EOSC-Life brings together the 13 Biological and Medical ESFRI research infrastructures (BMS RIs) to create an open collaborative space for digital biology.
It is our joint response to the challenge of analysing and reusing the prodigious amounts of data produced by life-science. Managing and integrating this data is beyond the capabilities of most individual end-users and institutes. By publishing data and tools in a Europe-wide cloud EOSC-Life aims to bring the capabilities of big science projects to the wider research community. Federated user access (AAI) will allow transnational resource access and authorisation. EOSC-Life establishes a novel access model for the BMS RI: through EOSC scientists would gain direct access to FAIR data and tools in a cloud environment available throughout the European Research Area.
EOSC-Life will make BMS RIs data resources FAIR and publish them in the EOSC following guidelines and standards (e.g. EDMI). Overall this will drive the evolution of the RI repository infrastructure for EOSC and integration of the BMS RI repositories. EOSC-Life will implement workflows that cross disciplines and RI boundaries and address the needs of interdisciplinary science. Through open hackathons and bring-your-own-data events we will co-create EOSC-Life with our user communities , providing a blueprint for how the EOSC supports wide-spread and excellent data-driven life science research. EOSC-Life will address the data policies needed for human research data under GDPR. Interoperable provenance information describe history of sample and data to ensure reproducibility and adherence to regulatory requirements.
Expertise: Data management, integration and access, training and user engagement, advanced imaging technologies, Industry engagement.
The European Molecular Biology Laboratory (EMBL) was established in 1974 and is supported by over twenty countries. EMBL is a centre of excellence for research in molecular biology.
It is a distributed international research organization (24 member states) with its main laboratory in Heidelberg. Research at EMBL emphasizes experimental analysis at multiple levels of biological organisation, from the molecule to the organism. One of EMBL’s five core missions is to develop and make available new technologies for the Life Sciences.
Expertise: Access to biobanks and biomolecular resources, access, data, ELSI, innovation.
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.
Members: Austria, Belgium, Bulgaria, Czech Republic, Estonia, Finland, France, Germany, Greece, Italy, Latvia, Malta, the Netherlands, Norway, Poland, Sweden, and the United Kingdom. Observer Countries: Cyprus, Switzerland, Turkey, IARC/WHO
Expertise: Translational research, personalised medicine, biomarker development.
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
Expertise: Multinational clinical trials, Clinical trial ethics and regulation, Clinical trial governance and management, Clinical trial data management, International collaboration.
The European Clinical Research Infrastructure Network (ECRIN, www.ecrin.org) is a sustainable, not-for-profit, distributed infrastructure with the legal status of a European Research Infrastructure Consortium (ERIC). ECRIN provides support for the planning and implementation of multinational clinical research projects in Europe. ECRIN currently has eight Member Countries (France, Germany, Spain, Italy, Portugal, Hungary, Czech Republic and Norway) and one Observer Country (Switzerland). Additional countries are about to join.ECRIN
Expertise: Marine Biology, Acquaculture, Environmental research, Marine Ecology, Blue Biotechnology
The European Marine Biological Resource Centre is established as a European Research Infrastructure Consortium, with the name of “EMBRC-ERIC”, a legal entity created under Union law. It is a distributed research Infrastructure of pan-European relevance. Part of the ESFRI roadmap since 2008, and adopted as an ERIC in February 2018, it is designed to further fundamental and applied marine biology and ecology research and help promote the development of blue biotechnologies the food, health and environmental sectors.
EMBRC-ERIC has the Statute of French Association, with its Headquarters located at the Pierre et Marie campus of Sorbonne Université in Paris, France. Its legal personality and extensive legal capacity are recognised in all EU Member States.EMBRC
Expertise: plant phenotyping data management, plant modelling, advanced imaging technologies, bioinformatics, automation and robotics
Forschungszentrum Jülich GmbH belongs to the Helmholtz Association of German Research Centres that was created in 1995 to formalise existing relationships between several globally renowned independent research centres. Within the Helmholtz Association almost 36,000 staff use the most modern scientific infrastructure, including, in particular, large-scale facilities and instrumentation, which are also open to use by members of the international scientific community. Working on behalf of the state, Helmholtz scientists pursue an ambitious goal: To make an essential contribution to solving the grand challenges which society faces.FZ Juelich
Expertise: Infectious diseases, Pathogens, BSL4, Public health
European Research Infrastructure on Highly Pathogenic Agents AISBL is a pan-European Research Infrastructure from ESFRI roadmap of leading European Biosafety level 4 facilities and national research institutes. It provides a coordinated transnational access to its members’ cutting-edge high containment and connecting facilities in order to enhance and accelerate research on risk group 4 and unknown emerging pathogens and contribute to outbreak preparedness of Europe and globally.
ERINHA provides the expertise, capacities, functions, as well as a pool of scientists and trained specialists required to lead or support research studies into human diseases caused by the most highly pathogenic agents, as well as applied research to develop new countermeasures and other interventions against these diseases. ERINHA has currently four full members with long track experience in the research on highly infectious diseases and data management: The National Institute of Health and Medical Research (Jean Mérieux BSL4 laboratory), Public Health Agency of Sweden (operating a BSL4 laboratory and connecting facilities), Ministry of Health of Hungary (NPHI with a BSL4 laboratory) and National Institute of Health Dr Ricardo Jorge of Portugal (BSL3 labs and connecting facilities).ERINHA
Expertise: Chemical Biology, Screening, Medicinal Chemistry
EU-OPENSCREEN (EU-OS) was included in the European ESFRI (European Strategy Forum for Research Infrastructures) Roadmap in 2008, officially founded in April 2018, and was awarded ESFRI `Landmark`status in June 2018. The ERIC is currently supported by the seven member countries Czech Republic, Finland, Germany, Latvia, Norway, Poland and Spain while Denmark has observer status and will join as full member on January 2019. The EU-OS network currently comprises chemical biology networks as well as 20 screening and medicinal chemistry centres. The primary activity of EU-OS is to provide access to its distributed research infrastructure for scientists seeking a better understanding on how fundamental molecular processes act to govern biological function at the organismal, tissue, cellular and pathway levels.
EU OS 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 microbiology; synthetic and medicinal chemistry; pharmacology and early drug discovery. EU OS 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-OS in EOSC-Life consists in the 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-OS and the creation of 15-20 large data sets from the Bioprofiling of the commercial collection of 100k compounds.
In WP1, the EU-OS 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 chemi-informatics tools into the cloud. EU-OS will directly participate in management work package (WP11).EU Openscreen
Expertise: Phenotyping and archiving of model mammalian genomes. Access to first-class tools and data for biomedical research.
INFRAFRONTIER is the European Research Infrastructure for the development, phenotyping, archiving and distribution of model mammalian genomes. The INFRAFRONTIER Research Infrastructure provides access to first-class tools and data for biomedical research, and thereby contributes to improving the understanding of gene function in human health and disease using mice.
The INFRAFRONTIER network currently consisting of 29 partners is engaged in several EC funded projects, such as INFRAFRONTIER2020, IPAD-MD and CORBEL, and contributes to the International Mouse Phenotyping Consortium (IMPC).INFRAFRONTIER
Expertise: Structural biology infrastructure: access, training, integrated technology provision.
Instruct is a distributed research infrastructure providing access to structural biology infrastructure. Instruct has ERIC status as of July 2017 comprising 11 member countries. Instruct infrastructure is provided at Instruct Centres (nodes) and a Central Instruct administrative Hub, located in Oxford UK, which serves as the host country for Instruct-ERIC.
Instruct has been providing access, training and other services to its member community since April 2011. Instruct-ERIC is sustained by in-kind contributions from members to fund the infrastructure running costs at nodes and by a cash contribution which funds the Hub and provides support for access and training activities.INSTRUCT ERIC
Expertise: systems biology; modeling predictive computational multi-scale models of living systems; systems metabolomics
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, Phycology, Science, Sociology and Education. In less than 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
Expertise: plant phenotyping data management, plant modelling, computer science for Information Technologies, advanced imaging technologies, data repositories federation, Biological Resource Center, taxonomy, bioinformatics, microbial genomics, Data management, workflow deployment, Galaxy
The French research institute INRA is Europe’s top agricultural research institute and the world’s number two center for the agricultural sciences; research is dedicated to food, nutrition, agriculture and the environment. INRA focuses on competitiveness, regional land use, health, sustainable development and bioeconomy. INRA employs over 12000 people including 8165 permanent staff. It has an annual budget of over 880 M€ for running 250 laboratories dispatched in 17 research centers in France.INRA
Expertise: Bioinformatics, Cloud compute, High performance computing, data analysis, Galaxy
Charité is Europe’s largest university hospital. All clinical care, research and teaching is delivered by physicians and researchers of the highest international standard. The co-lead of EOSC-Live WP7 will be assigned to Charité. It will act as the beneficiary organization for one of the biggest scientific clouds in Europe, the de.NBI Cloud. It is the German solution to enable integrative analyses for the entire life sciences community and the efficient use of data in research and application.
The de.NBI Cloud will contribute substantially to the EOSC Life project. The cloud will dedicate high performance computational and storage resources to support the activities of EOSC Life. The Platform Federation will receive essential support by the de.NBI Cloud experts. de.NBI Cloud will be head some tasks in WP7. Cloud appliances will allow adequate access to resources.
The de.NBI Cloud in Freiburg will extend the already existing Galaxy platform to make all existing and upcoming workflows and software packages available for EOSC. The de.NBI Cloud will be responsible for leading the respective training courses in collaboration with WP9.Charite Berlin
Expertise: Bioinformatics, Data analysis, Galaxy, Software engineering, Cloud deployment, Training
Founded in 1457, the University of Freiburg is one of the oldest German universities and is now one of the nation’s leading research and teaching institutions, evidenced inter alia by its membership in the League of European Research Universities (LERU). It actively fosters interdisciplinary research, and it is one of the few universities offering world-class research environments in the classical as well as in the modern disciplines.
Dedicated to defining and pioneering new research areas, the university actively promotes international exchange, and its central location in Europe and its proximity to Switzerland and France additionally supports its internationality. The University of Freiburg has a strong record in training and interdisciplinary research with the Center for Biological Systems Analysis and the BIOSS Centre for Biological Signalling Studies.
The Department of Computer Science, in close cooperation with the local compute center, do have years of experience with HPC and cloud computing. As one partner of the BW-Cloud project and as owner of the NEMO supercomputer the University of Freiburg is empowering the European wide Galaxy server.Uni Freiburg
Expertise: Data management, Scientific Data standards, FAIR, Scholarly publishing, Structural Biology
According to the 2014 Research Excellence Framework, the official UK-wide assessment of all university research, the University of Oxford has the largest volume of world-leading research in the country. The University of Oxford makes available its resources to Instruct-ERIC through established service level agreements (SLAs) with the Wellcome Centre for Human Genetics.
A number of facilities (The Division of Structural Biology – STRUBI www.strubi.ox.ac.uk, Oxford Protein Imaging Centre – OPIC www.opic.ox.ac.uk, Oxford Mass Spectrometry Centre) within the University of Oxford form sites within the Instruct-ERIC UK Centre. The University of Oxford also provides employment contracts for some staff seconded to Instruct-ERIC.
As such, some of the action to be carried out by UOXF (0.0625 PM in WP5, 0.125 PM in WP9 and 1 PM in WP11) will be carried out by these staff seconded from the University of Oxford to Instruct-ERIC and as such the University of Oxford will receive the personnel and indirect costs.University of Oxford
Expertise: Marine Biology, Marine outstations, Blue Biotechnology, Marine ecology, Acquaculture
Born from the merger of Université Pierre et Marie Curie and Université Paris Sorbonne, whose campuses are in the heart of Paris, Sorbonne Université (SU) covers all major disciplinary fields and offers new transversal academic and research programs. Sorbonne Université becomes a fully multidisciplinary research-intensive university with three faculties: Humanities and Social Sciences, Medicine and Sciences & Engineering. With more than 53 400 students (among 10 200 international students), 4400 doctoral students and 6300 researchers, Sorbonne Université is one of the leading French universities.
The European Affairs office, which is in charge of the EU projects at the university, has managed so far 150 FP7 and 85 H2020 projects (35 ERC grants and 45 industry-sponsored research chairs). The EU office will manage all the financial, administrative and legal aspects for the participation of Sorbonne Université in this project. SU hosts the Headquarters of the ESFRI infrastructure “European Marine Biological Research Centre” (EMBRC: www.embrc.eu) in Paris.
Together with the Centre National de la Recherche Scientifique (CNRS), SU also coleads EMBRC-France (www.embrc-france.org), the French national node of EMBRC. EMBRC-France is a distributed research infrastructure with sites at the 3 SU/CNRS marine biological stations: the Station Biologique de Roscoff (SBR) located in Brittany on the Atlantic coast (northwest France) and the Observatoire Océanologique de Villefranche-sur-mer (OOV) and Observatoire Océanologique de Banyuls-sur-mer (OOB) located at either extremity of the French Mediterranean coast.Universite Sorbonne
Expertise: Data management, HPC, Grid, Cloud, Software Engineering, Data standards
INSERM – France (ERINHA AISBL national node) The French National Institute of Health and Medical Research (Inserm) is a public scientific and technological institute, which operates under the joint authority of the French Ministry of Health and the French Ministry of Research. As the only French public research institute to focus entirely on human health, in 2008 Inserm took on the responsibility for the strategic, scientific and operational coordination of biomedical research.
This key role as coordinator comes naturally to Inserm thanks to the scientific quality of its teams and its ability to conduct translational research, from the laboratory to the patient’s bed. National coordination is strengthened since 2009 by the Alliance nationale pour les sciences de la vie et de la santé (French National Alliance for Life and Health Sciences), which Inserm co-founded with other research institutes and the Conférence des présidents d’université (Association of University Presidents). To extend the strategic and programmatic coordination of research to all life and health sciences, the Alliance relies on 9 multi-body thematic institutes jointly overseen by two research institutes (Inserm, CNRS, French Atomic Energy Commission/CEA or French National Institute for Agricultural Research/Inra), depending on the research field.INSERM
Expertise: Advanced imaging technologies, innovative imaging probes, preclinical image data processing.
The University of Torino (UNITO) participates in INFRAEOSC-04 project through the Center of Molecular Imaging (CIM, established by the Italian Ministry of University and Research in 2001). CIM is an interdisciplinary research initiative (ca. 25 research fellows) aimed at developing innovative “in vivo” diagnostic imaging probes.
It consists of chemistry and biology laboratories and is equipped with several scanners for the major imaging modalities thus covering the entire chain from the design of the imaging agents to their application in dedicated cellular and animal models. In 2007 UNITO-CIM implemented (with the contribution of the Piemonte government) an Industry / University laboratory devoted to support the activities of the Regional Platform for Medical Imaging.Universita Torino
Expertise: Image Data Management, data integration and access, open source software development.
The School of Life Sciences (SLS), University of Dundee, houses over 60 groups and 1000 scientists dedicated to discovering basic mechanisms in cell and developmental biology and the development of new diagnostics and therapies for neglected diseases. SLS houses 14 confocal and wide-field imaging systems and a 600 TB data management system for use by all researchers.
These facilities are made available to all SLS investigators. SLS hosts the Open Microscopy Environment project, an international software development consortium led by Prof Jason Swedlow that builds tools for accessing, managing, viewing, analysing, sharing and publishing large image datasets.University of Dundee
Expertise: Image Data Management, data integration and access, biological imaging
Åbo Akademi University (ABO) is the oldest university in Finland, and imaging has been one of the key focus areas of the university for a long time. Turku BioImaging (TBI, www.bioimaging.fi) is an interdisciplinary organization in the city of Turku, lead by Åbo Akademi University, bringing together biological and biomedical imaging, and responsible for coordinating imaging infrastructure development and operations both nationally and internationally.
TBI has long-standing expertise in providing access and training to imaging technologies and services, with strongholds in areas such as super-resolution and label-free imaging technology development, software development for bioimage informatics and infrastructure operations, and in vivo imaging technologies and probes. TBI includes several internationally known imaging units, such as Finland’s largest microscopy core facility, The Cell Imaging Core of the Turku Centre for Biotechnology, The Laboratory of Biophysics, where the development of the Nobel-winning super-resolution technologies was initiated, and the national PET center.
TBI also coordinates the Finnish BioImaging (FiBI) network, which provides services to nearly 1000 users annually, Associated with document Ref. Ares(2018)5778128 – 12/11/2018 EOSC-Life: Providing an open collaborative space for digital biology in Europe 824087 EOSC-Life — Part B 79 including numerous Centres of Excellence and ERC grant holders. TBI facilities are also closely associated with proteomics and computational modelling.Åbo Akademi
The Fraunhofer-Gesellschaft, is the leading organization for applied research in Europe.
It’s research activities are conducted by 67 institutes and it employs a staff of 24,000, with an annual research budget of 2.1 billion euros. The Fraunhofer IME ScreeningPort Department in Hamburg, has around 30 staff. The main scientific work of Fraunhofer IME ScreeningPort covers the identification, functional characterization and validation of targets which play a role in human health, disease and toxicity.
The work of the teams covers 5 major themes: i) Drug Discovery; ii) Structure Based Drug Design; iii) Biomarker and Translational Research; iv) R&D Information Technologies; and v) Enabling Technologies. IME will co-lead WP1 (Philip Gribbon) with Andrea Zaliani acting as technical lead in the WP. In WP2. IME will support the cloudification of tools and services related to small molecule based drug discovery and chemical biology and will work closely with IMIM to deliver this capability.IME FRAUNHOFER
Expertise: Mouse models of disease, Model organisms, mouse breeding, advanced phenotyping
Helmholtz Zentrum München (HMGU) is the German Research Center for Environmental Health. It investigates important common diseases, which develop from the interaction of lifestyle, environmental factors and personal genetic background, focusing particularly on diabetes mellitus and chronic lung diseases. Helmholtz Zentrum München is a research institution of the Federal Republic of Germany and the Free State of Bavaria. It is a member of the Helmholtz Association of German Research Centers, the largest research organization in Germany. The Helmholtz Zentrum München has 40 different institutes and departments at ten different locations in Germany and employs a workforce of around 2200, among them 720 scientists and postdocs.
The Institute of Experimental Genetics (Director Prof. Hrabé de Angelis) from the Helmholtz Zentrum München (IEG-HMGU) is interested in the functional analysis of mammalian genomes using the mouse as a model organism to carry out analyses of gene function and to elucidate the pathogenesis of diseases. The IEG-HMGU has established the German Mouse Clinic (GMC), which offers standardized and comprehensive phenotypic analyses of mouse mutants to internal and external users. In addition, the IEG-HMGU represents the German node of the European Mouse Mutant Archive (EMMA). The Helmholtz Zentrum München is one of the founding members of the INFRAFRONTIER GmbH and hosts the company on its campus. The HMGU did coordinate all related and previous INFRAFRONTIER projects. Helmholtz Zentrum München will contribute to WP1.Helmholtz München
Expertise: Mouse models of disease, Model organisms, mouse breeding, advanced phenotyping
The CERBM is a non-profit biomedical research organization funded and controlled by an alliance of French research agencies (CNRS and INSERM) and by the University of Strasbourg. The Institut Clinique de la Souris (ICS) is part of the CERBM, under the direction of Dr Yann Hérault and is located between the University of Strasbourg’s southern campus and the Biotech Innovation Park, in Illkirch.
The ICS, founded by P. Chambon in 2002, is a national infrastructure devoted to translational research and functional genomics. Under the direction of Yann Hérault since 2010, the ICS comprises around 100 scientists, engineers and technicians. The ICS is a member of the French INFRASTRUCTURE for Biology and Health, called PHENOMIN, laureate of the Investment for the future call in 2011 and which will contribute to the project.
Both IGBMC and ICS operate in accord with the National alliance AVIESAN for life science and Health, including INSERM and CNRS, and INFRAFRONTIER the European Infrastructure for Mouse genetics. The ICS and Yann Hérault have a strong expertise in generating and analyzing mouse models of human diseases with more than 2 000 models delivered in the last 13 years; in addition more than 40 mouse models for conditional activation of the inducible Cre-ERT2 recombinase have been developed and made available to the scientific community.
In the International Mouse Phenotyping consortium (IMPC), the ICS contributes to the development and standardized phenotypic analysis of about 250 mouse models for genes of interest nominated by the French scientific community. The ICS is a founding member of European Infrastructure INFRAFRONTIER GMBH. CERBM-GIE will contribute to WP1.IGBMC
Expertise: Mouse models of disease, Model organisms, mouse breeding, advanced phenotyping
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 was established in 1998, and operates under the supervision of the General Secretariat for Research and Technology (GSRT) of the Hellenic Ministry of Education. Competitive funding each year amounts to 75-85% of the total budget of the Center, an achievement that underlies Fleming’s strategic prioritization of research and innovation, which falls tightly within Europe 2020 priorities. In a 2014 evaluation by an international scientific committee organized by GSRT, Fleming was ranked first among Greek Research Centers active in biomedical sciences.
Over the last decade Fleming has established state-of-the-art facilities that offer services for translational research to the Center internally, but also to researchers and companies in Greece and abroad. 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 Alexander Fleming
Expertise: Mouse models of disease, Model organisms, mouse breeding, advanced phenotyping
The University of Oulu (UOULU) is a non-profit, higher education providing organization funded largely by the Finnish government. UOULU was founded in 1958 and is among the largest universities in Finland with 16 000 students and 3000 staff members working in ten faculties. UOULU has high-quality research environments for international research groups.
The university strategy is based on five thematic, internationally significant research focus areas: Creating sustainability by materials and systems, molecular and environmental basis of life-long health, digital solutions in sensing and interactions, earth and near-space system environmental change, understanding humans in change. In addition, UOULU has several national and international responsibilities with regards research infrastructures and specific research themes.
University of Oulu has the responsibility of Finnish coordination of the following four international infrastructural networks (ESFRI): Eiscat, Infrafrontier Finland (EMMA), Max IV, XFEL/XBI. The UOULU has experience in participating in European and international projects (including NIH funded projects) and networks, and is well equipped to manage also large-scale projects with multiple international partners. UOULU has been involved in the EU R&D Framework programs since FP4, and has participated in more than 260 projects and networks, of which over 20 have been coordinated by UOULU.
The UOULU was awarded the European Credit Transfer and Accumulation System (ECTS) Label in December 2013 as the first research university in Finland. UOULU follows the guidelines laid out in the European Charter for Researchers and the Code of Conduct for the Recruitment of Researchers. The Finnish Education Evaluation Centre (FINEEC) has conducted an audit of University of Oulu and awarded the institution a quality label that is valid for six years from 28 February 2018.
The quality system of University of Oulu fulfils the national criteria set for the quality management of higher education institutions, and the system corresponds to the European quality assurance principles and recommendations for higher education institutions.Oulun Yliopisto
Expertise: Transnational access, user training, community outreach, software development (for structural biology).
The Interuniversity Consortium CIRMMP together with CERM constitutes an infrastructure for Life Sciences, which provides a unique environment for research in the field of Structural Biology. 200 protein structures were solved in the laboratory using NMR and/or X-ray spectroscopies. The research activity of the infrastructure encompasses bioinformatics, computational biology, cellular structural biology, molecular biology, drug discovery, NMR methodology, relaxometry, metabolomics.
The Infrastructure has a wide range of high-resolution spectrometers, for solution and solid-state NMR as well as for metabolomics. The CERM/CIRMMP Infrastructure is a centre of the ESFRI Landmark Instruct -ERIC and a node of a European Grid Infrastructure, with a dedicated IT group.CIRMMP
Expertise: Image processing in electron and x-ray microscopy, information integration, community software production.
The CSIC (Spanish National Research Council) is Spain’s largest public research institution, and ranks third among Europe’s largest research organization. The CSIC is attached to the Spanish Ministry of Economy, Industry and Competitiveness through the State Secretariat for Research, Development and Innovation, and plays a key role in scientific and technological policy in Spain and worldwide.
According to its Statute (Article 4), CSIC has 4 main missions: – to foster multidisciplinary scientific and technological research – Knowledge transfer to industry and society- – Education and training of scientific and technical staff – Creation of Technology Based Companies CSIC supports research and training across a wide range of knowledge, from the most basic or fundamental aspects of science to the most complex technological developments; from human and social sciences to food science and technology, including biology, biomedicine, physics, chemistry and materials, natural resources and agricultural sciences.
As the third largest research organization in Europe, CSIC carries out research in all fields of knowledge, throughout its 123 Institutes distributed in eight areas: Humanities and Social Sciences, Biology and Biomedicine, Natural Resources, Agricultural Sciences, Physical Science and Technologies, Materials Science and Technology, Food Science and Technology and Chemical Science and Technology.CSIC
Expertise: Systems Biology, Mathematical modelling, Clinimetrics, Epidemiology, Systems Medicine.
ISBE.NL is the Netherlands node of the Infrastructure Systems Biology Europe (ISBE) that provides stewardship and insight into biological data and their acquisition. It consists of a Central Office (Gennaro Piccialli, Director, and Massimiliano Borsani, Manager) and 4 interconnected infrastructure pillars:
1) The Do Me an Experiment pillar (ISBE.it) helps generating systems’ data, e.g. related to enzyme kinetics, metabolomics, and epigenetics (http://www.sysbio.it/isbe/)
2) The Make Me My Model (M4) pillar helps customers to make various types of data (genome sequence, transcriptome, proteome, metabolome, physiological, kinetic etc. n-related) predictive and understood. Providing modelling most appropriate for the data set, M4 performs both dynamic data analysis via building phenomenological models with a top-down approach (ISBE.si), and bottom-up mechanism-based modelling (ISBE.NL) (www.isbe.nl). Both activities are followed by a model analysis that helps understand the system under study, e.g. predicts the effects of therapeutic or biotechnological interventions useful for model-driven experimental design and bioengineering, or for therapeutic practice. M4 can do this for a customer, assist the customer to do this himself or herself, or train the customer in person or in online tutorials, to do this.
3) The Live Model Repository pillar of ISBE 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/).
4) The Data and Model Stewardship pillar of ISBE is called FAIRDOM (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 eInfrastructures in Norway (NeLS) and Slovenia (p-ISA).
For the time being, FAIRDOM and M4 have been serving CORBEL clients providing them with online modelling services using the FAIRDOM HUB website (https://fairdomhub.org/) and www.ISBE.NL environments.
Former Centraalbureau voor Schimmelcultures (previously known as CBS-KNAW)
Expertise: Largest fungal culture collection in the world with strong taxonomic and bioinformatics expertise. Longstanding experience in software, algorithms, databases and websites (including web services) developments.
The Westerdijk Fungal Biodiversity Institute (WI) is part of the Royal Netherlands Academy of Arts and Sciences and is situated at Utrecht Science campus. WI maintains a world-renowned microbial biological resource centre of living filamentous fungi, yeasts and bacteria. The institute’s research programs principally focus on the taxonomy and evolution of fungi as well as on functional aspects of fungal biology and ecology, increasingly making use of molecular and genomics approaches.
The institute employs circa 70 personnel, among whom 20 scientists. In our microbial biological resource centre (brc) we maintain over 100.000 strains of micro-organisms, representing a large percentage of the species in the fungal kingdom that have been cultured to date. In diversity of species it is unchallenged as a reference centre for mycological research.
The task to preserve the organisms while maintaining their original characters is a perpetuating challenge to technicians and scientists alike. Because the increase in the number of organism acquisitions is not proportional to an increase in assistance, preservation on agar has been minimized, thus placing high demands upon long-term preservation. The value of a brc depends not only on the quality of the strains, but equally on the amount and accuracy of the data attached to them.
Although there are considerable differences among the various taxonomic groups, efforts are taken to increase the amount of information linked to the strains. The available databases allow random information retrieval and give not only access to strain data, but also a large series of scientific data. Many of our databases are freely available online via one of the many specialized websites that we are maintaining. Westerdijk Fungal Biodiversity Institute is a centre of expertise, advising on mycological problems of a scientific, health-related or industrial nature.
It offers various services including identifications, patent deposits and courses. Research projects for third parties can be carried out on a strictly confidential base. The institute also publishes books and the journals Studies in Mycology, CBS Biodiversity Series and Persoonia.KNAW
Expertise: culture collection, taxonomy, bioinformatics, microbiology
Associated with document Ref. Ares(2018)5778128 – 12/11/2018 EOSC-Life: Providing an open collaborative space for digital biology in Europe 824087 EOSC-Life — Part B 98 The University of Valencia is a leading academic organisation at national level, with a remarkable international dimension, which ranks among the top 300 in Europe as per university ranks, such as ARWU “Shanghai” Ranking (top 200 in Europe), THE (Times Higher Education) Ranking and QS World University Ranking. Shanghai 2016 ranks Universitat de València among the top 500 universities in the world, and 4th best university in Spain. The Spanish Type Culture Collection (CECT) is a central service of the University of Valencia.
Expertise: Data management and integration, Web Services, workflow management systems, microbial data information systems.
The IRCCS Ospedale Policlinico San Martino (USMI) of Genova, Italy, is the main city Hospital. It is a University Hospital and as such it includes clinical and research units tightly connected to the activity of the University of Genova and/or led by University professors. It has been recognized by the Italian Ministry of Health as “Istituto di Ricovero e Cura a Carattere Scientifico” (Scientific Institute for Research, Hospitalisation and Health Care), which is the highest certification in Italy for Institutes involved in Health Research.
It provides better care and prevention of diseases through basic, translational and clinical research. Fields of research activity include epidemiology, risk factors and primary prevention, cellular, molecular and structural biology, genomics and proteomics, tumour immunology, integrated approaches to cancer therapy. USMI has the WIPO International Depositary Authority (IDA) status. It is member of the European Culture Collections’ Organisation (ECCO) and of the World Federation for Culture Collections (WFCC).Ospedale San Martino
Expertise: cybersecurity, AAI, cloud and grid services, tools for data analytics, storage and data management, clinical trials, regulatory and legislative support
Masaryk University, established in 1919, is the second largest Czech university with around 36,000 students and 4,500 staff in 9 faculties and 2 university Institutes. Masaryk University is involved in several biomedical research infrastructures, as a partner or as a national leading institution.
1) Institute of Computer Science, one of the university Institutes, with its staff of around 140 persons, is a leading national institute in the area of e-infrastructures and cybersecurity. It hosts national research infrastructure CERITSC (CERIT Scientific Cloud) and the Czech Cybercrime Centre of Excellence (C4E) and recently is taking national leadership and coordination in the GDPR implementation for the university/academic environment in the Czech Republic. The RI CERIT-SC will be directly involved in the EOSC Life project. It is dedicated to the development and management of a grid/cloud combined e-infrastructure experimental facility, focusing on research in high performance computing in grids and clouds using multi-core and many-core accelerators (e.g. GPGPU cards or Xeon Phi systems), on research in (big) data analytics and pattern search in unstructured data, and performing additional research in areas where the e-infrastructure is used in wide range of sciences. CERIT-SC is a founding partner of the Czech ELIXIR CZ node, together with CESNET responsible for its e-infrastructure needs. CERIT-SC and CESNET are co-developing Perun, the core of advanced ELIXIR AAI, and used also as part of the EGI AAI. Recently, CERIT-SC leads a capacity building program for ELIXIR CZ, coordinating a project funded through the national structural funds program. CERIT-SC, together with CSC FI, is responsible for the ELIXIR AAI development and management, primary within the ELIXIR EXCELERATE project and supported also by ELIXIR Implementation studies. CERIT-SC has been developing national IT infrastructure for BBMRI.cz since 2011, which dealt with findability and accessibility of biological material from the Czech biobanks. This infrastructure has become an early concept of what has become an access pipeline for the European BBMRI-ERIC in 2016-2017.
CERIT-SC has also worked with Masaryk Memorial Cancer Institute (hosting node of BBMRI.cz) on implementing scalable proteomics workflows as a part of EGI-Engage project. CERIT-SC provides BBMRI-ERIC Authentication and Authorization Infrastructure since second half of 2016. CERIT-SC has been also involved in number of medical informatics and bioinformatics projects, such as building data management platform for THALAMOSS project focused on developing new treatments for rare disease of beta-thalassaemia. It is leading an e-infrastructure dedicated work package in the West-life project, with a strong emphasis on the AAI and cloud delivery for the structural biology environments. Similarly, CERIT-SC is a partner of the just started EDIREX project that builds the distributed infrastructure for research on patient-derived cancer xenografts, again with the responsibility for the e-infrastructure and also for the data analytics.
2) CZECRIN (Czech Clinical Research Infrastructure Network) is headquartered in the Department of Pharmacology in the Faculty of Medicine of Masaryk University, Brno. CZECRIN is recognised as a Large Infrastructure by the Czech Government and is included in the Roadmap for Large Research, Development and Innovation Infrastructures in the Czech Republic of the Ministry of Education, Youth and Sports. At the centre of CZECRIN is a collaboration between Masaryk University, which leads the University Module of CZECRIN, and St. Anne´s University Hospital, Brno, which leads the Clinical Module. The University Module groups together clinical trials centres located in universities.
The clinical trials centres provide coordination and service support for investigator-initiated clinical trials, training activities and methodological support. The Clinical Module currently comprises six clinical trials units at various medical facilities. The clinical trials units conduct trials and communicate with regulatory authorities. The modules are connected to each other and to ECRIN via Masaryk University.Masaryk University
Expertise: Storage, network, computing, information management and scientific application support and resources for academia, institutes and companies.
The LUMC is a university medical centre for research, education and patient care with a high-quality profile and a strong scientific orientation and ranks as the 6th best medical research institute in Europe (Shanghai 2015/2014). It has a unique research practice, ranging from pure fundamental medical research to applied clinical research. This enables LUMC to offer patient care and education that is in line with the latest international insights and standards – and helps it to improve medicine and healthcare both internally and externally.
LUMC is well-structured and productive research and training environment annually produces ~115 PhD theses and ~1750 scientific publications.
LUMC’s BioSemantics group (PIs Roos, Mons) focuses on the automated discovery of new biological knowledge and development of the FAIR data concept as substrate for knowledge discovery. It develops algorithms for the purpose of finding novel genotype – phenotype relationships, drug targets and drug repurposing, and develops FAIR Linked Data technologies and innovative approaches towards enhanced interoperability of biological and health datasets.
Together with the DTL FAIR engineering team and the so-called FAIR skunk team, the BioSemantics engineering team has developed a suite of FAIR data tools to create, publish, index and annotate FAIR data sources. Over the past 2 years, the BioSemantics group has (co)organized 10+ BYODs in a wide range of Life Science domains, including rare-disease, OMICS and plant science. It has a leading role in European-wide efforts to harmonize data and establish FAIR-compliant infrastructure for rare diseases.
PI Roos is co-leading the Rare Disease Work package within ELIXIR, Mons helped organise the interoperability platform in ELIXIR, was chair of the high-level expert group for developing the European Open Science Cloud, and is leading the organisation of GO FAIR implementation networks. The group is one of the founders of the Dutch Techcentre for the Life Sciences (DTL), the Dutch node in ELIXIR. DTL and the BioSemantics group has a leading role in organising the development of FAIR principles ever since the founding at the Lorentz workshop in Leiden in 2014.Academisch ziekenhuis Leiden
Expertise: Storage, network, computing, information management and scientific application support and resources for academia, institutes and companies.
CSC – IT Center for Science Ltd (http://www.csc.fi), is the Finnish national HPC center providing highperformance and cloud computing, networking and data services to academia, research institutes, public sector and industry.
CSC is a non-profit limited company whose shares are fully owned by Finnish Government and Finnish universities. Established in 1971, it currently has over 300 employees, and supports a European-wide customer base of thousands of researchers in disciplines such as biosciences, environmental science, linguistics, chemistry and mathematical modelling.
CSC provides Finland’s widest selection of scientific software and databases, training and expert support, storage and data services, and Finland’s most powerful supercomputing environment, and operates the Finnish national research and education network Funet. CSC is the Finnish ELIXIR node, initiator and coordinator of the collaborative data infrastructure EUDAT and a committed actor in the development of the European Open Science Cloud through leading roles in EOSCpilot and EOSC-hub. As responsible for national eInfrastructures, CSC is also member of PRACE and EGI.CSC – Tieteen tietotekniikan keskus Oy
Expertise: Chemical Biology, High-throughput screening, Cheminformatics; Advanced Phenotyping, Transgenic Rodent Models, Metabolomics
The Institute of Molecular Genetics AS CR, v. v. i. (IMG) is one of the 54 public research institutes of the Academy of Sciences of the Czech Republic and is located in the Biomedical campus on the southern outskirts of Prague. The Institute was founded in 1962 and since that time it has become a leading biomedical institution in the Czech Republic. With ~ 560 employees and 29 research groups, the Institute carries out 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.
IMG is financed by the institutional support of the Czech Academy of Sciences and by a number of national and foreign research grants. The Institute operates several core facilities such as facilities Genomic and Bioinformatics core units, as well as three large national research infrastructure with several state-of-the-art technology platforms, providing their services not only to the whole national research community but they are opened via trans-national open access to international community. IMG thus hosts CZ-OPENSCREEN (National Infrastructure for Chemical Biology; https://www.openscreen.cz), The Czech Centre for Phenogenomics (CCP, http://www.phenogenomics.cz), and the Czech-Bioimaging (https://www.czech-bioimaging.cz). In 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.stav molekularni genetiky akademie
Expertise: Cheminformatics, QSAR, toxicology, bioinformatics, data integration, molecular modelling, systems biology
The Fundació Institut Mar d’Investigacions Mèdiques (IMIM) (http://www.imim.cat/en_index.html) is a biomedical research institute that manages the translational and clinical research carried out by the Parc de Salut Mar (https://www.parcdesalutmar.cat/en_index.html), a public healthcare organisation located in Barcelona.
The IMIM is located in the Barcelona Biomedical Research Park (PRBB) (https://www.prbb.org/). IMIM takes part in the project through the Research Programme on Biomedical Informatics (GRIB) (http://grib.imim.es/), which is a research programme of the IMIM, as well as of the Universitat Pompeu Fabra (UPF). The Research Group on Systems Pharmacology performs research at the interface between chemistry, biology, and informatics aiming at providing a fundamental mechanistic understanding of drug efficiency and safety. To this aim, the group currently focuses its research in three lines: i) collection, storage, management, and analysis of pharmacology and safety data; ii) development of novel integrative computational approaches for predicting the pharmacology and safety of small molecules; and iii) application of these methods in drug discovery and chemical biology projects. At present, it is composed of 8 researchers (1 Head, 2 Post-doctoral researchers, 3 PhD students, and 2 Master students) integrated within the Research Program on Biomedical Informatics composed of over 60 researchers.IMIM
Expertise: Model organisms, Bioinformatics, Data Management, Advanced phenotyping, cloud compute, Galaxy
Consiglio Nazionale delle Ricerche (National Research Council, CNR; establ. in 1923), with more than 8000 employees, is the largest multidisciplinary public research institution of Italy. its duty is to carry out, promote, spread, transfer and improve research activities in the main sectors of knowledge growth and of its applications for the scientific, technological, economic and social development of the Country.
CNR is distributed all over Italy through a network of 102 institutes aiming at promoting a wide diffusion of its competences throughout the national territory and at facilitating contacts and cooperation with local firms and organizations. The project includes the participation of two research Institutes with expertise in different areas of the interest in the proposal.Consiglio nazionale delle ricerche
Expertise: workflow systems, registries, data management, integration and access, training and user engagement, semantic technologies, ontologies.
The University of Manchester is one of the UK’s top research-led universities. The school plays important roles in the two EU FET flagship projects, Graphene and Human Brain Project and two of the BMS EU Research Infrastructures: ISBE (Systems Biology) and ELIXIR (Life Science Data). In this proposal, UNIMAN is represented by the School of Computer Science.
The Information Management Group, co-led by Goble, is large (50+). Goble’s e-Science sub group focus on the application of semantic and distributed computing technologies to accelerating computational science, scientific reproducibility and FAIR results management and scholarship, producing software and data platforms that are production quality and widely used. Innovations address resource-interoperability through workflows, web-based resource sharing, and semantic-driven infrastructures. Developed core components of EU Research Infrastructures: (i) ELIXIR, the TeSS training portal and; (ii) ISBE, the FAIRDOM-SEEK platform for managing data, models, SOPS and workflows for collaborative projects and data management bridging local, national and European infrastructures.The University of Manchester
Expertise: Systems Biology, Bioinformatics, training, data management
National Institute of Biology (NIB), founded in 1960, is a public non-profit organization performing basic and applied research in the fields of biology, biotechnology, medicine, ecology as well as interdisciplinary fields, joining biosciences with statistics and bioinformatics. It is the third largest research institute of natural sciences in Slovenia with 130 researchers organised into 5 departments.
One of these is the Department of Biotechnology and Systems Biology which is part of this consortium is the largest among them. The department is well-versed in analysis of high-throughput data, focusing mainly on the transcriptomics level (Next generation sequencing, DNA microarrays and quantitative real-time PCR), while complementing this level with proteomics and metabolomics data. After data acquisition initial data analysis is performed, covering statistical modelling, multivariate analysis, data mining and mathematical modelling.
Additionally, several tools helping this analysis were developed within department, recently also a local data management system, built in accordance with isa-tab standard and FAIR data principles and is compatible with FAIRDOMhub. NIB is also coordinator of Slovenian node of ISBE and member of Slovenian Elixir node.NIB
Expertise: Data management, e-infrastructure, web development, marine biological observations, data analysis and visualisation
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. The VLIZ is a government funded but autonomous institute with the legal status of a non-profit organization and employs 65 FTE’s. VLIZ set up a strong collaborative network through 21 cooperation agreements with Flemish research groups and administrations and integrates its activities in 7 national and 25 international networks. Associated with document Ref. Ares(2018)5778128 – 12/11/2018 EOSC-Life:Providing an open collaborative space for digital biology in Europe 824087 EOSC-Life — Part B 120 The participation of the VLIZ in the project will be undertaken by the VLIZ Data Centre department.
The VLIZ Data Centre provides assistance, technologies and tools to scientists and policymakers to support marine data management. Within international networks VLIZ participates in the development of data infrastructures. VLIZ data centre is heavily involved in the management of international e-infrastructures: the central portal for the European Marine Observation and Data network (EMODnet), LifeWatch Taxonomic Backbone and data systems, World Register of Marine Species (WoRMS), Global Sea Level Observing System (GLOSS), Ocean Biogeographic Information System (EurOBIS), Marine Data Archive, Integrated Marine Information System, Marine Regions. VLIZ is a National Oceanographic Data Centre in the network the IODE programme of IOC-UNESCO and a regular member of the ICSU World Data System. VLIZ also contributes to the organisation of the EMBRC data infrastructure by chairing the EMBRC Working group on E-infrastructure and leading the virtual access work package of the ASSEMBLEPLUS project.Flanders Marine Institut
Expertise: bioinformatics, biological resource biology and management
The Centro de Ciências do Mar (CCMAR) is a non-profit research organisation at the University of Algarve with the mission to promote research and education on processes in the marine environment, with emphasis on biological interactions and the sustainable use of living resources. CCMAR was evaluated Excellent in 2015 by the Foundation for Science and Technology of Portugal. CCMAR leads the national node for EMBRC and a member of the national nodes for ELIXIR and EMSO.
In coordination with WP2, CCMAR will undertake the implementation of a genome annotation platform: Marine Eukaryote Genomics Portal – access to tools and data-flows for marine genome annotation. The platform is designed to address the fragmented research landscape for genome annotation of marine organisms. We propose a portal to marine genomic resources and a community driven annotation platform for marine eukaryotes, which would provide a focus for post-assembly genomic workflows and data access and complement access services such as EMBRIC Configurator, ELIXIR ontologies, and meta-data standards. Together these resources would expose the workflow from genome data collection to publication using open access and FAIR compliant standards and procedures. Although taxon agnostic, initially the platform will focus on pelagic fishes (the closely related Sardinha and Alosa) and the use primarily of comparative methods of gene prediction and validation.CCMAR
Expertise: Marine Training and Education, web development, Marine Ecology of Soft-Bottom Communities
Ghent University attracts yearly over 41,000 students, employs around 6,500 academic staff members and invested over 265 million Euros in research projects on behalf of public and private partners. The University has participated in more than 260 projects in the Seventh Framework Programme. Ghent University is in the top 100 (71) of the Shanghai Ranking of World Universities.
Ghent University has a strong mission to promote and facilitate interdisciplinary fundamental and applied research and education on marine ecosystems, providing a strong knowledge base to support ecosystem-based management of marine resources for current and future generations. Core facilities available for internal and external use include climate rooms and aquaculture facilities, integrated omics platforms for biodiscovery, state-of-the-art microalgae culturing facilities and units equipped for histological sectioning and staining techniques. UGent offers access to a variety of model organisms (diatoms, bacteria, nematodes, crustaceans).
UGent will, in collaboration with the other EMBRC parties, shape the contribution to WP9. More specifically UGent will contribute to training the EOSC-Life end users and contributing to the training impact assessment.
Expertise: Marine Biological Resources, Access to genetic resources in compliance with Access and Benefit Sharing Regulatory framework
A Spanish academic and research institution, the University of the Basque Country (UPV/EHU) is the only public university in the Basque Country and one of biggest universities in Spain conforming an Euroregional Campus of Excellence with the Univ. of Bordeaux. It accounts for about 45,000 students and 4,500 research and academic staff.
The university has ample experience in participating and coordinating a wide variety of European, international, national and regional projects. The participation of the UPV/EHU in the project will be undertaken by the Plentzia Marine Station (PiEUPV/EHU) which is the Marine Research Station of the University. Together with ECIMAT in the University of Vigo it forms the Spanish node of EMBRC-ERIC.UPV/EHU
Expertise: Marine Biological Resources, Access to genetic resources in compliance with Access and Benefit Sharing Regulatory framework.
Universidad de Vigo is a Spanish academic and research institution. It accounts for about 22,000 students and 2,500 research and academic staff. The university has ample experience in participating and coordinating a wide variety of European, international, national and regional projects.
The participation of the UVIGO in the project will be undertaken by Toralla Marine Science Station of (ECIMAT; www.ecimat.org) which is the University of Vigo´s marine research station. It provides state of the art marine research facilities to more than 150 researchers from the University of Vigo and other 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 (European Marine Biological Resource Centre).
The collection ad provision of Marine Biological Resources (MBRs) for research and the development of Functional Preservation Technologies for marine organisms are among the main contributions of ECIMAT to the services provided by the EMBRC.University of Vigo
Expertise: Bioinformatics training development and delivery at both undergraduate and postgraduate level, training impact assessment, health data science training
The University of Cambridge is one of the most renowned Research/Higher Education Institute and is frequently ranked amongst the top 5 in international academic rankings such as ARWU and Shanghai Ranking. It has a longstanding history of academic and scientific excellence backed up with rich culture, learning, research and creativity. Many affiliates of University of Cambridge have won Nobel Prizes for their significant advances. University of Cambridge is also a major participant in European projects and is one of the top recipients of FP7 funding.
The Bioinformatics Training Programme of the University of Cambridge offers a wide-ranging portfolio of training courses in bioinformatics and data science, at both undergraduate and post-graduate level. In 2017, it comprised 102 postgraduate training events and hosted 83 undergraduate training sessions; 2,600 postgraduates and 760 undergraduates are trained on average each year. Such training activities are open to all members of UK academic institutions, research institutes, public and government bodies, as well as industry partners.University of Cambridge
Expertise: FAIR, data sharing, knowledge discovery, machine learning, data mining, semantic web, ontology, linked data
Maastricht University is a top-ranked international university, renowned for the quality of the research undertaken in many areas. The Institute of Data Science (IDS) at Maastricht University will co-lead Task 6.1 of Work Package 6 given their exceptional expertise in the FAIR principles and technology to support their implementation. IDS is an interfaculty program for collaborative innovation around data science.
The main task will be to co-develop FAIRassist, a digital assistant to provide personalized guidance through the form of a wizard-like interface to walk users through various aspects related to the FAIR principles. The main deliverable of this task is the consolidation of material in a manner digestible to diverse set of stakeholders, the development of a digital assistant to provide advice on how to make a data resource FAIR, to assess the level of FAIRness, and to provide a new avenue for training and dissemination.University Maastricht
WP1 will publish data and data resources for use by WP2 and WP3, in support of the open calls and for the benefit of the EOSC and biomedical user communities. It will supply data/data resources needed by WP2 and will develop strategies for use of EOSC for different data types based on thematic groupings. A Data Catalogue will be implemented, initially at the level of each infrastructure by the RI Data experts, and then at cross-infrastructure and cross-demonstrator levels on a thematic basis, taking advantage of previous work within Corbel.
This catalogue will describe the data/data resources and will implement the minimal meta-data model developed in WP6. The sustainability of data/data resources will be addressed to determine sustainability best practice. Specifically, WP1 will:
- Development of cloud compatible FAIR-compliant data resources
- Assessment of cloud feasibility of data/data resources and publication these repositories in EOSC for data reuse
- Advance the evolution of RI repository infrastructure for EOSC (sustainability) and the interfaces between the repositories supporting the RI demonstrators and open calls
- Provide consented data repositories and deployments (in support of WP4)
- Implementation of FAIR services and WP1 standards for RI data/data resources (delivered in WP6)
- Provide implementation strategies and exemplar implementations for cloud accessibility of RIs archival and added value data resources
- Integrate repository/data access with workflows (supporting WP2)
- Develop a technical sustainability strategy for data/data resources deployed
D1.1 : EOSC Cloud feasibility assessment for demonstrators
D1.2 : EOSC repository deployment for project demonstrators
D1.3 : EOSC FAIR services deployment for open call
D1.4 : EOSC Sustainability best practice
WP Leads: Helen Parkinson (ELIXIR/EMBL-EBI), Philip Gribbon (EU-OpenScreen/Fraunhofer)
The BMS RIs harbour a large, vibrant and geographically diverse community of tool developers. The core purpose of this work package is to make the collective toolbox of BMR RIs (e.g. bio.tools have over 8000 entries) findable, accessible, interoperable and reusable in the cloud so that users across the BMS RIs as well as the broad scientific community can take full advantage of the European OpenScience Cloud.
To support this general goal, WP2 will engage both tool developers and end-users (i.e. scientists and research teams who want to make use of the EOSC to analyse data) to deliver an integrated EOSC environment by addressing three major points: software and tools packaging, workflow composition and execution, and registries.
Specifically, WP2 aims to: 1) Make BMS RI tools ready for deployment in the EOSC following FAIR principles. 2)Drive implementation of workflows that cross disciplines and RI boundaries. 3) Promote and develop use of the EOSC by fostering tool-focused collaborations and sharing between communities via cloud implementation and sharing of workflows that integrate the data and data analysis methods of different BMS RI.
Task 2.1 Make tools and workflows interoperable and reusable in the EOSC across RIs [M1-48]
Task 2.2 Tool findability and registries [M1-48]
Task 2.3 Address demonstrators from WP3 [M1-48]
Task 2.4 The Tools Collaboratory
Task 2.5 Sustainability
D2.1 : Cloud implementation of exemplary workflows selected by the RIs/communities including demonstrators
D2.2 : A common environment (Tools Collaboratory) that can run cross-RIs workflows following the hackathons/ workshops/WP3 use cases
D2.3 : Implementation of a comprehensive workflow registry solution for publishing and sharing workflows across instances of the Tools Collaboratory
The general objective of this WP aims at identifying key elements of data and processes providing a fast, coordinated and user-oriented way to start building RI’s connection to EOSC. Actual scientific and technological projects representing a broad scope of different domains in the life sciences will be selected to guide and structure the work in order to allow implementation of processes with concrete exemplary projects at hand. Specifically, WP3 will:
- Support an initial set of selected demonstrators to start their work with the start of the EOSC project
- Develop practical guidelines based on the experience with the initial set of demonstrators to inform the organization of topic-specific Open Calls
- Organisation of several Open Calls for specific topics
D3.1 : Publication of generic guidelines for the organization of topic-specific Open Calls
D3.2 : Report on the work of the initial Demonstrators
D3.3 : Report on the work of the Open Call Projects
WP Leads: Frauke Leitner (EuroBioImaging), Jose-Maria Carazo (Instruct/CSIC)
WP4 will address policies and specifications for the storage, processing, access, sharing and reuse of biological and medical data for research purposes, with a special focus on sensitive data. This is an essential step to build the European Health and Innovation Cloud, able to handle health data and health research data in a transnational environment. WP4 will therefore:
- Promote and improve pan-European policies, standards and risk analyses to ensure full regulatory compliance of data within the EOSC, especially sensitive or classified data.
- Propose and improve standardized solutions for working with multi-source (partitioned) environments, where datasets are not directly available for integration and in many cases not even metadata is disclosed in detail.
- Propose solutions enabling secure federated storage, access and sharing of sensitive research or health data.
- Promote the integration and knowledge of privacy-enhancing technologies.
Task 4.1 Regulatory compliance of sensitive health data and biological and medical research data management: policies, code of conduct, national implementation, de-identification
Task 4.2 Policy and guidance on sharing and reusing biomedical research data, images, and samples
Task 4.3 Reuse of hospital data (electronic health records) and data collected at home through electronic data capture for observational or interventional clinical research
Task 4.4 Transnational reuse of national health databases and national registries for research purposes
Task 4.5 Current requirements for hosting/distributing and access control mechanisms for sensitive data
D4.1 : Requirements for hosting/distributing and access control for sensitive data
D4.2 : Report on requirements for regulatory compliance of sensitive health data and biological and medical research data management
D4.3 : Guidance and policy on standards and tools to facilitate sharing and reuse of multimodal data (including imaging), cohort integration, and biosamples
D4.4 : Report on data standards for observational and interventional studies, and on interoperability between healthcare and research data
D4.5 : Public database inventorying the national health databases and registries and describing their access procedures for reuse for research purposes
WP Leads: Michaela Mayrhofer (BBMRI), Jacques Demotes (ECRIN)
BMS RIs need an access and user management system based on common identity authentication and authorisation infrastructure (AAI) that supports the identification of the user, allows users to specify their needs, keeping control over access to the resources strictly conforming to what a particular user is allowed to see and use. We also need to jointly manage access to services and facilities (e.g. via calls) through services such as provided by Instruct’s ARIA. The e-infrastructures within EOSC are paving the way to common denominator services. EOSC AAI will be a part of this service ecosystem, however, its general architecture is still discussed as part of the AARC2 project and plans to implement it lay in the future as part of the EOSC-Hub project. Therefore, we aim to:
- To specify/define a convergent access and user management system to enable multi-RI applications and workflows that build on existing approaches (LS AAI, ARIA, Negotiator service, etc) and
- To support access to sensitive data with their specific requirements
- To implement federated life science authentication and authorization infrastructure (AAI) and access proposal/control system supporting access through different user entry points, managing user life cycle and controlling and providing fine grained access control to the resources;
- To support management and operation of this access and user management system including its connection to life science RIs service providers (e.g. cloud, data resources and other RI services)
- To ensure sustainability of the access and user management system; including its funding and governance model after the project;
- To make the whole access and user management system fully interoperable with the EOSC ecosystem, connecting it into the forthcoming EOSC AAI.
- To provide training for the whole pipeline for life science RIs resource providers, developers and users.
Task 5.1 Requirement gathering, blueprint, sustainability
Task 5.2 Complex LS AAI implementation
Task 5.3 Management and operation of complex LS AAI
Task 5.4 Training and community engagement
D5.1 : Access and User Management System for Life Science (LS AAI) – the blueprint
D5.2 : Access and User Management System for Life Science (LS AAI) – the implementation and usage report
D5.3 : Access and User Management System for Life Science – the blueprint: 1st update
D5.4 : Access and User Management System for Life Science – the blueprint: 2nd update of the initial document
D5.5 : Access and User Management System for Life Science (LS AAI) – final implementation and usage report
WP Leads: Susan Daenke (Instruct), Ludek Matyska (ELIXIR/MU)
WP6 will deliver the common services and standards needed to make data FAIR (namely for WP1 “Data resources”, WP2 “Tools and workflows”, and WP4 “Policies and tools for sensitive data reuse”), ensuring that these are consistently applied across infrastructures. WP6 will also enhance interlinked repository of registries and identifier, as a common basis of metadata models and interoperability in the EOSC-integrated data sets. Last, but not least, WP6 will deliver interoperable provenance information in order to describe history of biological material and data in order to supporting meaningful data integration and to address reproducibility problems revealed in the biomedical research in the past decade. Specifically:
- Development of a personalized guidance to understanding and implementing the FAIR principles.
- Implementation of a common metadata model to interconnect existing core registries and ontology services needed for implementing Findability and Interoperability in data and services.
- Developing common interoperable provenance standard. Provenance will enable machine readable description of history from biological material to data generation and data processing, in order to assess fitness for purpose and this reusability of data.
- Use the common provenance standard to support traceability of genetic material in order to implement support for Nagoya Protocol.
Task 6.1: Personalized guidance to understanding and implementing the FAIR principles for data resources
Task 6.2: Identification and application of registries for FAIR data infrastructures – Identifying and interconnecting registries with common metadata models, identifiers
Task 6.3: Provenance
Task 6.4 FAIR data management standards for protecting genetic resources
D6.1 : FAIR Requirements document
D6.2 : Provenance proposed model
D6.3 : Launch of FAIRsharing webpage
D6.4 : FAIRassist software
D6.5 : Report on identification and application of registries for FAIR data infrastructures
D6.6 : Common provenance model for processing biological material, data generation and computational workflows
WP Leads: Petr Holub (BBMRI), Isabelle Perseil (ERINHA/INSERM)
The overall goal of WP7 is to provide 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. Through the provided cloud resources, this work package will also promote the implementation and adoption of cloud interoperability standardsto ensure EOSC cloud providers are compatible with life-science services and with each other. To do this we will provide:
- An integrated set of public sector community cloud providers appearing in the EOSC Service Catalogue with access managed using the LS AAI (WP5)
- Procure commercial cloud providers using a cloud procurement framework (e.g. HNSciCloud, GEANT, …) that are integrated with the LS AAI and appearing in the EOSC Service Catalogue.
- Allocate resources from the supported EOSC-Life cloud providers in the EOSC Service Catalogue to the selected workflows and demonstrators from the EOSC-Life project, and compensate the cloud providers for the usage made at the agreed rates.
- Provide a technical support and consultancy function that will work with the selected demonstrators and workflows to support their deployment onto the allocated cloud resources to eventually establish a sustainable ResOps “Community of Practice” for cloud-enabled workflows.
- Establish a set of quantifiable capabilities needed for the secure hosting of sensitive data and identify which of the supported cloud providers in the EOSC Service Catalogue have these characteristics.
- The implementation of the principles for a secure and trusted cloud will be implemented in cooperation with WP4 which will collect the requirements for the BMS RI so that cloud solutions offered for the storage and computation of human research data comply with the legal requirements for sensitive data.
- Data access controls for sensitive data on cloud target systems are enforced in collaboration with WP5, and leverage technologies (e.g. OAuth2 based implementation) from previous projects (CORBEL, EXCELERATE).
- Provide deployable platforms for e.g. Galaxy and CWL based workflows (using GA4GH Cloud-WG compatible service).
D7.1 : Initial EOSC-LS Cloud Observatory Report
D7.2 : Final EOSC-LS Cloud Observatory Report
WP Leads: Steven Newhouse (ELIXIR/EMBL-EBI), Chris Lawerenz (ELIXIR/Charite)
Long-term sustainability in research infrastructures has been linked to their ability to ensure excellent science, unlock their innovation potential, facilitate exploitation of their data and to interlink with a global environment. At the same time the overall sustainability of the EOSC depends on the active involvement of all relevant stakeholders in the EOSC Governance model. To address these important aspects of international impact, innovation and sustainability, WP8 will:
- Integrate EOSC-Life with the developing EOSC governance and coordination structures and with the other EOSC cluster projects.
- Broaden the engagement and opportunities for Europe’s SMEs to use open life science data.
- Extend the quality management framework developed in CORBEL towards service management in line with the Rules of Engagement / service management framework to be adopted by EOSC.
- Develop metrics to assess impact of life-science open data in the cloud on data reproducibility.
D8.1 : Report on a methodology framework to assess
D8.2 : Common Framework for Quality, Data and Service Management
D8.3 : Summary Report Stakeholder Forum Meetings
D8.4 : Report on reproducibility
WP Leads: Michael Raess (INFRAFRONTIER), Anton Ussi (EATRIS)
Develop and deliver training to enable effective data access and preservation for immediate and future sharing, and re-use, of data in the Biological and Medical Sciences. The training will address two target communities that have distinct needs and different roles towards establishing an European Open Science Cloud (EOSC): (i) the BMS Research Infrastructures (data) staff and (ii) the end-user of the (data) services offered. For BMS RI staff it will provide skills training in:
- deployment of data resources in selected EOSC-Life cloud environment;
- workflow composition, deployment and execution in selected EOSC-Life cloud environments;
- data stewardship, architecture and operation of data services within EOSC-Life; and
- how to support cloud deployment and long-term FAIR data management for the cluster RIs. For EOSC-Life end-users, WP9 will provide hands-on training and expertise in:
- using EOSC-Life data resources, analytical workflows and other services developed in the project,
- effective re-use of publicly available data; and • best practices that users should adopt in managing their own data.
Task 9.1 Analysis of the training needs of different EOSC-Life users
Task 9.2 Train EOSC-Life end users
Task 9.3 Train EOSC-Life staff including data experts
Task 9.4 Assessing training impact
D9.1 : Final report of analysis of the training needs of different EOSC-Life
D9.2 : Review of EOSC-Life training activities, their impact and potential adaptations
D9.3 : Final report on EOSC-Life training activities and their impact
WP Leads: Gabriella Rustici (ELIXIR/UNICAM), Rebecca Ludwig (EATRIS)
The goal of the WP Outreach is to increase the visibility of the activities and developments, especially the demonstrators, through transparent and active internal communication within the Research Infrastructures, and coordinated intensive external communications between the participants of the consortium and their main stakeholders. Specifically, the WP aims to:
- Ensure awareness of the project’s aims, goals and context with all stakeholders, in particular in relation to the specific role of the participating BMS RIs in a coherent and controlled way through the development of communication strategic map
- Ensure the promotion and dissemination of project deliverables to all stakeholders through the involvement of each participating RI and the generation of a communication tool kit.
- Provide active support for the dissemination, visibility and attractiveness of publicly organised events during the project
- Provide strategic outreach to other projects and relevant initiatives to support the implementation of demonstrators developed.
Task 10.1 Communication Plan and Branding
Task 10.2 Stakeholders Engagement
Task 10.3 Events and dissemination
D10.1 : Strategic Marketing and Stakeholder mapping report
D10.2 : Review of effectiveness and impact of outreach and stakeholder engagement
WP Leads: Erik Steinfelder (BBMRI), Jacques Demotes (ECRIN)
- Establish and implement the Project Administration and Management functions
- Effectively integrate EOSC-Life deliverables with long-term planning and strategy of BMS RI through BMS RI strategy board
- Organise and deliver project management, advisory board and project open annual meetings
- Develop and implement a risk management plan to ensure project objectives are achieved
Task 11.1 Establish and implement the Project Administration
Task 11.2 Establish close integration with BMS RI long-term planning and strategy
Task 11.3 Organise and deliver all project management, partner and advisory board meetings
Task 11.4 Develop and implement a management contingency plan
D11.1 : EOSC-Life Data Management Plan
D11.2 : Life Science in EOSC: Summary of EOSC-Life impact and key results
D11.3 : Summary of EOSC-Life Main Achievements, Impacts, and Sustainability and Exploitation Plans
WP Lead: Niklas Blomberg (ELIXIR, Project Coordinator)
The objective is to ensure compliance with the ‘ethics requirements’ set out in this work package. The ‘ethics requirements’ that the project must comply with are included as deliverables in this work package.
D12.1 : POPD – Requirement No. 1
4.1. The applicant must check if a declaration on compliance and/or authorisation is required under national law for collecting and processing personal data as described in the proposal. If yes, the declaration on compliance and/or authorisation must be submitted as a deliverable. 4.2. If no declaration on compliance or authorisation is required under the applicable national law, a statement from the designated Data Protection Officer that all personal data collection and processing will be carried out according to EU and national legislation must be submitted as a deliverable. 4.4. Detailed information on the procedures for data collection, storage, protection, retention, and destruction, and confirmation that they comply with national and EU legislation must be submitted as a deliverable. 4.7. Templates of the informed consent forms and information sheets (in language and terms intelligible to the participants) must be kept on file. 4.9. In case of further processing of previously collected personal data, relevant authorisations must be kept on file.