Monthly Archives: November 2016

NormSys & CHARME Tutorial/Conference: Future needs – today’s requirements, Building Bridges with Standards in the Life Sciences, December 5-6 – Potsdam, Germany

This meeting will take place December 5-6, 2016 at the Fraunhofer conference center in Potsdam, Germany. The tutorial will also cover an introduction into the FAIRDOM/SEEK platform for data management.

Standardisation issues are addressed in many fields in the life sciences, e.g. basic research, industrial R&D, education, technology transfer and application but these areas are often poorly connected.
The conference intends to explore the needs and the dimension of the relation between standardisation and innovation. Representatives from academia, industry and standardisation bodies who have been making exceptional contributions to develop and disseminate standards will inform and discuss with the participants the pros and cons of the use and implementation of standards in the daily workflows.
The tutorial will give interested staff insights in standard operation procedures (SOPs), experimental design, modelling design and a brief introduction into FAIRDOM ata management. This training will give an overview and hints how to plan an experiment to generate standardised data which are consistent and suitable for mathematic analysis, as well as how this can be handled and used to setup simulatable computer models.

The conference is free of charge.  For the tutorial we ask for a small fee.

Please find more information at or

To register for the tutorial please visit:

To register the panel discussion and / or the conference please send an E-mail to with the subject line
NORMSYS-Conference for participation at the conference or
NORMSYS-Panel for participation at the panel discussion.

You can download the conference tutorial in PDF format here: Conference tutorial

ERACoBioTech: Cofund on Biotechnologies Announced

About CoBioTech

The ERA-Net Cofund on Biotechnologies is a new ERA-Net Cofund Action under Horizon 2020 that will build upon the achievements of ERA-IB2 (ERA-Net for Industrial Biotechnology 2), ERASysAPP (ERA-Net for Applied Systems Biology) and ERASynBio (ERA-Net for Synthetic Biology).
The key mission of ERA CoBioTech is to

  • maximise synergies between current mechanisms of biotechnology research funding in Europe
  • foster the exchange of knowledge across borders
  • highlight the benefits of a bio-based economy for society
  • maintain and strengthen Europe’s position in biotechnology.

For more information please visit:

The pre-announcement is available here as a pdf download: [pdf download]

New Blog: The Digital Salmon Knowledge Base

Our Partners, Digital Salmon, write about their experience of using FAIRDOM tools and expertise in managing their data and models in our new blog “Data and model management needs for a knowledge base of salmon physiology: The Digital Salmon”

To read more please visit:

For more information on the Digital Salmon project please visit:

Data and model management needs for a knowledge base of salmon physiology: The Digital Salmon

By Tina Graceline and Jon Olav Vik, Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences.

Systems biology for salmon farming is the topic of the Digital Salmon, a FAIRDOM partner and active user of Our use-case was highlighted at the first FAIRDOM user meeting in Barcelona, 15 Sept 2016. The Digital Salmon currently has two projects, DigiSal and GenoSysFat, which comprise a model-driven, tightly integrated theoretical-experimental study of mechanistic interactions among genetic and feed factors. By combining experiment and modelling we aim to deliver a predictive understanding of a whole range of possible diets, much more efficiently than by traditional feeding trials alone. From a data management perspective, we have a lot of data and models that can potentially be linked via common languages; genes code for enzymes, which catalyze biochemical reactions, which transform molecules whose concentrations we can manipulate, measure and model.

Atlantic salmon farming generates approximately 6 billion euro every year and is projected to generate 20 billion euro in 2050. To support this growth, many challenges must be addressed. Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, climate change, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges. Project DigiSal lays the foundations for a Digital Salmon: an ensemble of mathematical descriptions of salmon physiology, combining mathematics, high-dimensional data analysis, computer science and measurement technology along with genomics and experimental biology. We chose to begin with the challenges associated with novel feedstuffs.

Salmon are carnivores but today aquaculture provides more than half their fat and protein from plants, challenging the metabolic system and affecting fish health and nutritional value of salmon meat. The effects of the novel feed ingredients on the salmon body are complex and involve many organs. The newly sequenced salmon genome and related resources will enable a tightly integrated theoretical-experimental study of mechanistic interactions among genetic and feed factors. This brings us to systems biology: understanding the living body as a set of components that both affect each other and depend on each other. By combining experiment and modelling we aim to deliver a predictive understanding of a whole range of possible diets, much more efficiently than by traditional feeding trials alone.

In late 2015, the Digital Salmon became a FAIRDOM partner. We have been using the FAIRDOMHub, an online instance of the SEEK software, and it has proved very useful in contextualizing our research assets—data, operating procedures, and models—in an investigation-study-assay structure, adapted to our research. We have saved much time and explanation and avoided many misunderstandings by being able to point coworkers to a data file that automatically links to experimental protocols and the wider research motivation.

Members of the FAIRDOM team have provided training, help, and advice on planning how we should structure and manage our data within the FAIRDOMHub. We are currently seeking a dedicated biosemantician to improve the semantic interoperability of our data and ultimately our ability to query over related data. If this sounds like an attractive challenge to you, please contact project leader Jon Olav Vik.

The project also faces difficult design decisions in managing large, non-public data. The raw data make up a few TB per year, and we would prefer to catalogue rather than store this data in the FAIRDOMHub, perhaps linking to our homebrew, lightweight LIMS system which keeps track of our biological samples. We are also eagerly anticipating FAIRDOM development in interfacing the SEEK with Git version control of analysis reports and computer code, and programmatic access to data and models on the FAIRDOMHub.

Overall, FAIRDOM software and expertise has greatly improved our ability to implement data and model management protocol across our project. We see this being hugely valuable as our project matures. We’re looking forward to growing our relationship with the FAIRDOM team, in particular our contact persons Natalie Stanford and Stuart Owen.

DigiSal is funded by the Research Council of Norway grant 248792 as part of its Digital Life initiative. It is hosted by the Norwegian University of Life Sciences, with partners at universities in Trondheim, Bergen, Tromsø, Wageningen and Stirling, the Institute for Marine Research, and the industry companies AquaGen and EWOS. We also collaborate closely with the Foods of Norway centre for research-driven innovation.