EOSC-Life brings together the 13 BMS RIs (biomedical science research infrastructures) on the ESFRI Roadmap. The project consortium comprises all the legal entities of the established BMS RIs, including a set of national centres that provide access to leading international scientific service platforms. It also includes the coordinating centres and key institutes of the preparatory phase infrastructures – in total 63 partners and linked third parties in 14 countries. The EOSC-Life consortium represents a truly continent-scale effort. Collectively the BMS RIs have national nodes in 23 European countries, and EOSC-Life will benefit from the established outreach and technical coordination functions among them.
Learn more about European research infrastructures here.
The following is a list of partners – click expand to learn about what they do and their roles in EOSC-Life!
ELIXIR*, the European life-science infrastructure for biological information, is a unique initiative that consolidates Europe’s national centres, services, and core bioinformatics resources into a single, coordinated infrastructure.
ELIXIR brings together Europe’s major life-science data archives and connects these with national bioinformatics infrastructures throughout ELIXIR’s members, of which there are 22 across Europe. ELIXIR’s organisational team (‘Hub’) is based in the UK, within the European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI).
ELIXIR supports users addressing the Grand Challenges in diverse domains ranging from marine research via agriculture to health research and medical sciences. By consolidating the expertise and outputs of such a broad range of institutes, ELIXIR offers researchers access to bioinformatics expertise, data, tools, compute resources and training for their research.
* ELIXIR is represented in the project by EMBL, the European Molecular Biology Laboratory
ELIXIR has a multitude of connections both across other research infrastructures in Europe and further afield, but also through the Node network of academic institutes and industry connections. ELIXIR’s users range from wet-lab scientists, to bioinformaticians, to service providers across a broad spectrum of scientific domains. ELIXIR understands the needs of researchers striving to find the best methods for data analysis and discovery, but also the needs of service providers who require rapid access to novel and diverse datasets.
As coordinator ELIXIR is the lead organisation involved in the Project Management (WP11) of EOSC-Life, and offers the underlying technical, financial and administrative management for the project to run smoothly and meet all objectives. ELIXIR is well placed for this task as it has extensive experience in managing large, EU-funded project consortia, such as the CORBEL and FAIRPlus projects. ELIXIR has existing connections and collaborations with the other European research infrastructures, and through the Project Management role will facilitate other organisations involved in EOSC-Life to fulfil their obligations.
Other individuals that are part of ELIXIR through the Nodes are also involved in WPs of the CORBEL project. ELIXIR Partners co-lead the following WPs:
WP1 – Helen Parkinson (EMBL-EBI)
WP5 – Ludek Matyska (ELIXIR-CZ)
WP7 – Steven Newhouse (EMBL-EBI) and Chris Lawerenz (ELIXIR-DE)
WP9 – Gabriella Rustici (ELIXIR-UK)
WP11 – Niklas Blomberg, Friederike Schmidt-Tremmel (ELIXIR Hub)
The pan-European Biobanking and BioMolecular resources Research Infrastructure – European Research Infrastructure Consortium (BBMRI-ERIC) improves the accessibility and interoperability of the existing comprehensive collections, either population-based or clinical-oriented, of biological samples from different (sub)populations of Europe. With 20 member states and one international organisation, BBMRI-ERIC is one of the largest research infrastructures in Europe. Its Directory lists over 600 biobanks and over 100 million samples and datasets, accessible through the Negotiator tool. BBMRI-ERIC also supports members through its CS IT, Quality Management and ELSI services.
BBMRI-ERIC is Work Package Co-Leader for WP4, WP6 and WP10, supported by our Linked Third Parties.Website
EATRIS, the European Infrastructure for Translational Research offers a new collaboration model for fostering innovation. The infrastructure plays a fundamental role in the advancement of knowledge and technology in translational research and drug development. With over 90 leading institutes, across 12 EU Member States, EATRIS provides access to the entire pipeline of academic translational infrastructure and expertise, and optimises the route from discovery to proof-of-concept in medicines development. It provides a new development pathway, open to researchers and companies in need of support for advancing biomedical innovations.
EATRIS helps pooling and exploiting the translational academic capacities of the infrastructure in omics technologies to enable researchers to better address the scientific and societal challenges of Personalised Medicine.
Under EOSC-Life, together with BBMRI, EATRIS will co-lead the open call on sensitive data foreseen under WP3. In addition EATRIS is WP co-lead for Education and Training (WP9) and contribute to the communication WP (WP10).
EATRIS also works closely with EATRIS data core team formed by five EATRIS linked third parties: University of Helsinki (FI), IMTM (CZ), Lygature (NL), VHIR (ES), and Mario Negri Institute (IT). EATRIS linked third parties will contribute to the project through WP1 Publishing FAIR RI data resources in EOSC; WP2 Make tools and workflows interoperable and reusable in the EOSC across RIs and WP4 Policies, specifications and tools for the management of data for biological and medical research. Under WP8, Mario Negri Institute will lead a task on assessing the impact of life-science open data in the cloud on data reproducibility.
ECRIN is a not-for-profit intergovernmental organisation that supports the conduct of multinational clinical trials in Europe.
Multinational clinical trials provide greater access to patients, facilities and medical expertise; raise methodological standards; enable the sharing of costs, tools and procedures; increase the potential for broad implementation of research outcomes; and prevent duplication of research.
However, various trial obstacles – from infrastructure interoperability to regulatory and ethical requirements and management and funding issues – deter many investigators from attempting multinational trials. This is especially the case for independent or academic trials which are more frequently conducted in a single country than industry-sponsored trials. This limited scope means reduced potential impact on global public health.
ECRIN provides a means to overcome the above challenges by offering researchers support to prepare and implement multinational trials. Support areas include the preparation of applications for funding, protocol evaluation, trial management, quality assurance and more. The clinical research ecosystem is currently undergoing a digital revolution, with the possibility to reuse data already collected in the context of research projects (trials, cohorts, registries), or healthcare and health systems (electronic health records, hospital datawarehouses, health databases) for research purposes.
EOSC needs a framework for secure archiving, discovery, dissemination and analysis of human -omics, translational research, clinical research and health research data. Services for access-controlled human data will need to meet the challenges of 1) limited sharing, needed in transnational collaborative research projects, as well as 2) long-term sharing, where the opportunity for reuse of data will increase the rate of scientific discovery and validation, leading to greater impact in the scientific and medical/healthcare fields. A secure authentication and authorisation process is essential to enable the scientific community to use human data without compromising privacy and informed consent. So are guidelines and compliance processes.
It is incumbent on the BMS RIs to define and drive secure human data services in the EOSC. This should include:
– Data governance and support to the user-driven deployment of workflows within a secure and compliant cloud environment.
– ELSI Guidelines, ELSI helpdesk, GDPR compliance, Code-of-conducts, etc.
ECRIN, as a co-leader of WP4, will develop and promote policy recommendations and specifications to work with multi-source environments, and propose solutions enabling secure federated storage, access and sharing of sensitive health data for research purposes.
The European Marine Biological Resource Centre (EMBRC-ERIC) is a pan-European Research Infrastructure for marine biology and ecology research. It provides researchers a variety of unique resources that are custom to the demand of the user and is a driver in the development of blue biotechnologies, supporting both fundamental and applied research activities for sustainable solutions in the food, health and environmental sectors.
With 6 of its marine research infrastructures involved in the project, EMBRC brings its expertise in FAIR data management, data integration, data policies, trainings and ABS principles and legislations. The RI is involved in WP3, WP4, WP6, WP8 and WP11 and will work to provide specialized expertise to bring the capabilities of big science projects to the wider research community and direct access to FAIR data and tools in a cloud environment. EMBRC will also address data policies and overall creating an open, continent-scale, collaborative and interdisciplinary environment for data science to help create a solution to the problem EOSC-Life is tackling.Website
EMPHASIS is the European infrastructure for plant phenotyping. Currently in the preparatory phase, EMPHASIS will enable researchers to use facilities, resources and services for multi-scale plant phenotyping from 2021 onwards. In particular, EMPHASIS will facilitate research on plant performance in different agro-climatic scenarios in Europe to address the challenge of food security in a changing climate.
Role in EOSC-Life
Within the framework of EOSC-Life, EMPHASIS will enable interoperability of plant phenotyping data according to the FAIR principle, making them re-useable for the plant phenotyping community and beyond. In addition, EMPHASIS will develop data analysis tools to address specific scientific challenges related to plant sciences in general, plant breeding, and development of technologies including imaging, robotics and automation. In its activities, EMPHASIS will build on existing initiatives to make data management FAIR such as MIAPPE and BrAPI, which will directly contribute to the development of joint standards and ontologies as well as incorporation of both plant genetic and phenomic information. EMPHASIS is involved in four Work Packages of EOSC-Life (WP 1, WP 2, WP 3, WP 8) and will demonstrate how to link phenomics and other omics data.Website
European Research Infrastructure on Highly Pathogenic Agents AISBL (ERINHA-AISBL) is the Pan-European distributed Research Infrastructure dedicated to the study of highly infectious emerging and re-emerging diseases classified as Risk Group 4 (RG4).
ERINHA brings together European high containment and complementary research facilities and expertise in the field of highly infectious diseases and preparedness to outbreaks of high consequences pathogens.
It provides access to the rare resources – Biosafety Level 4 laboratories – to perform excellence-driven research (developing diagnostic capabilities, increasing the understanding of diseases, developing new interventions (e.g. therapeutics, vaccines), helping to translate interventions to the market).
ERINHA contributes to the enhancement of the European and global capacity, capability and emergency preparedness in response to global outbreaks.
Within EOSC-Life project ERINHA, along with its French national node INSERM, is involved in WP1 “Publishing Fair RI data resources in EOSC”, WP4 “Policies, specifications and tools for secure management of sensitive data for research purposes”, co-leads WP6 “FAIRification and provenance services”.
ERINHA deals with sensitive and highly sensitive data in the framework of its research activities on high-consequence pathogens of outbreak concern. Its main contributions concern the field of hosting, distribution, access control mechanisms for sensitive data, sensitive data hosting and processing Policy Framework, as well as FAIRification of data.Website
EU-OPENSCREEN ERIC (EU-OS) is a non-profit research infrastructure, which operates on a global scale. We are funded by European countries (currently Czech Republic, Denmark, Finland, Latvia, Norway, Poland, Spain with Germany as host country) and offer access to academic high-throughput screening facilities and medicinal chemistry groups in these countries. Scientists from academia and industry can implement their screening projects at EU-OS partner laboratories using our European Chemical Biology Library (ECBL), which is composed of 100,000 commercial compounds plus a growing number of compounds collected from academic chemistry groups. Hit optimisation can be done at our medicinal chemistry sites. All compounds will be profiled in a panel of about 20 non-project specific assays, which will deliver extensive information on physico-chemical, cellular toxicity and anti-microbial properties.
Compound structures and primary screening data will be made public in the European Chemical Biology Database (ECBD), with the possibility to request an embargo period of up to three years so that data can be patented or published.
The primary activity of EU-OPENSCREEN is to provide access to its distributed research infrastructure for scientist seeking a better understanding on how fundamental molecular processes act to govern biological function at the organismal, tissue, cellular and pathway levels. EU‑OPENSCREEN will extend the application of Chemical Biology and will develop novel research ‘tools’ for all fields of the Life Sciences, incl. molecular, cell, plant, structural and micro -biology; synthetic and medicinal chemistry; pharmacology and early drug discovery. EU‑OPENSCREEN will drive quality and consistency in the generation and analysis of biological data by creating consistency in the process of target validation through the application of agreed experimental and data analysis standards across its network.
The main contribution of EU-OPENSCREEN in EOSC is to work in cooperation with its RI partner sites IME, IMG, CSC and IMIM to deliver the demonstrator project on Chemical and Structural biology (WP3). This aligns well with the European Chemical Biology Database resource, which will be developed by EU-OPENSCREEN and the creation of 15-20 large data sets from the Bioprofiling of the commercial collection of 100k compounds.
In WP1, the EU-OPENSCREEN partner IME will manage the process of cloudification of data sources as co-lead of this WP and as a partner in WP2 working on implementation of chemo-informatics tools into the cloud. EU-OPENSCREEN will directly participate in the management work package (WP11).Website
Euro-BioImaging’s mission is to allow imaging research to flow unhindered, thereby ensuring excellent research and development across the life sciences. In practical terms, Euro-BioImaging offers all scientists – regardless of affiliation, area of expertise, or field of activity – open access to imaging instruments, expertise, training opportunities, and data management services that they do not find at their home institutions or among their collaboration partners. Euro-BioImaging has 15 members hosting 21 Nodes, located across 9 countries and EMBL and offers access to over 40 different imaging technologies.
In terms of data, Euro-BioImaging offers a wide range of image data services – the Nodes support their users in data management and quality control, primary data analysis and the transfer of large data sets to the home base. In addition, collaboration with the BioImage Archive (www.ebi.ac.uk/bioimage-archive/ ) which was launched as public central archive for biological and biomedical image data, which will make it easier for researchers around the world to store, share, access and analyse images. This wealth of scientific images can now start to be reused, reanalysed, and interconnected to create new knowledge. New computational tools for image analysis and processing accessible via the cloud will complement the offered services.
With the advances in modern imaging technologies, the wealth of digital imaging data is rising exponentially. While this will lead to exciting breakthroughs, new challenges are also presenting themselves such as image data storage and interoperability. Euro-BioImaging co-leads Work Packages 2 and 3 in EOSC-Life.Website
INFRAFRONTIER is the European Research Infrastructure for the development, phenotyping, archiving and distribution of genetically modified mouse models for basic biomedical research. It is our mission to provide unique scientific resources, services, and expertise to advance the understanding, prevention and treatment of human diseases using rodent models (mouse and rat).
The main services we offer to the scientific community are:
In EOSC-Life, INFRAFRONTIER is cooperating with many partners on the FAIRification and cloud deployment of animal model resources (e.g. IMPC data). Seven of our core consortium partners are involved in publishing FAIR RI resources (WP1). These include heterogeneous types of data and workflows which enable applications in various fields of work within and beyond the INFRAFRONTIER research infrastructure.
One of our key tasks is to enhance the usability of RI resources for a broad user community and to create links to research areas with human data. Therefore, we are developing user driven analysis workflows in WP2.
Moreover, the INFRAFRONTIER coordination office is co-leading WP8 – International Impact, Innovation and Sustainability and is contributing to WP5 – User management and access services.
Instruct-ERIC is the single point of access to technology and expertise for structural biology research. Through its specialist research centres in Europe, Instruct-ERIC offers funded research visits, training, internships and R&D awards. By promoting integrative methods, Instruct-ERIC enables excellent science and technological development for the benefit of all life scientists.
Instruct-ERIC is utilising its cross-research infrastructure support tool, ARIA, to support the project activities and enhance integration with other research infrastructures in the life-sciences domain. As co-leads of WP5, Instruct-ERIC will also be supporting the delivery of Life Science Login, a single sign-on technology that will allow for seamless data sharing across multiple life-science domains.
Due to Instruct-ERIC’s core focus on training, the Instruct Hub is also involved in the training activities within EOSC-Life through WP9.
The Instruct-ERIC community includes data experts within the structural biology domain who also take a leading role in EOSC-Life activities. WP2 Workflows is co-led by Instruct-IT and WP3 Demonstrators and Open calls is co-led by Instruct-ES.
ISBE – Infrastructure for Systems Biology Europe – is a coordination effort to interconnect the best experimental and modeling facilities for Systems Biology in Europe. ISBE provides stewardship and insight into biological data and their acquisition. It is composed by one pillar, FAIRDOM, and three national candidate nodes: ISBE.NL, ISBE.SI, ISBE.IT. Each node provides different services to the user community, and has its own budget, but ISBE Italy is in charge of the interim coordination of the ESFRI project ISBE (ISBE Europe).
FAIRDOM is the Data and Model Stewardship pillar of ISBE prep phase (http://fair-dom.org). FAIRDOM platform and resources support Systems Biology to make Data (models, data, SOPs, samples, workflows) FAIR, and generalisable to any kind of FAIR management. The FAIRDOM has been integrated with national data e-Infrastructures in Norway (NeLS) and Slovenia (p-ISA).
ISBE.IT is an organized, multidisciplinary and inclusive scientific community devoted to the understanding of biological complexity for biosociety development. The Systems Metabolomics service at ISBE.IT (sysbio.it/isbe-service) provides a complete metabolomic platform to perform ad hoc experiments. These techniques, coupled with constraint-based modeling approach and/or validated through flow study technique (Metabolic Flux Analysis) is becoming an important example of systems biology applied to precision medicine, in particular if integrated with other omics data.
ISBE.NL is the Netherlands node of ISBE. Services are listed at http://isbe.nl/, but, in particular, the Make Me My Model (M4) pillar help customers to make various types of data (e.g. omics data , kinetic data, etc.) predictive and understood. M4 performs both dynamic data analysis via building phenomenological models with a top-down approach (with ISBE.SI), and bottom-up mechanism-based modelling (ISBE.NL). The Live Model Repository pillar of ISBE.NL develops systems biology tools for construction, modification and simulation of kinetic models and for the storage of curated models through JWS Online (https://jjj.bio.vu.nl/).
ISBE.SI NIB bring into consortium hands on experience in handling heterogenous plant sciences datasets, that NIB hold and will be used in the project. NIB has developed and is developing tools to assist with easing the end biological user experience, like plantBIOMINE, a tool assisting knowledge discovery (biomine.ijs.si), QuantGenious (quantgenius.nib.si), a tool allowing robust high-throughput quality analysis, and, in collaboration with FAIRDOM, pISA that allows for easy data management in real-time from the sampling to the mathematical modeling.
Role in EOSC-Life
CIRM (Centre International de Ressources Microbiennes) is a network of five Biological Resource Centres of the microbial domain (mBRCs). This network belongs to the Institut national de la recherche agronomique (INRA), the leading European agricultural research institute and the world’s second largest in agricultural research; INRA’s research is dedicated to food, nutrition, agriculture and the environment.
CIRM preserves the microbial resources generated by a large number of projects conducted by INRA since its creation in 1946. As a distributed infrastructure, CIRM is composed of five thematic mBRCs: food bacteria, human and animal pathogenic bacteria, plant-associated bacteria, filamentous fungi and yeasts of biotechnological interest. It currently preserves and distributes more than 22,000 isolates. The majority of these isolates are natural, but CIRM also maintains mutants and reference strains for research. This unique set of biological resources with which many data are associated (date of access, geographical origin, substrate of isolation, phenotypic, molecular and taxonomic characteristics, etc.) has a socio-economic impact in fields as varied as food fermentations, white and green biotechnologies as well as the control of plant pathogens and bacterial infections in animals. As a supplier of authenticated and reliable strains with their associated data, CIRM participates in research partnerships with university and private scientists. In addition to the conservation and distribution of strains, CIRM offers a wide range of services to the scientific community (identification and characterization of strains, molecular typing, confidential security deposit, field collection, etc.). The expertise of CIRM’s five mBRCs covers taxonomy, genomics, biotechnology, etc.
CIRM operates according to ISO 9001 certified processes to (i) ensure the quality of strains, associated data and services provided and (ii) provide assurance that the regulatory and legal framework is respected.
CIRM is participating in the construction of the MIRRI Information System, the objective of which is to display data associated with mBRC isolates from all MIRRI partners. CIRM will be involved, within WP1, in the exposure of mBRC data from France and other countries (Poland, Belgium…) in EOSC.
INRA will also be involved within WP2 in the deployment of tools and pipelines for the analysis of data associated with MIRRI biological resources. The set of workflows will be designed, using a modular approach and packaged to be easily deployed on cloud platforms, following the guidelines co-constructed within the WP2.Website (MIRRI)
Charité in Berlin is one of the largest university hospitals in Europe. All of the clinical care, research and teaching is delivered by physicians and researchers of the highest international standard. The Berlin Institute of Health (BIH) aims to translate innovations from the lab to the clinic. BIH focuses on developing new therapies and diagnostics that not only improve or maintain quality of life, but also create value.
The co-head of EOSC-Live WP Cloud Deployment Services is assigned to Charité. It acts as the beneficiary organization for one of Europe’s largest scientific clouds, the de.NBI Cloud. This German federated cloud provides EOSC-Life with powerful computing and storage resources. The supported cloud appliances enable adequate access to resources. The cloud platforms enable the use of existing and future workflows and software packages. Strong focuses are training courses and extensive measures within the scope of data protection and IT security according to GDPR.Website
The Data Readiness Group, based at the Oxford e-Research Centre in Engineering Science, researches and develops methods and tools to improve data reuse; works for data transparency, research integrity and the evolution of scholarly publishing.
Working with and for researchers, service providers, journal publishers, library science experts, funders and learned societies in the academic as well as in the commercial and governmental setting, we design and develop open source software, to improve collection, representation, sharing and publication of multi-dimensional data. We also build interoperability standards; we run informative, educational registries to enable data quality and readiness, essential in Data Science.
Role in EOSC-Life
Authors of the FAIR principles, we are the centre of many FAIR-enabling international efforts, as part of ELIXIR, the USA NIH, the Research Data Alliance and GO-FAIR. In EOSC-Life, we lead on the FAIRification Task in WP6, contributing via our community-driven FAIRsharing, FAIR maturity indicators and FAIRassist activities.Website
The Fraunhofer organisation is Europe’s largest application-oriented research organization. It’s research efforts are geared entirely to people’s needs: health, security, communication, energy and the environment. Fraunhofer IME is one of the Partner organisations of EU-OPENSCREEN, the European Infrastructure for Chemical Biology and Screening. The focus of Fraunhofer IME is to contribute steadily and substantially to the development of new approaches for the diagnosis and treatment of diseases. One research covers the development of bioinformatics and data management processes to help drug discovery and target validation. Areas of interest include FAIR and Federated data approaches, as well as the application of machine learning for hypothesis generation in target validation. For example, the Fraunhofer “Medical Data Space“ Modeled on the basic functionalities offered by the “Industrial Data Space“, the Medical Data Space offers decentralized data management for medical bioinformatics allowing autonomous and secure data storage as well as data exchange between networked databases.
With EOSC-LIFE, Fraunhofer is working to facilitate the cloudification of RI data sources within WP1. Fraunhofer-IME has extensive expertise in scientific data management and technical implementation of cloud-based resources that will be used to help RI-based users get their data sets to point where they are suitable for deployment.Website
BSRC Fleming is a top-ranked Greek non-profit research organisation focusing on scientific and technological excellence, training and innovation in biomedical sciences. The Center has gained international recognition for its pioneering research towards understanding the molecular and cellular basis of human diseases such as autoimmune diseases, cancer, neurodegenerative disorders, osteoporosis, pulmonary fibrosis and others, and the development of new approaches for their diagnosis and treatment. The Center is internationally recognized for its projects in translational research on pathway, target and biomarker identification and validation, preclinical evaluation of therapeutics in animal models and novel drug development and screening.
Fleming’s strength and international visibility lies on its focus and success in developing and characterizing animal models that mimic human disease and the Center has consequently invested heavily on related infrastructures. Over the last decade Fleming has established state-of-the-art facilities, including an Animal House (currently with the highest capacities in Greece), as well as Transgenesis and Cryopreservation, Genomics, Proteomics, Flow Cytometry, Bioimaging, MicroCT, Endoscopy and Histopathology Units. Fleming is the Coordinator of 2 National Research Infrastructures: InfraforntieGR/Phenotypos and ELIXIR-GR, active in the areas of generation, archiving and phenotyping of animal models of disease and bioinformatics/biocomputing resources, respectively.
BSRC Fleming has a long standing expertise in developing and characterizing animal models and transgenic tools. The Center is an EMMA Node since 2009 and is now developing into a large Research Infrastructure for “disease-oriented” characterization of mutations (secondary to tertiary phenotyping). Over the last decade BSRC Fleming has contributed variable data types (clinical, -omics and imaging data) to in-house and international data repositories that are growing exponentially.
With its internationally attributed expertise and data dissemination record, Fleming has become an advocate of data sharing and database interoperability. The Center is an active Infrafrontier RI partner and already a highly involved contributor in the first phase of implementation in the EOSC-Life WP1. As a contributor, BSRC Fleming provides its long and diverse expertise in life science data and its specialized knowledge and experience from the field of specific animal models of autoimmune diseases, cancer, neurodegenerative disorders and others. In the context of EOSC-Life the Center serves as a data expert in one of the selected EOSC-Life use cases and will continue to support the project implementation and cloud readiness within WP1 as the project progresses.Website
Biocenter Oulu (BCO) RI operates in the University of Oulu, is open-access and serves academic and non-academic customers in research and R&D projects. BCO Transgenic Core is part of the ESFRI INFRAFRONTIER acting as the Finnish European Mouse Mutant Archive (EMMA) node and BCO Electron Microscopy (EM) Core is part of the EuBI RI through BCO Tissue Imaging Center. EM Core provides services and training in EM techniques and it is specialized in the ultrastructural analysis of gene-modified mouse tissues.
Role in EOSC-Life
We are producing original EM images on wild-type mouse tissues in the WP1. The goal is to collect images showing tissue-specific ultrastructures, which can be utilized as a reference by researchers studying gene-modified mice. Images are not subject of any ownership or confidentiality issues, are readily available and can be made open-access. Image data is being used to develop data handling and cloudification practices.Website
CIRMMP, in collaboration with the Magnetic Resonance Center (CERM), constitute an infrastructure for Life Sciences, which provides a unique environment for research in Structural Biology.
CERM/CIRMMP infrastructure is specialised in structural biology, molecular biology, protein/complex structure determination, functional characterisation, drug discovery, structure-based vaccine design, bioinformatics, NMR methodology, relaxometry and metabolomics.
Both orgnisations feature 12 spectrometers for solution and solid-state NMR covering the widest range of magnetic fields available, from high resolution NMR (950 MHz) down to 0.01 MHz with relaxometry, equipped with several probes that allows to meet all conceivable experimental conditions.
CERM/CIRMMP has a long-standing experience in access provision dating back to the 90s. Thanks to our scientist’s expertise and a dedicated technical staff we can support both expert and non-expert NMR users coming from many different fields of biological sciences: biomaterials, pharmaceutical, food industries and agricultural sciences. A taste of NMR applicability is available here (http://bit.ly/introNMR)
CERM/CIRMMP is an Instruct-ERIC Core Center for NMR.
CIRMMP has a long-term expertise in the provisioning of computational workflows via web interfaces, exploiting grid and cloud computational infrastructures. A main development to be achieved in EOSC-Life is to deploy approaches ensuring data FAIRness using methods shared with other RIs. In other words, we aim to further develop our protocols in order to make them compliant with the FAIR principles, thereby supporting users in achieving openness of their data.
CIRMMP will lead WP2 and is also involved in WP1, for data aspects. It will contribute to the optimal use of structural biology data by all other involved RIs.
The National Center for Biotechnology (CNB) is part of the Spanish Research Council (CSIC) and it hosts the “Instruct Cryo EM Image Processing Center” (I2PC). It is because of this tight connection with Instruct (the Research Infrastructure for Structural Biology) that we participate in EOSC-Life.
Our expertise is in the handling and processing of image data obtained by modern electron microscopies across Europe that are observing vital molecular machines at quasi atomic resolution. Naturally, we aim at making these data, together with the analysis workflows required for their proper interpretation, accessible in the EOSC. We refer to large data sets (one single microscope produces daily several TeraBytes of data) that are very noisy and with complex information. In fact, they are very similar to the well-known “CT scanners” in biomedical imaging, only that the “patient” is not a human being but a very tiny (in the tens of nanometers range) molecular machine.Website
The Spanish Type Culture Collection (CECT) is a broad scope collection that currently maintains circa 10,000 microbial strains (most are prokaryotes, followed by yeasts and filamentous fungi). It is a Service of the University of Valencia (UVEG). As a Biological Resource Centre, it maintains and supplies authenticated and reliable strains and associated data. Strains information is available through the CECT on-line catalogue, allowing users to find suitable strains for research and quality control among other uses. The catalogue is integrated in other tools like WDCM. The CECT also provides an on-line yeast identification service (www.yeast-id.org) based on genetic profiles.
The UVEG-CECT is involved in the construction of the MIRRI Information System and as part of the Statutory Seat (SS) will host the Collaborative Working Environment (CWE). Through this platform data associated with mBRC isolates from all MIRRI partners will be available. UVEG-CECT will be involved in EOSC-Life WP1 to expose the resources data in a FAIR compliant manner.Website
The Ospedale Policlinico San Martino (USMI) is a University Hospital, including both clinical and research units, tightly connected to the University of Genova. Recognized as an Institute of Excellence in Health Research for Oncology and Neurosciences.
It has a tradition in management of biological resources. It’s a member of the European Culture Collections’ Organisation (ECCO) and of the World Federation for Culture Collections (WFCC). It also is a WIPO International Depositary Authority (IDA).
After having partnered in many EU funded projects for Biological Resource Centers, it is now participating in the setting up of the Microbial Resource Research Infrastructure (MIRRI) and it is a member of MIRRI-IT, a Joint Research Unit aimed at building the Italian National Node of MIRRI.
The Bioinformatics laboratory has a long experience in data management for biological resources. It is maintaining since 2000 the Common Access to Biological Resources and Information (CABRI) Network Services (www.cabri.org), devoted to availability of quality microbial resources in Europe, as a result of the homonymous EU funded project.
Its expertise is witnessed by various publications on advanced data sharing technologies, including e.g. early implementation of Web Services, definition of workflows and development of workflow management services, and their adoption for biological resource information.
It currently coordinates the activities of MIRRI-IT for data sharing and distribution with the aim of supporting data export to the information system of MIRRI and providing autonomous services for access to data of Italian microbial resources.
The USMI contribution in the EOSC-Life project include participation in WP1, WP2 and WP5.
For WP1, USMI will support and contribute to the setting up of the tools needed for exposing data on microbial resources from MIRRI to EOSC. It will contribute to the definition of best technologies to be adopted in the Tools Collaboratory, WP2. Finally, USMI will participate in the definition of special needs of the Research Infrastructure for user access and management (WP5), including identification of special access rights for reserved/restricted data provided by the biological resource centers.
USMI will contribute also to training and outreach initiatives, according to the needs of the project and its expertise.Website
Masaryk University (MU) is the second largest Czech university with around 32,000 students and 4,500 staff in 9 faculties and 2 university Institutes, with Faculty of Medicine and Institute of Computer Science (ICS) directly involved in the project. MU is also partner or a national leader of several biomedical research infrastructures, e.g. ELIXIR, ECRIN, EATRIS and EuroBioImaging.
ICS is a leading national institute in the area of e-infrastructures and cybersecurity. It hosts national research infrastructure CERIT Scientific Cloud (CERIT-SC) and the Czech Cybercrime Centre of Excellence (C4E).
Through faculties of Medicine and National Sciences together with CEITEC Institute MU is a national leader in the biomedical research.
This creates at MU a unique environment where many research areas interact together supported with a strong information technology research and development that is tailored to the need of interdisciplinary activities.
In EOSC-Life, both ICS and Faculty of Medicine are involved in the work on policies and tools for a secure environment able to deal with sensitive data (the scope of WP4). This reflects the increasing need of MU researchers in different life science areas to be able to store and analyse growing datasets while guaranteeing strict legal requirements on the work with sensitive human data.
With its expertise in cybersecurity and building international e-infrastructures, ICS and its centre CERIT-SC leads a capacity building project for ELIXIR CZ. CERIT-SC, together with CSC FI (ELIXIR FI), is responsible for the ELIXIR AAI development, management and operation. CERIT-SC has been developing national e-infrastructure for BBMRI.cz since 2011. This infrastructure has become an early concept of what has become an access pipeline for European BBMRI-ERIC in 2016-2017. CERIT-SC also provides AAI for BBMRI-ERIC since second half of 2016. CERIT-SC has long standing interaction with other biomedical institutions, e.g. as a member of West-life and now EDIReX projects (related mostly to the INSTRUCT RI).
With this expertise MU (CERIT-SC) is co-leading the User management and Access services workpackage (WP5) and is also involved in the Cloud deployment workpackage (WP7).Website
CSC – IT Center for Science is a Finnish center of expertise in information technology owned by the Finnish state and higher education institutions. We provide internationally high-quality ICT expert services for higher education institutions, research institutes, culture, public administration and enterprises to help them thrive and benefit society at large.
CSC has expertise in the design, implementation and maintenance of user identification across organisational boundaries, such as the Haka identity federation service and Virtu trust domain for public servants, EduuniID and REMS. We have also applied our expertise in the management of sensitive biomedical research data in the international ELIXIR network.
The ELIXIR Node in Finland is hosted at CSC – IT Center for Science. Node provides cloud and storage resource and training for life sciences, with integrated computational access to very large biological data resources.
We are focusing on WP5 User management and access services AAI implementing federated life science authentication and authorization infrastructure and access proposal/control system. In addition we support management and operation of this system including its connection to life science RIs service providers.
We are focusing as well on WP7 Cloud Deployment Services. It provides a set of integrated cloud resources to support the cloud based FAIR RI data resources (WP1), workflows (WP2) and science demonstrators (WP3) that are being supported within the project.Website
Institute of Molecular Genetics is a leading biomedical institution performing basic research in molecular biology and genetics oriented on microbial and mammalian genomics, oncogenes and retroviruses, mechanisms and regulation of gene expression, structure and topology of cells, cell signalling, molecular immunology, and molecular developmental biology.
Czech Centre for Phenogenomics (CCP) is a large research infrastructure unique in combining genetic engineering capabilities, advanced phenotyping and imaging modalities, specific pathogen free (SPF) animal housing and husbandry, as well as cryopreservation and archiving, all in one central location – at BIOCEV campus.
National Infrastructure for Chemical Biology (CZ-OPENSCREEN) is a state-of-the-art infrastructure for chemical biology and genetics, whose mission is to identify new molecular probes and to develop new tools for research of chemical compounds – candidates for the development of new potential therapeutics.
CCP goal is to produce high-quality data that will not only function as a scientific reference catalogue, but will also enable comprehensive meta-analyses that could uncover otherwise hidden disease relationships and functional interactions.
CZ-OPENSCREEN offers to its users cooperation in assay development, high-throughput screening, data validation, chemical compound optimization and cheminformatic support, and it also operates the National compound collection.
In the INFRAEOSC-04 project, CZ-OPENSCREEN will deliver, in cooperation with EU-OS, the demonstrator project on Chemical and Structural biology (WP3). The Czech Centre for Phenogenomics will deliver data for WP1 (Publishing FAIR RI data resources in EOSC).Website
Consiglio Nazionale delle Ricerche (CNR; Italian National Research Council) is the largest multidisciplinary public research institution of Italy. It carries out advanced research activities in all sectors of knowledge and promotes their applications for the scientific and socio-economical development of Italy. CNR operates all over the Country, with more than 90 institutes diffusing its competences and promoting cooperation with local and international institutions and companies.
EOSC-Life includes two CNR’s Institutes with expertise in different areas of the project.
Institute of Biochemistry and Cell Biology (CNR-IBBC): INFRAFRONTIER RI
CNR is a founding partner of the European Mouse Mutant Archive (EMMA) and Infrafrontier networks and has established their Italian node and the new Mouse Clinic at the “A. Buzzati-Traverso” Campus, Monterotondo (Rome). Since June 2019 these infrastructures are part of the new IBBC. They are integrated components of Infrafrontier and Intern. Mouse Phenotyping Consortium (IMPC), for generation, phenotyping, cryopreservation and dissemination of mutant models of human diseases, with their bioinformatics resources. Advanced imaging modalities are also major research areas, in collaboration with IBBC’s multi-sited cellular/ biological node of EuroBioImaging.
Fabio Mammano, Associate Researcher of CNR-IBBC and Full Professor of Applied Physics at the Dept. of Physics and Astronomy “G. Galilei”, University of Padua, is the Italian Delegate for INFRAFRONTIER and IMPC, by appointment of the Italian Ministry of University and Research.
Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (CNR-IBIOM): ELIXIR RI
IBIOM is in charge of the management of the Italian node of ELIXIR, led by CNR and involving other 16 Institutions under a Joint Research Unit agreement. It offers a vast portfolio of high quality bioinformatics services, tools and data resources for the life science community. Publicly available bioinformatics services are complemented with downloadable, stand-alone tools used in structural bioinformatics, genomics and proteomics. The node hosts several flagship data resources and databases.
Graziano Pesole, Associate Researcher of CNR-IBIOM and Full Professor of Molecular Biology at the “A. Moro” University of Bari, is the Manager of the Joint Research Unit and Coordinator of the Italian node of ELIXIR.
Institute of Biochemistry and Cell Biology (CNR-IBBC):
Complete infrastructures, equipment and services are readily available to international users for mouse mutant model production, phenotypic and advanced imaging analysis, cryopreservation and distribution, genotypic/phenotypic data curation and disease model annotation, as well as related training activities, according to the international reference standards.
EMMA-Infrafrontier staff at IBBC will be involved in particular in WP1, Tasks 1.2 and 3.1, participating in the implementation of specific support of RI-nominated data/data resources (e.g. EMMA-Infrafrontier, IMPC disease model’s genotypic/phenotypic data, etc.) and open calls and actively implementing specific curatorial activities for the robust accessibility and required sustainability of WP1 data/data resources and services.
Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (CNR-IBIOM):
Computational resources, including high performance and cloud computing services, are operational and readily available to international users. Bioinformatics services are complemented with extensive training activities, oriented to the international life science community.
IBIOM, with the ELIXIR-IT associated staff, will be specifically involved in WP7, task 7.4.3. Its role will be to use the container execution platform developed in 7.4.3 as an environment for an orchestrated Galaxy deployment on cloud resources. This will be used to test and support the workflows selected in WP2. The Galaxy platform will be made available with all its workflows and software packages by utilizing the life science’s authentication and authorisation infrastructure. This task will support the portable Galaxy deployment at scale of this environment, drawing on knowledge from across the Biomedical Sciences RIs.
National Institute of Biology (NIB; http://www.nib.si/eng) is a public non-profit organisation performing basic and applied research in the fields of biology, biotechnology, medicine, ecology as well as interdisciplinary fields, joining biosciences with physics, chemistry, statistics and bioinformatics. It employs approximately 135 people and was awarded the ISO 9001 quality certificate for all its activities. NIB was granted ISO 17025 accreditation for detection of genetically modified organisms and their products in foodstuffs and agricultural products of plant origin as well as for detection of microorganisms. We are also European reference laboratory in the area of plant health.
Its Department of Biotechnology and Systems Biology, participating in the project, is focused in bioinformatics and systems biology of plants, gene expression quantification and plant biotic stress. The Department is an active member in EU Infrastructures for Systems Biology (ISBE) and Bioinformatics (ELIXIR). We are also actively promoting the setup of FAIR data management system and have developed a user friendly tool pISA-tree enabling both the wet and the dry lab scientist in the group to organise, analyse and access data in FAIR manner
Role in EOSC-Life
NIB is involved in the demonstrator Plant A+ (Taking Plant Omics Data through Annotation, Acquisition, and Analysis to Application) within the WP3. With long-time experience with omics technologies, as well as standardisation initiatives, NIB is contributing its potato datasets that will be properly annotated and deposited to cloud. NIB have been involved in development of tools, using ontologies (eg. GoMapMan), which can be integrated into analysis pipelines for better data annotation. We will also implement pISA-tree to locally organise the data in FAIR manner and then perform batch upload to cloud.Website
The Flanders Marine Institute (VLIZ) acts as the coordination and information platform for marine and coastal-related scientific research in Flanders, and serves as an international contact point. VLIZ has set up a strong collaborative network through numerous cooperation agreements with Flemish research groups and administrations and integrates its activities in multiple national and international networks.
The VLIZ Data Centre provides assistance, technologies and tools to support marine data management. Within international networks, VLIZ participates in the development of data infrastructures, and is heavily involved in the management of international e-infrastructures: EMODnet, LifeWatch WoRMS, GLOSS, EurOBIS. VLIZ hosts marine data archives and catalogue systems, and MarineRegions. VLIZ also contributes to the organisation of the EMBRC data infrastructurs, and leadings the virtual access work package of the ASSEMBLE Plus project.
In EOSC-Life VLIZ participates mainly in WP 1. 2, and 6. VLIZ’s experience working with numerous data systems for and with different Research Infrastructures is important here: in particular its archives, catalogues, virtual research environments. Within WP1, VLIZ will provide the data experts that will work on connecting the data resources to the EOSC and support the related demonstrators and calls. Within WP2 VLIZ will contribute to the developments of the tools collaboratory and support the related demonstrators and calls. Within WP6, along with UVIGO and UPV, VLIZ will design specific mechanisms that contribute to the compliance of data with ABS (the Nagoya Protocol).Website
The University of the Basque Country (UPV/EHU) is one of biggest Universities in Spain (about 45,000 students and 4,500 research/academic staff), conforming an Euroregional Campus of Excellence with the Univ. of Bordeaux. UPV/EHU participates in EOSC-Life through the Plentzia Marine Station (PiE-UPV/EHU) which is the Marine Research Station of the University. Together with ECIMAT in the UVIGO it forms the Spanish node of EMBRC-ERIC offering services to researchers utilizing marine bioresources.
UPV/EHU along with UVIGO, under the auspices of EMBRC-ERIC, will work in the development of data policies in relation to the utilization of genetic resources in compliance with Access and Benefit Sharing (ABS) regulations that will be carried out in WP4, identifying relevant cases in which BMS RIs may be affected by ABS regulations and proposing a BMS-RI ABS Data policy in accordance with the identified cases. UPV/EHU will also work in WP6 towards the design of specific mechanisms that may contribute to the compliance of biological data with ABS principles.
Universidade de Vigo (UVIGO) is a Spanish academic and research institution with circa 22,000 students and 2,500 research and academic staff. The participation of the UVIGO in the project will be undertaken by Toralla Marine Science Station of (ECIMAT; www.ecimat.org). ECIMAT provides state-of-the-art marine research facilities to more than 150 researchers from the CIM (Centre of Marine Research, University of Vigo) and other users from public and private institutions. Since 2014 ECIMAT is one of the two facilities that integrate the Spanish national node of the European Infrastructure (ESFRI) EMBRC-ERIC (European Marine Biological Resource Centre).
UVIGO along with UPV/EHU, will explore the impact of Access and Benefit Sharing (ABS) regulations in the utilization of biological, non-human genetic resources: identifying relevant cases in which BMS RIs may be affected by ABS regulations and proposing a BMS-RI ABS Data policy in accordance with the identified cases. Moreover, together with UPV/EHU and VLIZ, it will propose technical solutions that contribute to the compliance of data with ABS principles.Website
The University of Cambridge (UNICAM) is one of the world’s leading academic institutions; it comprises 31 constituent Colleges, 150 faculties and departments, organised into six schools.
UNICAM is a member organization of the UK Node of ELIXIR and plays a significant role in the training landscape, not just in the UK, but across the whole of the European ELIXIR project. UNICAM co-leads the ELIXIR training platform and supports the development of training to address key skills gaps amongst UK scientists; it is also responsible for the development and implementation of a framework for assessing training quality and impact of the entire ELIXIR training programme.
In particular, the Bioinformatics Training Programme of the UNICAM’s School of Biological Sciences is an ELIXIR-UK Node Service and is dedicated to address the shortage of bioinformatics training in traditional education by offering a wide-ranging portfolio of hands on training courses in bioinformatics and data science, at both undergraduate and post-graduate level.
Each year, on average, this programme organizes 100 short hands on courses, training 2,300 postgraduates and 1000 undergraduates. The team running this programme, led by Dr Gabriella Rustici, collaborates with many international partners (including the Carpentries, the ISCB Education Committee and GOBLET) to identify training gaps, develop training solutions to address such gaps and build training capacity on a global scale. Dr Rustici co-leads the ELIXIR Training Platform and is also Associate Director of Training for Health Data Research UK, a multi-funder institute for health and biomedical informatics.
UNICAM, in partnership with EATRIS, has the coordination of EOSC-Life WP9, “Training of the EOSC Life community”, including overseeing its execution, monitoring its progresses, and ensuring the accomplishments of its deliverables. Specifically, UNICAM will be co-leading the following tasks:
(i) training EOSC-Life staff including data experts,
(ii) allocation of the central budget available for the development of new training solutions based on training needs analysis, and
(iii) lead the strategy development for training impact assessment.Website
The Institute of Data Science (IDS) aims to involve students, researchers’ partners and stakeholders coming from different disciplinary backgrounds, to train the next generation of data scientists.
Science has evolved in such way that multiple disciplines are now fully reliant on each other. It is the era of multi – and – interdisciplinarity; where distinct disciplines work together to develop their own fields, and integrate with each other, so that new scientific approaches can also be developed.
Vast amounts of data being generated across all segments of society. If taken advantage of, these data offer an unprecedented opportunity to accelerate scientific discovery, to improve healthcare and wellbeing, and to strengthen our communities
Our organization has experience in developing a data-driven research culture in fields that are not traditionally familiar with novel methods for collecting, managing, and analysing data.
Currently, the appropriate management of data is a major concern across the broad scientific community; that is because existing data often gets lost, and that prevents the many benefits that the reuse of data has to offer. Scientific data can be reused for validating existing findings, answering new research questions, and testing new methods. Our goal is to provide researchers with the necessary knowledge and tools to do so, in a comprehensive way so that researchers with a non-technical background also can understand.
One of the core aspects of EOSC Life is the commitment with making data Findable, Accessible, Interoperable and Reusable – i.e. FAIR. We can offer researchers our expertise in developing training and tools for the implementation of the FAIR principles to their practice.
Within the spectrum of EOSC Life, the IDS has collaborated with ELIXIR, BBMRI and FAIRsharing. We are mainly involved in “WP6: FAIRification and provenance services”, but also aim to collaborate with other work packages such as WP4 “Policies, specifications and tools for secure management of sensitive data for research purposes” and WP9 “Training of the EOSC Life community”.Website
CRS4 is one of the leading centres in Italy for research and development activities in information technology, bioinformatics, distributed and high-performance computing. The interdisciplinary centre’s research activities focus on the development of enabling technologies and applied computing science in high priority areas recognized as strategic at the regional, national and European levels.
The interdisciplinary expertise found at CRS4 will allow it to contribute to task 2.5, providing automated testing of EOSC-Life tools, workflows and infrastructure. Beyond system failures caused by technical issues, higher level constructs, like workflows, can easily be invalidated by updates to model data sets or changes in tools. Automated deployment and verification will ensure that unexpected results from these instruments are promptly detected and signalled so that contributors can provide corrections and users are warned before relying on the results.Website
The Università degli Studi di Milano-Bicocca (UNIMIB) is a public university located in Milan, Italy, providing undergraduate, graduate and post-graduate education. The University of Milano-Bicocca has fourteen departments in the fields of Economics-Statistics, Law, Medicine, Psychology, Science, Sociology and Education. In twenty years the Bicocca University has achieved the highest national and international honours: 3rd largest university in Lombardy by student population; 2nd highest ranked Italian university among those comparable in size (according to ANVUR); number 55 on the list for best 150 universities less than 50 years’ old, according to THE Times Higher Education; 11 out of 14 departments are defined as “of excellence” by the Italian Ministry (MIUR). With about 900 teachers and researchers, Bicocca offers a wide range of degree courses: 32 Bachelor, 36 Master’s Degree, and 5 Unified Master’s Degree courses. There are 33,000 enrolled students, of which over 2200 are international.
UNIMIB hosted the ISBE Italy candidate node in 2013-2019, and is the representing entities of ISBE Europe in the EOSC-Life consortium. The majority of ISBE Italy initiatives take place here.Website