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The categorisation includes the type of sequence (e.g. spin echo, gradient echo), the weighting (e.g. T1W, T2W, DCE, ...), the presence of fat suppression and the detection of non-relevant / junk series (e.g. localizers, calibrations, screenshots...).", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab", "biotoolsID": "ml_model_for_mr_series_categorisation", "biotoolsCURIE": "biotools:ml_model_for_mr_series_categorisation", "version": [ "1.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2990", "term": "Classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": null, "cmd": "docker run -it --rm --name my-container \\\n -v \"<input_path>:/input\" \\\n -v \"<output_path>:/output\" \\\n harbor.eucaim.cancerimage.eu/processing-tools/ml_model_for_mr_series_categorisation:<version> \\\n --config-string \"{'output_name': 'classification_results.json'}\"" } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3316", "term": "Computer science" }, { "uri": "http://edamontology.org/topic_3077", "term": "Data acquisition" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://drive.google.com/file/d/1lIUixmLItQXOyBPIXL_AzPg_jlqDKwNE/view?usp=drive_link", "type": [ "User manual" ], "note": null }, { "url": "https://drive.google.com/file/d/1jF44iszmmiHd2paD8-YhFhW2uQJ0QBAZ/view?usp=drive_link", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1186/s40537-025-01086-w", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Automatic magnetic resonance imaging series labelling for large repositories", "abstract": "", "date": "2025-12-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Journal of Big Data" } } ], "credit": [ { "name": "GIBI230 - HULAFE", "email": "gibi230@iislafe.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Armando Gomis-Maya", "email": "armago@alumni.uv.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9527-8093", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pedro-Miguel Martinez-Girones", "email": "pedromiguel_martinez@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-9506-9451", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Carina Soler-Pons", "email": "carina_soler@iislafe.es", "url": null, "orcidid": "https://orcid.org/0009-0000-2991-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Leonor Cerda-Alberich", "email": "leonor_cerda@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-5567-4278", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Luis Marti-Bonmati", "email": "luis_marti@iislafe.es", "url": null, "orcidid": "https://orcid.org/0000-0002-8234-010X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "pedromiguel_martinez_HULAFE", "additionDate": "2025-11-25T09:58:37.569343Z", "lastUpdate": "2025-12-03T15:35:26.140884Z", "editPermission": { "type": "group", "authors": [ "casopon" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AutoProSeq - automatic classification of sequence types for prostate mpMRI", "description": "XGBoost-based automatic classification of sequence types for prostate mpMRI into T2W, DWI, ADC, DCE and others (any other sequence type) using metadata alone. Works as a CLI, allows direct application to DICOM datasets or CSV/tsv/Excel/parquet datasets, features integration for Orthanc and DICOM-web as RESTful APIs. This was applied to all data on ProCAncer-I to derive initial results for sequence types. Refines predictions using rule-based heuristics for T2W, DWI and ADC.", "homepage": "https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/champ-autoproseq", "biotoolsID": "auto-prostate-sequence-classifier", "biotoolsCURIE": "biotools:auto-prostate-sequence-classifier", "version": [ "v0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3553", "term": "Image annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3424", "term": "Raw image" }, "format": [ { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0968", "term": "Keyword" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "The input can be provided as a DICOM dataset (which will require --dicom-recursion, details below or in the documentation) or as a single DICOM study. This command will print a CSV with 5 columns: i) patient_id, ii) study_uid, iii) series_uid, iv) classification from the XGBoost model, v) classification after heuristics-based corrections.\nThe sequence classification is performed between T2W, DWI, ADC, DCE or others. The provided <dicom-recursion> refers to the number of folders until a DICOM series is found. So if the provided input is a patient folder with nested studies with nested series, the level of DICOM recursion should be 2. If the provided input is a directory with patient folders, the level of DICOM recursion should be 3.", "cmd": "docker run -v <dir-with-dicom>:/data harbor.eucaim.cancerimage.eu/processing-tools/champ-autoproseq --dicom_recursion <dicom-recursion> --input_paths /data" } ], "toolType": [ "Web API", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/CCIG-Champalimaud/metadata-classification", "type": [ "Repository" ], "note": "Repository containing code, README and additional usage information for this tool." } ], "download": [], "documentation": [ { "url": "https://github.com/CCIG-Champalimaud/metadata-classification", "type": [ "Other" ], "note": "Repository containing the code, README and additional information on how to run the tool. If used as an API (when integrated with Orthanc or DICOM-web), the documentation is available upon launching the API at <api-url>/docs." } ], "publication": [ { "doi": "10.1186/s13244-025-01938-2", "pmid": "40146375", "pmcid": "PMC12187622", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Automatic sequence identification in multicentric prostate multiparametric MRI datasets for clinical machine-learning", "abstract": "", "date": "2025-12-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Insights into Imaging" } } ], "credit": [ { "name": "José Guilherme de Almeida", "email": "jose.almeida@research.fchampalimaud.org", "url": "https://josegcpa.net", "orcidid": "https://orcid.org/0000-0002-1887-0157", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Nikolaos Papanikolaou", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3298-2072", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "josegcpa", "additionDate": "2025-12-02T17:37:57.215347Z", "lastUpdate": "2025-12-03T09:27:04.489071Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "gigaScience-Multi-Omics and High-Spatial-Resolution Omics", "description": "Multi-Omics and High-Spatial-Resolution Omics: Deciphering Complexity in Neurological Disorders", "homepage": "https://www.editorialmanager.com/giga/default2.aspx", "biotoolsID": "gigascience-multi-omics_and_high-spatial-resolution_omics", "biotoolsCURIE": "biotools:gigascience-multi-omics_and_high-spatial-resolution_omics", "version": [ "1.1" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/gigascience/giaf137", "pmid": null, "pmcid": null, "type": [ "Review" ], "version": "1.1", "note": "Multi-Omics and High-Spatial-Resolution Omics: Deciphering Complexity in Neurological Disorders", "metadata": null } ], "credit": [], "owner": "Liuxiuyun", "additionDate": "2025-11-28T16:33:36.583067Z", "lastUpdate": "2025-11-28T16:33:36.588376Z", "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/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": [ "Web application", "Workflow", "Command-line tool" ], "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": { "title": "Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" } }, { "doi": "10.1109/ISBI56570.2024.10635469", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble with Adaptive Post-Processing", "abstract": "", "date": "2024-01-01T00:00:00Z", "citationCount": 1, "authors": [], "journal": "Proceedings - International Symposium on Biomedical Imaging" } }, { "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": "2025-11-28T13:57:34.393084Z", "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). 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Based on MITK, there is the MITK Workbench, a powerful and free application to view, process, and segment medical images.", "homepage": "https://www.mitk.org/", "biotoolsID": "mitk", "biotoolsCURIE": "biotools:mitk", "version": [ "v2023.04" ], "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_3551", "term": "nrrd" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3551", "term": "nrrd" }, { "uri": "http://edamontology.org/format_3548", "term": "DICOM format" }, { "uri": "http://edamontology.org/format_3549", "term": "nii" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Workbench", "Desktop application", "Library" ], "topic": [], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "C++" ], "license": "BSD-3-Clause", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/MITK/MITK/", "type": [ "Repository" ], "note": null }, { "url": "https://lists.sourceforge.net/lists/listinfo/mitk-users", "type": [ "Mailing list" ], "note": "If you have any questions related to the use of or the development with MITK, please use the official mailing list.\n\nNote that you have to subscribe to the mailing list in order to send mails" } ], "download": [ { "url": "https://www.mitk.org/wiki/Downloads", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://docs.mitk.org/2023.04/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.media.2005.04.005", "pmid": "15896995", "pmcid": null, "type": [], "version": null, "note": "Nolden, Marco, et al. \"The Medical Imaging Interaction Toolkit: challenges and advances: 10 years of open-source development.\"\nInternational journal of computer assisted radiology and surgery 8 (2013): 607-620", "metadata": { "title": "The medical imaging interaction toolkit", "abstract": "Thoroughly designed, open-source toolkits emerge to boost progress in medical imaging. The Insight Toolkit (ITK) provides this for the algorithmic scope of medical imaging, especially for segmentation and registration. But medical imaging algorithms have to be clinically applied to be useful, which additionally requires visualization and interaction. The Visualization Toolkit (VTK) has powerful visualization capabilities, but only low-level support for interaction. In this paper, we present the Medical Imaging Interaction Toolkit (MITK). The goal of MITK is to significantly reduce the effort required to construct specifically tailored, interactive applications for medical image analysis. MITK allows an easy combination of algorithms developed by ITK with visualizations created by VTK and extends these two toolkits with those features, which are outside the scope of both. MITK adds support for complex interactions with multiple states as well as undo-capabilities, a very important prerequisite for convenient user interfaces. Furthermore, MITK facilitates the realization of multiple, different views of the same data (as a multiplanar reconstruction and a 3D rendering) and supports the visualization of 3D+t data, whereas VTK is only designed to create one kind of view of 2D or 3D data. MITK reuses virtually everything from ITK and VTK. Thus, it is not at all a competitor to ITK or VTK, but an extension, which eases the combination of both and adds the features required for interactive, convenient to use medical imaging software. MITK is an open-source project (www.mitk.org) © 2005 Elsevier B.V. All rights reserved.", "date": "2005-12-01T00:00:00Z", "citationCount": 378, "authors": [ { "name": "Wolf I." }, { "name": "Vetter M." }, { "name": "Wegner I." }, { "name": "Bottger T." }, { "name": "Nolden M." }, { "name": "Schobinger M." }, { "name": "Hastenteufel M." }, { "name": "Kunert T." }, { "name": "Meinzer H.-P." } ], "journal": "Medical Image Analysis" } }, { "doi": "10.1007/s11548-013-0840-8", "pmid": "23588509", "pmcid": null, "type": [], "version": null, "note": "Nolden, Marco, et al. \"The Medical Imaging Interaction Toolkit: challenges and advances: 10 years of open-source development.\"\nInternational journal of computer assisted radiology and surgery 8 (2013): 607-620", "metadata": { "title": "The medical imaging interaction toolkit: Challenges and advances: 10 years of open-source development", "abstract": "Purpose: The Medical Imaging Interaction Toolkit (MITK) has been available as open-source software for almost 10 years now. In this period the requirements of software systems in the medical image processing domain have become increasingly complex. The aim of this paper is to show how MITK evolved into a software system that is able to cover all steps of a clinical workflow including data retrieval, image analysis, diagnosis, treatment planning, intervention support, and treatment control. Methods: MITK provides modularization and extensibility on different levels. In addition to the original toolkit, a module system, micro services for small, system-wide features, a service-oriented architecture based on the Open Services Gateway initiative (OSGi) standard, and an extensible and configurable application framework allow MITK to be used, extended and deployed as needed. A refined software process was implemented to deliver high-quality software, ease the fulfillment of regulatory requirements, and enable teamwork in mixed-competence teams. Results: MITK has been applied by a worldwide community and integrated into a variety of solutions, either at the toolkit level or as an application framework with custom extensions. The MITK Workbench has been released as a highly extensible and customizable end-user application. Optional support for tool tracking, image-guided therapy, diffusion imaging as well as various external packages (e.g. CTK, DCMTK, OpenCV, SOFA, Python) is available. MITK has also been used in several FDA/CE-certified applications, which demonstrates the high-quality software and rigorous development process. Conclusions: MITK provides a versatile platform with a high degree of modularization and interoperability and is well suited to meet the challenging tasks of today's and tomorrow's clinically motivated research. © 2013 CARS.", "date": "2013-01-01T00:00:00Z", "citationCount": 354, "authors": [ { "name": "Nolden M." }, { "name": "Zelzer S." }, { "name": "Seitel A." }, { "name": "Wald D." }, { "name": "Muller M." }, { "name": "Franz A.M." }, { "name": "Maleike D." }, { "name": "Fangerau M." }, { "name": "Baumhauer M." }, { "name": "Maier-Hein L." }, { "name": "Maier-Hein K.H." }, { "name": "Meinzer H.-P." }, { "name": "Wolf I." } ], "journal": "International Journal of Computer Assisted Radiology and Surgery" } } ], "credit": [ { "name": "German Cancer Research Center (DKFZ)", "email": null, "url": "https://www.dkfz.de/de", "orcidid": null, "gridid": "grid.7497.d", "rorid": "04cdgtt98", "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "sschaum", "additionDate": "2023-06-26T12:38:15.108087Z", "lastUpdate": "2025-11-28T09:27:43.812008Z", "editPermission": { "type": "group", "authors": [ "ASHISR" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioContextAI Registry", "description": "The BioContextAI Registry is a community-driven catalog of Model Context Protocol (MCP) servers for agentic AI-supported biomedical research. 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"2025-10-31T10:28:34.411099Z", "lastUpdate": "2025-11-04T15:05:08.990137Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "UM - RQS 2.0 with RRLs", "description": "Radiomics is a medical imaging analysis tool that supports precision oncology by providing quantitative insights for clinical decision-making. The updated Radiomics Quality Score 2.0 (RQS 2.0) enhances the original RQS framework by integrating concepts of fairness, explainability, quality control, and harmonization, ensuring more rigorous and transparent evaluation of radiomics studies. It also introduces Radiomics Readiness Levels (RRLs)—a nine-stage framework inspired by technology readiness levels—to track progress from research to clinical implementation. Together, RQS 2.0 and RRLs provide a structured path to accelerate the clinical translation of radiomics and advance precision oncology.", "homepage": "https://www.radiomics.world/home", "biotoolsID": "um_rqs_2.0_with_rrls", "biotoolsCURIE": "biotools:um_rqs_2.0_with_rrls", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web service" ], "topic": [], "operatingSystem": [ "Windows", "Linux", "Mac" ], "language": [], "license": "Freeware", "collectionID": [ "EUCAIM" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.radiomics.world/rqs2", "type": [ "User manual" ], "note": "Framework to establish a structured, step-by-step approach to radiomics research." }, { "url": "https://www.radiomics.world/faq", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1038/s41571-025-01067-1", "pmid": "40903523", "pmcid": null, "type": [ "Review" ], "version": null, "note": null, "metadata": { "title": "Radiomics Quality Score 2.0: towards radiomics readiness levels and clinical translation for personalized medicine", "abstract": "", "date": "2025-11-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "Nature Reviews Clinical Oncology" } } ], "credit": [], "owner": "sinaamirrajab", "additionDate": "2025-11-04T15:00:53.996964Z", "lastUpdate": "2025-11-04T15:04:40.394407Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MAW", "description": "Metabolome Annotation Workflow for untargeted tandem mass spectrometry.", "homepage": "https://github.com/zmahnoor14/MAW", "biotoolsID": "maw", "biotoolsCURIE": "biotools:maw", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3643", "term": "Tag-based peptide identification" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "R" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/zmahnoor14/MAW-Benchmark", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s13321-023-00695-y", "pmid": "36871033", "pmcid": "PMC9985203", "type": [], "version": null, "note": null, "metadata": { "title": "MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry", "abstract": "Mapping the chemical space of compounds to chemical structures remains a challenge in metabolomics. Despite the advancements in untargeted liquid chromatography-mass spectrometry (LC–MS) to achieve a high-throughput profile of metabolites from complex biological resources, only a small fraction of these metabolites can be annotated with confidence. Many novel computational methods and tools have been developed to enable chemical structure annotation to known and unknown compounds such as in silico generated spectra and molecular networking. Here, we present an automated and reproducible Metabolome Annotation Workflow (MAW) for untargeted metabolomics data to further facilitate and automate the complex annotation by combining tandem mass spectrometry (MS2) input data pre-processing, spectral and compound database matching with computational classification, and in silico annotation. MAW takes the LC-MS2 spectra as input and generates a list of putative candidates from spectral and compound databases. The databases are integrated via the R package Spectra and the metabolite annotation tool SIRIUS as part of the R segment of the workflow (MAW-R). The final candidate selection is performed using the cheminformatics tool RDKit in the Python segment (MAW-Py). Furthermore, each feature is assigned a chemical structure and can be imported to a chemical structure similarity network. MAW is following the FAIR (Findable, Accessible, Interoperable, Reusable) principles and has been made available as the docker images, maw-r and maw-py. The source code and documentation are available on GitHub (https://github.com/zmahnoor14/MAW) The performance of MAW is evaluated on two case studies. MAW can improve candidate ranking by integrating spectral databases with annotation tools like SIRIUS which contributes to an efficient candidate selection procedure. The results from MAW are also reproducible and traceable, compliant with the FAIR guidelines. Taken together, MAW could greatly facilitate automated metabolite characterization in diverse fields such as clinical metabolomics and natural product discovery.", "date": "2023-12-01T00:00:00Z", "citationCount": 10, "authors": [ { "name": "Zulfiqar M." }, { "name": "Gadelha L." }, { "name": "Steinbeck C." }, { "name": "Sorokina M." }, { "name": "Peters K." } ], "journal": "Journal of Cheminformatics" } } ], "credit": [ { "name": "Mahnoor Zulfiqar", "email": "mahnoor.zulfiqar@uni-jena.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Christoph Steinbeck", "email": "christoph.steinbeck@uni-jena.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Kristian Peters", "email": "kristian.peters@ipb-halle.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Luiz Gadelha", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Maria Sorokina", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Pub2Tools", "additionDate": "2023-08-24T10:15:08.106111Z", "lastUpdate": "2025-11-03T16:47:22.668278Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "El-MAVEN", "description": "Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine for Metabolomics.", "homepage": "https://github.com/ElucidataInc/ElMaven", "biotoolsID": "El-MAVEN", "biotoolsCURIE": "biotools:El-MAVEN", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ElucidataInc/ElMaven", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/ElucidataInc/ElMaven/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://elucidatainc.github.io/ElMaven/Downloads/", "type": "Binaries", "note": null, "version": null }, { "url": "https://github.com/ElucidataInc/ElMaven/releases", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://elucidatainc.github.io/ElMaven/documentation/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1007/978-1-4939-9236-2_19", "pmid": "31119671", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "EL-MAVEN: A fast, robust, and user-friendly mass spectrometry data processing engine for metabolomics", "abstract": "", "date": "2019-01-01T00:00:00Z", "citationCount": 106, "authors": [], "journal": "Methods in Molecular Biology" } } ], "credit": [ { "name": null, "email": "info@elucidata.io", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": null, "email": "elmaven@elucidata.io", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hans", "additionDate": "2019-08-09T13:14:25Z", "lastUpdate": "2025-11-03T16:47:19.388844Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MSNovelist", "description": "De novo structure generation from mass spectra.", "homepage": "https://github.com/meowcat/MSNovelist", "biotoolsID": "msnovelist", "biotoolsCURIE": "biotools:msnovelist", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0476", "term": "Ab initio structure prediction" }, { "uri": "http://edamontology.org/operation_3860", "term": "Spectrum calculation" }, { "uri": "http://edamontology.org/operation_3454", "term": "Phasing" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_4009", "term": "Small molecule design" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0153", "term": "Lipids" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "Java" ], "license": "AGPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/S41592-022-01486-3", "pmid": "35637304", "pmcid": "PMC9262714", "type": [], "version": null, "note": null, "metadata": { "title": "MSNovelist: de novo structure generation from mass spectra", "abstract": "© 2022, The Author(s).Current methods for structure elucidation of small molecules rely on finding similarity with spectra of known compounds, but do not predict structures de novo for unknown compound classes. We present MSNovelist, which combines fingerprint prediction with an encoder–decoder neural network to generate structures de novo solely from tandem mass spectrometry (MS2) spectra. In an evaluation with 3,863 MS2 spectra from the Global Natural Product Social Molecular Networking site, MSNovelist predicted 25% of structures correctly on first rank, retrieved 45% of structures overall and reproduced 61% of correct database annotations, without having ever seen the structure in the training phase. Similarly, for the CASMI 2016 challenge, MSNovelist correctly predicted 26% and retrieved 57% of structures, recovering 64% of correct database annotations. Finally, we illustrate the application of MSNovelist in a bryophyte MS2 dataset, in which de novo structure prediction substantially outscored the best database candidate for seven spectra. MSNovelist is ideally suited to complement library-based annotation in the case of poorly represented analyte classes and novel compounds.", "date": "2022-07-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Stravs M.A." }, { "name": "Duhrkop K." }, { "name": "Bocker S." }, { "name": "Zamboni N." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Nicola Zamboni", "email": "zamboni@imsb.biol.ethz.ch", "url": null, "orcidid": "https://orcid.org/0000-0003-1271-1021", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Sebastian Böcker", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9304-8091", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Kai Dührkop", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9056-0540", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Michael A. Stravs", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-1426-8572", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-09-05T21:19:03.847868Z", "lastUpdate": "2025-11-03T16:47:18.329938Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "CANOPUS", "description": "CANOPUS is a tool for predicting compound classes directly from MS/MS. Because it does not depend on any database, CANOPUS is suitable for the classification of unknowns.", "homepage": "https://bio.informatik.uni-jena.de/software/canopus/", "biotoolsID": "canopus", "biotoolsCURIE": "biotools:canopus", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3860", "term": "Spectrum calculation" }, { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3801", "term": "Spectral library search" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" } ], "operatingSystem": [], "language": [], "license": "MIT", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/kaibioinfo/canopus_treemap", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/S41587-020-0740-8", "pmid": "33230292", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra", "abstract": "© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.Metabolomics using nontargeted tandem mass spectrometry can detect thousands of molecules in a biological sample. However, structural molecule annotation is limited to structures present in libraries or databases, restricting analysis and interpretation of experimental data. Here we describe CANOPUS (class assignment and ontology prediction using mass spectrometry), a computational tool for systematic compound class annotation. CANOPUS uses a deep neural network to predict 2,497 compound classes from fragmentation spectra, including all biologically relevant classes. CANOPUS explicitly targets compounds for which neither spectral nor structural reference data are available and predicts classes lacking tandem mass spectrometry training data. In evaluation using reference data, CANOPUS reached very high prediction performance (average accuracy of 99.7% in cross-validation) and outperformed four baseline methods. We demonstrate the broad utility of CANOPUS by investigating the effect of microbial colonization in the mouse digestive system, through analysis of the chemodiversity of different Euphorbia plants and regarding the discovery of a marine natural product, revealing biological insights at the compound class level.", "date": "2021-04-01T00:00:00Z", "citationCount": 24, "authors": [ { "name": "Duhrkop K." }, { "name": "Nothias L.-F." }, { "name": "Fleischauer M." }, { "name": "Reher R." }, { "name": "Ludwig M." }, { "name": "Hoffmann M.A." }, { "name": "Petras D." }, { "name": "Gerwick W.H." }, { "name": "Rousu J." }, { "name": "Dorrestein P.C." }, { "name": "Bocker S." } ], "journal": "Nature Biotechnology" } } ], "credit": [ { "name": "Sebastian Böcker", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Kigaard", "additionDate": "2021-01-18T11:58:45Z", "lastUpdate": "2025-11-03T16:47:13.400194Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PeakForest", "description": "A multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management.", "homepage": "https://peakforest.org", "biotoolsID": "peakforest", "biotoolsCURIE": "biotools:peakforest", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3801", "term": "Spectral library search" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0593", "term": "NMR" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data submission, annotation and curation" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java", "JavaScript" ], "license": "Other", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/peakforest", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1007/S11306-022-01899-3", "pmid": "35699774", "pmcid": "PMC9197906", "type": [], "version": null, "note": null, "metadata": { "title": "PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management", "abstract": "© 2022, The Author(s).Introduction: Accuracy of feature annotation and metabolite identification in biological samples is a key element in metabolomics research. However, the annotation process is often hampered by the lack of spectral reference data in experimental conditions, as well as logistical difficulties in the spectral data management and exchange of annotations between laboratories. Objectives: To design an open-source infrastructure allowing hosting both nuclear magnetic resonance (NMR) and mass spectra (MS), with an ergonomic Web interface and Web services to support metabolite annotation and laboratory data management. Methods: We developed the PeakForest infrastructure, an open-source Java tool with automatic programming interfaces that can be deployed locally to organize spectral data for metabolome annotation in laboratories. Standardized operating procedures and formats were included to ensure data quality and interoperability, in line with international recommendations and FAIR principles. Results: PeakForest is able to capture and store experimental spectral MS and NMR metadata as well as collect and display signal annotations. This modular system provides a structured database with inbuilt tools to curate information, browse and reuse spectral information in data treatment. PeakForest offers data formalization and centralization at the laboratory level, facilitating shared spectral data across laboratories and integration into public databases. Conclusion: PeakForest is a comprehensive resource which addresses a technical bottleneck, namely large-scale spectral data annotation and metabolite identification for metabolomics laboratories with multiple instruments. PeakForest databases can be used in conjunction with bespoke data analysis pipelines in the Galaxy environment, offering the opportunity to meet the evolving needs of metabolomics research. Developed and tested by the French metabolomics community, PeakForest is freely-available at https://github.com/peakforest.", "date": "2022-06-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Paulhe N." }, { "name": "Canlet C." }, { "name": "Damont A." }, { "name": "Peyriga L." }, { "name": "Durand S." }, { "name": "Deborde C." }, { "name": "Alves S." }, { "name": "Bernillon S." }, { "name": "Berton T." }, { "name": "Bir R." }, { "name": "Bouville A." }, { "name": "Cahoreau E." }, { "name": "Centeno D." }, { "name": "Costantino R." }, { "name": "Debrauwer L." }, { "name": "Delabriere A." }, { "name": "Duperier C." }, { "name": "Emery S." }, { "name": "Flandin A." }, { "name": "Hohenester U." }, { "name": "Jacob D." }, { "name": "Joly C." }, { "name": "Jousse C." }, { "name": "Lagree M." }, { "name": "Lamari N." }, { "name": "Lefebvre M." }, { "name": "Lopez-Piffet C." }, { "name": "Lyan B." }, { "name": "Maucourt M." }, { "name": "Migne C." }, { "name": "Olivier M.-F." }, { "name": "Rathahao-Paris E." }, { "name": "Petriacq P." }, { "name": "Pinelli J." }, { "name": "Roch L." }, { "name": "Roger P." }, { "name": "Roques S." }, { "name": "Tabet J.-C." }, { "name": "Tremblay-Franco M." }, { "name": "Traikia M." }, { "name": "Warnet A." }, { "name": "Zhendre V." }, { "name": "Rolin D." }, { "name": "Jourdan F." }, { "name": "Thevenot E." }, { "name": "Moing A." }, { "name": "Jamin E." }, { "name": "Fenaille F." }, { "name": "Junot C." }, { "name": "Pujos-Guillot E." }, { "name": "Giacomoni F." } ], "journal": "Metabolomics" } } ], "credit": [ { "name": "Franck Giacomoni", "email": "Franck.Giacomoni@inrae.fr", "url": null, "orcidid": "https://orcid.org/0000-0001-6063-4214", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Estelle Pujos-Guillot", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Christophe Junot", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "François Fenaille", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-09-04T23:10:37.868759Z", "lastUpdate": "2025-11-03T16:47:12.424836Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "BUDDY", "description": "Open-source cheminformatic software platform developed for MS-based metabolomics research.", "homepage": "https://github.com/HuanLab/BUDDY", "biotoolsID": "buddy", "biotoolsCURIE": "biotools:buddy", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3646", "term": "Peptide database search" }, { "uri": "http://edamontology.org/operation_3644", "term": "de Novo sequencing" }, { "uri": "http://edamontology.org/operation_2425", "term": "Optimisation and refinement" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" }, { "uri": "http://edamontology.org/topic_3407", "term": "Endocrinology and metabolism" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "C#" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://philipbear.github.io/BUDDY_Metabolomics", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1038/s41592-023-01850-x", "pmid": "37055660", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "BUDDY: molecular formula discovery via bottom-up MS/MS interrogation", "abstract": "A substantial fraction of metabolic features remains undetermined in mass spectrometry (MS)-based metabolomics, and molecular formula annotation is the starting point for unraveling their chemical identities. Here we present bottom-up tandem MS (MS/MS) interrogation, a method for de novo formula annotation. Our approach prioritizes MS/MS-explainable formula candidates, implements machine-learned ranking and offers false discovery rate estimation. Compared with the mathematically exhaustive formula enumeration, our approach shrinks the formula candidate space by 42.8% on average. Method benchmarking on annotation accuracy was systematically carried out on reference MS/MS libraries and real metabolomics datasets. Applied on 155,321 recurrent unidentified spectra, our approach confidently annotated >5,000 novel molecular formulae absent from chemical databases. Beyond the level of individual metabolic features, we combined bottom-up MS/MS interrogation with global optimization to refine formula annotations while revealing peak interrelationships. This approach allowed the systematic annotation of 37 fatty acid amide molecules in human fecal data. All bioinformatics pipelines are available in a standalone software, BUDDY (https://github.com/HuanLab/BUDDY)", "date": "2023-06-01T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Xing S." }, { "name": "Shen S." }, { "name": "Xu B." }, { "name": "Li X." }, { "name": "Huan T." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Tao Huan", "email": "thuan@chem.ubc.ca", "url": null, "orcidid": "http://orcid.org/0000-0001-6295-2435", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Pub2Tools", "additionDate": "2023-12-01T15:46:02.196263Z", "lastUpdate": "2025-11-03T16:45:48.375514Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MS-DIAL", "description": "MS-DIAL was launched as a universal program for untargeted metabolomics that supports multiple instruments (GC/MS, GC/MS/MS, LC/MS, and LC/MS/MS) and MS vendors (Agilent, Bruker, LECO, Sciex, Shimadzu, Thermo, and Waters)", "homepage": "http://prime.psc.riken.jp/compms/msdial/main.html", "biotoolsID": "ms_dial", "biotoolsCURIE": "biotools:ms_dial", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" }, { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" }, { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3636", "term": "MRM/SRM" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0153", "term": "Lipids" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial", "type": [ "General" ], "note": null }, { "url": "http://prime.psc.riken.jp/compms/msdial/faq.html", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1038/s41587-020-0531-2", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "A lipidome atlas in MS-DIAL 4", "abstract": "© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.We present Mass Spectrometry-Data Independent Analysis software version 4 (MS-DIAL 4), a comprehensive lipidome atlas with retention time, collision cross-section and tandem mass spectrometry information. We formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry. Using human, murine, algal and plant biological samples, we annotated and semiquantified 8,051 lipids using MS-DIAL 4 with a 1–2% estimated false discovery rate. MS-DIAL 4 helps standardize lipidomics data and discover lipid pathways.", "date": "2020-10-01T00:00:00Z", "citationCount": 38, "authors": [ { "name": "Tsugawa H." }, { "name": "Ikeda K." }, { "name": "Takahashi M." }, { "name": "Satoh A." }, { "name": "Mori Y." }, { "name": "Uchino H." }, { "name": "Okahashi N." }, { "name": "Yamada Y." }, { "name": "Tada I." }, { "name": "Bonini P." }, { "name": "Higashi Y." }, { "name": "Okazaki Y." }, { "name": "Zhou Z." }, { "name": "Zhu Z.-J." }, { "name": "Koelmel J." }, { "name": "Cajka T." }, { "name": "Fiehn O." }, { "name": "Saito K." }, { "name": "Arita M." }, { "name": "Arita M." } ], "journal": "Nature Biotechnology" } } ], "credit": [ { "name": "Makoto Arita", "email": "makoto.arita@riken.jp", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Hiroshi Tsugawa", "email": "hiroshi.tsugawa@riken.jp", "url": null, "orcidid": "https://orcid.org/0000-0002-2015-3958", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-05-26T20:56:35Z", "lastUpdate": "2025-11-03T16:45:45.835795Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MetaboAnalyst", "description": "Statistical, functional and integrative analysis of metabolomics data , interpretation, and integration with other omics data.", "homepage": "http://www.metaboanalyst.ca", "biotoolsID": "metaboanalyst", "biotoolsCURIE": "biotools:metaboanalyst", "version": [ "4.0", "5.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2497", "term": "Pathway or network analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" } ], "operatingSystem": [], "language": [ "R", "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://www.metaboanalyst.ca/faces/docs/Resources.xhtml", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://www.metaboanalyst.ca/faces/docs/Faqs.xhtml", "type": [ "General" ], "note": null }, { "url": "http://www.metaboanalyst.ca/faces/docs/Tutorial.xhtml", "type": [ "Training material" ], "note": null }, { "url": "http://www.metaboanalyst.ca/faces/docs/Contact.xhtml", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gky310", "pmid": "29762782", "pmcid": "PMC6030889", "type": [], "version": null, "note": null, "metadata": { "title": "MetaboAnalyst 4.0: Towards more transparent and integrative metabolomics analysis", "abstract": "We present a new update to MetaboAnalyst (version 4.0) for comprehensive metabolomic data analysis, interpretation, and integration with other omics data. Since the last major update in 2015, MetaboAnalyst has continued to evolve based on user feedback and technological advancements in the field. For this year's update, four newkey features have been added to MetaboAnalyst 4.0, including: (1) real-time R command tracking and display coupled with the release of a companion MetaboAnalystR package; (2) a MS Peaks to Pathways module for prediction of pathway activity from untargeted mass spectral data using themummichog algorithm; (3) a Biomarker Metaanalysis module for robust biomarker identification through the combination of multiple metabolomic datasets and (4) a Network Explorer module for integrative analysis of metabolomics, metagenomics, and/or transcriptomics data. The user interface of MetaboAnalyst 4.0 has been reengineered to provide a more modern look and feel, as well as to give more space and flexibility to introduce new functions. The underlying knowledgebases (compound libraries, metabolite sets, and metabolic pathways) have also been updated based on the latest data from the Human Metabolome Database (HMDB). A Docker image of MetaboAnalyst is also available to facilitate download and local installation of Metabo-Analyst.", "date": "2018-07-02T00:00:00Z", "citationCount": 2833, "authors": [ { "name": "Chong J." }, { "name": "Soufan O." }, { "name": "Li C." }, { "name": "Caraus I." }, { "name": "Li S." }, { "name": "Bourque G." }, { "name": "Wishart D.S." }, { "name": "Xia J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1038/s41596-022-00710-w", "pmid": "35715522", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data", "abstract": "Liquid chromatography coupled with high-resolution mass spectrometry (LC–HRMS) has become a workhorse in global metabolomics studies with growing applications across biomedical and environmental sciences. However, outstanding bioinformatics challenges in terms of data processing, statistical analysis and functional interpretation remain critical barriers to the wider adoption of this technology. To help the user community overcome these barriers, we have made major updates to the well-established MetaboAnalyst platform (www.metaboanalyst.ca) This protocol extends the previous 2011 Nature Protocol by providing stepwise instructions on how to use MetaboAnalyst 5.0 to: optimize parameters for LC–HRMS spectra processing; obtain functional insights from peak list data; integrate metabolomics data with transcriptomics data or combine multiple metabolomics datasets; conduct exploratory statistical analysis with complex metadata. Parameter optimization may take ~2 h to complete depending on the server load, and the remaining three stages may be executed in ~60 min.", "date": "2022-08-01T00:00:00Z", "citationCount": 730, "authors": [ { "name": "Pang Z." }, { "name": "Zhou G." }, { "name": "Ewald J." }, { "name": "Chang L." }, { "name": "Hacariz O." }, { "name": "Basu N." }, { "name": "Xia J." } ], "journal": "Nature Protocols" } } ], "credit": [ { "name": null, "email": "jeff.xia@mcgill.ca", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-07-03T00:07:39Z", "lastUpdate": "2025-11-03T16:45:45.351615Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "tidyMass", "description": "An Object-oriented Reproducible Analysis Framework for LC-MS Data.", "homepage": "https://www.tidymass.org/", "biotoolsID": "tidymass", "biotoolsCURIE": "biotools:tidymass", "version": [], "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_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/tidymass", "type": [ "Repository" ], "note": null }, { "url": "https://tidymass.tidymass.org/", "type": [ "Other" ], "note": null } ], "download": [ { "url": "https://hub.docker.com/r/jaspershen/tidymass-case-study", "type": "Container file", "note": null, "version": null }, { "url": "https://hub.docker.com/r/jaspershen/tidymass", "type": "Container file", "note": null, "version": null }, { "url": "https://www.tidymass.org/start/tidymass_docker/", "type": "Container file", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1038/s41467-022-32155-w", "pmid": "35902589", "pmcid": "PMC9334349", "type": [], "version": null, "note": null, "metadata": { "title": "TidyMass an object-oriented reproducible analysis framework for LC–MS data", "abstract": "Reproducibility, traceability, and transparency have been long-standing issues for metabolomics data analysis. Multiple tools have been developed, but limitations still exist. Here, we present the tidyMass project (https://www.tidymass.org/) a comprehensive R-based computational framework that can achieve the traceable, shareable, and reproducible workflow needs of data processing and analysis for LC-MS-based untargeted metabolomics. TidyMass is an ecosystem of R packages that share an underlying design philosophy, grammar, and data structure, which provides a comprehensive, reproducible, and object-oriented computational framework. The modular architecture makes tidyMass a highly flexible and extensible tool, which other users can improve and integrate with other tools to customize their own pipeline.", "date": "2022-12-01T00:00:00Z", "citationCount": 28, "authors": [ { "name": "Shen X." }, { "name": "Yan H." }, { "name": "Wang C." }, { "name": "Gao P." }, { "name": "Johnson C.H." }, { "name": "Snyder M.P." } ], "journal": "Nature Communications" } } ], "credit": [ { "name": "Caroline H. Johnson", "email": "caroline.johnson@yale.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Michael P. Snyder", "email": "mpsnyder@stanford.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Xiaotao Shen", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0002-9608-9964", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Hong Yan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-11-25T21:43:37.501728Z", "lastUpdate": "2025-11-03T16:45:44.856713Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "UmetaFlow", "description": "Untargeted metabolomics workflow for high-throughput data processing and analysis.", "homepage": "https://github.com/biosustain/snakemake_UmetaFlow", "biotoolsID": "umetaflow", "biotoolsCURIE": "biotools:umetaflow", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3557", "term": "Imputation" }, { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/biosustain/pyOpenMS_UmetaFlow", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s13321-023-00724-w", "pmid": "37173725", "pmcid": "PMC10176759", "type": [], "version": null, "note": null, "metadata": { "title": "UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis", "abstract": "Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication are required. Here, we present UmetaFlow, a computational workflow for untargeted metabolomics that combines algorithms for data pre-processing, spectral matching, molecular formula and structural predictions, and an integration to the GNPS workflows Feature-Based Molecular Networking and Ion Identity Molecular Networking for downstream analysis. UmetaFlow is implemented as a Snakemake workflow, making it easy to use, scalable, and reproducible. For more interactive computing, visualization, as well as development, the workflow is also implemented in Jupyter notebooks using the Python programming language and a set of Python bindings to the OpenMS algorithms (pyOpenMS). Finally, UmetaFlow is also offered as a web-based Graphical User Interface for parameter optimization and processing of smaller-sized datasets. UmetaFlow was validated with in-house LC–MS/MS datasets of actinomycetes producing known secondary metabolites, as well as commercial standards, and it detected all expected features and accurately annotated 76% of the molecular formulas and 65% of the structures. As a more generic validation, the publicly available MTBLS733 and MTBLS736 datasets were used for benchmarking, and UmetaFlow detected more than 90% of all ground truth features and performed exceptionally well in quantification and discriminating marker selection. We anticipate that UmetaFlow will provide a useful platform for the interpretation of large metabolomics datasets. Graphical Abstract: [Figure not available: see fulltext.]", "date": "2023-12-01T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Kontou E.E." }, { "name": "Walter A." }, { "name": "Alka O." }, { "name": "Pfeuffer J." }, { "name": "Sachsenberg T." }, { "name": "Mohite O.S." }, { "name": "Nuhamunada M." }, { "name": "Kohlbacher O." }, { "name": "Weber T." } ], "journal": "Journal of Cheminformatics" } } ], "credit": [ { "name": "Tilmann Weber", "email": "tiwe@biosustain.dtu.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Pub2Tools", "additionDate": "2024-01-02T02:11:50.145026Z", "lastUpdate": "2025-11-03T16:16:27.787938Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "IsoCor", "description": "IsoCor is a scientific software dedicated to the correction of low- and high-resolution mass spectrometry (MS) data for naturally occuring isotopes. IsoCor corrects raw MS data (mass fractions) for naturally-occurring isotopes of all elements and purity of the isotopic tracer. The output of IsoCor is the isotopologue distribution of the molecule (i.e. the relative fractions of molecular entities differing only in the number of isotopic substitutions of the tracer). IsoCor also calculates the mean enrichment (i.e. the mean isotopic content in the molecule) in metabolites.", "homepage": "https://github.com/MetaSys-LISBP/IsoCor", "biotoolsID": "IsoCor", "biotoolsCURIE": "biotools:IsoCor", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool", "Library", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3955", "term": "Fluxomics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Compute" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/MetaSys-LISBP/IsoCor", "type": [ "Repository" ], "note": "GitHub repository" }, { "url": "https://isocor.readthedocs.io/en/latest/", "type": [ "Helpdesk" ], "note": "Documentation" }, { "url": "https://toolshed.g2.bx.psu.edu/view/gmat/isocor/96f7617b4848", "type": [ "Galaxy service" ], "note": "Galaxy tool shed" }, { "url": "https://pypi.org/project/IsoCor/", "type": [ "Repository" ], "note": "PyPi repository" }, { "url": "https://anaconda.org/bioconda/isocor", "type": [ "Repository" ], "note": "Bioconda repository" } ], "download": [ { "url": "https://github.com/MetaSys-LISBP/IsoCor", "type": "Source code", "note": null, "version": "2" } ], "documentation": [ { "url": "https://isocor.readthedocs.io/en/latest/", "type": [ "API documentation", "Command-line options", "FAQ", "Installation instructions", "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btz209", "pmid": "30903185", "pmcid": null, "type": [ "Method" ], "version": "2", "note": null, "metadata": { "title": "IsoCor: Isotope correction for high-resolution MS labeling experiments", "abstract": "© 2019 The Author(s) 2019. Published by Oxford University Press. All rights reserved.Summary: Mass spectrometry (MS) is widely used for isotopic studies of metabolism and other (bio)chemical processes. Quantitative applications in systems and synthetic biology require to correct the raw MS data for the contribution of naturally occurring isotopes. Several tools are available to correct low-resolution MS data, and recent developments made substantial improvements by introducing resolution-dependent correction methods, hence opening the way to the correction of high-resolution MS (HRMS) data. Nevertheless, current HRMS correction methods partly fail to determine which isotopic species are resolved from the tracer isotopologues and should thus be corrected. We present an updated version of our isotope correction software (IsoCor) with a novel correction algorithm which ensures to accurately exploit any chemical species with any isotopic tracer, at any MS resolution. IsoCor v2 also includes a novel graphical user interface for intuitive use by end-users and a command-line interface to streamline integration into existing pipelines. Availability and implementation: IsoCor v2 is implemented in Python 3 and was tested on Windows, Unix and MacOS platforms. The source code and the documentation are freely distributed under GPL3 license at https://github.com/MetaSys-LISBP/IsoCor/ and https://isocor.readthedocs.io/.", "date": "2019-11-01T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Millard P." }, { "name": "Delepine B." }, { "name": "Guionnet M." }, { "name": "Heuillet M." }, { "name": "Bellvert F." }, { "name": "Letisse F." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Pierre Millard", "email": "millard@insa-toulouse.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-8136-9963", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Matthieu Guionnet", "email": "guionnet@insa-toulouse.fr", "url": null, "orcidid": "https://orcid.org/0000-0001-5326-0357", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Baudoin Delépine", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-6288-425X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "millard", "additionDate": "2020-01-21T09:25:21Z", "lastUpdate": "2025-11-03T16:16:25.029297Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Krona", "description": "Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).", "homepage": "https://github.com/marbl/Krona/wiki", "biotoolsID": "krona", "biotoolsCURIE": "biotools:krona", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "JavaScript", "Perl" ], "license": "Proprietary", "collectionID": [ "Animal and Crop Genomics" ], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/marbl/Krona/wiki/Help", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2105-12-385", "pmid": "21961884", "pmcid": "PMC3190407", "type": [], "version": null, "note": null, "metadata": { "title": "Interactive metagenomic visualization in a Web browser", "abstract": "Background: A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables.Results: Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools.Conclusions: Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net. © 2011 Ondov et al; licensee BioMed Central Ltd.", "date": "2011-09-30T00:00:00Z", "citationCount": 1386, "authors": [ { "name": "Ondov B.D." }, { "name": "Bergman N.H." }, { "name": "Phillippy A.M." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "B.D. Ondov", "email": "ondovb@nbacc.net", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "GitHub Issues", "email": null, "url": "https://github.com/marbl/Krona/issues", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "seqwiki_import", "additionDate": "2017-01-13T13:15:12Z", "lastUpdate": "2025-10-29T15:10:11.949158Z", "editPermission": { "type": "group", "authors": [ "animalandcropgenomics", "ELIXIR-CZ", "Bioinformatics_project" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "The MINERVA Platform", "description": "The MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform is a standalone webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format, including files produced using CellDesigner or SBGN editors. Visualization of uploaded networks generated by the platform is accessible via a web browser to all viewers with the weblink to the resource.\n\nThe MINERVA Platform is a webservice using the Java Server Faces 2 technology. The server side, including data parsing, integration, annotation and verification, is implemented in Java. The platform uses the Postgres SQL database for data storage and the Hibernate framework as a middle layer between web server and database. The user web-interface is generated using React.js. The displayed content is visualized by OpenLayers API, dedicated JavaScript and CSS.", "homepage": "https://minerva.uni.lu", "biotoolsID": "MINERVA_Platform", "biotoolsCURIE": "biotools:MINERVA_Platform", "version": [ "13.1.3", "13.2.0", "14.0.13", "15.0.3", "16.4.0", "17.1.3", "18.1.1", "19.1.0" ], "otherID": [], "relation": [ { "biotoolsID": "pathvisio", "type": "uses" }, { "biotoolsID": "sbgn", "type": "uses" }, { "biotoolsID": "libsbml", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3926", "term": "Pathway visualisation" } ], "input": [], "output": [], "note": "Visualise systems biology diagrams online, on a standalone web server", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0571", "term": "Expression data visualisation" } ], "input": [], "output": [], "note": "Visualise omics data from multiple datasets on top of the diagrams", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3434", "term": "Conversion" } ], "input": [], "output": [], "note": "Convert between main systems biology layout formats: CellDeslgners SBML, SBML layout+render, SBGN-ML, GPML", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [], "output": [], "note": "Use MINERVA API to access systems biology formats for modelling", "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_3342", "term": "Translational medicine" }, { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" } ], "operatingSystem": [], "language": [], "license": "AGPL-3.0", "collectionID": [ "LCSB", "ELIXIR-LU" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Luxembourg" ], "elixirCommunity": [], "link": [ { "url": "https://gitlab.lcsb.uni.lu/minerva/core/", "type": [ "Repository" ], "note": "GiLab repository for core functionalities (data and format handling, service stability, API access)" }, { "url": "https://gitlab.lcsb.uni.lu/minerva/core/-/issues", "type": [ "Issue tracker" ], "note": "Issue tracker for core functionalities (data and format handling, service stability, API access)" }, { "url": "https://gitlab.lcsb.uni.lu/minerva/frontend", "type": [ "Repository" ], "note": "GiLab repository for frontend functionalities" }, { "url": "https://gitlab.lcsb.uni.lu/minerva/frontend/-/issues", "type": [ "Issue tracker" ], "note": "Issue tracker for frontend functionalities" } ], "download": [ { "url": "https://minerva.pages.uni.lu/doc/install/", "type": "Other", "note": "Installation instructions, including debian package, virtual machine images and docker containers.", "version": "13.1.3 - 18.1.1" } ], "documentation": [ { "url": "https://minerva.uni.lu", "type": [ "Quick start guide", "Release notes", "User manual", "API documentation", "Citation instructions", "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1038/npjsba.2016.20", "pmid": "28725475", "pmcid": "PMC5516855", "type": [ "Primary" ], "version": "10.0", "note": null, "metadata": { "title": "MINERVA—A platform for visualization and curation of molecular interaction networks", "abstract": "", "date": "2016-01-01T00:00:00Z", "citationCount": 71, "authors": [], "journal": "npj Systems Biology and Applications" } }, { "doi": "10.1093/bioinformatics/btz286", "pmid": "31074494", "pmcid": "PMC6821317", "type": [ "Primary" ], "version": "12.2.3", "note": null, "metadata": { "title": "MINERVA API and plugins: Opening molecular network analysis and visualization to the community", "abstract": "", "date": "2019-11-01T00:00:00Z", "citationCount": 26, "authors": [], "journal": "Bioinformatics" } }, { "doi": "10.1093/bib/bbz067", "pmid": "31273380", "pmcid": "PMC7373180", "type": [ "Primary" ], "version": "13.1.1", "note": null, "metadata": { "title": "Closing the gap between formats for storing layout information in systems biology", "abstract": "", "date": "2019-07-10T00:00:00Z", "citationCount": 18, "authors": [], "journal": "Briefings in Bioinformatics" } }, { "doi": "10.1089/big.2015.0057", "pmid": "27441714", "pmcid": "PMC4932659", "type": [ "Usage" ], "version": "10.0", "note": null, "metadata": { "title": "Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases", "abstract": "", "date": "2016-06-01T00:00:00Z", "citationCount": 40, "authors": [], "journal": "Big Data" } }, { "doi": "10.1016/j.envpol.2019.04.005", "pmid": "30991279", "pmcid": null, "type": [], "version": "13.1.1", "note": null, "metadata": { "title": "Genes associated with Parkinson's disease respond to increasing polychlorinated biphenyl levels in the blood of healthy females", "abstract": "", "date": "2019-07-01T00:00:00Z", "citationCount": 5, "authors": [], "journal": "Environmental Pollution" } } ], "credit": [], "owner": "mjostaszewski", "additionDate": "2019-08-26T14:34:55Z", "lastUpdate": "2025-10-29T08:54:40.647322Z", "editPermission": { "type": "group", "authors": [ "sascha.herzinger" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NetStart", "description": "Prediction of eukaryotic translation initiation sites using a protein language model.\n\nNetStart 2.0 is a deep learning-based model that predicts canonical translation initiation sites in mRNA transcripts in species across the eukaryotic domain, including vertebrates, invertebrates, plants, fungi, and protists. \n\nThe model integrates the ESM-2 protein language model for assessing transitions from non-coding to coding regions with local start codon sequence context and taxonomical information. It has been trained on sequences from 60 phylogenetically diverse eukaryotic species.\n\nIf you need help with the bioinformatics programs, see the \"Getting Help\" section at the server site at the link.", "homepage": "https://services.healthtech.dtu.dk/services/NetStart-2.0/", "biotoolsID": "netstart_2.0", "biotoolsCURIE": "biotools:netstart_2.0", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" }, { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" }, { "uri": "http://edamontology.org/operation_0439", "term": "Translation initiation site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_0108", "term": "Protein expression" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/lsandvad/netstart2", "type": [ "Repository" ], "note": "GitHub with code and instructions and to download and run the program locally" }, { "url": "https://services.healthtech.dtu.dk/services/NetStart-2.0/", "type": [ "Service" ], "note": "NetStart 2.0 server where sequences can be uploaded directly without having to download the program (hosted by DTU Health Tech)." } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/S12859-025-06220-2", "pmid": "40830753", "pmcid": "PMC12366053", "type": [ "Method" ], "version": "2.0", "note": null, "metadata": { "title": "NetStart 2.0: prediction of eukaryotic translation initiation sites using a protein language model", "abstract": "", "date": "2025-12-01T00:00:00Z", "citationCount": 0, "authors": [], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Line Sandvad Nielsen", "email": "line.s.nielsen@bio.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Henrik Nielsen", "email": "henni@dtu.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "linesandvad", "additionDate": "2025-10-27T16:27:24.014603Z", "lastUpdate": "2025-10-28T17:34:39.042070Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Thor", "description": "Spatial transcriptomics integrates transcriptomics data with histological tissue images, offering deeper insights into cellular organization and molecular functions. However, existing computational platforms mainly focus on genomic analysis, leaving a gap in the seamless integration of genomic and imaging modalities. Thor is a comprehensive spatial transcriptomics analysis tool designed to bridge this gap by enabling efficient co-analysis of gene expression profiles and high-resolution tissue images. It provides scalable workflows for spatial feature extraction, cell segmentation, gene–spatial correlation, and visualization, facilitating multi-omic insights into tissue architecture and cellular heterogeneity.", "homepage": "https://github.com/GuangyuWangLab2021/Thor", "biotoolsID": "Thor", "biotoolsCURIE": "biotools:Thor", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3891", "term": "Essential dynamics" }, { "uri": "http://edamontology.org/operation_3557", "term": "Imputation" }, { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://wanglab.tech/thor", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://wanglab.tech/thor/", "type": [ "Quick start guide" ], "note": null } ], "publication": [ { "doi": "10.21203/RS.3.RS-4909620/V1", "pmid": "40162205", "pmcid": "PMC11952649", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Pengzhi Zhang", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-6920-1490", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Weiqing Chen", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3539-9210", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "udayaraja", "additionDate": "2025-10-27T16:15:48.531662Z", "lastUpdate": "2025-10-27T16:59:57.862356Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MS Annika", "description": "MS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra. It can deal with a wide variety of cross-linkers and provides robust and transparent FDR control based on a target-decoy approach. 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