CORBEL Project
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CORBEL News | Issue 13

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Update on COVID-19

Spread out across Europe, the Life Science Research Infrastructures of CORBEL are working hard to continue operations at this time, with some understandable limitations. Thanks to technology we are able to continue moving ahead on many fronts – including making resources available for research on SARS-CoV-2 and COVID-19. Please check this newsletter and the CORBEL website periodically to be informed of event cancellations and project progress. Feel free to get in touch with us with any questions or concerns.

The CORBEL project consortium

 
 
 

NEWS

CORBEL Final AGM

The Final AGM of the CORBEL project took place March 2, 2020 at The Hotel in Brussels. During the final meeting, the CORBEL consortium members presented solutions for harmonising user access to the European life science research infrastructures (LS RIs). Topics included access, data, quality management, training, ELSI, innovation support, and more. Presentations by scientists from the biological and medical user communities illustrated how concerted access to multiple RIs advanced their projects, thus demonstrating the benefit of CORBEL for European life science research.

The one-day meeting was open to European scientists from the biological and medical field, potential users of the CORBEL common services as well as other stakeholders generally interested in CORBEL and the European life science RIs.

A full report of the meeting will be published as a deliverable forthcoming.

View the presentations here.

 

New CORBEL legal template available

The CORBEL Innovation Office made a new legal template available on the CORBEL’s portal for Material Transfer & Data Transfer Agreements. To view all templates available, please click here.

 

New CORBEL deliverables published

Assessment of animal model phenotypes against outcome measures

Animal models play a crucial role in understanding the mechanisms of diseases and symptoms, and to test the efficacy and safety of treatments before conducting clinical trials. Selecting human diseases and developing core sets of clinical outcome measures as well as complementary sets of mouse phenotyping measures will contribute to narrow the gap between animal models and human trials. The overall objective of the CORBEL task 3.2 is to promote convergence between outcome measures used for clinical trials in humans and phenotyping techniques used for testing treatments in animal models.

Report on user engagement activities

This deliverable aims to give a comprehensive overview about the user engagement and user experience activities that were developed and executed by the CORBEL consortium in order to establish contacts to various scientific user communities and to support opening of the services developed in the project to a wide community. Based on the stakeholder analysis and the communication strategy that were developed at the beginning of the project, user engagement activities started right at the beginning of CORBEL. In order to ensure effective communication with all user communities, activities have been performed by all work packages.

Sustainability plan for extended BMS RI Innovation Office

In this deliverable proposals are outlined to continue some of the Innovation Office activities of CORBEL beyond the formal termination of the project. Based on the breakdown of requests and other activities handled during the project and taking account of resources available options have been developed to provide Help Desk support for innovation as well as continuing the web portal and innovation email facilities and providing training and other materials. Opportunities to link into new initiatives will be pursued for mutual benefit. Relationships with other CORBEL work package products will be taken into account to simplify access to information and resources and to continue to share best practices post CORBEL.

Report on final assessment and generalization of integration platform

Task 3.4 in CORBEL (“Data integration and management services for image-driven and genomics-driven biomarker studies”) was designed to develop a common IT framework to support data handling and analysis for both clinical and preclinical biomarker research, across disease areas. The effectiveness of the selected approaches has been demonstrated using national and international research projects in this domain. It was investigated whether the data integration and imaging solutions implemented for the selected use cases are not only operational and used, but can also serve as best practices within the framework of shared services between the (ESFRI) Biological and Medical Research Infrastructures in the medical domain. This has been demonstrated with four independent use cases across the spectrum from preclinical to clinical biomarker research.

 

New CORBEL brochure available

 "For the advancement of science: Working with European Life Science Research Infrastructures" is a new brochure created out of CORBEL to introduce the Life Science RIs, and it is now available. Please click here to download the PDF (4.8 Mb).

In the brochure, we want to explain why access to services and technologies offered by the RIs, the collaborative work of RIs, and in particular, the creation of common service pipelines are advancing life science research. We would like to feature the RIs in our WP4 impact brochure, which are committed to continue their joint efforts independently of CORBEL, and which have indicated that they willing to set up bilateral collaboration agreements.

A website presenting the LS RIs will launch in Spring 2020. 

Explore the many advantages of working with Life Science Research Infrastructures! 

 

EOSC-Life Featured in Article on COVID-19 and the EOSC

The European Open Science Cloud (EOSC) will accelerate research to address future global challenges such as COVID-19.

Niklas Blomberg, coordinator of CORBEL and EOSC-Life, was featured in an article highlighting the need for the EOSC to address global health crises such as Coronavirus. As we collaborate to build the EOSC, a few use cases are already showing the potential benefit of the EOSC to global health.

Blomberg argues that open science allows faster, more efficient research, which he has experienced first-hand while collaborating with ELIXIR-Belgium and de.NBI/ELIXIR-Germany on an initiative addressing COVID-19.

Open data and open reproducible workflow also allow European scientists to collaborate globally,” says Blomberg. “Our recent collaboration on COVID-19 genomes is a great example: four teams – two European, one in Australia, one in US work together to make reproducible workflows openly available to scientists globally.

This is the core of EOSC – fast, open access to as wide a pool of data and tools as possible for scientific collaborations.” EOSC-Life is one of the EOSC projects accelerating open science through open data, open reproducible tools and workflows in the life sciences field.

Read the full article here.

 

Marie Curie Alumni meeting cancelled

The Marie Curie Alumni meeting on March 28-29 in Zagreb was just cancelled. Please visit the website for any further information: https://www.mariecuriealumni.eu/2020-conference/home.

 
 

RI in the SPOTLIGHT

This section will focus on one of the thirteen research infrastructures participating in CORBEL, providing useful information for current and future users. In this issue, ERINHA (European Research Infrastructure on Highly Pathogenic Agents) is introduced to the research community.

 

ERINHA is a pan-European distributed life sciences research Infrastructure dedicated to the study of highly infectious emerging and re-emerging high-consequence pathogens (RG4 & unknown). It brings together leading European high containment and complementary research facilities and expertise required to perform cutting-edge research on highly infectious diseases. ERINHA provides access to its state of art BSL-4 laboratories and complementary capacities and expertise to perform excellence orientated in-vitro and in-vivo research projects, trainings and advise. A wide range of capabilities and functions from high basic research laboratory capacities to NHP modeling research are provided by ERINHA, as well as expertise of senior scientists and access to complementary functions (from BSL1 to BSL4, genomics, proteomics etc.).

ERINHA produces the ideal environment to facilitate coordination of research on high-consequence pathogens in Europe. The infrastructure will contribute to the enhancement of the European and global capacity, capability and emergency preparedness in the response to global outbreaks.

Its National Nodes are based in France (Inserm), Portugal (INSA), Sweden (FOHM), Hungary (Ministry of Human Capacities), Netherlands (ERASMUS MC) and Belgium (KUL).

Since 2018, ERINHA has been granted landmark status by the European Strategy Forum on Research Infrastructures (ESFRI).

 
 

SUCCESS STORY

This section will illustrate how consecutive access to multiple research infrastructures offered via CORBEL was able to help European scientists to progress with their research projects.

 

Integrating EU-wide cardiovascular research datasets

Service Providers:
Adriano Barbosa da Silva, Queen Mary University of London (QMUL), United Kingdom

EATRIS Coordination Office, Amsterdam, The Netherlands

BBMRI Headquarters, Graz, Austria

Euro-BioImaging, Population Imaging Node Rotterdam (BIGR), Rotterdam, The Netherlands

Projects like the UK Biobank aim to improve the prevention, diagnosis and treatment of several diseases, by following the health status of 500,000 volunteer participants, and anonymously capturing changes that could give clues on alterations of health condition, lifestyle or environment that could be associated with the onset of diseases, such as cardiovascular diseases (CVD).

Dr. Adriano Barbosa’s CORBEL project aims to extend the impact of large population studies, such as the UK Biobank, by identifying and collecting additional European CVD datasets that could be analysed in parallel in order to validate insights observed in the UK Biobank on an independent dataset. In this respect it was of critical importance for him to gain access to European Research Infrastructures (RIs) that could help with this task.

A bulk search conducted by BBMRI using their negotiator service towards the BBMRI catalogue of biobanks identified 465 matches. In parallel, EATRIS coordination and support office, through its proprietary database of capacity available within the RI partner institutions, identified five institutions. Further discussions between Adriano and principal investigators at the identified institutions enabled by EATRIS allowed to scale down to two institutions with the datasets fully matching Adriano’s CVD query: Fondazione Ri.MED (Italy) and St. Anne's University Hospital (Czech Republic).

EATRIS helped to establish a Data Protection Agreement between Adriano’s university and Ri.MED via engagement with the respective data protection officers. Additionally, EATRIS supported Adriano with setting up a Memorandum of Understanding between his university and the Czech hospital as a first step to establish the necessary framework to have their data used in the scope of the project.

Through the Euro-BioImaging Node in Rotterdam, preliminary work was performed for the deployment of the XNAT.bmia.nl imaging archive key for the integration of imaging datasets. Further support will be provided for the extraction of imaging features from the medical imaging data sets allowing QMUL to apply machine learning methods to stratify cardiovascular patients based on machine learning.

Adriano Barbosa da Silva: "CORBEL support during my project was fundamental to address the legal requirements needed prior to data sharing. Without RI support it would have been particularly challenging to liaise with the matched biobanks and make sure that their datasets could be used in my research."

© Photo: Adriano Barbosa da Silva

 
 

UPCOMING EVENTS

Webinar - Course design and delivery: guidance and tips for impactful training

27 March 2020, 15:30 - 16:30 CET

CORBEL and EOSC-Life organise the webinar series "Engaging with your community through events and training", and the 3rd webinar in the series will be presented by Sarah Morgan (EMBL-EBI) and Gabriella Rustici, on 27th March.

This webinar will provide a practical look at course design and delivery, giving guidance on the key elements you need to consider to ensure your training meets the needs of your intended audience. It will also provide some tips for successful delivery and a brief look at how you can assess the impact your training has in the short and long term.

Please note that the 4th and final webinar of this series, The Best Practices that was scheduled for this date, will be scheduled thereafter; the new date will be announced shortly.

Register here in the CORBEL webinar section.

 

CORBEL webinar: ‘The BBMRI ELSI Services across the Nodes & BMS RIs’
21 April 2020, 15:30 - 16:30

The CORBEL webinar series offers a presentation by Michaela Mayrhofer from BBMRI-ERIC. The BBMRI-ERIC ELSI Services supports facilitating compliance with regulatory requirements and best practice standards. The service started working for the biobanking community and subsequently extend to the BMS community and includes:

  • The ELSI Knowledge Base is an open-access resource platform, containing practical knowledge and information on relevant ELSI topics.
  • The Ethics Check is a support service for researchers who are applying for H2020 research projects or similar. We assist with the compulsory Ethics Self-Assessment section during the application phase.
  • The ELSI Policy Monitoring follows relevant policy and regulatory developments at European level. We organise coordinated responses to relevant public consultations, as well as other interventions.

Please note that this webinar was postponed from 25th February.

More information & Register Online.

 

ONLINE! Implementing Biomedical Research Projects: The Complete Workflow from Concept, ELSI and Privacy Considerations to High-Quality Biobanking
11-15 May 2020

**Note: This workshop will be moved to a web-based format. Updated programme and details to come.

This workshop, co-organised by EJP RD, EASI-Genomics and BBMRI-ERIC, with support from MedUniGraz, BBMRI.at, CBmed and QIAGEN, is aimed at biomedical researchers, medical professionals and biobank managers who want to organise biomedical research projects on human biological samples. In two modules we will use several use-cases to address the key issues in biomedical research involving human subjects, human biological samples and associated medical data: ethics, legal issues, privacy and data protection, data standardisation and the implementation of sample workflows in a clinical context that are compatible with the In Vitro Diagnostic Regulation.

For further information and registration please visit: https://www.ejprarediseases.org/index.php/biomedical-research-training-workshop-biomedical-research-projects/

Registration deadline has been extended until the end of April!

 

Workshop - Sample preparation and multiscale imaging of plankton
27-29 May 2020, Villefranche sur mer, France

The Sample Preparation and Multiscale Imaging of Plankton workshop will be held at Villefranche-sur-Mer, from May 27th to May 29th, 2020. The workshop is organized by Euro-BIoImaing and EMBRC. The workshop contains practical demos and lectures and will allow participants to exchange about on-field sample preparation and discuss new strategies to prepare and observe cells at the nanoscale level using different imaging platforms.

The main goal of this workshop is to share about state-of-the-art skills and expertise in imaging and preparation of marine samples in an interdisciplinary atmosphere that will foster discussions and networking.

Please note that the registration deadline is 31 March. Any further information and the registration form is to be found on https://www.eventbrite.com/e/sample-preparation-and-multiscale-imaging-of-plankton-tickets-92710506621

 
 

UPDATES FROM PARTNERS

EU-OPENSCEREEN:
Bioactive compounds part of EU-OPENSCREEN compound library

Bioactive compounds are now part of EU-OPENSCREEN compound library. The bioactive compounds were selected from compounds contained in the Probes & Drugs portal, an up-to-date public resource for high-quality chemical tools. The bioactives’ library was designed with a strategy to cover wide target space, prioritizing selective, potent compounds. The final bioactives’ library of ~2,400 compounds covers almost 2,000 protein targets, containing several hundred compounds labeled as chemical probes and approved drugs.

EU-OPENSCREEN is ready to welcome compound donations from chemists to be included into the jointly used EU-OPENSCREEN compound collection. The donated compounds will be screened against a wide range of biological assays, thereby delivering extensive information about their biological activities. For more info visit the pages "How to donate your compound" and "Screening of donated compounds" on the EU-OPENSCREEN website.

 

EMPHASIS:
Ministry Meeting

As the preparatory project EMPHASIS-PREP will be finalised towards the end of 2020, EMPHASIS progresses in developing its business plan in discussion with national ministries. To this end, EMPHASIS brought together representatives from 14 countries that have expressed interest in supporting the implementation of EMPHASIS in a web-based meeting on 19 February. The participants discussed specific activities required to implement this service organisation, comprising firstly the establishment of the governance supporting service provision and testing parts of the service portfolio. The group plans to meet the next time towards the end of April, following up on this exchange and starting to take concrete decisions towards realising the implementation of EMPHASIS.

Update on continued EMPHASIS Coordination and Support Office operation during restrictions related to COVID-19

Across Europe, restrictions are put in place in order to protect the population against the spread of SARS-CoV-2. The EMPHASIS Coordination and Support Office continues its work making enhanced use of digital communication channels. Please note that phones can currently not be answered; if you would like to get in touch with us, please contact us via email (emphasis@fz-juelich.de or email addresses of specific team members provided on our homepage).

 

EMBRC:
Joint EUROMARINE-EMBRC 2020 Call for proposals

In 2020, EuroMarine and EMBRC jointly launch a new call offering access to EMBRC services to early career researchers affiliated with a EuroMarine member organisation.

EMBRC offers 50 k€ worth of services to 10 EuroMarine early career scientists (as defined by the EuroMarine OYSTER (early career scientists) group, i.e., PhD students or researchers within 5 years of their PhD degree. Applicants must belong to an organisation that is a 2020 member of EuroMarine. Each successful applicant will benefit up to 5 k€.

Applications will be pre-selected and ranked on the basis of their description of the research project to which the targeted EMBRC services will contribute, considering its intrinsic scientific value, its novelty and its relevance to the general scientific strategy of EuroMarine, as outlined in the EuroMarine Ocean Frontier manifesto.

Proposals must involve mobility on the part of the young researchers, who must visit at least one EMBRC facility located outside the country they are based in.

  • 19 April 2020: Deadline for proposal submission
  • 20 Apr.-3 May 2020: Pre-selection
  • 4-15 May: Feasibility assessment and costing; notification of outcome Second half of 2020: Research visit / Service provisioning

More information on the timeline, the application and further contact via the website at http://euromarinenetwork.eu/calls/joint-euromarine-embrc-2020-call-proposals.

 
 

JOB VACANCY

IBG-2

Vacancy: Research Scientist for Bioinformatics and Data Management

The Institute of Bio- and Geosciences, Plant Sciences Division (IBG-2) is looking to recruit a Research scientist in the field of Bioinformatics and Data Management. IBG-2 is a world leader in plant phenotyping, with excellent knowledge of the dynamic interaction between plants and the environment, combined with technology development, engineering and bioinformatics. The department develops and operates relevant next-generation infrastructure platforms and technologies and makes them available to external users.

You will be responsible for managing and operating interdisciplinary research projects in the framework of EPPN 2020, EMPHASIS and EOSC-Life aiming at enabling interoperability of plant data in the European scientific community. 

Do you want to know more about this position and to apply? Please visit https://www.fz-juelich.de/SharedDocs/Stellenangebote/_common/dna/2020-031-EN-IBG-2.html

 

EU-OPENSCREEN

Vacancy: Analytical Chemist

EU-OPENSCREEN is looking for an Analytical Chemist for the head office in Berlin, Germany. The position will initially be available for two years. Interested candidates should submit their updated CV with supporting documents and a motivational letter to jobs@eu-openscreen.eu. Applications are accepted until the position is filled. More information about the role can be obtained from wolfgang.fecke@eu-openscreen.eu, +49 30 9489 2420.

 

BBMRI

Vacancy: Systems Administrator

BBMRI-ERIC is searching for a Systems Administrator for its headquarters in Graz, Austria. This is a full-time (40 hr/week) position. The Systems Administrator is responsible for supporting all office operations regarding IT and the infrastructure operations of Common Service IT. Application deadline: March 27. Learn more here: Link: https://www.bbmri-eric.eu/wp-content/uploads/BBMRI-ERIC_VacancyNote_SystemsAdmin_2020March_Final.pdf

This project receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 654248.

This publication reflects the view only of the author(s), and the European Union cannot be held responsible for any use which may be made of the information contained therein.

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