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  description: 'The tool performs a DICOM quality check in terms of correct number
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  cost: Free of charge
  credit:
  - email: h.kucukali+biotools@uu.nl
    fundrefid: null
    gridid: null
    name: Hüseyin Küçükali
    note: null
    orcidid: https://orcid.org/0000-0003-1669-3107
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  description: An open platform for sharing, discussing and reusing causal graphs.
  documentation: []
  download: []
  editPermission:
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  function: []
  homepage: https://opencausal.org/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-23T14:56:55.440549Z'
  license: null
  link: []
  maturity: Emerging
  name: Open Causal
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2019-07-06T06:35:25Z'
  biotoolsCURIE: biotools:StructureProfiler
  biotoolsID: StructureProfiler
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: rarey@zbh.uni-hamburg.de
    fundrefid: null
    gridid: null
    name: Matthias Rarey
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Tool for 3D protein structure profiling.
  documentation: []
  download:
  - note: NAOMI ChemBio Suite including the package
    type: Downloads page
    url: https://software.zbh.uni-hamburg.de/pages/getPackage
    version: null
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Protein geometry calculation
      uri: http://edamontology.org/operation_0249
    - term: Protein structure validation
      uri: http://edamontology.org/operation_0321
    - term: Protein-ligand docking
      uri: http://edamontology.org/operation_0482
    output: []
  homepage: https://www.zbh.uni-hamburg.de/forschung/amd/software/structureprofiler.html
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-23T14:50:37.487104Z'
  license: Other
  link: []
  maturity: Mature
  name: StructureProfiler
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1093/bioinformatics/bty692
    metadata:
      abstract: Motivation Three-dimensional protein structures are important starting
        points for elucidating protein function and applications like drug design.
        Computational methods in this area rely on high quality validation datasets
        which are usually manually assembled. Due to the increase in published structures
        as well as the increasing demand for specially tailored validation datasets,
        automatic procedures should be adopted. Results StructureProfiler is a new
        tool for automatic, objective and customizable profiling of X-ray protein
        structures based on the most frequently applied selection criteria currently
        in use to assemble benchmark datasets. As examples, four dataset configurations
        (Astex, Iridium, Platinum, combined), all results of the combined tests and
        the list of all PDB Ids passing the combined criteria set are attached in
        theSupplementary Material.
      authors:
      - name: Meyder A.
      - name: Kampen S.
      - name: Sieg J.
      - name: Fahrrolfes R.
      - name: Friedrich N.-O.
      - name: Flachsenberg F.
      - name: Rarey M.
      citationCount: 4
      date: '2019-03-01T00:00:00Z'
      journal: Bioinformatics
      title: 'StructureProfiler: An all-in-one tool for 3D protein structure profiling'
    note: null
    pmcid: null
    pmid: '30124779'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Protein structural motifs and surfaces
    uri: http://edamontology.org/topic_0166
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  validated: 1
  version: []
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-28T23:55:08.439649Z'
  biotoolsCURIE: biotools:dicom_image_similarity-duplicate_checker
  biotoolsID: dicom_image_similarity-duplicate_checker
  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'Detects duplicate or visually similar DICOM series using a tiered
    approach that combines metadata analysis, hash-based comparison, and pixel-level
    similarity metrics.

    Ideal for:

    1. High-level series comparison and classification, and

    2. Detecting duplicates even after post-processing (e.g., denoising, filtering).


    For scenarios requiring strict, image-level deduplication based on pixel content,
    fully agnostic to metadata changes, consider using [https://bio.tools/image_duplicate_check_tool]'
  documentation:
  - note: null
    type:
    - General
    url: https://docs.google.com/document/d/10GsrgRCeyrZrdus04iI-967llth0o9yE/edit?usp=drive_link&ouid=108776251279939449410&rtpof=true&sd=true
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  function: []
  homepage: https://www.med.auth.gr/en/content/laboratory-computing-medical-informatics-and-biomedical-imaging-technologies
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-23T13:24:16.938179Z'
  license: Apache-2.0
  link:
  - note: Link to the Harbor image
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/deduplication_tool
  maturity: Mature
  name: Image Duplicates Checker
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: difoto
  publication: []
  relation:
  - biotoolsID: data_integration_quality_check_tool_diqct
    type: includedIn
  toolType:
  - Command-line tool
  topic:
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 0
  version:
  - '2.0'
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T10:38:08.771699Z'
  biotoolsCURIE: biotools:ct-based_neuroblastoma_tumour_detection_and_segmentation
  biotoolsID: ct-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: 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
    - Developer
    - Support
    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
    typeEntity: Person
    typeRole:
    - 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:
    - Support
    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 by deep learning an automatic segmentation of the
    possible neuroblastoma tumours on Contrast Enhanced CT images (CE-CTs). Model
    architecture is Unet-based with residual operations, atrous dilation convolution
    and specific batch generator. It applies preprocessing steps as RAS conversion,
    resizing, z-score normalization, patching; and postprocessing operations. It takes
    DICOM images as input and generates tumoral masks in DICOM SEG or NIFTI formats.
  documentation:
  - note: null
    type:
    - Terms of use
    url: https://drive.google.com/file/d/1mvGl_fexQIqBR7njGl73V81VdZ7ycPBs/view?usp=drive_link
  download: []
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    - pedromiguel_martinez_HULAFE
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  function:
  - cmd: "docker run --rm --gpus all \\\n\t-v /path/to/input:/input \\\n\t-v /path/to/output:/output\
      \ \\\n\tharbor.eucaim.cancerimage.eu/processing-tools/ct-based_neuroblastoma_tumour_detection_and_segmentation:2.0.0\
      \ \\\n\t--series_csv /output/config/series_to_segment.csv \\\n\t--output_dir\
      \ /output"
    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/ct-based_neuroblastoma_tumour_detection_and_segmentation/artifacts-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-23T03:53:03.484226Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ct-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: CT-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-022_T-01-02-005)
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: casopon
  publication:
  - doi: 10.3390/app11083508
    metadata:
      abstract: ''
      authors: []
      citationCount: 10
      date: '2021-04-02T00:00:00Z'
      journal: Applied Sciences (Switzerland)
      title: 'Franken-ct: Head and neck mr-based pseudo-ct synthesis using diverse
        anatomical overlapping mr-ct scans'
    note: null
    pmcid: null
    pmid: null
    type:
    - Usage
    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:
  - 2.0.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T09:19:51.404419Z'
  biotoolsCURIE: biotools:mr-based_dipg_tumour_detection_and_segmentation
  biotoolsID: mr-based_dipg_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
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    typeEntity: Institute
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  - email: matias_fernandez@iislafe.es
    fundrefid: null
    gridid: null
    name: Matias Fernandez-Paton
    note: null
    orcidid: https://orcid.org/0000-0001-9374-1411
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Support
    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
    typeEntity: Person
    typeRole:
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    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
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    - Support
    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
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    typeEntity: Person
    typeRole:
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    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: The tool performs an automatic segmentation of the possible DIPG tumours
    on MR images. DIPG (Diffuse Intrinsic Pontine Glioma), or more recently, DMG (Diffuse
    Midline Glioma) is a H3 K27M–mutant pediatric brainstem cancer detected in T1W
    and Flair/T2-weighted magnetic resonance images. The tool includes a complete
    workflow from DICOM images to DICOM seg tumoral masks.
  documentation:
  - note: null
    type:
    - General
    url: https://link.springer.com/article/10.1007/s10278-025-01557-9
  - note: null
    type:
    - Terms of use
    url: https://drive.google.com/file/d/1KjFvpsxLndP7M7ugVy0uF2vSsWUgUZEY/view?usp=drive_link
  download: []
  editPermission:
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    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input \\\n  -v /path/to/output:/output\
      \ \\\nharbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest\
      \ \\\n  --series-selector /input/config/series.csv"
    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 -v /path/to/output:/output\
      \ harbor.eucaim.cancerimage.eu/processing-tools/mr-based_dipg_tumour_detection_and_segmentation:latest\
      \ \\\n  --json-args '{\"dataset_id\":\"DS1\",\"patient_id\":\"P1\",\"study_id\"\
      :\"S1\",\"sequences\":{\"T1w\":\"/input/DICOM/DS1/P1/S1/T1\",\"FLAIR\":\"/input/DICOM/DS1/P1/S1/FLAIR\"\
      }}'"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
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        uri: http://edamontology.org/format_3549
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        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
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        term: Image
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      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_dipg_tumour_detection_and_segmentation/artifacts-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-22T13:54:01.962965Z'
  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_dipg_tumour_detection_and_segmentation/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: MR-based DIPG tumour detection and segmentation (EUCAIM-SW-020_T-01-02-003)
  operatingSystem:
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  - Linux
  - Windows
  otherID: []
  owner: casopon
  publication:
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    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-01-01T00:00:00Z'
      journal: Journal of Imaging Informatics in Medicine
      title: Deep Learning Auto-segmentation of Diffuse Midline Glioma on Multimodal
        Magnetic Resonance Images
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  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: '2025-05-29T12:09:16.704255Z'
  biotoolsCURIE: biotools:mr-based_glioblastoma_tumour_detection_and_segmentation
  biotoolsID: mr-based_glioblastoma_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:
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    url: null
  - email: maria_beser@iislafe.es
    fundrefid: null
    gridid: null
    name: Maria Beser-Robles
    note: null
    orcidid: https://orcid.org/0000-0002-0072-5525
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
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    - Developer
    - Support
    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
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    typeEntity: Person
    typeRole:
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    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
    gridid: null
    name: Leonor Cerda-Alberich
    note: null
    orcidid: https://orcid.org/0000-0002-5567-4278
    rorid: null
    typeEntity: Person
    typeRole:
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  - email: luis_marti@iislafe.es
    fundrefid: null
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    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
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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:
  - note: null
    type:
    - General
    url: https://pubmed.ncbi.nlm.nih.gov/38849632/
  - note: null
    type:
    - Terms of use
    url: https://drive.google.com/file/d/1eqM5V0oILLlcuv5NF0ib4Gb6p2kA5EzU/view?usp=drive_link
  download: []
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  elixirNode: []
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  elixir_badge: 0
  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:
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  description: The GlobalAMFungi Database is an open-access, global repository of
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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:
    - 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: []
  elixirPlatform: []
  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:
  - 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
  additionDate: '2025-12-15T14:17:14.627791Z'
  biotoolsCURIE: biotools:asafind
  biotoolsID: asafind
  collectionID:
  - ELIXIR-CZ
  - Czech Republic
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: mvohnoutova@jcu.cz
    fundrefid: null
    gridid: null
    name: Marta Vohnoutová
    note: null
    orcidid: https://orcid.org/0000-0002-8915-8626
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    - Maintainer
    url: https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Vohnoutova_Marta_61699
  - email: agruber@prf.jcu.cz
    fundrefid: null
    gridid: null
    name: Ansgar Gruber
    note: null
    orcidid: https://orcid.org/0000-0002-5876-4391
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    url: https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gruber_Ansgar_118401
  description: "ASAFind is a software that predicts the intracellular location of\
    \ proteins in cells with four membrane-bound complex plastids of red algal origin.\
    \ \nThese plastids evolved via eukaryote-eukaryote endosymbiosis and for example\
    \ can be found in diatoms and cryptophytes. ASAFind uses protein sequence data\
    \ and external predictions of signal peptides (by the tools SignalP and TargetP),\
    \ and predicts plastid proteins, and proteins that are targeted to the periplastidic\
    \ compartment from these data; optionally, a graphical output can generated."
  documentation:
  - note: null
    type:
    - Installation instructions
    url: https://asafind.jcu.cz/download-page/
  download:
  - note: Download page on web-service, links to repository
    type: Downloads page
    url: https://asafind.jcu.cz/download-page/
    version: '2.0'
  editPermission:
    authors:
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    type: group
  elixirCommunity:
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  - Marine Metagenomics
  - Microbial Biotechnology
  elixirNode:
  - Czech Republic
  elixirPlatform:
  - Tools
  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: Open access
  additionDate: '2025-12-15T11:29:08.759624Z'
  biotoolsCURIE: biotools:mitsorter
  biotoolsID: mitsorter
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: sharonnatasha.cox@uniba.it
    fundrefid: null
    gridid: null
    name: Sharon Natasha Cox
    note: Researcher at University of Bari
    orcidid: https://orcid.org/0000-0002-8488-440X
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: angelovarvara94@gmail.com
    fundrefid: null
    gridid: null
    name: Angelo Sante Varvara
    note: PhD Student at SEMM Institute
    orcidid: https://orcid.org/0009-0005-3559-8430
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://www.linkedin.com/in/angelo-sante-varvara-b514661a6/
  description: Stand-alone tool for methylation-based discrimination of mitochondrial
    DNA ONT reads
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://github.com/asvarvara/MitSorter/blob/main/README.md
  download: []
  editPermission:
    authors:
    - sharonnatasha.cox
    type: group
  elixirCommunity:
  - Federated Human Data
  elixirNode:
  - Italy
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function: []
  homepage: https://github.com/asvarvara/MitSorter
  homepage_status: 0
  language:
  - Python
  - Shell
  lastUpdate: '2025-12-15T11:29:47.221679Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/asvarvara/MitSorter
  maturity: Emerging
  name: MitSorter
  operatingSystem:
  - Linux
  otherID: []
  owner: asvarvara
  publication:
  - doi: 10.1093/bioadv/vbaf135
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-01-01T00:00:00Z'
      journal: Bioinformatics Advances
      title: 'MitSorter: a standalone tool for accurate discrimination of mtDNA and
        NuMT ONT reads based on differential methylation'
    note: null
    pmcid: PMC12275464
    pmid: '40688360'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Workflow
  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  validated: 0
  version: []
- 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:
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    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:
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    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:
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  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
  - biotoolsID: pdb
    type: uses
  - biotoolsID: rfam
    type: uses
  - biotoolsID: 3d-beacons
    type: uses
  toolType:
  - Desktop application
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 1
  version:
  - 2.11.5.1
- accessibility: Open access
  additionDate: '2025-12-08T13:54:29.684754Z'
  biotoolsCURIE: biotools:oct-to-tiff
  biotoolsID: oct-to-tiff
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A command line tool for converting optical coherence tomography angiography
    (OCTA) data.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/camlloyd/oct-to-tiff
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-10T22:41:05.503948Z'
  license: BSD-3-Clause
  link: []
  maturity: null
  name: oct-to-tiff
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: camlloyd
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Tomography
    uri: http://edamontology.org/topic_3452
  - term: Ophthalmology
    uri: http://edamontology.org/topic_3417
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version:
  - 0.6.0
- accessibility: Open access
  additionDate: '2023-03-23T00:11:45.508771Z'
  biotoolsCURIE: biotools:protcad
  biotoolsID: protcad
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: roland.dunbrack@fccc.edu
    fundrefid: null
    gridid: null
    name: Roland L. Dunbrack Jr.
    note: null
    orcidid: http://orcid.org/0000-0001-7674-6667
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Qifang Xu
    note: null
    orcidid: http://orcid.org/0000-0002-1606-7045
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: The Protein Common Assembly Database (ProtCAD) – A comprehensive structural
    resource of protein complexes.
  documentation: []
  download: []
  editPermission:
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  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
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    input:
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        term: PDB ID
        uri: http://edamontology.org/data_1127
      format: []
    - data:
        term: Pfam clan ID
        uri: http://edamontology.org/data_2758
      format: []
    - data:
        term: Protein name (UniProt)
        uri: http://edamontology.org/data_2764
      format: []
    note: null
    operation:
    - term: Sequence assembly
      uri: http://edamontology.org/operation_0310
    - term: Clustering
      uri: http://edamontology.org/operation_3432
    - term: Protein architecture recognition
      uri: http://edamontology.org/operation_2475
    output: []
  homepage: http://dunbrack2.fccc.edu/protcad
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-10T20:33:43.896057Z'
  license: null
  link: []
  maturity: null
  name: ProtCAD
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Jennifer
  publication:
  - doi: 10.1093/nar/gkac937
    metadata:
      abstract: ''
      authors: []
      citationCount: 4
      date: '2023-01-06T00:00:00Z'
      journal: Nucleic Acids Research
      title: The protein common assembly database (ProtCAD)––a comprehensive structural
        resource of protein complexes
    note: null
    pmcid: PMC9825537
    pmid: '36300618'
    type: []
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: X-ray diffraction
    uri: http://edamontology.org/topic_2828
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-12-10T13:18:28.703003Z'
  biotoolsCURIE: biotools:emapper2gbk
  biotoolsID: emapper2gbk
  collectionID:
  - AuReMe
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Arnaud
    note: null
    orcidid: https://orcid.org/0000-0003-1170-0785
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://github.com/ArnaudBelcour
  description: creation of genbank files from Eggnog-mapper annotation outputs
  documentation:
  - note: null
    type:
    - Installation instructions
    - User manual
    url: https://github.com/AuReMe/emapper2gbk
  download:
  - note: null
    type: Source code
    url: https://github.com/AuReMe/emapper2gbk.git
    version: 0.3.2
  - note: null
    type: Software package
    url: https://pypi.org/project/emapper2gbk/#files
    version: 0.3.2
  editPermission:
    authors:
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    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: genomes -fn genome.fna -fp proteome.faa -gff genome.gff -n "Escherichia coli"
    input:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence set (protein)
        uri: http://edamontology.org/data_1233
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
    note: Genomic -single mode
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: GenBank-like format (text)
        uri: http://edamontology.org/format_2205
  homepage: https://github.com/AuReMe/emapper2gbk
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-10T16:49:05.332576Z'
  license: LGPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/AuReMe/emapper2gbk
  - note: Access to Python library
    type:
    - Software catalogue
    url: https://pypi.org/project/emapper2gbk/
  maturity: Mature
  name: emapper2gbk
  operatingSystem:
  - Linux
  otherID: []
  owner: Noe_Robert
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Data rescue
    uri: http://edamontology.org/topic_4011
  validated: 0
  version:
  - 0.3.2
- accessibility: Open access
  additionDate: '2025-12-09T11:58:09.082995Z'
  biotoolsCURIE: biotools:specieshub
  biotoolsID: specieshub
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit: []
  description: SpeciesHub is a privacy-friendly platform that empowers you to manage
    biodiversity data—replacing spreadsheets, paper forms, and custom software for
    each project. It's an all-in-one resource for individual biologists and large
    teams, offering advanced tools to keep your data private, secure, and shared only
    on your terms.
  documentation: []
  download: []
  editPermission:
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    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data editing
      uri: http://edamontology.org/operation_3096
    output: []
  homepage: https://specieshub.io
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-10T08:59:19.493457Z'
  license: null
  link: []
  maturity: Emerging
  name: SpeciesHub
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: danas
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-11-14T17:30:28.515260Z'
  biotoolsCURIE: biotools:raptor-rnaseq
  biotoolsID: raptor-rnaseq
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: RAPTOR intelligently recommends and benchmarks RNA-seq pipelines by
    analyzing 20+ data characteristics (biological variation, depth, zero-inflation,
    sample size). Multi-criteria scoring provides personalized pipeline recommendations
    from eight production-ready workflows (STAR-RSEM-DESeq2, Salmon-edgeR, Kallisto-Sleuth,
    etc.) in 30 seconds with clear reasoning. Comprehensive benchmarking quantifies
    accuracy, efficiency, and reproducibility metrics across all pipelines on user
    data with customizable priority modes.
  documentation:
  - note: null
    type:
    - Citation instructions
    - Code of conduct
    - Command-line options
    - FAQ
    - General
    - Installation instructions
    - Quick start guide
    - Release notes
    - Terms of use
    - Training material
    - User manual
    url: https://github.com/AyehBlk/RAPTOR
  download:
  - note: null
    type: Source code
    url: https://github.com/AyehBlk/RAPTOR
    version: v2.1.0
  editPermission:
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    type: private
  elixirCommunity: []
  elixirNode:
  - Belgium
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: raptor profile --counts your_counts.csv --metadata metadata.csv --output
      report.html
    input:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: 'Comprehensive statistical characterization of RNA-seq datasets: library
      size statistics and variation, zero-inflation percentage, gene-level count distribution,
      biological coefficient of variation (BCV), mean-variance relationships, sequencing
      depth assessment, and experimental design balance.'
    operation:
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: JSON
        uri: http://edamontology.org/format_3464
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
  - cmd: raptor run --pipeline 3 --data your_fastq/ --output results/
    input:
    - data:
        term: Statistical estimate score
        uri: http://edamontology.org/data_0951
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: 'Intelligent recommendation system analyzing data characteristics (library
      size variation, zero-inflation, BCV, sample size, sequencing depth, design complexity)
      and matching them to pipeline strengths using multi-criteria scoring (0-200).
      Recommends from 8 pipelines: STAR-RSEM-DESeq2 (high accuracy), HISAT2-StringTie-Ballgown
      (novel transcripts), Salmon-edgeR (balanced), Kallisto-Sleuth (ultra-fast),
      STAR-HTSeq-limma (complex designs), STAR-featureCounts-NOISeq (non-parametric),
      Bowtie2-RSEM-EBSeq (Bayesian), HISAT2-Cufflinks-Cuffdiff (legacy). Priority
      modes: accuracy, speed, memory, or balanced.'
    operation:
    - term: Prediction and recognition
      uri: http://edamontology.org/operation_2423
    - term: Optimisation and refinement
      uri: http://edamontology.org/operation_2425
    - term: Comparison
      uri: http://edamontology.org/operation_2424
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ-like format (text)
        uri: http://edamontology.org/format_2182
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: 'Comprehensive benchmarking framework comparing 8 RNA-seq pipelines. Evaluates:
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      (2) Efficiency metrics: runtime, memory, CPU utilization, disk space; (3) Reproducibility
      metrics: between-run concordance, fold-change correlation, p-value correlation.
      Benchmark datasets: simulated data (Polyester), SEQC/MAQC validation, and user
      data. Runtime: 2-4 hours (small datasets) to 8-24 hours (large datasets). Outputs:
      HTML dashboard, CSV/TSV tables, publication-ready figures.'
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Validation
      uri: http://edamontology.org/operation_2428
    - term: Comparison
      uri: http://edamontology.org/operation_2424
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Gene expression profile
        uri: http://edamontology.org/data_0928
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
    - data:
        term: Matrix
        uri: http://edamontology.org/data_2082
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/AyehBlk/RAPTOR
  homepage_status: 0
  language:
  - Shell
  - Python
  - R
  lastUpdate: '2025-12-10T08:58:59.523684Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/AyehBlk/RAPTOR
  maturity: Emerging
  name: RAPTOR
  operatingSystem:
  - Linux
  otherID:
  - type: doi
    value: doi:10.5281/zenodo.17607161
    version: v2.1.0
  owner: AyehBlk
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  validated: 0
  version:
  - v2.1.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-12-09T09:22:22.735091Z'
  biotoolsCURIE: biotools:instanovo
  biotoolsID: instanovo
  collectionID:
  - proteomics
  - ms-utils
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: k.eloff@instadeep.com
    fundrefid: null
    gridid: null
    name: Kevin Eloff
    note: null
    orcidid: https://orcid.org/0000-0003-1355-8743
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: konka@dtu.dk
    fundrefid: null
    gridid: null
    name: Konstantinos Kalogeropoulos
    note: null
    orcidid: https://orcid.org/0000-0003-3907-9281
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: r.catzel@instadeep.com
    fundrefid: null
    gridid: null
    name: Rachel Catzel
    note: null
    orcidid: https://orcid.org/0000-0002-2983-9833
    rorid: null
    typeEntity: null
    typeRole:
    - Maintainer
    url: null
  - email: j.vangoey@instadeep.com
    fundrefid: null
    gridid: null
    name: Jeroen Van Goey
    note: null
    orcidid: https://orcid.org/0000-0003-4480-5567
    rorid: null
    typeEntity: null
    typeRole:
    - Maintainer
    url: null
  - email: tpaje@dtu.dk
    fundrefid: null
    gridid: null
    name: Timothy P. Jenkins
    note: null
    orcidid: https://orcid.org/0000-0003-2979-5663
    rorid: null
    typeEntity: null
    typeRole:
    - Support
    url: null
  description: InstaNovo is a transformer neural network with the ability to translate
    fragment ion peaks into the sequence of amino acids that make up the studied peptide(s).
  documentation:
  - note: null
    type:
    - General
    url: https://instadeepai.github.io/InstaNovo/
  - note: null
    type:
    - Installation instructions
    url: https://instadeepai.github.io/InstaNovo/tutorials/getting_started/#installation
  - note: null
    type:
    - Quick start guide
    url: https://instadeepai.github.io/InstaNovo/tutorials/getting_started/
  - note: null
    type:
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  - term: Proteomics experiment
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  description: This preprocessing tool is design for 2D digital mammograms in DICOM  format.
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    note: Command Arguments
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  description: D-GENIES – for Dot plot large Genomes in an Interactive, Efficient
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  validated: 0
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  description: Docker images developped at the Euro-BioImaging MED-Hub  and National
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  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Fernando Aguilar
    note: 'Creator and devloper of the main package FAIR EVA.

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

    This software started to be developed within IFCA-Advanced-Computing receives
    funding from the European Union’s Horizon 2020 research and innovation programme
    under grant agreement No 857647.'
  documentation:
  - note: Documentation for the main package, EUCAIM plugin specific documentation
      not included.
    type:
    - General
    url: https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.md
  - note: Wiki page with FAIR EVA for EUCAIM specific instructions.
    type:
    - User manual
    url: https://gitlabpages.ifca.es/fair-eva-guide-608baa/
  download: []
  editPermission:
    authors:
    - ines.ifca
    - davrodgon
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: python scripts/batch_runner.py --plugin eucaim_catalogue --out faireva_out
    input:
    - data:
        term: URL
        uri: http://edamontology.org/data_1052
      format: []
    note: null
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output:
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
  homepage: https://github.com/IFCA-Advanced-Computing/FAIR_eva
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-04T10:57:20.901575Z'
  license: Apache-2.0
  link:
  - note: Repository for FAIR EVA, without the EUCAIM specific plugin
    type:
    - Repository
    url: https://github.com/IFCA-Advanced-Computing/FAIR_eva
  maturity: Mature
  name: FAIR EVA for EUCAIM
  operatingSystem:
  - Linux
  otherID: []
  owner: davrodgon
  publication:
  - doi: 10.1038/s41597-023-02652-8
    metadata:
      abstract: null
      authors: []
      citationCount: 0
      date: null
      journal: null
      title: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Plug-in
  - Command-line tool
  - Web service
  topic:
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  validated: 0
  version:
  - EUCAIM_plugin_0.3
  - EUCAIM_plugin_0.3.1
  - EUCAIM_plugin_0.4.0
  - EUCAIM_0.4.2
- accessibility: Open access (with restrictions)
  additionDate: '2025-11-25T09:58:37.569343Z'
  biotoolsCURIE: biotools:ml_model_for_mr_series_categorisation
  biotoolsID: ml_model_for_mr_series_categorisation
  collectionID:
  - 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:
    - Provider
    url: null
  - email: armago@alumni.uv.es
    fundrefid: null
    gridid: null
    name: Armando Gomis-Maya
    note: null
    orcidid: https://orcid.org/0000-0002-9527-8093
    rorid: null
    typeEntity: Person
    typeRole:
    - 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:
    - Support
    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:
    - Support
    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:
    - Contributor
    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:
    - Contributor
    url: null
  description: A tool based on artificial intelligence that is able to perform a categorisation
    of MRI series by using standardized DICOM tags. The categorisation includes the
    type of sequence (e.g. spin echo, gradient echo), the weighting (e.g. T1W, T2W,
    DCE, ...), the presence of fat suppression and the detection of non-relevant /
    junk series (e.g. localizers, calibrations, screenshots...).
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.google.com/file/d/1lIUixmLItQXOyBPIXL_AzPg_jlqDKwNE/view?usp=drive_link
  - note: null
    type:
    - Terms of use
    url: https://drive.google.com/file/d/1jF44iszmmiHd2paD8-YhFhW2uQJ0QBAZ/view?usp=drive_link
  download: []
  editPermission:
    authors:
    - casopon
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run -it --rm --name my-container \\\n  -v \"<input_path>:/input\"\
      \ \\\n  -v \"<output_path>:/output\" \\\n  harbor.eucaim.cancerimage.eu/processing-tools/ml_model_for_mr_series_categorisation:<version>\
      \ \\\n  --config-string \"{'output_name': 'classification_results.json'}\""
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Classification
      uri: http://edamontology.org/operation_2990
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-03T15:35:26.140884Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: ML model for MR series categorisation (EUCAIM-SW-011_T-01-01-011)
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication:
  - doi: 10.1186/s40537-025-01086-w
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-12-01T00:00:00Z'
      journal: Journal of Big Data
      title: Automatic magnetic resonance imaging series labelling for large repositories
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  - term: Data acquisition
    uri: http://edamontology.org/topic_3077
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
  - 1.1.0
- accessibility: Open access
  additionDate: '2025-11-26T09:26:04.357618Z'
  biotoolsCURIE: biotools:mdpath
  biotoolsID: mdpath
  collectionID:
  - gpcr
  confidence_flag: null
  cost: null
  credit: []
  description: MDPath is a tool for calculating allosteric communication pathways
    in proteins by analyzing the mutual information of residue dihedral angle movements
    throughout an MD simulation.
  documentation: []
  download: []
  editPermission:
    authors:
    - Aaminah
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/wolberlab/mdpath
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-03T12:50:00.977035Z'
  license: null
  link: []
  maturity: null
  name: MDPath
  operatingSystem: []
  otherID: []
  owner: Aaminah
  publication:
  - doi: 10.1021/acs.jcim.5c01590
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-10-27T00:00:00Z'
      journal: Journal of Chemical Information and Modeling
      title: 'MDPath: Unraveling Allosteric Communication Paths of Drug Targets through
        Molecular Dynamics Simulations'
    note: null
    pmcid: PMC12570139
    pmid: '41030225'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Molecular dynamics
    uri: http://edamontology.org/topic_0176
  - term: Computational chemistry
    uri: http://edamontology.org/topic_3332
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2023-01-25T22:49:31.072923Z'
  biotoolsCURIE: biotools:soluprotmutsupdb
  biotoolsID: soluprotmutsupdb
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: 222755@mail.muni.cz
    fundrefid: null
    gridid: null
    name: David Bednar
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: mazurenko@mail.muni.cz
    fundrefid: null
    gridid: null
    name: Stanislav Mazurenko
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Jan Velecký
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Marie Hamsikova
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: A manually curated database of protein solubility changes upon mutations.
  documentation: []
  download: []
  editPermission:
    authors:
    - velda
    - m.musil
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Protein solubility prediction
      uri: http://edamontology.org/operation_0409
    - term: Aggregation
      uri: http://edamontology.org/operation_3436
    - term: Variant effect prediction
      uri: http://edamontology.org/operation_0331
    output: []
  homepage: http://loschmidt.chemi.muni.cz/soluprotmutdb
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-03T12:49:50.125351Z'
  license: null
  link: []
  maturity: null
  name: SoluProtMutsupDB
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: velda
  publication:
  - doi: 10.1016/J.CSBJ.2022.11.009
    metadata:
      abstract: © 2022 The Author(s)Protein solubility is an attractive engineering
        target primarily due to its relation to yields in protein production and manufacturing.
        Moreover, better knowledge of the mutational effects on protein solubility
        could connect several serious human diseases with protein aggregation. However,
        we have limited understanding of the protein structural determinants of solubility,
        and the available data have mostly been scattered in the literature. Here,
        we present SoluProtMutDB – the first database containing data on protein solubility
        changes upon mutations. Our database accommodates 33 000 measurements of 17
        000 protein variants in 103 different proteins. The database can serve as
        an essential source of information for the researchers designing improved
        protein variants or those developing machine learning tools to predict the
        effects of mutations on solubility. The database comprises all the previously
        published solubility datasets and thousands of new data points from recent
        publications, including deep mutational scanning experiments. Moreover, it
        features many available experimental conditions known to affect protein solubility.
        The datasets have been manually curated with substantial corrections, improving
        suitability for machine learning applications. The database is available at
        loschmidt.chemi.muni.cz/soluprotmutdb.
      authors:
      - name: Velecky J.
      - name: Hamsikova M.
      - name: Stourac J.
      - name: Musil M.
      - name: Damborsky J.
      - name: Bednar D.
      - name: Mazurenko S.
      citationCount: 0
      date: '2022-01-01T00:00:00Z'
      journal: Computational and Structural Biotechnology Journal
      title: 'SoluProtMutDB: A manually curated database of protein solubility changes
        upon mutations'
    note: null
    pmcid: PMC9678803
    pmid: '36420168'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Data submission, annotation and curation
    uri: http://edamontology.org/topic_0219
  - term: Literature and language
    uri: http://edamontology.org/topic_3068
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2025-12-02T17:37:57.215347Z'
  biotoolsCURIE: biotools:auto-prostate-sequence-classifier
  biotoolsID: auto-prostate-sequence-classifier
  collectionID:
  - EUCAIM
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit:
  - email: jose.almeida@research.fchampalimaud.org
    fundrefid: null
    gridid: null
    name: José Guilherme de Almeida
    note: null
    orcidid: https://orcid.org/0000-0002-1887-0157
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://josegcpa.net
  - email: null
    fundrefid: null
    gridid: null
    name: Nikolaos Papanikolaou
    note: null
    orcidid: https://orcid.org/0000-0003-3298-2072
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: XGBoost-based automatic classification of sequence types for prostate
    mpMRI into T2W, DWI, ADC, DCE and others (any other sequence type) using metadata
    alone. Works as a CLI, allows direct application to DICOM datasets or CSV/tsv/Excel/parquet
    datasets, features integration for Orthanc and DICOM-web as RESTful APIs. This
    was applied to all data on ProCAncer-I to derive initial results for sequence
    types. Refines predictions using rule-based heuristics for T2W, DWI and ADC.
  documentation:
  - note: Repository containing the code, README and additional information on how
      to run the tool. If used as an API (when integrated with Orthanc or DICOM-web),
      the documentation is available upon launching the API at <api-url>/docs.
    type:
    - Other
    url: https://github.com/CCIG-Champalimaud/metadata-classification
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: docker run -v <dir-with-dicom>:/data  harbor.eucaim.cancerimage.eu/processing-tools/champ-autoproseq
      --dicom_recursion <dicom-recursion> --input_paths /data
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: 'The input can be provided as a DICOM dataset (which will require --dicom-recursion,
      details below or in the documentation) or as a single DICOM study. This command
      will print a CSV with 5 columns:  i) patient_id, ii) study_uid, iii) series_uid,
      iv) classification from the XGBoost model, v) classification after heuristics-based
      corrections.

      The sequence classification is performed between T2W, DWI, ADC, DCE or others.
      The provided <dicom-recursion> refers to the number of folders until a DICOM
      series is found. So if the provided input is a patient folder with nested studies
      with nested series, the level of DICOM recursion should be 2. If the provided
      input is a directory with patient folders, the level of DICOM recursion should
      be 3.'
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Keyword
        uri: http://edamontology.org/data_0968
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/champ-autoproseq
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-03T09:27:04.489071Z'
  license: MIT
  link:
  - note: Repository containing code, README and additional usage information for
      this tool.
    type:
    - Repository
    url: https://github.com/CCIG-Champalimaud/metadata-classification
  maturity: Emerging
  name: AutoProSeq - automatic classification of sequence types for prostate mpMRI
  operatingSystem:
  - Linux
  otherID: []
  owner: josegcpa
  publication:
  - doi: 10.1186/s13244-025-01938-2
    metadata:
      abstract: ''
      authors: []
      citationCount: 1
      date: '2025-12-01T00:00:00Z'
      journal: Insights into Imaging
      title: Automatic sequence identification in multicentric prostate multiparametric
        MRI datasets for clinical machine-learning
    note: null
    pmcid: PMC12187622
    pmid: '40146375'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web API
  - Command-line tool
  topic:
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  validated: 0
  version:
  - v0.1
- accessibility: Open access
  additionDate: '2025-11-26T13:27:32.776575Z'
  biotoolsCURIE: biotools:iqa_dce_tool
  biotoolsID: iqa_dce_tool
  collectionID:
  - EUCAIM
  confidence_flag: null
  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:
  - note: null
    type: Container file
    url: https://hub.docker.com/r/billykforth/iqa_dce_tool
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://hub.docker.com/repository/docker/billykforth/iqa_dce_tool/general
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-03T06:46:13.717361Z'
  license: EUPL-1.1
  link: []
  maturity: Mature
  name: IQA DCE tool
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: billyk
  publication:
  - doi: 10.3390/jimaging11110417
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  validated: 0
  version:
  - '1.0'
- 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
    url: https://asparaginasedb.cz/help.html
  download: []
  editPermission:
    authors: []
    type: private
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  elixirNode:
  - Czech Republic
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://asparaginasedb.com/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-02T22:00:20.857626Z'
  license: CC-BY-4.0
  link: []
  maturity: Mature
  name: Asparaginase database
  operatingSystem:
  - Linux
  otherID: []
  owner: spiwokv
  publication: []
  relation: []
  toolType:
  - Database portal
  - Bioinformatics portal
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-04-30T10:28:37.002350Z'
  biotoolsCURIE: biotools:eucaim_wizard_tool
  biotoolsID: eucaim_wizard_tool
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Computational BioMedicine Laboratory, Foundation for Research and Technology
      Hellas (FORTH)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.ics.forth.gr/cbml/?lang=en
  description: The EUCAIM Wizard Tool performs an analysis of data re-identification
    risks of imaging and clinical data that follow the EUCAIM CDM. It includes and
    uses an EUCAIM specific configuration of the ARX Data Anonymization Tool (biotools:arx),
    by supporting a wide variety of privacy and risk models as well methods for analyzing
    the usefulness of output data.
  documentation:
  - note: null
    type:
    - User manual
    url: https://docs.google.com/document/d/1pi-7SvDKzVSYS78MhvnBX7PcXF3kZAc6/edit?usp=sharing&ouid=115998150174651530097&rtpof=true&sd=true
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Anonymisation
      uri: http://edamontology.org/operation_3283
    output: []
  homepage: https://github.com/cbml-forth/eucaim_wizard_tool
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2025-12-02T12:53:14.408095Z'
  license: EUPL-1.1
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/cbml-forth/eucaim_wizard_tool
  maturity: Emerging
  name: EUCAIM Wizard Tool
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: vkalokyri
  publication: []
  relation:
  - biotoolsID: arx
    type: includes
  - biotoolsID: arx
    type: uses
  toolType:
  - Desktop application
  topic:
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  - term: Data protection
    uri: http://edamontology.org/topic_4044
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  validated: 0
  version:
  - beta1.0
- accessibility: Open access
  additionDate: '2025-12-02T12:03:53.282983Z'
  biotoolsCURIE: biotools:aggreprot
  biotoolsID: aggreprot
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    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
    name: David Bednar
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Jiri Damborsky
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Simeon Borko
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  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.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Proteomics
  elixirNode:
  - Czech Republic
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function: []
  homepage: https://loschmidt.chemi.muni.cz/aggreprot/
  homepage_status: 0
  language:
  - Java
  - JavaScript
  lastUpdate: '2025-12-02T12:03:53.285771Z'
  license: Proprietary
  link: []
  maturity: Mature
  name: AggreProt
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: m.musil
  publication:
  - doi: 10.1093/nar/gkae420
    metadata:
      abstract: ''
      authors: []
      citationCount: 17
      date: '2024-07-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'AggreProt: A web server for predicting and engineering aggregation prone
        regions in proteins'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web service
  topic:
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  validated: 0
  version:
  - '1.0'
next: ?page=2
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