Resource List
List all resources, or create a new resource.
GET /api/t
{ "count": 31891, "next": "?page=2", "previous": null, "list": [ { "name": "msnpy", "description": "A Python package for processing and annotating multi-stage (MSⁿ) mass spectral data", "homepage": "https://github.com/computational-metabolomics/msnpy", "biotoolsID": "msnpy", "biotoolsCURIE": "biotools:msnpy", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "ralf", "additionDate": "2026-02-05T20:50:33.563257Z", "lastUpdate": "2026-02-05T20:50:33.567057Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "dimspy", "description": "Python package for processing direct-infusion mass spectrometry-based metabolomics and lipidomics data", "homepage": "https://github.com/computational-metabolomics/dimspy", "biotoolsID": "dimspy", "biotoolsCURIE": "biotools:dimspy", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "ralf", "additionDate": "2026-02-05T20:40:40.977533Z", "lastUpdate": "2026-02-05T20:40:40.981305Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Liana+", "description": "LIANA+ is a scalable framework for inference of cell‑cell communication (CCC) from single-cell and spatially resolved omics data. It integrates multiple ligand‑receptor inference methods and expert curated resources into a unified pipeline, supports consensus ranking across methods, and facilitates differential and contextual CCC analyses. LIANA+ accepts AnnData/MuData formats and interfaces with single‑cell ecosystems like scverse for flexible, interoperable workflows.", "homepage": "https://liana-py.readthedocs.io/en/latest/", "biotoolsID": "liana", "biotoolsCURIE": "biotools:liana", "version": [ "1.7.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0313", "term": "Expression profile clustering" }, { "uri": "http://edamontology.org/operation_2939", "term": "Principal component visualisation" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [ { "uri": "http://edamontology.org/format_3590", "term": "HDF5" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3768", "term": "Clustered expression profiles" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_4028", "term": "Single-cell sequencing" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" } ], "operatingSystem": [], "language": [ "Python" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/saezlab/liana-py", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://liana-py.readthedocs.io/en/latest/api.html", "type": [ "API documentation" ], "note": null }, { "url": "https://liana-py.readthedocs.io/en/latest/installation.html", "type": [ "Installation instructions" ], "note": null }, { "url": "https://liana-py.readthedocs.io/en/latest/notebooks/index.html", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1038/s41556-024-01469-w", "pmid": "39223377", "pmcid": "PMC11392821", "type": [], "version": "1.7.1", "note": "The growing availability of single-cell and spatially resolved transcriptomics has led to the development of many approaches to infer cell-cell communication, each capturing only a partial view of the complex landscape of intercellular signalling. Here we present LIANA+, a scalable framework built around a rich knowledge base to decode coordinated inter- and intracellular signalling events from single- and multi-condition datasets in both single-cell and spatially resolved data. By extending and unifying established methodologies, LIANA+ provides a comprehensive set of synergistic components to study cell-cell communication via diverse molecular mediators, including those measured in multi-omics data. LIANA+ is accessible at https://github.com/saezlab/liana-py with extensive vignettes ( https://liana-py.readthedocs.io/ ) and provides an all-in-one solution to intercellular communication inference.", "metadata": null }, { "doi": "10.1038/s41467-022-30755-0", "pmid": "35680885", "pmcid": "PMC9184522", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "attilagabor", "additionDate": "2024-11-11T08:56:21.437836Z", "lastUpdate": "2026-02-05T16:22:37.314374Z", "editPermission": { "type": "group", "authors": [ "khaled4" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "3DBIONOTES", "description": "Web based application designed to integrate protein structure, protein sequence and protein annotations in a unique graphical environment. The current version of the application offers a unified, enriched and interactive view of EMDB volumes, PDB structures and Uniprot sequences where the protein annotations stored in Uniprot, Immune Epitope DB, Phospho Site Plus, BioMuta and dSysMap can be explored interactively at sequence and structural level.", "homepage": "http://3dbionotes.cnb.csic.es/ws", "biotoolsID": "3dbionotes", "biotoolsCURIE": "biotools:3dbionotes", "version": [ "v3" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1146", "term": "EMDB ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1127", "term": "PDB ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] } ], "output": [], "note": "Integration of protein structure, protein sequence and protein annotations in a unique graphical environment.", "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "SQL" ], "license": "Apache-2.0", "collectionID": [ "ELIXIR-ES", "CNB-CSIC", "COVID-19", "INB", "IMPaCT-ISCIII" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Interoperability" ], "elixirNode": [ "Spain" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "http://3dbionotes.cnb.csic.es/ws/help", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.jsb.2016.02.007", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/btx483", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/btz118", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/btab397", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "INB", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ELIXIR-ES", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "cnb.csic.es", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Carlos Oscar Sorzano", "email": "coss@cnb.csic.es", "url": "http://3dbionotes.cnb.csic.es", "orcidid": "https://orcid.org/0000-0002-9473-283X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "EOSC-Life", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": "EOSC Life [INFRAEOSC-04-2018, Proposal: 824087]" }, { "name": "CORBEL", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": "CORBEL [INFRADEV-01-2014-1, Proposal 654248]" }, { "name": "CSIC", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": "CSIC [PIE/COVID-19 number 202020E079]" }, { "name": "Comunidad de Madrid", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": "Comunidad de Madrid through grant CAM [S2017/BMD-3817]" }, { "name": "Spanish Ministry of Science and Innovation", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": "Spanish Ministry of Science and Innovation through projects [SEV 2017-0712, FPU-2015/264, PID2019-104757RB-I00/AEI/10.13039/501100011033]" }, { "name": "Instituto de Salud Carlos III", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": "Instituto de Salud Carlos III: PT17/0009/0010 [ISCIII-SGEFI/ERDF]" } ], "owner": "coss", "additionDate": "2016-07-11T10:42:10Z", "lastUpdate": "2026-02-05T14:26:24.786970Z", "editPermission": { "type": "group", "authors": [ "coss" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "crabz", "description": "Like pigz, but rust", "homepage": "https://github.com/sstadick/crabz", "biotoolsID": "crabz", "biotoolsCURIE": "biotools:crabz", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "camlloyd", "additionDate": "2026-02-05T13:03:47.451732Z", "lastUpdate": "2026-02-05T13:03:47.454691Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BRENDA", "description": "Internationally leading information system on all aspects of enzymes, including function, structure, involvement in diseases, application, engineering, and molecular properties. The database includes hundreds of milllions of enzyme data and is compiled from manual literature annotation, data integration from other databases and predicted enzyme functions and locations.", "homepage": "http://www.brenda-enzymes.org", "biotoolsID": "brenda", "biotoolsCURIE": "biotools:brenda", "version": [], "otherID": [], "relation": [ { "biotoolsID": "bto", "type": "includes" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3208", "term": "Genome visualisation" }, { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" }, { "uri": "http://edamontology.org/operation_0338", "term": "Sequence database search" }, { "uri": "http://edamontology.org/operation_0306", "term": "Text mining" }, { "uri": "http://edamontology.org/operation_2241", "term": "Transmembrane protein visualisation" }, { "uri": "http://edamontology.org/operation_0360", "term": "Structural similarity search" }, { "uri": "http://edamontology.org/operation_0269", "term": "Transmembrane protein prediction" }, { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3083", "term": "Pathway or network visualisation" }, { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_3194", "term": "Genome feature comparison" }, { "uri": "http://edamontology.org/operation_0305", "term": "Literature search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2909", "term": "Organism name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0990", "term": "Compound name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2299", "term": "Gene name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1127", "term": "PDB ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2291", "term": "UniProt ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2108", "term": "Reaction ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2342", "term": "Pathway or network name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2365", "term": "Pathway or network accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1187", "term": "PubMed ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1046", "term": "Strain name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1179", "term": "NCBI taxonomy ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1051", "term": "Ontology name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1012", "term": "Enzyme name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1011", "term": "EC number" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2024", "term": "Enzyme kinetics data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2291", "term": "UniProt ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1127", "term": "PDB ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2108", "term": "Reaction ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2342", "term": "Pathway or network name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2365", "term": "Pathway or network accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1046", "term": "Strain name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2909", "term": "Organism name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1179", "term": "NCBI taxonomy ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1039", "term": "SCOP domain identifier" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2700", "term": "CATH identifier" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1012", "term": "Enzyme name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1011", "term": "EC number" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2024", "term": "Enzyme kinetics data" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" }, { "uri": "http://edamontology.org/topic_0821", "term": "Enzymes" }, { "uri": "http://edamontology.org/topic_3070", "term": "Biology" }, { "uri": "http://edamontology.org/topic_3297", "term": "Biotechnology" }, { "uri": "http://edamontology.org/topic_3473", "term": "Data mining" }, { "uri": "http://edamontology.org/topic_3344", "term": "Biomedical science" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "de.NBI", "DSMZ Digital Diversity" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [ "Data", "Tools", "Interoperability" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://www.dsmz.de/", "type": [ "Other" ], "note": null }, { "url": "https://hub.dsmz.de/#/", "type": [ "Service" ], "note": null }, { "url": "https://www.brenda-enzymes.org/", "type": [ "Service" ], "note": null }, { "url": "https://brenda-enzymes.org/support.php", "type": [ "Helpdesk" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.brenda-enzymes.org/copy.php", "type": [ "Terms of use" ], "note": null }, { "url": "http://www.brenda-enzymes.org/introduction.php", "type": [ "Citation instructions" ], "note": null }, { "url": "https://www.brenda-enzymes.org/tutorial.php", "type": [ "Training material" ], "note": null }, { "url": "https://www.brenda-enzymes.org/help.php", "type": [ "Training material" ], "note": null }, { "url": "https://www.brenda-enzymes.org/faq.php", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkaf1113", "pmid": "41206471", "pmcid": "PMC12807770", "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkaa1025", "pmid": "33211880", "pmcid": "PMC7779020", "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gky1048", "pmid": "30395242", "pmcid": "PMC6323942", "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1016/j.jbiotec.2017.04.020", "pmid": "28438579", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gku1068", "pmid": "25378310", "pmcid": "PMC4383907", "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkn820", "pmid": "18984617", "pmcid": "PMC2686525", "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkq1089", "pmid": "21062828", "pmcid": "PMC3013686", "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1186/1471-2105-12-329", "pmid": "21827651", "pmcid": "PMC3166944", "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkh081", "pmid": "14681450", "pmcid": "PMC308815", "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gks1049", "pmid": "23203881", "pmcid": "PMC3531171", "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1016/s0968-0004(01)02027-8", "pmid": "11796225", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkl972", "pmid": "17202167", "pmcid": "PMC1899097", "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/30.1.47", "pmid": "11752250", "pmcid": "PMC99121", "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkq968", "pmid": "21030441", "pmcid": "PMC3013802", "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "BMBF", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": null, "email": "contact@brenda-enzymes.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures", "email": null, "url": "https://www.dsmz.de/", "orcidid": null, "gridid": "grid.420081.f", "rorid": "02tyer376", "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "matkrull", "additionDate": "2016-02-03T14:20:28Z", "lastUpdate": "2026-02-05T07:01:46.010390Z", "editPermission": { "type": "group", "authors": [ "AJaede", "juh22", "lje" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Denoising-Inhomogeneity Correction Tool (EUCAIM-SW-015_T-01-01-015)", "description": "The tool is designed to perform a customisable image pre-processing to reduce noise and inhomogeneity field effect, thus improving image quality and reproducibility of radiomics features. This tool consists of two independent steps: one for denoising using one of the 5 integrated filters (Bilateral Filter, Anisotropic Diffusion Filter (ADF), Curvature Flow Filter (CFF), SUSAN and Non Local Means (NLM)), and another for the ANTs N4 and another for the ANT's N4 bias correction filter. The parameter configuration of this tool has been optimised for TW1, T2W, DWI and DCE sequences in neuroblastoma (NB) and paediatric brain tumours, but it can also be configured with some of their parameters using a JSON parameter configuration file.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/artifacts-tab", "biotoolsID": "denoising-inhomogeneity_correction_tool", "biotoolsCURIE": "biotools:denoising-inhomogeneity_correction_tool", "version": [ "1.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run -it --rm --name container_name -v \"<input_path>:/input\" -v \"<output_path>:/output\" -v \"<config_path>:/config\" harbor.eucaim.cancerimage.eu/processing-tools/denoising_inhomogeneity_correction_tool:1.1.0 --config /config/config.json" }, { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processin-tools/denoising_inhomogeneity_correction_tool:1.1.0 --paths /input/Dataset/Patient_1/Study/T1W /input/Dataset/Patient_2/Study/T2W --output /output --series_number 2000 --series_description_suffix \"_harmonized\" --denoising adf --conductance 0.5 --iterations 3 --time_step 0.0625 --n4 --bspline_size 50 --n4_iterations 50 30 --shrink_factor 2" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0219", "term": "Data curation and archival" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/artifacts-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://drive.eucaim.cancerimage.eu/s/wYJ7Fttnk6Dp7gc", "type": [ "User manual" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/oseiKoeFZqwoRCA", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=HkHqFGXGEbo&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=9", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1007/s10278-021-00512-8", "pmid": "34505958", "pmcid": "PMC8554919", "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1186/s41747-020-00150-9", "pmid": "32246291", "pmcid": "PMC7125275", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Matias Fernandez-Paton", "email": "matias_fernandez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0001-9374-1411", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Documentor", "Support" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor", "Support" ], "note": null }, { "name": "Leonor Cerda-Alberich", "email": "leonor_cerda@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5567-4278", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T08:55:46.088021Z", "lastUpdate": "2026-02-04T15:33:01.249605Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CORToViz", "description": "CORToViz (CORD-19 Topic Visualizer) is a computational method and interactive visualization tool designed to explore and analyze the evolution of research topics within large text corpora. In the referenced work, it was applied to the COVID-19 Open Research Dataset (CORD-19), which contains over a million scientific abstracts related to the COVID-19 pandemic. CORToViz combines modern machine learning and natural language processing techniques to cluster documents, extract temporal topic trends, and present results through an interactive dashboard. The dashboard supports visualization of topic contents (e.g., with word clouds), time-series plots of topic trends over time, and statistical testing to assess significant changes in topic prominence within user-selected time windows. While demonstrated on CORD-19, the pipeline and visualization components are general and can be adapted to other textual datasets with temporal structure.", "homepage": "http://gmql.eu/cortoviz", "biotoolsID": "cortoviz", "biotoolsCURIE": "biotools:cortoviz", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://hub.docker.com/r/frinve/cortoviz/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://hub.docker.com/r/frinve/cortoviz/", "type": "Software package", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1016/j.eswa.2024.124028", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "abernasconi", "additionDate": "2026-02-04T11:00:35.227720Z", "lastUpdate": "2026-02-04T11:00:41.026549Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RecombinHunt", "description": "RecombinHunt is a data-driven computational tool developed for detecting and characterizing recombinant viral genomes — sequences formed by combining genetic material from two (or more) different viral lineages. It uses statistical analyses of mutations in viral genome sequences to identify contributing parental lineages and the positions (breakpoints) where recombination occurred, doing so with high specificity and sensitivity and relatively fast performance compared with other methods. Originally applied to SARS-CoV-2 and shown to also work with viruses like monkeypox, it helps improve genomic surveillance of evolving viruses and can support early warning systems for future pandemics.", "homepage": "https://doi.org/10.5281/zenodo.8123832", "biotoolsID": "recombinhunt", "biotoolsCURIE": "biotools:recombinhunt", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/tomalf2/recombinhunt-cov", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/s41467-024-47464-5", "pmid": "38632281", "pmcid": "PMC11024102", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "abernasconi", "additionDate": "2026-02-04T10:55:57.317793Z", "lastUpdate": "2026-02-04T10:56:03.581236Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GRAPH-SEARCH", "description": "GRAPH-SEARCH allows users to explore a network of 130K biomedical entities and 48M relations by formulating or adapting graph queries; it produces a bibliography of COVID-19-related publications, which are globally ranked; and each publication is further associated with the specific parts of the query that it explains, thereby allowing the user to understand each aspect of the matching.", "homepage": "https://gmql.eu/graph-search", "biotoolsID": "graph-search", "biotoolsCURIE": "biotools:graph-search", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/FrInve/graph-search/wiki", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://hub.docker.com/r/frinve/graph-search", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/FrInve/graph-search/wiki/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.2196/52655", "pmid": "38814687", "pmcid": "PMC11176882", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "abernasconi", "additionDate": "2026-02-04T10:08:58.628807Z", "lastUpdate": "2026-02-04T10:09:02.499031Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FluWarning", "description": "FluWarning is a computational early-warning system to detect early genetic signals in influenza A viruses that may indicate a risk of cross-species transmission (“spillover”) and potential epidemic or pandemic events.", "homepage": "https://doi.org/10.5281/zenodo.15498406", "biotoolsID": "fluwarning", "biotoolsCURIE": "biotools:fluwarning", "version": [ "2" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0605", "term": "Informatics" }, { "uri": "http://edamontology.org/topic_4019", "term": "Biosciences" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://doi.org/10.5281/zenodo.15498406", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/DEIB-GECO/flu-warning-system", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/DEIB-GECO/flu-warning-system/blob/main/README.md", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1126/sciadv.adz7312", "pmid": "41134898", "pmcid": "PMC12551695", "type": [], "version": "2", "note": null, "metadata": null } ], "credit": [], "owner": "abernasconi", "additionDate": "2026-02-04T10:02:52.405439Z", "lastUpdate": "2026-02-04T10:03:01.978429Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SCIPI", "description": "Hepatocyte Ploidy Identification Pipeline on the Stereo-cell Platform for Accurate Liver Polyploidy Classification via Fluorescence Staining and Deep Learning Tools", "homepage": "https://github.com/JeffLuo9/Hep_Ploidy_protocol", "biotoolsID": "scipi", "biotoolsCURIE": "biotools:scipi", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "jiahui", "additionDate": "2026-02-04T03:24:52.473123Z", "lastUpdate": "2026-02-04T03:26:06.350767Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GuaCAMOLE", "description": "Detects and corrects GC bias in metagenomic libraries", "homepage": "https://github.com/CIbiv/guaCAMOLE", "biotoolsID": "guacamole", "biotoolsCURIE": "biotools:guacamole", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "florian", "additionDate": "2026-02-04T02:24:49.967847Z", "lastUpdate": "2026-02-04T02:24:49.969863Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SMIntegration", "description": "SMIntegration is an innovative open-source platform for integrated analysis of spatial transcriptomics and metabolomics data. It integrates spatial pattern recognition, differential comparison, network construction, and functional annotation into a unified workflow. Designed to address key challenges in spatial multi-omics correlation analysis, SMIntegration enables researchers to explore gene-metabolite co-regulation mechanisms through an intuitive web interface, revealing spatial heterogeneity in tissue development and disease progression.", "homepage": "https://metax.genomics.cn/app/smintegration", "biotoolsID": "smintegration", "biotoolsCURIE": "biotools:smintegration", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "haoke", "additionDate": "2026-02-04T01:48:29.964334Z", "lastUpdate": "2026-02-04T01:48:29.966207Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "hopsworks-chef", "description": "Chef Cookbook for Hopsworks, providing automation scripts for deployment and configuration.", "homepage": "https://github.com/HEAP-EXPOSOME/hopsworks-chef", "biotoolsID": "hopsworks_chef", "biotoolsCURIE": "biotools:hopsworks_chef", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "HEAP" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "HEAP", "email": "roxana.martinez@ki.se", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T01:21:28.611408Z", "lastUpdate": "2026-02-04T01:21:28.613392Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "metagenomics-ML", "description": "ML-based sequence classification pipeline for metagenomics data.", "homepage": "https://github.com/HEAP-EXPOSOME/metagenomics-ML", "biotoolsID": "metagenomics_ml", "biotoolsCURIE": "biotools:metagenomics_ml", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "HEAP" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "HEAP", "email": "roxana.martinez@ki.se", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T01:21:16.133156Z", "lastUpdate": "2026-02-04T01:21:16.135430Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HEAP exposome demo", "description": "Chemical exposome pipeline with a sample dataset. The Docker container includes all dependencies, which can be run in RStudio or installed via Docker. R scripts process the dataset, producing output data and an HTML report.", "homepage": "https://github.com/HEAP-EXPOSOME/exposome-demo", "biotoolsID": "heap_exposome_demo", "biotoolsCURIE": "biotools:heap_exposome_demo", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "HEAP" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "HEAP", "email": "roxana.martinez@ki.se", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T01:21:04.370412Z", "lastUpdate": "2026-02-04T01:21:04.372560Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HEAP streaming demo", "description": "Streaming tutorial notebooks for PPG data. Demonstrates producing and consuming streaming data from an external Kafka topic into Hopsworks using dummy PPG data. Requires a Kafka cluster and a pre-created topic.", "homepage": "https://github.com/HEAP-EXPOSOME/streaming-demo", "biotoolsID": "heap_streaming_demo", "biotoolsCURIE": "biotools:heap_streaming_demo", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "HEAP" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "HEAP", "email": "roxana.martinez@ki.se", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T01:20:40.952325Z", "lastUpdate": "2026-02-04T01:20:40.954643Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FAIR data self-assessment service", "description": "The Self Assessment Service (SAS) is an online questionnaire guiding researchers on how Findable, Accessible, Interoperable and Reusable (FAIR) their data is.", "homepage": "https://heap.bibbox.org/surveys/?s=XC8YLX8W8R", "biotoolsID": "fair_data_self_assessment_service", "biotoolsCURIE": "biotools:fair_data_self_assessment_service", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "HEAP" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "HEAP", "email": "roxana.martinez@ki.se", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T01:20:25.653675Z", "lastUpdate": "2026-02-04T01:20:25.655691Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BIBBOX", "description": "The BIBBOX allows researchers to publish their data and associated data management software (Apps) in a FAIR manner, by incorporating a FAIR Data Point into the Apps. The architecture is modular and flexible, enabling integration with existing open-source software and publication in the App Store.", "homepage": "https://github.com/bibbox", "biotoolsID": "bibbox", "biotoolsCURIE": "biotools:bibbox", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "HEAP" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "HEAP", "email": "roxana.martinez@ki.se", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T01:20:11.704347Z", "lastUpdate": "2026-02-04T01:20:11.709239Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Spatial Agent-based Modeling of Urban Health Interventions", "description": "Repository containing methods and models for urban health interventions, including spatial synthetic population generation (GenSynthPop), routing setup with OSRM, environmental spatial layer preparation, NLP knowledge extraction, and GAMA agent-based simulation models.", "homepage": "https://github.com/TabeaSonnenschein/Spatial-Agent-based-Modeling-of-Urban-Health-Interventions", "biotoolsID": "spatial_agent_based_modeling_urban_health_interventions", "biotoolsCURIE": "biotools:spatial_agent_based_modeling_urban_health_interventions", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "EXPANSE", "IHEN" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Tabea Sonnenschein", "email": "t.s.sonnenschein@uu.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "EXPANSE", "email": "expanse@uu.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:57:35.249500Z", "lastUpdate": "2026-02-04T00:57:35.255232Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GenSynthPop", "description": "Sample-free tool to construct synthetic populations from mixed-aggregation contingency tables. Prepares stratified census datasets, generates conditional propensities, combines with spatial marginals, and validates generated populations for simulations such as agent-based models.", "homepage": "https://github.com/TabeaSonnenschein/GenSynthPop", "biotoolsID": "gensynthpop", "biotoolsCURIE": "biotools:gensynthpop", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "EXPANSE", "IHEN" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Tabea Sonnenschein", "email": "t.s.sonnenschein@uu.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "EXPANSE", "email": "expanse@uu.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:56:31.885816Z", "lastUpdate": "2026-02-04T00:56:31.887941Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CellAutDisp", "description": "Python package for dispersion modeling of traffic-related NO2, including hourly and monthly calculations, model calibration, and a genetic algorithm for calibration. Supports cellular automata dispersion modeling with adjustable parameters.", "homepage": "https://github.com/TabeaSonnenschein/CellAutDisp", "biotoolsID": "cellautdisp", "biotoolsCURIE": "biotools:cellautdisp", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "EXPANSE" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Tabea Sonnenschein", "email": "t.s.sonnenschein@uu.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "EXPANSE", "email": "expanse@uu.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:56:20.148531Z", "lastUpdate": "2026-02-04T00:56:20.150784Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "UrbHealth-ABM: Urban Health Scenario Agent-based Model", "description": "An Agent-Based Model (ABM) simulating individual-level activity schedules, mobility choices, traffic, air pollution, and exposure to air pollution and transport-related physical activity under different urban scenarios.", "homepage": "https://github.com/TabeaSonnenschein/UrbHealth-ABM", "biotoolsID": "urbhealth_abm", "biotoolsCURIE": "biotools:urbhealth_abm", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "EXPANSE" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Tabea Sonnenschein", "email": "t.s.sonnenschein@uu.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "EXPANSE", "email": "expanse@uu.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:56:03.219737Z", "lastUpdate": "2026-02-04T00:56:03.223237Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Expanseeker", "description": "Expanseeker is the official app of the Urban Labs study within the EXPANSE project. It engages users in Challenges and Activities to help researchers collect exposome data and understand the relationship between the exposome and health.", "homepage": "https://play.google.com/store/apps/details?id=com.GamesForHealth.Expanse", "biotoolsID": "expanseeker", "biotoolsCURIE": "biotools:expanseeker", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "EXPANSE" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "EXPANSE", "email": "expanse@uu.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:55:34.163174Z", "lastUpdate": "2026-02-04T00:55:34.165389Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Exposome Maps", "description": "Exposome Maps is a data catalogue of geospatially resolved datasets on environmental exposure estimates. It contains more than 20,000 datasets on several Exposome dimensions including Physico-Chemical Environment, Built Environment, Food Environment, and Social Environment. It provides harmonized data collections across Europe for following environmental factors: PM10, PM2.5, NO2, O3, Temperature, Ultra Violet Radiation, Road Traffic Noise, Urbanicity, NDVI (Normalized Difference Vegetation Index ), MSAVI (Modified Soil Adjusted Vegetation Index), Green spaces, Blue spaces, Imperviousness, Light at night, Walkability Index.", "homepage": "https://exposome.uu.nl/", "biotoolsID": "exposome_maps", "biotoolsCURIE": "biotools:exposome_maps", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" }, { "uri": "http://edamontology.org/topic_3855", "term": "Environmental sciences" } ], "operatingSystem": [], "language": [], "license": "Other", "collectionID": [ "EXPANSE", "EHEN" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://expanseproject.eu/", "type": [ "Other" ], "note": "Project information page" } ], "download": [], "documentation": [ { "url": "https://surfdrive.surf.nl/files/index.php/s/uqUORDrd428H2F9", "type": [ "User manual" ], "note": "Description of Environmental variables available through Exposome Maps" }, { "url": "https://surfdrive.surf.nl/files/index.php/s/fI0Gmuu5O1MJAI9", "type": [ "Terms of use" ], "note": "Exposome-NL data platform Data Access and Publication Policy" } ], "publication": [ { "doi": "10.1126/science.aay3164", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1097/EE9.0000000000000162", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Roel Vermeulen", "email": "R.C.H.Vermeulen@uu.nl", "url": null, "orcidid": "https://orcid.org/0000-0003-4082-8163", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "Zimbo Boudewijns", "email": "z.s.r.m.boudewijns@uu.nl", "url": null, "orcidid": "https://orcid.org/0000-0002-9383-9571", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Maintainer" ], "note": null }, { "name": "Lloyd Roga", "email": "l.q.roga@uu.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null } ], "owner": "Channel2291", "additionDate": "2025-03-17T14:01:59.601345Z", "lastUpdate": "2026-02-04T00:46:44.590787Z", "editPermission": { "type": "group", "authors": [ "hkucukali" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "sharp: Stability-enHanced Approaches using Resampling Procedures", "description": "An R package providing a unified framework for stability-enhanced variable selection, graphical modelling, and clustering using resampling-based approaches. In stability selection and consensus clustering, resampling techniques are used to enhance the reliability of the results. In this package, hyper-parameters are calibrated by maximising model stability, which is measured under the null hypothesis that all selection (or co-membership) probabilities are identical. Functions are readily implemented for the use of LASSO regression, sparse PCA, sparse (group) PLS or graphical LASSO in stability selection, and hierarchical clustering, partitioning around medoids, K means or Gaussian mixture models in consensus clustering.", "homepage": "https://cran.r-project.org/web/packages/sharp/index.html", "biotoolsID": "sharp-r", "biotoolsCURIE": "biotools:sharp-r", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "LongITools", "Unverified", "EXPANSE", "IHEN" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Barbara Bodinier", "email": "barbara.bodinier@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "LongITools", "email": "teija.juola@oulu.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-03T23:14:10.223819Z", "lastUpdate": "2026-02-04T00:45:04.049849Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Calculation of the working life expectancy and working years lost", "description": "Calculates working life expectancy (WLE) and working years lost (WYL), including healthy working life expectancy (HWLE), based on cumulative labor market attachment and health status.", "homepage": "https://www.we-expose.eu/tool-on-calculating-the-working-life-expectancy-and-working-years-lost", "biotoolsID": "working_life_expectancy_and_working_years_lost", "biotoolsCURIE": "biotools:working_life_expectancy_and_working_years_lost", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "EPHOR" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "EPHOR", "email": "eelco.kuijpers@tno.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:35:46.144285Z", "lastUpdate": "2026-02-04T00:35:46.146687Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ephorhia", "description": "A Stata program for flexible simulation studies on occupational exposures, allowing users to define custom parameters and replicate intervention scenarios from EPHOR analyses.", "homepage": "https://www.we-expose.eu/open-access-stata-statistical-package-program-ephorhia2019", "biotoolsID": "ephorhia", "biotoolsCURIE": "biotools:ephorhia", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "EPHOR", "IHEN" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "EPHOR", "email": "eelco.kuijpers@tno.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:34:37.175666Z", "lastUpdate": "2026-02-04T00:34:37.178401Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Disease multiple exposure hierarchical and penalization models", "description": "Hierarchical and penalization models developed for agnostic exploration of exposure-disease associations, applied to lung cancer risk in pooled case-control populations. Includes sample code on GitHub.", "homepage": "https://github.com/cb-ge/ephor_wp4_agnostic_models", "biotoolsID": "disease_multiple_exposure_hierarchical_penalization_models", "biotoolsCURIE": "biotools:disease_multiple_exposure_hierarchical_penalization_models", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "EPHOR" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "EPHOR", "email": "eelco.kuijpers@tno.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:33:51.163186Z", "lastUpdate": "2026-02-04T00:33:51.165530Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Multiple exposures-response (MER)", "description": "A suite of statistical approaches for multiple exposure-response modelling in the working-life exposome context, guiding analyses of combined occupational and non-occupational risk factors.", "homepage": "https://github.com/Wenxin-Wan/ephor_wp4_method_tutorial", "biotoolsID": "multiple_exposures_response", "biotoolsCURIE": "biotools:multiple_exposures_response", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "EPHOR" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Wenxin Wan", "email": "w.wan@uu.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "EPHOR", "email": "eelco.kuijpers@tno.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:31:27.401743Z", "lastUpdate": "2026-02-04T00:31:27.404506Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EuroJEM", "description": "EuroJEM is a comprehensive job-exposure matrix instrument providing harmonized occupational exposure data across Europe for systematic evaluation where individual-level data is unavailable.", "homepage": "https://ki.se/en/imm/eurojem", "biotoolsID": "eurojem", "biotoolsCURIE": "biotools:eurojem", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "EPHOR" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "EuroJEM", "email": "eurojem@ki.se", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null }, { "name": "EPHOR", "email": "eelco.kuijpers@tno.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:29:49.187393Z", "lastUpdate": "2026-02-04T00:29:49.189225Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Inventory of Occupational Exposure Tools", "description": "Provides a meta-data inventory of existing occupational exposure information and tools, including job-exposure matrices, exposure databases, and occupational coding systems, to facilitate harmonization and research replication.", "homepage": "https://occupationalexposuretools.net/", "biotoolsID": "inventory_of_occupational_exposure_tools", "biotoolsCURIE": "biotools:inventory_of_occupational_exposure_tools", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "EPHOR" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Susan Peters", "email": "s.peters@uu.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Michelle C Turner", "email": "michelle.turner@isglobal.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Svetlana Solovieva", "email": "svetlana.solovieva@ttl.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "EPHOR", "email": "eelco.kuijpers@tno.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:29:17.402450Z", "lastUpdate": "2026-02-04T00:29:17.404465Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Automatic job code crosswalking tool: ISCO-08 to ISCO-88", "description": "This tool converts job codes from ISCO-08 to ISCO-88, allowing users to upload a CSV file and receive a translated output with corrected occupational codes.", "homepage": "https://diamonds.tno.nl/shiny/ephor/diamonds/", "biotoolsID": "isco08_to_isco88", "biotoolsCURIE": "biotools:isco08_to_isco88", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "EPHOR" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "EPHOR", "email": "eelco.kuijpers@tno.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:28:41.678903Z", "lastUpdate": "2026-02-04T00:28:41.680635Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Occupational Cohorts", "description": "OccupationalCohorts.net provides an inventory of active cohorts in Europe and globally, supporting research on occupation, work-related exposures, employment, and health relationships.", "homepage": "https://occupationalcohorts.net/", "biotoolsID": "occupational-cohorts", "biotoolsCURIE": "biotools:occupational-cohorts", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "EPHOR" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Michelle C Turner", "email": "michelle.turner@isglobal.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Esther Brinquis", "email": "esther.brinquis@isglobal.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "EPHOR", "email": "eelco.kuijpers@tno.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:28:04.541550Z", "lastUpdate": "2026-02-04T00:28:04.543389Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Substance Information System (SIS)", "description": "SIS allows users to search and find information on hazardous substances. The tool integrates diverse data sources using AI to provide information on substance properties, safety, health effects, exposure, and application by business sectors.", "homepage": "https://diamonds.tno.nl/projects/sis", "biotoolsID": "substance_information_system", "biotoolsCURIE": "biotools:substance_information_system", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "EPHOR" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "EPHOR", "email": "eelco.kuijpers@tno.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:27:19.876941Z", "lastUpdate": "2026-02-04T00:27:19.878820Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "European Occupational Exposure Viewer (OEV)", "description": "OEV is a tree-map style interactive tool that allows the exploration of work exposures by European country, year, and sex, based on exposures included in the EuroJEM series of job-exposure matrices.", "homepage": "https://diamonds.tno.nl/shiny/ephor-eurojem/diamonds/", "biotoolsID": "occupational_exposure_viewer", "biotoolsCURIE": "biotools:occupational_exposure_viewer", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "EPHOR", "IHEN" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "EPHOR", "email": "eelco.kuijpers@tno.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-04T00:26:55.580831Z", "lastUpdate": "2026-02-04T00:26:55.583155Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "dsSyntheticClient", "description": "A DataSHIELD client-side R package for generating synthetic data to support privacy-preserving federated analysis.", "homepage": "https://github.com/tombisho/dsSyntheticClient", "biotoolsID": "dssyntheticclient", "biotoolsCURIE": "biotools:dssyntheticclient", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "LongITools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Tom R. P. Bishop", "email": "trpb2@cantab.net", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "LongITools", "email": "teija.juola@oulu.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-03T23:35:43.761259Z", "lastUpdate": "2026-02-03T23:35:43.764352Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "dsExposome", "description": "A DataSHIELD server-side R package providing exposome analysis functions for privacy-preserving federated analysis of sensitive data.", "homepage": "https://github.com/isglobal-brge/dsExposome", "biotoolsID": "dsexposome", "biotoolsCURIE": "biotools:dsexposome", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "LongITools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Juan R. Gonzalez", "email": "juanr.gonzalez@isglobal.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "LongITools", "email": "teija.juola@oulu.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-03T23:35:21.313155Z", "lastUpdate": "2026-02-03T23:35:21.315021Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "TriplotGUI", "description": "A molecular epidemiology toolbox for exploring and interpreting complex associations between exposures, omics profiles, and health outcomes through interactive visualization.", "homepage": "https://github.com/MetaboComp/TriplotGUI", "biotoolsID": "triplotgui", "biotoolsCURIE": "biotools:triplotgui", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "LongITools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Carl Brunius", "email": "carl.brunius@chalmers.se", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "LongITools", "email": "teija.juola@oulu.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-03T23:14:37.390224Z", "lastUpdate": "2026-02-03T23:14:37.392097Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "fake: Flexible Data Simulation Using the Multivariate Normal Distribution", "description": "An R package for generating artificial multivariate normal data conditional on predefined relationships between variables, enabling benchmarking of variable selection, graphical modelling, and clustering methods.", "homepage": "https://github.com/barbarabodinier/fake", "biotoolsID": "fake", "biotoolsCURIE": "biotools:fake", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "LongITools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Barbara Bodinier", "email": "barbara.bodinier@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "LongITools", "email": "teija.juola@oulu.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-03T23:10:57.883512Z", "lastUpdate": "2026-02-03T23:10:57.885352Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Bayesian Life-course Structural Equation Models (BLSEM)", "description": "A modelling tool for investigating causal linkages, mediation effects, and pathways between life-course exposures and health outcomes using Bayesian structural equation models.", "homepage": "https://github.com/alexlewin24/BLSEM", "biotoolsID": "blsem", "biotoolsCURIE": "biotools:blsem", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "LongITools", "Unverified", "IHEN" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Marjo-Riitta Järvelin", "email": "m.jarvelin@imperial.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "LongITools", "email": "teija.juola@oulu.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-03T23:09:49.036485Z", "lastUpdate": "2026-02-03T23:09:49.038255Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Earth Metabolome Initiative Ontology", "description": "The EMI (Earth Metabolome Initiative) ontology is a knowledge representation framework designed to describe the metabolic content of all known species. Where applicable, it reuses and repurposes several general-purpose and domain-specific ontologies including SOSA (Sensor, Observation, Sample, and Actuator), SKOS (Simple Knowledge Organization System), RO (Relation Ontology), QUDT (Quantities, Units, Dimensions, and Types), and ENPKG. The EMI ontology contains over 100 new concepts and relations to describe chemical compounds, organism traits and interactions, geolocation, and sample metadata.", "homepage": "https://github.com/earth-metabolome-initiative/earth_metabolome_ontology", "biotoolsID": "earth_metabolome_initiative_ontology", "biotoolsCURIE": "biotools:earth_metabolome_initiative_ontology", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/earth-metabolome-initiative/earth_metabolome_ontology", "type": [ "Repository" ], "note": null }, { "url": "https://w3id.org/emi#", "type": [ "Other" ], "note": "Link to ontology documentation" } ], "download": [], "documentation": [ { "url": "https://w3id.org/emi#", "type": [ "Other" ], "note": null } ], "publication": [ { "doi": "10.1101/2025.08.20.671289", "pmid": null, "pmcid": null, "type": [ "Preprint" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Tarcisio Mendes de Farias", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-3175-5372", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Pierre-Marie Allard", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3389-2191", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Disha Tandon", "email": null, "url": null, "orcidid": "https://orcid.org/0009-0005-5515-1230", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Emmanuel Defossez", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-3279-9190", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "disha6", "additionDate": "2026-02-03T22:34:15.942389Z", "lastUpdate": "2026-02-03T22:34:27.003707Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Geocoder", "description": "A Python-based geocoding tool that converts human-readable addresses into geographic coordinates using the geopy package and outputs the results as a CSV file.", "homepage": "https://www.hedimed.eu/toolbox/geocoder/", "biotoolsID": "hedimed_geocoder", "biotoolsCURIE": "biotools:hedimed_geocoder", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "HEDIMED", "Unverified", "IHEN" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Lauri Häme", "email": "lauri.hame@terramonitor.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "HEDIMED", "email": "hedimed.administration@tuni.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-03T22:01:45.022969Z", "lastUpdate": "2026-02-03T22:01:45.026703Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HEDIMED Research Platform", "description": "A scalable, container-based research analytics platform enabling secure, centralized analysis of cohort data through PostgreSQL, Teiid data virtualization, JupyterLab, and RStudio.", "homepage": "https://www.hedimed.eu/toolbox/hedimed-research-platform/", "biotoolsID": "hedimed_research-platform", "biotoolsCURIE": "biotools:hedimed_research-platform", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "HEDIMED" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Juha Pajula", "email": "juha.pajula@vtt.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "HEDIMED", "email": "hedimed.administration@tuni.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-03T21:57:33.359515Z", "lastUpdate": "2026-02-03T21:57:33.363592Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HEDIMED Public Platform", "description": "A GDPR-compliant public analytics platform providing secure access to cohort-integrated exposome-health visualizations, interactive dashboards, and educational materials.", "homepage": "https://www.hedimed.eu/toolbox/hedimed-public-platform/", "biotoolsID": "hedimed_public-platform", "biotoolsCURIE": "biotools:hedimed_public-platform", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "HEDIMED" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Apostolia Karabatea", "email": "a.karabatea@gnomon.com.gr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "HEDIMED", "email": "hedimed.administration@tuni.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-03T21:57:08.386890Z", "lastUpdate": "2026-02-03T21:57:08.390253Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Simulation model for investigating the cost-effectiveness of preventing and screening celiac disease", "description": "An open-source simulation model to compare the cost-effectiveness of population-based screening and prevention strategies for celiac disease, supporting evidence-based healthcare decision-making.", "homepage": "https://www.hedimed.eu/toolbox/open-source-simulation-model-for-investigating-the-cost-effectiveness-of-preventing-and-screening-celiac-disease/", "biotoolsID": "hedimed_celiac-disease-cost-effectiveness-model", "biotoolsCURIE": "biotools:hedimed_celiac-disease-cost-effectiveness-model", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "HEDIMED" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Jani Mäkinen", "email": "jani.j.makinen@tuni.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "HEDIMED", "email": "hedimed.administration@tuni.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-03T21:56:32.322745Z", "lastUpdate": "2026-02-03T21:56:32.325314Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Population Dynamics Model for Type 1 Diabetes", "description": "A simulation model of the natural history of type 1 diabetes that evaluates the impact of primary and secondary prevention strategies on disease incidence.", "homepage": "https://www.hedimed.eu/toolbox/population-dynamics-model-for-type-1-diabetes/", "biotoolsID": "hedimed_population-dynamics-model-t1d", "biotoolsCURIE": "biotools:hedimed_population-dynamics-model-t1d", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "HEDIMED" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Jyri Rökman", "email": "jyri.rokman@vtt.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "HEDIMED", "email": "hedimed.administration@tuni.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-03T21:55:23.069777Z", "lastUpdate": "2026-02-03T21:55:23.075670Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Data analysis methods for analysing Olink proteomics data", "description": "A set of interlocked R functions providing a standardized syntax to accelerate and harmonize the analysis of Olink proteomics data across multiple cohorts, datasets, and endpoints.", "homepage": "https://github.com/jonathanth/OlinkAnalysisHEDIMED", "biotoolsID": "hedimed_olinkanalysis", "biotoolsCURIE": "biotools:hedimed_olinkanalysis", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "HEDIMED", "Unverified", "IHEN" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Jonathan Thorsen", "email": "jonathan.thorsen@dbac.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "HEDIMED", "email": "hedimed.administration@tuni.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-03T21:53:38.804928Z", "lastUpdate": "2026-02-03T21:53:38.807176Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Geosampler", "description": "Terramonitor Geosampler calculates zonal statistics (e.g. mean, maximum, minimum) from raster files around coordinate points within a given radius and outputs a CSV file with statistics appended to the points.", "homepage": "https://www.hedimed.eu/toolbox/geosampler/", "biotoolsID": "hedimed_geosampler", "biotoolsCURIE": "biotools:hedimed_geosampler", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Unverified", "IHEN", "HEDIMED" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Lauri Häme", "email": "lauri.hame@terramonitor.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "HEDIMED", "email": "hedimed.administration@tuni.fi", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": null } ], "owner": "hkucukali", "additionDate": "2026-02-03T21:52:20.746663Z", "lastUpdate": "2026-02-03T21:52:33.290463Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }