate smoothly with our data management platforms.

After working closely with our Norwegian Digital Life partners, the new releases of SEEK and NeLS now integrate with each other. This allows access to Norwegian infrastructure for storage, computing and archiving of research data as well as a rich toolbox for FAIR project data management. NeLS supports Norwegian life science researchers in executing Bioinformatics analysis on their data. Using SEEK with NeLS, data or analysis generated within projects can easily be shared among the project participants and made accessible when they are ready for publication.

If you are interested in working with FAIRDOM to integrate with your local or national resources, you can contact us here:

The integration work of NeLS and SEEK has been funded by the Centre for Digital Life Norway and has been performed in collaboration with ELIXIR Norway and FAIRDOM partners at the University of Manchester. Several Digital Life projects have participated in testing of the new versions.

Digital Life Norway have written a blog post that goes into some more detail:

Useful links:




Job Posting: Senior Advisor (2.5 yr) in Data Management for the Digital Salmon

Join our Norwegian partners as a Data Manager. Working with colleagues accross Norway, with continued support from the FAIRDOM Team and network. Would suit an early career data manager making their first steps, or a more experienced scientist transitioning into support a role.

Senior Advisor (2.5 yr) in Data Management for the Digital Salmon – 18/03082

Required qualifications: PhD or MSc in relevant field of bioinformatics, systems biology, informatics, librarianship, or similar.

The Data Manager will be associated with the project “Towards the Digital Salmon: from a reactive to a pre-emptive research strategy in aquaculture (DigiSal)“. The project is part of the national consortium for biotechnology, Centre for Digital Life Norway, and a partner in the FAIRDOM foundation for scientific data management according to the FAIR principles: Findable, Accessible, Interoperable, Reusable. Main tasks:
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. Users include bioinformaticians and wet-lab researchers who generate omics data and microscopy images, and systems biologists who develop physiological models e.g. of salmon metabolism.
Be our contact point with the FAIRDOM consortium, benefitting from community support and training in cutting-edge tools and workflows, and contributing to FAIRDOM’s future development.
Be involved on the national level in Digital Life Norway’s development of data and model management.

Join us at “FAIR Data Management in Life-Sciences” a workshop and user meeting in Lyon France, Sat 27th Oct.

We are hosting a workshop and user meeting entitled “FAIR Data Management in Life-Sciences”, as a satellite of this year’s ICSB 2018, in Lyon, France ( To register, please fill in the google form below (or follow this link directly to the form, which also provides some additional information about the workshop and user meeting. If you can not view the google form, or do not wish to register your details using a google form, please mail and one of the team will collect your registration data via email or phone.

ELIXIR Webinar on the Systems Biology Implementation Study

Representatives from ELIXIR France will present the outcomes from the Systems Biology Implementation Study to define the requirements for a European bioinformatics resource for microbial metabolism as well as providing a practical demonstration of how existing funded resources from ELIXIR partners could be integrated to meet those needs.

The webinar will take place on Wendesday 13 June 2018 at 14.00 BST (to be confirmed!).

For more information please visit:

CORBEL launches 2nd Open Call for research projects!

The CORBEL Open Call invites researchers to apply to access technologies and services from more than 20 facilities from 10 different research infrastructures across Europe. Selected projects will gain unprecedented opportunities to utilise a wide range of high-end technologies and services. These include state-of-the-art offers from the fields of advanced imaging, biobanking, clinical and translational research, curated databases, marine model organisms, mouse mutant phenotyping, high-throughput screening, structural biology as well as systems biology.

Costs for travel to partner sites will be reimbursed by CORBEL and access to service providers will be granted without access fee (extra costs for consumables may apply). Projects will be supported at every stage, with CORBEL project managers at hand to help scientists navigate between different service providers and exploit the full potential of the offers available. Learn more about the CORBEL Open Call by visiting our website (

CORBEL – Coordinated Research Infrastructures Building Enduring Life-science services – is an EC Horizon2020 project uniting 13 Biological and Medical Science Research Infrastructures (RIs). In CORBEL, the participating RIs expand their cooperation in order to harmonise researchers’ access to their cutting-edge technologies and services by establishing a sustainable platform of aligned services that will enable faster admission to a wider portfolio of technologies and services to boost research projects.

“NETTAB 2018: Building a FAIR Bioinformatics environment” Call for Abstracts.

NETTAB 2018 is organised in collaboration with ELIXIR Nodes of the UK and Italy as well as the Italian Society of Bioinformatics, BITS.
The main focus will be on FAIR principles in bioinformatics, a challenging topic that we hope will attract many researchers from all over the world, including but not limited to, Bioinformaticians, Biologists, Computer Scientists, and others working or interested in the above research scope.
The FAIR Guiding Principles for scientific data management and stewardship, published in 2016, has sparked worldwide interest across the biology community: from grassroots to policymakers, and from data providers to publishers.
In order to make the FAIR concept a reality, we need to answer many questions, like: What is FAIRness? How to make FAIR data a reality? How to facilitate the translation to FAIR data? How to measure it? On these topics, there are many ongoing projects, such as EOSCpilot, FAIRmetrics, FAIRsharing, and GO-FAIR.
Now is the perfect time to discuss on these topics and related actions, and to move on from FAIR principles to FAIR practice. The workshop will provide an excellent environment and a range of opportunities to present and discuss methods, theoretical approaches, algorithms, tools, platforms, practical applications and experiences of FAIR in Bioinformatics.
Methods, theoretical approaches, algorithms, tools, platforms, practical applications and experiences of FAIR in Bioinformatics including, but not limited to:
FAIR concept
•       Specification and revision of components, conceptual issues.
•       Criticisms and review of FAIR principles
Development tools
•       FAIR Web Services, metadata for FAIR tools, revision of standard formats.
FAIRification methodologies
•       FAIRification best practices and training
•       Experiences of FAIR methods
•       Best practices and lessons learned from domains outside bioinformatics.
FAIRness evaluation
•       FAIRness validation and correction tools.
•       FAIR metrics: Levels of FAIRness, FAIRness scores, FAIRness minimal levels.
FAIR environment
•       Integration and interoperation of FAIR data and systems.
•       FAIR and its demonstrated contribution to open science and reproducible results
•       FAIR principles and practices of research outputs other than data: workflows, scripts, tools, models, training materials, SOPs etc
•       Surveys of FAIR resources and methods
FAIR value
•       Examples of FAIR in practice and the benefits of FAIR resources
•       Related initiatives to FAIR: for example Data Commons and EOSC
•       The economics of FAIR
•       Incentives for FAIR stewardship throughout the data lifecycle
The topics of NETTAB 2018 also include the usual topics of NETTAB workshops.
Submission of abstracts for oral communications: Sunday May 20, 2018
Notification: Monday June 18, 2018
Abstracts of maximum four A4 pages must be submitted through EasyChair at:
See full instructions at:
Visit the website at: