Single-Cell Omics services
| Name | Description | ELIXIR Node |
|---|---|---|
| ELIXIR Czech Republic | ||
Cellular and molecular biology are fundamental to ELIXIR's mission. As part of our 2024–28 Programme, we are committed to advancing data services and software for research on nucleic acids, proteins and other biomolecules. This initiative will address new demands for multi-omics and multi-modal analyses, including imaging, by developing methods and partnerships. We will also expand expertise in reusable data and software to incorporate FAIR models, ensuring robust solutions for modelling at all scales. The following projects are key to connecting the latest developments with established data resources, unlocking the potential of cellular and molecular biology:
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ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Israel, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR UK, EMBL-EBI | |
| ELIXIR Finland, ELIXIR Germany, ELIXIR Netherlands, ELIXIR Slovenia, ELIXIR Sweden | ||
| EMBL-EBI | ||
NeoSpan will focus on designing a prototype workflow for retrieving and spatially mapping neoantigens from spatial omics datasets. As interest in spatially resolved biology is growing, researchers need tools to combine mutation detection, neoantigen prediction, gene expression and spatial coordinates in a unified analysis. As part of this Staff Exchange, Greek and Dutch teams will develop the initial framework for this pipeline, drawing on their combined expertise in single-cell and spatial omics, cancer immunology and computational method development. There will be several phases involved in the project, including requirements-gathering, development of core modules, integration, usability improvements and visualisation, followed by testing and refinement. A pilot workshop will be held near the end of the exchange to introduce the prototype to interested ELIXIR Nodes. The intention is that the workflow will later be adapted for wider use and maintained through established workflow communities. Beyond the technical outputs, the exchange will strengthen cross-Node collaboration in spatial omics, contribute to SCONE-related activities and provide substantial training opportunities for the participating researcher. |
ELIXIR Greece, ELIXIR Netherlands | |
The ELIXIR Metabolomics Community relies on standards, formats and data treatment solutions development and adoption, but it remains challenging to ensure high-quality reported metadata, sufficiently contextualised results, interoperable and reusable datasets and to integrate these metabolomics data with other omics or studies. This project is designed to address these issues and aims to connect key international standards with ELIXIR resources, as well as creating associated community guidelines and training materials. Based on the FAIRification framework, activities in the project will:
As a first necessary step, the project will create a Semantic Metabolomics Data Model to standardise metadata, ensuring unambiguous reuse of metabolomics projects. This model will focus on integrating key ontologies, providing open training initiative and enhancing the interoperability of metabolomics data through the production of open guidelines for annotation steps. By linking with ELIXIR’s Deposition databases, ISA Framework and other services, the project seeks to boost interconnection with ELIXIR platforms, other ELIXIR communities (Systems Biology, Food and Nutrition, Galaxy, Proteomics, Toxicology, Research Data Alliance Focus Group, etc.), the FAIR Cookbook and BioSchemas.org communities. Project outcomes are expected to promote the emergence of ambitious and innovative semantic-based solutions for inter-comparison of studies in healthcare, clinical and plant domains. |
ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Italy, ELIXIR Spain, ELIXIR France, ELIXIR Netherlands, ELIXIR Sweden, 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 | |
Spatial transcriptomics (ST) was named ‘Method of the Year 2020’ by Nature Methods and was more recently featured in Nature’s Seven technologies to watch in 2024. ST is now a prerequisite for researching transcriptional pathology at the cellular and molecular levels. Current use of ST is ubiquitously applied to multiple pathologies, including neurodegenerative disease, cancer, cardiomyopathy and nephrology. There is also an emerging application of ST in plant and microbiome research. While there are a plethora of spatial analysis applications, these are not unified or easily manageable by research scientists and they lack any hope of delivering FAIR and reproducible results. To address this challenge, we will implement Spatial2Galaxy (S2G) – a self-contained, reproducible, scalable FAIR spatial transcription analysis platform for researchers and bioinformaticians alike. We will develop S2G based on our success with developing Galaxy workflows, training materials and ST and single-cell analysis pipelines. S2G will provide state-of-the-art ST tools and workflows with proven high performance in benchmarking studies, ensuring the uptake of best practices. These tools will be demonstrated on datasets that connect various ST databases. This will consolidate community guidelines for integrative multi-modal single-cell omics and imaging analysis. Compared to non-spatial single-cell sequencing, presented as the Nature ‘Method of the Year 2013', it took six years until practical training and workflows for its analysis were FAIRified and available in Galaxy by 2019. In contrast, S2G aims to reduce this gap between technologies becoming relevant and provision of FAIR resources to the life science community for ST. |
ELIXIR Germany, ELIXIR France, ELIXIR Netherlands, ELIXIR UK | |
A new training course in spatial transcriptomics will be developed and delivered in Lausanne as part of this Staff Exchange. Spatial omics has grown rapidly in recent years, yet many ELIXIR Nodes have limited capacity to train researchers in these methods. The need for coordinated training was highlighted in the 2023 skills gap survey conducted by the ELIXIR Single-Cell Omics Community and the ELIXIR Training Platform. The new multi-Node training course will combine expertise from Belgium, Switzerland, Germany, Greece, Spain, the Netherlands and Sweden. Trainers will collaborate on preparing reusable and FAIR training materials and deliver an in-person course designed to help participants gain practical experience in analysing spatial transcriptomics data. Beyond supporting the course delivery, the activity will contribute to building long-term training capacity within ELIXIR by seeding a network of trainers who can adapt and reuse the materials in their own Nodes. The expectation is that the course will become a foundation for future offerings as the field continues to evolve. |
ELIXIR Belgium, ELIXIR Germany, ELIXIR Spain, ELIXIR Switzerland | |
TELLME will develop an AI service that generates clear, unbiased explanations of complex systems biology and multi-omics models. These models capture rich biological information but are difficult to interpret holistically. Using large language models, TELLME will translate pathway graphs, knowledge networks and multi-omics maps into clear narratives enriched with literature. This will reduce time-consuming manual interpretation and improve the accessibility, FAIRness and clarity of complex data. The tool will integrate with ELIXIR resources through open APIs, containerisation and AAI compatibility. Predicted outcomes:
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ELIXIR Netherlands, ELIXIR Spain, ELIXIR UK | |
| ELIXIR Belgium |