count: 32977
list:
- 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:
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  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
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    note: null
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    typeEntity: Institute
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    url: null
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    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
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    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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    - Support
    - Documentor
    - Developer
    url: null
  - email: carina_soler@iislafe.es
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    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
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    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
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  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:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/tS2W8nb38Zs2ZzK
  - note: null
    type:
    - General
    url: https://www.mdpi.com/2072-6694/14/15/3648
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/44BxMSNpxwgsZiE
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=c7XOEGRA9aQ&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=12
  download: []
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  function:
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      \ \\\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:
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        term: Image
        uri: http://edamontology.org/data_2968
      format:
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        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
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        uri: http://edamontology.org/format_3464
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
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        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/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-30T11:37:29.346721Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
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    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/info-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: MR-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-019_T-01-02-002)
  operatingSystem:
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  - Windows
  - Linux
  otherID: []
  owner: casopon
  publication:
  - doi: 10.3390/cancers14153648
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
  - doi: 10.3390/cancers15051622
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
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  topic:
  - term: Oncology
    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 (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:
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  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
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    rorid: null
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    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
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    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
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    - Documentor
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    url: null
  - email: adrian_galiana@iislafe.es
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    name: Adrian Galiana-Bordera
    note: null
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    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
    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: '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
    url: https://drive.eucaim.cancerimage.eu/s/LAKqSQZY4Bjqz5W
  - note: null
    type:
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    url: https://drive.eucaim.cancerimage.eu/s/EEqjraK574HrwMf
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=oUebkjLYeSs&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=3
  download:
  - note: EUCAIM user needed
    type: Container file
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab
    version: 2.1.0
  editPermission:
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  elixir_badge: 0
  function:
  - cmd: "docker run -it --rm --name my-container \\\n  -v \"<input_path>:/input\"\
      \ \\\n  -v \"<output_path>:/output\" \\\n  -v \"<config_path>:/config\" \\\n\
      \  harbor.eucaim.cancerimage.eu/ingestion-tools/dicom_file_integrity_checker:latest"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: For Data Holders (ingestion-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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        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: JSON
        uri: http://edamontology.org/format_3464
  - cmd: "docker run -it --rm --name my-container \\\n  -v \"<input_path>:/input\"\
      \ \\\n  -v \"<output_path>:/output\" \\\n  harbor.eucaim.cancerimage.eu/processing-tools/dicom_file_integrity_checker:latest\
      \ \\\n  /app/entrypoint.sh --config-string \"{'QA': {'sequence_selection': ['ALL'],\
      \ 'modality_selection': ['ALL'], 'input_directory': 'dataset_id'}}\""
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    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:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
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        uri: http://edamontology.org/format_2331
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-30T11:36:53.934680Z'
  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:
    - Software catalogue
    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:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/dicom_file_integrity_checker/artifacts-tab
  maturity: Mature
  name: DICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  - term: Data acquisition
    uri: http://edamontology.org/topic_3077
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
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  - 2.1.0
  - 2.1.1
- accessibility: null
  additionDate: '2025-05-29T08:55:46.088021Z'
  biotoolsCURIE: biotools:denoising-inhomogeneity_correction_tool
  biotoolsID: denoising-inhomogeneity_correction_tool
  collectionID:
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  confidence_flag: null
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  - email: matias_fernandez@iislafe.es
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    name: Matias Fernandez-Paton
    note: null
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    rorid: null
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    typeRole:
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    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
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    name: Pedro-Miguel Martinez-Girones
    note: null
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    url: null
  - email: carina_soler@iislafe.es
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    url: null
  - email: leonor_cerda@iislafe.es
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    name: Leonor Cerda-Alberich
    note: null
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    typeRole:
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  - email: luis_marti@iislafe.es
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  description: 'The tool is designed to perform a customisable image pre-processing
    to reduce noise and inhomogeneity field effect, thus improving image quality and
    reproducibility of radiomics features. This tool consists of two independent steps:
    one for denoising using one of the 5 integrated filters (Bilateral Filter, Anisotropic
    Diffusion Filter (ADF), Curvature Flow Filter (CFF), SUSAN and Non Local Means
    (NLM)), and another for the ANTs N4 and another for the ANT''s N4 bias correction
    filter. The parameter configuration of this tool has been optimised for TW1, T2W,
    DWI and DCE sequences in neuroblastoma (NB) and paediatric brain tumours, but
    it can also be configured with some of their parameters using a JSON parameter
    configuration file.'
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/wYJ7Fttnk6Dp7gc
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/oseiKoeFZqwoRCA
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=HkHqFGXGEbo&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=9
  download: []
  editPermission:
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  function:
  - cmd: docker run -it --rm --name container_name -v "<input_path>:/input" -v "<output_path>:/output"
      -v "<config_path>:/config" harbor.eucaim.cancerimage.eu/processing-tools/denoising_inhomogeneity_correction_tool:1.1.0
      --config /config/config.json
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
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    output:
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      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processin-tools/denoising_inhomogeneity_correction_tool:1.1.0
      --paths /input/Dataset/Patient_1/Study/T1W /input/Dataset/Patient_2/Study/T2W
      --output /output --series_number 2000 --series_description_suffix "_harmonized"
      --denoising adf --conductance 0.5 --iterations 3 --time_step 0.0625 --n4 --bspline_size
      50 --n4_iterations 50 30 --shrink_factor 2
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
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    output:
    - data:
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      format:
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        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-30T11:36:34.414003Z'
  license: CC-BY-NC-ND-4.0
  link:
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  maturity: null
  name: Denoising-Inhomogeneity Correction Tool (EUCAIM-SW-015_T-01-01-015)
  operatingSystem:
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  - Windows
  - Linux
  otherID: []
  owner: casopon
  publication:
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    metadata: null
    note: null
    pmcid: PMC8554919
    pmid: '34505958'
    type:
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    version: null
  - doi: 10.1186/s41747-020-00150-9
    metadata: null
    note: null
    pmcid: PMC7125275
    pmid: '32246291'
    type: []
    version: null
  relation: []
  toolType:
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  topic:
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  validated: 0
  version:
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- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T10:41:57.535794Z'
  biotoolsCURIE: biotools:cluster_based_harmonization
  biotoolsID: cluster_based_harmonization
  collectionID:
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  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
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    note: null
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    rorid: null
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    fundrefid: null
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  description: 'The tool is designed to perform radiomics harmonization on large and
    heterogeneous datasets, where the risk of over-harmonization is present. Instead
    of directly applying harmonization based on predefined batch labels, the tool
    first identifies groups of batches that share similar characteristics through
    clustering of the radiomics data. It then performs harmonization using these cluster-derived
    labels. The tool allows the harmonization of radiomics variables using two methods:
    (1) original ComBat (Rabinovic, 2007) method, where each original batch group
    is considered for the harmonization process and (2) cluster-based ComBat method,
    where batch groups with similar radiomics characteristics form clusters and the
    latter are being considered for the harmonization process.'
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/Kz3jfQYQZjezpxK
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    note: null
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      format:
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/cluster_based_harmonization/info-tab
  homepage_status: 0
  language:
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  license: CC-BY-NC-ND-4.0
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  name: Cluster based harmonization (EUCAIM-SW-044_T-01-03-006)
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  toolType:
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  validated: 0
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  description: This preprocessing tool is design for 2D digital mammograms in DICOM  format.
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  - cmd: docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processing-tools/2d_digital_mammography_harmonization:1.1.0
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      format:
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    note: Command Arguments
    operation:
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    output:
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/2d_digital_mammography_harmonization/info-tab
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    uri: http://edamontology.org/topic_3071
  validated: 0
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  description: A tool based on artificial intelligence that is able to perform a categorisation
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    junk series (e.g. localizers, calibrations, screenshots...).
  documentation:
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    url: https://www.youtube.com/watch?v=gudDCiuJIf8&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=11
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    note: null
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/info-tab
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  maturity: Mature
  name: ML model for MR series categorisation (EUCAIM-SW-011_T-01-01-011)
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  owner: pedromiguel_martinez_HULAFE
  publication:
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    metadata: null
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  - term: Data management
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  validated: 0
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  additionDate: '2025-11-21T13:49:36.578343Z'
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  description: "Tool that aims to validate visually the chronological order and logical\
    \ consistency of dates associated with a patient's medical history. It generates\
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/time_coherence_tool/info-tab
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  validated: 0
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  description: A machine learning-based tool to estimate the overall survival probability
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  description: A fully automated service which can be applied on any kind of tabular
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  description: Whole-gland, zonal & lesion prostate segmentation from multi-parametric
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  description: Python library for computing the mosaic Q and Q_alt structural descriptors,
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    type:
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    url: https://osf.io/42kjn/wiki?wiki=zmh9d
  download:
  - note: null
    type: Software package
    url: https://pypi.org/project/protein-mosaic-q/
    version: 0.3.3
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: mosaicq protein.pdb [--metric Q_alt]
    input: []
    note: Computes mosaic Q and Q_alt parameters quantifying spatial clustering of
      amino acids by chemical type in protein 3D structures.
    operation:
    - term: Protein geometry calculation
      uri: http://edamontology.org/operation_0249
    output: []
  homepage: https://proteins-mosaic-q.org/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-29T11:29:15.749301Z'
  license: MIT
  link:
  - note: null
    type:
    - Software catalogue
    url: https://pypi.org/project/protein-mosaic-q/
  - note: null
    type:
    - Repository
    url: https://github.com/UPO-Sevilla-Fco-Javier-Lobo-Cabrera/clustering_trait_proteins
  - note: null
    type:
    - Other
    url: https://citizenscience.eu/project/686
  - note: null
    type:
    - Other
    url: https://scistarter.org/proteins-mosaic-q-project
  - note: null
    type:
    - Other
    url: https://proteins-mosaic-q.org/
  - note: null
    type:
    - Other
    url: https://ciencia-ciudadana.es/project/392
  - note: null
    type:
    - Other
    url: https://osf.io/42kjn/overview
  - note: null
    type:
    - Other
    url: https://huggingface.co/ProteinsMosaicQ
  maturity: Emerging
  name: protein-mosaic-q
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: fjlobo
  publication:
  - doi: 10.1101/500025
    metadata: null
    note: Earlier version of the manuscript. Updated version available in the project
      repository.
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: null
  relation:
  - biotoolsID: biopython
    type: uses
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  validated: 0
  version:
  - 0.3.3
- accessibility: Open access (with restrictions)
  additionDate: '2025-11-07T18:15:49.962044Z'
  biotoolsCURIE: biotools:prostate_zone_segmentation_tool
  biotoolsID: prostate_zone_segmentation_tool
  collectionID:
  - EUCAIM
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit:
  - email: jose.almeida@research.fchampalimaud.org
    fundrefid: null
    gridid: null
    name: José Guilherme de Almeida
    note: null
    orcidid: https://orcid.org/0000-0002-1887-0157
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    url: https://josegcpa.net
  - email: null
    fundrefid: null
    gridid: null
    name: Nickolas Papanikolaou
    note: null
    orcidid: https://orcid.org/0000-0003-3298-2072
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Nuno Rodrigues
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: 'This tool automatically segments the the prostate into two zones:
    the central and transition zones (TZ+CZ) and the peripheral zone (PZ). It takes
    as input a T2-weighted image and produces a segmentation in the same input format.


    Three datasets were used to train this model: ProstateX (n=152), Prostate158 (n=119)
    and ProstateNet (the ProCAncer-I dataset; n=532). We used the T2-weighted images
    available in each dataset and trained a standard three-class nnU-Net model with
    three classes: background, peripheral zone and the combination of the transition
    and central zones as annotated by radiologists. Using 149 cases from the three
    previously noted datasets, this model achieved DSC=0.81 (95% CI=[0.59, 0.92])
    for PZ and 0.87 (95% CI=[0.60, 0.96]) for CZ+TZ. In a clinical validation using
    ProCAncer-I data, this model achieved, for PZ and TZ+CZ, DSC=0.65 and DSC=0.77,
    respectively, comparable to the observed between-radiologist DSC for a subset
    of cases (DSC=0.61 and DSC=0.73, respectively).'
  documentation:
  - note: This is the repository containing all of the code together with a comprehensive
      README for deployment and examplar files.
    type:
    - API documentation
    url: https://github.com/josegcpa/nnunet_serve
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: docker run --shm-size=1gb -v $(pwd)/example:/data/input:ro -v $(pwd)/test_output:/data/output:rw
      --gpus="all" test-eucaim:latest nnunet-predict --study_path /data/input --series_folders
      <series-folder> --output_dir /data/output
    input:
    - data:
        term: MRI image
        uri: http://edamontology.org/data_3442
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    note: 'Image annotation for individual DICOM and Nifti images: Please note that
      it is easier to mount the input and output paths path and keep `--study_path`
      always as `/data/input` and `--output_dir` always as `/data/output`. This way
      only `--series_folders` requires any change. `--series_folders` can refer both
      to a Nifti file (if the input is Nifti) or the a DICOM series folder.


      If the input is DICOM, `--is_dicom` should be used.'
    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
      - term: nii
        uri: http://edamontology.org/format_3549
  - cmd: docker run --shm-size=1gb -v $(pwd)/example_dataset:/data/input:ro -v $(pwd)/test_output:/data/output:rw
      --gpus="all" test-eucaim:latest nnunet-predict-batch {{--data_json /data/input/<dataset_json>.json|--data_dir
      /data/input --output_dir /data/output}}
    input:
    - data:
        term: MRI image
        uri: http://edamontology.org/data_3442
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    note: "Batch image annotation for DICOM and Nifti images using dataset JSON and\
      \ data directory supports two methods: using a dataset JSON and using a data\
      \ directory. \n\nThe dataset JSON-based method relies on having a dataset JSON\
      \ which has a list of dictionaries that follow this structure: `{\"study_path\"\
      : str, \"series_folders\": [[str]], \"output_dir\": str}`. These are analogous\
      \ to the previous modes. Be mindful that paths should be specified accordingly\
      \ for the Docker file-system. The dataset JSON should be specified using `--data_json`.\n\
      \nThe data directory-based method relies on having a directory structured as\
      \ patient/study/series, where each series follows an nnU-Net-like convention\
      \ (i.e. `<series_id>_0000`, `<series_id>_0001`, etc.). In this case, it should\
      \ be `<series-id>_0000`. The data directory should be specified using `--data_dir`\
      \ and requires the specification of an `--output_dir`.\n\nIf the input is DICOM,\
      \ `--is_dicom` should be specified."
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: MRI image
        uri: http://edamontology.org/data_3442
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/champ-prostate-zone-segmentation
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-29T10:36:29.272637Z'
  license: CC-BY-NC-4.0
  link:
  - note: This is the nnunet_serve repository, containing the generic nnU-Net building
      and serving functionalities used by the Computational Clinical Imaging Group
      at Champalimaud Foundation. This should also be used as documentation.
    type:
    - Repository
    url: https://github.com/josegcpa/nnunet_serve
  - note: Contains the EUCAIM model card for this model.
    type:
    - Other
    url: https://kdrive.infomaniak.com/app/share/1928123/f7bf2733-0454-47b0-a29c-0beacb51fe68
  maturity: Emerging
  name: Prostate zone segmentation tool
  operatingSystem:
  - Linux
  otherID: []
  owner: josegcpa
  publication:
  - doi: 10.1016/j.compbiomed.2024.108216
    metadata: null
    note: null
    pmcid: null
    pmid: '38442555'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: nnunet
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-04-29T07:18:42.908173Z'
  biotoolsCURIE: biotools:immune-checkpoint-inhibitor-development-services-for-cancer
  biotoolsID: immune-checkpoint-inhibitor-development-services-for-cancer
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Alfa Cytology provides comprehensive preclinical research and development
    services aimed at advancing the field of cancer therapy by facilitating the discovery
    and optimization of novel immune checkpoint inhibitors. With our expertise and
    experience, we collaborate with research organizations and pharmaceutical companies
    to accelerate the development of innovative therapies.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.alfacytology.com/immune-checkpoint-inhibitor-development-services-for-cancer.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-29T07:18:42.912150Z'
  license: null
  link: []
  maturity: null
  name: Immune Checkpoint Inhibitor Development Services for Cancer
  operatingSystem: []
  otherID: []
  owner: AlfaCytology
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-04-29T07:14:08.932295Z'
  biotoolsCURIE: biotools:virtual-cell-modeling-service
  biotoolsID: virtual-cell-modeling-service
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Virtual cell modeling represents an emerging frontier at the intersection
    of artificial intelligence and biology, aiming to predict quantities such as responses
    to diverse perturbations quantitatively. However, autonomously building computational
    models for virtual cells is challenging due to the complexity of biological systems,
    the heterogeneity of data modalities, and the need for domain-specific expertise
    across multiple disciplines.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/virtual-cell-modeling-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-29T07:14:50.625887Z'
  license: null
  link: []
  maturity: null
  name: Virtual Cell Modeling Service
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-11-05T11:45:08.078589Z'
  biotoolsCURIE: biotools:sub-saharan_africa_brain_glioma_segmenter
  biotoolsID: sub-saharan_africa_brain_glioma_segmenter
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: daniel.capellan@upm.es
    fundrefid: null
    gridid: null
    name: Daniel Capellán-Martín
    note: null
    orcidid: https://orcid.org/0000-0002-9743-0845
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Developer
    - Contributor
    - Support
    url: null
  - email: pabhijeet@childrensnational.org
    fundrefid: null
    gridid: null
    name: Abhijeet Parida
    note: null
    orcidid: https://orcid.org/0000-0002-4978-0576
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    - Contributor
    - Support
    - Maintainer
    url: null
  - email: zjiang@childrensnational.org
    fundrefid: null
    gridid: null
    name: Zhifan Jiang
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    - Developer
    - Support
    url: null
  - email: mj.ledesma@upm.es
    fundrefid: null
    gridid: null
    name: María Jesus Ledesma-Carbayo
    note: null
    orcidid: https://orcid.org/0000-0001-6846-3923
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Contributor
    url: null
  - email: mlingura@childrensnational.org
    fundrefid: null
    gridid: null
    name: Marius George Linguraru
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Contributor
    url: null
  description: The Sub-Saharan Africa Brain Glioma Segmenter is a software tool developed
    by researchers from Universidad Politécnica de Madrid and Children’s National
    Hospital for the segmentation and analysis of intercranial meningiomas in magnetic
    resonance imaging (MRI). Built in Python, it enables precise quantitative analysis
    of gliomas in brain MRI scans to support clinical decision-making in both diagnosis
    and prognosis. This tool was trained on a cohort of patients from Sub-Saharan
    Africa.
  documentation:
  - note: null
    type:
    - API documentation
    - Citation instructions
    - Terms of use
    - Code of conduct
    - Release notes
    - User manual
    - General
    - Quick start guide
    url: https://docs.hope4kids.io/HOPE-Segmenter-Kids/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output: []
  homepage: https://github.com/BIT-UPM/EUCAIM/tree/main/sub_saharan_africa_brain_glioma_segmenter
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-28T09:51:14.743240Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: Main app webpage
    type:
    - Other
    url: https://segmenter.hope4kids.io/
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids
  - note: EUCAIM harbor link
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ssa-brain-glioma-segmenter/info-tab
  maturity: Mature
  name: Sub-Saharan Africa Brain Glioma Segmenter
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: dani-capellan
  publication:
  - doi: 10.1007/978-3-031-76163-8_20
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1109/ISBI56570.2024.10635469
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04094
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04111
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  - Command-line tool
  - Workflow
  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: '2025-11-05T10:35:32.782850Z'
  biotoolsCURIE: biotools:intercranial_meningioma_segmenter
  biotoolsID: intercranial_meningioma_segmenter
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: daniel.capellan@upm.es
    fundrefid: null
    gridid: null
    name: Daniel Capellán-Martín
    note: null
    orcidid: https://orcid.org/0000-0002-9743-0845
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Developer
    - Contributor
    - Support
    url: null
  - email: pabhijeet@childrensnational.org
    fundrefid: null
    gridid: null
    name: Abhijeet Parida
    note: null
    orcidid: https://orcid.org/0000-0002-4978-0576
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    - Contributor
    - Support
    - Maintainer
    url: null
  - email: zjiang@childrensnational.org
    fundrefid: null
    gridid: null
    name: Zhifan Jiang
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    - Developer
    - Support
    url: null
  - email: mj.ledesma@upm.es
    fundrefid: null
    gridid: null
    name: María Jesus Ledesma-Carbayo
    note: null
    orcidid: https://orcid.org/0000-0001-6846-3923
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Contributor
    url: null
  - email: mlingura@childrensnational.org
    fundrefid: null
    gridid: null
    name: Marius George Linguraru
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
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    - Contributor
    url: null
  description: The Intercranial Meningioma Segmenter is a software tool developed
    by researchers from Universidad Politécnica de Madrid and Children’s National
    Hospital for the segmentation and analysis of intercranial meningiomas in magnetic
    resonance imaging (MRI). Built in Python, it enables precise quantitative analysis
    of intercranial meningiomas in brain MRI scans to support clinical decision-making
    in both diagnosis and prognosis.
  documentation:
  - note: null
    type:
    - API documentation
    - Citation instructions
    - Terms of use
    - Code of conduct
    - Release notes
    - User manual
    - General
    - Quick start guide
    url: https://docs.hope4kids.io/HOPE-Segmenter-Kids/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output: []
  homepage: https://github.com/BIT-UPM/EUCAIM/tree/main/intercranial_meningioma_segmenter
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-28T09:50:24.781513Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: Main app webpage
    type:
    - Other
    url: https://segmenter.hope4kids.io/
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids
  - note: EUCAIM harbor link
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/intracranial-meningioma-segmenter/info-tab
  maturity: Mature
  name: Intercranial Meningioma Segmenter
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: dani-capellan
  publication:
  - doi: 10.1007/978-3-031-76163-8_20
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1109/ISBI56570.2024.10635469
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04094
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04111
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  - Command-line tool
  - Workflow
  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: '2025-11-04T18:24:22.573039Z'
  biotoolsCURIE: biotools:brain_metastasis_segmenter
  biotoolsID: brain_metastasis_segmenter
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: daniel.capellan@upm.es
    fundrefid: null
    gridid: null
    name: Daniel Capellán-Martín
    note: null
    orcidid: https://orcid.org/0000-0002-9743-0845
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Developer
    - Contributor
    - Support
    url: null
  - email: pabhijeet@childrensnational.org
    fundrefid: null
    gridid: null
    name: Abhijeet Parida
    note: null
    orcidid: https://orcid.org/0000-0002-4978-0576
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    - Contributor
    - Support
    - Maintainer
    url: null
  - email: zjiang@childrensnational.org
    fundrefid: null
    gridid: null
    name: Zhifan Jiang
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    - Developer
    - Support
    url: null
  - email: mj.ledesma@upm.es
    fundrefid: null
    gridid: null
    name: María Jesus Ledesma-Carbayo
    note: null
    orcidid: https://orcid.org/0000-0001-6846-3923
    rorid: null
    typeEntity: null
    typeRole:
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    - Contributor
    url: null
  - email: mlingura@childrensnational.org
    fundrefid: null
    gridid: null
    name: Marius George Linguraru
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
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    - Contributor
    url: null
  description: The Brain Metastasis Segmenter is a software tool developed by researchers
    from Universidad Politécnica de Madrid and Children’s National Hospital for the
    segmentation and analysis of brain metastases in magnetic resonance imaging (MRI).
    Built in Python, it enables precise quantitative analysis of brain metastases
    in MRI scans to support clinical decision-making in both diagnosis and prognosis.
  documentation:
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  - doi: 10.1109/ISBI56570.2024.10635469
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  description: The Brain Glioma Segmenter is a software tool developed by researchers
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  - doi: 10.1109/ISBI56570.2024.10635469
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  toolType:
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  topic:
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  description: The Pediatric Brain Tumor Segmenter is a software tool developed by
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  - doi: 10.1109/ISBI56570.2024.10635469
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  validated: 0
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  description: The purpose of the tool is to provide a complete framework for automatic
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  description: The EUCAIM Wizard Tool performs an analysis of data re-identification
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  description: RACLAHE (Region-Adaptive Contrast Limited Adaptive Histogram Equalization)
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  documentation:
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  - note: null
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  topic:
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  validated: 0
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  additionDate: '2025-12-04T11:29:17.647406Z'
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  description: A fully convolutional (with no pooling layers) model was trained on
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    - Developer
    url: null
  description: "A DICOM Anonymization pipeline in a Docker container. This pipeline\
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    \ the following steps:\n\nStep 1 (Optional): Perform OCR on DICOM pixel data to\
    \ remove sensitive information (burned-in information).\nStep 2: Deidentify DICOM\
    \ metadata using the RSNA CTP Anonymizer and the EUCAIM anonymization script.\
    \ \nStep 3 (Optional): Deidentify clinical data provided in CSV files so that\
    \ the referenced patient id is anonymized the same way CTP does in Step 2."
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  - note: null
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    input:
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    note: null
    operation:
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/lethe-dicom-anonymizer/info-tab
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  lastUpdate: '2026-04-28T06:53:40.880240Z'
  license: EUPL-1.2
  link:
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  owner: vkalokyri
  publication:
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    metadata: null
    note: null
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    type: []
    version: null
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  toolType:
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  topic:
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  - term: Data protection
    uri: http://edamontology.org/topic_4044
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  validated: 0
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  - 0.10.1
  - 0.11.2
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T10:38:08.771699Z'
  biotoolsCURIE: biotools:ct-based_neuroblastoma_tumour_detection_and_segmentation
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  description: The tool performs by deep learning an automatic segmentation of the
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    resizing, z-score normalization, patching; and postprocessing operations. It takes
    DICOM images as input and generates tumoral masks in DICOM SEG or NIFTI formats.
  documentation:
  - note: null
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  function:
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    note: null
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  language:
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  lastUpdate: '2026-04-27T11:04:03.859531Z'
  license: CC-BY-NC-ND-4.0
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  maturity: Mature
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  toolType:
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  topic:
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  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
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  additionDate: '2025-05-29T09:19:51.404419Z'
  biotoolsCURIE: biotools:mr-based_dipg_tumour_detection_and_segmentation
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  description: The tool performs an automatic segmentation of the possible DIPG tumours
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    workflow from DICOM images to DICOM seg tumoral masks.
  documentation:
  - note: null
    type:
    - General
    url: https://link.springer.com/article/10.1007/s10278-025-01557-9
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    url: https://drive.eucaim.cancerimage.eu/s/5CL2H8tyMDzFHex
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  function:
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        term: Image
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    note: null
    operation:
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      }}'"
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  language:
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  lastUpdate: '2026-04-27T11:03:42.973594Z'
  license: CC-BY-NC-ND-4.0
  link:
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  maturity: Mature
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    metadata: null
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    version: null
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  toolType:
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    uri: http://edamontology.org/topic_3474
  - 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'
  biotoolsCURIE: biotools:mr-based_glioblastoma_tumour_detection_and_segmentation
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  description: 'The tool performs an automatic segmentation of the possible glioblastoma
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    among others. It takes DICOM images as input and generates tumoral masks in DICOM
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  documentation:
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    url: https://pubmed.ncbi.nlm.nih.gov/38849632/
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    url: https://drive.eucaim.cancerimage.eu/s/otrYTickHjDxnkP
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  function:
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  - 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\
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      }]' \\\n  --target total-fused \\\n  --emit-config true"
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    note: null
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  homepage_status: 0
  language:
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  lastUpdate: '2026-04-27T11:02:32.526898Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
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    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/info-tab
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  maturity: Mature
  name: MR-based glioblastoma tumour detection and segmentation (EUCAIM-SW-021_T-01-02-004)
  operatingSystem:
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  operatingSystem: []
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  owner: johangustafsson
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  - doi: 10.1101/2025.06.14.659707
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1101/2024.11.19.624167
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1038/s41592-022-01488-1
    metadata: null
    note: Cite if you use automatic MSA generation.
    pmcid: PMC9184281
    pmid: '35637307'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-04-20T07:17:03.131774Z'
  biotoolsCURIE: biotools:biobakery_workflows
  biotoolsID: biobakery_workflows
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: bioBakery workflows is a collection of workflows for common microbial
    community analyses using standardized tools and parameters, performing quality
    control and generating summary statistics.
  documentation:
  - note: null
    type:
    - Installation instructions
    - Command-line options
    url: https://github.com/biobakery/biobakery_workflows
  download: []
  editPermission:
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    type: private
  elixirCommunity: []
  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output:
    - data:
        term: Nucleic acid report
        uri: http://edamontology.org/data_2084
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://huttenhower.sph.harvard.edu/biobakery_workflows
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-20T07:26:03.529372Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/biobakery/biobakery_workflows
  maturity: Mature
  name: bioBakery Workflows
  operatingSystem:
  - Linux
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.1093/bioinformatics/btx754
    metadata: null
    note: null
    pmcid: PMC6030947
    pmid: '29194469'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - 4.0.0
- accessibility: null
  additionDate: '2015-03-05T10:30:40Z'
  biotoolsCURIE: biotools:3d-dart
  biotoolsID: 3d-dart
  collectionID:
  - WeNMR
  - EOSC-Hub
  - EGI
  - INSTRUCT
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: a.m.j.j.bonvin@uu.nl
    fundrefid: null
    gridid: null
    name: Bonvin Lab
    note: null
    orcidid: http://orcid.org/0000-0001-7369-1322
    rorid: null
    typeEntity: Division
    typeRole:
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    - Maintainer
    - Provider
    - Primary contact
    url: http://www.bonvinlab.org
  - email: null
    fundrefid: null
    gridid: null
    name: Utrecht University
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: http://www.uu.nl
  description: A web server for generation of 3D-structural DNA models with a defined
    conformation by providing control over both ‘global’ and ‘local’ conformational
    features.
  documentation:
  - note: null
    type:
    - User manual
    url: https://milou.science.uu.nl/services/3DDART/DARTusage.html
  download: []
  editPermission:
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    type: group
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  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: 3DNA driven - DNA Analysis and Rebuilding Tools. Provides a means of analyzing
      nucleic acid structures and generating custom models.
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Molecular dynamics
      uri: http://edamontology.org/operation_2476
    - term: Nucleic acid structure analysis
      uri: http://edamontology.org/operation_2481
    output: []
  homepage: https://milou.science.uu.nl/services/3DDART/
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-19T09:24:16.551817Z'
  license: null
  link: []
  maturity: Mature
  name: 3D-DART
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: esraa9
  publication:
  - doi: 10.1093/nar/gkp287
    metadata:
      abstract: There is a growing interest in structural studies of DNA by both experimental
        and computational approaches. Often, 3D-structural models of DNA are required,
        for instance, to serve as templates for homology modeling, as starting structures
        for macro-molecular docking or as scaffold for NMR structure calculations.
        The conformational adaptability of DNA when binding to a protein is often
        an important factor and at the same time a limitation in such studies. As
        a response to the demand for 3D-structural models reflecting the intrinsic
        plasticity of DNA we present the 3D-DART server (3D NA-Driven D NA A nalysis
        and R ebuilding T ool). The server provides an easy interface to a powerful
        collection of tools for the generation of DNA-structural models in custom
        conformations. The computational engine beyond the server makes use of the
        3DNA software suite together with a collection of home-written python scripts.
        The server is freely available at http://haddock.chem.uu.nl/dna without any
        login requirement.
      authors:
      - name: van Dijk M.
      - name: Bonvin A.M.J.J.
      citationCount: 279
      date: '2009-08-04T00:00:00Z'
      journal: Nucleic Acids Research
      title: '3D-DART: A DNA structure modelling server'
    note: null
    pmcid: PMC2703913
    pmid: '19417072'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Structural biology
    uri: http://edamontology.org/topic_1317
  - term: NMR
    uri: http://edamontology.org/topic_0593
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  validated: 1
  version:
  - '1'
- accessibility: Open access
  additionDate: '2026-03-04T16:50:34.235195Z'
  biotoolsCURIE: biotools:pathway-subtyping
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  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: Disease-agnostic Python framework for discovering molecular subtypes
    using pathway-level analysis and Gaussian mixture model clustering with built-in
    validation gates
  documentation:
  - note: null
    type:
    - User manual
    url: https://codeberg.org/pathways/pathway-subtyping-framework/src/branch/main/docs
  download:
  - note: 'pip install pathway-subtyping

      Or with all extras:

      pip install pathway-subtyping[viz,graph]'
    type: Software package
    url: https://pypi.org/project/pathway-subtyping/
    version: 0.3.1
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Expression analysis
      uri: http://edamontology.org/operation_2495
    - term: Clustering
      uri: http://edamontology.org/operation_3432
    - term: Data analysis
      uri: http://edamontology.org/operation_2945
    output: []
  homepage: https://codeberg.org/pathways/pathway-subtyping-framework
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-19T05:06:05.234645Z'
  license: MIT
  link:
  - note: Python Library Repository
    type:
    - Software catalogue
    url: https://pypi.org/project/pathway-subtyping/
  - note: Documentation
    type:
    - Other
    url: https://codeberg.org/pathways/pathway-subtyping-framework/src/branch/main/docs
  - note: Source code repository
    type:
    - Other
    url: https://codeberg.org/pathways/pathway-subtyping-framework
  maturity: Mature
  name: pathway-subtyping
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: pathways
  publication:
  - doi: 10.21203/rs.3.rs-8913089/v1
    metadata: null
    note: 'Title: Pathway-Based Molecular Subtyping Reveals a GABA-Collapsed Autism
      Subgroup and Cross-Disease Convergence with Schizophrenia in Human Cerebral
      Cortex'
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: null
  relation: []
  toolType:
  - Library
  - Command-line tool
  topic:
  - term: Omics
    uri: http://edamontology.org/topic_3391
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Biosciences
    uri: http://edamontology.org/topic_4019
  validated: 0
  version:
  - 0.4.0
  - 0.3.1
  - 0.5.0
  - 0.6.2
  - 0.6.3
- accessibility: Open access
  additionDate: '2023-08-30T13:03:57.407598Z'
  biotoolsCURIE: biotools:shic
  biotoolsID: shic
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: magnus.palmblad@gmail.com
    fundrefid: null
    gridid: null
    name: Magnus Palmblad
    note: null
    orcidid: https://orcid.org/0000-0002-5865-8994
    rorid: null
    typeEntity: null
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Veit Schwämmle
    note: null
    orcidid: https://orcid.org/0000-0002-9708-6722
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Dirk Winkelhardt
    note: null
    orcidid: https://orcid.org/0000-0001-8770-2221
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Vedran Kasalica
    note: null
    orcidid: https://orcid.org/0000-0002-0097-1056
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Anna-Lena Lamprecht
    note: null
    orcidid: https://orcid.org/0000-0003-1953-5606
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: shic is a collection of shims for use in automated workflow composition
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/magnuspalmblad/shic/blob/main/README.md
  download: []
  editPermission:
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    type: group
  elixirCommunity:
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  - Galaxy
  - Metabolomics
  elixirNode: []
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  elixir_badge: 0
  function:
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    input:
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        term: Protein report
        uri: http://edamontology.org/data_0896
      format:
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        uri: http://edamontology.org/format_3747
    note: null
    operation:
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    output:
    - data:
        term: ID list
        uri: http://edamontology.org/data_2872
      format:
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        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
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        term: Mass spectrometry data
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      format:
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        uri: http://edamontology.org/format_3651
    note: null
    operation:
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    output:
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
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  - cmd: null
    input:
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      format:
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    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence distance matrix
        uri: http://edamontology.org/data_0870
      format:
      - term: mega
        uri: http://edamontology.org/format_1991
  - cmd: null
    input:
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      format:
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    note: null
    operation:
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    output:
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      format:
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  - cmd: null
    input:
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      format:
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    note: null
    operation:
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    output:
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      format:
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  - cmd: null
    input:
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      format:
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    note: null
    operation:
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    output:
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      format:
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        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
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    note: null
    operation:
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    output:
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      format:
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        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
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      format:
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    note: null
    operation:
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    input:
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    note: null
    operation:
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    output:
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        term: ID list
        uri: http://edamontology.org/data_2872
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
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      format:
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    note: null
    operation:
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    output:
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      format:
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        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
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      format:
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    note: null
    operation:
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    output:
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        term: Protein name (UniProt)
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      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://github.com/magnuspalmblad/shic
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-17T13:21:28.211937Z'
  license: MIT
  link:
  - note: null
    type:
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  maturity: null
  name: shic
  operatingSystem: []
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication: []
  relation: []
  toolType:
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  topic: []
  validated: 0
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