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HULAFE", "email": "gibi230@iislafe.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "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", "Developer", "Documentor", "Maintainer" ], "note": null }, { "name": "Adrian Galiana-Bordera", "email": "adrian_galiana@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8324-8284", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "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": [ "Contributor", "Documentor" ], "note": null } ], "owner": "pedromiguel_martinez_HULAFE", "additionDate": "2025-04-15T17:42:40.968987Z", "lastUpdate": "2025-12-29T09:32:44.020187Z", "editPermission": { "type": "group", "authors": [ "casopon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Open Causal", "description": "An open platform for sharing, discussing and reusing causal graphs.", "homepage": "https://opencausal.org/", "biotoolsID": "opencausal", "biotoolsCURIE": "biotools:opencausal", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Hüseyin Küçükali", "email": "h.kucukali+biotools@uu.nl", "url": null, "orcidid": "https://orcid.org/0000-0003-1669-3107", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hkucukali", "additionDate": "2025-12-23T13:32:58.320710Z", "lastUpdate": "2025-12-23T14:56:55.440549Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "StructureProfiler", "description": "Tool for 3D protein structure profiling.", "homepage": "https://www.zbh.uni-hamburg.de/forschung/amd/software/structureprofiler.html", "biotoolsID": "StructureProfiler", "biotoolsCURIE": "biotools:StructureProfiler", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0249", "term": "Protein geometry calculation" }, { "uri": "http://edamontology.org/operation_0321", "term": "Protein structure validation" }, { "uri": "http://edamontology.org/operation_0482", "term": "Protein-ligand docking" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" }, { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Other", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://software.zbh.uni-hamburg.de/pages/getPackage", "type": "Downloads page", "note": "NAOMI ChemBio Suite including the package", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1093/bioinformatics/bty692", "pmid": "30124779", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "StructureProfiler: An all-in-one tool for 3D protein structure profiling", "abstract": "Motivation Three-dimensional protein structures are important starting points for elucidating protein function and applications like drug design. Computational methods in this area rely on high quality validation datasets which are usually manually assembled. Due to the increase in published structures as well as the increasing demand for specially tailored validation datasets, automatic procedures should be adopted. Results StructureProfiler is a new tool for automatic, objective and customizable profiling of X-ray protein structures based on the most frequently applied selection criteria currently in use to assemble benchmark datasets. As examples, four dataset configurations (Astex, Iridium, Platinum, combined), all results of the combined tests and the list of all PDB Ids passing the combined criteria set are attached in theSupplementary Material.", "date": "2019-03-01T00:00:00Z", "citationCount": 4, "authors": [ { "name": "Meyder A." }, { "name": "Kampen S." }, { "name": "Sieg J." }, { "name": "Fahrrolfes R." }, { "name": "Friedrich N.-O." }, { "name": "Flachsenberg F." }, { "name": "Rarey M." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Matthias Rarey", "email": "rarey@zbh.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ehrt", "additionDate": "2019-07-06T06:35:25Z", "lastUpdate": "2025-12-23T14:50:37.487104Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Image Duplicates Checker", "description": "Detects duplicate or visually similar DICOM series using a tiered approach that combines metadata analysis, hash-based comparison, and pixel-level similarity metrics.\nIdeal for:\n1. 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Model architecture is Unet-based with residual operations, atrous dilation convolution and specific batch generator. It applies preprocessing steps as RAS conversion, resizing, z-score normalization, patching; and postprocessing operations. 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DIPG (Diffuse Intrinsic Pontine Glioma), or more recently, DMG (Diffuse Midline Glioma) is a H3 K27M–mutant pediatric brainstem cancer detected in T1W and Flair/T2-weighted magnetic resonance images. 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The tool outputs Excel files containing the mean and median for each metric and scan, as well as PNG files with corresponding histogram plots.", "homepage": "https://github.com/FerielRamdhane/XNAT-Quality-Metrics/tree/main", "biotoolsID": "image_quality_assessment_metrics_iqa_for_xnat_platform", "biotoolsCURIE": "biotools:image_quality_assessment_metrics_iqa_for_xnat_platform", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "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_3603", "term": "PNG" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Script", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python", "MATLAB" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/FerielRamdhane/XNAT-Quality-Metrics/tree/main", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://docs.google.com/document/d/17goRA76d9vViR93HbhIcjPPxsCdtGhS9/edit?usp=sharing&ouid=114076787312989347088&rtpof=true&sd=true", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Feriel Romdhane", "email": "ferielromdhane@yahoo.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-5854-9341", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Euro-BioImaging ERIC", "email": "preclinicaldata@eurobioimaging.eu", "url": "https://www.eurobioimaging.eu/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "National Research Council", "email": null, "url": "https://www.ibb.cnr.it/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Feriel", "additionDate": "2025-10-15T07:25:34.085350Z", "lastUpdate": "2025-12-05T14:40:30.073701Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FAIR EVA for EUCAIM", "description": "FAIR EVA: Evaluator, Validator & Advisor has been developed to check the FAIRness level of digital objects from different repositories or data portals. It requires the object identifier (preferably persistent and unique identifier) and the repository to check. It also provides a generic and agnostic way to check digital objects.\nThis software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647.", "homepage": "https://github.com/IFCA-Advanced-Computing/FAIR_eva", "biotoolsID": "fair_eva_4_eucaim", "biotoolsCURIE": "biotools:fair_eva_4_eucaim", "version": [ "EUCAIM_plugin_0.3", "EUCAIM_plugin_0.3.1", "EUCAIM_plugin_0.4.0", "EUCAIM_0.4.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" }, { "uri": "http://edamontology.org/operation_2428", "term": "Validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1052", "term": "URL" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "note": null, "cmd": "python scripts/batch_runner.py --plugin eucaim_catalogue --out faireva_out" } ], "toolType": [ "Plug-in", "Command-line tool", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/IFCA-Advanced-Computing/FAIR_eva", "type": [ "Repository" ], "note": "Repository for FAIR EVA, without the EUCAIM specific plugin" } ], "download": [], "documentation": [ { "url": "https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.md", "type": [ "General" ], "note": "Documentation for the main package, EUCAIM plugin specific documentation not included." }, { "url": "https://gitlabpages.ifca.es/fair-eva-guide-608baa/", "type": [ "User manual" ], "note": "Wiki page with FAIR EVA for EUCAIM specific instructions." } ], "publication": [ { "doi": "10.1038/s41597-023-02652-8", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": null, "abstract": null, "date": null, "citationCount": 0, "authors": [], "journal": null } } ], "credit": [ { "name": "Fernando Aguilar", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-9462-4831", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer", "Documentor" ], "note": "Creator and devloper of the main package FAIR EVA.\nThis software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647." }, { "name": "David Rodríguez", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9160-5106", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": "Developer of the EUCAIM plugin." }, { "name": "Inés Victoria", "email": null, "url": null, "orcidid": "https://orcid.org/0009-0003-7950-3937", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Developer of the EUCAIM plugin." } ], "owner": "davrodgon", "additionDate": "2025-06-30T08:52:48.500476Z", "lastUpdate": "2025-12-04T10:57:20.901575Z", "editPermission": { "type": "group", "authors": [ "ines.ifca", "davrodgon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ML model for MR series categorisation (EUCAIM-SW-011_T-01-01-011)", "description": "A tool based on artificial intelligence that is able to perform a categorisation of MRI series by using standardized DICOM tags. The categorisation includes the type of sequence (e.g. spin echo, gradient echo), the weighting (e.g. T1W, T2W, DCE, ...), the presence of fat suppression and the detection of non-relevant / junk series (e.g. localizers, calibrations, screenshots...).", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab", "biotoolsID": "ml_model_for_mr_series_categorisation", "biotoolsCURIE": "biotools:ml_model_for_mr_series_categorisation", "version": [ "1.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2990", "term": "Classification" } ], "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_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": null, "cmd": "docker run -it --rm --name my-container \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n harbor.eucaim.cancerimage.eu/processing-tools/ml_model_for_mr_series_categorisation:<version> \\\n --config-string \"{'output_name': 'classification_results.json'}\"" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3316", "term": "Computer science" }, { "uri": "http://edamontology.org/topic_3077", "term": "Data acquisition" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/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.google.com/file/d/1lIUixmLItQXOyBPIXL_AzPg_jlqDKwNE/view?usp=drive_link", "type": [ "User manual" ], "note": null }, { "url": "https://drive.google.com/file/d/1jF44iszmmiHd2paD8-YhFhW2uQJ0QBAZ/view?usp=drive_link", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1186/s40537-025-01086-w", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Automatic magnetic resonance imaging series labelling for large repositories", "abstract": "", "date": "2025-12-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Journal of Big Data" } } ], "credit": [ { "name": "GIBI230 - HULAFE", "email": "gibi230@iislafe.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Armando Gomis-Maya", "email": "armago@alumni.uv.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9527-8093", "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": [ "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": [ "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": [ "Contributor" ], "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": [ "Contributor" ], "note": null } ], "owner": "pedromiguel_martinez_HULAFE", "additionDate": "2025-11-25T09:58:37.569343Z", "lastUpdate": "2025-12-03T15:35:26.140884Z", "editPermission": { "type": "group", "authors": [ "casopon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MDPath", "description": "MDPath is a tool for calculating allosteric communication pathways in proteins by analyzing the mutual information of residue dihedral angle movements throughout an MD simulation.", "homepage": "https://github.com/wolberlab/mdpath", "biotoolsID": "mdpath", "biotoolsCURIE": "biotools:mdpath", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0176", "term": "Molecular dynamics" }, { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" }, { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "gpcr" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1021/acs.jcim.5c01590", "pmid": "41030225", "pmcid": "PMC12570139", "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "MDPath: Unraveling Allosteric Communication Paths of Drug Targets through Molecular Dynamics Simulations", "abstract": "", "date": "2025-10-27T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Journal of Chemical Information and Modeling" } } ], "credit": [], "owner": "Aaminah", "additionDate": "2025-11-26T09:26:04.357618Z", "lastUpdate": "2025-12-03T12:50:00.977035Z", "editPermission": { "type": "group", "authors": [ "Aaminah" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SoluProtMutsupDB", "description": "A manually curated database of protein solubility changes upon mutations.", "homepage": "http://loschmidt.chemi.muni.cz/soluprotmutdb", "biotoolsID": "soluprotmutsupdb", "biotoolsCURIE": "biotools:soluprotmutsupdb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0409", "term": "Protein solubility prediction" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_0331", "term": "Variant effect prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data submission, annotation and curation" }, { "uri": "http://edamontology.org/topic_3068", "term": "Literature and language" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1016/J.CSBJ.2022.11.009", "pmid": "36420168", "pmcid": "PMC9678803", "type": [], "version": null, "note": null, "metadata": { "title": "SoluProtMutDB: A manually curated database of protein solubility changes upon mutations", "abstract": "© 2022 The Author(s)Protein solubility is an attractive engineering target primarily due to its relation to yields in protein production and manufacturing. Moreover, better knowledge of the mutational effects on protein solubility could connect several serious human diseases with protein aggregation. However, we have limited understanding of the protein structural determinants of solubility, and the available data have mostly been scattered in the literature. Here, we present SoluProtMutDB – the first database containing data on protein solubility changes upon mutations. Our database accommodates 33 000 measurements of 17 000 protein variants in 103 different proteins. The database can serve as an essential source of information for the researchers designing improved protein variants or those developing machine learning tools to predict the effects of mutations on solubility. The database comprises all the previously published solubility datasets and thousands of new data points from recent publications, including deep mutational scanning experiments. Moreover, it features many available experimental conditions known to affect protein solubility. The datasets have been manually curated with substantial corrections, improving suitability for machine learning applications. The database is available at loschmidt.chemi.muni.cz/soluprotmutdb.", "date": "2022-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Velecky J." }, { "name": "Hamsikova M." }, { "name": "Stourac J." }, { "name": "Musil M." }, { "name": "Damborsky J." }, { "name": "Bednar D." }, { "name": "Mazurenko S." } ], "journal": "Computational and Structural Biotechnology Journal" } } ], "credit": [ { "name": "David Bednar", "email": "222755@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Stanislav Mazurenko", "email": "mazurenko@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Jan Velecký", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Marie Hamsikova", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "velda", "additionDate": "2023-01-25T22:49:31.072923Z", "lastUpdate": "2025-12-03T12:49:50.125351Z", "editPermission": { "type": "group", "authors": [ "velda", "m.musil" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "AutoProSeq - automatic classification of sequence types for prostate mpMRI", "description": "XGBoost-based automatic classification of sequence types for prostate mpMRI into T2W, DWI, ADC, DCE and others (any other sequence type) using metadata alone. Works as a CLI, allows direct application to DICOM datasets or CSV/tsv/Excel/parquet datasets, features integration for Orthanc and DICOM-web as RESTful APIs. This was applied to all data on ProCAncer-I to derive initial results for sequence types. Refines predictions using rule-based heuristics for T2W, DWI and ADC.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/champ-autoproseq", "biotoolsID": "auto-prostate-sequence-classifier", "biotoolsCURIE": "biotools:auto-prostate-sequence-classifier", "version": [ "v0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0968", "term": "Keyword" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "The input can be provided as a DICOM dataset (which will require --dicom-recursion, details below or in the documentation) or as a single DICOM study. This command will print a CSV with 5 columns: i) patient_id, ii) study_uid, iii) series_uid, iv) classification from the XGBoost model, v) classification after heuristics-based corrections.\nThe sequence classification is performed between T2W, DWI, ADC, DCE or others. The provided <dicom-recursion> refers to the number of folders until a DICOM series is found. So if the provided input is a patient folder with nested studies with nested series, the level of DICOM recursion should be 2. If the provided input is a directory with patient folders, the level of DICOM recursion should be 3.", "cmd": "docker run -v <dir-with-dicom>:/data harbor.eucaim.cancerimage.eu/processing-tools/champ-autoproseq --dicom_recursion <dicom-recursion> --input_paths /data" } ], "toolType": [ "Web API", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/CCIG-Champalimaud/metadata-classification", "type": [ "Repository" ], "note": "Repository containing code, README and additional usage information for this tool." } ], "download": [], "documentation": [ { "url": "https://github.com/CCIG-Champalimaud/metadata-classification", "type": [ "Other" ], "note": "Repository containing the code, README and additional information on how to run the tool. If used as an API (when integrated with Orthanc or DICOM-web), the documentation is available upon launching the API at <api-url>/docs." } ], "publication": [ { "doi": "10.1186/s13244-025-01938-2", "pmid": "40146375", "pmcid": "PMC12187622", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Automatic sequence identification in multicentric prostate multiparametric MRI datasets for clinical machine-learning", "abstract": "", "date": "2025-12-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Insights into Imaging" } } ], "credit": [ { "name": "José Guilherme de Almeida", "email": "jose.almeida@research.fchampalimaud.org", "url": "https://josegcpa.net", "orcidid": "https://orcid.org/0000-0002-1887-0157", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Nikolaos Papanikolaou", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3298-2072", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "josegcpa", "additionDate": "2025-12-02T17:37:57.215347Z", "lastUpdate": "2025-12-03T09:27:04.489071Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "IQA DCE tool", "description": "The purpose of the tool is to provide a complete framework for automatic detection of image quality for Breast DCE MR images. The assessment is performed on the first post-contrast dynamic phase in order to assess the most clinically relevant sequence among a number of identical acquisitions. Two categories are available for image classification, i.e. high and low quality, depending on the level of noise, degree of blurring and presence of artifacts.", "homepage": "https://hub.docker.com/repository/docker/billykforth/iqa_dce_tool/general", "biotoolsID": "iqa_dce_tool", "biotoolsCURIE": "biotools:iqa_dce_tool", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "EUPL-1.1", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://hub.docker.com/r/billykforth/iqa_dce_tool", "type": "Container file", "note": null, "version": "1.0" } ], "documentation": [ { "url": "https://docs.google.com/document/d/1hG_M21gvO4D8zkHmwtbavT8Dp6bliRU4/edit", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.3390/jimaging11110417", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "billyk", "additionDate": "2025-11-26T13:27:32.776575Z", "lastUpdate": "2025-12-03T06:46:13.717361Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Asparaginase database", "description": "Asparaginases are one of the most successful biopharmaceuticals that play a pivotal role in the treatment of acute lymphoblastic leukemia. In order to find new asparaginases with improved properties (stability, substrate affinity, immunogenicity) or to achieve these goals by enzyme engineering, it is essential to collect and accurately classify asparaginases from various sources. The database covers 101 experimentally studied proteins from the literature, a manually curated set of 127 sequences from SwissProt, and more than 100,000 automatically curated enzymes.", "homepage": "https://asparaginasedb.com/", "biotoolsID": "asparaginase_database", "biotoolsCURIE": "biotools:asparaginase_database", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Database portal", "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "CC-BY-4.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://asparaginasedb.cz/help.html", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [], "owner": "spiwokv", "additionDate": "2025-11-29T18:03:55.516541Z", "lastUpdate": "2025-12-02T22:00:20.857626Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EUCAIM Wizard Tool", "description": "The EUCAIM Wizard Tool performs an analysis of data re-identification risks of imaging and clinical data that follow the EUCAIM CDM. It includes and uses an EUCAIM specific configuration of the ARX Data Anonymization Tool (biotools:arx), by supporting a wide variety of privacy and risk models as well methods for analyzing the usefulness of output data.", "homepage": "https://github.com/cbml-forth/eucaim_wizard_tool", "biotoolsID": "eucaim_wizard_tool", "biotoolsCURIE": "biotools:eucaim_wizard_tool", "version": [ "beta1.0" ], "otherID": [], "relation": [ { "biotoolsID": "arx", "type": "includes" }, { "biotoolsID": "arx", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3283", "term": "Anonymisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" }, { "uri": "http://edamontology.org/topic_4044", "term": "Data protection" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "EUPL-1.1", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/cbml-forth/eucaim_wizard_tool", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://docs.google.com/document/d/1pi-7SvDKzVSYS78MhvnBX7PcXF3kZAc6/edit?usp=sharing&ouid=115998150174651530097&rtpof=true&sd=true", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [ { "name": "Computational BioMedicine Laboratory, Foundation for Research and Technology Hellas (FORTH)", "email": null, "url": "https://www.ics.forth.gr/cbml/?lang=en", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "vkalokyri", "additionDate": "2025-04-30T10:28:37.002350Z", "lastUpdate": "2025-12-02T12:53:14.408095Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AggreProt", "description": "AggreProt is a web server to predict and engineer protein aggregation. The tool provides a per-residue numerical aggregation propensity value and an overall protein aggregation propensity profile. Along with the protein solvent accessibility area and its transmembrane propensity, AggreProt predictions aid the users on designing soluble proteins.", "homepage": "https://loschmidt.chemi.muni.cz/aggreprot/", "biotoolsID": "aggreprot", "biotoolsCURIE": "biotools:aggreprot", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java", "JavaScript" ], "license": "Proprietary", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "Proteomics" ], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkae420", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "AggreProt: A web server for predicting and engineering aggregation prone regions in proteins", "abstract": "", "date": "2024-07-05T00:00:00Z", "citationCount": 17, "authors": [], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Joan Planas-Iglesias", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "David Bednar", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Jiri Damborsky", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Simeon Borko", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "m.musil", "additionDate": "2025-12-02T12:03:53.282983Z", "lastUpdate": "2025-12-02T12:03:53.285771Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" } ] }
