Resource List
List all resources, or create a new resource.
GET /api/t/?creditTypeRole=Developer
{ "count": 1056, "next": "?page=2", "previous": null, "list": [ { "name": "Deep Learning Noise Reduction (DLNR)", "description": "A fully convolutional (with no pooling layers) model was trained on a set of noisy images with the ground truth being the original image without the (synthetic) noise. Different levels of noise and types were incorporated into the training set. The experiments showed reduction in noise levels, but it can impact image quality when T2ws without noise is provided to the model.", "homepage": "https://github.com/trivizakis/DLNR", "biotoolsID": "deep_learning_noise_reduction_dlnr", "biotoolsCURIE": "biotools:deep_learning_noise_reduction_dlnr", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "EUPL-1.2", "collectionID": [ "EUCAIM" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/trivizakis/DLNR", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://docs.google.com/document/d/197LZH1EASYfOhwzo_I1ZfATiv8gh9Vyu/edit?usp=sharing&ouid=115998150174651530097&rtpof=true&sd=true", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1109/SACI66288.2025.11030174", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Eleftherios Trivizakis", "email": "trivizakis@ics.forth.gr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null } ], "owner": "vkalokyri", "additionDate": "2025-12-04T11:29:17.647406Z", "lastUpdate": "2026-03-12T10:23:37.808636Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Intercranial Meningioma Segmenter", "description": "The Intercranial Meningioma Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of intercranial meningiomas in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of intercranial meningiomas in brain MRI scans to support clinical decision-making in both diagnosis and prognosis.", "homepage": "https://github.com/BIT-UPM/EUCAIM/tree/main/intercranial_meningioma_segmenter", "biotoolsID": "intercranial_meningioma_segmenter", "biotoolsCURIE": "biotools:intercranial_meningioma_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow", "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Contributor", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Contributor", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-11-05T10:35:32.782850Z", "lastUpdate": "2026-03-12T09:18:54.512989Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Brain Metastasis Segmenter", "description": "The Brain Metastasis Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of brain metastases in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of brain metastases in MRI scans to support clinical decision-making in both diagnosis and prognosis.", "homepage": "https://github.com/BIT-UPM/EUCAIM/tree/main/brain_metastasis_segmenter", "biotoolsID": "brain_metastasis_segmenter", "biotoolsCURIE": "biotools:brain_metastasis_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web application", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Contributor", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Contributor", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-11-04T18:24:22.573039Z", "lastUpdate": "2026-03-12T09:18:35.170132Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Sub-Saharan Africa Brain Glioma Segmenter", "description": "The Sub-Saharan Africa Brain Glioma Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of intercranial meningiomas in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of gliomas in brain MRI scans to support clinical decision-making in both diagnosis and prognosis. This tool was trained on a cohort of patients from Sub-Saharan Africa.", "homepage": "https://github.com/BIT-UPM/EUCAIM/tree/main/sub_saharan_africa_brain_glioma_segmenter", "biotoolsID": "sub-saharan_africa_brain_glioma_segmenter", "biotoolsCURIE": "biotools:sub-saharan_africa_brain_glioma_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow", "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Developer", "Contributor", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Contributor", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-11-05T11:45:08.078589Z", "lastUpdate": "2026-03-12T09:18:25.525211Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Brain Glioma Segmenter", "description": "The Brain Glioma Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of brain gliomas in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of brain gliomas in MRI scans to support clinical decision-making in both diagnosis and prognosis.", "homepage": "https://github.com/BIT-UPM/EUCAIM/tree/main/brain_glioma_segmenter", "biotoolsID": "brain_glioma_segmenter", "biotoolsCURIE": "biotools:brain_glioma_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web application", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor", "Developer", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-11-05T10:49:02.917891Z", "lastUpdate": "2026-03-12T09:17:40.450265Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Pediatric Brain Tumor Segmenter", "description": "The Pediatric Brain Tumor Segmenter is a software tool developed by researchers from Universidad Politécnica de Madrid and Children’s National Hospital for the segmentation and analysis of pediatric brain tumors in magnetic resonance imaging (MRI). Built in Python, it enables precise quantitative analysis of pediatric brain tumors in MRI scans to support clinical decision-making in both diagnosis and prognosis.", "homepage": "https://github.com/BIT-UPM/EUCAIM/tree/main/pediatric_brain_tumor_segmenter", "biotoolsID": "pediatric_brain_tumor_segmenter", "biotoolsCURIE": "biotools:pediatric_brain_tumor_segmenter", "version": [ "v1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web application", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-SA-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://segmenter.hope4kids.io/", "type": [ "Other" ], "note": "Main app webpage" }, { "url": "https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids", "type": [ "Repository" ], "note": "GitHub repository" } ], "download": [], "documentation": [ { "url": "https://docs.hope4kids.io/HOPE-Segmenter-Kids/", "type": [ "API documentation", "Citation instructions", "Terms of use", "Code of conduct", "Release notes", "User manual", "General", "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-031-76163-8_20", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04094", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.48550/arXiv.2412.04111", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Capellán-Martín", "email": "daniel.capellan@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9743-0845", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Contributor", "Support" ], "note": null }, { "name": "Abhijeet Parida", "email": "pabhijeet@childrensnational.org", "url": null, "orcidid": "https://orcid.org/0000-0002-4978-0576", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Contributor", "Support", "Maintainer" ], "note": null }, { "name": "Zhifan Jiang", "email": "zjiang@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Developer", "Support" ], "note": null }, { "name": "María Jesus Ledesma-Carbayo", "email": "mj.ledesma@upm.es", "url": null, "orcidid": "https://orcid.org/0000-0001-6846-3923", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null }, { "name": "Marius George Linguraru", "email": "mlingura@childrensnational.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "dani-capellan", "additionDate": "2025-10-28T18:31:05.926498Z", "lastUpdate": "2026-03-12T09:16:46.032652Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WEBnma", "description": "WEBnm@ provides quick, automated computation and analysis of low-frequency normal modes for protein structures.", "homepage": "http://apps.cbu.uib.no/webnma", "biotoolsID": "webnma", "biotoolsCURIE": "biotools:webnma", "version": [ "3.5" ], "otherID": [], "relation": [ { "biotoolsID": "numpy", "type": "uses" }, { "biotoolsID": "biopython", "type": "uses" }, { "biotoolsID": "matplotlib", "type": "uses" }, { "biotoolsID": "mustang", "type": "uses" }, { "biotoolsID": "dssp", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_0244", "term": "Protein flexibility and motion analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1354", "term": "Sequence profile" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Constructs elastic network model from alpha carbon coordinates of the protein, and computes properties to describe large scale conformations. Computes normal modes, fluctuation profiles, inter-residue correlations, conformational overlap analysis and vector field representations. Structural amino acid profiles, and normal mode characteristics describing protein motion, visualized in plots and decorated structure visualizations. White space delimited tabular data for normal modes and the provided plots", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2487", "term": "Protein structure comparison" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0886", "term": "Structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_2200", "term": "FASTA-like (text)" } ] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_0889", "term": "Structural profile" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Performs comparative analysis of the normal modes of protein structures. Computes the Bhattacharyya Coefficient (BC) and the Root Mean Squared Inner Product (RMSIP) of aligned parts of the proteins. Alignment of sets of proteins to be compared. Multiple protein structures Heatmaps, dendrograms and structural amino acid profiles for visual comparison of structural similarity. White space delimited tabular data for the provided plots", "cmd": null } ], "toolType": [ "Web API", "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "BiB tools", "CBU tools", "UiB tools", "ELIXIR-NO", "ELIXIR-Norway" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Norway" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [ { "url": "https://github.com/reuter-group/webnma3", "type": [ "Repository", "Issue tracker" ], "note": null }, { "url": "https://elixir.no/helpdesk", "type": [ "Helpdesk" ], "note": "Helpdesk and support for ELIXIR Norway services." } ], "download": [], "documentation": [ { "url": "http://apps.cbu.uib.no/webnma3/howto/single", "type": [ "Quick start guide" ], "note": null }, { "url": "http://apps.cbu.uib.no/webnma3/qanda", "type": [ "FAQ" ], "note": null }, { "url": "http://apps.cbu.uib.no/webnma3/about", "type": [ "General", "Citation instructions" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-014-0427-6", "pmid": "25547242", "pmcid": "PMC4339738", "type": [ "Primary" ], "version": "2.0", "note": null, "metadata": { "title": "WEBnmat v2.0: Web server and services for comparing protein flexibility", "abstract": "Background: Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. Results: We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnmat, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the. In addition, programmatic access to WEBnmat is now available through a SOAP-based web service. WEBnmat is available at. Conclusion: WEBnmat v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnmat facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.", "date": "2014-12-30T00:00:00Z", "citationCount": 87, "authors": [ { "name": "Tiwari S.P." }, { "name": "Fuglebakk E." }, { "name": "Hollup S.M." }, { "name": "Skjaerven L." }, { "name": "Cragnolini T." }, { "name": "Grindhaug S.H." }, { "name": "Tekle K.M." }, { "name": "Reuter N." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1186/1471-2105-6-52", "pmid": "15762993", "pmcid": "PMC1274249", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "WEBnm@: A web application for normal mode analyses of proteins", "abstract": "Background: Normal mode analysis (NMA) has become the method of choice to investigate the slowest motions in macromolecular systems. NMA is especially useful for large biomolecular assemblies, such as transmembrane channels or virus capsids. NMA relies on the hypothesis that the vibrational normal modes having the lowest frequencies (also named soft modes) describe the largest movements in a protein and are the ones that are functionally relevant. Results: We developed a web-based server to perform normal modes calculations and different types of analyses. Starting from a structure file provided by the user in the PDB format, the server calculates the normal modes and subsequently offers the user a series of automated calculations; normalized squared atomic displacements, vector field representation and animation of the first six vibrational modes. Each analysis is performed independently from the others and results can be visualized using only a web browser. No additional plug-in or software is required. For users who would like to analyze the results with their favorite software, raw results can also be downloaded. The application is available on http://www.bioinfo.no/tools/normalmodes. We present here the underlying theory, the application architecture and an illustration of its features using a large transmembrane protein as an example. Conclusion: We built an efficient and modular web application for normal mode analysis of proteins. Non specialists can easily and rapidly evaluate the degree of flexibility of multi-domain protein assemblies and characterize the large amplitude movements of their domains. © 2005 Hollup et al; licensee BioMed Central Ltd.", "date": "2005-03-11T00:00:00Z", "citationCount": 105, "authors": [ { "name": "Hollup S.M." }, { "name": "Salensminde G." }, { "name": "Reuter N." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Nathalie Reuter", "email": "Nathalie.Reuter@uib.no", "url": "http://www.cbu.uib.no/reuter/", "orcidid": "https://orcid.org/0000-0002-3649-7675", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Sandhya P Tiwari", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-0747-3826", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Kidane M Tekle", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Tristan Cragnolini", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Svenn H Grindhaug", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Lars Skjærven", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Gisle Salensminde", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Edvin Fuglebakk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Siv M Hollup", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Department of Molecular Biology, University of Bergen, Norway", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Computational Biology Unit, Department of Informatics, University of Bergen, Norway", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "UiB", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "UiB", "additionDate": "2016-03-17T13:51:10Z", "lastUpdate": "2026-03-11T08:56:55.566213Z", "editPermission": { "type": "group", "authors": [ "eca008", "korbinib" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "QMRITools", "description": "QMRITools is a collection of tools for quantitative muscle MRI analysis, enabling the assessment of neuromuscular disorders and conditions. The software utilizes various MRI sequences and processing pipelines to generate metrics for comparative evaluation.", "homepage": "https://github.com/mfroeling/QMRITools", "biotoolsID": "qmri", "biotoolsCURIE": "biotools:qmri", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" }, { "uri": "http://edamontology.org/operation_3799", "term": "Quantification" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3444", "term": "MRI" }, { "uri": "http://edamontology.org/topic_3407", "term": "Endocrinology and metabolism" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3379", "term": "Preclinical and clinical studies" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.qmritools.com/assets/htmldoc/html/guide/qmritools", "type": [ "User manual" ], "note": null }, { "url": "https://www.qmritools.com/doc/instal/", "type": [ "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.21105/joss.01204", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1002/jmri.23608", "pmid": "22334539", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1002/mrm.22477", "pmid": "20725932", "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1002/nbm.4119", "pmid": "31313867", "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Martijn Froeling", "email": "m.froeling@gmail.com", "url": "https://www.qmritools.com/", "orcidid": "https://orcid.org/0000-0003-3841-0497", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null } ], "owner": "martijn", "additionDate": "2026-01-14T16:51:46.442030Z", "lastUpdate": "2026-03-04T12:17:03.094179Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Lab Integrated Data (LabID)", "description": "Lab Integrated Data (LabID) is an open-source web-based platform for research data management in life science institutes, featuring sample and dataset management, an inventory management system and an electronic lab notebook. LabID allows recording extensive experimental information about the provenance of data (samples, reagents, instrument, protocols, assay parameters) and is designed to help individual scientists, research groups and core facilities better manage, annotate and share their research according to FAIR principles.", "homepage": "https://grp-gbcs.embl-community.io/labid-user-docs/", "biotoolsID": "labid", "biotoolsCURIE": "biotools:labid", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3070", "term": "Biology" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data curation and archival" }, { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [], "language": [], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://gitlab.com/lab-integrated-data", "type": [ "Repository" ], "note": "Open source repositories for the LabID subprojects (UI, Server, Command Line Interface, Library)" }, { "url": "https://labintegrateddata.slack.com/", "type": [ "Discussion forum" ], "note": "Channel for questions from externals" }, { "url": "https://www.embl.org/groups/modis/", "type": [ "Other" ], "note": "Website of the MODIS team behind LabID" } ], "download": [], "documentation": [ { "url": "https://grp-gbcs.embl-community.io/labid-user-docs/", "type": [ "General" ], "note": "Main documentation including installation instructions and training" }, { "url": "https://labid-demo.embl.de/", "type": [ "Training material" ], "note": "Test server for e.g LabID and trainings" } ], "publication": [], "credit": [ { "name": "Charles Girardot", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-4301-3920", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer", "Primary contact", "Developer" ], "note": "Head of MODIS team at EMBL Heidelberg" }, { "name": "Jelle Scholtalbers", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6090-2482", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Support" ], "note": "Former MODIS team member, now working as a freelance (LabRise solutions)" }, { "name": "Matthias Monfort", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer", "Developer", "Support" ], "note": null }, { "name": "Nayeem Reza", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-2068-5812", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer", "Support" ], "note": null }, { "name": "Laurent Thomas", "email": "laurent.thomas@embl.de", "url": null, "orcidid": "https://orcid.org/0000-0001-7686-3249", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL Heidelberg", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "03mstc592", "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null } ], "owner": "laurent_s._v.", "additionDate": "2026-03-02T15:35:15.926607Z", "lastUpdate": "2026-03-02T19:41:16.788202Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Random Number Lab", "description": "An interactive set of tools including randomization of data (even stratified random sampling) and random assignments for studies, generation of random numbers following specific probability distributions, generation of random and quasi-random point distributions and sampling patterns, noise in one or two dimensions with adjustable spectral properties, random walks and Lévy flights. Own data tables can be provided for random sampling in a privacy-friendly way, as data processing takes place directly in the browser and no data is transferred to anywhere else. The Random Number Lab also offers some educational material and worksheets and can be used for scientific and educational purposes.", "homepage": "https://randomnumberlab.org", "biotoolsID": "random_number_lab", "biotoolsCURIE": "biotools:random_number_lab", "version": [], "otherID": [ { "value": "RRID:SCR_028010", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0364", "term": "Random sequence generation" } ], "input": [], "output": [], "note": "Generation of sequences of random numbers or elements, spatial point patterns, random walks", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": "Visualization of random distributions and random processes", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [], "output": [], "note": "Randomization and permutation of data in a privacy-preserving way", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" }, { "uri": "http://edamontology.org/topic_3678", "term": "Experimental design and studies" } ], "operatingSystem": [ "Linux", "iOS", "Mac", "Android", "Windows" ], "language": [ "JavaScript" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Thomas Amthor", "email": "hello@randomnumberlab.org", "url": null, "orcidid": "https://orcid.org/0000-0002-1456-6131", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null } ], "owner": "thomas9", "additionDate": "2026-02-27T17:39:14.144907Z", "lastUpdate": "2026-02-27T18:10:10.460700Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PLAST", "description": "PLAST is a heuristical method to search for highest scoring local alignments between a DNA sequence query and a graphical pangenome. It takes as input a plain DNA sequence and a pangenome which may either be a set of (multiple) FASTA or FASTQ files or a sequence graph constructed by the tool Bifrost. It then outputs statistically meaningful (gapped) alignments in the style of the NCBI BLAST standard output format. Alignments are calculated based on a \"seed-and-extend approach\" while traversing the sequence graph. Biologically meaningful alignments are filtered by using an alignment statistic explicitly developed for sequence-to-graph alignments involving graphical pangenomes.", "homepage": "https://github.com/tischulz1/plast", "biotoolsID": "pangenome-blast", "biotoolsCURIE": "biotools:pangenome-blast", "version": [ "0.0.1-0.2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0495", "term": "Local alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1211", "term": "unambiguous pure nucleotide" } ] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_3975", "term": "GFA 1" }, { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1333", "term": "BLAST results" } ] } ], "note": "In order to search for alignments within the pangenome graph, \nA pangenome graph used to search for alignments consists of (1) a file in GFA format containing all sequences of the graph, (2) a binary file produced by the tool itself or the software \"Bifrost\" and (3) a program-specific index data structure in binary format.", "cmd": "PLAST Search -i pangenomeGraphCommonFilePrefix -q fileContainingOneQueryPerLine" }, { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_3975", "term": "GFA 1" }, { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "note": "If a pangenome graph already exists and only an index has to be built, FASTA/FASTQ files are not needed.", "cmd": "PLAST Build -i pangenomeGraphCommonFilePrefix -R *.fasta" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://gitlab.ub.uni-bielefeld.de/gi/plast", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/tischulz1/plast", "type": [ "Mirror" ], "note": null } ], "download": [], "documentation": [ { "url": "https://gitlab.ub.uni-bielefeld.de/gi/plast/-/blob/master/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btab077", "pmid": "33532821", "pmcid": "PMC8388040", "type": [ "Primary", "Method", "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Detecting high-scoring local alignments in pangenome graphs", "abstract": "Motivation: Increasing amounts of individual genomes sequenced per species motivate the usage of pangenomic approaches. Pangenomes may be represented as graphical structures, e.g. compacted colored de Bruijn graphs, which offer a low memory usage and facilitate reference-free sequence comparisons. While sequence-to-graph mapping to graphical pangenomes has been studied for some time, no local alignment search tool in the vein of BLAST has been proposed yet. Results: We present a new heuristic method to find maximum scoring local alignments of a DNA query sequence to a pangenome represented as a compacted colored de Bruijn graph. Our approach additionally allows a comparison of similarity among sequences within the pangenome. We show that local alignment scores follow an exponential-tail distribution similar to BLAST scores, and we discuss how to estimate its parameters to separate local alignments representing sequence homology from spurious findings. An implementation of our method is presented, and its performance and usability are shown. Our approach scales sublinearly in running time and memory usage with respect to the number of genomes under consideration. This is an advantage over classical methods that do not make use of sequence similarity within the pangenome.", "date": "2021-08-15T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Schulz T." }, { "name": "Wittler R." }, { "name": "Rahmann S." }, { "name": "Hach F." }, { "name": "Stoye J." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Bielefeld University", "email": null, "url": "https://www.uni-bielefeld.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Genome Informatics", "email": null, "url": "https://gi.cebitec.uni-bielefeld.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Tizian Schulz", "email": "plast-service@cebitec.uni-bielefeld.de", "url": null, "orcidid": "https://orcid.org/0000-0003-0744-7078", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "tizian", "additionDate": "2021-05-06T06:18:52Z", "lastUpdate": "2026-02-26T11:22:02.485629Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Helix Insight", "description": "AI-powered variant interpretation platform for clinical genetics laboratories. Automates ACMG/AMP 2015 classification using Bayesian point-based framework (Tavtigian et al. 2018) with BayesDel ClinGen SVI-calibrated thresholds (Pejaver et al. 2022). Integrates 8 reference databases (gnomAD v4.1, ClinVar, dbNSFP 4.9c, SpliceAI, gnomAD Constraint, HPO, ClinGen, Ensembl VEP) for comprehensive variant annotation. Supports HPO-based phenotype matching with semantic similarity scoring, automated biomedical literature mining across 2M+ PubMed publications, and structured clinical report generation. Delivers full clinical interpretation of whole genome sequencing (WGS) in under 15 minutes. EU-hosted on dedicated infrastructure in Helsinki, Finland (GDPR-compliant).", "homepage": "https://helixinsight.bio", "biotoolsID": "HelixInsight", "biotoolsCURIE": "biotools:HelixInsight", "version": [ "3.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0920", "term": "Genotype/phenotype report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1622", "term": "Disease report" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0305", "term": "Literature search" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "Proprietary", "collectionID": [], "maturity": "Emerging", "cost": "Commercial", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://helixinsight.bio/docs", "type": [ "General" ], "note": null }, { "url": "https://helixinsight.bio/docs/getting-started", "type": [ "API documentation" ], "note": null }, { "url": "https://helixinsight.bio/how-it-works", "type": [ "Installation instructions" ], "note": null }, { "url": "https://helixinsight.bio/terms", "type": [ "Terms of use" ], "note": null }, { "url": "https://helixinsight.bio/privacy", "type": [ "Other" ], "note": "Privacy policy" } ], "publication": [], "credit": [ { "name": "Helena Bioinformatics", "email": "contact@helena.bio", "url": "https://helena.bio", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Developer" ], "note": null } ], "owner": "helenabio", "additionDate": "2026-02-23T13:56:07.187145Z", "lastUpdate": "2026-02-24T22:17:23.859555Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "FANTASIA", "description": "FANTASIA (Functional ANnoTAtion based on embedding space SImilArity) is a pipeline for protein annotating via GO term transference using the embedding space. FANTASIA’s latest developments include additional protein language models and provide enhanced functionalities.", "homepage": "https://github.com/CBBIO/", "biotoolsID": "fantasiav2", "biotoolsCURIE": "biotools:fantasiav2", "version": [ "4.0", "LITE" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3945", "term": "Molecular evolution" }, { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" }, { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" }, { "uri": "http://edamontology.org/topic_4010", "term": "Open science" } ], "operatingSystem": [ "Linux" ], "language": [ "Python", "SQL" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Spain" ], "elixirCommunity": [ "3D-BioInfo", "Proteomics" ], "link": [ { "url": "https://github.com/CBBIO/FANTASIA", "type": [ "Repository" ], "note": "Main repository contains documentation from latest version" }, { "url": "https://github.com/MetazoaPhylogenomicsLab/FANTASIA", "type": [ "Repository" ], "note": "Main repository contains documentation from linitial version based on Bioembeddings implementation." }, { "url": "https://www.earthbiogenome.org/report-on-annotation-recommended-tools", "type": [ "Software catalogue" ], "note": "Recommended tool for the Earth Biogenome Project" }, { "url": "https://github.com/CBBIO/FANTASIA-Lite", "type": [ "Software catalogue" ], "note": "This is the LITE version of FANTASIA for a quick and custom annotation" }, { "url": "https://gitlab.com/ifb-elixirfr/cluster/tools/-/tree/master/tools/fantasia/0.1.0?ref_type=heads", "type": [ "Repository" ], "note": "This is a repository for FANTASIA-LITE available in Elixir France" } ], "download": [], "documentation": [ { "url": "https://fantasia.readthedocs.io/en/latest/", "type": [ "General" ], "note": "Full documetnation with user cases, benchmarking, and cluster implementations" } ], "publication": [ { "doi": "10.1093/nargab/lqae078", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1007/978-1-0716-4623-6_8", "pmid": "40601255", "pmcid": null, "type": [ "Method" ], "version": "2.8.0", "note": "This protocol describes the use of the first version of FANTASIA", "metadata": null }, { "doi": "10.1038/s42003-025-08651-2", "pmid": "40813894", "pmcid": "PMC12354702", "type": [ "Primary" ], "version": "4.0", "note": "Application of FANTASIA to annotate 24 million of genes of 1000 animal species", "metadata": null } ], "credit": [ { "name": "Francisco Miguel Pérez Canales", "email": "fmpercan@upo.es", "url": "http://www.bioinfocb.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer", "Support", "Provider" ], "note": "Programmer" }, { "name": "Ana M Rojas Mendoza", "email": "a.rojas.m@csic.es", "url": "http://www.bioinfocb.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Contributor", "Documentor", "Support" ], "note": "Scientific concept and functionalities" }, { "name": "Rosa Fernandez", "email": "rosa.fernandez@ibe.upf-csic.es", "url": "https://www.metazomics.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor", "Documentor" ], "note": "Scientific concept and functionalities" }, { "name": "Francisco J. Ruiz Mota", "email": "fraruimot@alum.us.es", "url": "http://www.bioinfocb.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Junior developer" }, { "name": "Gemma Martinez Redondo", "email": "gemma.martinez@ibe.upf-csic.es", "url": "https://www.metazomics.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Developer" ], "note": "Contributed as developer of the first version of FANTASIA V1" }, { "name": "Alex Dominguez Rodriguez", "email": "adomrod4@upo.es", "url": "http://www.bioinfocb.es/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact", "Maintainer", "Documentor" ], "note": "Implemented the LITE version of FANTASIA" } ], "owner": "arojas", "additionDate": "2025-06-25T13:31:29.384393Z", "lastUpdate": "2026-02-22T21:19:22.986918Z", "editPermission": { "type": "group", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Poly Pipeline", "description": "A data analysis pipeline for Spatial Transcriptomics data tailored to polyploid organisms.", "homepage": "https://github.com/capuccino26/POLY_PIPELINE", "biotoolsID": "poly_pipeline", "biotoolsCURIE": "biotools:poly_pipeline", "version": [ "v1.0.0" ], "otherID": [ { "value": "doi:10.5281/zenodo.18655692", "type": "doi", "version": "v1.0.0" } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0313", "term": "Expression profile clustering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3917", "term": "Count matrix" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3768", "term": "Clustered expression profiles" }, "format": [] } ], "note": "Clustering of GEF files.", "cmd": "ANALYSIS=1" }, { "operation": [ { "uri": "http://edamontology.org/operation_3925", "term": "Network visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3917", "term": "Count matrix" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [] } ], "note": "Generation of Nodes and Edges.", "cmd": "ANALYSIS=3" }, { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [] } ], "note": "Data converter.", "cmd": "ANALYSIS=0" }, { "operation": [ { "uri": "http://edamontology.org/operation_3800", "term": "RNA-Seq quantification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3917", "term": "Count matrix" }, "format": [] } ], "note": "Generation of count matrix.", "cmd": "ANALYSIS=1" }, { "operation": [ { "uri": "http://edamontology.org/operation_3695", "term": "Data filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [] } ], "note": "Filtering of GEF files.", "cmd": "ANALYSIS=1" } ], "toolType": [ "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [ "Linux" ], "language": [ "R", "Bash", "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [], "elixirCommunity": [ "Plant Sciences" ], "link": [ { "url": "https://github.com/capuccino26/POLY_PIPELINE", "type": [ "Repository" ], "note": "Github Repository" }, { "url": "https://zenodo.org/records/18655692", "type": [ "Other" ], "note": "Zenodo Insert" } ], "download": [ { "url": "https://github.com/capuccino26/POLY_PIPELINE/releases/tag/v1.0.0", "type": "Source code", "note": "Github Release", "version": "v1.0.0" } ], "documentation": [ { "url": "https://github.com/capuccino26/POLY_PIPELINE#poly_pipeline", "type": [ "User manual" ], "note": "Github Documentation" } ], "publication": [ { "doi": "10.5281/zenodo.18655692", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": "v1.0.0", "note": "Zenodo Insertion", "metadata": null } ], "credit": [ { "name": "Pedro Cristovão Carvalho", "email": "pccrvl@gmail.com", "url": "https://cafinvest.com.br/resume.php", "orcidid": "https://orcid.org/0000-0001-9242-6911", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact", "Maintainer", "Provider", "Support" ], "note": "Main developer of the pipeline" } ], "owner": "pedro", "additionDate": "2026-02-19T07:51:45.702608Z", "lastUpdate": "2026-02-19T08:19:12.181956Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "GRNsight", "description": "Web application and service for visualizing small- to medium-scale models of gene regulatory networks. It automatically lays out either an unweighted or weighted network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. It is best-suited for visualizing networks of fewer than 35 nodes and 70 edges and has general applicability.", "homepage": "http://dondi.github.io/GRNsight/", "biotoolsID": "grnsight", "biotoolsCURIE": "biotools:grnsight", "version": [ "7.4.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_1781", "term": "Gene regulatory network analysis" }, { "uri": "http://edamontology.org/operation_3083", "term": "Pathway or network visualisation" } ], "input": [], "output": [], "note": "GRNsight automatically lays out a network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. When a user uploads a spreadsheet with an unweighted adjacency matrix, GRNsight automatically lays out the graph using black lines and pointed arrowheads. When a user uploads a spreadsheet with a weighted adjacency matrix, GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (positive for activation or negative for repression) and magnitude of the weight parameter. Nodes are rectangular and support gene labels of up to 12 characters. The edges are arcs, which become straight lines when the nodes are close together. Self-regulatory edges are indicated by a loop on the lower-right side of a node. Visualizations can be modified by sliders that adjust D3.js's force graph layout parameters and through manual node dragging.", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0204", "term": "Gene regulation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "JavaScript" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/dondi/GRNsight", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/dondi/GRNsight/archive/refs/heads/main.zip", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://dondi.github.io/GRNsight/documentation.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.7717/peerj-cs.85", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.5281/zenodo.7411630", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Ngoc Kim Ngan Tran", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Cecilia Zaragoza", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "A’Kaia Phelps", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Ona O. Igbinedion", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Ahmad R. Mersaghian", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Ian M. Green", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Lauren L. Amparo", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Alexia M. Filler", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Kevin B. Patterson", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "John L. Lopez", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Justin Kyle T. Torres", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Eileen Choe", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jen Shin", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Mihir Samdarshi", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Anindita Varshneya", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Nicole A. Anguiano", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Britain J. Southwick", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Ben G. Fitzpatrick", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Loyola Marymount University", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "NSF award 0921038; LMU Rains Research Assistant Program; LMU Summer Undergraduate Research Program", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "lmu.edu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Kam D. Dahlquist", "email": "kdahlquist@lmu.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "John David N. Dionisio", "email": "dondi@lmu.edu", "url": null, "orcidid": "https://orcid.org/0000-0001-8655-4693", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "dondi@lmu.edu", "additionDate": "2016-08-13T19:15:03Z", "lastUpdate": "2026-02-17T08:19:18.244542Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)", "description": "The tool performs a DICOM quality check in terms of correct number of files per sequence, corrupted files, precise directory hierarchy, separated dynamic series merging them, interest series filtering/selection by specific series description lists and diffusion sequence identification by b-values. It applies the desired changes to the dataset and generates a report containing information about the selected sequences, corrupted files, missing files and merged files.\n\nStatus: Deployed", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "biotoolsID": "dicom_file_integrity_checker_by_gibi230", "biotoolsCURIE": "biotools:dicom_file_integrity_checker_by_gibi230", "version": [ "2.0.0", "2.1.0", "2.1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "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_3620", "term": "xlsx" }, { "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" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "For Data Holders (ingestion-tools)", "cmd": "docker run -it --rm --name my-container \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n -v \"<config_path>:/config\" \\\n harbor.eucaim.cancerimage.eu/ingestion-tools/dicom_file_integrity_checker:latest" }, { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "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" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "For Data Users (processing-tools)", "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/dicom_file_integrity_checker:latest \\\n /app/entrypoint.sh --config-string \"{'QA': {'sequence_selection': ['ALL'], 'modality_selection': ['ALL'], 'input_directory': 'dataset_id'}}\"" } ], "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": [ "Mac", "Linux", "Windows" ], "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://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "type": [ "Software catalogue" ], "note": "Link to EUCAIM's Harbor for Data Holders" }, { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/dicom_file_integrity_checker/artifacts-tab", "type": [ "Software catalogue" ], "note": "Link to EUCAIM's Harbor for Data Users" } ], "download": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab", "type": "Container file", "note": "EUCAIM user needed", "version": "2.1.0" } ], "documentation": [ { "url": "https://drive.eucaim.cancerimage.eu/s/LAKqSQZY4Bjqz5W", "type": [ "User manual" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/EEqjraK574HrwMf", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=oUebkjLYeSs&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=3", "type": [ "Training material" ], "note": null } ], "publication": [], "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": "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 }, { "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": "pedromiguel_martinez_HULAFE", "additionDate": "2025-04-15T17:42:40.968987Z", "lastUpdate": "2026-02-16T17:32:26.457200Z", "editPermission": { "type": "group", "authors": [ "casopon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Segmentation evaluation", "description": "This tool calculates segmentation metrics (Dice score, intersection over union, Hausdorff distance, and normalised surface distance) between two sets of masks. It can be used to quickly calculate a number of metrics for segmentation models.", "homepage": "https://github.com/josegcpa/eucaim-metrics/tree/master", "biotoolsID": "segmentation_evaluation", "biotoolsCURIE": "biotools:segmentation_evaluation", "version": [ "v0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "This is the core command which can be used to calculate image segmentation metrics. For more options please run `uv run eval_segmentation --help`", "cmd": "uv run eval_segmentation \\\n --pred test_data/predicted/ \\\n --gt test_data/groundtruth/ \\\n --output test.json \\\n --n_classes 2 \\\n --verbose \\\n --params '{\"normalised_surface_distance\": {\"max_distance\": 100.0}}'" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_3444", "term": "MRI" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/josegcpa/eucaim-metrics/tree/master", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/josegcpa/eucaim-metrics/tree/master", "type": [ "Quick start guide", "API documentation" ], "note": null } ], "publication": [], "credit": [ { "name": "José Guilherme de Almeida", "email": "jose.almeida@research.fchampalimaud.org", "url": null, "orcidid": "https://orcid.org/0000-0002-1887-0157", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer" ], "note": null }, { "name": "Nickolas 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": "2026-02-12T14:54:22.759092Z", "lastUpdate": "2026-02-12T15:01:23.363666Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "decompTumor2Sig", "description": "R package for identification of mutational signatures active in individual tumors. It decomposes an individual tumor genome into a given set of Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution of the corresponding mutational processes to the somatic mutations identified in the tumor.", "homepage": "http://rmpiro.net/decompTumor2Sig/", "biotoolsID": "decompTumor2Sig", "biotoolsCURIE": "biotools:decompTumor2Sig", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0239", "term": "Sequence motif recognition" }, { "uri": "http://edamontology.org/operation_1812", "term": "Parsing" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/rmpiro/decompTumor2Sig/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/rmpiro/decompTumor2Sig", "type": [ "Repository" ], "note": null }, { "url": "https://bioconductor.org/packages/release/bioc/html/decompTumor2Sig.html", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://rmpiro.net/index.html#downloads", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/rmpiro/decompTumor2Sig/blob/master/decompTumor2Sig-manual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-019-2688-6", "pmid": "30999866", "pmcid": "PMC6472187", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "DecompTumor2Sig: Identification of mutational signatures active in individual tumors", "abstract": "© 2019 The Author(s).Background: The somatic mutations found in a tumor have in most cases been caused by multiple mutational processes such as those related to extrinsic carcinogens like cigarette smoke, and those related to intrinsic processes like age-related spontaneous deamination of 5-methylcytosine. The effect of such mutational processes can be modeled by mutational signatures, of which two different conceptualizations exist: the model introduced by Alexandrov et al., Nature 500:415-421, 2013, and the model introduced by Shiraishi et al., PLoS Genetics 11(12):e1005657, 2015. The initial identification and definition of mutational signatures requires large sets of tumor samples. Results: Here, we present decompTumor2Sig, an easy to use R package that can decompose an individual tumor genome into a given set of Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution of the corresponding mutational processes to the somatic mutations identified in the tumor. Until now, such tools were available only for Alexandrov signatures. We demonstrate the correctness and usefulness of our approach with three test cases, using somatic mutations from 21 breast cancer genomes, from 435 tumor genomes of ten different tumor entities, and from simulated tumor genomes, respectively. Conclusions: The decompTumor2Sig package is freely available and has been accepted for inclusion in Bioconductor.", "date": "2019-04-18T00:00:00Z", "citationCount": 8, "authors": [ { "name": "Kruger S." }, { "name": "Piro R.M." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Prof. Dr. Rosario M. Piro", "email": "r.piro@fu-berlin.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null } ], "owner": "rosario7", "additionDate": "2019-06-20T14:18:28Z", "lastUpdate": "2026-02-12T13:42:21.288130Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-POLIMI" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Sarek", "description": "Sarek is part of nf-core and has changed to the nf-core-sarek id.", "homepage": "https://nf-co.re/sarek", "biotoolsID": "sarek", "biotoolsCURIE": "biotools:sarek", "version": [ "2.0.0", "2.1.0", "2.2.0", "2.2.1", "2.2.2", "2.3", "2.3.FIX1" ], "otherID": [], "relation": [ { "biotoolsID": "caw", "type": "isNewVersionOf" }, { "biotoolsID": "nf-core-sarek", "type": "hasNewVersion" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3731", "term": "Sample comparison" }, { "uri": "http://edamontology.org/operation_0361", "term": "Sequence annotation" }, { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3497", "term": "DNA sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3673", "term": "Whole genome sequencing" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Linux" ], "language": [ "Groovy" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/nf-core/sarek", "type": [ "Repository" ], "note": "Github Repository" }, { "url": "https://nfcore.slack.com/channels/sarek", "type": [ "Social media" ], "note": "Slack channel" } ], "download": [], "documentation": [ { "url": "https://nf-co.re/sarek", "type": [ "General" ], "note": null }, { "url": "https://nf-co.re/sarek/usage", "type": [ "User manual" ], "note": null }, { "url": "https://nf-co.re/usage/installation", "type": [ "Installation instructions" ], "note": null }, { "url": "https://github.com/nf-core/sarek/blob/master/LICENSE", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1101/316976", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": "This is the publication about the nf-core framework", "metadata": null }, { "doi": "10.12688/f1000research.16665.2", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": "This is the publication about the nf-core framework", "metadata": null }, { "doi": "10.1038/s41587-020-0439-x", "pmid": "32055031", "pmcid": null, "type": [ "Other" ], "version": null, "note": "This is the publication about the nf-core framework", "metadata": { "title": "The nf-core framework for community-curated bioinformatics pipelines", "abstract": "", "date": "2020-03-01T00:00:00Z", "citationCount": 935, "authors": [ { "name": "Ewels P.A." }, { "name": "Peltzer A." }, { "name": "Fillinger S." }, { "name": "Patel H." }, { "name": "Alneberg J." }, { "name": "Wilm A." }, { "name": "Garcia M.U." }, { "name": "Di Tommaso P." }, { "name": "Nahnsen S." } ], "journal": "Nature Biotechnology" } } ], "credit": [ { "name": "Maxime U. Garcia", "email": "maxime.garcia@scilifelab.se", "url": "https://maxulysse.github.io/", "orcidid": "https://orcid.org/0000-0003-2827-9261", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Szilvester Juhos", "email": "szilveszter.juhos@scilifelab.se", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Science for Life Laboratory - SciLifeLab", "email": null, "url": "https://www.scilifelab.se/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "National Genomics Infrastructure - NGI", "email": null, "url": "https://ngisweden.scilifelab.se/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "National Bioinformatics Infrastructure Sweden - NBIS", "email": null, "url": "https://nbis.se/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "Barntumörbanken", "email": null, "url": "https://ki.se/forskning/barntumorbanken", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null } ], "owner": "MaxUlysse", "additionDate": "2017-05-24T12:15:33Z", "lastUpdate": "2026-02-04T22:38:39.196636Z", "editPermission": { "type": "group", "authors": [ "malinlarsson", "szilva", "fhanssen", "ewels", "JoseEspinosa", "gelpi@ub.edu" ] }, "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": "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": "Image duplication check", "description": "A CLI tool for detecting duplicate DICOM images by analyzing pixel data, generating content-based hashes, and comparing them to identify identical images, even when metadata, file format, or size differs", "homepage": "https://docs.google.com/presentation/d/1guNJkm0E5YSsbIVKaaEevFnNGG4WR_m6XGsL695e3_A/edit?slide=id.g370e96e3b29_0_111#slide=id.g370e96e3b29_0_111", "biotoolsID": "image_duplicate_check_tool", "biotoolsCURIE": "biotools:image_duplicate_check_tool", "version": [ "v1.0.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3384", "term": "Medical imaging" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "JavaScript" ], "license": "MIT", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/helghast79/eucaim-image-duplication-check-tool", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/helghast79/eucaim-image-duplication-check-tool/releases/tag/v1.0.0", "type": "Downloads page", "note": "scroll to bottom of github release page to find the executable download for each OS", "version": "v1.0.0" } ], "documentation": [ { "url": "https://github.com/helghast79/eucaim-image-duplication-check-tool/blob/main/README.md", "type": [ "General", "Command-line options", "Installation instructions", "User manual", "Release notes" ], "note": null } ], "publication": [], "credit": [ { "name": "Miguel Chambel", "email": "miguel.chambel@research.fchampalimaud.org", "url": null, "orcidid": "https://orcid.org/0000-0002-6099-4110", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Contributor", "Documentor" ], "note": null }, { "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": [ "Maintainer", "Support" ], "note": null }, { "name": "Nickolas 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": "helghast", "additionDate": "2025-10-31T09:19:51.388544Z", "lastUpdate": "2026-02-03T15:36:48.615645Z", "editPermission": { "type": "group", "authors": [ "josegcpa" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Cluster based harmonization (EUCAIM-SW-044_T-01-03-006)", "description": "The tool is designed to perform radiomics harmonization on large and heterogeneous datasets, where the risk of over-harmonization is present. Instead of directly applying harmonization based on predefined batch labels, the tool first identifies groups of batches that share similar characteristics through clustering of the radiomics data. It then performs harmonization using these cluster-derived labels. The tool allows the harmonization of radiomics variables using two methods: (1) original ComBat (Rabinovic, 2007) method, where each original batch group is considered for the harmonization process and (2) cluster-based ComBat method, where batch groups with similar radiomics characteristics form clusters and the latter are being considered for the harmonization process.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/cluster_based_harmonization/artifacts-tab", "biotoolsID": "cluster_based_harmonization", "biotoolsCURIE": "biotools:cluster_based_harmonization", "version": [ "1.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3432", "term": "Clustering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3835", "term": "TIDE TXT" } ] } ], "note": null, "cmd": "docker run --rm --cpus CPUS -v input_path:/input -v output_path:/output -v config_path:/config harbor.eucaim.cancerimage.eu/processing-tools/cluster_based_harmonization:1.1.0 --config /config/config.json" }, { "operation": [ { "uri": "http://edamontology.org/operation_3432", "term": "Clustering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] }, { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3835", "term": "TIDE TXT" } ] } ], "note": null, "cmd": "docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processing-tools/cluster_based_harmonization:1.1.0 --file_path /input/data.xlsx --identifier patient_id --start_col original_shape_Elongation --end_col lbp-3D-k_ngtdm_Strength --batch_col software_versions --output_dir /output/results --min_clusters 2 --max_clusters 100 --results full --approach soft --small_groups merge" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0219", "term": "Data curation and archival" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "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/cluster_based_harmonization/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/Kz3jfQYQZjezpxK", "type": [ "User manual" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/5bMA2jsZTfS8eoZ", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=0GJqNJv-Qf8&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=31", "type": [ "Training material" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/LkczHCMZH5nd8QR", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Aikaterini Vraka", "email": "aikaterini_vraka@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0001-5984-904X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martínez-Gironés", "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", "Support" ], "note": null } ], "owner": "casopon", "additionDate": "2025-05-29T10:41:57.535794Z", "lastUpdate": "2026-02-03T12:10:11.102129Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "2D Digital Mammography Harmonization (EUCAIM-SW-046_T-01-03-008)", "description": "This preprocessing tool is design for 2D digital mammograms in DICOM format. It standardizes and harmonizes images through a configurable pipeline that includes spatial reorientation, pseudo-3D stacking, isotropic resampling, intensity normalization, optional denoising, contrast enhancement, and mask processing (if available).", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/2d_digital_mammography_harmonization/artifacts-tab", "biotoolsID": "2d_digital_mammography_harmonization", "biotoolsCURIE": "biotools:2d_digital_mammography_harmonization", "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/2d_digital_mammography_harmonization:1.1.0 /app/entrypoint.sh --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": "Command Arguments", "cmd": "docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processing-tools/2d_digital_mammography_harmonization:1.1.0 --input_directory dataset_id --output_directory gaussian_output --num_workers 4 --series_number 2301101 --series_description_suffix _harmonized --zscore_enabled true --zscore_p_low 1.0 --zscore_p_high 99.0 --denoise_method gaussian --gaussian_ksize 3 --gaussian_sigma 0.8 --clahe_enabled true --clahe_clip_limit 0.01" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0219", "term": "Data curation and archival" }, { "uri": "http://edamontology.org/topic_3316", "term": "Computer science" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "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/2d_digital_mammography_harmonization/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/CC3yJTjPz9N7Ggg", "type": [ "User manual" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/rdHWqMkNf7frQRY", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=IrZhMp2lB7g&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=13", "type": [ "Training material" ], "note": null } ], "publication": [], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Manuel Marfil-Trujillo", "email": "manuel_marfil@iislafe.es", "url": null, "orcidid": null, "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", "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 } ], "owner": "pedromiguel_martinez_HULAFE", "additionDate": "2025-06-06T10:00:26.469620Z", "lastUpdate": "2026-02-03T12:05:59.818541Z", "editPermission": { "type": "group", "authors": [ "casopon" ] }, "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", "Mac", "Linux" ], "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.eucaim.cancerimage.eu/s/rpm56rD5FfXAHyb", "type": [ "User manual" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/8r3CzyQXrd7ERFp", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=gudDCiuJIf8&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=11", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1186/s40537-025-01086-w", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "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": "2026-02-03T12:02:23.334589Z", "editPermission": { "type": "group", "authors": [ "casopon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Time Coherence Tool (EUCAIM-SW-001_T-01-01-001)", "description": "Tool that aims to validate visually the chronological order and logical consistency of dates associated with a patient's medical history. It generates a timeline visualization for each patient from an Excel file and highlights rule violations.\n \nStatus : Containerized", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/time_coherence_tool/artifacts-tab", "biotoolsID": "time_coherence_tool", "biotoolsCURIE": "biotools:time_coherence_tool", "version": [ "1.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Data analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": null, "cmd": "docker run -it --rm --name my-container -v \"<input_path>:/input\" -v \"<output_path>:/output\" harbor.eucaim.cancerimage.eu/processing-tools/time_coherence_tool:2.1.0 --config-string \"{'data_file': 'my_data.xlsx', 'generate_pdf': 'true'}\"" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_3316", "term": "Computer science" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "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/time_coherence_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/M23wDa4RWXenzxX", "type": [ "User manual" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/9QbdWjnLBeMYSWR", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=j4J_UPQqYR4&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=10", "type": [ "Training material" ], "note": null } ], "publication": [], "credit": [ { "name": "GIBI230 - HULAFE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "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": "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": [ "Developer", "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 } ], "owner": "casopon", "additionDate": "2025-11-21T13:49:36.578343Z", "lastUpdate": "2026-02-03T12:00:24.202390Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CT-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-022_T-01-02-005)", "description": "The tool performs by deep learning an automatic segmentation of the possible neuroblastoma tumours on Contrast Enhanced CT images (CE-CTs). 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. It takes DICOM images as input and generates tumoral masks in DICOM SEG or NIFTI formats.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ct-based_neuroblastoma_tumour_detection_and_segmentation/artifacts-tab", "biotoolsID": "ct-based_neuroblastoma_tumour_detection_and_segmentation", "biotoolsCURIE": "biotools:ct-based_neuroblastoma_tumour_detection_and_segmentation", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "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" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n\t-v /path/to/input:/input \\\n\t-v /path/to/output:/output \\\n\tharbor.eucaim.cancerimage.eu/processing-tools/ct-based_neuroblastoma_tumour_detection_and_segmentation:2.0.0 \\\n\t--series_csv /output/config/series_to_segment.csv \\\n\t--output_dir /output" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "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/ct-based_neuroblastoma_tumour_detection_and_segmentation/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/GxJrJPrYBnzecqT", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=JQ0dtAE_6uc&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=37", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.3390/app11083508", "pmid": null, "pmcid": null, "type": [ "Usage" ], "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": "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", "Support" ], "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": [ "Support" ], "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": "2025-05-29T10:38:08.771699Z", "lastUpdate": "2026-02-03T11:47:41.029073Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MR-based glioblastoma tumour detection and segmentation (EUCAIM-SW-021_T-01-02-004)", "description": "The tool performs an automatic segmentation of the possible glioblastoma tumours on MRI images and its subregions: necrosis (Intratumoral necrotic core), edema (Peritumoral vasogenic edema), enhancing (Contrast-enhancing tumor region), total (Total tumor including edema and necrosis by a single model) and total-fused (Total tumor fusioning of necrosis+edema+enhancing). It applies preprocessing steps as skull stripping, intra-patient registration, z-score normalization, patching, among others. It takes DICOM images as input and generates tumoral masks in DICOM SEG or NIFTI formats.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/artifacts-tab", "biotoolsID": "mr-based_glioblastoma_tumour_detection_and_segmentation", "biotoolsCURIE": "biotools:mr-based_glioblastoma_tumour_detection_and_segmentation", "version": [ "2.1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "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" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/input:/input \\\n -v /path/to/output:/output \\\n harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest \\\n --series-selector /input/config/series.csv \\\n --target total \\\n --emit-config true" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "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" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/input:/input \\\n -v /path/to/output:/output \\\n harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest \\\n --series-list '[{\"dataset_id\":\"DS001\",\"patient_id\":\"PAT001\",\"study_id\":\"ST001\",\"series_path\":\"/input/DICOM/DS001/PAT001/ST001/T1_POST\"}]' \\\n --target total-fused \\\n --emit-config true" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "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/mr-based_glioblastoma_tumour_detection_and_segmentation/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://pubmed.ncbi.nlm.nih.gov/38849632/", "type": [ "General" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/otrYTickHjDxnkP", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=8_OJPTQUKAw&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=22", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1007/s11548-024-03205-z", "pmid": null, "pmcid": null, "type": [ "Primary" ], "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": "Maria Beser-Robles", "email": "maria_beser@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-0072-5525", "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", "Developer", "Support" ], "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": [ "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": "2025-05-29T12:09:16.704255Z", "lastUpdate": "2026-02-03T11:47:01.186875Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MR-based DIPG tumour detection and segmentation (EUCAIM-SW-020_T-01-02-003)", "description": "The tool performs an automatic segmentation of the possible DIPG tumours on MR images. 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. The tool includes a complete workflow from DICOM images to DICOM seg tumoral masks.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_tumour_detection_and_segmentation/artifacts-tab", "biotoolsID": "mr-based_dipg_tumour_detection_and_segmentation", "biotoolsCURIE": "biotools:mr-based_dipg_tumour_detection_and_segmentation", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "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" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/input:/input \\\n -v /path/to/output:/output \\\nharbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest \\\n --series-selector /input/config/series.csv" }, { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3549", "term": "nii" }, { "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_3549", "term": "nii" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "note": null, "cmd": "docker run --rm --gpus all \\\n -v /path/to/input:/input -v /path/to/output:/output harbor.eucaim.cancerimage.eu/processing-tools/mr-based_dipg_tumour_detection_and_segmentation:latest \\\n --json-args '{\"dataset_id\":\"DS1\",\"patient_id\":\"P1\",\"study_id\":\"S1\",\"sequences\":{\"T1w\":\"/input/DICOM/DS1/P1/S1/T1\",\"FLAIR\":\"/input/DICOM/DS1/P1/S1/FLAIR\"}}'" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "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/mr-based_dipg_tumour_detection_and_segmentation/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://link.springer.com/article/10.1007/s10278-025-01557-9", "type": [ "General" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/5CL2H8tyMDzFHex", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=f3DPS56z6oI&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=36", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1007/s10278-025-01557-9", "pmid": null, "pmcid": null, "type": [ "Primary" ], "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", "Developer", "Documentor", "Support" ], "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": [ "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": "2025-05-29T09:19:51.404419Z", "lastUpdate": "2026-02-03T11:45:32.223088Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MR-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-019_T-01-02-002)", "description": "This tool is specifically designed and validated for automated detection and segmentation of neuroblastic tumours in T2-weighted magnetic resonance images (T2-MR) using deep learning. It processes DICOM or NIfTI input data and outputs in NIFTI or DICOM SEG.\n\nTRAINING & VALIDATION COHORTS:\n\nInitial Development (Veiga-Canuto 2022):\n-Training: 106 patients, 5-fold CV (median DSC 0.965 ± 0.018).\n-Internal validation: 26 patients (median DSC 0.918 ± 0.067).\n-Sources: La Fe (Spain), SIOPEN HR-NBL1/LINES, St. Anna (Austria), Pisa (Italy).\n-Mean age: 37.6 ± 39.3 months.\n-Median tumor volume: 116,518 mm³.\n\nExternal Validation (Veiga-Canuto 2023):\n-300 patients, 535 independent T2 MRI scans (486 at diagnosis, 49 post-chemotherapy).\n-Performance: median DSC 0.997 (0.944–1.000), 94% successful detection.\n-Sources: 12 European countries (HR-NBL1/SIOPEN 119, LINES/SIOPEN 107, German Registry 62, others 12).\n-Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105), Canon (3).", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/artifacts-tab", "biotoolsID": "mr-based_neuroblastoma_tumour_detection_and_segmentation", "biotoolsCURIE": "biotools:mr-based_neuroblastoma_tumour_detection_and_segmentation", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "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" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "note": null, "cmd": "docker run --rm \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n --gpus all \\\n harbor.eucaim.cancerimage.eu/processing-tools/mr_based_neuroblastoma_tumour_detection_and_segmentation:2.0.0 \\\n --mode dicom-seg \\\n --series-selector /output/config/series_to_segment.csv \\\n --seg-series-number 2302001 \\\n --seg-algorithm-name \"nnUNet_Neuroblastoma_Primage_training\" \\\n --seg-coordinating-center \"EUCAIM Consortium\" \\\n --keep-nifti false" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "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/mr_based_neuroblastoma_tumour_detection_and_segmentation/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://www.mdpi.com/2072-6694/14/15/3648", "type": [ "General" ], "note": null }, { "url": "https://drive.eucaim.cancerimage.eu/s/44BxMSNpxwgsZiE", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.youtube.com/watch?v=c7XOEGRA9aQ&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=12", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.3390/cancers14153648", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.3390/cancers15051622", "pmid": null, "pmcid": null, "type": [ "Primary" ], "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": "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": [ "Developer" ], "note": null }, { "name": "Diana Veiga Canuto", "email": "dianaveigac@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0002-6048-2940", "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", "Support", "Documentor", "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": [ "Support", "Documentor" ], "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": "2025-05-29T09:08:44.174795Z", "lastUpdate": "2026-02-03T11:40:55.741817Z", "editPermission": { "type": "group", "authors": [ "pedromiguel_martinez_HULAFE" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Cloud-based Workflow Manager (CloWM)", "description": "Data analysis in the life sciences often suffers from reproducibility, standardization and accessibility issues and these problems become even more severe with the escalating volume and complexity of data. While best-practice data analysis workflows try to tackle these challenges, many existing workflows still grapple with scalability issues, limited portability due to tight coupling with the execution environment and accessibility constraints arising from the absence of user-friendly interfaces. To overcome these issues, we created CloWM, a comprehensive cloud-based workflow management platform that allows the generic transformation of command-line driven workflows into user-friendly web-based services. CloWM offers the seamless integration of (1) scientific workflows written in the Nextflow DSL, (2) robust data storage, (3) a highly scalable compute layer for data-intensive analysis tasks and (4) a user-friendly interface.", "homepage": "https://clowm.bi.denbi.de", "biotoolsID": "clowm", "biotoolsCURIE": "biotools:clowm", "version": [], "otherID": [], "relation": [ { "biotoolsID": "sans", "type": "includes" } ], "function": [], "toolType": [ "Web service", "Bioinformatics portal", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [], "language": [ "Python", "JavaScript" ], "license": "Apache-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://gitlab.ub.uni-bielefeld.de/cmg/clowm", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://clowm.bi.denbi.de/api/v1/openapi.json", "type": "API specification", "note": null, "version": null }, { "url": "https://gitlab.ub.uni-bielefeld.de/cmg/clowm", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://clowm.bi.denbi.de/api/v1/docs", "type": [ "API documentation" ], "note": null }, { "url": "https://clowm.bi.denbi.de/terms", "type": [ "Terms of use" ], "note": null }, { "url": "https://wiki.clowm.de", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.5281/zenodo.14039069", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Göbel", "email": "dgoebel@techfak.uni-bielefeld.de", "url": "https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=223066601", "orcidid": "https://orcid.org/0009-0009-9985-3823", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer", "Developer", "Primary contact" ], "note": null }, { "name": "Michael Beckstette", "email": "mbeckste@cebitec.uni-bielefeld.de", "url": null, "orcidid": "https://orcid.org/0000-0002-3707-1692", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Documentor" ], "note": null }, { "name": "Xaver Stiensmeier", "email": "xaver.stiensmeier@uni-bielefeld.de", "url": "https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=386908541", "orcidid": "https://orcid.org/0009-0005-3274-122X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Bielefeld University", "email": null, "url": "https://www.uni-bielefeld.de", "orcidid": null, "gridid": null, "rorid": "02hpadn98", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Genome Informatics", "email": null, "url": "https://gi.cebitec.uni-bielefeld.de", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "NFDI4Microbiota", "email": null, "url": "https://nfdi4microbiota.de", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null } ], "owner": "dgoebel", "additionDate": "2025-04-09T13:19:17.715967Z", "lastUpdate": "2026-01-30T13:23:10.333194Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ITSoneDB", "description": "A comprehensive collection of the fungal ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences aimed at supporting metagenomic surveys of fungal environmental communities.", "homepage": "https://itsonedb.cloud.ba.infn.it/", "biotoolsID": "itsonedb", "biotoolsCURIE": "biotools:itsonedb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data" ], "elixirNode": [ "Italy" ], "elixirCommunity": [ "Marine Metagenomics" ], "link": [], "download": [], "documentation": [ { "url": "https://itsonedb.cloud.ba.infn.it/", "type": [ "General" ], "note": "HELP button in the homepage" } ], "publication": [ { "doi": "10.1093/bib/bbs036", "pmid": "22786784", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "C.N.R. - IBIOM", "email": null, "url": "http://www.ibiom.cnr.it/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "C.N.R. - ITB, Bari", "email": null, "url": "http://www.ba.itb.cnr.it", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "ELIXIR-ITA-CNR", "email": null, "url": "http://elixir-italy.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Provider" ], "note": null }, { "name": "Graziano Pesole", "email": "graziano.pesole@uniba.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-CNR", "additionDate": "2015-02-05T13:59:31Z", "lastUpdate": "2026-01-30T10:26:56.768452Z", "editPermission": { "type": "group", "authors": [ "flavioli" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Bakta", "description": "Rapid & standardized annotation of bacterial genomes, MAGs & plasmids", "homepage": "https://github.com/oschwengers/bakta", "biotoolsID": "bakta", "biotoolsCURIE": "biotools:bakta", "version": [ "v1.12.0" ], "otherID": [], "relation": [ { "biotoolsID": "diamond", "type": "uses" }, { "biotoolsID": "hmmer3", "type": "uses" }, { "biotoolsID": "infernal", "type": "uses" }, { "biotoolsID": "trnascan-se", "type": "uses" }, { "biotoolsID": "blast", "type": "uses" }, { "biotoolsID": "aragorn", "type": "uses" }, { "biotoolsID": "pilercr", "type": "uses" }, { "biotoolsID": "deepsig", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0925", "term": "Sequence assembly" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2914", "term": "Sequence features metadata" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [ { "uri": "http://edamontology.org/format_1975", "term": "GFF3" } ] }, { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1364", "term": "Hidden Markov model" }, "format": [ { "uri": "http://edamontology.org/format_3329", "term": "HMMER3" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" }, { "uri": "http://edamontology.org/format_1975", "term": "GFF3" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1927", "term": "EMBL format" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2887", "term": "Nucleic acid sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": "bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fasta" } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/oschwengers/bakta", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://bioconda.github.io/recipes/bakta/README.html", "type": [ "Other" ], "note": null }, { "url": "https://bakta.computational.bio", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://zenodo.org/records/14916843", "type": "Other", "note": "Mandatory annotation database", "version": "v6.0" } ], "documentation": [ { "url": "https://github.com/oschwengers/bakta/blob/main/README.md", "type": [ "General" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.md", "type": [ "Contributions policy" ], "note": null }, { "url": "https://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.md", "type": [ "Code of conduct" ], "note": null }, { "url": "https://bakta.readthedocs.io/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1099/mgen.0.000685", "pmid": "34739369", "pmcid": "PMC8743544", "type": [ "Primary" ], "version": "1.1", "note": null, "metadata": null }, { "doi": "10.1093/nar/gkaf335", "pmid": "40271661", "pmcid": "PMC12230652", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Oliver Schwengers", "email": "oliver.schwengers@cb.jlug.de", "url": "https://github.com/oschwengers", "orcidid": "https://orcid.org/0000-0003-4216-2721", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Justus Liebig University Giessen", "email": null, "url": "https://www.uni-giessen.de", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "oschwengers", "additionDate": "2021-05-08T17:25:21Z", "lastUpdate": "2026-01-29T12:11:19.042627Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ", "bebatut" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Goslin", "description": "Goslin is the Grammar of succinct lipid nomenclature project. It defines multiple grammers compatible with ANTLRv4 for different sources of shorthand lipid nomenclature. This allows to generate parsers based on the defined grammars, which provide immediate feedback whether a processed lipid shorthand notation string is compliant with a particular grammar, or not.", "homepage": "https://github.com/lifs-tools/goslin", "biotoolsID": "goslin", "biotoolsCURIE": "biotools:goslin", "version": [ "1.1.2", "2.0.0", "2.1.0", "2.2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_1812", "term": "Data parsing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0984", "term": "Molecule name" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0984", "term": "Molecule name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0153", "term": "Lipidomics" }, { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "LIFS", "BioInfra.Prot" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "Metabolomics" ], "link": [ { "url": "https://github.com/lifs-tools/goslin", "type": [ "Repository" ], "note": null }, { "url": "https://lifs-tools.org/support", "type": [ "Helpdesk" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/lifs-tools/goslin/blob/master/docs/README.adoc", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1101/2020.04.17.046656", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": "1.1.2", "note": "Preprint publication.", "metadata": null }, { "doi": "10.1021/acs.analchem.0c01690", "pmid": "32589019", "pmcid": "PMC7467413", "type": [ "Primary" ], "version": "1.1.2", "note": "Final, accepted version.", "metadata": null }, { "doi": "10.1021/acs.analchem.1c05430", "pmid": "35404045", "pmcid": "PMC9047418", "type": [ "Primary" ], "version": "2.0.0", "note": null, "metadata": null } ], "credit": [ { "name": "Nils Hoffmann", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6540-6875", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer", "Developer" ], "note": null }, { "name": "Dominik Kopczynski", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-5885-4568", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer", "Developer" ], "note": null }, { "name": "Bing Peng", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-5006-7041", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Robert Ahrends", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0232-3375", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "nils.hoffmann", "additionDate": "2020-06-23T10:03:06Z", "lastUpdate": "2026-01-28T08:20:52.068084Z", "editPermission": { "type": "group", "authors": [ "de.NBI_Service_Team" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioMaS (Bioinformatic analysis of Metagenomic amplicons)", "description": "BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills.", "homepage": "http://itsonewb.cloud.ba.infn.it/galaxy/tool_runner?tool_id=biomas2_wrapper", "biotoolsID": "biomas_bioinformatic_analysis_of_metagenomic_amplicons", "biotoolsCURIE": "biotools:biomas_bioinformatic_analysis_of_metagenomic_amplicons", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0232", "term": "Sequence merging" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0496", "term": "Global alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3391", "term": "Omics" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "Bash", "Python" ], "license": "Not licensed", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Italy" ], "elixirCommunity": [ "Marine Metagenomics" ], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s12859-015-0595-z", "pmid": "26130132", "pmcid": "PMC4486701", "type": [ "Method" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Bruno Fosso", "email": "b.fosso@ibiom.cnr.it", "url": null, "orcidid": "https://orcid.org/0000-0003-2324-086X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Researcher at CNR-IBIOM" }, { "name": "Graziano Pesole", "email": "graziano.pesole@uniba.it", "url": null, "orcidid": "https://orcid.org/0000-0003-3663-0859", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "Full Professor of Molecular Biology at University of Bari" }, { "name": "Monica Santamaria", "email": "m.santamaria@ibiom.cnr.it", "url": null, "orcidid": "https://orcid.org/0000-0003-1488-6052", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "Researcher at CNR-IBIOM" } ], "owner": "bfosso", "additionDate": "2021-03-31T15:26:55Z", "lastUpdate": "2026-01-27T17:22:28.785300Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "madbot", "description": "madbot, developed by IFB, simplifies scientific data management and sharing. As research data grows, ensuring accessibility and reusability becomes complex.\nUnlike other tools, madbot automates data organization and description, saving time and ensuring consistency. It connects to repositories like Zenodo and ENA, enabling seamless submissions. Its user-friendly interface requires no technical skills, while its backend ensures data accuracy and high-quality metadata.\nWith an extensible architecture, madbot integrates with diverse storage systems and standards, adapting to researchers' needs. By streamlining data sharing, it promotes open science and global collaboration.", "homepage": "https://madbot.france-bioinformatique.fr", "biotoolsID": "madbot", "biotoolsCURIE": "biotools:madbot", "version": [ "1.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Data deposition" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3778", "term": "Text annotation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" }, { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data curation and archival" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_3345", "term": "Data identity and mapping" }, { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python", "TypeScript", "Other" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://gitlab.com/ifb-elixirfr/madbot", "type": [ "Repository" ], "note": null }, { "url": "https://madbot.france-bioinformatique.fr/", "type": [ "Service" ], "note": null }, { "url": "https://tree.taiga.io/project/julozi-1-madbot/backlog", "type": [ "Technical monitoring" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "IFB - Institut Français de Bioinformatique", "email": null, "url": "https://www.ifb-elixir.fr/", "orcidid": null, "gridid": null, "rorid": "045f7pv37", "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "Julien Seiler", "email": "julien.seiler@france-bioinformatique.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-4549-5188", "gridid": null, "rorid": "045f7pv37", "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Thomas Denecker", "email": "thomas.denecker@france-bioinformatique.fr", "url": null, "orcidid": "https://orcid.org/0000-0003-1421-7641", "gridid": null, "rorid": "045f7pv37", "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Imane Messak", "email": "imane.messak@france-bioinformatique.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-1654-6652", "gridid": null, "rorid": "045f7pv37", "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Developer" ], "note": null }, { "name": "Baptiste Rousseau", "email": "baptiste.rousseau@france-bioinformatique.fr", "url": null, "orcidid": "https://orcid.org/0009-0002-1723-2732", "gridid": null, "rorid": "045f7pv37", "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Elora Vigo", "email": "elora.vigo@france-bioinformatique.fr", "url": null, "orcidid": "https://orcid.org/0009-0001-5597-2427", "gridid": null, "rorid": "045f7pv37", "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Laurent BOURI", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-2297-1559", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Matéo HIRIART", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Nadia GOUÉ", "email": "nadia.goue@uca.fr", "url": null, "orcidid": "https://orcid.org/0000-0003-2750-1473", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "thomas", "additionDate": "2026-01-26T13:51:57.135345Z", "lastUpdate": "2026-01-27T09:21:23.918487Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Atomic Charge Calculator II", "description": "Atomic Charge Calculator II (ACC II) is a web application for fast calculation of partial atomic charges.", "homepage": "https://acc2.ncbr.muni.cz", "biotoolsID": "atomic-charge-calculator-ii", "biotoolsCURIE": "biotools:atomic-charge-calculator-ii", "version": [ "2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3438", "term": "Calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_3814", "term": "SDF" }, { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" } ] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" } ] } ], "output": [], "note": "Calculation of partial atomic charges", "cmd": null } ], "toolType": [ "Web API", "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" } ], "operatingSystem": [], "language": [ "JavaScript", "Python", "C++" ], "license": "MIT", "collectionID": [ "ELIXIR-CZ" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [ { "url": "https://github.com/krab1k/AtomicChargeCalculator", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/krab1k/ChargeFW2", "type": [ "Repository" ], "note": "Computational core" } ], "download": [], "documentation": [ { "url": "https://github.com/sb-ncbr/AtomicChargeCalculator/wiki", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkaa367", "pmid": "32402071", "pmcid": "PMC7319571", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Radka Svobodová", "email": "radka.svobodova@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-3840-8760", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Provider" ], "note": null }, { "name": "Tomáš Raček", "email": "tomas.racek@muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-0296-2452", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null } ], "owner": "ELIXIR-CZ", "additionDate": "2021-01-18T09:10:00Z", "lastUpdate": "2026-01-26T06:46:06.259892Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MicrobiomeR", "description": "MicrobiomeR is an R package for microbiome analysis that incorporates phyloseq, metacoder, taxa, and microbiome in order to standardize and simplify common microbiome workflows.", "homepage": "https://vallenderlab.github.io/MicrobiomeR/", "biotoolsID": "MicrobiomeR", "biotoolsCURIE": "biotools:MicrobiomeR", "version": [ "0.6.1" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Windows", "Linux" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/vallenderlab/MicrobiomeR/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://github.com/vallenderlab/MicrobiomeR", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/vallenderlab/MicrobiomeR/releases/download/v0.6.1/MicrobiomeR_0.6.1.tar.gz", "type": "Software package", "note": null, "version": "0.6.1" } ], "documentation": [ { "url": "https://microbiomer.vallenderlab.science/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.21105/joss.01299", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Robert Gilmore", "email": "rgilmore@umc.edu", "url": null, "orcidid": "http://orcid.org/0000-0001-8096-0180", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Shaurita D. Hutchins", "email": "shutchins2@umc.edu", "url": null, "orcidid": "http://orcid.org/0000-0002-7687-0059", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "sdhutchins", "additionDate": "2019-08-13T22:07:01Z", "lastUpdate": "2026-01-21T04:08:50.540139Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CTDquerier", "description": "Comparative Toxicogenomics Database data extraction, visualization and enrichment of environmental and toxicological studies.", "homepage": "https://github.com/isglobal-brge/CTDquerier", "biotoolsID": "ctdquerier", "biotoolsCURIE": "biotools:ctdquerier", "version": [], "otherID": [], "relation": [ { "biotoolsID": "rexposome", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2840", "term": "Toxicology" }, { "uri": "http://edamontology.org/topic_3077", "term": "Data acquisition" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "R" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://bioconductor.org/packages/CTDquerier", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://bioconductor.org/packages/release/bioc/src/contrib/CTDquerier_2.6.0.tar.gz", "type": "Software package", "note": null, "version": "2.6.0" } ], "documentation": [ { "url": "https://github.com/isglobal-brge/CTDquerier", "type": [ "General" ], "note": null }, { "url": "https://bioconductor.org/packages/release/bioc/html/CTDquerier.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bty326", "pmid": "29688259", "pmcid": "PMC6137994", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Carles Hernandez-Ferrer", "email": "carles.hernandez@isglobal.org", "url": null, "orcidid": "https://orcid.org/0000-0002-8029-7160", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Xavier Escribà Montagut", "email": "xavier.escriba@isglobal.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "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 } ], "owner": "d.gabrielaitis", "additionDate": "2018-06-01T15:37:38Z", "lastUpdate": "2026-01-20T14:55:22.826687Z", "editPermission": { "type": "group", "authors": [ "brgelab", "chernan3" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "summarized.science", "description": "summarized.science is an independent, web-based literature monitoring resource that provides monthly curated, topic-focused summaries of recent peer-reviewed scientific research. The platform helps researchers stay up to date with the large volume of publications in their field by offering structured overviews that link directly to primary literature. The summaries are designed to support literature discovery and orientation, not to replace the underlying research papers. The platform includes topic-specific pages covering areas such as bioinformatics and computational biology.", "homepage": "https://summarized.science/", "biotoolsID": "summarized.science", "biotoolsCURIE": "biotools:summarized.science", "version": [ "1.1" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_4019", "term": "Biosciences" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://summarized.science/#newsletter", "type": [ "Mailing list" ], "note": "GDPR complient newsletter" } ], "download": [], "documentation": [ { "url": "https://summarized.science/about", "type": [ "Other" ], "note": "About page for the project" }, { "url": "https://summarized.science/faq", "type": [ "FAQ" ], "note": "FAQ page for the project" } ], "publication": [], "credit": [ { "name": "Niek Maas", "email": "hello@summarized.science", "url": "https://summarized.science/contact", "orcidid": "https://orcid.org/0000-0002-8745-4405", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "sybren", "additionDate": "2026-01-15T17:20:26.339869Z", "lastUpdate": "2026-01-15T17:25:05.336276Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "muscadet", "description": "Multiomics single-cell copy number alterations detection: an R package for CNV profiling in cancer cells, using one to multiple single-cell modalities.", "homepage": "https://icagen.github.io/muscadet/", "biotoolsID": "muscadet", "biotoolsCURIE": "biotools:muscadet", "version": [], "otherID": [], "relation": [ { "biotoolsID": "seurat", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3964", "term": "Complex CNV detection" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3958", "term": "Copy number variation" } ], "operatingSystem": [ "Windows", "Mac", "Linux" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ICAGEN/muscadet", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://icagen.github.io/muscadet/articles/muscadet.html", "type": [ "Quick start guide" ], "note": null }, { "url": "https://icagen.github.io/muscadet/news/index.html", "type": [ "Release notes" ], "note": null } ], "publication": [], "credit": [ { "name": "Marie Denoulet", "email": "marie.denoulet@univ-nantes.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-9668-0439", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Nils Giordano", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-2549-6631", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Stéphane Minvielle", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-1389-312X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Céline Vallot", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-1601-2359", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Eric Letouzé", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6369-2839", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "BiRD bioinformatics facility", "email": "pf-bird@univ-nantes.fr", "url": "https://pf-bird.univ-nantes.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null } ], "owner": "marie3", "additionDate": "2026-01-12T16:01:46.296229Z", "lastUpdate": "2026-01-13T15:28:27.343905Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Humess", "description": "Humess is an analysis pipeline using Snakemake to automatically generate specific human metabolic models from 3'SRP RNA-seq dataset. It depends on a modified version of CarveMe which uses a top-down approach to build specific metabolic models from a universal model. Humess can also perform an optional analysis on the generated metabolic models using a sampling procedure.", "homepage": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/humess", "biotoolsID": "humess", "biotoolsCURIE": "biotools:humess", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3660", "term": "Metabolic network modelling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [] } ], "note": "Snakemake based pipeline", "cmd": "snakemake -pa --configfile config.json --cores 1" } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [], "language": [ "Bash", "R", "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/humess", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/humess", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/humess/-/wikis/home", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btaf448", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "HUMESS: integrating quantitative transcriptomic analysis and metabolic modeling to unveil condition-specific gene signatures", "abstract": "", "date": "2025-08-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Louis Paré", "email": "louis.pare@univ-nantes.fr", "url": "https://pf-bird.univ-nantes.fr/about_us/", "orcidid": "https://orcid.org/0009-0002-4772-8042", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Maintainer", "Developer" ], "note": null }, { "name": "BiRD bioinformatics facility", "email": "pf-bird@univ-nantes.fr", "url": "https://pf-bird.univ-nantes.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Support", "Provider" ], "note": null }, { "name": "Philippe Bordron", "email": "philippe.bordron@inrae.fr", "url": "https://miat.inrae.fr/member/bordronphilippe/", "orcidid": "https://orcid.org/0000-0003-1975-0920", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Developer" ], "note": null }, { "name": "Laurent David", "email": "laurent.david@univ-nantes.fr", "url": "https://www.univ-nantes.fr/laurent-david", "orcidid": "https://orcid.org/0000-0003-3594-0353", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Maxime Mahé", "email": "maxime.mahe@univ-nantes.fr", "url": "https://www.univ-nantes.fr/maxime-mahe", "orcidid": "https://orcid.org/0000-0003-2560-193X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Audrey Bihouée", "email": "audrey.bihouee@univ-nantes.fr", "url": "https://www.univ-nantes.fr/audrey-bihouee", "orcidid": "https://orcid.org/0000-0002-8689-2083", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Damien Eveillard", "email": "damien.eveillard@univ-nantes.fr", "url": "https://www.univ-nantes.fr/damien-eveillard", "orcidid": "https://orcid.org/0000-0002-8162-7360", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "louis-pare", "additionDate": "2026-01-06T14:04:52.944419Z", "lastUpdate": "2026-01-06T14:05:11.572162Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Winnow", "description": "A confidence rescoring and FDR estimation workflow for de novo peptide sequencing.", "homepage": "https://github.com/instadeepai/winnow", "biotoolsID": "winnow", "biotoolsCURIE": "biotools:winnow", "version": [ "1.0.3" ], "otherID": [], "relation": [ { "biotoolsID": "instanovo", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3644", "term": "de Novo sequencing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3651", "term": "MGF" } ] }, { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": "winnow predict --data-source instanovo --dataset-config-path test_config.yaml --method winnow --fdr-threshold 0.01 --confidence-column confidence --output-folder ./predictions" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "proteomics", "Proteomics" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/instadeepai/winnow", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/instadeepai/winnow/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/instadeepai/winnow/archive/refs/tags/v1.0.3.zip", "type": "Source code", "note": null, "version": "1.0.3" } ], "documentation": [ { "url": "https://instadeepai.github.io/winnow/api/datasets/", "type": [ "API documentation" ], "note": null }, { "url": "https://instadeepai.github.io/winnow/cli/", "type": [ "Command-line options" ], "note": null }, { "url": "https://instadeepai.github.io/winnow/contributing/", "type": [ "Contributions policy" ], "note": null }, { "url": "https://instadeepai.github.io/winnow/#bibtex-entry-and-citation-info", "type": [ "Citation instructions" ], "note": null }, { "url": "https://instadeepai.github.io/winnow/#installation", "type": [ "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.48550/arXiv.2509.24952", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "2", "note": null, "metadata": null } ], "credit": [ { "name": "Jemma Daniel", "email": "j.daniel@instadeep.com", "url": null, "orcidid": "https://orcid.org/0000-0002-1964-3976", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Documentor", "Maintainer" ], "note": null }, { "name": "Amandla Mabona", "email": null, "url": null, "orcidid": "https://orcid.org/0009-0009-7514-677X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Jeroen van Goey", "email": "j.vangoey@instadeep.com", "url": null, "orcidid": "https://orcid.org/0000-0003-4480-5567", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Maintainer" ], "note": null }, { "name": "Konstantinos Kalogeropoulos", "email": "konka@dtu.dk", "url": null, "orcidid": "https://orcid.org/0000-0003-3907-9281", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Contributor" ], "note": null } ], "owner": "Jemma", "additionDate": "2026-01-05T15:29:05.686915Z", "lastUpdate": "2026-01-06T07:50:06.065478Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "The Chemistry Development Kit", "description": "Open source Java library for bio- and cheminformatics.", "homepage": "http://github.com/cdk/cdk/", "biotoolsID": "cdk", "biotoolsCURIE": "biotools:cdk", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java" ], "license": "LGPL-2.1", "collectionID": [ "ELIXIR-NL" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://github.com/cdk/cdk/", "type": [ "Repository" ], "note": null }, { "url": "https://fosstodon.org/@cdk", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/cdk/cdk/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s13321-017-0220-4", "pmid": "29086040", "pmcid": "PMC5461230", "type": [], "version": null, "note": null, "metadata": { "title": "The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching", "abstract": "", "date": "2017-06-06T00:00:00Z", "citationCount": 381, "authors": [], "journal": "Journal of Cheminformatics" } }, { "doi": "10.1021/ci025584y", "pmid": "12653513", "pmcid": "PMC4901983", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics", "abstract": "", "date": "2003-01-01T00:00:00Z", "citationCount": 935, "authors": [], "journal": "Journal of Chemical Information and Computer Sciences" } }, { "doi": "10.2174/138161206777585274", "pmid": "16796559", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Recent developments of the Chemistry Development Kit (CDK) - An open-source Java library for chemo- and bioinformatics", "abstract": "", "date": "2006-06-01T00:00:00Z", "citationCount": 445, "authors": [], "journal": "Current Pharmaceutical Design" } } ], "credit": [ { "name": "Christoph Steinbeck", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Rajarshi Guha", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "John May", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Egon Willighagen", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "maastrichtuniversity.nl", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": null, "url": "https://sourceforge.net/p/cdk/mailman/?source=navbar", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "egonw", "additionDate": "2015-12-01T14:33:26Z", "lastUpdate": "2025-12-29T19:08:00.918429Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Spatial Proteomics", "description": "End-to-end spatial proteomics analysis workflow with QuPath integration. Our workflow consists of cell segmentation, batch correction, unsupervised clustering, validation of clusters on the image, and cell type clustering results visualization.", "homepage": "https://github.com/BioDepot/SpatialProteomics", "biotoolsID": "spatial_proteomics", "biotoolsCURIE": "biotools:spatial_proteomics", "version": [], "otherID": [ { "value": "RRID:SCR_027835", "type": "rrid", "version": null } ], "relation": [], "function": [], "toolType": [ "Workflow" ], "topic": [], "operatingSystem": [], "language": [ "Python", "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://youtu.be/vHjdCAZQhfE", "type": [ "Other" ], "note": "Demo video" } ], "download": [ { "url": "https://github.com/BioDepot/SpatialProteomics", "type": "Source code", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1101/2025.05.23.655879", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": "1", "note": null, "metadata": null } ], "credit": [ { "name": "Ling-Hong Hung", "email": "lhhung@uw.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-5209-2248", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Ka Yee Yeung", "email": "kayee@uw.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-1754-7577", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null }, { "name": "Bryce Fukuda", "email": "fukudab@uw.edu", "url": null, "orcidid": "https://orcid.org/0009-0003-7203-5261", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null } ], "owner": "kayee", "additionDate": "2025-12-23T00:16:25.679615Z", "lastUpdate": "2025-12-23T00:29:13.711774Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "D-GENIES", "description": "D-GENIES – for Dot plot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualization.", "homepage": "https://dgenies.toulouse.inrae.fr/", "biotoolsID": "d-genies", "biotoolsCURIE": "biotools:d-genies", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3182", "term": "Genome alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2161", "term": "Sequence similarity plot" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0490", "term": "Dot plot plotting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2161", "term": "Sequence similarity plot" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python", "Shell" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/genotoul-bioinfo/dgenies", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://dgenies.readthedocs.io/en/latest/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.7717/peerj.4958", "pmid": "29888139", "pmcid": "PMC5991294", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "D-GENIES: Dot plot large genomes in an interactive, efficient and simple way", "abstract": "", "date": "2018-01-01T00:00:00Z", "citationCount": 493, "authors": [], "journal": "PeerJ" } } ], "credit": [ { "name": "Floréal Cabanettes", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Christophe Klopp", "email": "christophe.klopp@inrae.fr", "url": null, "orcidid": "https://orcid.org/0000-0001-7126-5477", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Philippe Bordron", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-1975-0920", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Vincent Dominguez", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "GenoToul bioinformatics facility", "email": null, "url": "http://bioinfo.genotoul.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-07-29T10:31:55Z", "lastUpdate": "2025-12-18T10:02:18.098079Z", "editPermission": { "type": "group", "authors": [ "pbordron" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "omicRexposome", "description": "It systematizes the association evaluation between exposures and omic data, taking advantage of MultiDataSet for coordinated data management, rexposome for exposome data definition and limma for association testing. Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA).", "homepage": "http://bioconductor.org/packages/release/bioc/html/omicRexposome.html", "biotoolsID": "omicrexposome", "biotoolsCURIE": "biotools:omicrexposome", "version": [ "1.2.0" ], "otherID": [], "relation": [ { "biotoolsID": "rexposome", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3809", "term": "Differentially-methylated region identification" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2424", "term": "Comparison" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3659", "term": "Regression analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3295", "term": "Epigenetics" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0204", "term": "Gene regulation" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "MIT", "collectionID": [ "BioConductor", "Proteomics" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://bioconductor.org/packages/omicRexposome/", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://bioconductor.org/packages/release/bioc/src/contrib/omicRexposome_1.2.0.tar.gz", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/manuals/omicRexposome/man/omicRexposome.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btz526", "pmid": "31243429", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Comprehensive study of the exposome and omic data using rexposome Bioconductor Packages", "abstract": "", "date": "2019-12-15T00:00:00Z", "citationCount": 23, "authors": [], "journal": "Bioinformatics" } }, { "doi": "10.1038/s41467-022-34422-2", "pmid": "36411288", "pmcid": "PMC9678903", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Multi-omics signatures of the human early life exposome", "abstract": "", "date": "2022-12-01T00:00:00Z", "citationCount": 112, "authors": [], "journal": "Nature Communications" } } ], "credit": [ { "name": "Carles Hernandez-Ferrer", "email": "carles.hernandez@isglobal.org", "url": "http://www.carleshf.com", "orcidid": "https://orcid.org/0000-0002-8029-7160", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Xavier Escribà Montagut", "email": "xavier.escriba@isglobal.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Juan R Gonzalez", "email": "juanr.gonzalez@isglobal.org", "url": "https://brge.isglobal.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "chernan3", "additionDate": "2018-07-24T09:43:16Z", "lastUpdate": "2025-12-18T07:01:33.292198Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "chernan3", "rodney" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "globalamfungi", "description": "The GlobalAMFungi Database is an open-access, global repository of arbuscular mycorrhizal (AM) fungal occurrence data compiled from high-throughput sequencing studies. It aggregates millions of DNA sequence observations of AM fungi from thousands of geographically referenced environmental samples, together with rich metadata on sampling location and environmental context, to map the global distribution and diversity of these key plant symbionts. The resource is designed to be community-driven and FAIR (Findable, Accessible, Interoperable, Reusable), supporting research into AM fungal ecology, biogeography, and how environmental factors shape their diversity.", "homepage": "https://globalamfungi.com/", "biotoolsID": "globalamfungi", "biotoolsCURIE": "biotools:globalamfungi", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Data deposition" }, { "uri": "http://edamontology.org/operation_0226", "term": "Annotation" }, { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [ { "uri": "http://edamontology.org/format_2310", "term": "FASTA-HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3050", "term": "Biodiversity" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_3810", "term": "Agricultural science" } ], "operatingSystem": [], "language": [ "R" ], "license": "CC-BY-4.0", "collectionID": [ "ELIXIR-CZ", "Czech Republic" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "Plant Sciences" ], "link": [ { "url": "https://globalamfungi.com/", "type": [ "Helpdesk", "Repository", "Service" ], "note": null } ], "download": [], "documentation": [ { "url": "https://globalamfungi.com/", "type": [ "User manual", "Citation instructions", "Quick start guide", "Contributions policy", "General" ], "note": null } ], "publication": [ { "doi": "10.1111/nph.19283", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": null, "abstract": null, "date": null, "citationCount": 0, "authors": [], "journal": null } } ], "credit": [ { "name": "Tomas Vetrovsky", "email": "vetrovsky@biomed.cas.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-0831-486X", "gridid": null, "rorid": "02p1jz666", "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Contributor" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null } ], "owner": "TomasVetrovsky", "additionDate": "2025-12-16T11:00:25.334832Z", "lastUpdate": "2025-12-16T11:00:25.337448Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ASAFind", "description": "ASAFind is a software that predicts the intracellular location of proteins in cells with four membrane-bound complex plastids of red algal origin. \nThese plastids evolved via eukaryote-eukaryote endosymbiosis and for example can be found in diatoms and cryptophytes. ASAFind uses protein sequence data and external predictions of signal peptides (by the tools SignalP and TargetP), and predicts plastid proteins, and proteins that are targeted to the periplastidic compartment from these data; optionally, a graphical output can generated.", "homepage": "https://asafind.jcu.cz/", "biotoolsID": "asafind", "biotoolsCURIE": "biotools:asafind", "version": [ "2.0" ], "otherID": [], "relation": [ { "biotoolsID": "signalp", "type": "uses" }, { "biotoolsID": "targetp", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2489", "term": "Subcellular localisation prediction" }, { "uri": "http://edamontology.org/operation_0239", "term": "Sequence motif recognition" }, { "uri": "http://edamontology.org/operation_0422", "term": "Protein cleavage site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Script", "Command-line tool", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python" ], "license": "CC-BY-SA-4.0", "collectionID": [ "ELIXIR-CZ", "Czech Republic" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "Plant Sciences", "Marine Metagenomics", "Microbial Biotechnology" ], "link": [ { "url": "https://asafind.jcu.cz", "type": [ "Service" ], "note": "Web Service" }, { "url": "https://github.com/ASAFind/ASAFind-2", "type": [ "Repository" ], "note": "Information and source code, for local installation or development" } ], "download": [ { "url": "https://asafind.jcu.cz/download-page/", "type": "Downloads page", "note": "Download page on web-service, links to repository", "version": "2.0" } ], "documentation": [ { "url": "https://asafind.jcu.cz/download-page/", "type": [ "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1111/tpj.70138", "pmid": "40464854", "pmcid": "PMC12136025", "type": [ "Primary" ], "version": "2.0", "note": "Publication of the current version of ASAFind (2.0)", "metadata": { "title": "ASAFind 2.0: multi-class protein targeting prediction for diatoms and algae with complex plastids", "abstract": "", "date": "2025-06-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Plant Journal" } }, { "doi": "10.1111/tpj.12734", "pmid": "25438865", "pmcid": "PMC4329603", "type": [ "Other" ], "version": "1.0", "note": "Publication of the first version of ASAFind", "metadata": { "title": "Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage", "abstract": "", "date": "2015-02-01T00:00:00Z", "citationCount": 138, "authors": [], "journal": "Plant Journal" } }, { "doi": "10.48550/arXiv.2303.02509", "pmid": null, "pmcid": null, "type": [ "Benchmarking study" ], "version": "1.0", "note": "Benchmarking of the performance of the first version of ASAFind", "metadata": null } ], "credit": [ { "name": "Marta Vohnoutová", "email": "mvohnoutova@jcu.cz", "url": "https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Vohnoutova_Marta_61699", "orcidid": "https://orcid.org/0000-0002-8915-8626", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Developer", "Maintainer" ], "note": null }, { "name": "Ansgar Gruber", "email": "agruber@prf.jcu.cz", "url": "https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gruber_Ansgar_118401", "orcidid": "https://orcid.org/0000-0002-5876-4391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor" ], "note": null } ], "owner": "martavohnoutova", "additionDate": "2025-12-15T14:17:14.627791Z", "lastUpdate": "2025-12-15T17:36:43.189214Z", "editPermission": { "type": "group", "authors": [ "agruber" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MitSorter", "description": "Stand-alone tool for methylation-based discrimination of mitochondrial DNA ONT reads", "homepage": "https://github.com/asvarvara/MitSorter", "biotoolsID": "mitsorter", "biotoolsCURIE": "biotools:mitsorter", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" } ], "operatingSystem": [ "Linux" ], "language": [ "Python", "Shell" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Italy" ], "elixirCommunity": [ "Federated Human Data" ], "link": [ { "url": "https://github.com/asvarvara/MitSorter", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/asvarvara/MitSorter/blob/main/README.md", "type": [ "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.1093/bioadv/vbaf135", "pmid": "40688360", "pmcid": "PMC12275464", "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "MitSorter: a standalone tool for accurate discrimination of mtDNA and NuMT ONT reads based on differential methylation", "abstract": "", "date": "2025-01-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Bioinformatics Advances" } } ], "credit": [ { "name": "Sharon Natasha Cox", "email": "sharonnatasha.cox@uniba.it", "url": null, "orcidid": "https://orcid.org/0000-0002-8488-440X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "Researcher at University of Bari" }, { "name": "Angelo Sante Varvara", "email": "angelovarvara94@gmail.com", "url": "https://www.linkedin.com/in/angelo-sante-varvara-b514661a6/", "orcidid": "https://orcid.org/0009-0005-3559-8430", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "PhD Student at SEMM Institute" } ], "owner": "asvarvara", "additionDate": "2025-12-15T11:29:08.759624Z", "lastUpdate": "2025-12-15T11:29:47.221679Z", "editPermission": { "type": "group", "authors": [ "sharonnatasha.cox" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }