Field 6 – Open Digital Research Services
These services aim to combine the complex landscape of reusable biomedical data and analytic tools in the context of tumour biology complexity, to provide unprecedented opportunities for the cancer community for the development of novel techniques and understanding of the impact of cancer diagnostics and treatment from a molecular to a population level
| Unique ID | Country | Service Name | Description of Service | Research Infrastructure | Service Provider | Unit of access | Website |
|---|---|---|---|---|---|---|---|
| 9.1_IFO-IRE | IT | Transcriptomics,bulk and/or single-cell transcriptomics analysis and/or Immune Repertoire and/or deconvolution | Transcriptomics,bulk and/or single-cell transcriptomics analysis and/or Immune Repertoire and/or deconvolution | BIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC) | IFO-IRE | bulk and sing. cell transcriptomics analysis | https://www.ifo.it/ |
| 9.1_Lubeck Inst. Derm | DE | Transcriptomics,bulk and/or single-cell transcriptomics analysis and/or Immune Repertoire and/or deconvolution | The entire workflow for analysis of scRNAseq and immunoreceptor repertoire data is provided. | BIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC) | LIED | Bulk &/or sing. cell transcript.analysis | https://www.uksh.de/ |
| 9.1_CRG | ES | Analysis of bulk/ single cell RNA sequencing data from tumor and normal samples | Analysis of bulk RNA sequencing/ single-cell RNA sequencing/ Immune Repertoire profiling data from tumor and normal samples | BIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC) | Centro Nacional de Análisis Genómico | Bulk &/or sing.cell transcript.analysis | https://www.cnag.crg.eu/ |
| 9.2_UNIMIB | IT | Whole exome sequencing / whole genome sequencing analysis / cancer evolution analysis | Whole exome sequencing / whole genome sequencing analysis / cancer evolution analysis | BIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC) | UNIMIB | Whole Exome Seq./ whole genome seq. | https://www.unimib.it/ |
| 9.2_CRG | ES | Analysis of whole exome sequencing / whole genome sequencing data from tumor and normal samples | Analysis of whole exome sequencing and/or whole genome sequencing data from tumor and normal samples | BIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC) | Centro Nacional de Análisis Genómico | Whole exome seqen./whole genome sequen. | https://www.cnag.crg.eu/ |
| 9.1_Biogem | IT | Transcriptomics/ whole exome sequencing | Transcriptomic | BIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC) | Biogem S.c.a.r.l | RNA-SEQ | https://www.biogem.it/index.php/it/ |
| 9.4_Uni.of Oulu | FI | Biological and Biomedical image analysis (Digital Pathology/Radiomics) and modeling | For digital image data analysis of histological tissue slides, this service provides tailored analysis protocol packages (APPs) to customers using Visiopharm software (equipped with tissue align module. APPs are custom designed according to the specific research question and they are modified to work with specific staining. ML is trained for efficient detection and analysis of structural features (e.g. tumors, blood vessels, connective tissue), specific to the research question. | INFRAFRONTIER ERIC | University of Oulu | Biomed. imaging analysis | https://www.oulu.fi/en/university/faculties-and-units/biocenter-oulu |
| 9.4_CCMAR | PT | BioMedical Image Processing & Analysis | Biomedical image reconstruction, processing, analysis and visualization services, including workflows to enable accelerated scans and extract quantitative information from biomedical images (e.g. microscopy, mesoscopic optical imaging, Tomography, Magnetic Resonance Imaging) | EUROPEAN MARINE BIOLOGICAL RESOURCE CENTRE EUROPEAN RESEARCH INFRASTRUCTURE CONSORTIUM (EMBRC-ERIC) | EMBRC-PT | Biomed. imaging analysis | https://www.ccmar.ualg.pt/en |
| 9.21_EATRIS | DE | Digital Analysis Service plus expert support for EATRIS clinical cancer research support | Digital Analysis Service plus expert support for EATRIS clinical cancer research support | EATRIS ERIC (EATRIS) | EATRIS | Digital Analysis Service | https://eatris.eu/ |
| 9.23_Weitzmann | IL | Image data analysis | The bioimage analysis service supports researchers with image visualization and extraction of quantitative information from biological images using a variety of tailor-made, open source and commercial tools. The analysis workflow is devised and automated for the specific research application, by combining the most relevant tools using both classical and AI based algorithms. 2D-5D data from a variety of imaging modalities can be processed, including: digital pathology, live imaging ,confocal and spinning disk imaging, lightsheet microscopy, electron microscopy and also some MRI imaging. | EURO-BIOIMAGING ERIC (EURO-BIOIMAGING) | Israel BioImaging | Biomed. imaging analysis | https://www.eurobioimaging.eu/nodes/israel-bioimaging |
| 9.7_ELIXIR | IO | Consultation of Elixir services - core data services | Consultation to aid with selection , integration & use of Elixir core data services | ELIXIR/EMBL/EBI | ELIXIR | Selection , integration & use of | https://elixir-europe.org |
| 9.8_Elixir Hub | IO | Consultation of Elixir services - deposition databases | Consultation to aid with selection , integration & use of Elixir deposition databases | ELIXIR/EMBL/EBI | ELIXIR | Selection, integration & use of | https://elixir-europe.org |
| 9.9_ELIXIR Hub | IO | Consultation of Elixir services - FAIRification of software | Consultation of Elixir services - FAIRification of software | ELIXIR/EMBL/EBI | ELIXIR | FAIRification of software | https://elixir-europe.org |
| 9.17_BPE | NL | Machine Learning for prognostics, predictive | Provision of ML expertise focused on predictive diagnosis | IBISBA (WAGENINGEN UNIVERSITY) | Wageningen University | Digi. Support Service | https://www.ibisba.eu |
| 9.33_INRAE | NL | Machine Learnning for multi-omics data integration | Machine Learnig integration of multi-omics data | IBISBA (WAGENINGEN UNIVERSITY) | Wageningen University | ML/AI for multi-omic data | https://www.ibisba.eu |
| 9.34_LIFE | NL | AI-based decision support system for stratification and decision making | AI-based decision support system for stratification and decision making | IBISBA (WAGENINGEN UNIVERSITY) | Wageningen University | AI-based decision support system | https://www.ibisba.eu |
| 9.35_Biotech NL | NL | Support for biomarker identification and validation | ML/AI expert support for identification and validation of biomarkers | IBISBA (WAGENINGEN UNIVERSITY) | Wageningen University | support for biomarker ident. | https://www.ibisba.eu |
| 9.20_Wageningen Uni | NL | Digital Analysis Service plus expert support for clinical cancer research | Provision of expert support for digital analytics in cancer research and clinics | IBISBA (WAGENINGEN UNIVERSITY) | Wageningen University | Digi. analysis service | https://www.ibisba.eu |
| 9.6_UNITO | IT | 3D interactive visualization and analysis of multidimensional cancer genomic data. | User’s genomic data will be processed to be visualised and analysed with GenomeCruzer, a software for interactive 3D visualization and analysis of multidimensional cancer genomic data. User-provided genomic data will be processed and loaded in the GenomeCruzer database. The database will be tested by the service provider and released to the user. The user can then use the database with the GenomeCruzer software, freely available for download from the web (support for installation and use will be provided). | EurOPDX (UNIVERSITA DEGLI STUDI DI TORINO) | University of Torino | 1 genomic dataset processing | https://www.oncology.unito.it/ |
| 13. 2.6_9.18_I2PC | ES | Electron Microscopy Image Analysis, I2PC, Madrid, Spain - canSERV | This platform will provide personalised support to projects requiring specialised processing of either electron or X-ray microscopy images. It will also help developers in integrating their methods into generally accessible analysis workflows. The Instruct Image Processing Centre (I2PC) in Madrid will assign personnel to this analysis, as well as the required computational resources. | INSTRUCT-ERIC | Instruct Centre ES - Instruct Image Processing Centre | 1day | |
| 14. 2.45_9.19_Instruct_NKI | NL | PDB-REDO, Amsterdam, Netherlands - canSERV | PDB-REDO is a procedure to optimise crystallographic structure models, providing algorithms that make a fully automated decision making system for refinement, rebuilding and validation. With PDB-REDO you can obtain updated and optimised versions of existing entries of the PDB from our DataBank, or you can optimise your own structure model using our Server. Due to robust automation, the procedure can be run at scales from individual structures to high-throughput optimization of thousands of structures. If you want to know more, please check https://pdb-redo.eu | INSTRUCT-ERIC | Instruct Centre NL - Netherlands Cancer Institute | 1 day | |
| 9.4_ATMA | IT | Biomedical imaging analysis (digital) | Collection, curation and analysis of diagnostic images (MR, CT, PT) of cancer patients | BIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC) | ATMA | Biomed. imaging analysis | https://sdn.synlab.it/ |
More information about individual services, please contact us.