Date: 7th of May 2024 09:00 - 10:30

Online event: Zoom registration

Organised by: Life Science RDM Group Norway

ELIXIR Code of Conduct: https://elixir-europe.org/events/code-of-conduct

Background:

The data steward profession is internationally among the fastest growing jobs (report from DANS - NL). Despite this, there is currently no defined career and educational pathway in Norway to become accredited as a Data Steward. On top of this, this highly demanded position is not presently represented in a suitable job category in the Norwegian public sector. The evaluation committee for the Norwegian Research Infrastructure program already wrote in 2021: The committee recommends that “RCN, together with the RPOs [research performing organisations], promote training of highly skilled people needed for operating RIs in the research system. We would especially mention data stewards as a new category that does not yet have a place in the system” (Evaluation of the INFRASTRUKTUR initiative, page 6).

Due to their transdisciplinary competence and their broad range of responsibilities, Data Stewards are currently employed across different job categories. This often results in misaligned career progression matrices and poor career progress (see also NIFU report: Technical-administrative employees in the university and higher education sector)

In this event, we aim to learn about the approaches adopted by other countries in defining and integrating the profession of Data Steward in the public sector and discuss together with the Norwegian unions, research and education institutions and Data Stewardship Experts on potential ways to anchor this role better in Norway.

 

 

Time	Topic	Speaker(s)
09:00	Welcome	Korbinian Bösl (Data Management Coordinator, ELIXIR Norway)
09:05	Example: Data Stewards in the Dutch system 12+3min Q+A	Fieke Schoots (Training Coordinator FAIR Data, Health RI NL)
09:20	Example: Data Stewards in the Swedish system 12+3min Q+A	Niclas Jareborg (Data Management team in the SciLifeLab Bioinformatics platform - NBIS)
09:35	Panel discussion	Moderation: Live Kvale (UiO library - Section for open research) Participants: Jon Iddeng (Forskerforbundet) Dag Endersen (UiO NHM, GBIF-NO & Tekna UiO) Katrine Weisteen Bjerde (HKDIR) Erik Sandquist (Senior Research Infrastructure Advisor, Division of Research and Innovation UiB) Even Birkeland (Data Steward FHI)
10:25	Sum up
10:30	End

 

 

In February 2024, a great milestone was reached for the human omics data community: the first datasets are now available in the Federated European Genome-phenome Archive (FEGA). These datasets - hosted by national nodes in Poland, Norway, and Sweden - are discoverable in the EGA portal and accessible according to national laws.

These datasets include:

• From FEGA Poland - The Genomic Map Of Poland
• From FEGA Norway - CRCbiome: Gut metagenome of Norwegian screening participants using FIT sampling
• Also from FEGA Norway - Single cell transcriptomics in expanded Tregs of APS-1 patients
• From FEGA Sweden - A Combined Omics and Tissue Biobank for Paediatric Cancers

The first Norwegian data set that has now been made available consists of data from research on the bacterial flora in the human intestinal system. The Norwegian researcher behind the first shared data set that was recently published in the journal Nature Communications, Professor Trine Rounge, states that "for us, FEGA Norway is the only available solution for sharing sensitive data. It is essential to share such data securely between researchers to ensure reproducibility and reuse in other projects”.

The establishment of these datasets represents a significant step towards achieving the broader objectives of the FEGA; to facilitate the sharing of high-quality human genomic and phenotypic data across borders. “The value for users is twofold: it becomes easier to make data available securely compared to storing data locally, and data becomes easier to find for other researchers. The possibility of reuse improves the chances of both verifying scientific discoveries and reaching groundbreaking conclusions, of benefit to the research community and later also patients,” said Anna Hagwall, project manager and head of human data at FEGA Sweden, NBIS.

About Federated EGA
FEGA was launched in 2022 as a network to store and lawfully share sensitive human omics data safely. It relies on the technology originally developed by the EGA and support from ongoing collaborations with ELIXIR - a European life sciences infrastructure. FEGA has contributed to and benefitted from the implementation of community standards for sensitive data management including those developed by the Global Alliance for Genomics and Health (GA4GH). “The FEGA concept and the development of the Nordic FEGA nodes have been made possible thanks to several projects coordinated by NeIC,” said Kjell Petersen, FEGA Norway technical lead.

Managing human omics data is challenging due to its sheer size and privacy concerns, often resulting in restrictions on how and where sensitive data can be shared. The FEGA network follows a federated data access model whereby sensitive data is stored securely within a local or national jurisdiction, while discovery across the network for data of interest is enabled via a central portal.

As of February 2024, the FEGA network comprises seven European national nodes with tens of additional national partners working towards establishing a FEGA node. As the FEGA network continues to onboard nodes from around the world, populated with more and more data, we move closer to a vision of a truly global resource for discovery of and access to sensitive human omics data to accelerate disease research and improve human health. "The Federated EGA network is entering a key phase where the first research datasets are now available across the network. In coming years, we look forward to expanding these datasets to cover key areas such as cancer and rare diseases for the benefit of patients" said Thomas Keane, Group Leader at EMBL-EBI.

[cross post: https://blog.ega-archive.org/first-datasets-available-in-Federated-EGA ]

On behalf of BioMedData and ELIXIR Norway, we would are delighted to extend to you an invitation to the National Stakeholder Meeting on Life Science Data Management, scheduled for November 22-23, 2023. This meeting brings together all our partners in data management related projects covering several national infrastructures,  life sciences data  and sensitive data. 

Event Details:

Event Name: National Stakeholder Meeting on Life Science Data Management in Norway

Date: November 22-23, 2023

Location: SALONGEN, Ibsenkvartalet, C.J. Hambros plass 2, Oslo

Important Links:

Agenda: 2022-11-22_National_stakeholder_meeting

Registration:  https://nettskjema.no/a/366854 

Agenda Highlights:

Day 1: Wednesday, November 22, 2023

12:00-13:00: Lunch

13:00-13:30: General scope of the meeting, and introduction round

13:30-14:00: Highlights from BioMedData

14:00-14:30: European Life Science RDM ecosystem

14:30-14:45: Coffee break

14:45-15:30: Stakeholder needs - Monitoring, CRIS issues, Incident response, Accessibility, Cataloging

15:30-16:30: Persona - ‘RDM takes a village’ & Measuring the impact of data availability

Day 2: Thursday, November 23, 2023

9:00-10:30: Future perspectives - EOSC, Joint strategic statement, Lack of detailed (institutional) policies, Funding situation, Service Gaps, Infrastructure gaps

10:30-10:45: Coffee break

10:30-12:00: Special category data - Federated genome phenome archive (FEGA)- Norway, Policy issues, Streamlining consent/REK/…, Data processing framework agreements

12:00-13:00: Lunch

This gathering brings together esteemed stakeholders. We aim with this agenda to address key issues and foster meaningful discussions around life science data management in Norway and Europe.

We believe that your valuable insights and expertise will greatly contribute to the success of this event.

To secure your spot, kindly register through the following link: https://nettskjema.no/a/366854 

Should you have any questions or require further information, please do not hesitate to contact us at: contact@elixir.no 

About the Department of Informatics

Digitization of businesses, industry, public administration, and education makes informatics play an increasingly important role in the development of society. Research and education in informatics are crucial for the digital transformation of society to succeed. If you want to be a part of an international work environment, and a contributor to leading research projects, apply for a job at the Department of Informatics. The Department is in rapid growth regarding its number of students, research directions, and employees. We have today about 1000 students, and almost 40 different nationalities represented among our 150 employees.

These positions will be a part of our technical team at Computational Biology Unit (CBU), which is the research center for computational biology and bioinformatics at University of Bergen. CBU coordinates ELIXIR Norway, the Norwegian node of the pan-European ELIXIR infrastructure (an ESFRI landmark) for life science data.

Senior Engineer/ Chief Engineer (System Developer)

At the Department of Informatics there is a vacancy for up to two positions as senior egngineers, funded by external projects. If there are no qualified candidates for one or both the senior engineer positions, we will consider hiring as chief engineer, with requirements for qualifications and experience lowered accordingly.

Duties

The announced position is in the CBU Service Group, and main work tasks include software development in a scientific environment with a focus on e-infrastructure for bioinformatics and computational biology. The position contributes to the development work undertaken in the context of ELIXIR Norway, and related national and international e-infrastructure projects associated with ELIXIR Norway. One central project focuses on secure archiving and controlled access to human genome datasets and related information in a federated solution.

Qualifications and personal attributes

• Master's in computer science or equivalent is required. Long relevant practical experience from software and system development, may compensate for not meeting the formal education requirements.
• Experience from both Python and Java development is required, with in depth experience from one of these languages, including familiarity with micro service based system architecture. Experience also from Go (Golang) will be regarded as very beneficial.
• Good experience with version control systems like git is a requirement, as well as knowledge on agile/iterative software development methodology.

We hope you also fulfill one or several of the points below:

• Our system platform is Linux, with extensive use of virtualization technology. Solid knowledge within both of these areas is desirable but not required.
• Working experience with containers, such as Docker (building and management) is strongly desirable.
• Experience from development of distributed systems and relevant technologies is advantageous (i.e. message queueing)
• Previous work experience from a geographically distributed software development team, in a multi-cultural environment, are both desirable.
• As we develop e-infrastructure services for the life sciences, basic knowledge within molecular biology/biomedicine would be a plus, but not a requirement

Personal qualities are important, and will be emphasized:

• Applicants must have excellent skills in oral and written English.
• A high level of independence and integrity is required.
• We expect enthusiasm and the ability to perform well in a cross-disciplinary team.
• As an employee in a research and teaching institution you must be willing and capable of learning new things as required to solve tasks

Senior Engineer/Chief Engineer (DevOps system administrator)

Duties

The announced positions are in the CBU Service Group. This is a team of engineers and researchers who together develop and operate e-infrastructure for the life sciences. The main work tasks include development and operation of Linux based infrastructure across
multiple deployment platforms. The position contributes to the development work undertaken in the context of ELIXIR Norway, and related national and international e-infrastructure projects associated with ELIXIR Norway. The work in the team is done in close interaction and collaboration with researchers and IT staff at the Department of Informatics and the University of Bergen central IT-department.

Examples of other kinds of duties can be:

• Implement and automate continuous integration and continuous delivery (CI/CD) for e-infrastructure development projects
• Monitor system performance and perform proactive troubleshooting and optimalization
• Design and implement security protocols and security policies
• Contribute to development work, including national and international infrastructure projects
• Cooperate with research groups and technical personell to understand their needs and give technical support and advice
• Document processes and procedures, and stay updated on new technology and best practice

Qualifications and personal attributes

• 3 - 5 years relevant higher education within IT is required. Long relevant practical experience combined with relevant courses may compensate for not meeting the formal education requirements.
• Experience from Linux system administration in a team with responsibility of medium complexity server IT-infrastructure, including use of virtualization technology and security management, is a requirement.
• Experience with “infrastructure as code” is required, either using ansible or other relevant related technology.
• We require good knowledge and experience with using Git versioning software and services.

We hope you also fulfill one or several of the points below:

• Knowledge on development and operations best practices (DevOps) including CI/CD, would be highly advantageous.
• Experience from FreeBSD system administration is desirable.
• Experience with large scale storage/file servers, batch job scheduling or network administration is an advantage.
• Experience with programming i.e. Web, Java and Python is desirable.
• Experience from working in a software development team is a clear advantage.
• Knowledge on research data within life science and bioinformatics is an advantage.

Personal qualities are important, and will be emphasized:

• Applicants must have excellent skills in oral and written English.
• A high level of independence and integrity is required.
• We expect enthusiasm and the ability to perform well in a cross-disciplinary team.
• As an employee in a research and teaching institution you must be willing and capable of learning new things as required to solve tasks

 

Special requirements for all positions

The University of Bergen is subjected to the regulation for export control system. The regulation will be applied in the processing of the applications.

We can offer:

 

• Exciting development opportunities as part of your role in a strong professional environment
• A position as Senior Engineer (code 1181) at salary grade 66 - 75 on the State Salary Scale depending on seniority and qualifications. This currently amounts to an annual salary of NOK NOK 646 000 - 759 100,- before taxes. Alternative as a chief engineer with salary pay grade 59 - 68 (code 1087). This currently amounts to an annual salary of NOK 575 400 - 667 700, -. A higher salary may be considered for a particularly well qualified applicant.
• Enrolment in the Norwegian Public Service Pension Fund
• Good welfare benefits

Your application must include

• A brief account of the applicant's interests and motivation for applying for the position
• Transcripts and diplomas, and relevant certificates
• The names and contact information for two referees
• CV

General information:

Detailed information about the positions can be obtained by contacting:

Head of Department, Professor Inge Jonassen, Inge.Jonassen@uib.no or group leader Kjell Petersen, Kjell.Petersen@uib.no.

For HR related matters, please contact Karoline Christiansen, karoline.christiansen@uib.no.

The hired staff for this position may be assigned other tasks and responsibilities within the same area of work, at the Department of Informatics or University of Bergen.

The state labour force shall reflect the diversity of Norwegian society to the greatest extent possible. People with immigrant backgrounds and people with disabilities are encouraged to apply for the position.
Information about applicants may be made public even if the applicant has asked not to be named on the list of persons who have applied. The applicant must be notified if the request to be omitted is not met.

For further information about the recruitment process, click here.

Please apply on Jobbnorge:

https://www.jobbnorge.no/en/available-jobs/job/249094/senior-engineer-chief-engineer-system-developer

https://www.jobbnorge.no/en/available-jobs/job/249066/senior-engineer-chief-engineer-devops-system-administrator

 

"Are you a bioinformatician looking for a multifaceted position? Do you enjoy connecting with people, looking for variation in daily tasks, and having a service minded-attitude? Come and join the Bioinformatics Core Facility as our senior bioinformatician/coordinator. We have an open 3-years position with the possibility of extension in a competent and interdisciplinary research environment."

The Bioinformatics Core Facility is funded by the South-East Health region (HSØ), and is an approved core facility for all HSØ institutions, as well as for the University of Oslo. We are located at the Institute for Cancer Research at Radiumhospitalet, formally organized under the Department of Core Facilities at Oslo University Hospital.

Here we reside in a basic, translational, and clinical research environment, together with 6 other core facilities offering cutting-edge technologies, services and analysis support (https://www.ous-research.no/corefacilities/). The Bioinformatics Core Facility is tightly connected to the Oslo node of the national Norwegian ELIXIR bioinformatics infrastructure (which is also a part of the European bioinformatics infrastructure (ESFRI). The core facility also collaborates with the Bioinformatics Center at the Department of Informatics, the University Center for Information Technology (USIT), as well as the Oslo Centre for Biostatistics and Epidemiology (OCBE) - all located at the University of Oslo.

Our work focuses on providing high-quality services on a wide range of data analysis topics. We work primarily with -omics data (genomics, transcriptomics, epigenomics, and proteomics), and our services also include workflow development/scripting, support using national web- and other services, biostatistics, access to databases and specialized license-based software to mention some. The majority of projects are related to human health research, as the core facility is immersed in Norway’s strongest cancer research environment.

The candidate will spend approximately 80 % of their time working on research-related service projects on behalf of users. This includes providing bioinformatics analysis of their data, developing custom workflows, and researching state-of-the-art analysis strategies to ensure optimal analysis. Approximately 20% of their time will be used for coordinating our daily activities together with the core facility management and personnel. This includes answering incoming requests and providing price quotes, invoicing, and supporting the management with reports and applications to our funding agencies. Some outreach activity to relevant research institutions is to be expected. Finally, there will be joint Bioinformatics Core Facility / ELIXIR helpdesk activities. This encompasses monthly joint meetings at the University of Oslo and assisting with the national ELIXIR helpdesk support system.

 

Oslo University Hospital is a workplace with great diversity. We believe this is absolutely crucial to solving the tasks required of us. We therefore want this diversity to be reflected among the applicants for our positions and encourage everyone to apply regardless of who you are and what background you have.

Duties and responsibilities:

Bioinformatics:

The successful candidate will participate in providing bioinformatics data analysis as requested by the users. We handle all omics data, but most projects use bulk and single-cell RNA, exome and whole genome sequencing, and epigenetic data. We also see an increased demand for spatial data (RNA/protein) analysis and high-dimensionality mass/flow cytometry data. Services may vary from quality control of raw data to in-depth exploration of biological patterns. Common analyses include variant calling on tumor-normal pairs, differential gene expression of bulk and single-cell data, and clinical annotation of analysis outputs. We also offered development of custom solutions, long-term support for large projects, and support for users setting up their analysis environments within Tjenester for Sensitive Data (TSD), and advice for Data Management Plans.

 

Coordination:

The successful candidate will support the core facility management with everyday tasks related to our users. This encompasses answering any incoming requests, researching and setting up suggestions for analysis workflows, and generating price quotes and contracts. We also do yearly outreach efforts where we visit relevant research environments and present our services. Finally, the candidate will support the management by providing the data foundation for reports and applications.

 

ELIXIR Norway:

There will be shared activity between The Bioinformatics Core Facility and the Oslo node of ELIXIR with respect to the ELIXIR helpdesk. Here, the candidate will attend monthly meetings, the yearly ELIXIR all-hands meeting, and answer any incoming tickets to the helpdesk system when relevant. In this setting, the candidate will get to interact with key personnel and competence from both USIT/TSD and ELIXIR Oslo being part of a resourceful network.

Qualifications required:

• A master’s degree with 5 years of experience in the field of bioinformatics or similar. A PhD degree in a relevant field is beneficial.
• Knowledge of UNIX, Python and R, and preferably one more workflow language (e.g. NextFlow)
• Experience with high-performance computing (HPC) and containers (Docker, singularity, biocontainers or similar)
• Advanced bioinformatics skills and experience with handling large biological datasets
• Excellent verbal and written communication skills (English)
• Excellent documentation skills to support FAIR principle.

Qualifications preferred:

• Good grasp of basic molecular biology
• Experience with machine learning
• Experience with workflows provided today by the core facility (described above)
• Some experience with UNIX/Linux systems with respect to software installation and similar
• Experience with database installation and maintenance

 

Personal characteristics:

• The candidate should be able to work independently as well as a part of the team
  Good communication skills are required as the successful candidate is expected to interact closely with the members of core facility and research groups

 

We offer:

• A 3 years position with the possibility of extension in an interdisciplinary and international research environment
• Variation in the daily work tasks
• Possibility to grow and develop competencies in different areas
• A team of supportive colleagues

 

Apply

Description:Online course on using the Norwegian e-infrastructure for Life Science (NeLS) and the national supported Galaxy (usegalaxy.no). The course will consist of lessons covering the necessary topics alternating with hands-on sessions to gain practical experience.

More information on TeSS: https://tess.elixir-europe.org/events/using-the-norwegian-e-infrastructure-for-life-science-nels-and-usegalaxy-no

Agenda: https://elixir.mf.uni-lj.si/enrol/index.php?id=87
Register at: https://nettskjema.no/a/281563

We are pleased to announce the Data Management planning workshop for Life Scientists in Norway by ELIXIR Norway and Digital Life Norway.

All Norwegian universities require a DMP for all projects. All projects that receive funding from the Norwegian RCN are required to submit a data management plan as soon as possible after the contract with the RCN has been signed. This workshop focuses on how-to generate a data management plan for a Life Science research project that will meet both requirements.

 

We would like to invite researchers (PhD candidates, Post Doctoral Fellows, Researchers, Associate Professors and Professors) in existing and upcoming Life Science projects to develop their DMP in this workshop.

 

 

Maximum number of participants: 45

The workshop will take place if there is at least 10 participants

26.09.2022

0830 - 0900 Login support

0900 - 0915 Introduction

0915 - 0930 Requirements from the RCN

0930 - 1000 Parallel session: Local recommendations & storage infrastructures Institutional DMP guidelines

1000 - 1015 Short break

1015 - 1100 Introduction DSW

1100 - 1120 Information on national storage infrastructures

NeLS/StoreBioInfo
NIRD
TSD
1120 - 1135 Short break

1135 - 1230 Persistent identifiers, Controlled Vocabularies & Ontologies

 

27.09.2022

0900 - 1000 Key legal requirements for research in the GDPR and Health research act

Personal Data Act
Health Research Act
1000 - 1015 Short break

1015 - 1045 Relevant deposition repositories/ data archives

domain specific archives (ELIXIR/EMBL-EBI, NCBI)
Dataverse NO
EGA
NIRD archive
NSD
1045 - 1100 Short break

1100 - 1115 Licensing of data, biological material and software

1115 - 1300 Hands on training and assistance to generate a data management plan

Requirements: Join us online and bring your project proposal . You will get the opportunity to set up a data management plan for your project with help of the Data Stewardship Wizard tool using a structured and detailed questionnaire with references to relevant resources.

Looking forward to see you at the workshop.

 

Register here on nettskjema

Monday, May 9, 2022
online

It has been a while since the FAIRDOM community got together to exchange ideas and share our FAIRDOM-SEEK related experiences. We’re therefore very excited to announce a new series of FAIRDOM user meetings, with the first meeting scheduled for 9th of May, 2022 at 14:00 CEST.

The purpose is to establish an active FAIRDOM user community to allow networking between various FAIRDOM-SEEK users and learn from each other’s experiences. Within the two-hours event the FAIRDOM team will give an introduction on current developments and the invited users will showcase the use of FAIRDOMHub and other FAIRDOM-SEEK instances for their research projects. After the presentations we’ll have plenty of time for discussions and networking.

Confirmed invited speakers:

Cyril Pommier
Frank Meineke - Leipzig Health Atlas (https://www.health-atlas.de)
Jasper Koehorst - WorkflowHub (https://workflowhub.eu)
Andrej Blejec - Bulk uploading from pISA-tree to FAIRDOM using SEEK API and R package seekr
Please register for free to get the Zoom access details.

 

Salmobase is a tool for making molecular genomic resources for salmonid species publicly available in a framework of visualisations and analytic tools. The site has now been rebuilt with new features and more planned to come in the near future.

Open access life science resources such as data and software, are fundamental for breakthrough discoveries, scientific excellence and entrepreneurial endeavours. ELIXIR’s latest report is an up-to-date analysis on the benefit of open data to industry and innovation, with an extensive survey, testimonials, and analysis of the hotspots of European innovation. 

Read more

 

In the context of CONVERGE, ELIXIR-Norway organized two contentathon to extend the RDMkit with tool assemblies - carefully curated and selected set of tools to facilitate research data management in the Life Science domains with a focus on local availability or need of a specific domain. During 4 days in May and June 2021 over 30 research data management experts from all over Europe compiled several tool assemblies for Data Stewards and Researchers.

"We hope this examples will help others to do their data management in a better and more efficient manner." - said Korbinian Bösl, who has been organizing the contentathons.

"We are super happy that the joint proposal of ELIXIR-Norway and ELIXIR-Belgium to extend the RDMkit further has just been selected for the Biohackathon 2021 and we are looking forward to meet exciting people to enable more knowledge transfer."

 

In a joint effort representatives from all research infrastructures in BioMedData have gathered for a 2 day online workshop to perform the first steps towards domain specific guidance for researchers in their data management. This work will result in the near future in expert recommendation for different domains and technologies which can be imported to new data management plans, forming the basis for more efficient research.

One important factor to accelerate these efforts was the advise from the Data Stewardship Wizard development team on collective editing of Knowledge Models in the Data Stewardship Wizard during the workshop.

The 11 Norwegian Life Science Research Infrastructures in the BioMedData project have published their "Report on data management plan needs/gaps".

This report marks the conclusion of the first phase within the project, aimed at assessing the data management routines at the Norwegian Life Science infrastructures and the gap with respect to the FAIR data principles. This report is a basis for the infrastructures to plan and implement further steps to improve the data management at the infrastructures and facilitate good data management by the researchers using the infrastructures.

Read more in the report (public available on zenodo under CC BY 4.0)

ELIXIR.NO newsletter number 5, January 2018, is now out. Can be downloaded here.