European Life Sciences Research Articles

Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities

In recent years, modern life sciences research underwent a rapid development driven mainly by the technical improvements in analytical areas leading to miniaturization, parallelization, and high throughput processing of biological samples. This has led to the generation of huge amounts of experimental data. To meet these rising demands, the German Network for Bioinformatics Infrastructure (de.NBI) was established in 2015 as a national bioinformatics consortium aiming to provide high quality bioinformatics services, comprehensive training, powerful computing capacities (de.NBI Cloud) as well as connections to the European Life Science Infrastructure ELIXIR, with the goal to assist researchers in exploring and exploiting data more effectively.
 Since its foundation, de.NBI Cloud has formed the scientific and collaborative backbone for new major German initiatives like NFDI or EOSC-Life in the European sector of computational biosciences. Above all, the cooperation with various NFDI consortia such as NFDI4Biodiversity, DataPLANT, GHGA, FAIRagro or NFDI4Microbiota showcases the power, range and flexibility of the de.NBI Cloud, especially for the national life science community.
 In conclusion, the de.NBI Cloud provides the ability to unlock the full potential of research data and enables easier collaboration across different ecosystems and research areas, which in turn enables scientists to innovate and scale-up their data-driven research, not only in the life and computational biosciences, but across the different science domains addressed by the NFDI.

Towards Connecting Molecular Data and the Biodiversity Research Community: An ENA and ELIXIR biodiversity community perspective

Global and regional efforts for generating molecular sequencing data are fundamental to characterise and monitor the Earth’s biodiversity. However, exploiting the full potential of molecular data for biodiversity monitoring and conservation is still a challenge. There is still the need to fully connect the generation and archiving of sequence data with other biodiversity infrastructures, thereby promoting Findability, Accessability, Interoperability and Reusability (FAIR) of data. Here we present the ongoing activities and future plans of the European Life-Science Infrastructure (ELIXIR) and the European Molecular Biology Laboratory European Bioinformatics Institute’s (EMBL-EBI) European Nucleotide Archive (ENA, the European node of the International Nucleotide Sequence Database Collaboration - INSDC) towards an enriched set of sequence data connected to the wider biodiversity research community. ELIXIR has an emerging Biodiversity Community that was originally created as a focus group in 2019, to better align the work in biodiversity across the ELIXIR Nodes and with global initiatives in the biodiversity domain. This group has been working on understanding the capabilities, interests and ongoing projects that exist across the Nodes, developing connections with external partners in the biodiversity area (e.g. Global Biodiversity Information Facilitiy, GBIF; LifeWatch Eric) and developing a longer term strategy for support of biodiversity by ELIXIR. A recent opinion piece by the group (Waterhouse et al. 2021) highlights opportunities for infrastructure developments in the area of biodiversity and provides recommendations for closer integration of molecular data with biodiversity research. These recommendations include the alignment of taxonomies across domains and the general adoption of standardized metadata. ELIXIR and EMBL-EBI are involved in several biodiversity genomics initiatives, including the Earth BioGenome Project (EBP), the Darwin Tree of Life Project (DToL), the European Reference Genome Atlas (ERGA), and the BIOSCAN Europe, where support is being provided to data curation, submission and visibility and in the definition of standards for the associated metadata (e.g. Lawniczak et al. 2022). Moreover, EMBL-EBI is a partner of UniEuk, an initiative that is working towards building a flexible universal taxonomic framework for eukaryotes. ELIXIR and EMBL-EBI are also part of the Biodiversity Community Integrated Knowledge Library (BiCIKL), an Horizon 2020 project that is working towards establishing FAIR practices in the biodiversity domain, and thereby developing tools and workflows for connecting data along the biodiversity research cycle (Penev et al. 2022). These projects and community efforts are contributing to improving metadata standards and pushing the development of tools and workflows to support enriched metadata and increased linkage with other biodiversity infrastructures. Overall, we need to continue to work towards a strong foundation of interlinked knowledge to be able to effectively respond to global challenges such as biodiversity loss and ecosystem change.

A CONVERSATION WITH… Isabelle de Cremoux, CEO and Managing Partner of European Life Science VC Seventure Partners

Inside Precision MedicineVol. 9, No. 2 In Conversation WithA CONVERSATION WITH… Isabelle de Cremoux, CEO and Managing Partner of European Life Science VC Seventure PartnersBacking the Microbiome: The Investor PerspectiveHelen AlbertHelen AlbertHelen Albert is Senior Editor at Inside Precision Medicine and a freelance science journalist. Prior to going freelance, she was Editor-in-Chief at Labiotech, an English-language, digital publication based in Berlin focusing on the European biotech industry. Before moving to Germany, she worked at a range of different science and health-focused publications in London. She was Editor of The Biochemist magazine and blog, but also worked as a Senior Reporter at Springer Nature's medwireNews for a number of years, as well as freelancing for various international publications. She has written for New Scientist, Chemistry World, Biodesigned, The BMJ, Forbes, Science Business, Cosmos magazine, and GEN. Helen has academic degrees in genetics and anthropology, and also spent some time early in her career working at the Sanger Institute in Cambridge before deciding to move into journalism.Senior EditorSearch for more papers by this authorPublished Online:14 Apr 2022https://doi.org/10.1089/ipm.09.02.14AboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View articleFiguresReferencesRelatedDetails Volume 9Issue 2Apr 2022 InformationCopyright © GEN PublishingTo cite this article:Helen Albert.A CONVERSATION WITH… Isabelle de Cremoux, CEO and Managing Partner of European Life Science VC Seventure Partners.Inside Precision Medicine.Apr 2022.50-52.http://doi.org/10.1089/ipm.09.02.14Published in Volume: 9 Issue 2: April 14, 2022PDF download

Euro-BioImaging – Interdisciplinary research infrastructure bringing together communities and imaging facilities to support excellent research

Euro-BioImaging – Interdisciplinary research infrastructure bringing together communities and imaging facilities to support excellent research

Innovations strategy for moving from created regional clusters to co-creation in life sciences for health care and well-being ecosystems.

Over the last decades, the demographic changes have all altered the population structure and influenced the social, economic, and political characteristics of countries over the world. Therefore, the creation of novel ecosystems, new clusters and systems which involved technology and industry, business, education, science, and innovation are increased rapidly. However, in order to solve the future global challenges, the created various types of clusters, public and private sector systems should cooperate and work together as a unit. Therefore, one of the proposed solutions is unified regional ecosystems' building. The Interreg European Life Science Ecosystems (ELISE) project addresses the societal challenge which is common to the European regions: to promote better health for all. This covers the need to improve health and well-being outcomes, to promote market growth, job creation, and EU competitiveness. Based on the project, three different regions of the European countries-Poland, Italy, and Germany-are selected in order to perform the analysis of drivers directly influencing the move from the existing clusters to unified regional ecosystem. The performed analysis showed that the government of a country and regional public authorities have the direct influence and play the central role in shaping unified regional ecosystems. The common economic, social, and political situation in a country is dependent on the government and it is influenced by the regional public authorities. Therefore, the collaboration and conversation among such institutions is the important factor defining how quickly different countries will create unified ecosystems and will solve the future problems.

The Collaborative Potential of Research Infrastructures in Addressing Global Scientific Questions

Research Infrastructures (RIs) are facilities, resources and services used by scientists to perform research and support innovation. A number of EU research infrastructures [e.g. e-Science and Technology European Infrastructure for Biodiversity and Ecosystem Research (LifeWatch) European Research Iinfrastructures Consortium (ERIC); The European life-sciences Infrastructure for biological Information (ELIXIR); the European Marine Biological Resource Centre (EMBRC ERIC); the European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences (uroBioImaging ERIC)] have been building Virtual Research Environments (VREs), which include many virtual laboratories (vLabs) offering, one stop data access to scientists, high computational capacity and collaborative research platforms in support of the requirements of the digital science. This presentation gives examples on the use of the vLabs developed by LifeWatch ERIC which have subsequently been taken up as web services by other RIs. The RvLab operates on a high-performance computer cluster, and has been used in order to analyse various properties of taxon equality, with a focus on marine species. This taxonomic information on marine biota is organized and made publicly available through the World Register of Marine Species (WoRMS) that delivers more than 250,000 described valid species names. Although scientists consider an equal status (in terms of contribution to overall diversity) to each taxon used in taxonomy, biogeography, ecology and biodiversity, the question “are all taxa equal?” has never been tested at a global scale. We present evidence that this question can be addressed by applying relatedness indices (Taxonomic Distinctness) over the entire WoRMS metazoan tree. The virtual micro-CT laboratory (Micro-CT vLab), which can be used by the members of the scientific community interested in the digitisation methods and biological collections, makes the micro-CT data exploration of natural history specimens freely available over the internet. Micro-CT vLab makes it possible the online exploration and dissemination of micro-CT datasets, which are only rarely made available to the public due to their very large size and a lack of dedicated online platforms supporting the interactive manipulation of 3D data. Examples of how these vLabs can be used by other RIs are provided.

New indicators and indexes for benchmarking university\u2013industry\u2013government innovation in medical and life science clusters: results from the European FP7 Regions of Knowledge HealthTIES project

BackgroundWhile the European Union is striving to become the ‘Innovation Union’, there remains a lack of quantifiable indicators to compare and benchmark regional innovation clusters. To address this issue, a HealthTIES (Healthcare, Technology and Innovation for Economic Success) consortium was funded by the European Union’s Regions of Knowledge initiative, research and innovation funding programme FP7. HealthTIES examined whether the health technology innovation cycle was functioning differently in five European regional innovation clusters and proposed regional and joint actions to improve their performance. The clusters included BioCat (Barcelona, Catalonia, Spain), Medical Delta (Leiden, Rotterdam and Delft, South Holland, Netherlands), Oxford and Thames Valley (United Kingdom), Life Science Zürich (Switzerland), and Innova Észak-Alföld (Debrecen, Hungary).MethodsAppreciation of the ‘triple helix’ of university–industry–government innovation provided the impetus for the development of two quantifiable innovation indexes and related indicators. The HealthTIES H-index is calculated for disease and technology platforms based on the h-index proposed by Hirsch. The HealthTIES Innovation Index is calculated for regions based on 32 relevant quantitative and discriminative indicators grouped into 12 categories and 3 innovation phases, namely ‘Input’ (n = 12), ‘Innovation System’ (n = 9) and ‘Output’ (n = 11).ResultsThe HealthTIES regions had developed relatively similar disease and technology platform profiles, yet with distinctive strengths and weaknesses. The regional profiles of the innovation cycle in each of the three phases were surprisingly divergent. Comparative assessments based on the indicators and indexes helped identify and share best practice and inform regional and joint action plans to strengthen the competitiveness of the HealthTIES regions.ConclusionThe HealthTIES indicators and indexes provide useful practical tools for the measurement and benchmarking of university–industry–government innovation in European medical and life science clusters. They are validated internally within the HealthTIES consortium and appear to have a degree of external prima facie validity. Potentially, the tools and accompanying analyses can be used beyond the HealthTIES consortium to inform other regional governments, researchers and, possibly, large companies searching for their next location, analyse and benchmark ‘triple helix’ dynamics within their own networks over time, and to develop integrated public–private and cross-regional research and innovation strategies in Europe and beyond.

Finding your way through the science maze.

Asifa Akhtar is Director at the Max Planck Institute of Immunobiology and Epigenetics. Her lab focuses on chromatin and epigenetic regulation. A member of the European Molecular Biology Organisation, she received the European Life Science Organization award in 2008 and the Wilhelm Feldberg Prize in 2017.

Proceedings of the “Think Tank Hackathon’’, Big Data Training School for Life Sciences Follow-up, Ljubljana 6th – 7th February 2018

On 6th and 7th February 2018, a Think Tank took place in Ljubljana, Slovenia. It was a follow-up of the “Big Data Training School for Life Sciences” held in Uppsala, Sweden, in September 2017. The focus was on identifying topics of interest and optimising the programme for a forthcoming “Advanced” Big Data Training School for Life Science, that we hope is again supported by the COST Action CHARME (Harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research - CA15110). The Think Tank aimed to go into details of several topics that were - to a degree - covered by the former training school. Likewise, discussions embraced the recent experience of the attendees in light of the new knowledge obtained by the first edition of the training school and how it comes from the perspective of their current and upcoming work. The 2018 training school should strive for and further facilitate optimised applications of Big Data technologies in life sciences. The attendees of this hackathon entirely organised this workshop.

Report on the “Big Data Training School for Life Sciences”, 18-22 September 2017, Uppsala, Sweden

In September 2017 a "Big Data Training School for Life Sciences" took place in Uppsala, Sweden, jointly organised by EMBnet and the COST Action CHARME (Harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research - CA15100). The week programme was divided into hands-on sessions and lectures. In both cases, insights into dealing with big amounts of data were given. This paper describes our personal experience as students’ by providing also some suggestions that we hope can help the organisers as well as other trainers to further increase the efficiency of such intensive courses for students with diverse backgrounds.

Merck and Qiagen to expand in U.K.

U.S. drugmaker Merck & Co. and German diagnostics firm Qiagen are separately planning major investments in the U.K. The moves accompany a raft of British government measures intended to bolster the life sciences sector as the country prepares to leave the European Union. Merck is set to invest $1.3 billion to build a new U.K. headquarters and drug research center in the London area. Scheduled to open in about 2020, the facility will house 150 new researchers plus 800 staffers currently working in Hoddesdon, north of London. “This new London location will enable us to … be an important contributor to the vibrant and rapidly growing London life sciences community, while providing access for more collaborations within the European life science ecosystem,” says Roger M. Perlmutter, president of Merck Research Laboratories. In the near term, Merck plans to establish a small temporary research facility in the London area. The firm

Matching Local and Global Dimensions: A Knowledge Based Approach to Classify European Life Sciences Clusters

It is now widely accepted that innovation is a territorially embedded process, which cannot be fully understood independent of the social and institutional conditions of individual places. On the basis of these considerations, some authors identified criteria to define the geographic confines for the innovative process, introducing the concept of the local systems of innovation (LIS), defined as networks of technologically specialized and locally situated firms, institutions and research agencies. Nevertheless empirical evidences show that especially in high tech industry like life sciences, relatively few clusters are completely self-sufficient in terms of the knowledge base from which they draw suggesting that the knowledge flows that feed innovation in a cluster are often both local and global.According to these considerations and starting from the knowledge based theory of innovations systems the paper proposes a theoretical framework that classifies the innovation systems considering the place of knowledge sourcing and the place of knowledge development. The framework has then been used to classify the European life sciences clusters. The empirical analysis shows that Local Innovation System is only a possible configuration of technology clusters that can be assumes also the configurations of Imported Innovation Systems, Exported Innovation Systems and Global Innovation Systems.

Bioinformatics on a national scale: an example from Switzerland.

Switzerland has been a pioneer in the field of bioinformatics since the early 1980s. As time passed, the need for one entity to gather and represent bioinformatics on a national scale was felt and, in 1998, the SIB Swiss Institute of Bioinformatics was created. Hence, 2018 marks the Institute’s 20th anniversary. Today, the Institute federates 65 research and service groups across the country—whose activity domains range from genomics, proteomics, medicine and health to structural biology, systems biology, phylogeny and evolution—and a group whose sole task is dedicated to training. The Institute hosts 12 competence centres that provide bioinformatics and biocuration expertise to life scientists across the country. SIB sensed early on that the wealth of data produced by modern technologies in medicine and the growing self-awareness of patients was about to revolutionize the way medical data are considered. In 2012, it created a Clinical Bioinformatics group to address the issue of personalized health, thus working towards a more global approach to patient management, and more targeted and effective therapies. In this respect, SIB has a major role in the Swiss Personalized Health Network to make patient-related data available to research throughout the country. The uniqueness of the Institute’s governance structure has also inspired the structure of other European life science organizations, notably ELIXIR.

Bioinformatics in Germany: toward a national-level infrastructure.

The German Network for Bioinformatics Infrastructure (de.NBI) is a national initiative funded by the German Federal Ministry of Education and Research (BMBF). The mission of de.NBI is (i) to provide high-quality bioinformatics services to users in basic and applied life sciences research from academia, industry and biomedicine; (ii) to offer bioinformatics training to users in Germany and Europe through a wide range of workshops and courses; and (iii) to foster the cooperation of the German bioinformatics community with international network structures such as the European life-sciences Infrastructure for biological Information (ELIXIR). The network was launched by the BMBF in March 2015 and now includes 40 service projects operated by 30 project partners that are organized in eight service centers. The de.NBI staff develops further and maintains almost 100 bioinformatics services for the human, plant and microbial research fields and provides comprehensive training courses to support users with different expertise levels in bioinformatics. In the future, de.NBI will expand its activities to the European level, as the de.NBI consortium was assigned by the BMBF to establish and run the German node of ELIXIR.

The European Lead Factory: A Blueprint for Public-Private Partnerships in Early Drug Discovery.

The European Lead Factory (ELF) is a public–private partnership (PPP) that provides researchers in Europe with a unique platform for translation of innovative biology and chemistry into high-quality starting points for drug discovery. It combines an exceptional collection of small molecules, high-throughput screening (HTS) infrastructure, and hit follow-up capabilities to advance research projects from both private companies and publicly funded researchers. By active interactions with the wider European life science community, ELF connects and unites bright ideas, talent, and experience from several disciplines. As a result, ELF is a unique, collaborative lead generation engine that has so far resulted in >4,500 hit compounds with a defined biological activity from 83 successfully completed HTS and hit evaluation campaigns. The PPP has also produced more than 120,000 novel innovative library compounds that complement the 327,000 compounds contributed by the participating pharmaceutical companies. Intrinsic to its setup, ELF enables breakthroughs in areas with unmet medical and societal needs, where no individual entity would be able to create a comparable impact in such a short time.

The ELIXIR channel in F1000Research.

ELIXIR, the European life science infrastructure for biological information, is a unique initiative to consolidate 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 - the ELIXIR Nodes. This editorial introduces the ELIXIR channel in F1000Research; the aim of the channel is to collect and present ELIXIR’s scientific and operational output, engage with the broad life science community and encourage discussion on proposed infrastructure solutions. Submissions will be assessed by the ELIXIR channel Advisory Board to ensure they are relevant to ELIXIR community, and subjected to F1000Research open peer review process.

The ELIXIR channel in F1000Research

ELIXIR, the European life science infrastructure for biological information, is a unique initiative to consolidate 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 - the ELIXIR Nodes. This editorial introduces the ELIXIR channel in F1000Research; the aim of the channel is to collect and present ELIXIR's scientific and operational output, engage with the broad life science community and encourage discussion on proposed infrastructure solutions. Submissions will be assessed by the ELIXIR channel Editorial Board to ensure they are relevant to ELIXIR community, and subjected to F1000Research open peer review process.

Stimulating translational research: several European life science institutions put their heads together

Translational research leaves no-one indifferent and everyone expects a particular benefit. We as EU-LIFE (www.eu-life.eu), an alliance of 13 research institutes in European life sciences, would like to share our experience in an attempt to identify measures to promote translational research without undermining basic exploratory research and academic freedom.

AQUA-TNET thematic network: an 18-year chronicle of development and achievement in European aquaculture education

The long-running higher education network AQUA-TNET, a tightly-knit collaboration of university departments, research institutes and other stakeholders from the aquaculture industry, was established in 1996 by AQUATT, a coordinating partner in the SOCRATES-ERASMUS Thematic Network DEMETER led by ICA (Association for European Life Sciences Universities). Later, AQUA-TNET activities continued under an umbrella organisation, the AFANET Thematic Network. Previous work on accreditation in European aquaculture courses carried out by AQUA-TNET’s first coordinator, the UETP (University Enterprise Training Partnership) AQUATT enabled the fledging network of 15 partners to publish details of aquaculture courses in all its 15 member countries and to focus on issues soon to be raised as part of the emergent Bologna Process (1999). AQUA-TNET’s ground-breaking work in educational reforms led to its steady expansion, with the result that in 2005 it was established as a stand-alone ERASMUS Thematic Network. Its achievements from 2005 to 2011 under the coordination of Gent University (Belgium) and from 2011 to 2014 of the University of Stirling (UK), demonstrate the incremental impact of AQUA-TNET’s long-term activities. AQUA-TNET played a leading co-operative role between higher education institutions, further education providers, research institutions and industry, defining and developing a high-quality European dimension within its academic disciplines. Activities included contributions to Bologna priorities such as student and staff mobility (M.Sc. and Ph.D. online portals detailing all members’ courses); development of innovative M.Sc., Ph.D., HE/VET and Lifelong Learning (LLL) programmes; organisation of hands-on workshops on new technologies (e-learning, ICT); identification of flexible pathways for lifelong learners (EQF and ECVET); developing diversified language learning for HE; excellent online forum ( www.aquatnet.com ) disseminating comprehensive information to all stakeholders, including industry.

ESA's Cooperative Strategy and Current Program in Materials Science in Space

The physical sciences research activities implemented by ESA in the framework of the European Life and Physical sciences in Space (ELIPS) programme build up on more than two decades of scientific progress and experience with developing and operating instruments on various space carriers. Research projects are mostly defined and developed in the context of International Topical Teams supported by ESA in coordination with other international partner agencies. Formal project proposals are eventually submitted to regular Announcements of Opportunity, reviewed by international independent peers and their technical feasibility is assessed by technical experts of the facilities considered for the implementation of the space experiments. For most projects, experiments and numerical modelling go hand in hand. As concerning Materials Sciences and the realisation of solidification experiments several platforms and facilities are utilised. This spans from centrifuges to - with increasing experiment duration - the Drop Tower in Bremen, the A-300 aircraft flying parabolic trajectories, sounding rockets and eventually the International Space Station (ISS). Several solidification instruments from typical Bridgman type furnaces to electromagnetic levitation and heating of spherical samples were developed, some of which are already operational in orbit. A dedicated X-ray set-up has also recently been operated on a sounding rocket to enable in-situ observations of the solidification of a metallic alloy. The paper will provide an overview of solidification projects, their objectives and corresponding instruments available for experimentation. It will lay out the objectives and strategy of ESA’s research programme, including the consolidating the international cooperation that prevails in Europe and in the ISS project.