CORBEL Project
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CORBEL News | Issue 11

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NEWS

Euro-BioImaging and EU-OPENSCREEN sign collaboration agreement

On 11 July 2019, EU-OPENSCREEN and Euro-BioImaging, two of the 13 research infrastructures (RIs) that are collaborating in CORBEL, signed a collaboration agreement in order to jointly support cutting-edge life science research in Europe. In signing this agreement, Euro-BioImaging and EU-OPENSCREEN acknowledge the value and importance of their own field of expertise being embedded in a larger scope of technologies and services offered by complementary life science RIs across Europe.

Within CORBEL, the two RIs were involved in the development of pipelines for combined service provision, which were evaluated by involving real user projects. By enabling several CORBEL user projects, EU-OPENSCREEN and Euro-BioImaging already demonstrated the feasibility and impact of cross-infrastructure user access and are now aiming at sustaining their achievements by the collaboration agreement. Harmonizing and facilitating user access across the life sciences RIs will increase the user community of the individual RIs, enable interdisciplinary research projects, and drive innovation and scientific progress.

Antje Keppler (Euro-BioImaging) and Wolfgang Fecke (EU-OPENSCREEN) sign the collaboration agreement between the two research infrastructures.

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New CORBEL deliverables published

‘Report on integrated biomedical data and project proposals for biomarker validation in clinical trial monitoring’
Pancreatic cancer is one of the most lethal forms of cancer, and there is a strong need to be able to identify it at an early stage in order to start a treatment as early as possible. The report describes how the challenge of identifying predictive biomarkers for the early stages of pancreatic cancer was tackled by making use of biobanked samples from five large European population cohorts. Via metabolomics analyses, two potentially interesting biomarkers - glutamine and histidine - were found, but turned out to have too low impact to have clinical utility. Via proteomics analyses, six proteins of oncological relevance were found as potential biomarkers: GZMH, VEGFR2, FGFBP1, GPNMB, CRTAC1 and ITGAV. As the next step, their clinical interest is being independently validated followed by integrated multi-omics analysis. The metabolomics part of the study resulted in a recent publication in Endocrinology.

‘Prototype implementation of distributed automated data access request, review and authorization and delivery systems’
This deliverable describes research infrastructures’ prototypes for granting a researcher an authorisation to access research data encouraging secondary use of data that is already collected. The main use case is that data access requires authorisation because of its sensitive nature, for instance, if it involves human samples. First, key concepts are presented, then previous work in life sciences and beyond as well as within relevant standards bodies are described. Finally eight prototype implementations are presented from the contributing research infrastructures. Before data access authorisation and delivery can be carried out, a researcher needs to be identified and their identity authenticated to a sufficient level of assurance. Existing approaches to researcher authentication are described here to the extent necessary for data access authorisation. The work outlined in this deliverable will be continued within the EOSC-Life project.

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‘Evaluation of repositories for sharing individual participant data from clinical studies’ – publication in Trials

A multi-stakeholder task force set up by the CORBEL consortium (Work Package 3) is developing procedures to provide the scientific community with access to individual patient-level data (IPD) from clinical trials. Access to IPD would ensure data quality and robustness of analyses, improve the accuracy of estimates of benefits from a treatment, and optimise the use of clinical trial data for re-analyses, secondary analyses and meta-analyses.

With publishing an ‘Evaluation of repositories for sharing individual-participant data from clinical studies’, a task force sub-group has now made an important contribution to the implementation of clinical study data sharing: they analysed existing data repositories using an indicator set to capture the maturity of the repositories’ procedures and their suitability for the hosting of IPD. Their analysis gives an overview about the currently available repositories and can actually help researchers to find a suitable repository for their datasets.

The group is now exploring the practical implementation of the quality criteria and requirements developed to assess the available repositories in a pilot demonstrator.

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CORBEL webinar recordings available

‘Genomics and clinical data at your fingertips with open-source software: tranSMART & cBioPortal’
4 June 2019, Speakers: Jan-Willem Boiten, Lygature, and Menno de Vries, Netherlands Cancer Institute

'Towards a GDPR Code of Conduct for Health Research: where are we today?'
19 June 2019, Speaker: Michaela Th. Mayrhofer, BBMRI-ERIC

Since 2017, CORBEL has been running a webinar series to address challenges and share best practices between the biological and medical European research infrastructures. Recordings of all webinars are publicly available on our website.

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Subscribe to the EOSC-Life Newsletter

EOSC-Life - the cluster project within the European Open Science Cloud (EOSC) aiming at creating an open collaborative space for digital biology in Europe - has recently launched its project website www.eosc-life.eu. Sign up here to be added to the EOSC-Life newsletter, launching this autumn! Stay up-to-date on the project's progress, open calls, research output and more.

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CORBEL Final Open Meeting & 1st EOSC-Life AGM

The final CORBEL meeting will take place on 2 March 2020 in Florence, Italy. The consortium will present their solutions for harmonising user access to the European life science research infrastructures (RIs), comprising topics such as access, data or quality management, training, ELSI and innovation support. Presentations by scientists from the biological and medical user communities will illustrate how concerted access to multiple RIs advanced their projects, thus demonstrating the benefit of CORBEL for European life science research. The one-day meeting will be 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. Registration will open soon - visit our news page for updates!

The final CORBEL meeting will be organised back-to-back with the 1st annual general meeting (AGM) of the EOSC-Life project on 3-4 March 2020. EOSC-Life is the new cluster project of the European life science RIs within the European Open Science Cloud (EOSC), aiming at creating an open collaborative space for digital biology in Europe. The 1st EOSC-Life AGM will comprise one day open to selected stakeholders and a second internal day for the consortium. 

 

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, MIRRI (Microbial Resource Research Infrastructure) is introduced to the researcher community.

MIRRI-ERIC provides a unique access point to biological resources, related information, services and expertise of 35 microbial resource centres (mBRCs) located in 10 countries. This means that about 450.000 resources (such as bacteria -including cyanobacteria-, archaea, fungi, yeasts, plant viruses, bacteriophages and their isolated DNA as well as human, animal and plant cell cultures) can be readily provided to users from academia, health and agriculture authorities, and the bio-industry. Pathogenic material is provided to risk group 2, selected risk group 3 organisms are available from a few mBRCs. In addition MIRRI-ERIC offers unrivalled expertise in the integrated analysis of complex microbial interactions, ranging from the isolation of a specimen from the environment to the description of novel species, deciphering the genomic information and its path to gene expression. Targeted identification of genes of interest for biotechnological exploitation as well as analysis of ‘microbiomes’ make MIRRI-ERIC an interesting partner not only for academic researchers but also for industry and ‘personalized medicine’.

Currently MIRRI-ERIC is under development, but basic services are already available. Full operability as well as the virtual entry point to all services will be achieved once the legal status is established.

 

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. In this issue, a user project selected in the 2nd Open Call, requesting access to Euro-BioImaging and EMBRC resources, is featured:

Revealing the morphological plasticity of a cell in planktonic symbioses

Service Providers:
Euro-BioImaging EMBL Node

EMBRC, CNRS Marine Observatory, Villefranche-sur-mer, France

Symbiosis with photosynthetic cells occurred several times in the evolutionary history of eukaryotes and led to the acquisition of the chloroplast– the organelle that performs photosynthesis. Chloroplast acquisition gave rise to a wide diversity of photosynthetic organisms and is considered to be one of the most important biological innovations in eukaryotes.
Living in symbiosis with microalgae is still a widespread phenomenon in today’s oceanic plankton. These ecological interactions contribute significantly to oceanic primary production and the functioning of marine ecosystems. Large-scale environmental sequencing projects (e.g. Tara-Oceans) have unveiled the worldwide prevalence of these cell-cell symbioses in the oceanic plankton.

Despite their key ecological roles in the oceans, the basic functioning of these symbiotic interactions, as well as the subcellular mechanisms by which a cell can accommodate and engineer an intracellular microalgal cell remain unknown. Dr. Johan Decelle, a young group leader at the University of Grenoble Alpes, who played an active role in the Tara-Ocean expeditions, has focused on revealing these mechanisms in his research. The goal of his project is to unveil the structural architecture of the symbiotic cells, in particular the chloroplasts, using cutting-edge imaging technologies. Working with the CNRS Marine Observatory of Villefranche-sur-mer, which is part of EMBRC, has allowed him to collect his study material despite being based away from the sea with his institute. This site offers a favorable oceanographic context for the presence of symbiotic plankton in near-shore waters, which facilitate experiments on live cells. At the Euro-BioImaging EMBL Node, he used the 3D imaging technique FIB-SEM (Focused Ion Beam scanning electron microscopy) to visualize subcellular modifications of the photosynthetic machinery and the microalgal cell at high imaging volume before and during symbiotic interaction.

What started as a project selected via the CORBEL Open Call developed into a long-term collaboration. All partners agree that this project will improve our knowledge of the functioning of planktonic symbioses and bring new evolutionary insights into chloroplast acquisition in eukaryotes.

‘Learning about these available resources and accessible technologies in Europe was such luck! To have the possibility to go all the way from collecting planktonic cells in the ocean to high-end cutting-edge imaging technologies is a unique opportunity to better understand these ecologically-important cells!’ - Johan Decelle

 

UPCOMING EVENTS

Sustainability of Mouse Informatics Resources (SMIR) - INFRAFRONTIER workshop at IMGC 2019
25-26 September 2019, Strasbourg, France

In an INFRAFRONTIER satellite workshop to the International Mouse Genetics Conference (IMGC) 2019, experts from leading institutions in Europe, North America and Asia will discuss the status quo and the future of international Mouse Informatics Resources and the strategic plans of the major mouse data providers.

 

2nd CORBEL Service Operator and User Meeting
1-2 October 2019, Heidelberg, Germany

The upcoming meeting at the EMBL in Heidelberg, organised by CORBEL WP4, will bring together European scientists who have been supported by CORBEL, and the research infrastructure Service Operators for exchange of experience. Project presentations by participants will illustrate how CORBEL support advanced their projects. Special requirements of industrial partners in accessing RI resources as well as future developments in the field of scientific collaborations and datasharing will be discussed.

 

Europe Biobank Week 2019
8-11 October 2019, Lübeck, Germany

Registration for Europe Biobank Week 2019, taking place from 8-11 October in Lübeck, Germany is possible here. Additional practical courses and pre-conference workshops will take place on 7 and October, respectively. Check out the extensive programme and social events here. Lufthansa Group Partner Airlines is partnering with the organisers to offer discounted flight rates for EBW 2019 attendees - find out more here.

 

Rare Diseases Data Integration (RDDI) - INFRAFRONTIER workshop at ASHG 2019
15 October 2019, Houston, USA

INFRAFRONTIER will organize an ancillary event to the annual meeting of the American Society of Human Genetics (ASHG) to bring together global Rare Disease communities, human and mouse geneticists, and clinicians from all over the world to facilitate the understanding and treatment of rare diseases. The RDDI workshop aims at aligning relevant genetic and phenotypic data from model organisms with Rare Diseases clinical data. It wants to create new communication channels between Rare Disease clinicians and mouse geneticists, and to showcase the already available, RD-relevant mouse lines to Rare Disease consortia worldwide.

 

ASCB|EMBO 2019 Meeting
7-11 December 2019, Washington, DC, USA

The joint meeting of the American Society for Cell Biology (ASCB) and European Molecular Biology Organization (EMBO) will focus on cell biology as the fundamental basis of biology, and will offer sessions on emerging topics such as nontraditional model organisms, and the use of computational modeling and biophysics.

 

Workshop 'Data Visualisation for Biology: A Practical Workshop on Design, Techniques and Tools’
16-20 March 2020, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge, UK

As biological datasets increase in size and complexity, we are moving more and more from a hypothesis-driven research paradigm to a data-driven one. As a result, exploration of that data has become even more crucial than in the past.
In this 5-day course, organised by EMBL-EBI in association with CORBEL, we will dive into the topic of biological data visualisation and how it can be used to gain insight into and get a "feel" for a dataset, so that targeted analyses can be defined. We will start by covering theoretical questions such as: What is data visualisation? How do we perceive images? How can we visualise data in the best possible way? It will be delivered through a mixture of lectures and workshop sessions, and will also provide hands-on experience in developing visualisations. The course will focus on working with omics (e.g. genomics, transcriptomics) data rather than e.g. imaging data.
This course is targeted at biologists who want to explore and gain further insight into their own data through the use of visualisation and design approaches.

Application opens: Tuesday 10 September 2019
Application deadline: Friday 29 November 2019 

 

REPORTS

Promoting access to European research infrastructures
Joint efforts to reach out to European scientists at the 44th FEBS Congress in Krakow, Poland, 6-11 July 2019

CORBEL, Instruct, Euro-BioImaging and EU-OPENSCREEN joined forces to raise awareness about the life science research infrastructures (RIs) among the 1,825 participants of this year’s congress of the Federation of European Biochemical Societies (FEBS).

The three RIs presented their fields of work and their offers in a special ‘Using international research infrastructures to boost your science’ session that attracted the interest of around 150 participants. The joint exhibition booth of the three RIs and CORBEL provided a continuous space for encounters with the congress participants. Some of them were familiar with the concept of RIs, but many of them had never heard about this kind of organisation before and were appreciative to learn how access to RI resources and expertise might benefit their own research projects. As the congress participants came from a large variety of research areas, the broad offer of the life science RIs covered almost all fields of interest.

Many questions were asked and answered - hopefully, fruitful collaborations will emerge based on the newly established contacts.

 

UPDATES FROM PARTNERS

BBMRI-ERIC:
Register for Europe Biobank Week 2019! Secure your registration now for the largest biobanking conference in Europe, taking place from 8-11 October in Lübeck, Germany. Join us for additional practical courses on Oct 7 and pre-conference workshops Oct 8. Check out our extensive programme and social events here. Book accommodations and take advantage of travel discounts for EBW19 - Lufthansa Group Partner Airlines is partnering with us to offer you discounted flight rates for EBW 2019 attendees! Find out more here.

EMBRC-ERIC:
EMBRC-NO Kicks Off In September: On 4 September, the Norwegian node of EMBRC had its kick-off meeting in Bergen. With coordination from the University of Bergen, the following 7 node partners came together to celebrate the milestone: University of Bergen, Institute of Marine Research, Norwegian University of Science and Technology, University of Oslo, Norwegian Institute for Water Research, University of Tromsø – The Arctic University of Norway, Nofima 

ASSEMBLE Plus Open Calls for Marine Research: Take the opportunity to carry out a part of your marine research project for free, at any of the over 30 marine stations and institutes in Europe and overseas. Apply to the “Transnational Access” of ASSEMBLE Plus! ASSEMBLE Plus is a consortium integrating over 30 marine biological stations and installations in 16 different countries in Europe and overseas. It provides scientists from academia, industry and policy with research services in the field of marine biology for ecosystem access, maintenance and culture of marine organisms, microscopy, molecular biology, biochemical and biological analysis, bioinformatics and more! In the Transnational Access programme, ASSEMBLE Plus will cover the costs for a maximum of two persons per project to gain access to laboratories, research services, and standard disposables, for a maximum of 30 days. In addition, the Access Provider will cover the costs of shipping biological resources, and costs of the visit (travel, accommodation and meals). Deadline for project submission: 11 October 2019 (5th call). Period of access: December 2019 - May 2020 (5th call). Apply on www.assembleplus.eu/access/transnational-access

ECRIN:
PERMIT Project on Methodological Standards for Personalised Medicine Now Funded:
The PERsonalised MedicIne Trials (‘PERMIT’) project on methodological standards for personalised medicine research has received a positive funding decision from Horizon 2020 (grant agreement number 874825). The PERMIT consortium is composed of pan-European research infrastructures (ECRIN, EATRIS, ELIXIR-LU/UNILU), funders (DLR), HTAs (KCE, ISCIII), patients (EPF), regulatory (ISS), data protection (TMF) and scientific experts. The objective of PERMIT is to establish, with all relevant stakeholders and invited experts, recommendations ensuring the robustness of personalised medicine trials, which also requires validation of the stratification methods.

Poland Joins ECRIN as an Observer Country:
ECRIN is pleased to announce that Poland has officially joined as an observer country. The Polish Medical Research Agency will be the national scientific partner. The addition of Poland brings ECRIN's total number of member and observer countries to 12, with 9 members (Czech Republic, France, Germany, Hungary, Ireland, Italy, Norway, Portugal and Spain) and 3 observers (Poland, Slovakia, Switzerland). This represents around 350 million European citizens. Learn more about ECRIN's member and observer countries here.

EMPHASIS:
On 11th June 2019, the 1st EMPHASIS Ministry Meeting took place in London where representatives of six countries (Belgium, Estonia, France, Germany, Italy and UK) discussed strategic options for the operational phase of EMPHASIS. They started off by introducing the phenotyping landscape of their respective countries and the need for pan-European integration. As a conclusion, the meeting participants agreed on concrete steps for the formal implementation phase of EMPHASIS. All participants emphasised that the entire process to establish EMPHASIS is open to all ESFRI countries.

On 25 and 26 September 2019, as part of the European Research & Innovation Days in Brussels, EMPHASIS invites visitors to the Science is wonderful! exhibition to uncover the secrets of plants and their relevance for our daily lives.

Infrafrontier:
Sustainability of Mouse Informatics Resources (SMIR)
- INFRAFRONTIER workshop at IMGC 2019 in Strasbourg:
For the global biomedical research community, the reliable access to mouse informatics resources like the databases of Jackson Laboratories, EMMA, IMPC, and others, are a prerequisite for the development of Precision Medicine. But the long-term sustainability of these tools is facing some challenges today. In an INFRAFRONTIER satellite workshop to the International Mouse Genetics Conference (IMGC) 2019 in Strasbourg on 25 and 26 September, experts from leading institutions in Europe, North America and Asia will present their tools and their ideas for improvements. They will openly discuss the status quo and the future of international Mouse Informatics Resources and the strategic plans of the major mouse data providers. Medical and genetics researchers from all over Europe are warmly invited to take part in the SMIR workshop and its panel discussion. 

Rare Diseases Data Integration (RDDI) - INFRAFRONTIER workshop at ASHG 2019 in Houston:
On Tuesday, 15 October 2019, INFRAFRONTIER will organize an interesting workshop in Houston, USA: As an ancillary event to the annual meeting of the American Society of Human Genetics (ASHG), it will bring together global Rare Disease communities, human and mouse geneticists, and clinicians from all over the world to facilitate the understanding and treatment of rare diseases. The RDDI workshop aims at aligning relevant genetic and phenotypic data from model organisms with Rare Diseases clinical data. It wants to create new communication channels between Rare Disease clinicians and mouse geneticists, and to showcase the already available, RD-relevant mouse lines to Rare Disease consortia worldwide. Involved are EJP-RD, the new European Joint Programme on Rare Diseases; RD-Connect - an integrated platform for Rare Disease research that connects databases, registries, biobanks and clinical bioinformatics; EMBL-EBI as a leading data integrator; the Centers for Mendelian Genomics, and Kids First. 

Instruct-ERIC:
We are delighted to announce that Instruct-ERIC will be participating of 2 newly awarded Horizon 2020 projects: EU-CELAC ResInfra and iNEXT Discovery. EU-CELAC ResInfra aims to identify a number of CELAC (Community of Latin American and Caribbean States) Research Infrastructures (RIs) that may be eligible for the construction of a bi-regional collaboration. This will be carried out through the definition of minimal key requirements these RIs would need to develop in the coming years. Within this project Instruct will be leading a task on infrastructure cooperation and coordination on Structural Biology for Health. The project will run for 30 months.

iNEXT discovery has been funded by the European Commission within the INFRAIA Horizon 2020 call. iNEXT discovery brings together a strong network of leading structural biology facilities including facilities in many Instruct Centres. The project will run for 4 years starting early next year using the Instruct developed ARIA for their proposal system. One of the core aims of iNEXT discovery is to bring the benefits of structural biological technology and expertise to scientists from new scientific communities, building on the achievements of the CORBEL and iNEXT transnational access projects. This will be done through interactions with industry and other ESFRI RIs METROFOOD, EU-OPENSCREEN, EATRIS and Euro-BioImaging who are also members of the iNEXT discovery consortium.

ELIXIR:
Three new ELIXIR Communities established: Structural bioinformatics, Intrinsically disordered proteins and Microbial biotechnology - these are the domains of three newly established ELIXIR Communities. Following the approval of the Communities' work plans by the ELIXIR Head of Nodes Committee, the three Communities are now starting their activities, working closely with other ELIXIR Communities and with ELIXIR Platforms. With these three new Communities, there are now eleven ELIXIR Communities, covering a wide spectrum of life science domains with applications in health research, environment, agriculture or marine industry.

ELIXIR has published a paper in Nature Reviews Genetics that explores how European research infrastructures can be leveraged to facilitate transnational access to at least one million human genomes. In the paper ‘Leveraging European infrastructures to access 1 million human genomes by 2022’, the authors detail challenges, opportunities, and recommendations around accessing whole-genome level sequencing data, as well as phenotypic and biomolecular data across country borders, without compromising on data security. The paper also carried the voices from individuals from the Biobanking and BioMolecular resources Research Infrastructure (BBMRI-ERIC), EMBL’s European Bioinformatics Institute (EMBL-EBI) and the Global Alliance for Genomics Health (GA4GH). 

 

PUBLICATIONS

'Unique, Persistent, Resolvable: Identifiers as the foundation of FAIR' (2019) Juty, N., Wimalaratne, S.M., Soiland-Reyes, S., Kunze, J., Goble, C.A., Clark, T., Zenodo, DOI: 10.5281/zenodo.3267433

'Search for Early Pancreatic Cancer Blood Biomarkers in Five European Prospective Population Biobanks Using Metabolomics' (2019) Fest J., Vijfhuizen L.S., Goeman J.J., Veth O., Joensuu A., Perola M., Männistö S., Ness-Jensen E., Hveem K., Haller T., Tonisson N., Mikkel K., Metspalu A., van Duijn C.M., Ikram A., Stricker B.H., Ruiter R., van Eijck C.H.J., van Ommen G.B., 't Hoen P.A.C., ENDOCRINOLOGY, DOI: 10.1210/en.2019-00165

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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