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CORBEL News | Issue 8

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Thank you very much for your interest in CORBEL! You receive this newsletter because you are a member of the CORBEL consortium and/or have subscribed to the newsletter and/or have been a recipient of the BioMedBridges newsletter. We would like to make you aware of the fact that if you do not want to receive this newsletter any more, you can unsubscribe at any time by clicking on the "unsubscribe from this list" link at the bottom of every newsletter. Alternatively, you can request a newsletter administration link here to be sent to your e-mail address, which provides you with the opportunity to unsubscribe or edit your subscription data.

 

NEWS

 

CORBEL extended until May 2020

In the course of a recent grant agreement amendment, the European Commission approved the cost neutral extension of CORBEL until the end of May 2020. The consortium is very grateful for the chance to extend and expand its efforts to support European biological and medical research by harmonising user access to biomedical research infrastructures, unifying data management, creating common ethical and legal services, and offering joint innovation support!

 

CORBEL 2nd Open Call for Research Projects – a Status Update

The CORBEL 2nd Open Call still accepts applications for access to high-end technologies and services. In the Open Call, more than 20 facilities from 10 biomedical research infrastructures offer their services to European scientists from academia and industry. The Open Call, launched in March 2018, has raised significant interest already - CORBEL has received applications covering all 5 available access tracks during the first three rounds of submission. Projects that have already passed the scientific and technical evaluation will take up their work shortly.

Scientists from industry, wanting to advance their R&D projects, can now find specific information concerning industrial applications on the CORBEL website.

The current submission round of the 2nd Open Call will close on 31 October 2018.

 

Legal templates available on the CORBEL Innovation Helpdesk portal

One of the objectives of the CORBEL Innovation work package is to provide guidelines or templates for legal agreements applying to research collaborations and material or data transfer situations. Although such agreements require tailor-made approaches, content wise there are common segments to be captured which are provided in templates and guidelines ('tools'). Recently the CORBEL Innovation Helpdesk website has been updated with two documents which provide help:

If you have questions or require further help please contact the Innovation Helpdesk.

 

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, INFRAFRONTIER is introduced to the researcher community.

INFRAFRONTIER

Europe urgently needs to find solutions for the grand challenges in the area of human health. Different forms of cancer, metabolic diseases such as diabetes and obesity, cardiovascular diseases, rare diseases, and infectious diseases are constant threats to socio-economic well-being – in Europe as well as globally.

Mammalian models have proven to be a vital resource for biomedical research to understand human diseases and to develop treatments for them. Mouse studies have been key to most of the Nobel Prizes in Medicine and Physiology awarded within the past 20 years and to breakthrough discoveries in the functional basis of human health and disease. They also play an important role in pre-clinical screening and drug development.

The INFRAFRONTIER Research Infrastructure provides access to high-quality, high-efficiency resources and data for the development, phenotyping, archiving and distribution of mammalian models. Access is open for individual researchers and for national, European and international research programmes.

The national Mouse Clinics organised in INFRAFRONTIER offer access to a comprehensive first-line systemic phenotypic screening, covering a wide range of physiological functions ranging from cardiovascular, neuro-behaviour and metabolism expertise, to detailed pathology assessments. They are perfectly equipped to provide customised deep-drilling analyses tailored to the specific needs of a research project.

The nodes of the European Mouse Mutant Archive (EMMA) establish and manage Europe’s largest non-profit repository for maintaining medically relevant mouse mutants and making them available to a global scientific community. EMMA comprises over 6,000 mutant mouse lines carrying targeted, transgenic, induced and other types of mutations.

INFRAFRONTIER also provides specialised services, such as the development of mouse and rat models for human diseases, access to mouse resources for cancer and for microbiome research, as well as training and consulting.

For more information visit www.infrafrontier.eu.

 

UPCOMING EVENTS

5th MIUF meeting

October 15, 2018 in Paris

The CORBEL Medical Infrastructure Users Forum (MIUF) meets for the fifth time on October 15, 2018 in Paris (France) to continue the discussion of efficient development and use of bio-medical RIs. The meeting is open to scientific communities interested in medical research and is intended to discuss

  • the structuring of medical research communities at the pan-European level
  • the emerging needs of medical research projects in the context of the big data and personalised/stratified medicine approach and
  • the challenges raised in terms of development and deployment of data services

The final program is available here.

Joint Institut Pasteur and INFRAFRONTIER meeting: Modeling microbial ecosystems of mammals

October 15-16, 2018 in Paris

Institut Pasteur in Paris and INFRAFRONTIER will offer a joint meeting featuring the challenges and the current tools used in modeling the microbial ecosystems of mammals. The microbiota plays an important role in the development, immunity and physiology of its mammalian host. The aim of the meeting is to bring together the specialists of the field to discuss novel insights into the microbiota-host mutualism and parasitism, and focus on the new models and approaches to explore this relationship. In the near future, these advances will lead to the development of preventive and therapeutic strategies based on microbiota manipulation, and allow the microbiota to become a key diagnostic component in precision medicine. For detailed informations and registration, please visit the meeting website.

ELIXIR Innovation and SME Forum: Data Driven Innovation in Industrial Biotechnology

October 15-16, 2018 in Frankfurt/Main

This free ELIXIR Innovation and SME Forum on Data Driven Innovation in Industrial Biotechnology in Frankfurt is open to both large and small companies and aims to inform about ELIXIR resources and create a space to network for industry and academia.

Topics:

  • Big Data Challenges and Opportunities
  • Data driven Biotechnology in Germany and Europe
  • Services offered by de.NBI and ELIXIR
  • Flash Talks from companies showcasing their products

More information can be found here.

3rd CORBEL Annual General Meeting

October 16-17, 2018 in Paris
 

Webinar: West-Life: Lessons learnt from developing a virtual research environment

October 23, 2018 15:30 CEST

The West-Life project (https://about.west-life.eu) is a Horizon 2020 project funded by the European Commission to provide data processing and data management services for structural biology, in particular to support integrative methods. It has developed important enhancements to existing web services for structure solution and analysis, new pipelines to link these services into more complex higher-level workflows, and new data management facilities. Through this work it has made the benefits of European e-Infrastructures more accessible to life-science researchers in general and structural biologists in particular. The presentation will discuss some lessons learned along the way. Participation in the webinar is free, please register here.

Machine Learning for Image Analysis

October 29-31, 2018 in Heidelberg

CORBEL, EMBL, German BioImaging and NEUBIAS are organizing a joint blended learning course on Machine Learning for Image Analysis. The course will be a great mix of intensive learning, extensive hands-on and community networking, consisting of

  • Up-front online sessions: Participants will review the fundamentals of machine learning in three up-front webinars complemented by online tutorials. The webinars will take place on 2nd, 9th and 16th October 2018, 12:00 - 14:00 but a recorded alternative can be provided.
  • On-site workshop: Next, they will apply their knowledge at an on-site workshop (EMBL Heidelberg, October 29-31), in small interactive groups (the workshop has 20 available seats and ~8 trainer/lecturer), to both reference datasets and their own data.
  • Follow-up online sessions (optional): After the on-site workshop, two optional advanced training webinar, complemented by a online tutorials, will be given on 9th and 16th November 2018. These will focus simulation of data, transfer learning and boosting.

After the course participants should be able to explain the fundamentals of machine learning methods suitable for image analysis, consult others in strategies to obtain ground truth, give advice in training and using a neural-network and perform simple quality control on the results of one selected ML approach. More information about the course (program & trainers) and venue, are available at the course website.


Training Course: Data Management in Clinical Research

November 15, 2018 in Paris

CORBEL Work Package 3 is organising a training course on Data Management in Clinical Research, taking place on 15 November 2018 in Paris. The course is designed for clinical research professionals who are not data management expert and aims to raise awareness on the new challenges raised by the digital revolution in clinical research. Presentations and discussions will cover a broad spectrum of issues related to data management, sharing, reuse, and analysis. Registration (free, but mandatory) is possible here. The program can be found here.


Workshop: Best practices in Public-private collaborations

December 12-13, 2018 in Ljubljana

The CORBEL Innovation Helpdesk team in conjunction with the EATRIS Slovenia National Node and the University of Ljubljana is organizing a best practice workshop on the theme of public-private collaboration on 12-13 December 2018 in Ljubljana, Slovenia. This 2-day event will focus on all relevant aspects of setting up such collaborations, from initial contacts through planning and negotiation to completion of legal agreements and project implementation. In addition to plenary lectures covering various aspects there will be a use case for participants to work on in teams.

The workshop is aimed primarily at academic researchers from the biological and medical research infrastructures and their affiliated institutes who are or expect to be involved in the organization and implementation of such collaborative research programmes.

Participation is free of charge. For more information, please contact innovation(at)corbel-project.eu. Please register for the workshop here. The draft agenda can be found here.

 

MEET US @

ELIXIR Innovation and SME Forum: Data Driven Innovation in Industrial Biotechnology
October 15-16 2018, Frankfurt/Main

ENABLE Conference
November 7-9 2018, Copenhagen
Exhibition at the career event on 7 November 2018

 

REPORTS

 

The challenges of sharing resources

From 1-4 July 2018, CORBEL participated in the third biennial Core Technologies for Life Sciences (CTLS) conference in Ghent, Belgium. The CTLS association aims to “bring together scientists, technical and administrative staff working in or in close association with shared resource laboratories, such as core facilities, technological platforms and research infrastructures” (ctls-org.eu) – an aim that was well achieved by means of the conference, which was organised by the VIB research institute.

Framed by several satellite events (one of which was prepared by Infrafrontier), the conference addressed topics such as data management, quality control and career paths in core facilities in a number of plenary and parallel sessions. CORBEL partner Ilaria Nardello gave a talk on the global-reach potential of EU research infrastructures, featuring the case of EMBRC-ERIC, in the plenary session on ‘International Alliances, Networks and Cooperation’. Michael Raess (Infrafrontier) and Cath Brooksbank (EMBL-EBI) addressed the topics of ‘Quality management in distributed research infrastructures’ and ‘Fostering interactions between core facilities and research infrastructures’. Mery Piña (MIRRI) introduced the European Marine Biological Research Infrastructure Cluster (EMBRIC), a cluster project related to CORBEL. During the poster session, CORBEL was presented with a focus on the 2nd Open Call. Many interested participants visited the CORBEL booth for information about the consortium or individual research infrastructures throughout the whole conference.

The historical conference venue Het Pand contributed just as much to the positive atmosphere of the conference as the framework programme that took the 300 conference participants to selected places within the beautiful city of Ghent, providing many opportunities to network.

Interested conference participants from academia and industry visited the CORBEL booth.

Marie Vidal (ISBE), Frauke Leitner (Euro-BioImaging), Michael Raess (Infrafrontier) and Christiane Hauk (MIRRI) were some of the CORBEL partners that represented the consortium at the conference.

 

‘Advance the World. Together.’

This was the ambitious motto under which participants from 59 different countries gathered from 12-14 September 2018 at the historical ‘Hofburg’ in Vienna for the biennial International Conference for Research Infrastructures (ICRI). The conference was organised by the Austrian Federal Ministry of Education, Science and Research within the framework of the Austrian Presidency of the Council of the European Union. Following up on the ICRI 2016 conference in Cape Town, the conference provided a forum for discussion about different aspects concerning national, pan-European as well as global research infrastructures, such as policy issues, internationalisation, human resources and the societal value of research infrastructures.

The European biomedical research infrastructures united in CORBEL were well represented at the conference. Ilaria Nardello (EMBRC-ERIC) was a panellist in the plenary session on ‘Sustainable research infrastructures on the global arena’, addressing the challenges of ERIC implementation and issues of long-term sustainability. CORBEL co-coordinator Erik Steinfelder (BBMRI-ERIC) and Andrew Smith (ELIXIR) gave talks in the parallel sessions ‘Research Infrastructures and Data’ and ‘Enhancing the Societal Value of Research Infrastructures’, respectively. In a number of sessions, the necessity to interconnect research infrastructures was emphasised – thus, projects like CORBEL seem to be of great importance for the further development of the research landscape.

The conference was preceded by the launch of the European Strategy Forum on Research Infrastructures (ESFRI) Roadmap on 11 September 2018. Niklas Blomberg, Director of ELIXIR and CORBEL coordinator, was invited as a panellist to introduce the integration of services across RIs as it is practiced in CORBEL. Recordings of the Roadmap launch event and the ICRI plenary sessions are available on YouTube. During the ESFRI Exchange of Experience meeting also preceding ICRI, Ilaria Nardello and Andrew Smith also shared their views with new ESFRI research infrastructures on how to progress effectively through their preparatory phases.

CORBEL stand-up displays underneath beautiful chandeliers.

Lecture hall at the 'Hofburg'.

 

UPDATES FROM PARTNERS

In the course of the recent update of the European Strategy Forum on Research Infrastructures (ESFRI) Roadmap, four biomedical research infrastructures that are also involved in CORBEL received the ‘Landmark’ status: Euro-BioImaging, EU-OPENSCREEN ERIC, ERINHA and EMBRC-ERIC. ESFRI Landmarks are research infrastructures that are fully implemented or in the advanced implementation phase, that are recognised for their excellence and ‘represent major elements of competitiveness of the ERA’ (ESFRI Roadmap 2018). The Roadmap 2018 was officially presented on 11 September 2018 in Vienna. A recording of the event is available here.

BBMRI-ERIC, ECRIN and EATRIS recently published a joint statement on Horizon Europe. It was handed over to the European Commissioner for Research, Science and Innovation, Carlos Moedas, during ICRI 2018 by Erik Steinfelder, the Director General of BBMRI-ERIC.

BBMRI-ERIC has published its Annual Report for 2017, highlighting the key achievements last year. In addition to a detailed section on BBMRI-ERIC’s main activities, the report contains an overview of the National Nodes’ activities and the EU projects that BBMRI-ERIC is currently involved in. BBMRI-ERIC has also launched a new webinar series on quality management. Anyone who is interested in quality management issues in biobanking will be able to join.

Slovakia applied to be observer country of ECRIN. A pilot audit for data centre certification was run in Asia.

EMPHASIS and ELIXIR, together with the European Plant Phenotyping Network 2020 (EPPN2020) as well as members of the MIAPPE initiative (Minimum Information about Plant Phenotyping Experiments) met to explore any possible collaboration in data management, data production and analyses, looking for common and complementary objectives and tasks (more information here).

On the EMPHASIS website, information is available about several newly founded plant phenotyping initiatives. A complete list of plant phenotyping events is available on the website of the EMPHASIS partner initiative IPPN (International Plant Phenotyping Network). 

ERINHA recently launched their new website.

The Finnish Euro-BioImaging node is currently looking for a Project Manager.

The EU-OPENSCREEN inauguration ceremony took place on 25 september 2018 in Berlin.

INFRAFRONTIER will organize its second INFRAFRONTIER Stakeholder Meeting together with the International Mouse Phenotyping Consortium (IMPC) on December 3 to 4, 2018, in Munich, Germany. The meeting will thematically focus on the use of animal models in the research of causes and cures for Rare Diseases and in the development of new gene therapies. Papers may be submitted until October 30. Details for submission and registration can be found here.

The European Commission support for Instruct-ERIC continues with 3 new Horizon 2020 projects awarded. Spain submitted their application for joining Instruct-ERIC as a full member and the Spanish Ministry of Science, Innovation and Universities and the Council for Scientific Research (CSIC) has confirmed a 8 millions Euros investment for the purchase and installation of a Cryo electron microscope at the National Centre for Biotechnology (CNB, Instruct-ERIC-Spain) located at the campus of the Universidad Autónoma de Madrid. For these and more news about Instruct-ERIC have a look at the latest newsletter.

MERIL has introduced an additional data visualisation tool that allows you to discover the MERIL dataset interactively and provides you with the visual ‘big picture’ of the research infrastructure landscape in Europe. The new tool gives you more freedom to choose how you filter the dataset and visualize the results in the different dashboards and is designed to help you discover information on research infrastructures, with the aim of encouraging new partnerships and collaborations.

The MERIL-2 project continues to evolve - in this course, the MERIL database now accepts nominations of research infrastructures that are only open to national users. Previously, MERIL's eligibility checklist stipulated that only research infrastructures of “more than national relevance” should be listed. As of 25 July 2018, the sixth criterion has been amended with the aim of expanding MERIL's coverage and to broaden its usefulness.

The second Call for Transnational Access to the EPPN2020 facilities has been finished with 30 applications and the third Call is open now.

 

PUBLICATIONS

Mind the Gap: From Tool to Knowledge Base (2018) Mayrhofer, M.T., Schlünder, I., BIOPRESERVATION AND BIOBANKING, DOI: 10.1089/bio.2018.0018

PiGx: Reproducible genomics analysis pipelines with GNU Guix (2018) Wurmus R. et al., Giga Science, DOI: 10.1093/gigascience/giy123

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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