CORBEL Project
shared services for life-science
 
 
 
 
 

CORBEL News | Issue 10

View this email in your browser  
 
 

NEWS

EOSC-Life – developing an open collaborative space for digital biology in Europe

On 1 March 2019, the cluster of the 13 European biomedical research infrastructures launched their next joint venture, the EOSC-Life project.

EOSC-Life is a four-year EU-funded cluster project within the European Open Science Cloud (EOSC), aiming at creating an open collaborative space for digital biology in Europe. Coordinated by the ELIXIR research infrastructure, EOSC-Life is facilitating the publication of life-science data according to FAIR principles (findable, accessible, interoperable, reusable) and link these FAIR databases to open and reusable tools and workflows accessible to users via Europe’s national and international life-science clouds. EOSC-Life will also connect users across Europe to a single login authentication and resource authorisation system and develop data policies needed to preserve and deepen the trust given by research participants and patients volunteering their data and samples. Thus, scientists will have access to advanced data services, technology platforms, samples and support services and the resulting data will be openly accessible for reuse through the EOSC.

The biomedical scientific community from academia and industry can actively engage with EOSC-Life – the consortium will run a series of open calls for user research which will allow the research community to adopt advanced data management practice and access data integration and large-scale analysis tools in the cloud.

                                                                      ----------

New CORBEL deliverables published

‘Industry Collaboration Best Practices Guide’
This guide was a joint effort by EATRIS and the Medical University of Graz. It brings together all the experience in industry engagement of the CORBEL project to date and provides a comprehensive listing of helpful additional sources and literature references in this area. Experience from the two-day workshop in December 2018 has also been incorporated. All aspects of industry collaboration, from networking to negotiation and project management, are given attention. The aim of this guide is to provide a comprehensive single source to aid the researcher when confronted with the need to set up an industry collaboration, taking into account and prioritizing all relevant aspects and working with all the parties involved.

'Report on Common Access Framework Concept'
This deliverable presents the Common Access Framework developed within CORBEL work package 5 to manage seamless access to multiple research infrastructures within individual research projects. The framework comprises the ARIA (Access to Research Infrastructure Administration) access management software, which was adapted and improved to meet the specifications of CORBEL and provides a pilot platform for accessing multiple biomedical research infrastructures. The platform was tested by scientists belonging to the different scientific communities with research questions at the boundaries of the different research infrastructures. In addition, WP5 worked on a pilot concept for a common authentication and authorisation tool, with the aim of establishing an authentication and authorisation infrastructure (AAI) which meets the combined requirements of the biomedical infrastructures. This would enable scientists to access resources with a single unified identity and single sign-on. This work culminated in a pilot Life Science AAI, which was developed in collaboration with the AARC2 project.

‘Delivery of Toolkit supporting community ontology mapping and development’
This report describes the tools and services developed by CORBEL work package 6 to enable access to ontologies and ontology mapping services through the Ontology Lookup Service (OLS) and associated tools. OLS is an ontology portal that enables the search for appropriate ontological terms, and provides a visualisation of ontologies and hierarchies. This report highlights recent developments within the OLS, the Zooma ontology annotation tool, and the Ontology Cross Reference (OxO) service (which enables term mapping between ontologies, specifically addressing clinical terminologies). These tools have been taken up by a number of different projects and communities, which will contribute to the tools' long term sustainability. As an example, the publication of the BiobankUniverse semantic mapping tool and the implementation of Bioschemas into the MOLGENIS platform has led to its adoption by the EUCAN-Connect project as a tool to aid data harmonisation. Additionally, the MOLGENIS data resource incorporates the EOSC minimal metadata guidelines for dataset descriptions (called ‘EDMI’), and is also findable via Google dataset search, consequently improving compliance with the FAIR data principles.

                                                                       ----------

‘A Basic Introduction to Bioimage Analysis’ - webinar recording available!

During the webinar on 11 April 2019, Christian Tischer from the EMBL Centre for Bioimage Analysis (CBA) explained basic concepts of bioimage analysis, starting with a short overview of what bioimage analysis actually is and why it is useful. Subsequently, the topics of image formation, restoration, filtering and segmentation, as well as object measurements and image analysis quality control were addressed.

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.

 

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, ISBE is introduced to the researcher community.

ISBE (Infrastructure for Systems Biology Europe) is a knowledge-based research infrastructure that will empower European researchers across academia, clinics and industry to implement systems biology approaches addressing how the dynamic interactions between biological components (molecules, cells, tissues, organs) leads to the functioning of living organisms. ISBE will actively support scientists in facilitating model-compliant data generation, accessing resources for storing and sharing research assets, making their research assets FAIR compliant (that is findable, accessible, interoperable, and reusable) and creating predictive computational multi-scale models of biological systems based on integration of highly diverse data sets. In addition, ISBE will provide training for infrastructure users and providers to offer efficient services.

During the Interim Phase, ISBE will start to offer web-based services, named ISBE light. Three types of interrelated service modules will be available and rely on in-kind contributions from the ISBE community:

  • Modelling & Theory
    Services for building, validating, exploiting and expanding predictive computational models of biological systems that enable research groups to implement systems biology strategies.
  • Stewardship
    Manage research assets (data, models, procedures, etc.) in a concerted manner to make them FAIR, i.e. Findable, Accessible, Interoperable and Re-usable (together with the FAIRDOM programme).
  • Education & Training
    Develop and make available a portfolio of MSc, doctoral and postdoctoral teaching and training programmes.

For more information visit http://isbe.eu or www.isbe.nl

 

UPCOMING EVENTS

CORBEL Webinar: Genomics and clinical data at your fingertips with open-source software: tranSMART & cBioPortal
04 June 2019, 15:30 CEST

Speakers: Jan-Willem Boiten (Lygature), Menno de Vries (Netherlands Cancer Institute)

The propelling importance of genomics data in present-day health research is not yet supported with user-friendly software solutions that expose these data in a manner easily appreciated by clinical researchers. Clearly, there is an obvious need for tools that integrate genomics and other molecular biology results with the phenotypic and clinical outcome data. This webinar presents two widely used open-source solutions that aim to address this gap, tranSMART and cBioPortal; their usage will be illustrated with some practical use cases taken from practical use in the Dutch context as well from projects supported by CORBEL WP3.

  1. tranSMART (http://transmartfoundation.org/) is a data integration, sharing, and analysis platform for clinical and translational research. It allows users to search, view, and analyze data through a web interface, thereby allowing easy access to explore such data from multiple domains at study level.
  2. The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-source resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from more than 20,000 tumor samples from almost 100 cancer studies.

This webinar intends to give a flavor of the potential of these solutions in practical translational research. For those scientists interested in a deep-dive, a CORBEL training will be scheduled for later this year.

 

INFRAFRONTIER / IMPC Conference 2019 - Genetic Variation, Big Data and Ageing
3-5 June 2019, Helsinki

This year´s joint annual meeting of the INFRAFRONTIER and the International Mouse Phenotyping Consortium (IMPC) will be focussing on Genetic Variation, Big Data and Ageing – three top prerequisites for a sustainable success of the upcoming era of precision medicine. It will provide an excellent opportunity to support a better alignment of the unique platforms and repositories of the two leading international associations for functional mouse genetics with current ageing and population genetics initiatives. At the same time, the conference will support interactions with human genetics centers and clinical consortia in Europe and all over the world.

CORBEL will be present at the congress with an exhibition stand, providing information about the project's work and the participating research infrastructures.

 

CORBEL Webinar: Towards a GDPR Code of Conduct for Health Research: where are we today?
11 June 2019, 14:30 CEST
Speaker: Michaela Mayrhofer (BBMRI-ERIC)

On 25 May 2019, exactly one year after the GDPR came into force with direct effect in the EC Member States, the European Data Protection Board (EDPB) will publish its final Guidelines 1/2019 on Codes of Conduct and Monitoring Bodies under Regulation 2016/679. The possibility of drawing up a Code of Conduct is specified in Article 40 of the GDPR. The Guidelines will specify the how, including how to seek approval and monitor the code’s adherence. The GDPR Code of Conduct for Health Research initiative is aiming for a sector specific code in the area of health. It shall help to demonstrate GDPR compliance and to navigate across the various national country derogations that apply for health research related data transfer.

The aim of the webinar is to present an update on the GDPR Code of Conduct for Health Research development: What has been achieved so far? What obstacles were encountered? What about the country derogations? Why is the timeline a moving target? When to expect public consultation? When will the code be finalized and operational? 

 

44th FEBS Congress 2019 - From Molecules to Living Systems
6-11 July 2019, Krakow

The 44th FEBS (Federation of European Biochemical Societies) Congress aims to provide an outstanding international forum in the area of Europe and neighbouring regions for the face to face exchange of knowledge and ideas across the molecular life sciences.

CORBEL will be present at the congress with an exhibition stand, providing information about the project's work and the participating research infrastructures.

 

REPORTS

Exchanging Industry Engagement Best Practices among Research Infrastructures

EATRIS recently represented the biomedical RI community and CORBEL at the CALIPSOplus / SINE 2020 second Industry Office meeting.

The CORBEL Innovation Help Desk and related activities were introduced to the research infrastructures in the neutrons/synchrotron domains. Although the scope of the physics infrastructures is quite different from that of the biomedical ones, similar challenges were identified and lively discussions emerged. Read more about it here.

                                                                       ----------

RI-PATHS project hosts second round of participatory workshops on measuring the impact of research infrastructures

The second round of RI-PATHS (Research Infrastructure imPact Assessment paTHways) workshops took place from 08-10 May 2019. These were participatory workshops contributing to the creation of a common methodology for assessing the socio-economic impact of research infrastructures. Facilitated by evaluation experts and economists, the workshops were attended by numerous research infrastructures, from Europe and beyond. Each workshop had a different focus:

  • at DESY (Hamburg, Germany), the focus was on quantifiable economic impacts of research infrastructures;
  • at ELIXIR (Cambridge, UK), it was on new ways of documenting network effects in research, innovation and training; and
  • at ALBA (Barcelona, Spain), it was on exploring impact-relevant interactions between research infrastructures and users.

The ELIXIR-hosted workshop, attended by research infrastructures ranging from biological and biomedical sciences, to astronomy and social sciences, was especially relevant to virtual and distributed research infrastructures. For these, a major challenge lies in demonstrating to funders the added-value of 'working together' - 'the whole being greater than the sum of its parts'. The workshop report is being drafted, and further information on the project are available at https://ri-paths.eu.

 

UPDATES FROM PARTNERS

Over the past few months, EMBRC headquarters has been taking shape. The RI has a new Executive Director, Dr. Nicolas Pade, as well as a new Scientific Officer and Project Manager. A Communications Officer and Access Officer are expected to join the team by the summer.

EMBRIC, a cluster group to improve technology transfer practices that EMBRC is a part of, recently published a position paper on the principles for preserving, accessing, exploring and sharing marine genetic resources. Read more about it here.

Fourth call for application for Transnational Access to European plant phenotyping facilities
Plant phenotyping is a major bottleneck for addressing the physiological questions and unraveling the genetic controls of traits and plant performance. The European Plant Phenotyping Network 2020 (EPPN2020) provides researchers belonging to academic and industry groups with access to its 31 phenotyping facilities located all over Europe. The facilities can be used for experiments with either scientific or technological objectives. EPPN2020 has just launched its fourth call for application for transnational access, open to European groups but also open (to a limited extent) to groups originating from emerging countries or international research centers. The call closes on 8th of July 2019. Costs of such experiments are supported by the project. EPPN2020 is funded by the Horizon 2020 programme of the EU with €10 million and has the goal of opening European facilities and developing methods and standards in imaging, information systems, and data analysis. EPPN2020 coordinates its activities with the ESFRI infrastructure project EMPHASIS, developing a long-term strategy for operation of phenotyping infrastructure in Europe. For more information on available facilities, rules for access, and application forms, please visit: https://eppn2020.plant-phenotyping.eu

In the framework of EMPHASIS and EOSC-Life, the position of a research scientist in the field of bioinformatics and data management is open at Forschungszentrum Jülich. Details can be found here.

INFRAFRONTIER2020 Trans-national Access Call: Precision rat model development
The main objective of this INFRAFRONTIER open call is to facilitate access for the wider biomedical research community to the unique infrastructure and scientific expertise of the participating INFRAFRONTIER partners, to deliver novel rat mutant models that will advance knowledge of human disease and will be of widespread use in biomedical science. Many cognitive and physiological characteristics make the rat an ideal human disease model and choice for laboratory studies in neurobiology, cardiobiology, and immunology. Recent advances in genome-editing technology will be used to develop new rat models of human disease. More information and the call application forms are available here. Proposal submission to proposals(at)infrafrontier.eu by 31 May 2019.

Advance your research project by benefiting from EU-OPENSCREEN-DRIVE funding to access our EU-OPENSCREEN screening partner sites and EU-OPENSCREEN-DRIVE partners. Apply now to the following transnational open calls:

- EU-OPENSCREEN-DRIVE Chemoproteomics Call: Under this call EU-OPENSCREEN-DRIVE offers funding to enable transnational access to chemical proteomics facilities. A total of six projects will be selected in two separate calls (scheduled May 2019 and November 2020). Within this first call, our partners will support three successful applicants providing collaboration on target identification and compound disposition studies. The call will be closed on July 31th, 2019, 20:00 CET.

- EU-OPENSCREEN-DRIVE Screening Call: Under this call, 12 EU-OPENSCREEN-DRIVE partner institutions will each offer one predefined screening technology to external users. The user will provide the biological question and the related assay matching the offered techniques. EU-OPENSCREEN will provide its collection of 100,000 chemical compounds for each of the 12 selected user projects in-kind. The first screening call will be launched on June 1st, 2019, and will be open until September 30th, 2019, 20:00 CET.

New people @ EU-OPENSCREEN ERIC: We are happy to welcome Federica Rossella (Federica.rossella@eu-openscreen.eu) as Compound Quality Technician and Kathy Skopelitou (Kathy.skopelitou@eu-openscreen.eu) as Administrative Project Manager as new employees at EU-OPENSCREEN.

Nanobiotechnology laboratory: Call for proposals
The European Commission’s Joint Research Center (JRC) Nanobiotechnology laboratory has opened a call for proposals: external researchers can apply for open access to their state-of-the-art equipped facilities designed to foster interdisciplinary studies. Special emphasis lies on characterisation of nanomaterials, microplastics, nanomedicines, advanced materials and their interactions with biological systems, as well as on the detection, identification and characterisation of nanomaterials in food and consumer products. The call will close on 7 June 2019. More information is available here.   

Rare Disease Models and Mechanisms-Europe registry open for registration
Solve-RD – Solving the unsolved Rare Diseases” is a large European research project funded by the EU for five years (2018-2022) under Horizon 2020. The consortium is collaborating with European reference networks (ERNs) to improve the diagnosis of rare diseases. Solve-RD is about to establish a European Rare Disease Models & Mechanisms Network (RDMM-Europe) using the successful Canadian blueprint as a role model. The goal of RDMM-Europe is to link clinicians discovering new genes in patients with rare diseases with basic scientists, who can functionally analyze equivalent genes and pathways in model organisms. Solve-RD will provide 50 Seeding Grants (€20,000 each) to fund projects that will allow rapid confirmation of potentially disease-causing genes and elucidation of the underlying molecular disease mechanisms. For more information please check the Solve-RD website or contact Sanja Hermanns (sanja.hermanns@med.uni-tuebingen.de).

MERIL final conference from 24-25 June in Lisbon
The MERIL-2 project Final Conference will take place from 24-25 June 2019 at the Calouste Gulbenkian Foundation in Lisbon (Portugal). This event will be the perfect opportunity to engage with the RI community, find out about the main project outputs and achievements, and explore future directions for MERIL. Following the main event, there will be a dedicated workshop on RI impact assessment organised by the RI-PATHS project.

International Clinical Trials Day (ICTD) Conference: ECRIN and its French scientific partner, the French Clinical Research Infrastructure Network (F-CRIN), organised a conference in Paris, France on May 20th, 2019 to celebrate International Clinical Trials Day (ICTD).The theme of this year’s conference was ‘Patient Stratification Studies: Challenges and Opportunities’. ICTD 2019 brought together around 150 people, including ECRIN’s internal stakeholders and partners, and additional scientists and policymakers from France, the rest of Europe, and beyond. The meeting objective was to engage participants in discussion on the issues and challenges of clinical research, and in particular patient-centred research in the (academic) European clinical research context. For more information, see here.

 

PUBLICATIONS

‘Evaluation of repositories for sharing individual participant data from clinical studies’ (2019) Banzi R., Canham S., Kuchinke W., Krleza-Jeric K., Demotes-Mainard J., Ohmann C., Trials, DOI: 10.1186/s13063-019-3253-3

'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., Mannisto 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., bioRxiv, DOI: 10.1101/543686

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.

Imprint