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  description: Local Windows-friendly R Shiny application for RNA-seq differential
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  description: DeepTaxa is a hybrid CNN-BERT deep learning framework for multi-rank
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  description: DANTE (Da Amazing NucleoTide Exposer) is an algorithm for genotyping
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- accessibility: Open access
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  biotoolsCURIE: biotools:bioexcel_building_blocks_tutorials_protein_md_setup_tutorial_through_rest_api
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  description: This tutorial aims to illustrate the process of setting up a simulation
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    metadata: null
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  description: This BioExcel Building Blocks library (BioBB) workflow provides a pipeline
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  - term: Nucleic acid structure analysis
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    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: NSF award 0921038; LMU Rains Research Assistant Program; LMU Summer Undergraduate
      Research Program
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: lmu.edu
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: null
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    fundrefid: null
    gridid: null
    name: Kam D. Dahlquist
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: dondi@lmu.edu
    fundrefid: null
    gridid: null
    name: John David N. Dionisio
    note: null
    orcidid: https://orcid.org/0000-0001-8655-4693
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: Web application and service for visualizing small- to medium-scale
    models of gene regulatory networks. It automatically lays out either an unweighted
    or weighted 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.
    It is best-suited for visualizing networks of fewer than 35 nodes and 70 edges
    and has general applicability.
  documentation:
  - note: null
    type:
    - General
    url: http://dondi.github.io/GRNsight/documentation.html
  download:
  - note: null
    type: Source code
    url: https://github.com/dondi/GRNsight/archive/refs/heads/main.zip
    version: null
  editPermission:
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  function:
  - cmd: null
    input: []
    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
      a weighted adjacency matrix, GRNsight uses pointed and blunt arrowheads, and
      colors the edges and adjusts their thicknesses based on the sign (positive for
      activation or negative for repression) and magnitude of the weight parameter.
      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:
    - term: Gene regulatory network analysis
      uri: http://edamontology.org/operation_1781
    - term: Pathway or network visualisation
      uri: http://edamontology.org/operation_3083
    output: []
  homepage: http://dondi.github.io/GRNsight/
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2026-06-07T23:16:02.636376Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/dondi/GRNsight
  maturity: Mature
  name: GRNsight
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: dondi@lmu.edu
  publication:
  - doi: 10.7717/peerj-cs.85
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.5281/zenodo.7411630
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Gene regulation
    uri: http://edamontology.org/topic_0204
  validated: 1
  version:
  - 7.8.0
- accessibility: Open access
  additionDate: '2020-06-05T08:52:25Z'
  biotoolsCURIE: biotools:calibracurve
  biotoolsID: calibracurve
  collectionID:
  - BioInfra.Prot
  - de.NBI
  - CUBiMed.RUB
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: martin.eisenacher@rub.de
    fundrefid: null
    gridid: null
    name: PD Dr. Martin Eisenacher
    note: If contacting use "SPARROW" in subject line to avoid mail deluge.
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: de.NBI
    note: Service provision and maintenance funded by de.NBI.
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    - Maintainer
    - Support
    url: https://www.denbi.de/
  - email: michael.kohl@rub.de
    fundrefid: null
    gridid: null
    name: Dr. Michael Kohl
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: A highly useful and flexible tool for calibration of targeted MS‐based
    measurements. CalibraCurve enables an automated batch-mode determination of dynamic
    linear ranges and quantification limits for both targeted proteomics and similar
    assays. The software uses a variety of measures to assess the accuracy of the
    calibration and provides intuitive visualizations.
  documentation:
  - note: null
    type:
    - Installation instructions
    - Citation instructions
    - General
    - User manual
    - Training material
    - Terms of use
    url: https://github.com/mpc-bioinformatics/CalibraCurve
  download:
  - note: null
    type: Downloads page
    url: https://github.com/mpc-bioinformatics/CalibraCurve
    version: '2.0'
  editPermission:
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    type: group
  elixirCommunity:
  - Proteomics
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Analysis
      uri: http://edamontology.org/operation_2945
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: tiff
        uri: http://edamontology.org/format_3591
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://github.com/mpc-bioinformatics/CalibraCurve
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-06-04T08:07:22.002962Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/mpc-bioinformatics/CalibraCurve
  maturity: Mature
  name: CalibraCurve
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: BioInfra.Prot
  publication:
  - doi: 10.1002/pmic.201900143
    metadata:
      abstract: Targeted proteomics techniques allow accurate quantitative measurements
        of analytes in complex matrices with dynamic linear ranges that span up to
        4–5 orders of magnitude. Hence, targeted methods are promising for the development
        of robust protein assays in several sensitive areas, for example, in health
        care. However, exploiting the full method potential requires reliable determination
        of the dynamic range along with related quantification limits for each analyte.
        Here, a software named CalibraCurve that enables an automated batch-mode determination
        of dynamic linear ranges and quantification limits for both targeted proteomics
        and similar assays is presented. The software uses a variety of measures to
        assess the accuracy of the calibration, namely precision and trueness. Two
        different kinds of customizable graphs are created (calibration curves and
        response factor plots). The accuracy measures and the graphs offer an intuitive,
        detailed, and reliable opportunity to assess the quality of the model fit.
        Thus, CalibraCurve is deemed a highly useful and flexible tool to facilitate
        the development and control of reliable SRM/MRM-MS-based proteomics assays.
      authors:
      - name: Kohl M.
      - name: Stepath M.
      - name: Bracht T.
      - name: Megger D.A.
      - name: Sitek B.
      - name: Marcus K.
      - name: Eisenacher M.
      citationCount: 4
      date: '2020-06-01T00:00:00Z'
      journal: Proteomics
      title: 'CalibraCurve: A Tool for Calibration of Targeted MS-Based Measurements'
    note: null
    pmcid: null
    pmid: '32086983'
    type:
    - Primary
    version: '2.0'
  relation: []
  toolType:
  - Workflow
  - Script
  - Desktop application
  - Plug-in
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Experimental design and studies
    uri: http://edamontology.org/topic_3678
  validated: 1
  version:
  - '2.0'
- accessibility: null
  additionDate: '2026-05-29T14:02:11.144137Z'
  biotoolsCURIE: biotools:MPLID
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  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Folorunsho Bright Omage
    note: null
    orcidid: https://orcid.org/0000-0002-9750-5034
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Goran Neshich
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Membrane Protein-Lipid Interaction Database. A large-scale experimentally
    validated dataset of 80685 residue-level lipid contact annotations across 4712
    membrane proteins derived from PDB crystal and cryo-EM structures. Provides pre-computed
    binary contact labels, continuous distance values, sequence-identity-based cluster
    assignments, and ready-made train-validation-test splits for machine learning.
  documentation: []
  download: []
  editPermission:
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  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: null
    operation:
    - term: Residue contact prediction
      uri: http://edamontology.org/operation_0272
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/omagefolorunsho/MPLID
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-29T14:02:11.146591Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/omagefolorunsho/MPLID
  maturity: null
  name: MPLID
  operatingSystem: []
  otherID: []
  owner: folorunsho_bright
  publication:
  - doi: 10.5281/zenodo.18487584
    metadata: null
    note: Dataset deposition. Manuscript under review at GigaScience.
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Database portal
  topic:
  - term: Membrane and lipoproteins
    uri: http://edamontology.org/topic_0820
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version: []
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T10:41:57.535794Z'
  biotoolsCURIE: biotools:cluster_based_harmonization
  biotoolsID: cluster_based_harmonization
  collectionID:
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  cost: Free of charge (with restrictions)
  credit:
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    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: null
  - email: aikaterini_vraka@iislafe.es
    fundrefid: null
    gridid: null
    name: Aikaterini Vraka
    note: null
    orcidid: https://orcid.org/0000-0001-5984-904X
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martínez-Gironés
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
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    - Support
    url: null
  description: 'The tool is designed to perform radiomics harmonization on large and
    heterogeneous datasets, where the risk of over-harmonization is present. Instead
    of directly applying harmonization based on predefined batch labels, the tool
    first identifies groups of batches that share similar characteristics through
    clustering of the radiomics data. It then performs harmonization using these cluster-derived
    labels. The tool allows the harmonization of radiomics variables using two methods:
    (1) original ComBat (Rabinovic, 2007) method, where each original batch group
    is considered for the harmonization process and (2) cluster-based ComBat method,
    where batch groups with similar radiomics characteristics form clusters and the
    latter are being considered for the harmonization process.'
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/Kz3jfQYQZjezpxK
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/5bMA2jsZTfS8eoZ
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=0GJqNJv-Qf8&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=31
  - note: null
    type:
    - General
    url: https://drive.eucaim.cancerimage.eu/s/LkczHCMZH5nd8QR
  download: []
  editPermission:
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    type: group
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  function:
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      config_path:/config harbor.eucaim.cancerimage.eu/processing-tools/cluster_based_harmonization:1.1.0
      --config /config/config.json
    input:
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        term: Text data
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      - term: xlsx
        uri: http://edamontology.org/format_3620
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
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    output:
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      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: TIDE TXT
        uri: http://edamontology.org/format_3835
  - cmd: docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processing-tools/cluster_based_harmonization:1.1.0
      --file_path /input/data.xlsx --identifier patient_id --start_col original_shape_Elongation
      --end_col lbp-3D-k_ngtdm_Strength --batch_col software_versions --output_dir
      /output/results --min_clusters 2 --max_clusters 100 --results full --approach
      soft --small_groups merge
    input:
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
    note: null
    operation:
    - term: Clustering
      uri: http://edamontology.org/operation_3432
    output:
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: TIDE TXT
        uri: http://edamontology.org/format_3835
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/cluster_based_harmonization/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:21:17.961394Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/cluster_based_harmonization/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Emerging
  name: Cluster based harmonization (EUCAIM-SW-044_T-01-03-006)
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: casopon
  publication: []
  relation: []
  toolType:
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  topic:
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  validated: 0
  version:
  - 1.1.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-06-06T10:00:26.469620Z'
  biotoolsCURIE: biotools:2d_digital_mammography_harmonization
  biotoolsID: 2d_digital_mammography_harmonization
  collectionID:
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  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
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    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: manuel_marfil@iislafe.es
    fundrefid: null
    gridid: null
    name: Manuel Marfil-Trujillo
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
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    - Support
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: This preprocessing tool is design for 2D digital mammograms in DICOM  format.
    It standardizes and harmonizes images through a configurable pipeline that includes
    spatial reorientation, pseudo-3D stacking, isotropic resampling, intensity normalization,
    optional denoising, contrast enhancement, and mask processing (if available).
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/CC3yJTjPz9N7Ggg
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/rdHWqMkNf7frQRY
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=IrZhMp2lB7g&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=13
  download: []
  editPermission:
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    - casopon
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: docker run -it --rm --name container_name -v "<input_path>:/input" -v "<output_path>:/output"
      -v "<config_path>:/config" harbor.eucaim.cancerimage.eu/processing-tools/2d_digital_mammography_harmonization:1.1.0
      /app/entrypoint.sh --config /config/config.json
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processing-tools/2d_digital_mammography_harmonization:1.1.0
      --input_directory dataset_id --output_directory gaussian_output --num_workers
      4 --series_number 2301101 --series_description_suffix _harmonized --zscore_enabled
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      3 --gaussian_sigma 0.8 --clahe_enabled true --clahe_clip_limit 0.01
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Command Arguments
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/2d_digital_mammography_harmonization/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:21:05.356361Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
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  description: The tool performs by deep learning an automatic segmentation of the
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  description: 'The tool performs an automatic segmentation of the possible glioblastoma
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  description: The tool performs an automatic segmentation of the possible DIPG tumours
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  description: 'This tool is specifically designed and validated for automated detection
    and segmentation of neuroblastic tumours in T2-weighted magnetic resonance images
    (T2-MR) using deep learning. It processes DICOM or NIfTI input data and outputs
    in NIFTI or DICOM SEG.


    TRAINING & VALIDATION COHORTS:


    Initial Development (Veiga-Canuto 2022):

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

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

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

    -Mean age: 37.6 ± 39.3 months.

    -Median tumor volume: 116,518 mm³.


    External Validation (Veiga-Canuto 2023):

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

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

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

    -Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105),
    Canon (3).'
  documentation:
  - note: null
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    url: https://drive.eucaim.cancerimage.eu/s/44BxMSNpxwgsZiE
  - note: null
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    url: https://www.youtube.com/watch?v=c7XOEGRA9aQ&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=12
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  function:
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      \ \\\n  --gpus all \\\n  harbor.eucaim.cancerimage.eu/processing-tools/mr_based_neuroblastoma_tumour_detection_and_segmentation:2.0.0\
      \ \\\n  --mode dicom-seg \\\n  --series-selector /output/config/series_to_segment.csv\
      \ \\\n  --seg-series-number 2302001 \\\n  --seg-algorithm-name \"nnUNet_Neuroblastoma_Primage_training\"\
      \ \\\n  --seg-coordinating-center \"EUCAIM Consortium\" \\\n  --keep-nifti false"
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        uri: http://edamontology.org/data_2968
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      - term: nii
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    - data:
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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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    output:
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      format:
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        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
  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: '2026-05-27T15:19:40.961989Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
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    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/info-tab
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  maturity: Mature
  name: MR-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-019_T-01-02-002)
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    metadata: null
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  - doi: 10.3390/cancers15051622
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  toolType:
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  topic:
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  - term: Machine learning
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  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  validated: 0
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  additionDate: '2025-05-29T08:55:46.088021Z'
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  description: 'The tool is designed to perform a customisable image pre-processing
    to reduce noise and inhomogeneity field effect, thus improving image quality and
    reproducibility of radiomics features. This tool consists of two independent steps:
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    (NLM)), and another for the ANTs N4 and another for the ANT''s N4 bias correction
    filter. The parameter configuration of this tool has been optimised for TW1, T2W,
    DWI and DCE sequences in neuroblastoma (NB) and paediatric brain tumours, but
    it can also be configured with some of their parameters using a JSON parameter
    configuration file.'
  documentation:
  - note: null
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    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/wYJ7Fttnk6Dp7gc
  - note: null
    type:
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    url: https://drive.eucaim.cancerimage.eu/s/oseiKoeFZqwoRCA
  - note: null
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    url: https://www.youtube.com/watch?v=HkHqFGXGEbo&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=9
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    input:
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      format:
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    note: null
    operation:
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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/processin-tools/denoising_inhomogeneity_correction_tool:1.1.0
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      --output /output --series_number 2000 --series_description_suffix "_harmonized"
      --denoising adf --conductance 0.5 --iterations 3 --time_step 0.0625 --n4 --bspline_size
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    input:
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      format:
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    note: null
    operation:
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    output:
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  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: '2026-05-27T15:19:25.220262Z'
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  operatingSystem:
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  publication:
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    metadata: null
    note: null
    pmcid: PMC8554919
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  - doi: 10.1186/s41747-020-00150-9
    metadata: null
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    pmcid: PMC7125275
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  topic:
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    uri: http://edamontology.org/topic_0219
  validated: 0
  version:
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- accessibility: Open access (with restrictions)
  additionDate: '2025-11-25T09:58:37.569343Z'
  biotoolsCURIE: biotools:ml_model_for_mr_series_categorisation
  biotoolsID: ml_model_for_mr_series_categorisation
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  cost: Free of charge (with restrictions)
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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
    url: https://drive.eucaim.cancerimage.eu/s/rpm56rD5FfXAHyb
  - note: null
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    url: https://drive.eucaim.cancerimage.eu/s/8r3CzyQXrd7ERFp
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    url: https://www.youtube.com/watch?v=gudDCiuJIf8&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=11
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    note: null
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/info-tab
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  lastUpdate: '2026-05-27T15:19:08.404060Z'
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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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  - term: Data management
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  validated: 0
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  biotoolsCURIE: biotools:time_coherence_tool
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  description: "Tool that aims to validate visually the chronological order and logical\
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/time_coherence_tool/info-tab
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  maturity: Emerging
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  validated: 0
  version:
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- accessibility: Open access (with restrictions)
  additionDate: '2025-04-15T17:42:40.968987Z'
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  - 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
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    name: Adrian Galiana-Bordera
    note: null
    orcidid: https://orcid.org/0000-0002-8324-8284
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - 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:
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    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:
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        term: Image
        uri: http://edamontology.org/data_2968
      format:
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        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: xlsx
        uri: http://edamontology.org/format_3620
    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: JSON
        uri: http://edamontology.org/format_3464
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: "docker run -it --rm --name my-container \\\n  -v \"<input_path>:/input\"\
      \ \\\n  -v \"<output_path>:/output\" \\\n  harbor.eucaim.cancerimage.eu/processing-tools/dicom_file_integrity_checker:latest\
      \ \\\n  /app/entrypoint.sh --config-string \"{'QA': {'sequence_selection': ['ALL'],\
      \ 'modality_selection': ['ALL'], 'input_directory': 'dataset_id'}}\""
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: For Data Users (processing-tools)
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:16:18.033519Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  - note: Link to EUCAIM's Harbor for Data Holders
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/dicom_file_integrity_checker/artifacts-tab
  - note: Link to EUCAIM's Harbor for Data Users
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/dicom_file_integrity_checker/artifacts-tab
  maturity: Mature
  name: DICOM File Integrity Checker (EUCAIM-SW-002_T-01-01-002)
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  - term: Data acquisition
    uri: http://edamontology.org/topic_3077
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
  - 2.0.0
  - 2.1.0
  - 2.1.1
- accessibility: Open access
  additionDate: '2022-05-16T13:26:15.720803Z'
  biotoolsCURIE: biotools:skm
  biotoolsID: skm
  collectionID:
  - Plant Systems Biology
  - ELIXIR-SI
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: National Institute of Biology, Department of Biotechnology and Systems Biology
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: http://www.nib.si/
  - email: carissarobyn.bleker@nib.si
    fundrefid: null
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    name: Carissa Bleker
    note: null
    orcidid: https://orcid.org/0000-0003-1617-7145
    rorid: null
    typeEntity: Person
    typeRole:
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    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Kristina Gruden
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Živa Ramšak
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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  - email: null
    fundrefid: null
    gridid: null
    name: Vid Podpečan
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
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    url: null
  description: 'Stress Knowledge Map:  A compilation of knowledge on mechanisms underlying
    responses of plants to stress, the so called stress signalling network.'
  documentation:
  - note: null
    type:
    - General
    url: https://skm.nib.si/documentation
  download: []
  editPermission:
    authors:
    - zagor
    type: group
  elixirCommunity:
  - Plant Sciences
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  elixirNode:
  - Slovenia
  elixirPlatform: []
  elixir_badge: 0
  function:
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    input:
    - data:
        term: Gene name
        uri: http://edamontology.org/data_2299
      format: []
    note: null
    operation:
    - term: Database search
      uri: http://edamontology.org/operation_2421
    output:
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: sif
        uri: http://edamontology.org/format_3619
  - cmd: null
    input: []
    note: null
    operation:
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    output:
    - data:
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      format:
      - term: SBML
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      - term: sif
        uri: http://edamontology.org/format_3619
      - term: SBGN-ML
        uri: http://edamontology.org/format_3692
  homepage: https://skm.nib.si/
  homepage_status: 0
  language: []
  lastUpdate: '2026-05-22T08:51:52.189929Z'
  license: null
  link:
  - note: null
    type:
    - Other
    url: https://skm.nib.si/contact
  maturity: Emerging
  name: SKM
  operatingSystem: []
  otherID: []
  owner: carissa
  publication:
  - doi: 10.1016/j.xplc.2024.100920
    metadata: null
    note: 'Stress Knowledge Map: A knowledge graph resource for systems biology analysis
      of plant stress responses'
    pmcid: null
    pmid: '38616489'
    type:
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    version: null
  relation:
  - biotoolsID: gomapman
    type: uses
  - biotoolsID: newt-ve
    type: uses
  toolType:
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  topic:
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-05-18T13:53:39.264896Z'
  biotoolsCURIE: biotools:gonetview
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    gridid: null
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    note: null
    orcidid: null
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    url: null
  description: Standalone browser-based Gene Ontology network viewer for exploring,
    filtering, searching, and exporting GO term and gene annotation neighborhoods
    from locally preprocessed GO OBO and GAF data.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/JonasMarx3007/GONetView/blob/main/README.md
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    type:
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  function:
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        term: GO concept ID
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      format: []
    note: null
    operation:
    - term: Ontology visualisation
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    output:
    - data:
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      - term: PNG
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  - cmd: null
    input:
    - data:
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    note: null
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    output: []
  homepage: https://jonasmarx3007.github.io/GONetView/
  homepage_status: 0
  language:
  - Python
  - TypeScript
  lastUpdate: '2026-05-18T14:12:26.229467Z'
  license: MIT
  link:
  - note: Web Application Homepage
    type:
    - Other
    url: https://jonasmarx3007.github.io/GONetView/
  - note: null
    type:
    - Repository
    url: https://github.com/JonasMarx3007/GONetView
  maturity: Emerging
  name: GONetView
  operatingSystem: []
  otherID: []
  owner: JonasMarx3007
  publication:
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    metadata: null
    note: null
    pmcid: null
    pmid: null
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  relation: []
  toolType:
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  topic:
  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  - term: Functional genomics
    uri: http://edamontology.org/topic_0085
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - 0.1.0
next: ?page=2
previous: null
