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 IDCountryService Name Description of ServiceResearch InfrastructureService ProviderUnit of accessWebsite
9.1_IFO-IREITTranscriptomics,bulk and/or single-cell transcriptomics analysis and/or Immune Repertoire and/or deconvolutionTranscriptomics,bulk and/or single-cell transcriptomics analysis and/or Immune Repertoire and/or deconvolutionBIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC) IFO-IREbulk and sing. cell transcriptomics analysishttps://www.ifo.it/
9.1_Lubeck Inst. DermDETranscriptomics,bulk and/or single-cell transcriptomics analysis and/or Immune Repertoire and/or deconvolutionThe entire workflow for analysis of scRNAseq and immunoreceptor repertoire data is provided. BIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC) LIEDBulk &/or sing. cell transcript.analysishttps://www.uksh.de/
9.1_CRGESAnalysis of bulk/ single cell RNA sequencing data from tumor and normal samplesAnalysis of bulk RNA sequencing/ single-cell RNA sequencing/ Immune Repertoire profiling data from tumor and normal samplesBIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC) Centro Nacional de Análisis GenómicoBulk &/or sing.cell transcript.analysishttps://www.cnag.crg.eu/
9.2_UNIMIBITWhole exome sequencing / whole genome sequencing analysis / cancer evolution analysisWhole exome sequencing / whole genome sequencing analysis / cancer evolution analysisBIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC) UNIMIBWhole Exome Seq./ whole genome seq.https://www.unimib.it/
9.2_CRGESAnalysis of whole exome sequencing / whole genome sequencing data from tumor and normal samplesAnalysis of whole exome sequencing and/or whole genome sequencing data from tumor and normal samplesBIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC) Centro Nacional de Análisis GenómicoWhole exome seqen./whole genome sequen.https://www.cnag.crg.eu/
9.1_BiogemITTranscriptomics/ whole exome sequencingTranscriptomicBIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC) Biogem S.c.a.r.lRNA-SEQhttps://www.biogem.it/index.php/it/
9.4_Uni.of OuluFIBiological 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 ERICUniversity of OuluBiomed. imaging analysishttps://www.oulu.fi/en/university/faculties-and-units/biocenter-oulu
9.4_CCMARPTBioMedical 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-PTBiomed. imaging analysishttps://www.ccmar.ualg.pt/en
9.21_EATRISDEDigital Analysis Service plus expert support for EATRIS clinical cancer research supportDigital Analysis Service plus expert support for EATRIS clinical cancer research supportEATRIS ERIC (EATRIS)EATRISDigital Analysis Servicehttps://eatris.eu/
9.23_WeitzmannILImage data analysisThe 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 BioImagingBiomed. imaging analysishttps://www.eurobioimaging.eu/nodes/israel-bioimaging
9.7_ELIXIRIOConsultation of Elixir services - core data servicesConsultation to aid with selection , integration & use of Elixir core data servicesELIXIR/EMBL/EBI ELIXIRSelection , integration & use ofhttps://elixir-europe.org
9.8_Elixir HubIOConsultation of Elixir services - deposition databasesConsultation to aid with selection , integration & use of Elixir deposition databasesELIXIR/EMBL/EBI ELIXIRSelection, integration & use ofhttps://elixir-europe.org
9.9_ELIXIR HubIOConsultation of Elixir services - FAIRification of softwareConsultation of Elixir services - FAIRification of softwareELIXIR/EMBL/EBI ELIXIRFAIRification of softwarehttps://elixir-europe.org
9.17_BPENLMachine Learning for prognostics, predictiveProvision of ML expertise focused on predictive diagnosis IBISBA (WAGENINGEN UNIVERSITY)Wageningen UniversityDigi. Support Servicehttps://www.ibisba.eu
9.33_INRAENLMachine Learnning for multi-omics data integrationMachine Learnig integration of multi-omics dataIBISBA (WAGENINGEN UNIVERSITY)Wageningen UniversityML/AI for multi-omic datahttps://www.ibisba.eu
9.34_LIFENLAI-based decision support system for stratification and decision makingAI-based decision support system for stratification and decision makingIBISBA (WAGENINGEN UNIVERSITY)Wageningen UniversityAI-based decision support systemhttps://www.ibisba.eu
9.35_Biotech NLNLSupport for biomarker identification and validationML/AI expert support for identification and validation of biomarkersIBISBA (WAGENINGEN UNIVERSITY)Wageningen Universitysupport for biomarker ident.https://www.ibisba.eu
9.20_Wageningen UniNLDigital Analysis Service plus expert support for clinical cancer researchProvision of expert support for digital analytics in cancer research and clinicsIBISBA (WAGENINGEN UNIVERSITY)Wageningen UniversityDigi. analysis servicehttps://www.ibisba.eu
9.6_UNITOIT3D 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 Torino1 genomic dataset processinghttps://www.oncology.unito.it/
13. 2.6_9.18_I2PCESElectron Microscopy Image Analysis, I2PC, Madrid, Spain - canSERVThis 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-ERICInstruct Centre ES - Instruct Image Processing Centre1day
14. 2.45_9.19_Instruct_NKINLPDB-REDO, Amsterdam, Netherlands - canSERVPDB-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-ERICInstruct Centre NL - Netherlands Cancer Institute1 day
9.4_ATMAITBiomedical imaging analysis (digital)Collection, curation and analysis of diagnostic images (MR, CT, PT) of cancer patientsBIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC) ATMABiomed. imaging analysishttps://sdn.synlab.it/

More information about individual services, please contact us.