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  description: 'GnpIS is an integrative and multi-species information system dedicated
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    - data:
        term: Database search results
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      format: []
    - data:
        term: Genotype/phenotype report
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      format: []
    - data:
        term: Identifier
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      format: []
  homepage: https://urgi.versailles.inrae.fr/gnpis
  homepage_status: 0
  language:
  - JavaScript
  - Java
  lastUpdate: '2025-12-19T17:15:16.754031Z'
  license: BSD-3-Clause
  link:
  - note: null
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      journal: Database
      title: 'GnpIS: An information system to integrate genetic and genomic data from
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      journal: Methods in Molecular Biology
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    type:
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      citationCount: 38
      date: '2016-11-23T00:00:00Z'
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  description: PoseEdit automatically generates 2D diagrams of protein-ligand complexes,
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  biotoolsCURIE: biotools:mr-based_dipg_tumour_detection_and_segmentation
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  description: The tool performs an automatic segmentation of the possible DIPG tumours
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    workflow from DICOM images to DICOM seg tumoral masks.
  documentation:
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    type:
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  function:
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    note: null
    operation:
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    output:
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    note: null
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    metadata:
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      journal: Journal of Imaging Informatics in Medicine
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    note: null
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  - term: Data architecture, analysis and design
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  validated: 0
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    fundrefid: null
    gridid: null
    name: Michel Salzet
    note: Professor Michel Salzet known for his work in immunology, oncology and proteomic
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    rorid: null
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    url: https://www.laboratoire-prism.fr/member/michel-salzet/
  description: 'Profiler is a peer-reviewed, open-source web platform and desktop
    version for end-to-end multi-omics data analysis, integrating statistical methods,
    machine learning, and artificial intelligence into a unified workflow.


    The platform supports proteomics, metabolomics, lipidomics, transcriptomics, genomics,
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    Designed for both bioinformaticians and experimental scientists, Profiler enables
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    Profiler is developed by the PRISM U1192 laboratory and protected by INSERM Transfer.'
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  download:
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    type: Source code
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  - note: null
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  editPermission:
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  - Proteomics
  - Rare Diseases
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  function: []
  homepage: https://prism-profiler.univ-lille.fr/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-16T08:20:49.442259Z'
  license: Other
  link:
  - note: softeware link
    type:
    - Other
    url: https://prism-profiler.univ-lille.fr/
  - note: dataset examples
    type:
    - Repository
    url: https://github.com/yanisZirem/Profiler_v1_requests_datatests
  - note: Desktop version
    type:
    - Repository
    url: https://github.com/yanisZirem/prism-profiler
  maturity: Mature
  name: Profiler
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID:
  - type: doi
    value: doi:10.1093/bioinformatics/btaf644
    version: '1.0'
  owner: YZirem
  publication:
  - doi: 10.1093/bioinformatics/btaf644
    metadata: null
    note: null
    pmcid: null
    pmid: '41324558'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Desktop application
  - Web application
  - Workflow
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2025-12-15T14:17:14.627791Z'
  biotoolsCURIE: biotools:asafind
  biotoolsID: asafind
  collectionID:
  - ELIXIR-CZ
  - Czech Republic
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: mvohnoutova@jcu.cz
    fundrefid: null
    gridid: null
    name: Marta Vohnoutová
    note: null
    orcidid: https://orcid.org/0000-0002-8915-8626
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    - Maintainer
    url: https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Vohnoutova_Marta_61699
  - email: agruber@prf.jcu.cz
    fundrefid: null
    gridid: null
    name: Ansgar Gruber
    note: null
    orcidid: https://orcid.org/0000-0002-5876-4391
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    url: https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gruber_Ansgar_118401
  description: "ASAFind is a software that predicts the intracellular location of\
    \ proteins in cells with four membrane-bound complex plastids of red algal origin.\
    \ \nThese plastids evolved via eukaryote-eukaryote endosymbiosis and for example\
    \ can be found in diatoms and cryptophytes. ASAFind uses protein sequence data\
    \ and external predictions of signal peptides (by the tools SignalP and TargetP),\
    \ and predicts plastid proteins, and proteins that are targeted to the periplastidic\
    \ compartment from these data; optionally, a graphical output can generated."
  documentation:
  - note: null
    type:
    - Installation instructions
    url: https://asafind.jcu.cz/download-page/
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    type: Downloads page
    url: https://asafind.jcu.cz/download-page/
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  - Marine Metagenomics
  - Microbial Biotechnology
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  elixirPlatform:
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  elixir_badge: 0
  function:
  - cmd: null
    input:
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        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format: []
    note: null
    operation:
    - term: Subcellular localisation prediction
      uri: http://edamontology.org/operation_2489
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    - term: Protein cleavage site prediction
      uri: http://edamontology.org/operation_0422
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format: []
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format: []
  homepage: https://asafind.jcu.cz/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-15T17:36:43.189214Z'
  license: CC-BY-SA-4.0
  link:
  - note: Web Service
    type:
    - Service
    url: https://asafind.jcu.cz
  - note: Information and source code, for local installation or development
    type:
    - Repository
    url: https://github.com/ASAFind/ASAFind-2
  maturity: Mature
  name: ASAFind
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: martavohnoutova
  publication:
  - doi: 10.1111/tpj.70138
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-06-01T00:00:00Z'
      journal: Plant Journal
      title: 'ASAFind 2.0: multi-class protein targeting prediction for diatoms and
        algae with complex plastids'
    note: Publication of the current version of ASAFind (2.0)
    pmcid: PMC12136025
    pmid: '40464854'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1111/tpj.12734
    metadata:
      abstract: ''
      authors: []
      citationCount: 138
      date: '2015-02-01T00:00:00Z'
      journal: Plant Journal
      title: Plastid proteome prediction for diatoms and other algae with secondary
        plastids of the red lineage
    note: Publication of the first version of ASAFind
    pmcid: PMC4329603
    pmid: '25438865'
    type:
    - Other
    version: '1.0'
  - doi: 10.48550/arXiv.2303.02509
    metadata: null
    note: Benchmarking of the performance of the first version of ASAFind
    pmcid: null
    pmid: null
    type:
    - Benchmarking study
    version: '1.0'
  relation:
  - biotoolsID: signalp
    type: uses
  - biotoolsID: targetp
    type: uses
  toolType:
  - Script
  - Command-line tool
  - Web service
  topic:
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - '2.0'
- accessibility: null
  additionDate: '2020-03-17T13:50:50Z'
  biotoolsCURIE: biotools:seqfu
  biotoolsID: seqfu
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: A collection of utilities to manipulate FASTA and FASTQ files, supporting
    Gzipped input.
  documentation:
  - note: null
    type:
    - User manual
    url: https://telatin.github.io/seqfu2/
  download:
  - note: null
    type: Software package
    url: https://github.com/telatin/seqfu2
    version: null
  - note: null
    type: Downloads page
    url: https://github.com/telatin/seqfu2/releases
    version: null
  - note: null
    type: Software package
    url: https://bioconda.github.io/recipes/seqfu/README.html
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  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: seqfu [subcommand] FASTX > FASTX
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    note: null
    operation:
    - term: Nucleic acid sequence analysis
      uri: http://edamontology.org/operation_2478
    output:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format: []
  homepage: https://telatin.github.io/seqfu2/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-12T21:43:34.328705Z'
  license: null
  link:
  - note: Documentation
    type:
    - Other
    url: https://telatin.github.io/seqfu2
  - note: null
    type:
    - Repository
    url: https://github.com/telatin/seqfu2/
  maturity: null
  name: seqfu
  operatingSystem: []
  otherID: []
  owner: telatin
  publication:
  - doi: 10.3390/bioengineering8050059
    metadata:
      abstract: ''
      authors: []
      citationCount: 36
      date: '2021-01-01T00:00:00Z'
      journal: Bioengineering
      title: 'Seqfu: A suite of utilities for the robust and reproducible manipulation
        of sequence files'
    note: null
    pmcid: PMC8148589
    pmid: '34066939'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Nucleic acids
    uri: http://edamontology.org/topic_0077
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
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  - 1.11.0
  - 1.12.0
  - 1.13.0
  - 1.14.0
  - 1.15.0
  - 1.16.0
  - 1.17.0
  - 1.19.0
  - 1.20.0
  - 1.21.0
  - 1.22.0
  - 1.22.3
- accessibility: null
  additionDate: '2025-05-29T09:54:35.422273Z'
  biotoolsCURIE: biotools:dicomseg_converter
  biotoolsID: dicomseg_converter
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: mario.verdicchio@synlab.it
    fundrefid: null
    gridid: null
    name: Mario Verdicchio
    note: null
    orcidid: https://orcid.org/0000-0002-3762-3100
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: marco.aiello@synlab.it
    fundrefid: null
    gridid: null
    name: Marco Aiello
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: 'This repository provides tools for segmentation files conversion in
    DicomSEG, with a primary focus on: DICOM RTSTRUCT to DICOM SEG: A Python script
    (rtstruct/rtstruct2dcmseg.py) converts DICOM Radiotherapy Structure Set (RTSTRUCT)
    files, along with their referenced DICOM image series, into DICOM Segmentation
    (SEG) objects. It can also optionally convert the individual Regions of Interest
    (ROIs) defined in the RTSTRUCT into separate NIfTI (.nii.gz) files. Nifti Conversions
    via dcmqi and Custom Scripts: The Docker image built from this repository also
    includes command-line tools from dcmqi (DICOM Quantitative Imaging Toolkit) and
    custom Python scripts for various conversions, such as: ITK image formats (NIfTI,
    NRRD) to/from DICOM SEG. DICOM series to NIfTI. DICOM SEG to NIfTI (custom alternative).'
  documentation:
  - note: null
    type:
    - Command-line options
    url: https://github.com/marver17/DICOMSEG_Converter
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/marver17/DICOMSEG_Converter
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-12T10:29:48.030239Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/marver17/DICOMSEG_Converter
  maturity: null
  name: Annotation Seg Converter
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: marioverd
  publication:
  - doi: 10.1186/s13244-021-01081-8
    metadata:
      abstract: ''
      authors: []
      citationCount: 34
      date: '2021-12-01T00:00:00Z'
      journal: Insights into Imaging
      title: How does DICOM support big data management? Investigating its use in
        medical imaging community
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  validated: 0
  version:
  - 1.4.0
- accessibility: null
  additionDate: '2025-12-10T19:41:16.987102Z'
  biotoolsCURIE: biotools:kmindex
  biotoolsID: kmindex
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: kmindex is a tool for indexing and querying sequencing samples. It
    is built on top of kmtricks.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://tlemane.github.io/kmindex/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-10T19:41:16.990159Z'
  license: AGPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/tlemane/kmindex
  maturity: null
  name: kmindex
  operatingSystem: []
  otherID: []
  owner: smeds
  publication:
  - doi: 10.1038/s43588-024-00596-6
    metadata:
      abstract: ''
      authors: []
      citationCount: 6
      date: '2024-02-01T00:00:00Z'
      journal: Nature Computational Science
      title: Indexing and real-time user-friendly queries in terabyte-sized complex
        genomic datasets with kmindex and ORA
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - v0.5.3
- accessibility: null
  additionDate: '2025-05-22T17:46:59.585364Z'
  biotoolsCURIE: biotools:mainzelliste
  biotoolsID: mainzelliste
  collectionID:
  - eucaim
  - EUCAIM
  - Samply
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Mainzelliste is a web-based first-level pseudonymization service. It
    allows for the creation of personal identifiers (PID) from identifying attributes
    (IDAT), and thanks to the record linkage functionality, this is even possible
    with poor quality identifying data. The functions are available through a RESTful
    web interface. Mainzelliste also includes built-in consent management and supports
    FHIR APIs.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://bitbucket.org/medicalinformatics/mainzelliste/src/master/doc/getting-started.md
  - note: null
    type:
    - Installation instructions
    url: https://bitbucket.org/medicalinformatics/mainzelliste/src/master/doc/configuration-handbook.md
  - note: null
    type:
    - Installation instructions
    url: https://bitbucket.org/medicalinformatics/mainzelliste/src/master/docker.md
  - note: null
    type:
    - API documentation
    url: https://medicalinformatics.github.io/mainzelliste.de/api-doc/
  - note: null
    type:
    - Installation instructions
    url: https://drive.eucaim.cancerimage.eu/s/oxK6GtGg46tfRcc
  - note: null
    type:
    - Installation instructions
    url: https://drive.eucaim.cancerimage.eu/s/NCckRbAjYCj3ReR
  - note: null
    type:
    - Quick start guide
    url: https://drive.eucaim.cancerimage.eu/s/8bW9YY4Lz9KaFb7
  - note: null
    type:
    - Installation instructions
    url: https://drive.eucaim.cancerimage.eu/s/HWfZxafrzwZRMbg
  - note: null
    type:
    - API documentation
    url: https://drive.eucaim.cancerimage.eu/s/K84ykkt58Ze4eme
  download: []
  editPermission:
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    - benamor
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://bitbucket.org/medicalinformatics/mainzelliste/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-10T14:03:09.546308Z'
  license: AGPL-3.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://helmholtz.software/software/mainzelliste
  - note: null
    type:
    - Repository
    url: https://bitbucket.org/medicalinformatics/mainzelliste
  - note: null
    type:
    - Repository
    url: https://github.com/medicalinformatics/mainzelliste-gui/
  - note: null
    type:
    - Other
    url: https://docs.google.com/spreadsheets/d/1ipAPipeZa-3cBDFwQGn7kr07OsrhKSf_
  maturity: Mature
  name: Mainzelliste
  operatingSystem:
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  - Mac
  - Windows
  otherID: []
  owner: enola
  publication:
  - doi: 10.1186/s12911-014-0123-5
    metadata:
      abstract: ''
      authors: []
      citationCount: 76
      date: '2015-02-07T00:00:00Z'
      journal: BMC Medical Informatics and Decision Making
      title: A RESTful interface to pseudonymization services in modern web applications
    note: null
    pmcid: PMC4350982
    pmid: '25656224'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  - Web API
  topic:
  - term: Data protection
    uri: http://edamontology.org/topic_4044
  - term: Data identity and mapping
    uri: http://edamontology.org/topic_3345
  validated: 0
  version:
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- accessibility: Open access (with restrictions)
  additionDate: '2025-12-09T09:22:22.735091Z'
  biotoolsCURIE: biotools:instanovo
  biotoolsID: instanovo
  collectionID:
  - proteomics
  - ms-utils
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: k.eloff@instadeep.com
    fundrefid: null
    gridid: null
    name: Kevin Eloff
    note: null
    orcidid: https://orcid.org/0000-0003-1355-8743
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: konka@dtu.dk
    fundrefid: null
    gridid: null
    name: Konstantinos Kalogeropoulos
    note: null
    orcidid: https://orcid.org/0000-0003-3907-9281
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: r.catzel@instadeep.com
    fundrefid: null
    gridid: null
    name: Rachel Catzel
    note: null
    orcidid: https://orcid.org/0000-0002-2983-9833
    rorid: null
    typeEntity: null
    typeRole:
    - Maintainer
    url: null
  - email: j.vangoey@instadeep.com
    fundrefid: null
    gridid: null
    name: Jeroen Van Goey
    note: null
    orcidid: https://orcid.org/0000-0003-4480-5567
    rorid: null
    typeEntity: null
    typeRole:
    - Maintainer
    url: null
  - email: tpaje@dtu.dk
    fundrefid: null
    gridid: null
    name: Timothy P. Jenkins
    note: null
    orcidid: https://orcid.org/0000-0003-2979-5663
    rorid: null
    typeEntity: null
    typeRole:
    - Support
    url: null
  description: InstaNovo is a transformer neural network with the ability to translate
    fragment ion peaks into the sequence of amino acids that make up the studied peptide(s).
  documentation:
  - note: null
    type:
    - General
    url: https://instadeepai.github.io/InstaNovo/
  - note: null
    type:
    - Installation instructions
    url: https://instadeepai.github.io/InstaNovo/tutorials/getting_started/#installation
  - note: null
    type:
    - Quick start guide
    url: https://instadeepai.github.io/InstaNovo/tutorials/getting_started/
  - note: null
    type:
    - Command-line options
    url: https://instadeepai.github.io/InstaNovo/reference/cli/
  - note: null
    type:
    - API documentation
    url: https://instadeepai.github.io/InstaNovo/API/summary/
  - note: null
    type:
    - Citation instructions
    url: https://instadeepai.github.io/InstaNovo/citation/
  download:
  - note: null
    type: Source code
    url: https://github.com/instadeepai/InstaNovo/releases/tag/1.2.2
    version: 1.1.2
  editPermission:
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    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: instanovo predict --data-path /path/to/your/spectra.mgf --output-path predictions.csv
    input:
    - data:
        term: Mass spectrum
        uri: http://edamontology.org/data_0943
      format:
      - term: mzML
        uri: http://edamontology.org/format_3244
      - term: mzXML
        uri: http://edamontology.org/format_3654
      - term: MGF
        uri: http://edamontology.org/format_3651
    note: null
    operation:
    - term: de Novo sequencing
      uri: http://edamontology.org/operation_3644
    output:
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/instadeepai/instanovo
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-09T21:41:17.117080Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/instadeepai/instanovo
  - note: null
    type:
    - Other
    url: https://instanovo.ai/
  - note: null
    type:
    - Issue tracker
    url: https://github.com/instadeepai/InstaNovo/issues
  - note: null
    type:
    - Discussion forum
    url: https://github.com/instadeepai/InstaNovo/discussions
  maturity: Mature
  name: InstaNovo
  operatingSystem:
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  - Mac
  - Linux
  otherID: []
  owner: BioGeek
  publication:
  - doi: 10.1038/s42256-025-01019-5
    metadata:
      abstract: ''
      authors: []
      citationCount: 7
      date: '2025-04-01T00:00:00Z'
      journal: Nature Machine Intelligence
      title: InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale
        proteomics experiments
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: 1.1.4
  relation:
  - biotoolsID: matchms
    type: uses
  - biotoolsID: pyteomics
    type: uses
  - biotoolsID: spectrum_utils
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
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- accessibility: null
  additionDate: '2025-05-29T08:55:46.088021Z'
  biotoolsCURIE: biotools:denoising-inhomogeneity_correction_tool
  biotoolsID: denoising-inhomogeneity_correction_tool
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  - email: null
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    name: GIBI230 - HULAFE
    note: null
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    typeEntity: null
    typeRole: []
    url: null
  description: 'The tool is designed to perform a customisable image pre-processing
    to reduce noise and inhomogeneity field effect, thus improving image quality and
    reproducibility of radiomics features. This tool consists of two independent steps:
    one for denoising using one of the 5 integrated filters (Bilateral Filter, Anisotropic
    Diffusion Filter (ADF), Curvature Flow Filter (CFF), SUSAN and Non Local Means
    (NLM)), and another for the ANTs N4 and another for the ANT''s N4 bias correction
    filter. The parameter configuration of this tool has been optimised for TW1, T2W,
    DWI and DCE sequences in neuroblastoma (NB) and paediatric brain tumours, but
    it can also be configured with some of their parameters using a JSON parameter
    configuration file.'
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.google.com/file/d/1W0aHAIG_bdU9Z1J3aDNsb1r39WBuX9Ot/view?usp=drive_link
  - note: null
    type:
    - Terms of use
    url: https://drive.google.com/file/d/1w1tdjaLdjBZYJTp_EpETN6nwyQIsy4vg/view?usp=drive_link
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  function:
  - cmd: docker run -it --rm --name container_name -v "<input_path>:/input" -v "<output_path>:/output"
      -v "<config_path>:/config" harbor.eucaim.cancerimage.eu/processing-tools/denoising_inhomogeneity_correction_tool:1.1.0
      --config /config/config.json
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processin-tools/denoising_inhomogeneity_correction_tool:1.1.0
      --paths /input/Dataset/Patient_1/Study/T1W /input/Dataset/Patient_2/Study/T2W
      --series_number 2000 --series_description_suffix "_harmonized" --denoising adf
      --conductance 0.5 --iterations 3 --time_step 0.0625 --n4 --bspline_size 50 --n4_iterations
      50 30 --shrink_factor 2
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/artifacts-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-09T10:49:57.094252Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  - note: Link to Bitbucket repository
    type:
    - Repository
    url: https://bitbucket.org/gibi230/harmonization_tool/src/master/
  maturity: null
  name: Denoising-Inhomogeneity Correction Tool (EUCAIM-SW-015_T-01-01-015)
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: casopon
  publication:
  - doi: 10.1007/s10278-021-00512-8
    metadata:
      abstract: ''
      authors: []
      citationCount: 12
      date: '2021-10-01T00:00:00Z'
      journal: Journal of Digital Imaging
      title: MR Denoising Increases Radiomic Biomarker Precision and Reproducibility
        in Oncologic Imaging
    note: null
    pmcid: PMC8554919
    pmid: '34505958'
    type:
    - Primary
    version: null
  - doi: 10.1186/s41747-020-00150-9
    metadata:
      abstract: ''
      authors: []
      citationCount: 57
      date: '2020-12-01T00:00:00Z'
      journal: European Radiology Experimental
      title: 'PRIMAGE project: predictive in silico multiscale analytics to support
        childhood cancer personalised evaluation empowered by imaging biomarkers'
    note: null
    pmcid: PMC7125275
    pmid: '32246291'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  validated: 0
  version:
  - 1.1.0
- accessibility: Open access
  additionDate: '2021-01-02T12:42:50Z'
  biotoolsCURIE: biotools:mgse
  biotoolsID: mgse
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Boas Pucker
    note: null
    orcidid: https://orcid.org/0000-0002-3321-7471
    rorid: null
    typeEntity: null
    typeRole:
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    - Developer
    url: https://www.pbb.uni-bonn.de
  description: Mapping-based Genome Size Estimation (MGSE) predicts the size of a
    genome based on a (short) read mapping to an existing genome assembly. Low complexity
    sequences are often collapsed in a genome assembly thus the assembly size is smaller
    than the genome size. The actual copy number of sequences in the assembly is identified
    based on the coverage (sequencing depth) which allows the calculation of a genome
    size.
  documentation: []
  download:
  - note: MGSE is available on GitHub
    type: Downloads page
    url: https://github.com/bpucker/MGSE
    version: null
  editPermission:
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  homepage: https://github.com/bpucker/MGSE
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-06T16:20:42.941757Z'
  license: null
  link:
  - note: Publication in BMC Genomics
    type:
    - Repository
    url: https://doi.org/10.1186/s12864-025-11640-8
  maturity: Mature
  name: Mapping-based Genome Size Estimation
  operatingSystem:
  - Linux
  otherID: []
  owner: bpucker
  publication:
  - doi: 10.1186/s12864-025-11640-8
    metadata:
      abstract: ''
      authors: []
      citationCount: 2
      date: '2025-12-01T00:00:00Z'
      journal: BMC Genomics
      title: Mapping-based genome size estimation
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Script
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Sequence composition, complexity and repeats
    uri: http://edamontology.org/topic_0157
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  validated: 0
  version: []
- accessibility: null
  additionDate: '2017-01-17T14:56:27Z'
  biotoolsCURIE: biotools:multidataset
  biotoolsID: multidataset
  collectionID:
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  confidence_flag: null
  cost: null
  credit:
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    fundrefid: null
    gridid: null
    name: Carles Hernandez-Ferrer
    note: null
    orcidid: https://orcid.org/0000-0002-8029-7160
    rorid: null
    typeEntity: Person
    typeRole:
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    url: http://www.carleshf.com
  - email: carlos.ruiz@isglobal.org
    fundrefid: null
    gridid: null
    name: Carlos Ruiz-Arenas
    note: null
    orcidid: http://orcid.org/0000-0002-6014-3498
    rorid: null
    typeEntity: null
    typeRole:
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    url: null
  - email: null
    fundrefid: null
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    name: Alba Beltran-Gomila
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    typeEntity: Person
    typeRole:
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    url: null
  - email: juanr.gonzalez@isglobal.org
    fundrefid: null
    gridid: null
    name: Juan R Gonzalez
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: https://brge.isglobal.org/
  description: Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology
    from Center for Research in Environmental Epidemiology) dataset and MethylationSet.
    It is designed for integrating multi omics data sets and MethylationSet to contain
    normalized methylation data. These package contains base classes for MEAL and
    rexposome packages.
  documentation:
  - note: null
    type:
    - User manual
    url: http://bioconductor.org/packages/release/bioc/html/MultiDataSet.html
  download:
  - note: null
    type: Source code
    url: http://bioconductor/packages/release/bioc/src/contrib/MultiDataSet_1.2.0.tar.gz
    version: null
  editPermission:
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  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output: []
  homepage: http://bioconductor.org/packages/release/bioc/html/MultiDataSet.html
  homepage_status: 0
  language:
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  lastUpdate: '2025-12-04T11:18:56.561908Z'
  license: null
  link:
  - note: null
    type:
    - Mirror
    url: http://www.bioconductor.org/packages/release/bioc/html/MultiDataSet.html
  maturity: null
  name: MultiDataSet
  operatingSystem:
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  - Mac
  - Linux
  otherID: []
  owner: chernan3
  publication:
  - doi: 10.1186/s12859-016-1455-1
    metadata:
      abstract: ''
      authors: []
      citationCount: 23
      date: '2017-01-17T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'MultiDataSet: An R package for encapsulating multiple data sets with
        application to omic data integration'
    note: null
    pmcid: PMC5240259
    pmid: '28095799'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: rexposome
    type: uses
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Omics
    uri: http://edamontology.org/topic_3391
  - term: DNA
    uri: http://edamontology.org/topic_0654
  - term: Epigenetics
    uri: http://edamontology.org/topic_3295
  validated: 1
  version:
  - 1.2.0
- accessibility: Open access
  additionDate: '2025-06-30T08:52:48.500476Z'
  biotoolsCURIE: biotools:fair_eva_4_eucaim
  biotoolsID: fair_eva_4_eucaim
  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Fernando Aguilar
    note: 'Creator and devloper of the main package FAIR EVA.

      This software started to be developed within IFCA-Advanced-Computing receives
      funding from the European Union’s Horizon 2020 research and innovation programme
      under grant agreement No 857647.'
    orcidid: https://orcid.org/0000-0001-9462-4831
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    - Documentor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: David Rodríguez
    note: Developer of the EUCAIM plugin.
    orcidid: https://orcid.org/0000-0002-9160-5106
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Inés Victoria
    note: Developer of the EUCAIM plugin.
    orcidid: https://orcid.org/0009-0003-7950-3937
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: 'FAIR EVA: Evaluator, Validator & Advisor has been developed to check
    the FAIRness level of digital objects from different repositories or data portals.
    It requires the object identifier (preferably persistent and unique identifier)
    and the repository to check. It also provides a generic and agnostic way to check
    digital objects.

    This software started to be developed within IFCA-Advanced-Computing receives
    funding from the European Union’s Horizon 2020 research and innovation programme
    under grant agreement No 857647.'
  documentation:
  - note: Documentation for the main package, EUCAIM plugin specific documentation
      not included.
    type:
    - General
    url: https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.md
  - note: Wiki page with FAIR EVA for EUCAIM specific instructions.
    type:
    - User manual
    url: https://gitlabpages.ifca.es/fair-eva-guide-608baa/
  download: []
  editPermission:
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    type: group
  elixirCommunity: []
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  elixir_badge: 0
  function:
  - cmd: python scripts/batch_runner.py --plugin eucaim_catalogue --out faireva_out
    input:
    - data:
        term: URL
        uri: http://edamontology.org/data_1052
      format: []
    note: null
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output:
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
  homepage: https://github.com/IFCA-Advanced-Computing/FAIR_eva
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-04T10:57:20.901575Z'
  license: Apache-2.0
  link:
  - note: Repository for FAIR EVA, without the EUCAIM specific plugin
    type:
    - Repository
    url: https://github.com/IFCA-Advanced-Computing/FAIR_eva
  maturity: Mature
  name: FAIR EVA for EUCAIM
  operatingSystem:
  - Linux
  otherID: []
  owner: davrodgon
  publication:
  - doi: 10.1038/s41597-023-02652-8
    metadata:
      abstract: null
      authors: []
      citationCount: 0
      date: null
      journal: null
      title: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Plug-in
  - Command-line tool
  - Web service
  topic:
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  validated: 0
  version:
  - EUCAIM_plugin_0.3
  - EUCAIM_plugin_0.3.1
  - EUCAIM_plugin_0.4.0
  - EUCAIM_0.4.2
- accessibility: Open access (with restrictions)
  additionDate: '2025-11-25T09:58:37.569343Z'
  biotoolsCURIE: biotools:ml_model_for_mr_series_categorisation
  biotoolsID: ml_model_for_mr_series_categorisation
  collectionID:
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  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: gibi230@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: null
  - email: armago@alumni.uv.es
    fundrefid: null
    gridid: null
    name: Armando Gomis-Maya
    note: null
    orcidid: https://orcid.org/0000-0002-9527-8093
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
    gridid: null
    name: Leonor Cerda-Alberich
    note: null
    orcidid: https://orcid.org/0000-0002-5567-4278
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: A tool based on artificial intelligence that is able to perform a categorisation
    of MRI series by using standardized DICOM tags. The categorisation includes the
    type of sequence (e.g. spin echo, gradient echo), the weighting (e.g. T1W, T2W,
    DCE, ...), the presence of fat suppression and the detection of non-relevant /
    junk series (e.g. localizers, calibrations, screenshots...).
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.google.com/file/d/1lIUixmLItQXOyBPIXL_AzPg_jlqDKwNE/view?usp=drive_link
  - note: null
    type:
    - Terms of use
    url: https://drive.google.com/file/d/1jF44iszmmiHd2paD8-YhFhW2uQJ0QBAZ/view?usp=drive_link
  download: []
  editPermission:
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  elixir_badge: 0
  function:
  - 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'}\""
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Classification
      uri: http://edamontology.org/operation_2990
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-03T15:35:26.140884Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: ML model for MR series categorisation (EUCAIM-SW-011_T-01-01-011)
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication:
  - doi: 10.1186/s40537-025-01086-w
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-12-01T00:00:00Z'
      journal: Journal of Big Data
      title: Automatic magnetic resonance imaging series labelling for large repositories
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  - term: Data acquisition
    uri: http://edamontology.org/topic_3077
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
  - 1.1.0
- accessibility: Open access
  additionDate: '2025-12-02T17:37:57.215347Z'
  biotoolsCURIE: biotools:auto-prostate-sequence-classifier
  biotoolsID: auto-prostate-sequence-classifier
  collectionID:
  - EUCAIM
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit:
  - email: jose.almeida@research.fchampalimaud.org
    fundrefid: null
    gridid: null
    name: José Guilherme de Almeida
    note: null
    orcidid: https://orcid.org/0000-0002-1887-0157
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://josegcpa.net
  - email: null
    fundrefid: null
    gridid: null
    name: Nikolaos Papanikolaou
    note: null
    orcidid: https://orcid.org/0000-0003-3298-2072
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  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.
  documentation:
  - 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.
    type:
    - Other
    url: https://github.com/CCIG-Champalimaud/metadata-classification
  download: []
  editPermission:
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: docker run -v <dir-with-dicom>:/data  harbor.eucaim.cancerimage.eu/processing-tools/champ-autoproseq
      --dicom_recursion <dicom-recursion> --input_paths /data
    input:
    - data:
        term: Raw image
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    uri: http://edamontology.org/topic_3474
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  version:
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- accessibility: Open access
  additionDate: '2025-10-28T18:31:05.926498Z'
  biotoolsCURIE: biotools:pediatric_brain_tumor_segmenter
  biotoolsID: pediatric_brain_tumor_segmenter
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  cost: Free of charge
  credit:
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    gridid: null
    name: Daniel Capellán-Martín
    note: null
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    rorid: null
    typeEntity: Person
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    - Developer
    - Contributor
    - Support
    url: null
  - email: pabhijeet@childrensnational.org
    fundrefid: null
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    name: Abhijeet Parida
    note: null
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    - Support
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    typeRole:
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    - Support
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    note: null
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    typeRole:
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    - Contributor
    url: null
  - email: mlingura@childrensnational.org
    fundrefid: null
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    name: Marius George Linguraru
    note: null
    orcidid: null
    rorid: null
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    typeRole:
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    url: null
  description: The Pediatric Brain Tumor Segmenter is a software tool developed by
    researchers from Universidad Politécnica de Madrid and Children’s National Hospital
    for the segmentation and analysis of pediatric brain tumors in magnetic resonance
    imaging (MRI). Built in Python, it enables precise quantitative analysis of pediatric
    brain tumors in MRI scans to support clinical decision-making in both diagnosis
    and prognosis.
  documentation:
  - note: null
    type:
    - API documentation
    - Citation instructions
    - Terms of use
    - Code of conduct
    - Release notes
    - User manual
    - General
    - Quick start guide
    url: https://docs.hope4kids.io/HOPE-Segmenter-Kids/
  download: []
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  function:
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    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_3553
    output: []
  homepage: https://github.com/BIT-UPM/EUCAIM/pediatric_brain_tumor_segmenter
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-11-28T13:55:19.273705Z'
  license: CC-BY-NC-SA-4.0
  link:
  - note: Main app webpage
    type:
    - Other
    url: https://segmenter.hope4kids.io/
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids
  maturity: Mature
  name: Pediatric Brain Tumor Segmenter
  operatingSystem:
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  - Mac
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  otherID: []
  owner: dani-capellan
  publication:
  - doi: 10.1007/978-3-031-76163-8_20
    metadata:
      abstract: ''
      authors: []
      citationCount: 2
      date: '2024-01-01T00:00:00Z'
      journal: Lecture Notes in Computer Science (including subseries Lecture Notes
        in Artificial Intelligence and Lecture Notes in Bioinformatics)
      title: Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1109/ISBI56570.2024.10635469
    metadata:
      abstract: ''
      authors: []
      citationCount: 1
      date: '2024-01-01T00:00:00Z'
      journal: Proceedings - International Symposium on Biomedical Imaging
      title: 'Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble
        with Adaptive Post-Processing'
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04094
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04111
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  - Workflow
  - Command-line tool
  topic:
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - v1.0
- accessibility: Open access
  additionDate: '2023-06-26T12:38:15.108087Z'
  biotoolsCURIE: biotools:mitk
  biotoolsID: mitk
  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: grid.7497.d
    name: German Cancer Research Center (DKFZ)
    note: null
    orcidid: null
    rorid: 04cdgtt98
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    url: https://www.dkfz.de/de
  description: The Medical Imaging Interaction Toolkit (MITK) is a free open-source
    software for the development of interactive medical image processing software.
    Based on MITK, there is the MITK Workbench, a powerful and free application to
    view, process, and segment medical images.
  documentation:
  - note: null
    type:
    - General
    url: https://docs.mitk.org/2023.04/
  download:
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    type: Downloads page
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    version: null
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  function:
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    input:
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        uri: http://edamontology.org/data_2968
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        uri: http://edamontology.org/format_3548
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    operation:
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      uri: http://edamontology.org/operation_3553
    output:
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        term: Image
        uri: http://edamontology.org/data_2968
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      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
  homepage: https://www.mitk.org/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2025-11-28T09:27:43.812008Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/MITK/MITK/
  - note: 'If you have any questions related to the use of or the development with
      MITK, please use the official mailing list.


      Note that you have to subscribe to the mailing list in order to send mails'
    type:
    - Mailing list
    url: https://lists.sourceforge.net/lists/listinfo/mitk-users
  maturity: Mature
  name: MITK
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  owner: sschaum
  publication:
  - doi: 10.1016/j.media.2005.04.005
    metadata:
      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.
      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.
      citationCount: 378
      date: '2005-12-01T00:00:00Z'
      journal: Medical Image Analysis
      title: The medical imaging interaction toolkit
    note: 'Nolden, Marco, et al. "The Medical Imaging Interaction Toolkit: challenges
      and advances: 10 years of open-source development."

      International journal of computer assisted radiology and surgery 8 (2013): 607-620'
    pmcid: null
    pmid: '15896995'
    type: []
    version: null
  - doi: 10.1007/s11548-013-0840-8
    metadata:
      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.'
      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.
      citationCount: 354
      date: '2013-01-01T00:00:00Z'
      journal: International Journal of Computer Assisted Radiology and Surgery
      title: 'The medical imaging interaction toolkit: Challenges and advances: 10
        years of open-source development'
    note: 'Nolden, Marco, et al. "The Medical Imaging Interaction Toolkit: challenges
      and advances: 10 years of open-source development."

      International journal of computer assisted radiology and surgery 8 (2013): 607-620'
    pmcid: null
    pmid: '23588509'
    type: []
    version: null
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  toolType:
  - Workbench
  - Desktop application
  - Library
  topic: []
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2025-11-26T16:15:53.903274Z'
  biotoolsCURIE: biotools:biocontextai_registry
  biotoolsID: biocontextai_registry
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit: []
  description: The BioContextAI Registry is a community-driven catalog of Model Context
    Protocol (MCP) servers for agentic AI-supported biomedical research. It enables
    researchers and developers to discover, access, and contribute specialized tools
    and databases through a standardized protocol.
  documentation:
  - note: null
    type:
    - General
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    type:
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  maturity: Emerging
  name: BioContextAI Registry
  operatingSystem: []
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  owner: maltekuehl
  publication:
  - doi: 10.1038/s41587-025-02900-9
    metadata:
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      authors: []
      citationCount: 0
      date: '2025-11-01T00:00:00Z'
      journal: Nature biotechnology
      title: BioContextAI is a community hub for agentic biomedical systems
    note: null
    pmcid: null
    pmid: '41199021'
    type:
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    version: null
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  toolType:
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  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Omics
    uri: http://edamontology.org/topic_3391
  - term: Open science
    uri: http://edamontology.org/topic_4010
  validated: 0
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  additionDate: '2025-10-29T09:07:43.796224Z'
  biotoolsCURIE: biotools:raclahe
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  collectionID:
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  confidence_flag: tool
  cost: null
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  description: RACLAHE (Region-Adaptive Contrast Limited Adaptive Histogram Equalization)
    is an image enhancement method specifically designed for improving CNN-based segmentation
    of the prostate and prostatic zones in T2-Weighted MR images.
  documentation:
  - note: null
    type:
    - Quick start guide
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  language:
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  link:
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  name: RACLAHE
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  otherID: []
  owner: dimzaridis
  publication:
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    metadata:
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      authors: []
      citationCount: 19
      date: '2023-12-01T00:00:00Z'
      journal: Scientific Reports
      title: Region-adaptive magnetic resonance image enhancement for improving CNN-based
        segmentation of the prostate and prostatic zones
    note: null
    pmcid: null
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    type:
    - Method
    version: null
  relation: []
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  topic:
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    uri: http://edamontology.org/topic_0092
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - '3.0'
- accessibility: Open access
  additionDate: '2019-08-09T13:13:30Z'
  biotoolsCURIE: biotools:TYGS
  biotoolsID: TYGS
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Markus Göker
    note: null
    orcidid: https://orcid.org/0000-0002-5144-6200
    rorid: null
    typeEntity: Person
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    url: null
  description: Automated high-throughput platform for state-of-the-art genome-based
    taxonomy.
  documentation:
  - note: null
    type:
    - FAQ
    url: https://tygs.dsmz.de/faqs
  download: []
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  lastUpdate: '2025-11-19T14:16:09.917238Z'
  license: Unlicense
  link: []
  maturity: Mature
  name: TYGS
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  - Mac
  - Linux
  otherID: []
  owner: mgoeker
  publication:
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    metadata: null
    note: null
    pmcid: null
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    type:
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  - doi: 10.1093/nar/gkab902
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      citationCount: 1496
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    note: null
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    type:
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  - doi: 10.1038/S41467-019-10210-3
    metadata:
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      authors: []
      citationCount: 2403
      date: '2019-12-01T00:00:00Z'
      journal: Nature Communications
      title: TYGS is an automated high-throughput platform for state-of-the-art genome-based
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    note: null
    pmcid: PMC6522516
    pmid: '31097708'
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  relation: []
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  topic:
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  - term: Phylogeny
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  - term: Microbiology
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  validated: 1
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  additionDate: '2025-03-20T09:46:51.356874Z'
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  biotoolsID: spacedust
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  cost: Free of charge
  credit: []
  description: Spacedust is a modular toolkit for identification of conserved gene
    clusters among multiple genomes based on homology and conservation of gene neighborhood.
    Spacedust adapts the fast and sensitive structure comparisons of Foldseek and
    homology search capabilities of MMseqs2. It introduces a novel approach of aggregating
    sets of homologous hits between pairs of genomes and identifies cluster of hits
    with conserved gene neighborhood between each using agglomerative hierarchical
    clustering algorithm.
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  link: []
  maturity: Emerging
  name: Spacedust
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  otherID: []
  owner: milot-mirdita
  publication:
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    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
  - doi: 10.1038/s41592-025-02816-x
    metadata:
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      citationCount: 0
      date: '2025-10-01T00:00:00Z'
      journal: Nature Methods
      title: De novo discovery of conserved gene clusters in microbial genomes with
        Spacedust
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
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  topic:
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  validated: 0
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- accessibility: null
  additionDate: '2022-02-08T20:08:58.318539Z'
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  description: Foldseek enables fast and sensitive comparisons of large structure
    sets. It reaches sensitivities similar to state-of-the-art structural aligners
    while being at least 20,000 times faster.
  documentation:
  - note: null
    type:
    - User manual
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      - term: mmCIF
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    note: null
    operation:
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    output:
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      format: []
  homepage: https://foldseek.com
  homepage_status: 0
  language:
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  lastUpdate: '2025-11-10T08:35:52.579233Z'
  license: GPL-3.0
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  - note: Webserver to search against multiple structural databases such as the AlphaFoldDB
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    type:
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  maturity: Emerging
  name: Foldseek
  operatingSystem:
  - Mac
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  otherID: []
  owner: milot-mirdita
  publication:
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    metadata:
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      authors: []
      citationCount: 977
      date: '2024-02-01T00:00:00Z'
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    note: null
    pmcid: PMC10869269
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    version: null
  - doi: 10.1101/2022.02.07.479398
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      citationCount: 15
      date: '2025-03-01T00:00:00Z'
      journal: Nature Methods
      title: Rapid and sensitive protein complex alignment with Foldseek-Multimer
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: mmseqs2
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  validated: 0
  version: []
- accessibility: null
  additionDate: '2023-06-07T03:22:25.847061Z'
  biotoolsCURIE: biotools:metabuli
  biotoolsID: metabuli
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'Metabuli: specific and sensitive metagenomic classification via joint
    analysis of DNA and amino acid'
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output: []
  homepage: https://metabuli.steineggerlab.com
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2025-11-10T08:34:05.350544Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/steineggerlab/Metabuli/issues
  maturity: Mature
  name: metabuli
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: milot-mirdita
  publication:
  - doi: 10.1038/s41592-024-02273-y
    metadata:
      abstract: ''
      authors: []
      citationCount: 14
      date: '2024-06-01T00:00:00Z'
      journal: Nature Methods
      title: 'Metabuli: sensitive and specific metagenomic classification via joint
        analysis of amino acid and DNA'
    note: null
    pmcid: null
    pmid: '38769467'
    type: []
    version: null
  - doi: 10.1101/2023.05.31.543018
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1093/bioinformatics/btaf557
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-10-02T00:00:00Z'
      journal: Bioinformatics (Oxford, England)
      title: Easy and interactive taxonomic profiling with Metabuli App
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: mmseqs2
    type: uses
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2019-07-03T16:03:27Z'
  biotoolsCURIE: biotools:MMseqs2
  biotoolsID: MMseqs2
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'MMseqs2 (Many-against-Many sequence searching) is a software suite
    to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open
    source software implemented in C++ for Linux, MacOS, and (as beta version, via
    cygwin) Windows. The software is designed to run on multiple cores and servers
    and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST.
    At 100 times its speed it achieves almost the same sensitivity. It can perform
    profile searches with the same sensitivity as PSI-BLAST at over 400 times its
    speed.


    MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales
    linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments
    in 10 h on a single server to 50% sequence identity.'
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/soedinglab/MMseqs2/blob/master/README.md
  - note: null
    type:
    - User manual
    url: https://github.com/soedinglab/mmseqs2/wiki
  - note: Tutorial material
    type:
    - Training material
    url: https://github.com/soedinglab/MMseqs2/wiki/Tutorials
  download:
  - note: null
    type: Source code
    url: https://github.com/soedinglab/MMseqs2/releases
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: mmseqs easy-search query.fasta target.fasta output.m8 tmp
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTQ-like format (text)
        uri: http://edamontology.org/format_2182
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format:
      - term: BLAST results
        uri: http://edamontology.org/format_1333
  - cmd: 'mmseqs easy-cluster input.fasta output tmp

      mmseqs easy-linclust input.fasta output tmp'
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTQ-like format (text)
        uri: http://edamontology.org/format_2182
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    note: null
    operation:
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    output:
    - data:
        term: Sequence cluster
        uri: http://edamontology.org/data_1235
      format: []
  - cmd: mmseqs easy-taxonomy query.fasta targetDB output tmp
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTQ-like format (text)
        uri: http://edamontology.org/format_2182
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format: []
  homepage: https://mmseqs.com
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2025-11-10T08:28:33.612233Z'
  license: MIT
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/soedinglab/mmseqs2/issues
  - note: null
    type:
    - Repository
    url: https://github.com/soedinglab/mmseqs2
  maturity: Mature
  name: MMseqs2
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: milot-mirdita
  publication:
  - doi: 10.1038/nbt.3988
    metadata:
      abstract: ''
      authors: []
      citationCount: 2439
      date: '2017-11-01T00:00:00Z'
      journal: Nature Biotechnology
      title: MMseqs2 enables sensitive protein sequence searching for the analysis
        of massive data sets
    note: null
    pmcid: null
    pmid: '29035372'
    type: []
    version: null
  - doi: 10.1101/079681
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1038/s41467-018-04964-5
    metadata:
      abstract: ''
      authors: []
      citationCount: 577
      date: '2018-12-01T00:00:00Z'
      journal: Nature Communications
      title: Clustering huge protein sequence sets in linear time
    note: null
    pmcid: PMC6026198
    pmid: '29959318'
    type:
    - Method
    version: null
  - doi: 10.1093/bioinformatics/bty1057
    metadata:
      abstract: ''
      authors: []
      citationCount: 366
      date: '2019-08-15T00:00:00Z'
      journal: Bioinformatics
      title: MMseqs2 desktop and local web server app for fast, interactive sequence
        searches
    note: null
    pmcid: PMC6691333
    pmid: '30615063'
    type:
    - Method
    version: null
  - doi: 10.1101/2020.11.27.401018
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1093/bioinformatics/btab184
    metadata:
      abstract: ''
      authors: []
      citationCount: 162
      date: '2021-09-15T00:00:00Z'
      journal: Bioinformatics
      title: Fast and sensitive taxonomic assignment to metagenomic contigs
    note: MMseqs2 Taxonomy
    pmcid: PMC8479651
    pmid: '33734313'
    type: []
    version: null
  - doi: 10.1101/2024.11.13.623350v1
    metadata: null
    note: MMseqs2-GPU preprint
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1038/s41592-025-02819-8
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-10-01T00:00:00Z'
      journal: Nature Methods
      title: GPU-accelerated homology search with MMseqs2
    note: MMseqs2-GPU
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: mmseqs
    type: isNewVersionOf
  - biotoolsID: plass
    type: usedBy
  - biotoolsID: linclust
    type: includes
  - biotoolsID: metaeuk
    type: usedBy
  - biotoolsID: conterminator
    type: usedBy
  - biotoolsID: spacepharer
    type: usedBy
  toolType:
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Nucleic acids
    uri: http://edamontology.org/topic_0077
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2025-10-31T10:28:34.411099Z'
  biotoolsCURIE: biotools:automated_detection_and_segmentation_nsclc
  biotoolsID: automated_detection_and_segmentation_nsclc
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Automated detection and segmentation of non-small cell lung cancer
    computed tomography images
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/primakov/DuneAI-Automated-detection-and-segmentation-of-non-small-cell-lung-cancer-computed-tomography-images
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-11-04T15:05:08.990137Z'
  license: null
  link: []
  maturity: null
  name: UM - Automated detection and segmentation NSCLC
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: sinaamirrajab
  publication:
  - doi: 10.1038/s41467-022-30841-3
    metadata:
      abstract: ''
      authors: []
      citationCount: 110
      date: '2022-12-01T00:00:00Z'
      journal: Nature Communications
      title: Automated detection and segmentation of non-small cell lung cancer computed
        tomography images
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-11-04T15:00:53.996964Z'
  biotoolsCURIE: biotools:um_rqs_2.0_with_rrls
  biotoolsID: um_rqs_2.0_with_rrls
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit: []
  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.
  documentation:
  - note: Framework to establish a structured, step-by-step approach to radiomics
      research.
    type:
    - User manual
    url: https://www.radiomics.world/rqs2
  - note: null
    type:
    - FAQ
    url: https://www.radiomics.world/faq
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.radiomics.world/home
  homepage_status: 0
  language: []
  lastUpdate: '2025-11-04T15:04:40.394407Z'
  license: Freeware
  link: []
  maturity: Emerging
  name: UM - RQS 2.0 with RRLs
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: sinaamirrajab
  publication:
  - doi: 10.1038/s41571-025-01067-1
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-11-01T00:00:00Z'
      journal: Nature Reviews Clinical Oncology
      title: 'Radiomics Quality Score 2.0: towards radiomics readiness levels and
        clinical translation for personalized medicine'
    note: null
    pmcid: null
    pmid: '40903523'
    type:
    - Review
    version: null
  relation: []
  toolType:
  - Web service
  topic: []
  validated: 0
  version:
  - '2.0'
- accessibility: Open access
  additionDate: '2023-08-24T10:15:08.106111Z'
  biotoolsCURIE: biotools:maw
  biotoolsID: maw
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: mahnoor.zulfiqar@uni-jena.de
    fundrefid: null
    gridid: null
    name: Mahnoor Zulfiqar
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: christoph.steinbeck@uni-jena.de
    fundrefid: null
    gridid: null
    name: Christoph Steinbeck
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: kristian.peters@ipb-halle.de
    fundrefid: null
    gridid: null
    name: Kristian Peters
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Luiz Gadelha
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Maria Sorokina
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Metabolome Annotation Workflow for untargeted tandem mass spectrometry.
  documentation: []
  download: []
  editPermission:
    authors:
    - recetox-specdatri
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Protein identification
      uri: http://edamontology.org/operation_3767
    - term: Natural product identification
      uri: http://edamontology.org/operation_3803
    - term: Tag-based peptide identification
      uri: http://edamontology.org/operation_3643
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output: []
  homepage: https://github.com/zmahnoor14/MAW
  homepage_status: 0
  language:
  - Python
  - R
  lastUpdate: '2025-11-03T16:47:22.668278Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/zmahnoor14/MAW-Benchmark
  maturity: null
  name: MAW
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1186/s13321-023-00695-y
    metadata:
      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.
      authors:
      - name: Zulfiqar M.
      - name: Gadelha L.
      - name: Steinbeck C.
      - name: Sorokina M.
      - name: Peters K.
      citationCount: 10
      date: '2023-12-01T00:00:00Z'
      journal: Journal of Cheminformatics
      title: 'MAW: the reproducible Metabolome Annotation Workflow for untargeted
        tandem mass spectrometry'
    note: null
    pmcid: PMC9985203
    pmid: '36871033'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Cheminformatics
    uri: http://edamontology.org/topic_2258
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2019-08-09T13:14:25Z'
  biotoolsCURIE: biotools:El-MAVEN
  biotoolsID: El-MAVEN
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: info@elucidata.io
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Support
    url: null
  - email: elmaven@elucidata.io
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine
    for Metabolomics.
  documentation:
  - note: null
    type:
    - User manual
    url: https://elucidatainc.github.io/ElMaven/documentation/
  download:
  - note: null
    type: Binaries
    url: https://elucidatainc.github.io/ElMaven/Downloads/
    version: null
  - note: null
    type: Source code
    url: https://github.com/ElucidataInc/ElMaven/releases
    version: null
  editPermission:
    authors:
    - recetox-specdatri
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/ElucidataInc/ElMaven
  homepage_status: 0
  language: []
  lastUpdate: '2025-11-03T16:47:19.388844Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ElucidataInc/ElMaven
  - note: null
    type:
    - Issue tracker
    url: https://github.com/ElucidataInc/ElMaven/issues
  maturity: Mature
  name: El-MAVEN
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: hans
  publication:
  - doi: 10.1007/978-1-4939-9236-2_19
    metadata:
      abstract: ''
      authors: []
      citationCount: 106
      date: '2019-01-01T00:00:00Z'
      journal: Methods in Molecular Biology
      title: 'EL-MAVEN: A fast, robust, and user-friendly mass spectrometry data processing
        engine for metabolomics'
    note: null
    pmcid: null
    pmid: '31119671'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2022-09-05T21:19:03.847868Z'
  biotoolsCURIE: biotools:msnovelist
  biotoolsID: msnovelist
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: zamboni@imsb.biol.ethz.ch
    fundrefid: null
    gridid: null
    name: Nicola Zamboni
    note: null
    orcidid: https://orcid.org/0000-0003-1271-1021
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Sebastian Böcker
    note: null
    orcidid: https://orcid.org/0000-0002-9304-8091
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Kai Dührkop
    note: null
    orcidid: https://orcid.org/0000-0002-9056-0540
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Michael A. Stravs
    note: null
    orcidid: https://orcid.org/0000-0002-1426-8572
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: De novo structure generation from mass spectra.
  documentation: []
  download: []
  editPermission:
    authors:
    - recetox-specdatri
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Ab initio structure prediction
      uri: http://edamontology.org/operation_0476
    - term: Spectrum calculation
      uri: http://edamontology.org/operation_3860
    - term: Phasing
      uri: http://edamontology.org/operation_3454
    - term: Deposition
      uri: http://edamontology.org/operation_3431
    - term: Small molecule design
      uri: http://edamontology.org/operation_4009
    output: []
  homepage: https://github.com/meowcat/MSNovelist
  homepage_status: 0
  language:
  - Python
  - Java
  lastUpdate: '2025-11-03T16:47:18.329938Z'
  license: AGPL-3.0
  link: []
  maturity: null
  name: MSNovelist
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Jennifer
  publication:
  - doi: 10.1038/S41592-022-01486-3
    metadata:
      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.
      authors:
      - name: Stravs M.A.
      - name: Duhrkop K.
      - name: Bocker S.
      - name: Zamboni N.
      citationCount: 1
      date: '2022-07-01T00:00:00Z'
      journal: Nature Methods
      title: 'MSNovelist: de novo structure generation from mass spectra'
    note: null
    pmcid: PMC9262714
    pmid: '35637304'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Lipids
    uri: http://edamontology.org/topic_0153
  validated: 1
  version: []
- accessibility: null
  additionDate: '2021-01-18T11:58:45Z'
  biotoolsCURIE: biotools:canopus
  biotoolsID: canopus
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Sebastian Böcker
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  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.
  documentation: []
  download: []
  editPermission:
    authors:
    - recetox-specdatri
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
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  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Spectrum calculation
      uri: http://edamontology.org/operation_3860
    - term: Natural product identification
      uri: http://edamontology.org/operation_3803
    - term: Spectral library search
      uri: http://edamontology.org/operation_3801
    - term: Deposition
      uri: http://edamontology.org/operation_3431
    output: []
  homepage: https://bio.informatik.uni-jena.de/software/canopus/
  homepage_status: 0
  language: []
  lastUpdate: '2025-11-03T16:47:13.400194Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/kaibioinfo/canopus_treemap
  maturity: null
  name: CANOPUS
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1038/S41587-020-0740-8
    metadata:
      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.
      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.
      citationCount: 24
      date: '2021-04-01T00:00:00Z'
      journal: Nature Biotechnology
      title: Systematic classification of unknown metabolites using high-resolution
        fragmentation mass spectra
    note: null
    pmcid: null
    pmid: '33230292'
    type: []
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2022-09-04T23:10:37.868759Z'
  biotoolsCURIE: biotools:peakforest
  biotoolsID: peakforest
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: Franck.Giacomoni@inrae.fr
    fundrefid: null
    gridid: null
    name: Franck Giacomoni
    note: null
    orcidid: https://orcid.org/0000-0001-6063-4214
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Estelle Pujos-Guillot
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Christophe Junot
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: François Fenaille
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: A multi-platform digital infrastructure for interoperable metabolite
    spectral data and metadata management.
  documentation: []
  download: []
  editPermission:
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    - recetox-specdatri
    type: group
  elixirCommunity: []
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  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Natural product identification
      uri: http://edamontology.org/operation_3803
    - term: Spectral library search
      uri: http://edamontology.org/operation_3801
    - term: Deposition
      uri: http://edamontology.org/operation_3431
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output: []
  homepage: https://peakforest.org
  homepage_status: 0
  language:
  - Java
  - JavaScript
  lastUpdate: '2025-11-03T16:47:12.424836Z'
  license: Other
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/peakforest
  maturity: null
  name: PeakForest
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Jennifer
  publication:
  - doi: 10.1007/S11306-022-01899-3
    metadata:
      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.'
      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.
      citationCount: 0
      date: '2022-06-01T00:00:00Z'
      journal: Metabolomics
      title: 'PeakForest: a multi-platform digital infrastructure for interoperable
        metabolite spectral data and metadata management'
    note: null
    pmcid: PMC9197906
    pmid: '35699774'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: NMR
    uri: http://edamontology.org/topic_0593
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Data submission, annotation and curation
    uri: http://edamontology.org/topic_0219
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2023-12-01T15:46:02.196263Z'
  biotoolsCURIE: biotools:buddy
  biotoolsID: buddy
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: thuan@chem.ubc.ca
    fundrefid: null
    gridid: null
    name: Tao Huan
    note: null
    orcidid: http://orcid.org/0000-0001-6295-2435
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Open-source cheminformatic software platform developed for MS-based
    metabolomics research.
  documentation:
  - note: null
    type:
    - User manual
    url: https://philipbear.github.io/BUDDY_Metabolomics
  download: []
  editPermission:
    authors:
    - recetox-specdatri
    type: group
  elixirCommunity: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Peptide database search
      uri: http://edamontology.org/operation_3646
    - term: de Novo sequencing
      uri: http://edamontology.org/operation_3644
    - term: Optimisation and refinement
      uri: http://edamontology.org/operation_2425
    output: []
  homepage: https://github.com/HuanLab/BUDDY
  homepage_status: 0
  language:
  - C#
  lastUpdate: '2025-11-03T16:45:48.375514Z'
  license: MIT
  link: []
  maturity: null
  name: BUDDY
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1038/s41592-023-01850-x
    metadata:
      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).
      authors:
      - name: Xing S.
      - name: Shen S.
      - name: Xu B.
      - name: Li X.
      - name: Huan T.
      citationCount: 21
      date: '2023-06-01T00:00:00Z'
      journal: Nature Methods
      title: 'BUDDY: molecular formula discovery via bottom-up MS/MS interrogation'
    note: null
    pmcid: null
    pmid: '37055660'
    type: []
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Cheminformatics
    uri: http://edamontology.org/topic_2258
  - term: Endocrinology and metabolism
    uri: http://edamontology.org/topic_3407
  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  validated: 0
  version: []
- accessibility: null
  additionDate: '2021-05-26T20:56:35Z'
  biotoolsCURIE: biotools:ms_dial
  biotoolsID: ms_dial
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: makoto.arita@riken.jp
    fundrefid: null
    gridid: null
    name: Makoto Arita
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: hiroshi.tsugawa@riken.jp
    fundrefid: null
    gridid: null
    name: Hiroshi Tsugawa
    note: null
    orcidid: https://orcid.org/0000-0002-2015-3958
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  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)
  documentation:
  - note: null
    type:
    - General
    url: https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial
  - note: null
    type:
    - FAQ
    url: http://prime.psc.riken.jp/compms/msdial/faq.html
  download: []
  editPermission:
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    type: group
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  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Deisotoping
      uri: http://edamontology.org/operation_3629
    - term: Peak detection
      uri: http://edamontology.org/operation_3215
    - term: Natural product identification
      uri: http://edamontology.org/operation_3803
    - term: MRM/SRM
      uri: http://edamontology.org/operation_3636
    output: []
  homepage: http://prime.psc.riken.jp/compms/msdial/main.html
  homepage_status: 0
  language: []
  lastUpdate: '2025-11-03T16:45:45.835795Z'
  license: null
  link: []
  maturity: null
  name: MS-DIAL
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1038/s41587-020-0531-2
    metadata:
      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.
      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.
      citationCount: 38
      date: '2020-10-01T00:00:00Z'
      journal: Nature Biotechnology
      title: A lipidome atlas in MS-DIAL 4
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Lipids
    uri: http://edamontology.org/topic_0153
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  validated: 0
  version: []
- accessibility: null
  additionDate: '2018-07-03T00:07:39Z'
  biotoolsCURIE: biotools:metaboanalyst
  biotoolsID: metaboanalyst
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: jeff.xia@mcgill.ca
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Statistical, functional and integrative analysis of metabolomics data
    , interpretation, and integration with other omics data.
  documentation:
  - note: null
    type:
    - General
    url: http://www.metaboanalyst.ca/faces/docs/Faqs.xhtml
  - note: null
    type:
    - Training material
    url: http://www.metaboanalyst.ca/faces/docs/Tutorial.xhtml
  - note: null
    type:
    - General
    url: http://www.metaboanalyst.ca/faces/docs/Contact.xhtml
  download:
  - note: null
    type: Source code
    url: http://www.metaboanalyst.ca/faces/docs/Resources.xhtml
    version: null
  editPermission:
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  function:
  - cmd: null
    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_3501
    output: []
  - cmd: null
    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_2409
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Pathway or network analysis
      uri: http://edamontology.org/operation_2497
    output: []
  homepage: http://www.metaboanalyst.ca
  homepage_status: 0
  language:
  - R
  - Java
  lastUpdate: '2025-11-03T16:45:45.351615Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: MetaboAnalyst
  operatingSystem: []
  otherID: []
  owner: aotamendi.1
  publication:
  - doi: 10.1093/nar/gky310
    metadata:
      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.'
      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.
      citationCount: 2833
      date: '2018-07-02T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MetaboAnalyst 4.0: Towards more transparent and integrative metabolomics
        analysis'
    note: null
    pmcid: PMC6030889
    pmid: '29762782'
    type: []
    version: null
  - doi: 10.1038/s41596-022-00710-w
    metadata:
      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.'
      authors:
      - name: Pang Z.
      - name: Zhou G.
      - name: Ewald J.
      - name: Chang L.
      - name: Hacariz O.
      - name: Basu N.
      - name: Xia J.
      citationCount: 730
      date: '2022-08-01T00:00:00Z'
      journal: Nature Protocols
      title: Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration
        and covariate adjustment of global metabolomics data
    note: null
    pmcid: null
    pmid: '35715522'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  validated: 1
  version:
  - '4.0'
  - '5.0'
- accessibility: Open access
  additionDate: '2022-11-25T21:43:37.501728Z'
  biotoolsCURIE: biotools:tidymass
  biotoolsID: tidymass
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: caroline.johnson@yale.edu
    fundrefid: null
    gridid: null
    name: Caroline H. Johnson
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: mpsnyder@stanford.edu
    fundrefid: null
    gridid: null
    name: Michael P. Snyder
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Xiaotao Shen
    note: null
    orcidid: http://orcid.org/0000-0002-9608-9964
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Hong Yan
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: An Object-oriented Reproducible Analysis Framework for LC-MS Data.
  documentation: []
  download:
  - note: null
    type: Container file
    url: https://hub.docker.com/r/jaspershen/tidymass-case-study
    version: null
  - note: null
    type: Container file
    url: https://hub.docker.com/r/jaspershen/tidymass
    version: null
  - note: null
    type: Container file
    url: https://www.tidymass.org/start/tidymass_docker/
    version: null
  editPermission:
    authors:
    - recetox-specdatri
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://www.tidymass.org/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-11-03T16:45:44.856713Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/tidymass
  - note: null
    type:
    - Other
    url: https://tidymass.tidymass.org/
  maturity: null
  name: tidyMass
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Jennifer
  publication:
  - doi: 10.1038/s41467-022-32155-w
    metadata:
      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.
      authors:
      - name: Shen X.
      - name: Yan H.
      - name: Wang C.
      - name: Gao P.
      - name: Johnson C.H.
      - name: Snyder M.P.
      citationCount: 28
      date: '2022-12-01T00:00:00Z'
      journal: Nature Communications
      title: TidyMass an object-oriented reproducible analysis framework for LC–MS
        data
    note: null
    pmcid: PMC9334349
    pmid: '35902589'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2024-01-02T02:11:50.145026Z'
  biotoolsCURIE: biotools:umetaflow
  biotoolsID: umetaflow
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: tiwe@biosustain.dtu.dk
    fundrefid: null
    gridid: null
    name: Tilmann Weber
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Untargeted metabolomics workflow for high-throughput data processing
    and analysis.
  documentation: []
  download: []
  editPermission:
    authors:
    - recetox-specdatri
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Imputation
      uri: http://edamontology.org/operation_3557
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Deisotoping
      uri: http://edamontology.org/operation_3629
    output: []
  homepage: https://github.com/biosustain/snakemake_UmetaFlow
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-11-03T16:16:27.787938Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/biosustain/pyOpenMS_UmetaFlow
  maturity: null
  name: UmetaFlow
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1186/s13321-023-00724-w
    metadata:
      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.]'
      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.
      citationCount: 7
      date: '2023-12-01T00:00:00Z'
      journal: Journal of Cheminformatics
      title: 'UmetaFlow: an untargeted metabolomics workflow for high-throughput data
        processing and analysis'
    note: null
    pmcid: PMC10176759
    pmid: '37173725'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2020-01-21T09:25:21Z'
  biotoolsCURIE: biotools:IsoCor
  biotoolsID: IsoCor
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: millard@insa-toulouse.fr
    fundrefid: null
    gridid: null
    name: Pierre Millard
    note: null
    orcidid: https://orcid.org/0000-0002-8136-9963
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: guionnet@insa-toulouse.fr
    fundrefid: null
    gridid: null
    name: Matthieu Guionnet
    note: null
    orcidid: https://orcid.org/0000-0001-5326-0357
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Baudoin Delépine
    note: null
    orcidid: https://orcid.org/0000-0001-6288-425X
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  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.
  documentation:
  - note: null
    type:
    - API documentation
    - Command-line options
    - FAQ
    - Installation instructions
    - User manual
    url: https://isocor.readthedocs.io/en/latest/
  download:
  - note: null
    type: Source code
    url: https://github.com/MetaSys-LISBP/IsoCor
    version: '2'
  editPermission:
    authors:
    - recetox-specdatri
    type: group
  elixirCommunity: []
  elixirNode:
  - France
  elixirPlatform:
  - Tools
  - Compute
  elixir_badge: 0
  function: []
  homepage: https://github.com/MetaSys-LISBP/IsoCor
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-11-03T16:16:25.029297Z'
  license: GPL-3.0
  link:
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/MetaSys-LISBP/IsoCor
  - note: Documentation
    type:
    - Helpdesk
    url: https://isocor.readthedocs.io/en/latest/
  - note: Galaxy tool shed
    type:
    - Galaxy service
    url: https://toolshed.g2.bx.psu.edu/view/gmat/isocor/96f7617b4848
  - note: PyPi repository
    type:
    - Repository
    url: https://pypi.org/project/IsoCor/
  - note: Bioconda repository
    type:
    - Repository
    url: https://anaconda.org/bioconda/isocor
  maturity: Mature
  name: IsoCor
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: millard
  publication:
  - doi: 10.1093/bioinformatics/btz209
    metadata:
      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/.'
      authors:
      - name: Millard P.
      - name: Delepine B.
      - name: Guionnet M.
      - name: Heuillet M.
      - name: Bellvert F.
      - name: Letisse F.
      citationCount: 21
      date: '2019-11-01T00:00:00Z'
      journal: Bioinformatics
      title: 'IsoCor: Isotope correction for high-resolution MS labeling experiments'
    note: null
    pmcid: null
    pmid: '30903185'
    type:
    - Method
    version: '2'
  relation: []
  toolType:
  - Command-line tool
  - Library
  - Desktop application
  topic:
  - term: Fluxomics
    uri: http://edamontology.org/topic_3955
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-01-13T13:15:12Z'
  biotoolsCURIE: biotools:krona
  biotoolsID: krona
  collectionID:
  - Animal and Crop Genomics
  confidence_flag: null
  cost: null
  credit:
  - email: ondovb@nbacc.net
    fundrefid: null
    gridid: null
    name: B.D. Ondov
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: GitHub Issues
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://github.com/marbl/Krona/issues
  description: Krona creates interactive HTML5 charts of hierarchical data (such as
    taxonomic abundance in a metagenome).
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/marbl/Krona/wiki/Help
  download: []
  editPermission:
    authors:
    - animalandcropgenomics
    - ELIXIR-CZ
    - Bioinformatics_project
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://github.com/marbl/Krona/wiki
  homepage_status: 0
  language:
  - JavaScript
  - Perl
  lastUpdate: '2025-10-29T15:10:11.949158Z'
  license: Proprietary
  link: []
  maturity: Mature
  name: Krona
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1186/1471-2105-12-385
    metadata:
      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.'
      authors:
      - name: Ondov B.D.
      - name: Bergman N.H.
      - name: Phillippy A.M.
      citationCount: 1386
      date: '2011-09-30T00:00:00Z'
      journal: BMC Bioinformatics
      title: Interactive metagenomic visualization in a Web browser
    note: null
    pmcid: PMC3190407
    pmid: '21961884'
    type: []
    version: null
  relation: []
  toolType:
  - Plug-in
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2019-08-26T14:34:55Z'
  biotoolsCURIE: biotools:MINERVA_Platform
  biotoolsID: MINERVA_Platform
  collectionID:
  - LCSB
  - ELIXIR-LU
  confidence_flag: null
  cost: Free of charge
  credit: []
  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.


    The 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.'
  documentation:
  - note: null
    type:
    - Quick start guide
    - Release notes
    - User manual
    - API documentation
    - Citation instructions
    - Terms of use
    url: https://minerva.uni.lu
  download:
  - note: Installation instructions, including debian package, virtual machine images
      and docker containers.
    type: Other
    url: https://minerva.pages.uni.lu/doc/install/
    version: 13.1.3 - 18.1.1
  editPermission:
    authors:
    - sascha.herzinger
    type: group
  elixirCommunity: []
  elixirNode:
  - Luxembourg
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Visualise systems biology diagrams online, on a standalone web server
    operation:
    - term: Pathway visualisation
      uri: http://edamontology.org/operation_3926
    output: []
  - cmd: null
    input: []
    note: Visualise omics data from multiple datasets on top of the diagrams
    operation:
    - term: Expression data visualisation
      uri: http://edamontology.org/operation_0571
    output: []
  - cmd: null
    input: []
    note: 'Convert between main systems biology layout formats: CellDeslgners SBML,
      SBML layout+render, SBGN-ML, GPML'
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output: []
  - cmd: null
    input: []
    note: Use MINERVA API to access systems biology formats for modelling
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output: []
  homepage: https://minerva.uni.lu
  homepage_status: 0
  language: []
  lastUpdate: '2025-10-29T08:54:40.647322Z'
  license: AGPL-3.0
  link:
  - note: GiLab repository for core functionalities (data and format handling, service
      stability, API access)
    type:
    - Repository
    url: https://gitlab.lcsb.uni.lu/minerva/core/
  - note: Issue tracker for core functionalities (data and format handling, service
      stability, API access)
    type:
    - Issue tracker
    url: https://gitlab.lcsb.uni.lu/minerva/core/-/issues
  - note: GiLab repository for frontend functionalities
    type:
    - Repository
    url: https://gitlab.lcsb.uni.lu/minerva/frontend
  - note: Issue tracker for frontend functionalities
    type:
    - Issue tracker
    url: https://gitlab.lcsb.uni.lu/minerva/frontend/-/issues
  maturity: Mature
  name: The MINERVA Platform
  operatingSystem: []
  otherID: []
  owner: mjostaszewski
  publication:
  - doi: 10.1038/npjsba.2016.20
    metadata:
      abstract: ''
      authors: []
      citationCount: 71
      date: '2016-01-01T00:00:00Z'
      journal: npj Systems Biology and Applications
      title: MINERVA—A platform for visualization and curation of molecular interaction
        networks
    note: null
    pmcid: PMC5516855
    pmid: '28725475'
    type:
    - Primary
    version: '10.0'
  - doi: 10.1093/bioinformatics/btz286
    metadata:
      abstract: ''
      authors: []
      citationCount: 26
      date: '2019-11-01T00:00:00Z'
      journal: Bioinformatics
      title: 'MINERVA API and plugins: Opening molecular network analysis and visualization
        to the community'
    note: null
    pmcid: PMC6821317
    pmid: '31074494'
    type:
    - Primary
    version: 12.2.3
  - doi: 10.1093/bib/bbz067
    metadata:
      abstract: ''
      authors: []
      citationCount: 18
      date: '2019-07-10T00:00:00Z'
      journal: Briefings in Bioinformatics
      title: Closing the gap between formats for storing layout information in systems
        biology
    note: null
    pmcid: PMC7373180
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  description: MS Annika is a crosslink search engine based on MS Amanda, aimed at
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  description: 'ViVo Platform is a free, open-access web application for the analysis
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    Designed to standardize in vivo efficacy analysis, improve research reproducibility,
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    by reducing the number of animals needed in preclinical efficacy studies.'
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next: ?page=2
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