count: 1074
list:
- accessibility: Open access
  additionDate: '2026-05-13T06:42:26.772110Z'
  biotoolsCURIE: biotools:exomeflow
  biotoolsID: exomeflow
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: itsrobintomar@gmail.com
    fundrefid: null
    gridid: null
    name: Robin Kumar
    note: null
    orcidid: https://orcid.org/0009-0002-9084-2019
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://pypi.org/project/exomeflow/
  description: 'ExomeFlow is a Python package that provides a complete, automated
    Whole Exome Sequencing (WES) analysis workflow from raw FASTQ files to functionally
    annotated variants in a single reproducible CLI command.


    It aims to be the standard high-level pipeline for WES analysis in Python, combining
    GATK best-practice variant calling, hard filtering, and ANNOVAR annotation into
    one modular, maintainable package. It handles cohort-level processing (multiple
    samples), checkpointing for resumable runs, structured logging, and parallel execution
    out of the box.'
  documentation:
  - note: null
    type:
    - General
    url: https://pypi.org/project/exomeflow/
  download:
  - note: null
    type: Software package
    url: https://pypi.org/project/exomeflow/
    version: 1.0.08
  editPermission:
    authors: []
    type: private
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  elixirNode: []
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  elixir_badge: 0
  function: []
  homepage: https://pypi.org/project/exomeflow/
  homepage_status: 0
  language:
  - Python
  - Bash
  lastUpdate: '2026-05-13T07:08:06.554344Z'
  license: Freeware
  link:
  - note: null
    type:
    - Repository
    url: https://pypi.org/project/exomeflow/
  maturity: Emerging
  name: ExomeFlow
  operatingSystem:
  - Linux
  otherID: []
  owner: robin_kumar
  publication: []
  relation:
  - biotoolsID: fastp
    type: uses
  - biotoolsID: bio-samtools
    type: includes
  - biotoolsID: gatk_haplotype_caller
    type: includes
  toolType:
  - Workflow
  - Command-line tool
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: DNA mutation
    uri: http://edamontology.org/topic_2533
  validated: 0
  version:
  - 1.0.9
  - 1.0.8
- accessibility: Open access
  additionDate: '2026-05-13T05:45:59.510938Z'
  biotoolsCURIE: biotools:framexplore
  biotoolsID: framexplore
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: vidhuvijay2003@gmail.com
    fundrefid: null
    gridid: null
    name: Vidhu S Vijay
    note: MS Bioinformatics student at Amrita Vishwa Vidyapeetham; creator and maintainer
      of FrameXplore.
    orcidid: https://orcid.org/0009-0009-1182-2089
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: https://github.com/Vidhusv
  description: FrameXplore is a Google Colab notebook that extends ColabFold to automatically
    identify and correct disulfide bonds in cysteine‑rich protein structures. After
    a standard ColabFold prediction, it extracts all cysteine residues, computes Cα–Cα
    and S–S distances, identifies true disulfide bonds using geometric cutoffs (Cα–Cα
    < 6.5 Å, S–S < 2.5 Å), writes a corrected PDB with proper CONECT records, and
    provides an interactive 3D view.
  documentation:
  - note: Quick start guide, example test case, methodology explanation, citation,
      and repository contents
    type:
    - General
    url: https://github.com/Vidhusv/FRAMEXPLORER/blob/main/README.md
  download:
  - note: Latest version of the complete repository as a ZIP file
    type: Source code
    url: https://github.com/Vidhusv/FRAMEXPLORER/archive/refs/heads/main.zip
    version: 1.0.0
  - note: Direct download of the Colab notebook (.ipynb file). Can be run locally
      or uploaded to Google Colab.
    type: Binaries
    url: https://raw.githubusercontent.com/Vidhusv/FRAMEXPLORER/main/FrameXplore.ipynb
    version: 1.0.0
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/Vidhusv/FRAMEXPLORER
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-13T06:23:55.557041Z'
  license: MIT
  link:
  - note: GitHub repository with source code, documentation, and logo
    type:
    - Repository
    url: https://github.com/Vidhusv/FRAMEXPLORER
  - note: Report bugs, suggest features, or ask questions
    type:
    - Issue tracker
    url: https://github.com/Vidhusv/FRAMEXPLORER/issues
  maturity: Emerging
  name: FrameXplore
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID:
  - type: doi
    value: doi:10.5281/zenodo.20135079
    version: null
  owner: vidhu
  publication:
  - doi: 10.1038/s41592-022-01488-1
    metadata: null
    note: 'ColabFold: making protein folding accessible to all. Nature Methods, 2022.'
    pmcid: PMC9184281
    pmid: '35637307'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Biosciences
    uri: http://edamontology.org/topic_4019
  validated: 0
  version:
  - 1.0.0
- accessibility: Open access
  additionDate: '2026-05-07T05:36:51.677460Z'
  biotoolsCURIE: biotools:glycombocli
  biotoolsID: glycombocli
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: chris@proteaglyco.com
    fundrefid: null
    gridid: null
    name: Christopher Ashwood
    note: null
    orcidid: https://orcid.org/0000-0001-5944-6179
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Maia Kelly
    note: null
    orcidid: https://orcid.org/0000-0002-9383-1107
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: GlyComboCLI is an open source command line interface for combinatorial
    glycan composition determination to identify glycans in MS acquisitions of glycan-containing
    samples in text or mzML formats. This application enables rapid extraction of
    precursor m/z values from mzML files, a vendor-neutral format that ensures cross-platform
    compatibility.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://glycombocli.readthedocs.io/en/latest/
  download:
  - note: null
    type: Downloads page
    url: https://github.com/Protea-Glycosciences/GlyComboCLI/releases/latest
    version: null
  - note: null
    type: Container file
    url: https://hub.docker.com/r/proteaglycosciences/glycombocli
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Systems Biology
  elixirNode: []
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: GlyComboCLI.exe -F=".\masses.txt" -D=Native -R=Reduced -T=Da -E=0.6 -A=Neutral
      -hMax=9 -nMin=2 -nMax=10
    input:
    - data:
        term: Mass spectrum
        uri: http://edamontology.org/data_0943
      format:
      - term: mzML
        uri: http://edamontology.org/format_3244
    note: Requires MS2 scans with precursor m/z annotated if using the mzml approach
    operation:
    - term: Spectral analysis
      uri: http://edamontology.org/operation_3214
    - term: Sequence composition calculation
      uri: http://edamontology.org/operation_0236
    output:
    - data:
        term: Carbohydrate accession
        uri: http://edamontology.org/data_2900
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/Protea-Glycosciences/GlyComboCLI
  homepage_status: 0
  language:
  - C#
  lastUpdate: '2026-05-09T12:56:21.726475Z'
  license: Apache-2.0
  link:
  - note: Monitored GitHub repository
    type:
    - Technical monitoring
    url: https://github.com/Protea-Glycosciences/GlyComboCLI
  maturity: Emerging
  name: GlyComboCLI
  operatingSystem:
  - Linux
  - Windows
  otherID: []
  owner: chrashwood
  publication: []
  relation:
  - biotoolsID: msconvert
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  - term: Omics
    uri: http://edamontology.org/topic_3391
  validated: 0
  version:
  - 0.1.0
- accessibility: Open access
  additionDate: '2026-05-08T10:33:02.567199Z'
  biotoolsCURIE: biotools:repeatafterme
  biotoolsID: repeatafterme
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Robert Hubley
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: RepeatAfterMe is a package for the extension of repetitive DNA cores.
    The tool automatically extends a multiple sequence alignment that may represent
    only a fragment of a longer repetitive sequence family.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: ./RAMExtend -ranges test/extension-test2.tsv -twobit test/extension-test2.2bit
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: 2bit
        uri: http://edamontology.org/format_3009
    - data:
        term: Sequence range
        uri: http://edamontology.org/data_1017
      format:
      - term: bed6
        uri: http://edamontology.org/format_3585
    note: null
    operation:
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/Dfam-consortium/RepeatAfterMe
  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-05-08T10:33:02.569259Z'
  license: CC0-1.0
  link: []
  maturity: Mature
  name: RepeatAfterMe
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: Pub2Tools
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - v0.0.7
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T09:08:44.174795Z'
  biotoolsCURIE: biotools:mr-based_neuroblastoma_tumour_detection_and_segmentation
  biotoolsID: mr-based_neuroblastoma_tumour_detection_and_segmentation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
    gridid: null
    name: Leonor Cerda-Alberich
    note: null
    orcidid: https://orcid.org/0000-0002-5567-4278
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: dianaveigac@gmail.com
    fundrefid: null
    gridid: null
    name: Diana Veiga Canuto
    note: null
    orcidid: https://orcid.org/0000-0002-6048-2940
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Support
    - Documentor
    - Developer
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    - Documentor
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  description: 'This tool is specifically designed and validated for automated detection
    and segmentation of neuroblastic tumours in T2-weighted magnetic resonance images
    (T2-MR) using deep learning. It processes DICOM or NIfTI input data and outputs
    in NIFTI or DICOM SEG.


    TRAINING & VALIDATION COHORTS:


    Initial Development (Veiga-Canuto 2022):

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

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

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

    -Mean age: 37.6 ± 39.3 months.

    -Median tumor volume: 116,518 mm³.


    External Validation (Veiga-Canuto 2023):

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

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

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

    -Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105),
    Canon (3).'
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/tS2W8nb38Zs2ZzK
  - note: null
    type:
    - General
    url: https://www.mdpi.com/2072-6694/14/15/3648
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/44BxMSNpxwgsZiE
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=c7XOEGRA9aQ&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=12
  download: []
  editPermission:
    authors:
    - pedromiguel_martinez_HULAFE
    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: JSON
        uri: http://edamontology.org/format_3464
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - 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/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-30T11:37:29.346721Z'
  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/info-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
  - Windows
  - Linux
  otherID: []
  owner: casopon
  publication:
  - doi: 10.3390/cancers14153648
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.3390/cancers15051622
    metadata: null
    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: '2025-04-15T17:42:40.968987Z'
  biotoolsCURIE: biotools:dicom_file_integrity_checker_by_gibi230
  biotoolsID: dicom_file_integrity_checker_by_gibi230
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: gibi230@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - 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
    - Documentor
    - Maintainer
    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:
    - Contributor
    - Documentor
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  description: 'The tool performs a DICOM quality check in terms of correct number
    of files per sequence, corrupted files, precise directory hierarchy, separated
    dynamic series merging them, interest series filtering/selection by specific series
    description lists and diffusion sequence identification by b-values. It applies
    the desired changes to the dataset and generates a report containing information
    about the selected sequences, corrupted files, missing files and merged files.


    Status: Deployed'
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/LAKqSQZY4Bjqz5W
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/EEqjraK574HrwMf
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=oUebkjLYeSs&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=3
  download:
  - note: EUCAIM user needed
    type: Container file
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab
    version: 2.1.0
  editPermission:
    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  -v \"<config_path>:/config\" \\\n\
      \  harbor.eucaim.cancerimage.eu/ingestion-tools/dicom_file_integrity_checker:latest"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: For Data Holders (ingestion-tools)
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: JSON
        uri: http://edamontology.org/format_3464
  - cmd: "docker run -it --rm --name my-container \\\n  -v \"<input_path>:/input\"\
      \ \\\n  -v \"<output_path>:/output\" \\\n  harbor.eucaim.cancerimage.eu/processing-tools/dicom_file_integrity_checker:latest\
      \ \\\n  /app/entrypoint.sh --config-string \"{'QA': {'sequence_selection': ['ALL'],\
      \ 'modality_selection': ['ALL'], 'input_directory': 'dataset_id'}}\""
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
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    note: For Data Users (processing-tools)
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        uri: http://edamontology.org/format_3620
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/info-tab
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  lastUpdate: '2026-04-30T11:36:53.934680Z'
  license: CC-BY-NC-ND-4.0
  link:
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  - note: Link to EUCAIM's Harbor for Data Holders
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  - note: Link to EUCAIM's Harbor for Data Users
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/dicom_file_integrity_checker/artifacts-tab
  maturity: Mature
  name: DICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)
  operatingSystem:
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  - Windows
  - Linux
  otherID: []
  owner: pedromiguel_martinez_HULAFE
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_3316
  - term: Data acquisition
    uri: http://edamontology.org/topic_3077
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
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  - 2.1.0
  - 2.1.1
- accessibility: null
  additionDate: '2025-05-29T08:55:46.088021Z'
  biotoolsCURIE: biotools:denoising-inhomogeneity_correction_tool
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  description: 'The tool is designed to perform a customisable image pre-processing
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    (NLM)), and another for the ANTs N4 and another for the ANT''s N4 bias correction
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    it can also be configured with some of their parameters using a JSON parameter
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  - cmd: docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processin-tools/denoising_inhomogeneity_correction_tool:1.1.0
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      --output /output --series_number 2000 --series_description_suffix "_harmonized"
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      format:
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    note: null
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    output:
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      format:
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        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/info-tab
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  language:
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  lastUpdate: '2026-04-30T11:36:34.414003Z'
  license: CC-BY-NC-ND-4.0
  link:
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  name: Denoising-Inhomogeneity Correction Tool (EUCAIM-SW-015_T-01-01-015)
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  publication:
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    metadata: null
    note: null
    pmcid: PMC8554919
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    version: null
  - doi: 10.1186/s41747-020-00150-9
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    pmid: '32246291'
    type: []
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  toolType:
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  biotoolsCURIE: biotools:cluster_based_harmonization
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  description: 'The tool is designed to perform radiomics harmonization on large and
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    where batch groups with similar radiomics characteristics form clusters and the
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    - data:
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      format:
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  - cmd: docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processing-tools/cluster_based_harmonization:1.1.0
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    - data:
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      format:
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/cluster_based_harmonization/info-tab
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  link:
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  maturity: Emerging
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  operatingSystem:
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  - Mac
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  otherID: []
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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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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/2d_digital_mammography_harmonization/info-tab
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  validated: 0
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    note: null
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    rorid: null
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  description: A tool based on artificial intelligence that is able to perform a categorisation
    of MRI series by using standardized DICOM tags. The categorisation includes the
    type of sequence (e.g. spin echo, gradient echo), the weighting (e.g. T1W, T2W,
    DCE, ...), the presence of fat suppression and the detection of non-relevant /
    junk series (e.g. localizers, calibrations, screenshots...).
  documentation:
  - note: null
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    - User manual
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  - note: null
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  - note: null
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    input:
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        term: Image
        uri: http://edamontology.org/data_2968
      format:
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    note: null
    operation:
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        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/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-30T11:35:20.523347Z'
  license: CC-BY-NC-ND-4.0
  link:
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  - note: null
    type:
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  maturity: Mature
  name: ML model for MR series categorisation (EUCAIM-SW-011_T-01-01-011)
  operatingSystem:
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  - Windows
  - Linux
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication:
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    metadata: null
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    version: null
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  topic:
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  - term: Data acquisition
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  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
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- accessibility: Open access (with restrictions)
  additionDate: '2025-11-21T13:49:36.578343Z'
  biotoolsCURIE: biotools:time_coherence_tool
  biotoolsID: time_coherence_tool
  collectionID:
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  confidence_flag: null
  cost: Free of charge (with restrictions)
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    note: null
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    url: null
  - email: adrian_galiana@iislafe.es
    fundrefid: null
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    name: Adrian Galiana-Bordera
    note: null
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    rorid: null
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    url: null
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  description: "Tool that aims to validate visually the chronological order and logical\
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    \ a timeline visualization for each patient from an Excel file and highlights\
    \ rule violations.\n \nStatus : Containerized"
  documentation:
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        uri: http://edamontology.org/format_3508
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/time_coherence_tool/info-tab
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  language:
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  lastUpdate: '2026-04-30T11:33:34.401478Z'
  license: CC-BY-NC-ND-4.0
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  name: Time Coherence Tool (EUCAIM-SW-001_T-01-01-001)
  operatingSystem:
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  toolType:
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  topic:
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  - term: Computer science
    uri: http://edamontology.org/topic_3316
  validated: 0
  version:
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  biotoolsCURIE: biotools:tabular_data_curator
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    name: Unit of Medical Technology and Intelligent Information Systems (MEDLAB)
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    note: null
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  - email: bpezoulas@gmail.com
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    note: null
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    rorid: null
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  description: A fully automated service which can be applied on any kind of tabular
    data (e.g. clinical) to automatically identify duplicated fields (lexically similar
    and/or highly correlated features), outliers, data inconsistencies. It can also
    deal with missing values through the application of data imputers.
  documentation:
  - note: null
    type:
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    url: https://drive.eucaim.cancerimage.eu/s/PfBxCXNsKdEccj3
  - note: null
    type:
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  - note: null
    type:
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  download:
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    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/tdc-app/artifacts-tab
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  lastUpdate: '2026-04-30T11:02:38.765878Z'
  license: EUPL-1.2
  link:
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    url: https://github.com/vpz4/TDC
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  name: Tabular Data Curator
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  publication:
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    metadata: null
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    pmid: '30878889'
    type:
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    version: null
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_3572
  validated: 0
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- accessibility: Open access
  additionDate: '2026-04-30T10:37:00.214036Z'
  biotoolsCURIE: biotools:prostate_anatomies_and_lesion_automatic_segmentor
  biotoolsID: prostate_anatomies_and_lesion_automatic_segmentor
  collectionID:
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  confidence_flag: tool
  cost: Free of charge
  credit:
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    gridid: null
    name: Foundation for Research and Technology Hellas (FORTH)
    note: null
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    name: Dimitrios I. Zaridis
    note: null
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    url: null
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    url: null
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    note: null
    orcidid: https://orcid.org/0000-0002-7362-5082
    rorid: null
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    url: null
  description: Whole-gland, zonal & lesion prostate segmentation from multi-parametric
    MRI. Cascaded nnU-Net v2 (anatomies) + ProLesA-Net (lesions).  A three-stage pipeline
    that segments the whole gland (WG), peripheral zone (PZ), transition zone (TZ)
    and (when ADC + DWI are provided) the prostate lesions from prostate MRI. The
    anatomies are produced by two cascaded nnU-Net v2 models on T2; the lesion mask
    is produced by ProLesA-Net (Keras / TensorFlow 2.11) operating on T2 + ADC + DWI
    inside the WG mask
  documentation:
  - note: Quick Start Commands for the Software, including pulling from Harbor Container
      Registry, input folders structure
    type:
    - Quick start guide
    url: https://github.com/dzaridis/Prostate-Anatomies-and-Lesion-Segmentor
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/S4qW2cRD6T5NYBQ
  - note: Video with input folders structure, docker image execution & visualisation
    type:
    - General
    url: https://drive.eucaim.cancerimage.eu/s/HEKfYpL9DrCqJ84
  download:
  - note: null
    type: Container file
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/prostate-anatomies-and-lesion-segmentor/info-tab
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    url: https://github.com/dzaridis/Prostate-Anatomies-and-Lesion-Segmentor
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      \ \\\nharbor.eucaim.cancerimage.eu/processing-tools/prostate-anatomies-and-lesion-segmentor:1.0.0\
      \ \\\n    --input /input --output /output"
    input:
    - data:
        term: MRI image
        uri: http://edamontology.org/data_3442
      format: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_3553
    output:
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        uri: http://edamontology.org/data_3442
      format: []
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/prostate-anatomies-and-lesion-segmentor/info-tab
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  language:
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  lastUpdate: '2026-04-30T10:39:39.868431Z'
  license: EUPL-1.2
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    type:
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    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/prostate-anatomies-and-lesion-segmentor/info-tab
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    type:
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    url: https://github.com/dzaridis/Prostate-Anatomies-and-Lesion-Segmentor
  maturity: Emerging
  name: Prostate Anatomies and Lesion Automatic Segmentor
  operatingSystem:
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  - Mac
  - Linux
  otherID: []
  owner: dimzaridis
  publication:
  - doi: 10.1016/j.patter.2024.100992
    metadata: null
    note: null
    pmcid: PMC11284496
    pmid: '39081575'
    type:
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    version: null
  relation: []
  toolType:
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  topic:
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  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2026-04-29T11:29:15.746883Z'
  biotoolsCURIE: biotools:protein-mosaic-q
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  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Francisco Javier Lobo-Cabrera
    note: PhD in Biotechnology, with publications in computational biology.
    orcidid: https://orcid.org/0000-0002-9592-6863
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    typeRole:
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    url: https://scholar.google.com/citations?user=D4NAEvEAAAAJ&hl=en
  - email: bassas@us.es
    fundrefid: null
    gridid: null
    name: José A. Prado-Bassas
    note: Professor at Universidad de Sevilla, Faculty of Mathematics.
    orcidid: https://orcid.org/0000-0002-5670-5400
    rorid: null
    typeEntity: Person
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  description: Python library for computing the mosaic Q and Q_alt structural descriptors,
    which quantify the degree of spatial clustering of amino acids by chemical type
    (acidic, basic, polar, hydrophobic, and also special for Q_alt) in protein three-dimensional
    structures. Operates on PDB and mmCIF files via Biopython. Associated with the
    Proteins Mosaic Q Project, a citizen-science initiative gathering evidence for
    a conserved structural clustering pattern across proteins.
  documentation:
  - note: null
    type:
    - General
    url: https://pypi.org/project/protein-mosaic-q/
  - note: null
    type:
    - General
    url: https://osf.io/42kjn/wiki?wiki=zmh9d
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    type: Software package
    url: https://pypi.org/project/protein-mosaic-q/
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  function:
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    input: []
    note: Computes mosaic Q and Q_alt parameters quantifying spatial clustering of
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    operation:
    - term: Protein geometry calculation
      uri: http://edamontology.org/operation_0249
    output: []
  homepage: https://proteins-mosaic-q.org/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-29T11:29:15.749301Z'
  license: MIT
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  - note: null
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    type:
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  - note: null
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  maturity: Emerging
  name: protein-mosaic-q
  operatingSystem:
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  - Linux
  otherID: []
  owner: fjlobo
  publication:
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    metadata: null
    note: Earlier version of the manuscript. Updated version available in the project
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    pmcid: null
    pmid: null
    type:
    - Preprint
    version: null
  relation:
  - biotoolsID: biopython
    type: uses
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  validated: 0
  version:
  - 0.3.3
- accessibility: Open access (with restrictions)
  additionDate: '2025-11-07T18:15:49.962044Z'
  biotoolsCURIE: biotools:prostate_zone_segmentation_tool
  biotoolsID: prostate_zone_segmentation_tool
  collectionID:
  - EUCAIM
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit:
  - email: jose.almeida@research.fchampalimaud.org
    fundrefid: null
    gridid: null
    name: José Guilherme de Almeida
    note: null
    orcidid: https://orcid.org/0000-0002-1887-0157
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    url: https://josegcpa.net
  - email: null
    fundrefid: null
    gridid: null
    name: Nickolas Papanikolaou
    note: null
    orcidid: https://orcid.org/0000-0003-3298-2072
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Nuno Rodrigues
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: 'This tool automatically segments the the prostate into two zones:
    the central and transition zones (TZ+CZ) and the peripheral zone (PZ). It takes
    as input a T2-weighted image and produces a segmentation in the same input format.


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


      If the input is DICOM, `--is_dicom` should be used.'
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
  - cmd: docker run --shm-size=1gb -v $(pwd)/example_dataset:/data/input:ro -v $(pwd)/test_output:/data/output:rw
      --gpus="all" test-eucaim:latest nnunet-predict-batch {{--data_json /data/input/<dataset_json>.json|--data_dir
      /data/input --output_dir /data/output}}
    input:
    - data:
        term: MRI image
        uri: http://edamontology.org/data_3442
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    note: "Batch image annotation for DICOM and Nifti images using dataset JSON and\
      \ data directory supports two methods: using a dataset JSON and using a data\
      \ directory. \n\nThe dataset JSON-based method relies on having a dataset JSON\
      \ which has a list of dictionaries that follow this structure: `{\"study_path\"\
      : str, \"series_folders\": [[str]], \"output_dir\": str}`. These are analogous\
      \ to the previous modes. Be mindful that paths should be specified accordingly\
      \ for the Docker file-system. The dataset JSON should be specified using `--data_json`.\n\
      \nThe data directory-based method relies on having a directory structured as\
      \ patient/study/series, where each series follows an nnU-Net-like convention\
      \ (i.e. `<series_id>_0000`, `<series_id>_0001`, etc.). In this case, it should\
      \ be `<series-id>_0000`. The data directory should be specified using `--data_dir`\
      \ and requires the specification of an `--output_dir`.\n\nIf the input is DICOM,\
      \ `--is_dicom` should be specified."
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: MRI image
        uri: http://edamontology.org/data_3442
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/champ-prostate-zone-segmentation
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-29T10:36:29.272637Z'
  license: CC-BY-NC-4.0
  link:
  - note: This is the nnunet_serve repository, containing the generic nnU-Net building
      and serving functionalities used by the Computational Clinical Imaging Group
      at Champalimaud Foundation. This should also be used as documentation.
    type:
    - Repository
    url: https://github.com/josegcpa/nnunet_serve
  - note: Contains the EUCAIM model card for this model.
    type:
    - Other
    url: https://kdrive.infomaniak.com/app/share/1928123/f7bf2733-0454-47b0-a29c-0beacb51fe68
  maturity: Emerging
  name: Prostate zone segmentation tool
  operatingSystem:
  - Linux
  otherID: []
  owner: josegcpa
  publication:
  - doi: 10.1016/j.compbiomed.2024.108216
    metadata: null
    note: null
    pmcid: null
    pmid: '38442555'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: nnunet
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-11-05T11:45:08.078589Z'
  biotoolsCURIE: biotools:sub-saharan_africa_brain_glioma_segmenter
  biotoolsID: sub-saharan_africa_brain_glioma_segmenter
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: daniel.capellan@upm.es
    fundrefid: null
    gridid: null
    name: Daniel Capellán-Martín
    note: null
    orcidid: https://orcid.org/0000-0002-9743-0845
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Developer
    - Contributor
    - Support
    url: null
  - email: pabhijeet@childrensnational.org
    fundrefid: null
    gridid: null
    name: Abhijeet Parida
    note: null
    orcidid: https://orcid.org/0000-0002-4978-0576
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    - Contributor
    - Support
    - Maintainer
    url: null
  - email: zjiang@childrensnational.org
    fundrefid: null
    gridid: null
    name: Zhifan Jiang
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    - Developer
    - Support
    url: null
  - email: mj.ledesma@upm.es
    fundrefid: null
    gridid: null
    name: María Jesus Ledesma-Carbayo
    note: null
    orcidid: https://orcid.org/0000-0001-6846-3923
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Contributor
    url: null
  - email: mlingura@childrensnational.org
    fundrefid: null
    gridid: null
    name: Marius George Linguraru
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Contributor
    url: null
  description: The Sub-Saharan Africa Brain Glioma Segmenter is a software tool developed
    by researchers from Universidad Politécnica de Madrid and Children’s National
    Hospital for the segmentation and analysis of intercranial meningiomas in magnetic
    resonance imaging (MRI). Built in Python, it enables precise quantitative analysis
    of gliomas in brain MRI scans to support clinical decision-making in both diagnosis
    and prognosis. This tool was trained on a cohort of patients from Sub-Saharan
    Africa.
  documentation:
  - note: null
    type:
    - API documentation
    - Citation instructions
    - Terms of use
    - Code of conduct
    - Release notes
    - User manual
    - General
    - Quick start guide
    url: https://docs.hope4kids.io/HOPE-Segmenter-Kids/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output: []
  homepage: https://github.com/BIT-UPM/EUCAIM/tree/main/sub_saharan_africa_brain_glioma_segmenter
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-28T09:51:14.743240Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: Main app webpage
    type:
    - Other
    url: https://segmenter.hope4kids.io/
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids
  - note: EUCAIM harbor link
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ssa-brain-glioma-segmenter/info-tab
  maturity: Mature
  name: Sub-Saharan Africa Brain Glioma Segmenter
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: dani-capellan
  publication:
  - doi: 10.1007/978-3-031-76163-8_20
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1109/ISBI56570.2024.10635469
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04094
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04111
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  - Command-line tool
  - Workflow
  topic:
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - v1.0
- accessibility: Open access
  additionDate: '2025-11-05T10:35:32.782850Z'
  biotoolsCURIE: biotools:intercranial_meningioma_segmenter
  biotoolsID: intercranial_meningioma_segmenter
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: daniel.capellan@upm.es
    fundrefid: null
    gridid: null
    name: Daniel Capellán-Martín
    note: null
    orcidid: https://orcid.org/0000-0002-9743-0845
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Developer
    - Contributor
    - Support
    url: null
  - email: pabhijeet@childrensnational.org
    fundrefid: null
    gridid: null
    name: Abhijeet Parida
    note: null
    orcidid: https://orcid.org/0000-0002-4978-0576
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    - Contributor
    - Support
    - Maintainer
    url: null
  - email: zjiang@childrensnational.org
    fundrefid: null
    gridid: null
    name: Zhifan Jiang
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    - Developer
    - Support
    url: null
  - email: mj.ledesma@upm.es
    fundrefid: null
    gridid: null
    name: María Jesus Ledesma-Carbayo
    note: null
    orcidid: https://orcid.org/0000-0001-6846-3923
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Contributor
    url: null
  - email: mlingura@childrensnational.org
    fundrefid: null
    gridid: null
    name: Marius George Linguraru
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Contributor
    url: null
  description: The Intercranial Meningioma Segmenter is a software tool developed
    by researchers from Universidad Politécnica de Madrid and Children’s National
    Hospital for the segmentation and analysis of intercranial meningiomas in magnetic
    resonance imaging (MRI). Built in Python, it enables precise quantitative analysis
    of intercranial meningiomas in brain MRI scans to support clinical decision-making
    in both diagnosis and prognosis.
  documentation:
  - note: null
    type:
    - API documentation
    - Citation instructions
    - Terms of use
    - Code of conduct
    - Release notes
    - User manual
    - General
    - Quick start guide
    url: https://docs.hope4kids.io/HOPE-Segmenter-Kids/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output: []
  homepage: https://github.com/BIT-UPM/EUCAIM/tree/main/intercranial_meningioma_segmenter
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-28T09:50:24.781513Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: Main app webpage
    type:
    - Other
    url: https://segmenter.hope4kids.io/
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids
  - note: EUCAIM harbor link
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/intracranial-meningioma-segmenter/info-tab
  maturity: Mature
  name: Intercranial Meningioma Segmenter
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: dani-capellan
  publication:
  - doi: 10.1007/978-3-031-76163-8_20
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1109/ISBI56570.2024.10635469
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04094
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04111
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  - Command-line tool
  - Workflow
  topic:
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - v1.0
- accessibility: Open access
  additionDate: '2025-11-04T18:24:22.573039Z'
  biotoolsCURIE: biotools:brain_metastasis_segmenter
  biotoolsID: brain_metastasis_segmenter
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: daniel.capellan@upm.es
    fundrefid: null
    gridid: null
    name: Daniel Capellán-Martín
    note: null
    orcidid: https://orcid.org/0000-0002-9743-0845
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Developer
    - Contributor
    - Support
    url: null
  - email: pabhijeet@childrensnational.org
    fundrefid: null
    gridid: null
    name: Abhijeet Parida
    note: null
    orcidid: https://orcid.org/0000-0002-4978-0576
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    - Contributor
    - Support
    - Maintainer
    url: null
  - email: zjiang@childrensnational.org
    fundrefid: null
    gridid: null
    name: Zhifan Jiang
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    - Developer
    - Support
    url: null
  - email: mj.ledesma@upm.es
    fundrefid: null
    gridid: null
    name: María Jesus Ledesma-Carbayo
    note: null
    orcidid: https://orcid.org/0000-0001-6846-3923
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Contributor
    url: null
  - email: mlingura@childrensnational.org
    fundrefid: null
    gridid: null
    name: Marius George Linguraru
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Contributor
    url: null
  description: The Brain Metastasis Segmenter is a software tool developed by researchers
    from Universidad Politécnica de Madrid and Children’s National Hospital for the
    segmentation and analysis of brain metastases in magnetic resonance imaging (MRI).
    Built in Python, it enables precise quantitative analysis of brain metastases
    in MRI scans to support clinical decision-making in both diagnosis and prognosis.
  documentation:
  - note: null
    type:
    - API documentation
    - Citation instructions
    - Terms of use
    - Code of conduct
    - Release notes
    - User manual
    - General
    - Quick start guide
    url: https://docs.hope4kids.io/HOPE-Segmenter-Kids/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output: []
  homepage: https://github.com/BIT-UPM/EUCAIM/tree/main/brain_metastasis_segmenter
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-28T09:49:42.518292Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: Main app webpage
    type:
    - Other
    url: https://segmenter.hope4kids.io/
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids
  - note: EUCAIM harbor link
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/brain-metastasis-segmenter/info-tab
  maturity: Mature
  name: Brain Metastasis Segmenter
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: dani-capellan
  publication:
  - doi: 10.1007/978-3-031-76163-8_20
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1109/ISBI56570.2024.10635469
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04094
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04111
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  - Command-line tool
  - Workflow
  topic:
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - v1.0
- accessibility: Open access
  additionDate: '2025-11-05T10:49:02.917891Z'
  biotoolsCURIE: biotools:brain_glioma_segmenter
  biotoolsID: brain_glioma_segmenter
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: daniel.capellan@upm.es
    fundrefid: null
    gridid: null
    name: Daniel Capellán-Martín
    note: null
    orcidid: https://orcid.org/0000-0002-9743-0845
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Contributor
    - Developer
    - Support
    url: null
  - email: pabhijeet@childrensnational.org
    fundrefid: null
    gridid: null
    name: Abhijeet Parida
    note: null
    orcidid: https://orcid.org/0000-0002-4978-0576
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    - Developer
    - Support
    - Maintainer
    url: null
  - email: zjiang@childrensnational.org
    fundrefid: null
    gridid: null
    name: Zhifan Jiang
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    - Developer
    - Support
    url: null
  - email: mj.ledesma@upm.es
    fundrefid: null
    gridid: null
    name: María Jesus Ledesma-Carbayo
    note: null
    orcidid: https://orcid.org/0000-0001-6846-3923
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Contributor
    url: null
  - email: mlingura@childrensnational.org
    fundrefid: null
    gridid: null
    name: Marius George Linguraru
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Contributor
    url: null
  description: The Brain Glioma Segmenter is a software tool developed by researchers
    from Universidad Politécnica de Madrid and Children’s National Hospital for the
    segmentation and analysis of brain gliomas in magnetic resonance imaging (MRI).
    Built in Python, it enables precise quantitative analysis of brain gliomas in
    MRI scans to support clinical decision-making in both diagnosis and prognosis.
  documentation:
  - note: null
    type:
    - API documentation
    - Citation instructions
    - Terms of use
    - Code of conduct
    - Release notes
    - User manual
    - General
    - Quick start guide
    url: https://docs.hope4kids.io/HOPE-Segmenter-Kids/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output: []
  homepage: https://github.com/BIT-UPM/EUCAIM/tree/main/brain_glioma_segmenter
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-28T09:48:25.050327Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: Main app webpage
    type:
    - Other
    url: https://segmenter.hope4kids.io/
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids
  - note: EUCAIM harbor link
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/brain-glioma-segmenter/info-tab
  maturity: Mature
  name: Brain Glioma Segmenter
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: dani-capellan
  publication:
  - doi: 10.1007/978-3-031-76163-8_20
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1109/ISBI56570.2024.10635469
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04094
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04111
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Web application
  - Workflow
  topic:
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - v1.0
- accessibility: Open access
  additionDate: '2025-10-28T18:31:05.926498Z'
  biotoolsCURIE: biotools:pediatric_brain_tumor_segmenter
  biotoolsID: pediatric_brain_tumor_segmenter
  collectionID:
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  cost: Free of charge
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  - email: daniel.capellan@upm.es
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    name: Daniel Capellán-Martín
    note: null
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    rorid: null
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  - email: pabhijeet@childrensnational.org
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    url: null
  - email: zjiang@childrensnational.org
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  - email: mj.ledesma@upm.es
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    name: María Jesus Ledesma-Carbayo
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    rorid: null
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    typeRole:
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  - email: mlingura@childrensnational.org
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    name: Marius George Linguraru
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  description: The Pediatric Brain Tumor Segmenter is a software tool developed by
    researchers from Universidad Politécnica de Madrid and Children’s National Hospital
    for the segmentation and analysis of pediatric brain tumors in magnetic resonance
    imaging (MRI). Built in Python, it enables precise quantitative analysis of pediatric
    brain tumors in MRI scans to support clinical decision-making in both diagnosis
    and prognosis.
  documentation:
  - note: null
    type:
    - API documentation
    - Citation instructions
    - Terms of use
    - Code of conduct
    - Release notes
    - User manual
    - General
    - Quick start guide
    url: https://docs.hope4kids.io/HOPE-Segmenter-Kids/
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  function:
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    input: []
    note: null
    operation:
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    output: []
  homepage: https://github.com/BIT-UPM/EUCAIM/tree/main/pediatric_brain_tumor_segmenter
  homepage_status: 0
  language:
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  lastUpdate: '2026-04-28T09:46:53.991351Z'
  license: CC-BY-NC-SA-4.0
  link:
  - note: Main app webpage
    type:
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    url: https://segmenter.hope4kids.io/
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/Pediatric-Accelerated-Intelligence-Lab/HOPE-Segmenter-Kids
  - note: EUCAIM harbor link
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/pediatric-brain-tumor-segmenter/info-tab
  maturity: Mature
  name: Pediatric Brain Tumor Segmenter
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: dani-capellan
  publication:
  - doi: 10.1007/978-3-031-76163-8_20
    metadata: null
    note: null
    pmcid: null
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    type: []
    version: null
  - doi: 10.1109/ISBI56570.2024.10635469
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04094
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.48550/arXiv.2412.04111
    metadata: null
    note: null
    pmcid: null
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    type: []
    version: null
  relation: []
  toolType:
  - Web application
  - Command-line tool
  - Workflow
  topic:
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - v1.0
- accessibility: null
  additionDate: '2025-10-29T09:07:43.796224Z'
  biotoolsCURIE: biotools:raclahe
  biotoolsID: raclahe
  collectionID:
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  confidence_flag: tool
  cost: null
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  - email: null
    fundrefid: null
    gridid: null
    name: Foundation for Research and Technology Hellas (FORTH)
    note: null
    orcidid: null
    rorid: null
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    typeRole:
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  - email: dimzaridis@gmail.com
    fundrefid: null
    gridid: null
    name: Dimitrios I. Zaridis
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    orcidid: https://orcid.org/0000-0003-2549-3887
    rorid: null
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    url: null
  - email: ntachos@gmail.com
    fundrefid: null
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    name: Nikolaos Tachos
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    rorid: null
    typeEntity: null
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    url: null
  - email: fotiadis@uoi.gr
    fundrefid: null
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    name: Dimitrios I. Fotiadis
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    orcidid: https://orcid.org/0000-0002-7362-5082
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: RACLAHE (Region-Adaptive Contrast Limited Adaptive Histogram Equalization)
    is an image enhancement method specifically designed for improving CNN-based segmentation
    of the prostate and prostatic zones in T2-Weighted MR images.
  documentation:
  - note: User Manual in the EUCAIM Drive
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/f/2359
  - note: null
    type:
    - Quick start guide
    url: https://github.com/dzaridis/RACLAHE_Image_Enhancement_for_CNN_model_segmentation/tree/main
  download:
  - note: 'EUCAIM Harbor RACLAHE Image,

      Can be pulled via the following command after successfull login to Harbor

      docker pull harbor.eucaim.cancerimage.eu/processing-tools/raclahe@sha256:b3e9d383dfed95b7a6f1cca9dcbd271379946c97188e162d66f0d96b92341047'
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  language:
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  lastUpdate: '2026-04-28T07:20:19.446249Z'
  license: EUPL-1.2
  link:
  - note: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/raclahe/info-tab
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/raclahe/info-tab
  - note: Official Git Repository of RACLAHE
    type:
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  maturity: null
  name: RACLAHE
  operatingSystem:
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  owner: dimzaridis
  publication:
  - doi: 10.1038/s41598-023-27671-8
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Method
    version: null
  relation: []
  toolType:
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  topic:
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
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  additionDate: '2025-12-04T11:29:17.647406Z'
  biotoolsCURIE: biotools:deep_learning_noise_reduction_dlnr
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  description: A fully convolutional (with no pooling layers) model was trained on
    a set of noisy images with the ground truth being the original image without the
    (synthetic) noise. Different levels of noise and types were incorporated into
    the training set. The experiments showed reduction in noise levels, but it can
    impact image quality when T2ws without noise is provided to the model.
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/f/2363
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    metadata: null
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  validated: 0
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  additionDate: '2025-10-29T08:08:30.731334Z'
  biotoolsCURIE: biotools:lethe_dicom_anonymizer
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  description: "A DICOM Anonymization pipeline in a Docker container. This pipeline\
    \ is designed to anonymize DICOM files according to the EUCAIM standard and includes\
    \ the following steps:\n\nStep 1 (Optional): Perform OCR on DICOM pixel data to\
    \ remove sensitive information (burned-in information).\nStep 2: Deidentify DICOM\
    \ metadata using the RSNA CTP Anonymizer and the EUCAIM anonymization script.\
    \ \nStep 3 (Optional): Deidentify clinical data provided in CSV files so that\
    \ the referenced patient id is anonymized the same way CTP does in Step 2."
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  - note: null
    type:
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        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Anonymisation
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    output:
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        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
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  license: EUPL-1.2
  link:
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    type:
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  name: Lethe DICOM Anonymizer
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  otherID: []
  owner: vkalokyri
  publication:
  - doi: 10.5281/zenodo.19097245
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
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  - Desktop application
  topic:
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    uri: http://edamontology.org/topic_3384
  - term: Data protection
    uri: http://edamontology.org/topic_4044
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  validated: 0
  version:
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  - 0.10.1
  - 0.11.2
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T10:38:08.771699Z'
  biotoolsCURIE: biotools:ct-based_neuroblastoma_tumour_detection_and_segmentation
  biotoolsID: ct-based_neuroblastoma_tumour_detection_and_segmentation
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  cost: Free of charge (with restrictions)
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  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.eucaim.cancerimage.eu/s/GxJrJPrYBnzecqT
  - note: null
    type:
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    url: https://www.youtube.com/watch?v=JQ0dtAE_6uc&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=37
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  function:
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      \ \\\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:
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        uri: http://edamontology.org/format_3549
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        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
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        uri: http://edamontology.org/format_3752
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
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      uri: http://edamontology.org/operation_3553
    output:
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      - 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/info-tab
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  language:
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  lastUpdate: '2026-04-27T11:04:03.859531Z'
  license: CC-BY-NC-ND-4.0
  link:
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    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ct-based_neuroblastoma_tumour_detection_and_segmentation/info-tab
  - note: null
    type:
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    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: CT-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-022_T-01-02-005)
  operatingSystem:
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  otherID: []
  owner: casopon
  publication:
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    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
  relation: []
  toolType:
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  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:
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- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T09:19:51.404419Z'
  biotoolsCURIE: biotools:mr-based_dipg_tumour_detection_and_segmentation
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  confidence_flag: null
  cost: Free of charge (with restrictions)
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  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:
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    url: https://drive.eucaim.cancerimage.eu/s/5CL2H8tyMDzFHex
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  function:
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    input: []
    note: 3DNA driven - DNA Analysis and Rebuilding Tools. Provides a means of analyzing
      nucleic acid structures and generating custom models.
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Molecular dynamics
      uri: http://edamontology.org/operation_2476
    - term: Nucleic acid structure analysis
      uri: http://edamontology.org/operation_2481
    output: []
  homepage: https://milou.science.uu.nl/services/3DDART/
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-19T09:24:16.551817Z'
  license: null
  link: []
  maturity: Mature
  name: 3D-DART
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: esraa9
  publication:
  - doi: 10.1093/nar/gkp287
    metadata:
      abstract: There is a growing interest in structural studies of DNA by both experimental
        and computational approaches. Often, 3D-structural models of DNA are required,
        for instance, to serve as templates for homology modeling, as starting structures
        for macro-molecular docking or as scaffold for NMR structure calculations.
        The conformational adaptability of DNA when binding to a protein is often
        an important factor and at the same time a limitation in such studies. As
        a response to the demand for 3D-structural models reflecting the intrinsic
        plasticity of DNA we present the 3D-DART server (3D NA-Driven D NA A nalysis
        and R ebuilding T ool). The server provides an easy interface to a powerful
        collection of tools for the generation of DNA-structural models in custom
        conformations. The computational engine beyond the server makes use of the
        3DNA software suite together with a collection of home-written python scripts.
        The server is freely available at http://haddock.chem.uu.nl/dna without any
        login requirement.
      authors:
      - name: van Dijk M.
      - name: Bonvin A.M.J.J.
      citationCount: 279
      date: '2009-08-04T00:00:00Z'
      journal: Nucleic Acids Research
      title: '3D-DART: A DNA structure modelling server'
    note: null
    pmcid: PMC2703913
    pmid: '19417072'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Structural biology
    uri: http://edamontology.org/topic_1317
  - term: NMR
    uri: http://edamontology.org/topic_0593
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  validated: 1
  version:
  - '1'
- accessibility: Open access
  additionDate: '2026-04-13T13:10:58.362596Z'
  biotoolsCURIE: biotools:covsnap
  biotoolsID: covsnap
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: akenes96@gmail.com
    fundrefid: null
    gridid: null
    name: Enes Ak
    note: null
    orcidid: https://orcid.org/0000-0001-5931-730X
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  description: Coverage inspector for targeted sequencing QC (hg38)
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/enes-ak/covsnap/blob/master/README.md
  download:
  - note: pip install covsnap
    type: Downloads page
    url: https://pypi.org/project/covsnap/
    version: 0.3.0
  - note: https://anaconda.org/channels/bioconda/packages/covsnap/overview
    type: Downloads page
    url: https://anaconda.org/channels/bioconda/packages/covsnap/overview
    version: null
  editPermission:
    authors: []
    type: private
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: covsnap sample.bam BRCA1,TP53,ETFDH --exons
    input:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
    note: null
    operation:
    - term: Sequence assembly validation
      uri: http://edamontology.org/operation_3180
    output:
    - data:
        term: Quality control report
        uri: http://edamontology.org/data_3914
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://github.com/enes-ak/covsnap
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-17T09:04:11.979465Z'
  license: Other
  link:
  - note: 'Install with: pip install covsnap'
    type:
    - Repository
    url: https://pypi.org/project/covsnap/
  - note: github repository
    type:
    - Repository
    url: https://github.com/enes-ak/covsnap
  - note: 'Install with: conda install -c bioconda covsnap'
    type:
    - Repository
    url: https://anaconda.org/channels/bioconda/packages/covsnap/overview
  maturity: Emerging
  name: covsnap
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: enes.ak
  publication: []
  relation: []
  toolType:
  - Desktop application
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 0
  version:
  - 0.3.0
  - 0.4.0
- accessibility: Open access
  additionDate: '2026-04-17T00:26:46.738101Z'
  biotoolsCURIE: biotools:glycombo
  biotoolsID: glycombo
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: chris@proteaglyco.com
    fundrefid: null
    gridid: null
    name: Christopher Ashwood
    note: null
    orcidid: https://orcid.org/0000-0001-5944-6179
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Maia Kelly
    note: null
    orcidid: https://orcid.org/0000-0002-9383-1107
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: GlyCombo is an open source software for combinatorial glycan composition
    determination to identify glycans in MS acquisitions of glycan-containing samples
    in text or mzML formats. This application enables rapid extraction of precursor
    m/z values from mzML files, a vendor-neutral format that ensures cross-platform
    compatibility.
  documentation:
  - note: Youtube video on getting started
    type:
    - Quick start guide
    url: https://www.youtube.com/watch?v=mIGxMTSfPOI
  download:
  - note: null
    type: Downloads page
    url: https://github.com/Protea-Glycosciences/GlyCombo/releases/latest
    version: null
  editPermission:
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    type: private
  elixirCommunity:
  - Systems Biology
  elixirNode: []
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Mass spectrum
        uri: http://edamontology.org/data_0943
      format:
      - term: mzML
        uri: http://edamontology.org/format_3244
    note: No command line interface
    operation:
    - term: Annotation
      uri: http://edamontology.org/operation_0226
    output:
    - data:
        term: Carbohydrate structure
        uri: http://edamontology.org/data_1462
      format: []
  homepage: https://github.com/Protea-Glycosciences/GlyCombo
  homepage_status: 0
  language:
  - C#
  lastUpdate: '2026-04-17T00:26:46.740543Z'
  license: Apache-2.0
  link:
  - note: Monitored GitHub repository
    type:
    - Technical monitoring
    url: https://github.com/Protea-Glycosciences/GlyCombo
  maturity: Mature
  name: GlyCombo
  operatingSystem:
  - Windows
  otherID: []
  owner: chrashwood
  publication:
  - doi: 10.1021/jasms.4c00188
    metadata: null
    note: null
    pmcid: null
    pmid: '39271475'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: msconvert
    type: uses
  toolType:
  - Desktop application
  topic:
  - term: Omics
    uri: http://edamontology.org/topic_3391
  validated: 0
  version:
  - '1.3'
- accessibility: Open access
  additionDate: '2026-04-02T11:29:54.022786Z'
  biotoolsCURIE: biotools:pathotypr
  biotoolsID: pathotypr
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Paula Ruiz-Rodriguez
    note: null
    orcidid: https://orcid.org/0000-0003-0727-5974
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Mireia Coscolla
    note: null
    orcidid: https://orcid.org/0000-0003-0752-0538
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: I2SysBio (CSIC - Universitat de València)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: PathoGenOmics Lab
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole:
    - Provider
    url: null
  description: 'A fast, offline, pathogen-agnostic toolkit for lineage classification
    and marker-driven genotyping from whole-genome sequencing data. Bring your own
    SNP marker panel for any microbial pathogen — pathotypr handles the rest. Ships
    with curated panels for Mycobacterium tuberculosis complex (MTBC): 3,707 lineage-defining
    SNPs and over 102,000 resistance-associated mutations. Works with assembled genomes
    (FASTA) and raw reads (FASTQ). Available as command-line interface and cross-platform
    desktop GUI (Tauri).'
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/PathoGenOmics-Lab/pathotypr/tree/main/docs
  download:
  - note: null
    type: Binaries
    url: https://github.com/PathoGenOmics-Lab/pathotypr/releases
    version: null
  - note: null
    type: Source code
    url: https://github.com/PathoGenOmics-Lab/pathotypr
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: train — Build a Random Forest classifier from labeled genomes.
    operation:
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output:
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: predict — Assign lineages to genomes using a pre-trained Random Forest model.
    operation:
    - term: Variant classification
      uri: http://edamontology.org/operation_3225
    output:
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: classify — Call known SNP markers in assembled genomes against a user-defined
      marker panel.
    operation:
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    - term: Variant classification
      uri: http://edamontology.org/operation_3225
    output:
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: split-fastq — Alignment-free genotyping directly from raw reads using k-mer
      matching.
    operation:
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output:
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: match — Find the closest reference genome from a set of references for raw
      reads.
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    output:
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://github.com/PathoGenOmics-Lab/pathotypr
  homepage_status: 0
  language:
  - Rust
  lastUpdate: '2026-04-02T11:29:54.029869Z'
  license: AGPL-3.0
  link: []
  maturity: Mature
  name: pathotypr
  operatingSystem: []
  otherID: []
  owner: paururo
  publication:
  - doi: 10.64898/2026.03.24.714002
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Public health and epidemiology
    uri: http://edamontology.org/topic_3305
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - 1.0.0
- accessibility: Open access
  additionDate: '2026-03-02T15:35:15.926607Z'
  biotoolsCURIE: biotools:labid
  biotoolsID: labid
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Charles Girardot
    note: Head of MODIS team at EMBL Heidelberg
    orcidid: https://orcid.org/0000-0003-4301-3920
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    - Primary contact
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Jelle Scholtalbers
    note: Former MODIS team member, now working as a freelance (LabRise solutions)
    orcidid: https://orcid.org/0000-0002-6090-2482
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Support
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Matthias Monfort
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    - Developer
    - Support
    url: null
  - email: null
    fundrefid: null
    gridid: null
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    note: null
    orcidid: https://orcid.org/0000-0003-2068-5812
    rorid: null
    typeEntity: Person
    typeRole:
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    - Maintainer
    - Support
    url: null
  - email: laurent.thomas@embl.de
    fundrefid: null
    gridid: null
    name: Laurent Thomas
    note: null
    orcidid: https://orcid.org/0000-0001-7686-3249
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: EMBL Heidelberg
    note: null
    orcidid: null
    rorid: 03mstc592
    typeEntity: Institute
    typeRole: []
    url: null
  description: Lab Integrated Data (LabID) is an open-source web-based platform for
    research data management in life science institutes, featuring sample and dataset
    management, an inventory management system and an electronic lab notebook. LabID
    allows recording extensive experimental information about the provenance of data
    (samples, reagents, instrument, protocols, assay parameters) and is designed to
    help individual scientists, research groups and core facilities better manage,
    annotate and share their research according to FAIR principles.
  documentation:
  - note: Main documentation including installation instructions and training
    type:
    - General
    url: https://grp-gbcs.embl-community.io/labid-user-docs/
  - note: Test server for e.g LabID and trainings
    type:
    - Training material
    url: https://labid-demo.embl.de/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://grp-gbcs.embl-community.io/labid-user-docs/
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-26T11:00:14.410278Z'
  license: MIT
  link:
  - note: Open source repositories for the LabID subprojects (UI, Server, Command
      Line Interface, Library)
    type:
    - Repository
    url: https://gitlab.com/lab-integrated-data
  - note: Channel for questions from externals
    type:
    - Discussion forum
    url: https://join.slack.com/t/labintegrateddata/shared_invite/zt-2eb4ivxyc-1C4RZP_For0uiWcHeiTw0Q
  - note: Website of the MODIS team behind LabID
    type:
    - Other
    url: https://www.embl.org/groups/modis/
  maturity: Mature
  name: Lab Integrated Data (LabID)
  operatingSystem: []
  otherID: []
  owner: laurent_s._v.
  publication: []
  relation: []
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Biology
    uri: http://edamontology.org/topic_3070
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2019-08-26T14:34:55Z'
  biotoolsCURIE: biotools:MINERVA_Platform
  biotoolsID: MINERVA_Platform
  collectionID:
  - LCSB
  - ELIXIR-LU
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Marek Ostaszewski
    note: null
    orcidid: https://orcid.org/0000-0003-1473-370X
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Piotr Gawron
    note: null
    orcidid: https://orcid.org/0000-0002-9328-8052
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Reinhard Schneider
    note: null
    orcidid: https://orcid.org/0000-0002-8278-1618
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Venkata Satagopam
    note: null
    orcidid: https://orcid.org/0000-0002-6532-5880
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Rudi Balling
    note: null
    orcidid: https://orcid.org/0000-0003-2902-5650
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: David Hoksza
    note: null
    orcidid: https://orcid.org/0000-0003-4679-0557
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ewa Smula
    note: null
    orcidid: https://orcid.org/0000-0001-7118-3164
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    url: null
  description: 'The MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform
    is a standalone webserver for visualization, exploration and management of molecular
    networks encoded in SBGN-compliant format, including files produced using CellDesigner
    or SBGN editors. Visualization of uploaded networks generated by the platform
    is accessible via a web browser to all viewers with the weblink to the resource.


    The MINERVA Platform is a webservice using the Java Server Faces 2 technology.
    The server side, including data parsing, integration, annotation and verification,
    is implemented in Java. The platform uses the Postgres SQL database for data storage
    and the Hibernate framework as a middle layer between web server and database.
    The user web-interface is generated using React.js. The displayed content is visualized
    by OpenLayers API, dedicated JavaScript and CSS.'
  documentation:
  - note: null
    type:
    - Quick start guide
    - Release notes
    - User manual
    - API documentation
    - Citation instructions
    - Terms of use
    url: https://minerva.uni.lu
  download:
  - note: Installation instructions, including debian package, virtual machine images
      and docker containers.
    type: Other
    url: https://minerva.pages.uni.lu/doc/install/
    version: 13.1.3 - 20.0.3
  editPermission:
    authors:
    - sascha.herzinger
    type: group
  elixirCommunity: []
  elixirNode:
  - Luxembourg
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Visualise systems biology diagrams online, on a standalone web server
    operation:
    - term: Pathway visualisation
      uri: http://edamontology.org/operation_3926
    output: []
  - cmd: null
    input: []
    note: Visualise omics data from multiple datasets on top of the diagrams
    operation:
    - term: Expression data visualisation
      uri: http://edamontology.org/operation_0571
    output: []
  - cmd: null
    input: []
    note: 'Convert between main systems biology layout formats: CellDeslgners SBML,
      SBML layout+render, SBGN-ML, GPML'
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output: []
  - cmd: null
    input: []
    note: Use MINERVA API to access systems biology formats for modelling
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output: []
  homepage: https://minerva.uni.lu
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-24T15:37:40.163855Z'
  license: AGPL-3.0
  link:
  - note: GiLab repository for core functionalities (data and format handling, service
      stability, API access)
    type:
    - Repository
    url: https://gitlab.lcsb.uni.lu/minerva/core/
  - note: Issue tracker for core functionalities (data and format handling, service
      stability, API access)
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  maturity: Mature
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  description: Web application and service for visualizing small- to medium-scale
    models of gene regulatory networks. It automatically lays out either an unweighted
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    matrix where regulators are named in the columns and target genes in the rows.
    It is best-suited for visualizing networks of fewer than 35 nodes and 70 edges
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    note: GRNsight automatically lays out a network graph based on an Excel input
      spreadsheet containing an adjacency matrix where regulators are named in the
      columns and target genes in the rows. When a user uploads a spreadsheet with
      an unweighted adjacency matrix, GRNsight automatically lays out the graph using
      black lines and pointed arrowheads.  When a user uploads a spreadsheet with
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      colors the edges and adjusts their thicknesses based on the sign (positive for
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      Nodes are rectangular and support gene labels of up to 12 characters.  The edges
      are arcs, which become straight lines when the nodes are close together.  Self-regulatory
      edges are indicated by a loop on the lower-right side of a node. Visualizations
      can be modified by sliders that adjust D3.js's force graph layout parameters
      and through manual node dragging.
    operation:
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      uri: http://edamontology.org/operation_3083
    - term: Gene regulatory network analysis
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  homepage: http://dondi.github.io/GRNsight/
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  language:
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  lastUpdate: '2026-03-21T21:29:18.172348Z'
  license: BSD-3-Clause
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  maturity: Mature
  name: GRNsight
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    metadata: null
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  - doi: 10.5281/zenodo.7411630
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  relation: []
  toolType:
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  topic:
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  - term: Gene regulation
    uri: http://edamontology.org/topic_0204
  validated: 1
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  description: PangyPlot is a tool for visualizing graph-based pangenome data, designed
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    type:
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_3056
  validated: 0
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  cost: Free of charge
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  description: WEBnm@ provides quick, automated computation and analysis of low-frequency
    normal modes for protein structures.
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    type:
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    url: http://apps.cbu.uib.no/webnma3/about
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      format:
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    note: Constructs elastic network model from alpha carbon coordinates of the protein,
      and computes properties to describe large scale conformations. Computes normal
      modes, fluctuation profiles, inter-residue correlations, conformational overlap
      analysis and vector field representations. Structural amino acid profiles, and
      normal mode characteristics describing protein motion, visualized in plots and
      decorated structure visualizations. White space delimited tabular data for normal
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    input:
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        uri: http://edamontology.org/data_1460
      format:
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        uri: http://edamontology.org/format_1476
    note: Performs comparative analysis of the normal modes of protein structures.
      Computes the Bhattacharyya Coefficient (BC) and the Root Mean Squared Inner
      Product (RMSIP) of aligned parts of the proteins. Alignment of sets of proteins
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      amino acid profiles for visual comparison of structural similarity. White space
      delimited tabular data for the provided plots
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        uri: http://edamontology.org/format_3508
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        term: Structural profile
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      format:
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        uri: http://edamontology.org/format_2330
  homepage: http://apps.cbu.uib.no/webnma
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  language:
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  lastUpdate: '2026-03-11T08:56:55.566213Z'
  license: GPL-3.0
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    type:
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  - note: Helpdesk and support for ELIXIR Norway services.
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  maturity: Mature
  name: WEBnma
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  owner: UiB
  publication:
  - doi: 10.1186/s12859-014-0427-6
    metadata:
      abstract: 'Background: Normal mode analysis (NMA) using elastic network models
        is a reliable and cost-effective computational method to characterise protein
        flexibility and by extension, their dynamics. Further insight into the dynamics-function
        relationship can be gained by comparing protein motions between protein homologs
        and functional classifications. This can be achieved by comparing normal modes
        obtained from sets of evolutionary related proteins. Results: We have developed
        an automated tool for comparative NMA of a set of pre-aligned protein structures.
        The user can submit a sequence alignment in the FASTA format and the corresponding
        coordinate files in the Protein Data Bank (PDB) format. The computed normalised
        squared atomic fluctuations and atomic deformation energies of the submitted
        structures can be easily compared on graphs provided by the web user interface.
        The web server provides pairwise comparison of the dynamics of all proteins
        included in the submitted set using two measures: the Root Mean Squared Inner
        Product and the Bhattacharyya Coefficient. The Comparative Analysis has been
        implemented on our web server for NMA, WEBnmat, which also provides recently
        upgraded functionality for NMA of single protein structures. This includes
        new visualisations of protein motion, visualisation of inter-residue correlations
        and the analysis of conformational change using the. In addition, programmatic
        access to WEBnmat is now available through a SOAP-based web service. WEBnmat
        is available at. Conclusion: WEBnmat v2.0 is an online tool offering unique
        capability for comparative NMA on multiple protein structures. Along with
        a convenient web interface, powerful computing resources, and several methods
        for mode analyses, WEBnmat facilitates the assessment of protein flexibility
        within protein families and superfamilies. These analyses can give a good
        view of how the structures move and how the flexibility is conserved over
        the different structures.'
      authors:
      - name: Tiwari S.P.
      - name: Fuglebakk E.
      - name: Hollup S.M.
      - name: Skjaerven L.
      - name: Cragnolini T.
      - name: Grindhaug S.H.
      - name: Tekle K.M.
      - name: Reuter N.
      citationCount: 87
      date: '2014-12-30T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'WEBnmat v2.0: Web server and services for comparing protein flexibility'
    note: null
    pmcid: PMC4339738
    pmid: '25547242'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1186/1471-2105-6-52
    metadata:
      abstract: 'Background: Normal mode analysis (NMA) has become the method of choice
        to investigate the slowest motions in macromolecular systems. NMA is especially
        useful for large biomolecular assemblies, such as transmembrane channels or
        virus capsids. NMA relies on the hypothesis that the vibrational normal modes
        having the lowest frequencies (also named soft modes) describe the largest
        movements in a protein and are the ones that are functionally relevant. Results:
        We developed a web-based server to perform normal modes calculations and different
        types of analyses. Starting from a structure file provided by the user in
        the PDB format, the server calculates the normal modes and subsequently offers
        the user a series of automated calculations; normalized squared atomic displacements,
        vector field representation and animation of the first six vibrational modes.
        Each analysis is performed independently from the others and results can be
        visualized using only a web browser. No additional plug-in or software is
        required. For users who would like to analyze the results with their favorite
        software, raw results can also be downloaded. The application is available
        on http://www.bioinfo.no/tools/normalmodes. We present here the underlying
        theory, the application architecture and an illustration of its features using
        a large transmembrane protein as an example. Conclusion: We built an efficient
        and modular web application for normal mode analysis of proteins. Non specialists
        can easily and rapidly evaluate the degree of flexibility of multi-domain
        protein assemblies and characterize the large amplitude movements of their
        domains. © 2005 Hollup et al; licensee BioMed Central Ltd.'
      authors:
      - name: Hollup S.M.
      - name: Salensminde G.
      - name: Reuter N.
      citationCount: 105
      date: '2005-03-11T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'WEBnm@: A web application for normal mode analyses of proteins'
    note: null
    pmcid: PMC1274249
    pmid: '15762993'
    type:
    - Primary
    version: '1.0'
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    type: uses
  - biotoolsID: biopython
    type: uses
  - biotoolsID: matplotlib
    type: uses
  - biotoolsID: mustang
    type: uses
  - biotoolsID: dssp
    type: uses
  toolType:
  - Web API
  - Suite
  topic:
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  validated: 1
  version:
  - '3.5'
- accessibility: null
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  biotoolsCURIE: biotools:qmri
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    fundrefid: null
    gridid: null
    name: Martijn Froeling
    note: null
    orcidid: https://orcid.org/0000-0003-3841-0497
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: https://www.qmritools.com/
  description: QMRITools is a collection of tools for quantitative muscle MRI analysis,
    enabling the assessment of neuromuscular disorders and conditions. The software
    utilizes various MRI sequences and processing pipelines to generate metrics for
    comparative evaluation.
  documentation:
  - note: null
    type:
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    url: https://www.qmritools.com/assets/htmldoc/html/guide/qmritools
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    operation:
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    - term: Standardisation and normalisation
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  owner: martijn
  publication:
  - doi: 10.21105/joss.01204
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Method
    version: null
  - doi: 10.1002/jmri.23608
    metadata: null
    note: null
    pmcid: null
    pmid: '22334539'
    type:
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    version: null
  - doi: 10.1002/mrm.22477
    metadata: null
    note: null
    pmcid: null
    pmid: '20725932'
    type:
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    version: null
  - doi: 10.1002/nbm.4119
    metadata: null
    note: null
    pmcid: null
    pmid: '31313867'
    type:
    - Usage
    version: null
  relation: []
  toolType: []
  topic:
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Endocrinology and metabolism
    uri: http://edamontology.org/topic_3407
  - term: Pathology
    uri: http://edamontology.org/topic_0634
  - term: Preclinical and clinical studies
    uri: http://edamontology.org/topic_3379
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-27T17:39:14.144907Z'
  biotoolsCURIE: biotools:random_number_lab
  biotoolsID: random_number_lab
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  confidence_flag: null
  cost: Free of charge
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    fundrefid: null
    gridid: null
    name: Thomas Amthor
    note: null
    orcidid: https://orcid.org/0000-0002-1456-6131
    rorid: null
    typeEntity: Person
    typeRole:
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    - Maintainer
    url: null
  description: An interactive set of tools including randomization of data (even stratified
    random sampling) and random assignments for studies, generation of random numbers
    following specific probability distributions, generation of random and quasi-random
    point distributions and sampling patterns, noise in one or two dimensions with
    adjustable spectral properties, random walks and Lévy flights. Own data tables
    can be provided for random sampling in a privacy-friendly way, as data processing
    takes place directly in the browser and no data is transferred to anywhere else.
    The Random Number Lab also offers some educational material and worksheets and
    can be used for scientific and educational purposes.
  documentation: []
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    input: []
    note: Generation of sequences of random numbers or elements, spatial point patterns,
      random walks
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    output: []
  - cmd: null
    input: []
    note: Visualization of random distributions and random processes
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  - cmd: null
    input: []
    note: Randomization and permutation of data in a privacy-preserving way
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output: []
  homepage: https://randomnumberlab.org
  homepage_status: 0
  language:
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  lastUpdate: '2026-02-27T18:10:10.460700Z'
  license: null
  link: []
  maturity: Mature
  name: Random Number Lab
  operatingSystem:
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  - iOS
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  - Android
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  otherID:
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    value: RRID:SCR_028010
    version: null
  owner: thomas9
  publication: []
  relation: []
  toolType:
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  topic:
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  - term: Experimental design and studies
    uri: http://edamontology.org/topic_3678
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2021-05-06T06:18:52Z'
  biotoolsCURIE: biotools:pangenome-blast
  biotoolsID: pangenome-blast
  collectionID: []
  confidence_flag: null
  cost: Free of charge
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    fundrefid: null
    gridid: null
    name: Bielefeld University
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: https://www.uni-bielefeld.de/
  - email: null
    fundrefid: null
    gridid: null
    name: Genome Informatics
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: https://gi.cebitec.uni-bielefeld.de/
  - email: plast-service@cebitec.uni-bielefeld.de
    fundrefid: null
    gridid: null
    name: Tizian Schulz
    note: null
    orcidid: https://orcid.org/0000-0003-0744-7078
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: PLAST is a heuristical method to search for highest scoring local alignments
    between a DNA sequence query and a graphical pangenome. It takes as input a plain
    DNA sequence and a pangenome which may either be a set of (multiple) FASTA or
    FASTQ files or a sequence graph constructed by the tool Bifrost. It then outputs
    statistically meaningful (gapped) alignments in the style of the NCBI BLAST standard
    output format. Alignments are calculated based on a "seed-and-extend approach"
    while traversing the sequence graph. Biologically meaningful alignments are filtered
    by using an alignment statistic explicitly developed for sequence-to-graph alignments
    involving graphical pangenomes.
  documentation:
  - note: null
    type:
    - General
    url: https://gitlab.ub.uni-bielefeld.de/gi/plast/-/blob/master/README.md
  download: []
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  function:
  - cmd: PLAST Search -i pangenomeGraphCommonFilePrefix -q fileContainingOneQueryPerLine
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: unambiguous pure nucleotide
        uri: http://edamontology.org/format_1211
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: GFA 1
        uri: http://edamontology.org/format_3975
      - term: Binary format
        uri: http://edamontology.org/format_2333
    note: "In order to search for alignments within the pangenome graph, \nA pangenome\
      \ graph used to search for alignments consists of (1) a file in GFA format containing\
      \ all sequences of the graph, (2) a binary file produced by the tool itself\
      \ or the software \"Bifrost\" and (3) a program-specific index data structure\
      \ in binary format."
    operation:
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: BLAST results
        uri: http://edamontology.org/format_1333
  - cmd: PLAST Build -i pangenomeGraphCommonFilePrefix -R *.fasta
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: If a pangenome graph already exists and only an index has to be built, FASTA/FASTQ
      files are not needed.
    operation:
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    output:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: GFA 1
        uri: http://edamontology.org/format_3975
      - term: Binary format
        uri: http://edamontology.org/format_2333
  homepage: https://github.com/tischulz1/plast
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-02-26T11:22:02.485629Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.ub.uni-bielefeld.de/gi/plast
  - note: null
    type:
    - Mirror
    url: https://github.com/tischulz1/plast
  maturity: Mature
  name: PLAST
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: tizian
  publication:
  - doi: 10.1093/bioinformatics/btab077
    metadata:
      abstract: 'Motivation: Increasing amounts of individual genomes sequenced per
        species motivate the usage of pangenomic approaches. Pangenomes may be represented
        as graphical structures, e.g. compacted colored de Bruijn graphs, which offer
        a low memory usage and facilitate reference-free sequence comparisons. While
        sequence-to-graph mapping to graphical pangenomes has been studied for some
        time, no local alignment search tool in the vein of BLAST has been proposed
        yet. Results: We present a new heuristic method to find maximum scoring local
        alignments of a DNA query sequence to a pangenome represented as a compacted
        colored de Bruijn graph. Our approach additionally allows a comparison of
        similarity among sequences within the pangenome. We show that local alignment
        scores follow an exponential-tail distribution similar to BLAST scores, and
        we discuss how to estimate its parameters to separate local alignments representing
        sequence homology from spurious findings. An implementation of our method
        is presented, and its performance and usability are shown. Our approach scales
        sublinearly in running time and memory usage with respect to the number of
        genomes under consideration. This is an advantage over classical methods that
        do not make use of sequence similarity within the pangenome.'
      authors:
      - name: Schulz T.
      - name: Wittler R.
      - name: Rahmann S.
      - name: Hach F.
      - name: Stoye J.
      citationCount: 6
      date: '2021-08-15T00:00:00Z'
      journal: Bioinformatics
      title: Detecting high-scoring local alignments in pangenome graphs
    note: null
    pmcid: PMC8388040
    pmid: '33532821'
    type:
    - Primary
    - Method
    - Benchmarking study
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - 0.0.1-0.2.0
- accessibility: Restricted access
  additionDate: '2026-02-23T13:56:07.187145Z'
  biotoolsCURIE: biotools:HelixInsight
  biotoolsID: HelixInsight
  collectionID: []
  confidence_flag: null
  cost: Commercial
  credit:
  - email: contact@helena.bio
    fundrefid: null
    gridid: null
    name: Helena Bioinformatics
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Developer
    url: https://helena.bio
  description: AI-powered variant interpretation platform for clinical genetics laboratories.
    Automates ACMG/AMP 2015 classification using Bayesian point-based framework (Tavtigian
    et al. 2018) with BayesDel ClinGen SVI-calibrated thresholds (Pejaver et al. 2022).
    Integrates 8 reference databases (gnomAD v4.1, ClinVar, dbNSFP 4.9c, SpliceAI,
    gnomAD Constraint, HPO, ClinGen, Ensembl VEP) for comprehensive variant annotation.
    Supports HPO-based phenotype matching with semantic similarity scoring, automated
    biomedical literature mining across 2M+ PubMed publications, and structured clinical
    report generation. Delivers full clinical interpretation of whole genome sequencing
    (WGS) in under 15 minutes. EU-hosted on dedicated infrastructure in Helsinki,
    Finland (GDPR-compliant).
  documentation:
  - note: null
    type:
    - General
    url: https://helixinsight.bio/docs
  - note: null
    type:
    - API documentation
    url: https://helixinsight.bio/docs/getting-started
  - note: null
    type:
    - Installation instructions
    url: https://helixinsight.bio/how-it-works
  - note: null
    type:
    - Terms of use
    url: https://helixinsight.bio/terms
  - note: Privacy policy
    type:
    - Other
    url: https://helixinsight.bio/privacy
  download: []
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  elixir_badge: 0
  function:
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    input:
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        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
    note: null
    operation:
    - term: Variant classification
      uri: http://edamontology.org/operation_3225
    output:
    - data:
        term: Sequence report
        uri: http://edamontology.org/data_2955
      format: []
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format: []
    - data:
        term: Disease report
        uri: http://edamontology.org/data_1622
      format: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genetic variation analysis
      uri: http://edamontology.org/operation_3197
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Literature search
      uri: http://edamontology.org/operation_0305
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    output: []
  homepage: https://helixinsight.bio
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-24T22:17:23.859555Z'
  license: Proprietary
  link: []
  maturity: Emerging
  name: Helix Insight
  operatingSystem:
  - Linux
  otherID: []
  owner: helenabio
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Human genetics
    uri: http://edamontology.org/topic_3574
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  validated: 0
  version:
  - '3.5'
- accessibility: Open access
  additionDate: '2025-06-25T13:31:29.384393Z'
  biotoolsCURIE: biotools:fantasiav2
  biotoolsID: fantasiav2
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: fmpercan@upo.es
    fundrefid: null
    gridid: null
    name: Francisco Miguel Pérez Canales
    note: Programmer
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    - Support
    - Provider
    url: http://www.bioinfocb.es/
  - email: a.rojas.m@csic.es
    fundrefid: null
    gridid: null
    name: Ana M Rojas Mendoza
    note: Scientific concept and functionalities
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Contributor
    - Documentor
    - Support
    url: http://www.bioinfocb.es/
  - email: rosa.fernandez@ibe.upf-csic.es
    fundrefid: null
    gridid: null
    name: Rosa Fernandez
    note: Scientific concept and functionalities
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    - Documentor
    url: https://www.metazomics.com/
  - email: fraruimot@alum.us.es
    fundrefid: null
    gridid: null
    name: Francisco J. Ruiz Mota
    note: Junior developer
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: http://www.bioinfocb.es/
  - email: gemma.martinez@ibe.upf-csic.es
    fundrefid: null
    gridid: null
    name: Gemma Martinez Redondo
    note: Contributed  as developer of the first version of FANTASIA V1
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    url: https://www.metazomics.com/
  - email: adomrod4@upo.es
    fundrefid: null
    gridid: null
    name: Alex Dominguez Rodriguez
    note: Implemented the LITE version of FANTASIA
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    - Maintainer
    - Documentor
    url: http://www.bioinfocb.es/
  description: FANTASIA (Functional ANnoTAtion based on embedding space SImilArity)
    is a pipeline for protein annotating via GO term transference using the embedding
    space. FANTASIA’s latest developments include additional protein language models
    and provide enhanced functionalities.
  documentation:
  - note: Full documetnation with user cases, benchmarking, and cluster implementations
    type:
    - General
    url: https://fantasia.readthedocs.io/en/latest/
  download: []
  editPermission:
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    type: group
  elixirCommunity:
  - 3D-BioInfo
  - Proteomics
  elixirNode:
  - Spain
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_3672
    output: []
  homepage: https://github.com/CBBIO/
  homepage_status: 0
  language:
  - Python
  - SQL
  lastUpdate: '2026-02-22T21:19:22.986918Z'
  license: MIT
  link:
  - note: Main repository contains documentation  from latest version
    type:
    - Repository
    url: https://github.com/CBBIO/FANTASIA
  - note: Main repository contains documentation  from linitial version based on Bioembeddings
      implementation.
    type:
    - Repository
    url: https://github.com/MetazoaPhylogenomicsLab/FANTASIA
  - note: Recommended tool for the Earth Biogenome Project
    type:
    - Software catalogue
    url: https://www.earthbiogenome.org/report-on-annotation-recommended-tools
  - note: This is the LITE version of FANTASIA for a quick and custom annotation
    type:
    - Software catalogue
    url: https://github.com/CBBIO/FANTASIA-Lite
  - note: This is a repository for FANTASIA-LITE available in Elixir France
    type:
    - Repository
    url: https://gitlab.com/ifb-elixirfr/cluster/tools/-/tree/master/tools/fantasia/0.1.0?ref_type=heads
  maturity: Mature
  name: FANTASIA
  operatingSystem:
  - Linux
  otherID: []
  owner: arojas
  publication:
  - doi: 10.1093/nargab/lqae078
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Usage
    version: null
  - doi: 10.1007/978-1-0716-4623-6_8
    metadata: null
    note: This protocol describes the use of the first version of FANTASIA
    pmcid: null
    pmid: '40601255'
    type:
    - Method
    version: 2.8.0
  - doi: 10.1038/s42003-025-08651-2
    metadata: null
    note: Application of FANTASIA to annotate 24 million of genes of 1000 animal species
    pmcid: PMC12354702
    pmid: '40813894'
    type:
    - Primary
    version: '4.0'
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Molecular evolution
    uri: http://edamontology.org/topic_3945
  - term: Natural language processing
    uri: http://edamontology.org/topic_0218
  - term: Functional genomics
    uri: http://edamontology.org/topic_0085
  - term: Open science
    uri: http://edamontology.org/topic_4010
  validated: 0
  version:
  - '4.0'
  - LITE
- accessibility: Open access
  additionDate: '2026-02-19T07:51:45.702608Z'
  biotoolsCURIE: biotools:poly_pipeline
  biotoolsID: poly_pipeline
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: pccrvl@gmail.com
    fundrefid: null
    gridid: null
    name: Pedro Cristovão Carvalho
    note: Main developer of the pipeline
    orcidid: https://orcid.org/0000-0001-9242-6911
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    - Maintainer
    - Provider
    - Support
    url: https://cafinvest.com.br/resume.php
  description: A data analysis pipeline for Spatial Transcriptomics data tailored
    to polyploid organisms.
  documentation:
  - note: Github Documentation
    type:
    - User manual
    url: https://github.com/capuccino26/POLY_PIPELINE#poly_pipeline
  download:
  - note: Github Release
    type: Source code
    url: https://github.com/capuccino26/POLY_PIPELINE/releases/tag/v1.0.0
    version: v1.0.0
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Plant Sciences
  elixirNode: []
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: ANALYSIS=1
    input:
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format: []
    note: Clustering of GEF files.
    operation:
    - term: Expression profile clustering
      uri: http://edamontology.org/operation_0313
    output:
    - data:
        term: Clustered expression profiles
        uri: http://edamontology.org/data_3768
      format: []
  - cmd: ANALYSIS=3
    input:
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format: []
    note: Generation of Nodes and Edges.
    operation:
    - term: Network visualisation
      uri: http://edamontology.org/operation_3925
    output:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format: []
  - cmd: ANALYSIS=0
    input:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
    note: Data converter.
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
  - cmd: ANALYSIS=1
    input:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
    note: Generation of count matrix.
    operation:
    - term: RNA-Seq quantification
      uri: http://edamontology.org/operation_3800
    output:
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format: []
  - cmd: ANALYSIS=1
    input:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
    note: Filtering of GEF files.
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
  homepage: https://github.com/capuccino26/POLY_PIPELINE
  homepage_status: 0
  language:
  - R
  - Bash
  - Python
  lastUpdate: '2026-02-19T08:19:12.181956Z'
  license: MIT
  link:
  - note: Github Repository
    type:
    - Repository
    url: https://github.com/capuccino26/POLY_PIPELINE
  - note: Zenodo Insert
    type:
    - Other
    url: https://zenodo.org/records/18655692
  maturity: Mature
  name: Poly Pipeline
  operatingSystem:
  - Linux
  otherID:
  - type: doi
    value: doi:10.5281/zenodo.18655692
    version: v1.0.0
  owner: pedro
  publication:
  - doi: 10.5281/zenodo.18655692
    metadata: null
    note: Zenodo Insertion
    pmcid: null
    pmid: null
    type:
    - Other
    version: v1.0.0
  relation: []
  toolType:
  - Command-line tool
  - Script
  topic:
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 0
  version:
  - v1.0.0
- accessibility: Open access
  additionDate: '2026-02-12T14:54:22.759092Z'
  biotoolsCURIE: biotools:segmentation_evaluation
  biotoolsID: segmentation_evaluation
  collectionID:
  - EUCAIM
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: jose.almeida@research.fchampalimaud.org
    fundrefid: null
    gridid: null
    name: José Guilherme de Almeida
    note: null
    orcidid: https://orcid.org/0000-0002-1887-0157
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Nickolas Papanikolaou
    note: null
    orcidid: https://orcid.org/0000-0003-3298-2072
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: This tool calculates segmentation metrics (Dice score, intersection
    over union, Hausdorff distance, and normalised surface distance) between two sets
    of masks. It can be used to quickly calculate a number of metrics for segmentation
    models.
  documentation:
  - note: null
    type:
    - Quick start guide
    - API documentation
    url: https://github.com/josegcpa/eucaim-metrics/tree/master
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "uv run eval_segmentation \\\n    --pred test_data/predicted/ \\\n    --gt\
      \ test_data/groundtruth/ \\\n    --output test.json \\\n    --n_classes 2 \\\
      \n    --verbose \\\n    --params '{\"normalised_surface_distance\": {\"max_distance\"\
      : 100.0}}'"
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: nii
        uri: http://edamontology.org/format_3549
    note: This is the core command which can be used to calculate image segmentation
      metrics. For more options please run `uv run eval_segmentation --help`
    operation:
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://github.com/josegcpa/eucaim-metrics/tree/master
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-12T15:01:23.363666Z'
  license: CC-BY-4.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/josegcpa/eucaim-metrics/tree/master
  maturity: Emerging
  name: Segmentation evaluation
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: josegcpa
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  - term: MRI
    uri: http://edamontology.org/topic_3444
  validated: 0
  version:
  - v0.1
- accessibility: null
  additionDate: '2019-06-20T14:18:28Z'
  biotoolsCURIE: biotools:decompTumor2Sig
  biotoolsID: decompTumor2Sig
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: r.piro@fu-berlin.de
    fundrefid: null
    gridid: null
    name: Prof. Dr. Rosario M. Piro
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    url: null
  description: R package for identification of mutational signatures active in individual
    tumors. It decomposes an individual tumor genome into a given set of Alexandrov-type
    or Shiraishi-type signatures, thus quantifying the contribution of the corresponding
    mutational processes to the somatic mutations identified in the tumor.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/rmpiro/decompTumor2Sig/blob/master/decompTumor2Sig-manual.pdf
  download:
  - note: null
    type: Downloads page
    url: http://rmpiro.net/index.html#downloads
    version: null
  editPermission:
    authors:
    - ELIXIR-ITA-POLIMI
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    - term: Parsing
      uri: http://edamontology.org/operation_1812
    output: []
  homepage: http://rmpiro.net/decompTumor2Sig/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-02-12T13:42:21.288130Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/rmpiro/decompTumor2Sig/issues
  - note: null
    type:
    - Repository
    url: https://github.com/rmpiro/decompTumor2Sig
  - note: null
    type:
    - Software catalogue
    url: https://bioconductor.org/packages/release/bioc/html/decompTumor2Sig.html
  maturity: Mature
  name: decompTumor2Sig
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: rosario7
  publication:
  - doi: 10.1186/s12859-019-2688-6
    metadata:
      abstract: '© 2019 The Author(s).Background: The somatic mutations found in a
        tumor have in most cases been caused by multiple mutational processes such
        as those related to extrinsic carcinogens like cigarette smoke, and those
        related to intrinsic processes like age-related spontaneous deamination of
        5-methylcytosine. The effect of such mutational processes can be modeled by
        mutational signatures, of which two different conceptualizations exist: the
        model introduced by Alexandrov et al., Nature 500:415-421, 2013, and the model
        introduced by Shiraishi et al., PLoS Genetics 11(12):e1005657, 2015. The initial
        identification and definition of mutational signatures requires large sets
        of tumor samples. Results: Here, we present decompTumor2Sig, an easy to use
        R package that can decompose an individual tumor genome into a given set of
        Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution
        of the corresponding mutational processes to the somatic mutations identified
        in the tumor. Until now, such tools were available only for Alexandrov signatures.
        We demonstrate the correctness and usefulness of our approach with three test
        cases, using somatic mutations from 21 breast cancer genomes, from 435 tumor
        genomes of ten different tumor entities, and from simulated tumor genomes,
        respectively. Conclusions: The decompTumor2Sig package is freely available
        and has been accepted for inclusion in Bioconductor.'
      authors:
      - name: Kruger S.
      - name: Piro R.M.
      citationCount: 8
      date: '2019-04-18T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'DecompTumor2Sig: Identification of mutational signatures active in individual
        tumors'
    note: null
    pmcid: PMC6472187
    pmid: '30999866'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
  - 2.0.0
- accessibility: Open access
  additionDate: '2017-05-24T12:15:33Z'
  biotoolsCURIE: biotools:sarek
  biotoolsID: sarek
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: maxime.garcia@scilifelab.se
    fundrefid: null
    gridid: null
    name: Maxime U. Garcia
    note: null
    orcidid: https://orcid.org/0000-0003-2827-9261
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://maxulysse.github.io/
  - email: szilveszter.juhos@scilifelab.se
    fundrefid: null
    gridid: null
    name: Szilvester Juhos
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Science for Life Laboratory - SciLifeLab
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole: []
    url: https://www.scilifelab.se/
  - email: null
    fundrefid: null
    gridid: null
    name: National Genomics Infrastructure - NGI
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole: []
    url: https://ngisweden.scilifelab.se/
  - email: null
    fundrefid: null
    gridid: null
    name: National Bioinformatics Infrastructure Sweden - NBIS
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole: []
    url: https://nbis.se/
  - email: null
    fundrefid: null
    gridid: null
    name: Barntumörbanken
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole: []
    url: https://ki.se/forskning/barntumorbanken
  description: Sarek is part of nf-core and has changed to the nf-core-sarek id.
  documentation:
  - note: null
    type:
    - General
    url: https://nf-co.re/sarek
  - note: null
    type:
    - User manual
    url: https://nf-co.re/sarek/usage
  - note: null
    type:
    - Installation instructions
    url: https://nf-co.re/usage/installation
  - note: null
    type:
    - Terms of use
    url: https://github.com/nf-core/sarek/blob/master/LICENSE
  download: []
  editPermission:
    authors:
    - malinlarsson
    - szilva
    - fhanssen
    - ewels
    - JoseEspinosa
    - gelpi@ub.edu
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence (raw)
        uri: http://edamontology.org/data_3497
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
    note: null
    operation:
    - term: Sample comparison
      uri: http://edamontology.org/operation_3731
    - term: Sequence annotation
      uri: http://edamontology.org/operation_0361
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: https://nf-co.re/sarek
  homepage_status: 0
  language:
  - Groovy
  lastUpdate: '2026-02-04T22:38:39.196636Z'
  license: MIT
  link:
  - note: Github Repository
    type:
    - Repository
    url: https://github.com/nf-core/sarek
  - note: Slack channel
    type:
    - Social media
    url: https://nfcore.slack.com/channels/sarek
  maturity: Mature
  name: Sarek
  operatingSystem:
  - Linux
  otherID: []
  owner: MaxUlysse
  publication:
  - doi: 10.1101/316976
    metadata: null
    note: This is the publication about the nf-core framework
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.12688/f1000research.16665.2
    metadata: null
    note: This is the publication about the nf-core framework
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.1038/s41587-020-0439-x
    metadata:
      abstract: ''
      authors:
      - name: Ewels P.A.
      - name: Peltzer A.
      - name: Fillinger S.
      - name: Patel H.
      - name: Alneberg J.
      - name: Wilm A.
      - name: Garcia M.U.
      - name: Di Tommaso P.
      - name: Nahnsen S.
      citationCount: 935
      date: '2020-03-01T00:00:00Z'
      journal: Nature Biotechnology
      title: The nf-core framework for community-curated bioinformatics pipelines
    note: This is the publication about the nf-core framework
    pmcid: null
    pmid: '32055031'
    type:
    - Other
    version: null
  relation:
  - biotoolsID: caw
    type: isNewVersionOf
  - biotoolsID: nf-core-sarek
    type: hasNewVersion
  toolType:
  - Command-line tool
  - Workflow
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  validated: 1
  version:
  - 2.0.0
  - 2.1.0
  - 2.2.0
  - 2.2.1
  - 2.2.2
  - '2.3'
  - 2.3.FIX1
- accessibility: Restricted access
  additionDate: '2025-03-17T14:01:59.601345Z'
  biotoolsCURIE: biotools:exposome_maps
  biotoolsID: exposome_maps
  collectionID:
  - EXPANSE
  - EHEN
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: R.C.H.Vermeulen@uu.nl
    fundrefid: null
    gridid: null
    name: Roel Vermeulen
    note: null
    orcidid: https://orcid.org/0000-0003-4082-8163
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: z.s.r.m.boudewijns@uu.nl
    fundrefid: null
    gridid: null
    name: Zimbo Boudewijns
    note: null
    orcidid: https://orcid.org/0000-0002-9383-9571
    rorid: null
    typeEntity: null
    typeRole:
    - Maintainer
    url: null
  - email: l.q.roga@uu.nl
    fundrefid: null
    gridid: null
    name: Lloyd Roga
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  description: 'Exposome Maps is a data catalogue of geospatially resolved datasets
    on environmental exposure estimates. It contains more than 20,000 datasets on
    several Exposome dimensions including Physico-Chemical Environment, Built Environment,
    Food Environment, and Social Environment. It provides harmonized data collections
    across Europe for following environmental factors: PM10, PM2.5, NO2, O3, Temperature,
    Ultra Violet Radiation, Road Traffic Noise, Urbanicity, NDVI (Normalized Difference
    Vegetation Index ), MSAVI (Modified Soil Adjusted Vegetation Index), Green spaces,
    Blue spaces, Imperviousness, Light at night, Walkability Index.'
  documentation:
  - note: Description of Environmental variables available through Exposome Maps
    type:
    - User manual
    url: https://surfdrive.surf.nl/files/index.php/s/uqUORDrd428H2F9
  - note: Exposome-NL data platform Data Access and Publication Policy
    type:
    - Terms of use
    url: https://surfdrive.surf.nl/files/index.php/s/fI0Gmuu5O1MJAI9
  download: []
  editPermission:
    authors:
    - hkucukali
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://exposome.uu.nl/
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-04T00:46:44.590787Z'
  license: Other
  link:
  - note: Project information page
    type:
    - Other
    url: https://expanseproject.eu/
  maturity: Mature
  name: Exposome Maps
  operatingSystem: []
  otherID: []
  owner: Channel2291
  publication:
  - doi: 10.1126/science.aay3164
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1097/EE9.0000000000000162
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  - term: Environmental sciences
    uri: http://edamontology.org/topic_3855
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-10-31T09:19:51.388544Z'
  biotoolsCURIE: biotools:image_duplicate_check_tool
  biotoolsID: image_duplicate_check_tool
  collectionID:
  - EUCAIM
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: miguel.chambel@research.fchampalimaud.org
    fundrefid: null
    gridid: null
    name: Miguel Chambel
    note: null
    orcidid: https://orcid.org/0000-0002-6099-4110
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Contributor
    - Documentor
    url: null
  - 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:
    - Maintainer
    - Support
    url: https://josegcpa.net/
  - email: null
    fundrefid: null
    gridid: null
    name: Nickolas Papanikolaou
    note: null
    orcidid: https://orcid.org/0000-0003-3298-2072
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: A CLI tool for detecting duplicate DICOM images by analyzing pixel
    data, generating content-based hashes, and comparing them to identify identical
    images, even when metadata, file format, or size differs
  documentation:
  - note: null
    type:
    - General
    - Command-line options
    - Installation instructions
    - User manual
    - Release notes
    url: https://github.com/helghast79/eucaim-image-duplication-check-tool/blob/main/README.md
  download:
  - note: scroll to bottom of github release page to find the executable download
      for each OS
    type: Downloads page
    url: https://github.com/helghast79/eucaim-image-duplication-check-tool/releases/tag/v1.0.0
    version: v1.0.0
  editPermission:
    authors:
    - josegcpa
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://docs.google.com/presentation/d/1guNJkm0E5YSsbIVKaaEevFnNGG4WR_m6XGsL695e3_A/edit?slide=id.g370e96e3b29_0_111#slide=id.g370e96e3b29_0_111
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2026-02-03T15:36:48.615645Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/helghast79/eucaim-image-duplication-check-tool
  maturity: Emerging
  name: Image duplication check
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: helghast
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version:
  - v1.0.0
next: ?page=2
previous: null
