Benefits of working together services
| Name | Description | ELIXIR Node |
|---|---|---|
| ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI | ||
| ELIXIR Spain | ||
| ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI | ||
| ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR France, ELIXIR Germany, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI | ||
| ELIXIR Czech Republic | ||
| ELIXIR Czech Republic, ELIXIR Netherlands | ||
| ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Netherlands, ELIXIR Spain, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI | ||
| ELIXIR Italy, ELIXIR Norway, ELIXIR Portugal, EMBL-EBI | ||
| ELIXIR Czech Republic | ||
| ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Ireland, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI | ||
| ELIXIR Belgium | ||
| ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI | ||
| ELIXIR Netherlands | ||
| ELIXIR Germany, ELIXIR Italy | ||
| ELIXIR Norway | ||
| ELIXIR Belgium, ELIXIR Germany, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Portugal, ELIXIR Spain, ELIXIR Sweden, ELIXIR UK | ||
| ELIXIR Czech Republic | ||
Demonstrating impact is central to ensuring the long-term sustainability of a research infrastructure. Building on existing impact assessment frameworks (e.g. developed by the Organisation for Economic Cooperation and Development OECD, or by the European Strategic Forum on Research Infrastructures ESFRI) focused on research infrastructures, we will collaborate to adapt and refine these approaches based on the needs and specificities of the Italian, Norwegian and Portuguese Nodes of ELIXIR. This effort by ELIXIR Portugal, Norway and Italy will be undertaken through continuous sharing among team members, and in close collaboration with the ELIXIR Hub. In addition, opportunities to collect contributions from other ELIXIR Nodes will be taken advantage of, namely via direct requests for feedback, short surveys and/or semi-structured interviews. Synergies with relevant ELIXIR activities will be sought, e.g. the RI-PATHS project (“Research Infrastructures Pathways of Impact”) and the ELIXIR-CONVERGE project. The project is being continued and expanded to more ELIXIR Nodes through Impact evaluation at Node-level - getting it done. For any question or query, contact Corinne Martin (corinne.martin [at] elixir-europe.org (subject: Empowering%20ELIXIR%20Nodes%20to%20measure%20and%20communicate%20their%20performance%20and%20impact) ). If you are part of ELIXIR, you can access impact-related resources (requires login) as part of ELIXIR's Impact Focus Group. |
ELIXIR Portugal, ELIXIR Italy, ELIXIR Norway | |
| ELIXIR Finland, ELIXIR Spain, ELIXIR UK, EMBL-EBI | ||
| ELIXIR Switzerland | ||
| ELIXIR Spain | ||
| ELIXIR UK | ||
| ELIXIR UK | ||
Life science and healthcare stakeholders need to use sensitive data in several ways. Sensitive data needs to be protected against unauthorized access. Protection of data may be required for legal or ethical reasons, for issues pertaining to personal privacy, or for proprietary considerations. Especially important but complicated this is when sensitive data comes from several sources and countries. CSC (ELIXIR Finland) has recently launched open beta sensitive data (SD) services to support secure data management through web-user interfaces accessible from the user's own computer. The services include Sensitive Data Connect (SD Connect) and Sensitive Data Desktop (SD Desktop). VEIL.AI, a University of Helsinki spinout, specializes in health data privacy protection powered by AI-driven technologies. These new technologies enable high-quality row-level anonymized data production with secure and easier data interoperability and federation for better research, education and innovation opportunities in life sciences. The data privacy protection technologies include:
Purpose of this project is to validate use of VEIL.AI technologies as part of the CSC SD solutions delivered for researchers, organizations and educational purposes, and negotiate for a licencing model for technology that would allow long-term sustainability of the technology collaboration and exchange. Individual technology interests for knowledge exchange include:
Licencing of technology from an SME to support service infrastructure building of an ELIXIR node is a broad target. In this scheme CSC and VEIL.AI will produce a focused example of a collaboration scheme. We will first identify technology components, and then discuss what kind of agreement would be necessary, with the intention for a sustainable, long-term collaboration. Outcome will be know-how on how to build and formalise public infrastructure partnering with a (ICT) technology start-up. Optimally, lessons learned could be applicable for other similar arrangements. |
ELIXIR Finland | |
| ELIXIR Czech Republic, ELIXIR Finland, ELIXIR Germany, ELIXIR Italy, ELIXIR Norway, ELIXIR Portugal, ELIXIR Spain, ELIXIR UK, EMBL-EBI | ||
Building on the knowledge and experience gained during the piloting of the RI-PATHS approach, an ELIXIR-funded Staff Exchange project, and related work done elsewhere in ELIXIR, this Strategic Implementation Study aimed to increase capacity in impact evaluation across a set of national ELIXIR Nodes. Led by three ELIXIR Nodes (Belgium, Norway and Portugal), and with support from the ELIXIR Hub, activities were undertaken in coordination with relevant work being done as part of the ELIXIR-CONVERGE project, and included:
A series of "Show and Tell" knowledge-exchange events was also run, e.g.:
The application of the new skills and knowledge was implemented by the Nodes themselves, focused on their chosen case studies (or “impact challenge”), with mentoring from relevant experts (impact, innovation and industry, communications, funding and stakeholders). This mentoring took the form of ad-hoc and informal requests for support and advice, along with more formal "support calls" where Nodes came with specific questions to ask to the experts, whom in turn provided dedicated feedback based on materials submitted ahead of the call. Case studies were chosen by the Nodes, based on their needs, as influenced by their national circumstances and particular sets of stakeholders. Outputs from this project are hyperlinked at the bottom this page, and include ELIXIR's Impact Toolkit (featured in the final webinar). The Toolkit collates a range of impact-related materials including training materials, worked examples, factsheets, lists of indicators, key published references, case studies, and slides. Its intended audience is operators, developers and managers wishing to demonstrate and communicate the performance, impact, and ultimately public value of their research infrastructure, to their particular set of funders and stakeholders. The main outcome from this project was an increased capacity at Node level to demonstrate and communicate public value to funders and other key stakeholders, thereby contributing to long-term sustainability of Node-led activities. This ambition aligns directly with one of the 2020 recommendations of a High-Level Expert Group which assessed the progress of ESFRI (European Strategy Forum for Research Infrastructures) and other world class research infrastructures towards implementation and long-term sustainability. In parallel to this, the project worked to reinforce an ELIXIR-wide ‘community of practice’ around impact evaluation. For any question or query, contact (info [at] elixir-europe.org (subject: Impact%20evaluation%20at%20Node-level%20-%20getting%20it%20done, body: %0AProject%20this%20message%20relates%20to%3A%0Ahttps%3A%2F%2Felixir-europe.org%2Finternal-projects%2Fcommissioned-services%2Fimpact-evaluation) ). If you are part of ELIXIR, you can access all resources related to this Study (requires login), and much more (also requires login) as part of ELIXIR's Impact Focus Group. Supported by  |
ELIXIR Portugal, ELIXIR Norway, ELIXIR Belgium, ELIXIR Italy, ELIXIR Greece, ELIXIR Netherlands, ELIXIR Switzerland, ELIXIR UK, ELIXIR France, ELIXIR Czech Republic, ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Israel, ELIXIR Germany | |
| ELIXIR Finland | ||
| ELIXIR Germany | ||
| ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Ireland, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI | ||
| ELIXIR Belgium, ELIXIR Germany | ||
| ELIXIR Belgium, ELIXIR Norway, ELIXIR Portugal | ||
This study will support OpenEBench in the goal to become an observatory of bioinformatics software quality regarding openness including:
WP1. A Core Benchmarking Service:Work Package 1 has the following aims:
Through four subtasks:
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ELIXIR Czech Republic, ELIXIR Italy, ELIXIR Norway, ELIXIR Spain, ELIXIR Switzerland | |
| ELIXIR Finland, ELIXIR Germany, ELIXIR Norway, ELIXIR Spain, ELIXIR Sweden | ||
| ELIXIR Spain | ||
| ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI | ||
This Implementation Study will allow the newly created Single-Cell Omics Community to tackle some of the main challenges identified and achieve the Community's short-term goals described in the white paper. SCONE will address the need for scalable training by training more trainers and by providing easy access to up-to-date training resources, including lecture videos. Efficient benchmarking of analysis tools will be achieved by providing curated benchmarking datasets. To effectively address shortfalls in current data/metadata standard paradigms, SCONE will monitor emerging technologies and organise workshops on standard and FAIR data management practices in use across the entire single-cell omics community, with involvement of key stakeholders including those providing standards, tools and data hosting solutions. The ELIXIR Compute Platform will be kept up to date with the computing requirements of SCO researchers by active information exchange including a workshop. Events and news
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ELIXIR Finland, ELIXIR Sweden, ELIXIR Germany, ELIXIR Italy, ELIXIR Switzerland, EMBL-EBI, ELIXIR Slovenia, ELIXIR Netherlands, ELIXIR UK, ELIXIR Belgium, ELIXIR Greece, ELIXIR Portugal, ELIXIR Ireland, ELIXIR Israel, ELIXIR Norway, ELIXIR Spain, ELIXIR France, ELIXIR Czech Republic, ELIXIR Luxembourg | |
This Implementation Study will allow the newly created Single-Cell Omics Community to tackle some of the main challenges identified and achieve the Community's short-term goals described in the white paper. SCONE will address the need for scalable training by training more trainers and by providing easy access to up-to-date training resources, including lecture videos. Efficient benchmarking of analysis tools will be achieved by providing curated benchmarking datasets. To effectively address shortfalls in current data/metadata standard paradigms, SCONE will monitor emerging technologies and organise workshops on standard and FAIR data management practices in use across the entire single-cell omics community, with involvement of key stakeholders including those providing standards, tools and data hosting solutions. The ELIXIR Compute Platform will be kept up to date with the computing requirements of SCO researchers by active information exchange including a workshop. Events and news
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ELIXIR Finland, ELIXIR Sweden, ELIXIR Germany, ELIXIR Italy, ELIXIR Switzerland, EMBL-EBI, ELIXIR Slovenia, ELIXIR Netherlands, ELIXIR UK, ELIXIR Belgium, ELIXIR Greece, ELIXIR Portugal, ELIXIR Ireland, ELIXIR Israel, ELIXIR Norway, ELIXIR Spain, ELIXIR France, ELIXIR Czech Republic, ELIXIR Luxembourg | |
| ELIXIR Switzerland | ||
An aim of systems biology is to understand biological functions by modelling metabolic interactions and processes. Different modelling techniques have been developed and applied. Out of these, the use of genome-scale metabolic models (GEMs) stands out as a widely applicable approach ranging from optimizing industrial production of commercially-relevant chemicals to studying disease patterns, be it within a set of human tissues or across animal model organisms. GEMs are complex and powerful tools. They comprise of thousands of reactions, mapping how metabolites are transformed through the activity of enzymes. Moreover, they aim to capture in vivo cellular behaviour under different phenotypic conditions by introducing the necessary abstractions for the entire metabolism. Most often, systems biology requires the collection and integration of experimental data, and the same applies to GEMs. In the process of analysing experimental data, one recurring step is the visualisation of analysis results, regardless if the experiment is done in an academic or industrial setting. Metabolic Atlas is dedicated to making GEMs easy to browse and analyse. Developed open-source by the Swedish ELIXIR node National Bioinformatics Infrastructure Sweden (NBIS) and freely available online at https://metabolicatlas.org, the web portal integrates high-value open source GEMs developed by the Nielsen Lab at Chalmers University of Technology, now community-curated, and facilitates the access to the content of these models without any requirements. Moreover, it provides both automatically-generated and manually-curated maps, onto which omics data can be overlaid. Additionally, the manually-created maps have been the foundation of the collaboration with Protein Atlas, an ELIXIR Core Data Resource. Metabolic Atlas has also been showcased in the context of omics data integration, as part of the ELIXIR-SE Omics integration workshop. The BioInnovation Institute Foundation (BII) is an international non-profit foundation supported by the Novo Nordisk Foundation, and it operates as an incubator to accelerate world-class life science innovations that drive the development of new solutions by early-stage life science start-ups for the benefit of people and society. A recent ELIXIR report on innovation in the life sciences highlights that “innovative life sciences projects require the essential use of open data, open-source software and common standards. Together, open resources allow industry, academia and the wider community to create novel services and products.” Acting as an interface between the academic community and industry, BII is aware of the importance of the open-source ecosystem as a startup need. The Swedish ELIXIR node has an established systems biology dimension. In addition to the software development of Metabolic Atlas, NBIS provides expert bioinformatics support to the scientific community and occasionally to the industry. Last but not least, NBIS is also active in the recently established Systems Biology Community. The goal of this project is to identify and retrospectively assess systems biology-themed activities geared towards industry with a focus on reproducibility, FAIRification and data management that can be carried out by NBIS. Specifically, the project will kick-off from how Metabolic Atlas can be leveraged by the industry and look further towards a long-term collaboration between BII and NBIS. |
ELIXIR Sweden | |
| ELIXIR Spain | ||
| ELIXIR Czech Republic, ELIXIR Netherlands | ||