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  description: A tool that checks the clinical metadata quality (validity, completeness),
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  description: D-GENIES – for Dot plot large Genomes in an Interactive, Efficient
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  biotoolsCURIE: biotools:microminer
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  description: MicroMiner assists in identifying single-residue substitutions in protein
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  description: JAMDA enables the preparation of individual protein structures and
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  description: PoseEdit automatically generates 2D diagrams of protein-ligand complexes,
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  - note: null
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  maturity: Mature
  name: BCFtools
  operatingSystem:
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  otherID: []
  owner: awhitwham
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  - doi: 10.1093/bioinformatics/btp352
    metadata:
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      journal: Bioinformatics
      title: The Sequence Alignment/Map format and SAMtools
    note: The Sequence Alignment/Map format and SAMtools.
    pmcid: PMC2723002
    pmid: '19505943'
    type:
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    version: null
  - doi: 10.1093/gigascience/giab008
    metadata:
      abstract: ''
      authors: []
      citationCount: 8157
      date: '2021-02-01T00:00:00Z'
      journal: GigaScience
      title: Twelve years of SAMtools and BCFtools
    note: Twelve years of SAMtools and BCFtools.
    pmcid: PMC7931819
    pmid: '33590861'
    type:
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    version: null
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    type: uses
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  topic:
  - term: Genetic variation
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  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: GWAS study
    uri: http://edamontology.org/topic_3517
  - term: Genotyping experiment
    uri: http://edamontology.org/topic_3516
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - '1.3'
  - 1.3.1
  - '1.4'
  - 1.4.1
  - '1.5'
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  - '1.9'
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  - '1.19'
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  - '1.21'
  - '1.22'
  - '1.23'
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  additionDate: '2025-07-21T09:36:40.711284Z'
  biotoolsCURIE: biotools:nnunet
  biotoolsID: nnunet
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  confidence_flag: null
  cost: null
  credit:
  - email: r.floca@Dkfz-Heidelberg.de
    fundrefid: null
    gridid: null
    name: DKFZ Heidelberg
    note: Group Lead and Board Member, Medical Image Computing department, DKFZ Heidelberg
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    - Contributor
    - Maintainer
    url: https://www.dkfz.de/
  description: "nnU-Net is a self-configuring method for deep learning-based biomedical\
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    \ Imaging and the Division of Medical Image Computing at the German Cancer Research\
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    \ the provided training cases to configure a matching U-Net-based segmentation\
    \ pipeline without requiring expertise from the user.\nThe tool provides pretrained\
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    \ segmentation, Abdominal organ segmentation, Liver and liver tumor segmentation,\
    \ Kidney and kidney tumor segmentation, Brain Tumor segmentation and Hippocampus\
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  documentation:
  - note: GitHub Readme
    type:
    - General
    url: https://github.com/MIC-DKFZ/nnUNet/tree/nnunetv1
  - note: Docker containers and other relevant instructions
    type:
    - User manual
    url: https://github.com/MIC-DKFZ/nnunet-eucaim-docker/
  download: []
  editPermission:
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    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet pretrained on Task007_Pancreas targeting are pancras and pancreas
      tumor
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-liver-tumour
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet model pretrained on Task029_LiTS targeting are liver and liver
      tumor
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-hippocampus-segmentation
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet pretrained on Task004_Hippocampus MRI data targeting posterior
      and anterior parts of the hippocampus
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-colon-cancer
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet pretrained on Task010_Colon targeting are colon cancer primaries.
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-brain-tumour-pet
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    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet pretrained on Task169_BrainTumorPET targeting are brain tumor
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
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    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUNet model pretrained on Task017_AbdominalOrganSegmentation targeting
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    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
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    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUNet model pretrained on Task135_KiTS2021 targeting are kidney, tumor
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    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://github.com/MIC-DKFZ/nnUNet/tree/nnunetv1
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  language:
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  lastUpdate: '2025-12-16T12:04:54.619598Z'
  license: Apache-2.0
  link: []
  maturity: Mature
  name: nnUNet
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  owner: ASHISR
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  - doi: 10.1038/s41592-020-01008-z
    metadata:
      abstract: ''
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      citationCount: 6593
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      journal: Nature Methods
      title: 'nnU-Net: a self-configuring method for deep learning-based biomedical
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    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
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  version:
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  description: The GlobalAMFungi Database is an open-access, global repository of
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    note: null
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  name: globalamfungi
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  owner: TomasVetrovsky
  publication:
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    metadata:
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    pmcid: null
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  topic:
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  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  validated: 0
  version: []
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T09:19:51.404419Z'
  biotoolsCURIE: biotools:mr-based_dipg_tumour_detection_and_segmentation
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  cost: Free of charge (with restrictions)
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    orcidid: null
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    orcidid: https://orcid.org/0000-0001-9374-1411
    rorid: null
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    url: null
  - email: pedromiguel_martinez@iislafe.es
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    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
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    - Developer
    - Documentor
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    url: null
  - email: adrian_galiana@iislafe.es
    fundrefid: null
    gridid: null
    name: Adrian Galiana-Bordera
    note: null
    orcidid: https://orcid.org/0000-0002-8324-8284
    rorid: null
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    typeRole:
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    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
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    note: null
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    rorid: null
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  description: The tool performs an automatic segmentation of the possible DIPG tumours
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  documentation:
  - note: null
    type:
    - General
    url: https://link.springer.com/article/10.1007/s10278-025-01557-9
  download: []
  editPermission:
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  function:
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    - data:
        term: Image
        uri: http://edamontology.org/data_2968
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      - term: DICOM format
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    - data:
        term: Report
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      - term: CSV
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    note: null
    operation:
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      - term: DICOM format
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  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input -v /path/to/output:/output\
      \ harbor.eucaim.cancerimage.eu/processing-tools/mr-based_dipg_tumour_detection_and_segmentation:latest\
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    input:
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    note: null
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    output:
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      format:
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      - term: DICOM format
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    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: MR-based DIPG tumour detection and segmentation (EUCAIM-SW-020_T-01-02-003)
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  otherID: []
  owner: casopon
  publication:
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      journal: Journal of Imaging Informatics in Medicine
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    note: null
    pmcid: null
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    type:
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  relation: []
  toolType:
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  topic:
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  - term: Machine learning
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  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  validated: 0
  version:
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  additionDate: '2025-05-29T12:09:16.704255Z'
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  description: 'The tool performs an automatic segmentation of the possible glioblastoma
    tumours on MRI images and its subregions: necrosis (Intratumoral necrotic core),
    edema (Peritumoral vasogenic edema), enhancing (Contrast-enhancing tumor region),
    total (Total tumor including edema and necrosis by a single model) and total-fused
    (Total tumor fusioning of necrosis+edema+enhancing). It applies preprocessing
    steps as skull stripping, intra-patient registration, z-score normalization, patching,
    among others. It takes DICOM images as input and generates tumoral masks in DICOM
    SEG or NIFTI formats.'
  documentation: []
  download: []
  editPermission:
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    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
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  function:
  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input \\\n  -v /path/to/output:/output\
      \ \\\n  harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest\
      \ \\\n  --series-selector /input/config/series.csv \\\n  --target total \\\n\
      \  --emit-config true"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input \\\n  -v /path/to/output:/output\
      \ \\\n  harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest\
      \ \\\n  --series-list '[{\"dataset_id\":\"DS001\",\"patient_id\":\"PAT001\"\
      ,\"study_id\":\"ST001\",\"series_path\":\"/input/DICOM/DS001/PAT001/ST001/T1_POST\"\
      }]' \\\n  --target total-fused \\\n  --emit-config true"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
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        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/artifacts-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-16T08:22:56.322315Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/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: MR-based glioblastoma tumour detection and segmentation (EUCAIM-SW-021_T-01-02-004)
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: casopon
  publication:
  - doi: 10.1007/s11548-024-03205-z
    metadata:
      abstract: ''
      authors: []
      citationCount: 8
      date: '2024-09-01T00:00:00Z'
      journal: International Journal of Computer Assisted Radiology and Surgery
      title: Deep learning automatic semantic segmentation of glioblastoma multiforme
        regions on multimodal magnetic resonance images
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - 2.1.1
- accessibility: Open access
  additionDate: '2025-12-16T08:20:17.123908Z'
  biotoolsCURIE: biotools:profiler
  biotoolsID: profiler
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: michel.salzet@univ-lille.fr
    fundrefid: null
    gridid: null
    name: Michel Salzet
    note: Professor Michel Salzet known for his work in immunology, oncology and proteomic
    orcidid: https://orcid.org/0000-0003-4318-0817
    rorid: null
    typeEntity: Person
    typeRole: []
    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,
    and other omics datasets from raw or tabular inputs. Profiler provides automated
    preprocessing, data exploration, biomarker discovery, AI-driven modeling, survival
    analysis, and biological interpretation using enrichment analysis.


    Designed for both bioinformaticians and experimental scientists, Profiler enables
    reproducible, explainable, and high-performance omics analysis through an intuitive
    web interface.


    Profiler is developed by the PRISM U1192 laboratory and protected by INSERM Transfer.'
  documentation:
  - note: null
    type:
    - Citation instructions
    url: https://prism-profiler.univ-lille.fr/citation/
  download:
  - note: null
    type: Source code
    url: https://doi.org/10.5281/zenodo.17478158
    version: null
  - note: null
    type: Test data
    url: https://github.com/yanisZirem/Profiler_v1_requests_datatests
    version: '1.0'
  - note: null
    type: Software package
    url: https://prism-profiler.univ-lille.fr/app/
    version: null
  editPermission:
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  - Proteomics
  - Rare Diseases
  elixirNode:
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  elixirPlatform:
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  - Training
  - Interoperability
  elixir_badge: 0
  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: Restricted access
  additionDate: '2025-12-16T08:08:29.575906Z'
  biotoolsCURIE: biotools:verdanta
  biotoolsID: verdanta
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit: []
  description: "Curated plant RNASeq data portal, focusing on multiple transcriptomes\
    \ of Capsicum annuum. The portal currently contains about 70 high quality hand-curated\
    \ studies, along with pre-computed quality charts, analysis-ready data in csv,\
    \ parquet and yaml (metadata) forms and advanced search that allows to pick not\
    \ just full studies but also individual samples into the dataset. \n\nFour curated\
    \ Capsicum transcriptomes are currently available.\n\nThe portal is free for academic\
    \ use, both for students and researchers. Working E-mail or social login is required\
    \ as protection from botnet attacks. Academic email automatically unlocks full\
    \ access, otherwise you can contact us to unlock it if you think you are eligible."
  documentation:
  - note: null
    type:
    - User manual
    url: https://verdanta.info/#data-organization
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Hierarchy
        uri: http://edamontology.org/data_2589
      format: []
    - data:
        term: Identifier
        uri: http://edamontology.org/data_0842
      format: []
    note: null
    operation:
    - term: Structure database search
      uri: http://edamontology.org/operation_0339
    output:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format: []
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format: []
  homepage: https://verdanta.info/
  homepage_status: 0
  language:
  - Rust
  lastUpdate: '2025-12-16T08:15:22.926670Z'
  license: Other
  link:
  - note: Project description, documentation
    type:
    - Other
    url: https://verdanta.info/
  - note: Register/login
    type:
    - Service
    url: https://verdanta.org/ca
  maturity: Mature
  name: Verdanta
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Bourumir
  publication: []
  relation:
  - biotoolsID: salmon
    type: uses
  - biotoolsID: fastqc
    type: uses
  - biotoolsID: fastp
    type: uses
  - biotoolsID: ncbi_resources
    type: uses
  - biotoolsID: thaf
    type: uses
  toolType:
  - Bioinformatics portal
  topic:
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  - term: Omics
    uri: http://edamontology.org/topic_3391
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 0
  version:
  - '1.0'
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T09:08:44.174795Z'
  biotoolsCURIE: biotools:mr-based_neuroblastoma_tumour_detection_and_segmentation
  biotoolsID: mr-based_neuroblastoma_tumour_detection_and_segmentation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    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:
    - Developer
    url: null
  - email: dianaveigac@gmail.com
    fundrefid: null
    gridid: null
    name: Diana Veiga Canuto
    note: null
    orcidid: https://orcid.org/0000-0002-6048-2940
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    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:
    - Primary contact
    - Support
    - Documentor
    - Developer
    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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    - Documentor
    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: 'This tool is specifically designed and validated for automated detection
    and segmentation of neuroblastic tumours in T2-weighted magnetic resonance images
    (T2-MR) using deep learning. It processes DICOM or NIfTI input data and outputs
    in NIFTI or DICOM SEG.


    TRAINING & VALIDATION COHORTS:


    Initial Development (Veiga-Canuto 2022):

    -Training: 106 patients, 5-fold CV (median DSC 0.965 ± 0.018).

    -Internal validation: 26 patients (median DSC 0.918 ± 0.067).

    -Sources: La Fe (Spain), SIOPEN HR-NBL1/LINES, St. Anna (Austria), Pisa (Italy).

    -Mean age: 37.6 ± 39.3 months.

    -Median tumor volume: 116,518 mm³.


    External Validation (Veiga-Canuto 2023):

    -300 patients, 535 independent T2 MRI scans (486 at diagnosis, 49 post-chemotherapy).

    -Performance: median DSC 0.997 (0.944–1.000), 94% successful detection.

    -Sources: 12 European countries (HR-NBL1/SIOPEN 119, LINES/SIOPEN 107, German
    Registry 62, others 12).

    -Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105),
    Canon (3).'
  documentation:
  - note: null
    type:
    - General
    url: https://www.mdpi.com/2072-6694/14/15/3648
  - note: null
    type:
    - Terms of use
    url: https://drive.google.com/file/d/1xzmrPQx9LfZr6WS5OR80RkipukoO_3Gw/view?usp=drive_link
  download: []
  editPermission:
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    type: group
  elixirCommunity: []
  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: "docker run --rm \\\n  -v \"<input_path>:/input\" \\\n  -v \"<output_path>:/output\"\
      \ \\\n  --gpus all \\\n  harbor.eucaim.cancerimage.eu/processing-tools/mr_based_neuroblastoma_tumour_detection_and_segmentation:2.0.0\
      \ \\\n  --mode dicom-seg \\\n  --series-selector /output/config/series_to_segment.csv\
      \ \\\n  --seg-series-number 2302001 \\\n  --seg-algorithm-name \"nnUNet_Neuroblastoma_Primage_training\"\
      \ \\\n  --seg-coordinating-center \"EUCAIM Consortium\" \\\n  --keep-nifti false"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/artifacts-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-16T01:53:35.476918Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/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: MR-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-019_T-01-02-002)
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: casopon
  publication:
  - doi: 10.3390/cancers14153648
    metadata:
      abstract: ''
      authors: []
      citationCount: 33
      date: '2022-08-01T00:00:00Z'
      journal: Cancers
      title: Comparative Multicentric Evaluation of Inter-Observer Variability in
        Manual and Automatic Segmentation of Neuroblastic Tumors in Magnetic Resonance
        Images
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.3390/cancers15051622
    metadata:
      abstract: ''
      authors: []
      citationCount: 16
      date: '2023-03-01T00:00:00Z'
      journal: Cancers
      title: Independent Validation of a Deep Learning nnU-Net Tool for Neuroblastoma
        Detection and Segmentation in MR Images
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
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    uri: http://edamontology.org/topic_2640
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  validated: 0
  version:
  - 2.0.0
- accessibility: Open access
  additionDate: '2025-12-15T14:17:14.627791Z'
  biotoolsCURIE: biotools:asafind
  biotoolsID: asafind
  collectionID:
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  - Czech Republic
  confidence_flag: tool
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Marta Vohnoutová
    note: null
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    rorid: null
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    - Developer
    - Maintainer
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  - 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:
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    - 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/
  download:
  - note: Download page on web-service, links to repository
    type: Downloads page
    url: https://asafind.jcu.cz/download-page/
    version: '2.0'
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  - Marine Metagenomics
  - Microbial Biotechnology
  elixirNode:
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  elixirPlatform:
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        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: Restricted access
  additionDate: '2025-05-22T14:58:20.772120Z'
  biotoolsCURIE: biotools:extended_a_priori_probability_tool
  biotoolsID: extended_a_priori_probability_tool
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit:
  - email: aarias@iti.es
    fundrefid: null
    gridid: null
    name: Ana María Arias Beltrán
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Instituto Tecnológico de Informática (ITI)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: The tool provides a semi-supervised metric (EAPP) for binary classification
    tasks that considers not only the a priori probability but also some possible
    bias present in the dataset, as well as other features that could provide a relatively
    trivial separability of the target classes. Therefore, it allows for evaluating
    the ease or complexity of the task or bias of the data beyond the well-established
    baseline for any binary classification.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://drive.eucaim.cancerimage.eu/s/Ld2AgbGZmm4qcke
  - note: Tool License Agreement in DOCX format
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/CAwxZaC4xDzkCA5
  - note: Tool License Summary in TXT format
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/Z8mYAoPk2JjZLFL
  download: []
  editPermission:
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    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: jobman submit -i image_batch_EAPP -r small gpu -- -i0 input_data_class0_path
      -i1 input_data_class1_path -o output_directory/results.json
    input:
    - data:
        term: Structure
        uri: http://edamontology.org/data_0883
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
    note: 'input_data_class0_path:  Input path for class 0 data; input_data_class1_path:
      Input path for class 1 data. In both cases it must be a CSV file, images stored
      in a folder or compressed into a ZIP file, or a 3D DICOM series file; output_path:
      directory and filename (JSON format) where the results will be saved'
    operation:
    - term: Data analysis
      uri: http://edamontology.org/operation_2945
    output:
    - data:
        term: Structure
        uri: http://edamontology.org/data_0883
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/image_batch_iti-eapp
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-15T12:21:49.565380Z'
  license: Proprietary
  link:
  - note: Scientific paper
    type:
    - Other
    url: https://ieeexplore.ieee.org/document/9950248
  - note: Harbor repository with the tool's Docker images
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/image_batch_iti-eapp
  maturity: Mature
  name: EAPP - Extended a Priori Probability tool
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: dsilveira
  publication:
  - doi: 10.1109/ACCESS.2022.3221936
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2022-01-01T00:00:00Z'
      journal: IEEE Access
      title: 'Extended a Priori Probability (EAPP): A Data-Driven Approach for Machine
        Learning Binary Classification Tasks'
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  validated: 0
  version:
  - v1.0.1
- accessibility: Restricted access
  additionDate: '2025-05-22T12:06:46.866961Z'
  biotoolsCURIE: biotools:breast_dense_tissue_segmentation
  biotoolsID: breast_dense_tissue_segmentation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit:
  - email: aarias@iti.es
    fundrefid: null
    gridid: null
    name: Ana María Arias Beltrán
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Instituto Tecnológico de Informática (ITI)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: The tool takes a digital mammogram and performs an automatic segmentation
    of the breast area and the dense tissue. After the mammogram segmentation, the
    tool returns a DICOM-SEG image with both the dense tissue and the breast tissue
    mask combined.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://drive.eucaim.cancerimage.eu/s/agktHMkYfy5pHes
  - note: Tool License Agreement in DOCX format
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/gPcqYKakCDSXGjN
  - note: Tool License Summary in TXT format
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/7ZPfQqsJ6YRjgpe
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: 'jobman submit -i mammography-density-segmenter -r small-gpu -- -p

      input_dcm_path -o output_directory'
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: 'input_dcm_path: input path to the 2D DICOM image (FFDM); output_directory:
      output directory to store the results'
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    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/image_batch_iti-breast
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-15T12:09:26.486490Z'
  license: Proprietary
  link:
  - note: Scientific paper
    type:
    - Other
    url: https://pubmed.ncbi.nlm.nih.gov/36010173/
  - note: Harbor repository with the tool's Docker images
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/image_batch_iti-breast
  maturity: Mature
  name: Breast Dense Tissue Segmentation
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: dsilveira
  publication:
  - doi: 10.3390/diagnostics12081822
    metadata:
      abstract: ''
      authors: []
      citationCount: 7
      date: '2022-08-01T00:00:00Z'
      journal: Diagnostics
      title: 'Breast Dense Tissue Segmentation with Noisy Labels: A Hybrid Threshold-Based
        and Mask-Based Approach'
    note: null
    pmcid: PMC9406546
    pmid: '36010173'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version:
  - v1.0.6
- accessibility: Open access
  additionDate: '2022-04-19T09:32:41.303637Z'
  biotoolsCURIE: biotools:metagwgs
  biotoolsID: metagwgs
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: claire.hoede@inrae.fr
    fundrefid: null
    gridid: null
    name: Claire Hoede
    note: null
    orcidid: https://orcid.org/0000-0001-5054-7731
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: GenoToul bioinformatics facility
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole:
    - Provider
    url: http://bioinfo.genotoul.fr/
  description: metagWGS is a workflow dedicated to the analysis of metagenomic data.
    It allows assembly, taxonomic annotation, and functional annotation of predicted
    genes. Since release 2.3, binning step with the possibility of cross-alignment
    is included. It has been developed in collaboration with several CATI BIOS4biol
    agents. Funded by Antiselfish Project (Labex Ecofect), ExpoMicoPig project (France
    Futur elevage) and SeqOccIn project (CPER - Occitanie Toulouse / FEDER), ATB_Biofilm
    funded by PNREST Anses, France genomique (ANR-10-INBS-09-08) and Resalab Ouest.
  documentation:
  - note: We provide up to date installation documentation, usage documentation, output
      description and functionnal test datasets and procedure.
    type:
    - User manual
    url: https://genotoul-bioinfo.pages-forge.inrae.fr/metagwgs/master/index.html
  download:
  - note: Functional tests data and script
    type: Test data
    url: https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets
    version: null
  editPermission:
    authors:
    - pbordron
    type: group
  elixirCommunity: []
  elixirNode:
  - France
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: Format
        uri: http://edamontology.org/format_1915
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Gene functional annotation
      uri: http://edamontology.org/operation_3672
    output:
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format:
      - term: Format
        uri: http://edamontology.org/format_1915
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    output:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://forgemia.inra.fr/genotoul-bioinfo/metagwgs
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-11T14:51:44.804907Z'
  license: GPL-3.0
  link:
  - note: See documentation, source code and functionnal test documentation.
    type:
    - Repository
    url: https://forge.inrae.fr/genotoul-bioinfo/metagwgs
  maturity: Mature
  name: metagWGS
  operatingSystem:
  - Linux
  otherID: []
  owner: choede
  publication: []
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version:
  - '2.3'
  - 2.5.0
- accessibility: Open access
  additionDate: '2025-12-11T14:36:21.061830Z'
  biotoolsCURIE: biotools:easy16s
  biotoolsID: easy16s
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: cedric.midoux@inrae.fr
    fundrefid: null
    gridid: null
    name: Cédric Midoux
    note: null
    orcidid: https://orcid.org/0000-0002-7964-0929
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Easy16S is designed to facilitate the exploration, visualization, and
    analysis of microbiome data.
  documentation:
  - note: null
    type:
    - General
    - User manual
    url: https://easy16s.migale.inrae.fr/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Multiple sample visualisation
      uri: http://edamontology.org/operation_3744
    output: []
  homepage: https://easy16s.migale.inrae.fr/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-12-11T14:36:21.065324Z'
  license: AGPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://forge.inrae.fr/migale/easy16s
  - note: null
    type:
    - Repository
    url: https://doi.org/10.57745/ZN1HXQ
  maturity: Mature
  name: easy16S
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: cmidoux
  publication:
  - doi: 10.21105/joss.06704
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType: []
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version:
  - v25.07
- accessibility: Open access
  additionDate: '2019-02-13T17:01:40Z'
  biotoolsCURIE: biotools:Jalview
  biotoolsID: Jalview
  collectionID:
  - ELIXIR-UK
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Jim Procter
    note: null
    orcidid: https://orcid.org/0000-0002-7865-7382
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.lifesci.dundee.ac.uk/people/jim-procter
  - email: null
    fundrefid: null
    gridid: null
    name: Geoff Barton
    note: null
    orcidid: https://orcid.org/0000-0002-9014-5355
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://www.lifesci.dundee.ac.uk/people/geoff-barton
  description: Jalview is a free cross-platform program for multiple sequence alignment
    editing, visualisation and analysis. Use it to align, view and edit sequence alignments,
    analyse them with phylogenetic trees and principal components analysis (PCA) plots
    and explore molecular structures and annotation.
  documentation:
  - note: null
    type:
    - Citation instructions
    url: https://www.jalview.org/about/citation
  - note: Hands-on exercises, Training courses and Training videos
    type:
    - Training material
    url: https://www.jalview.org/training/
  - note: null
    type:
    - FAQ
    url: https://www.jalview.org/help/faq
  - note: null
    type:
    - User manual
    url: https://www.jalview.org/help/documentation/
  download:
  - note: null
    type: Downloads page
    url: https://www.jalview.org/download
    version: null
  - note: null
    type: Source code
    url: https://www.jalview.org/download/source/
    version: null
  - note: Binaries for all platforms
    type: Binaries
    url: https://www.jalview.org/download/?os=all
    version: null
  - note: null
    type: Icon
    url: https://www.jalview.org/favicon.svg
    version: null
  - note: Executable JAR file
    type: Binaries
    url: https://www.jalview.org/download/other/jar/
    version: null
  editPermission:
    authors:
    - ben_s
    - jimprocter
    type: group
  elixirCommunity: []
  elixirNode:
  - UK
  elixirPlatform:
  - Tools
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: GFF2-seq
        uri: http://edamontology.org/format_1938
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: RNAML
        uri: http://edamontology.org/format_3311
      - term: Format
        uri: http://edamontology.org/format_1915
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: mmCIF
        uri: http://edamontology.org/format_1477
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: GFF3-seq
        uri: http://edamontology.org/format_1939
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
    - data:
        term: Structure alignment
        uri: http://edamontology.org/data_0886
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: 'Other Input formats:

      AMSA (.amsa);

      JnetFile (.concise, .jnet);

      PFAM (.pfam);

      Substitution matrix (.matrix);

      Jalview Project File (.jvp);

      Jalview Feature File (.features, .jvfeatures);

      Jalview Annotations File (.annotations, .jvannotations);

      Predicted Aligned Error (PAE) Matrix File (.json)

      ...

      Other Output formats:

      PFAM (.pfam);

      BioJS (.biojs) (interactive HTML/Javascript);

      Jalview Project File (.jvp);'
    operation:
    - term: Sequence alignment editing
      uri: http://edamontology.org/operation_3081
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: EPS
        uri: http://edamontology.org/format_3466
      - term: Format
        uri: http://edamontology.org/format_1915
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PNG
        uri: http://edamontology.org/format_3603
  homepage: https://www.jalview.org/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-11T14:16:30.074724Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Discussion forum
    url: https://discourse.jalview.org/
  - note: null
    type:
    - Issue tracker
    url: https://issues.jalview.org/
  - note: Latest development version
    type:
    - Other
    url: https://www.jalview.org/development/jalview_develop/
  - note: null
    type:
    - Repository
    url: https://gitlab.jalview.org/jalview/jalview.git
  - note: Twitter feed
    type:
    - Social media
    url: https://twitter.com/Jalview
  - note: YouTube training videos
    type:
    - Social media
    url: https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/104771886/
  maturity: Mature
  name: Jalview
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: ben_s
  publication:
  - doi: 10.1093/bioinformatics/btp033
    metadata:
      abstract: ''
      authors: []
      citationCount: 7717
      date: '2009-05-07T00:00:00Z'
      journal: Bioinformatics
      title: Jalview Version 2-A multiple sequence alignment editor and analysis workbench
    note: null
    pmcid: PMC2672624
    pmid: '19151095'
    type: []
    version: null
  relation:
  - biotoolsID: jabaws
    type: uses
  - biotoolsID: chimera
    type: uses
  - biotoolsID: chimerax
    type: uses
  - biotoolsID: pymol
    type: uses
  - biotoolsID: bioconda
    type: includedIn
  - biotoolsID: 3d-beacons
    type: uses
  - biotoolsID: uniprot
    type: uses
  - biotoolsID: pfam
    type: uses
  - biotoolsID: ensembl
    type: uses
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  topic:
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  description: Pathway Tools multiprocessing wrapper (for PathoLogic).
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  description: 'Detects duplicate or visually similar DICOM series using a tiered
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  biotoolsCURIE: biotools:instanovo
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  description: InstaNovo is a transformer neural network with the ability to translate
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  description: D-GENIES – for Dot plot large Genomes in an Interactive, Efficient
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  additionDate: '2021-01-02T12:42:50Z'
  biotoolsCURIE: biotools:mgse
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  description: Mapping-based Genome Size Estimation (MGSE) predicts the size of a
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    rorid: null
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    name: David Rodríguez
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    rorid: null
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  - email: null
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    name: Inés Victoria
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    orcidid: https://orcid.org/0009-0003-7950-3937
    rorid: null
    typeEntity: Person
    typeRole:
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  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:
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    url: https://gitlabpages.ifca.es/fair-eva-guide-608baa/
  download: []
  editPermission:
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  function:
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    input:
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        term: URL
        uri: http://edamontology.org/data_1052
      format: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_0336
    - term: Validation
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    output:
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        term: Score
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  homepage: https://github.com/IFCA-Advanced-Computing/FAIR_eva
  homepage_status: 0
  language:
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  lastUpdate: '2025-12-04T10:57:20.901575Z'
  license: Apache-2.0
  link:
  - note: Repository for FAIR EVA, without the EUCAIM specific plugin
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    url: https://github.com/IFCA-Advanced-Computing/FAIR_eva
  maturity: Mature
  name: FAIR EVA for EUCAIM
  operatingSystem:
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  otherID: []
  owner: davrodgon
  publication:
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      date: null
      journal: null
      title: null
    note: null
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  toolType:
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  topic:
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  validated: 0
  version:
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- accessibility: Open access (with restrictions)
  additionDate: '2025-11-25T09:58:37.569343Z'
  biotoolsCURIE: biotools:ml_model_for_mr_series_categorisation
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  cost: Free of charge (with restrictions)
  credit:
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  - email: carina_soler@iislafe.es
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    rorid: null
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    rorid: null
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    orcidid: https://orcid.org/0000-0002-8234-010X
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  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,
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  documentation:
  - note: null
    type:
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    url: https://drive.google.com/file/d/1lIUixmLItQXOyBPIXL_AzPg_jlqDKwNE/view?usp=drive_link
  - note: null
    type:
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  function:
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        term: Image
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        uri: http://edamontology.org/format_3548
    note: null
    operation:
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      uri: http://edamontology.org/operation_2990
    output:
    - data:
        term: Report
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      format:
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        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:
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    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:
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  - Linux
  - Mac
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication:
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    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:
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    version: null
  relation: []
  toolType:
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  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:
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- accessibility: null
  additionDate: '2024-04-18T08:31:46.459964Z'
  biotoolsCURIE: biotools:hictkpy
  biotoolsID: hictkpy
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: 'Python bindings for hictk: read and write .cool and .hic files directly
    from Python'
  documentation:
  - note: null
    type:
    - General
    url: https://hictkpy.readthedocs.io
  - note: null
    type:
    - Installation instructions
    url: https://hictkpy.readthedocs.io/en/stable/installation.html
  - note: null
    type:
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    url: https://hictkpy.readthedocs.io/en/stable/quickstart.html
  - note: null
    type:
    - API documentation
    url: https://hictkpy.readthedocs.io/en/stable/api/index.html
  download:
  - note: null
    type: Downloads page
    url: https://github.com/paulsengroup/hictkpy/releases
    version: null
  - note: null
    type: Binaries
    url: https://pypi.org/project/hictkpy/
    version: null
  - note: null
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  homepage_status: 0
  language:
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  lastUpdate: '2025-12-03T14:44:30.069607Z'
  license: MIT
  link:
  - note: null
    type:
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  - note: null
    type:
    - Issue tracker
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  - note: null
    type:
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    url: https://github.com/paulsengroup/hictkpy/discussions
  maturity: Mature
  name: hictkpy
  operatingSystem:
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  - Linux
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  owner: robomics
  publication:
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      authors: []
      citationCount: 1
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      journal: Bioinformatics
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    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
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    type: uses
  toolType:
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  topic:
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  - term: Sequence analysis
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  validated: 0
  version:
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  additionDate: '2025-11-26T13:27:32.776575Z'
  biotoolsCURIE: biotools:iqa_dce_tool
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  cost: Free of charge
  credit: []
  description: The purpose of the tool is to provide a complete framework for automatic
    detection of image quality for Breast DCE MR images. The assessment is performed
    on the first post-contrast dynamic phase in order to assess the most clinically
    relevant sequence among a number of identical acquisitions. Two categories are
    available for image classification, i.e. high and low quality, depending on the
    level of noise, degree of blurring and presence of artifacts.
  documentation:
  - note: null
    type:
    - General
    url: https://docs.google.com/document/d/1hG_M21gvO4D8zkHmwtbavT8Dp6bliRU4/edit
  download:
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    type: Container file
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  license: EUPL-1.1
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  maturity: Mature
  name: IQA DCE tool
  operatingSystem:
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  - Windows
  - Mac
  otherID: []
  owner: billyk
  publication:
  - doi: 10.3390/jimaging11110417
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
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  topic:
  - term: MRI
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  - term: Data quality management
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  - term: Oncology
    uri: http://edamontology.org/topic_2640
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- accessibility: Open access
  additionDate: '2025-11-29T18:03:55.516541Z'
  biotoolsCURIE: biotools:asparaginase_database
  biotoolsID: asparaginase_database
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Asparaginases are one of the most successful biopharmaceuticals that
    play a pivotal role in the treatment of acute lymphoblastic leukemia. In order
    to find new asparaginases with improved properties (stability, substrate affinity,
    immunogenicity) or to achieve these goals by enzyme engineering, it is essential
    to collect and accurately classify asparaginases from various sources. The database
    covers 101 experimentally studied proteins from the literature, a manually curated
    set of 127 sequences from SwissProt, and more than 100,000 automatically curated
    enzymes.
  documentation:
  - note: null
    type:
    - User manual
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  download: []
  editPermission:
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  homepage_status: 0
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  lastUpdate: '2025-12-02T22:00:20.857626Z'
  license: CC-BY-4.0
  link: []
  maturity: Mature
  name: Asparaginase database
  operatingSystem:
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  owner: spiwokv
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  toolType:
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  - Bioinformatics portal
  topic:
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  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-12-02T12:03:53.282983Z'
  biotoolsCURIE: biotools:aggreprot
  biotoolsID: aggreprot
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  confidence_flag: tool
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Joan Planas-Iglesias
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
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    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
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  description: AggreProt is a web server to predict and engineer protein aggregation.
    The tool provides a per-residue numerical aggregation propensity value and an
    overall protein aggregation propensity profile. Along with the protein solvent
    accessibility area and its transmembrane propensity, AggreProt predictions aid
    the users on designing soluble proteins.
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  function: []
  homepage: https://loschmidt.chemi.muni.cz/aggreprot/
  homepage_status: 0
  language:
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  - JavaScript
  lastUpdate: '2025-12-02T12:03:53.285771Z'
  license: Proprietary
  link: []
  maturity: Mature
  name: AggreProt
  operatingSystem:
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  owner: m.musil
  publication:
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    metadata:
      abstract: ''
      authors: []
      citationCount: 17
      date: '2024-07-05T00:00:00Z'
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    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
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  toolType:
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    uri: http://edamontology.org/topic_3510
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2021-01-18T10:10:48Z'
  biotoolsCURIE: biotools:ape
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  credit:
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    note: null
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    name: Anna-Lena Lamprecht
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    orcidid: https://orcid.org/0000-0003-1953-5606
    rorid: null
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  description: APE (the Automated Pipeline Explorer) as a command-line tool and API
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    a new application domain by providing it with a domain ontology and semantically
    annotated tools. It can then be used to synthesize purpose-specific workflows
    based on a specification of the available workflow inputs, desired outputs and
    possibly additional constraints.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://ape-framework.readthedocs.io/
  download:
  - note: Download APE java library or the CLI
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  function:
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    input:
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        term: Workflow metadata
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      format:
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        uri: http://edamontology.org/format_3464
    note: null
    operation:
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    output:
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      format:
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      - term: CWL
        uri: http://edamontology.org/format_3857
      - term: PNG
        uri: http://edamontology.org/format_3603
  homepage: https://github.com/sanctuuary/APE/
  homepage_status: 0
  language:
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  lastUpdate: '2025-12-01T13:47:56.062392Z'
  license: Apache-2.0
  link:
  - note: null
    type:
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    url: https://github.com/sanctuuary/ape
  maturity: Mature
  name: APE
  operatingSystem:
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  - Windows
  - Linux
  otherID: []
  owner: VKasalica
  publication:
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    metadata: null
    note: null
    pmcid: PMC7304703
    pmid: null
    type:
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    version: null
  - doi: 10.1021/acs.jproteome.0c00983
    metadata:
      abstract: ''
      authors: []
      citationCount: 7
      date: '2021-04-02T00:00:00Z'
      journal: Journal of Proteome Research
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    note: null
    pmcid: PMC8041394
    pmid: '33720735'
    type:
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    version: null
  relation: []
  toolType:
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  topic:
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  - term: Ontology and terminology
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  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 1
  version:
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- accessibility: Open access
  additionDate: '2017-08-03T18:45:53Z'
  biotoolsCURIE: biotools:hbat
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    gridid: null
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  description: "HBAT (Hydrogen Bond Analysis Tool) is a package to automate the analysis\
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    \ structures, available in Protein Data Bank (PDB) file format. HBAT uses a geometric\
    \ approach to identify molecular interactions by analysing distance and angular\
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    \ and a completed rewrite of original implementation with cross-platform support.\
    \ HBAT 2.0 is open sourced under MIT License."
  documentation:
  - note: null
    type:
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    - API documentation
    - Citation instructions
    - Command-line options
    - Installation instructions
    - Quick start guide
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    - General
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    url: https://docs.hope4kids.io/HOPE-Segmenter-Kids/
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  homepage: https://github.com/BIT-UPM/EUCAIM/brain_glioma_segmenter
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-11-28T13:56:29.777759Z'
  license: CC-BY-NC-ND-4.0
  link:
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    type:
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    url: https://segmenter.hope4kids.io/
  - note: GitHub repository
    type:
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    url: https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids
  maturity: Mature
  name: Brain Glioma Segmenter
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    metadata:
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      title: Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging
    note: null
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      journal: Proceedings - International Symposium on Biomedical Imaging
      title: 'Enhancing Generalizability in Brain Tumor Segmentation: Model Ensemble
        with Adaptive Post-Processing'
    note: null
    pmcid: null
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    type: []
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  - doi: 10.48550/arXiv.2412.04094
    metadata: null
    note: null
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  toolType:
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  topic:
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  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
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  biotoolsCURIE: biotools:pediatric_brain_tumor_segmenter
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    - Contributor
    - Support
    url: null
  - email: pabhijeet@childrensnational.org
    fundrefid: null
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    name: Abhijeet Parida
    note: null
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    typeRole:
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    url: null
  - email: mlingura@childrensnational.org
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    name: Marius George Linguraru
    note: null
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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/
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  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:
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    url: https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids
  maturity: Mature
  name: Pediatric Brain Tumor Segmenter
  operatingSystem:
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  owner: dani-capellan
  publication:
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    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
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  - doi: 10.48550/arXiv.2412.04111
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    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:
  - email: null
    fundrefid: null
    gridid: grid.7497.d
    name: German Cancer Research Center (DKFZ)
    note: null
    orcidid: null
    rorid: 04cdgtt98
    typeEntity: null
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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/
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        uri: http://edamontology.org/format_3548
      - term: nii
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    output:
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      - term: DICOM format
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      - term: nii
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  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'
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  maturity: Mature
  name: MITK
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  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
  relation: []
  toolType:
  - Workbench
  - Desktop application
  - Library
  topic: []
  validated: 0
  version:
  - v2023.04
- accessibility: Open access (with restrictions)
  additionDate: '2025-04-15T17:42:40.968987Z'
  biotoolsCURIE: biotools:dicom_file_integrity_checker_by_gibi230
  biotoolsID: dicom_file_integrity_checker_by_gibi230
  collectionID:
  - EUCAIM
  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: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
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    rorid: null
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    note: null
    orcidid: https://orcid.org/0000-0002-8324-8284
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
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    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: 'The tool performs a DICOM quality check in terms of correct number
    of files per sequence, corrupted files, precise directory hierarchy, separated
    dynamic series merging them, interest series filtering/selection by specific series
    description lists and diffusion sequence identification by b-values. It applies
    the desired changes to the dataset and generates a report containing information
    about the selected sequences, corrupted files, missing files and merged files.


    Status: Deployed'
  documentation:
  - note: null
    type:
    - User manual
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  - note: null
    type:
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    url: https://drive.google.com/file/d/1pO_td7uvlsFWy6AZi8AOq3__hm4L2xSv/view?usp=drive_link
  download:
  - note: EUCAIM user needed
    type: Container file
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    - data:
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      format:
      - term: xlsx
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      - term: JSON
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    note: For Data Holders (ingestion-tools)
    operation:
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    output:
    - data:
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    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: HTML
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      - term: xlsx
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      - term: JSON
        uri: http://edamontology.org/format_3464
  - cmd: "docker run -it --rm --name my-container \\\n  -v \"<input_path>:/input\"\
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    input:
    - data:
        term: Image
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      format:
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    note: For Data Users (processing-tools)
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
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    - data:
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      format:
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab
  homepage_status: 0
  language:
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  lastUpdate: '2025-11-27T13:23:38.501118Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  - note: Link to EUCAIM's Harbor for Data Holders
    type:
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    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab
  - note: Link to EUCAIM's Harbor for Data Users
    type:
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    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/dicom_file_integrity_checker/artifacts-tab
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  name: DICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)
  operatingSystem:
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  - Mac
  - Windows
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication: []
  relation: []
  toolType:
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  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:
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  - 2.1.0
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- accessibility: Open access
  additionDate: '2025-11-27T10:42:10.165590Z'
  biotoolsCURIE: biotools:ftag-finder
  biotoolsID: ftag-finder
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Carène Rizzon
    note: null
    orcidid: https://orcid.org/0000-0003-1194-4130
    rorid: 03jca6281
    typeEntity: null
    typeRole:
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    url: http://www.math-evry.cnrs.fr/members/crizzon/welcome
  - email: null
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    note: null
    orcidid: https://orcid.org/0009-0001-0971-497X
    rorid: null
    typeEntity: Person
    typeRole:
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    - Maintainer
    url: null
  description: 'Families and TAG Finder: a Snakemake workflow to identify gene families
    and detect Tandemly Arrayed Genes.'
  documentation: []
  download:
  - note: null
    type: Downloads page
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    version: null
  editPermission:
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  homepage_status: 0
  language:
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  - Bash
  - Python
  lastUpdate: '2025-11-27T10:42:10.168319Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.com/sortion/FTAG-Finder
  - note: null
    type:
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  name: FTAG-Finder
  operatingSystem:
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  description: The South Green Genome Hub is a suite of crop-specific community portals
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next: ?page=2
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