count: 9082
list:
- accessibility: Open access
  additionDate: '2026-06-07T04:02:15.529158Z'
  biotoolsCURIE: biotools:pepkio-well-plate-seeding-density-calculator
  biotoolsID: pepkio-well-plate-seeding-density-calculator
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Pepkio
    note: Pepkio develops software tools and bioinformatics solutions for life science
      researchers, including laboratory calculators and analysis services.
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: https://www.pepkio.com/
  description: Derives cells per well and suspension pipette volumes for standard
    6-, 12-, 24-, 48-, 96-, and 384-well plates from a hemocytometer stock count,
    trypan blue viability, and target seeding confluency, with QC flags for low viability
    and impractical transfers. A browser calculator supports interactive planning
    with cell-line presets; a Python library and command-line tool submit the same
    parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic
    is hosted remotely; the client transmits parameters and returns structured plate
    tables and shareable run identifiers.
  documentation:
  - note: null
    type:
    - General
    url: https://www.pepkio.com/tools/well-plate-seeding-density-calculator
  - note: null
    type:
    - User manual
    url: https://github.com/pepkio/pepkio-well-plate-seeding-density-calculator
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Web calculator for bench seeding; Python library and CLI for API-backed
      automation of the same cell seeding engine.
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output: []
  homepage: https://www.pepkio.com/tools/well-plate-seeding-density-calculator
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-06-07T04:02:36.627996Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/pepkio/pepkio-well-plate-seeding-density-calculator
  - note: null
    type:
    - Service
    url: https://www.pepkio.com/tools/well-plate-seeding-density-calculator
  - note: Python client on PyPI.
    type:
    - Other
    url: https://pypi.org/project/pepkio-well-plate-seeding-density-calculator/
  maturity: null
  name: Pepkio Cell Seeding Density Calculator
  operatingSystem: []
  otherID: []
  owner: pepkio
  publication: []
  relation: []
  toolType:
  - Command-line tool
  - Library
  - Web application
  topic:
  - term: Molecular biology
    uri: http://edamontology.org/topic_3047
  - term: Laboratory techniques
    uri: http://edamontology.org/topic_3361
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  validated: 0
  version:
  - 0.1.0
- accessibility: Open access
  additionDate: '2026-06-07T03:07:06.267031Z'
  biotoolsCURIE: biotools:pepkio-absorbance-curve-calculator
  biotoolsID: pepkio-absorbance-curve-calculator
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Pepkio
    note: Pepkio develops software tools and bioinformatics solutions for life science
      researchers, including laboratory calculators and analysis services.
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: https://www.pepkio.com/
  description: Processes 96-well plate absorbance data through blank subtraction,
    regression fitting, and dilution correction to report sample concentrations with
    QC flags for BCA, Bradford, and ELISA workflows. A browser calculator supports
    interactive grid entry with CSV and PDF export; a Python library and command-line
    tool submit the same parameters to the Pepkio Tools API for scripted and pipeline
    use. Calculator arithmetic is hosted remotely; the client transmits plate layout
    and absorbance values and returns model comparison, per-sample concentrations,
    and shareable run identifiers.
  documentation:
  - note: null
    type:
    - General
    url: https://www.pepkio.com/tools/absorbance-curve-calculator
  - note: null
    type:
    - User manual
    url: https://github.com/pepkio/pepkio-absorbance-curve-calculator
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Web calculator for plate-based standard-curve fitting; Python library and
      CLI for API-backed automation of the same absorbance-curve engine.
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    - term: Regression analysis
      uri: http://edamontology.org/operation_3659
    output: []
  homepage: https://www.pepkio.com/tools/absorbance-curve-calculator
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-06-07T03:07:30.306304Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/pepkio/pepkio-absorbance-curve-calculator
  - note: null
    type:
    - Service
    url: https://www.pepkio.com/tools/absorbance-curve-calculator
  maturity: null
  name: Pepkio Standard Curve Calculator
  operatingSystem: []
  otherID: []
  owner: pepkio
  publication: []
  relation: []
  toolType:
  - Web application
  - Command-line tool
  - Library
  topic:
  - term: Molecular biology
    uri: http://edamontology.org/topic_3047
  - term: Laboratory techniques
    uri: http://edamontology.org/topic_3361
  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  validated: 0
  version:
  - 0.1.0
- accessibility: Open access
  additionDate: '2026-06-07T01:12:57.723685Z'
  biotoolsCURIE: biotools:pepkio-tm-annealing-temperature-calculator
  biotoolsID: pepkio-tm-annealing-temperature-calculator
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Pepkio
    note: Pepkio develops software tools and bioinformatics solutions for life science
      researchers, including laboratory calculators and analysis services.
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: https://www.pepkio.com/
  description: Estimates PCR primer melting temperatures and polymerase-specific annealing
    temperatures from sequence and buffer inputs, with per-pair QC for hairpins, dimers,
    and Tm balance. A browser calculator supports interactive single-pair and batch
    entry (up to 200 pairs) with method comparison and export; a Python library and
    command-line tool submit the same parameters to the Pepkio Tools API for scripted
    and pipeline use. Calculator arithmetic for the API client is hosted remotely;
    sequences are transmitted for programmatic runs while the web interface performs
    calculations in the browser.
  documentation:
  - note: null
    type:
    - General
    url: https://www.pepkio.com/tools/tm-annealing-temperature-calculator
  - note: null
    type:
    - User manual
    url: https://github.com/pepkio/pepkio-tm-annealing-temperature-calculator
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Web calculator for in-browser Tm/Ta planning; Python library and CLI for
      API-backed automation of the same primer thermodynamics engine.
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Nucleic acid thermodynamic property calculation
      uri: http://edamontology.org/operation_0455
    output: []
  homepage: https://www.pepkio.com/tools/tm-annealing-temperature-calculator
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-06-07T01:12:57.725718Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/pepkio/pepkio-tm-annealing-temperature-calculator
  - note: null
    type:
    - Service
    url: https://www.pepkio.com/tools/tm-annealing-temperature-calculator
  - note: Python client on PyPI.
    type:
    - Other
    url: https://pypi.org/project/pepkio-tm-annealing-temperature-calculator/
  maturity: null
  name: Pepkio Tm Annealing Temperature Calculator
  operatingSystem: []
  otherID: []
  owner: pepkio
  publication: []
  relation: []
  toolType:
  - Web application
  - Command-line tool
  - Library
  topic:
  - term: Probes and primers
    uri: http://edamontology.org/topic_0632
  - term: Molecular biology
    uri: http://edamontology.org/topic_3047
  - term: Laboratory techniques
    uri: http://edamontology.org/topic_3361
  validated: 0
  version:
  - 0.1.0
- accessibility: Open access
  additionDate: '2026-06-07T00:51:25.740335Z'
  biotoolsCURIE: biotools:pepkio-ph-buffer-recipe-calculator
  biotoolsID: pepkio-ph-buffer-recipe-calculator
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Pepkio
    note: Pepkio develops software tools and bioinformatics solutions for life science
      researchers, including laboratory calculators and analysis services.
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: https://www.pepkio.com/
  description: Computes weighed laboratory buffer recipes from target pH, concentration,
    and volume, accounting for separate preparation and working temperatures when
    pKa shifts with temperature. Supports calculator mode from dry reagents and stock
    dilution mode, returning acid and base masses, ionic strength estimates, optional
    NaCl adjustment, gravimetric and titration routes, and stepwise protocols. A browser
    calculator supports interactive recipe entry with shareable links; a Python library
    and command-line tool submit the same parameters to the Pepkio Tools API for scripted
    and pipeline use. Calculator arithmetic is hosted remotely; the client transmits
    parameters and returns structured recipe tables, compatibility warnings, and shareable
    run identifiers.
  documentation:
  - note: null
    type:
    - General
    url: https://www.pepkio.com/tools/ph-buffer-recipe-calculator
  - note: null
    type:
    - User manual
    url: https://github.com/pepkio/pepkio-ph-buffer-recipe-calculator
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Web calculator for bench buffer planning; Python library and CLI for API-backed
      automation of the same pH buffer recipe engine.
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output: []
  homepage: https://www.pepkio.com/tools/ph-buffer-recipe-calculator
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-06-07T00:51:37.892323Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/pepkio/pepkio-ph-buffer-recipe-calculator
  - note: null
    type:
    - Service
    url: https://www.pepkio.com/tools/ph-buffer-recipe-calculator
  - note: Python client on PyPI.
    type:
    - Other
    url: https://pypi.org/project/pepkio-ph-buffer-recipe-calculator/
  maturity: null
  name: Pepkio pH Buffer Recipe Calculator
  operatingSystem: []
  otherID: []
  owner: pepkio
  publication: []
  relation: []
  toolType:
  - Command-line tool
  - Library
  - Web application
  topic:
  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  - term: Molecular biology
    uri: http://edamontology.org/topic_3047
  - term: Laboratory techniques
    uri: http://edamontology.org/topic_3361
  validated: 0
  version:
  - 0.1.0
- accessibility: Open access
  additionDate: '2026-06-06T10:17:59.613852Z'
  biotoolsCURIE: biotools:pepkio-pcr-master-mix-calculator
  biotoolsID: pepkio-pcr-master-mix-calculator
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Pepkio
    note: Pepkio develops software tools and bioinformatics solutions for life science
      researchers, including laboratory calculators and analysis services.
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: https://www.pepkio.com/
  description: Plans PCR and qPCR master-mix reagent volumes from stock and final
    concentrations, reaction counts, and pipetting overage, with consolidated totals
    when several assays are prepared together. A browser calculator supports interactive
    recipe entry with printable bench sheets; a Python library and command-line tool
    submit the same parameters to the Pepkio Tools API for scripted and pipeline use.
    Calculator arithmetic is hosted remotely; the client transmits parameters and
    returns structured volume tables, dilution warnings, and shareable run identifiers.
  documentation:
  - note: null
    type:
    - General
    url: https://www.pepkio.com/tools/pcr-master-mix-calculator
  - note: null
    type:
    - User manual
    url: https://github.com/pepkio/pepkio-pcr-master-mix-calculator
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Web calculator for bench planning; Python library and CLI for API-backed
      automation of the same PCR master-mix engine.
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output: []
  homepage: https://www.pepkio.com/tools/pcr-master-mix-calculator
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-06-06T10:17:59.615902Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/pepkio/pepkio-pcr-master-mix-calculator
  - note: null
    type:
    - Service
    url: https://www.pepkio.com/tools/pcr-master-mix-calculator
  - note: Python client on PyPI.
    type:
    - Other
    url: https://pypi.org/project/pepkio-pcr-master-mix-calculator/
  maturity: null
  name: Pepkio PCR Master Mix Calculator
  operatingSystem: []
  otherID: []
  owner: pepkio
  publication: []
  relation: []
  toolType:
  - Web application
  - Command-line tool
  - Library
  topic:
  - term: Molecular biology
    uri: http://edamontology.org/topic_3047
  - term: Laboratory techniques
    uri: http://edamontology.org/topic_3361
  validated: 0
  version:
  - 0.1.0
- accessibility: Open access
  additionDate: '2026-06-06T09:54:43.514157Z'
  biotoolsCURIE: biotools:pepkio-molarity-solution-calculator
  biotoolsID: pepkio-molarity-solution-calculator
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Pepkio
    note: Pepkio develops software tools and bioinformatics solutions for life science
      researchers, including laboratory calculators and analysis services.
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: https://www.pepkio.com/
  description: Computes laboratory solution preparation parameters—powder mass to
    weigh, stock and diluent volumes for single dilutions, and multi-step serial concentration
    tables—with correction for hydrated salts and supplier purity. A browser calculator
    supports interactive prep planning with saved recipes and shareable links; a Python
    client and command-line tool submit the same parameters to the Pepkio Tools API
    for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client
    transmits parameters and returns structured protocol steps and shareable run identifiers.
  documentation:
  - note: null
    type:
    - General
    url: https://www.pepkio.com/tools/molarity-solution-calculator
  - note: null
    type:
    - User manual
    url: https://github.com/pepkio/pepkio-molarity-solution-calculator
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Web calculator for powder, dilution, and serial modes; Python library and
      CLI for API-backed automation of the same solution-prep engine.
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output: []
  homepage: https://www.pepkio.com/tools/molarity-solution-calculator
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-06-06T09:55:01.920855Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/pepkio/pepkio-molarity-solution-calculator
  - note: null
    type:
    - Service
    url: https://www.pepkio.com/tools/molarity-solution-calculator
  - note: Python client on PyPI.
    type:
    - Other
    url: https://pypi.org/project/pepkio-molarity-solution-calculator/
  maturity: null
  name: Pepkio Molarity Solution Calculator
  operatingSystem: []
  otherID: []
  owner: pepkio
  publication: []
  relation: []
  toolType:
  - Web application
  - Command-line tool
  - Library
  topic:
  - term: Molecular biology
    uri: http://edamontology.org/topic_3047
  - term: Laboratory techniques
    uri: http://edamontology.org/topic_3361
  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  validated: 0
  version:
  - 0.1.0
- accessibility: Open access
  additionDate: '2026-06-05T11:49:37.977245Z'
  biotoolsCURIE: biotools:pepkio-serial-dilution-planner
  biotoolsID: pepkio-serial-dilution-planner
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Pepkio
    note: Pepkio develops software tools and bioinformatics solutions for life science
      researchers, including laboratory calculators and analysis services.
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    url: https://www.pepkio.com/
  description: Plans geometric serial dilution series for molecular biology and biochemistry
    workflows, rounding transfer volumes to declared pipette ranges and optional 96-
    or 384-well plate layouts. A browser calculator supports interactive protocol
    design; a Python client and command-line tool submit the same parameters to the
    Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted
    remotely; the client transmits parameters and returns structured step tables and
    shareable run identifiers.
  documentation:
  - note: null
    type:
    - General
    url: https://www.pepkio.com/tools/serial-dilution-planner
  - note: null
    type:
    - User manual
    url: https://github.com/pepkio/pepkio-serial-dilution-planner
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Web calculator for bench planning; Python library and CLI for API-backed
      automation of the same dilution engine.
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output: []
  homepage: https://www.pepkio.com/tools/serial-dilution-planner
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-06-05T11:49:37.979211Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/pepkio/pepkio-serial-dilution-planner
  - note: null
    type:
    - Service
    url: https://www.pepkio.com/tools/serial-dilution-planner
  - note: Archived client release on Zenodo.
    type:
    - Other
    url: https://doi.org/10.5281/zenodo.20555991
  maturity: null
  name: Pepkio Serial Dilution Planner
  operatingSystem: []
  otherID:
  - type: doi
    value: doi:10.5281/zenodo.20555991
    version: 0.1.2
  owner: pepkio
  publication: []
  relation: []
  toolType:
  - Command-line tool
  - Library
  - Web application
  topic:
  - term: Molecular biology
    uri: http://edamontology.org/topic_3047
  - term: Laboratory techniques
    uri: http://edamontology.org/topic_3361
  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  validated: 0
  version:
  - 0.1.2
- accessibility: Open access
  additionDate: '2015-06-11T13:36:28Z'
  biotoolsCURIE: biotools:ega
  biotoolsID: ega
  collectionID:
  - RD-connect
  - Rare Disease
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: EMBL-EBI Databases
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: helpdesk@ega-archive.org
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: European genome-phenome Archive (EGA) - service for permanent archiving
    and sharing of all types of personally identifiable genetic and phenotypic data
    resulting from biomedical research projects.
  documentation:
  - note: null
    type:
    - General
    url: https://ega-archive.org/
  download: []
  editPermission:
    authors:
    - ELIXIR-EE
    - amy_jean
    type: group
  elixirCommunity: []
  elixirNode:
  - Spain
  elixirPlatform:
  - Data
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: EGA accession
        uri: http://edamontology.org/data_2383
      format: []
    note: null
    operation:
    - term: Deposition
      uri: http://edamontology.org/operation_3431
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    - term: Aggregation
      uri: http://edamontology.org/operation_3436
    output:
    - data:
        term: Experiment report
        uri: http://edamontology.org/data_2531
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://ega-archive.org/
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2026-06-04T08:07:27.522383Z'
  license: null
  link: []
  maturity: Mature
  name: EGA
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: EMBL-EBI_Databases
  publication:
  - doi: 10.1038/ng.3312
    metadata:
      abstract: © 2015 Nature America, Inc. All rights reserved.The European Genome-phenome
        Archive (EGA) is a permanent archive that promotes the distribution and sharing
        of genetic and phenotypic data consented for specific approved uses but not
        fully open, public distribution. The EGA follows strict protocols for information
        management, data storage, security and dissemination. Authorized access to
        the data is managed in partnership with the data-providing organizations.
        The EGA includes major reference data collections for human genetics research.
      authors:
      - name: Lappalainen I.
      - name: Almeida-King J.
      - name: Kumanduri V.
      - name: Senf A.
      - name: Spalding J.D.
      - name: Ur-Rehman S.
      - name: Saunders G.
      - name: Kandasamy J.
      - name: Caccamo M.
      - name: Leinonen R.
      - name: Vaughan B.
      - name: Laurent T.
      - name: Rowland F.
      - name: Marin-Garcia P.
      - name: Barker J.
      - name: Jokinen P.
      - name: Torres A.C.
      - name: De Argila J.R.
      - name: Llobet O.M.
      - name: Medina I.
      - name: Puy M.S.
      - name: Alberich M.
      - name: De La Torre S.
      - name: Navarro A.
      - name: Paschall J.
      - name: Flicek P.
      citationCount: 161
      date: '2015-01-01T00:00:00Z'
      journal: Nature Genetics
      title: The European Genome-phenome Archive of human data consented for biomedical
        research
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web API
  - Web application
  - Database portal
  topic:
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Laboratory information management
    uri: http://edamontology.org/topic_0607
  - term: Data security
    uri: http://edamontology.org/topic_3263
  - term: Data integration and warehousing
    uri: http://edamontology.org/topic_3366
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 1
  version: []
- 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:
    authors:
    - karin
    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: Open access
  additionDate: '2026-05-16T23:32:20.372457Z'
  biotoolsCURIE: biotools:primerpickr
  biotoolsID: primerpickr
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Primerpickr is an open-source tool for rt-PCr primer picking powered
    by the aggregation of public usage of rt-pcr primers from open source papers.
    The database is validated with 154 genes and contains over 31,000 genes across
    10 species.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: PCR primer design
      uri: http://edamontology.org/operation_0308
    output: []
  homepage: https://www.primerpickr.com
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-03T16:56:05.104311Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Repository
    url: https://www.primerpickr.com/
  maturity: null
  name: PrimerPickr
  operatingSystem: []
  otherID: []
  owner: thomas1
  publication: []
  relation: []
  toolType:
  - Web service
  topic:
  - term: PCR experiment
    uri: http://edamontology.org/topic_3519
  - term: Probes and primers
    uri: http://edamontology.org/topic_0632
  validated: 0
  version:
  - '1.1'
- accessibility: Open access
  additionDate: '2026-06-03T08:48:08.426169Z'
  biotoolsCURIE: biotools:mpa-cloud
  biotoolsID: mpa-cloud
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Kay Schallert
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Daniel Kautzner
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Benjamin J. Saalfeld
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Prof. Dr.-Ing. Robert Heyer
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ludwig Knoche
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Malte Böttcher
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: The MetaProteomeAnalyzer Cloud (MPA Cloud) is an intuitive, open-source
    tool for metaproteomics data analysis and interpretation, designed to analyse
    comprehensive metaproteomics data from tandem mass spectrometry experiments through
    a web interface.
  documentation:
  - note: null
    type:
    - User manual
    url: https://mdoa-tools.bi.denbi.de/mpacloud/documentation
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Germany
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://mdoa-tools.bi.denbi.de/mpacloud/
  homepage_status: 0
  language:
  - Java
  - TypeScript
  lastUpdate: '2026-06-03T11:12:01.769057Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.com/mdoa-group/mpa-website
  - note: null
    type:
    - Repository
    url: https://gitlab.com/mdoa-group/mpa-cloud-server
  maturity: Mature
  name: MetaProteomeAnalyzer-Cloud
  operatingSystem: []
  otherID: []
  owner: benjamin4
  publication:
  - doi: 10.1038/s41596-020-0368-7
    metadata: null
    note: null
    pmcid: null
    pmid: '32859984'
    type: []
    version: null
  - doi: 10.3389/fmicb.2019.01883
    metadata: null
    note: null
    pmcid: PMC6707425
    pmid: '31474963'
    type: []
    version: null
  - doi: 10.1021/acs.analchem.7b03544
    metadata: null
    note: null
    pmcid: PMC5757220
    pmid: '29215871'
    type: []
    version: null
  - doi: 10.1021/pr501246w
    metadata: null
    note: null
    pmcid: null
    pmid: '25660940'
    type: []
    version: null
  relation:
  - biotoolsID: metaproteomeanalyzer
    type: isNewVersionOf
  - biotoolsID: mpa_portable
    type: isNewVersionOf
  toolType:
  - Web service
  topic:
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Metaproteomics
    uri: http://edamontology.org/topic_4060
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-06-03T01:24:52.152590Z'
  biotoolsCURIE: biotools:cellseekr
  biotoolsID: cellseekr
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: contact@cellseekr.com
    fundrefid: null
    gridid: null
    name: Sandro Matosevic
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: CellSeekr is a customizable discovery platform for the exploration
    and identification of immune signatures in a variety of tumors, patient and treatment
    settings through scRNAseq data analysis.
  documentation:
  - note: null
    type:
    - User manual
    url: http://cellseekr.com/documentation
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: RNA-Seq quantification
      uri: http://edamontology.org/operation_3800
    - term: Expression profile clustering
      uri: http://edamontology.org/operation_0313
    - term: Gene-set enrichment analysis
      uri: http://edamontology.org/operation_2436
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: http://cellseekr.com
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-03T01:37:06.670611Z'
  license: null
  link: []
  maturity: null
  name: CellSeekr
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: sandro
  publication: []
  relation: []
  toolType:
  - Web service
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Allergy, clinical immunology and immunotherapeutics
    uri: http://edamontology.org/topic_3400
  - term: Immunology
    uri: http://edamontology.org/topic_0804
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-06-01T13:34:32.262833Z'
  biotoolsCURIE: biotools:flexrl
  biotoolsID: flexrl
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Kayané Robach
    note: null
    orcidid: https://orcid.org/0000-0002-5725-623X
    rorid: 05grdyy37
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://www.amsterdamumc.org/en/research/researchers/kayane-robach
  description: A Flexible Model For Record Linkage
  documentation:
  - note: null
    type:
    - API documentation
    url: https://rdrr.io/cran/FlexRL/api/
  - note: null
    type:
    - Installation instructions
    - Quick start guide
    - Training material
    - User manual
    url: https://github.com/robachowyk/FlexRL
  download:
  - note: null
    type: Source code
    url: https://github.com/robachowyk/FlexRL
    version: null
  - note: null
    type: Software package
    url: https://cran.r-project.org/package=FlexRL
    version: null
  editPermission:
    authors: []
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/robachowyk/FlexRL
  homepage_status: 0
  language:
  - C++
  - R
  lastUpdate: '2026-06-02T11:29:08.508018Z'
  license: GPL-3.0-or-later
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/robachowyk/FlexRL
  - note: null
    type:
    - Issue tracker
    url: https://github.com/robachowyk/FlexRL/issues
  - note: null
    type:
    - Helpdesk
    url: https://github.com/robachowyk/FlexRL/issues
  - note: null
    type:
    - Discussion forum
    url: https://github.com/robachowyk/FlexRL/issues
  maturity: Emerging
  name: FlexRL
  operatingSystem: []
  otherID: []
  owner: tpronk
  publication:
  - doi: 10.1093/jrsssc/qlaf016
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.48550/arXiv.2407.06835
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Data identity and mapping
    uri: http://edamontology.org/topic_3345
  validated: 0
  version:
  - 0.1.1
- accessibility: Open access
  additionDate: '2026-06-01T13:54:56.279871Z'
  biotoolsCURIE: biotools:verbex
  biotoolsID: verbex
  collectionID: []
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit: []
  description: Verbex is a private, on-device Voice-to-ELN iOS app for scientists.
    It helps researchers capture experiment notes by voice as work happens, organize
    those notes into scientific sections, and prepare clean, reviewable, ELN-ready
    scientific records.
  documentation: []
  download:
  - note: AppStore Link
    type: Other
    url: https://apps.apple.com/us/app/verbex/id6758427118
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: http://www.verbalexperiment.com
  homepage_status: 0
  language: []
  lastUpdate: '2026-06-01T14:00:54.143012Z'
  license: Proprietary
  link:
  - note: null
    type:
    - Service
    url: http://www.verbalexperiment.com
  maturity: Emerging
  name: Verbex
  operatingSystem: []
  otherID: []
  owner: verbal
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - v1.2
- accessibility: Open access (with restrictions)
  additionDate: '2026-05-31T17:35:35.101105Z'
  biotoolsCURIE: biotools:ekokrati
  biotoolsID: ekokrati
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: ekokrati computes habitat connectivity metrics (PC, IIC, EC(PC), dPC
    and its decomposition into intra-patch, flux and connector components) for habitat
    patch networks. Users upload polygon data as GeoPackage or shapefile, set species-specific
    dispersal parameters, and receive patch importance scores and landscape-level
    indices. Designed for conservation planners, landscape ecologists and environmental
    consultants. No installation required.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Ecological data
        uri: http://edamontology.org/data_3736
      format: []
    note: null
    operation:
    - term: Network analysis
      uri: http://edamontology.org/operation_3927
    output:
    - data:
        term: Ecological data
        uri: http://edamontology.org/data_3736
      format: []
    - data:
        term: Biodiversity data
        uri: http://edamontology.org/data_3707
      format: []
  homepage: https://app.ekokrati.se
  homepage_status: 0
  language: []
  lastUpdate: '2026-05-31T17:47:42.227543Z'
  license: Proprietary
  link: []
  maturity: Emerging
  name: ekokrati
  operatingSystem: []
  otherID: []
  owner: mahir
  publication: []
  relation: []
  toolType: []
  topic:
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-05-13T16:57:58.086143Z'
  biotoolsCURIE: biotools:tendna_dna_format_converter
  biotoolsID: tendna_dna_format_converter
  collectionID:
  - File Exchange
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: Tool for converting raw DNA data files between 23andMe, AncestryDNA,
    MyHeritage, and FamilyTreeDNA formats.
  documentation:
  - note: GitHub repository with source code and documentation for raw DNA format
      conversion between major consumer genomics platforms.
    type:
    - Other
    url: https://github.com/milaza/dna-raw-data-converter-23andme-myheritage-ancestry/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://tendna.com/en/dna-converter
  homepage_status: 0
  language:
  - PHP
  lastUpdate: '2026-05-29T18:45:06.363655Z'
  license: MIT
  link:
  - note: Open-source documentation and source code for the TenDNA DNA Format Converter,
      including raw DNA format guides, compatibility notes, and conversion examples
      for 23andMe, AncestryDNA, MyHeritage, and FamilyTreeDNA.
    type:
    - Repository
    url: https://github.com/milaza/dna-raw-data-converter-23andme-myheritage-ancestry/
  - note: 'The tool supports DNA file format compatibility, raw genotype data restructuring,
      and cross-platform conversion for genealogy and personal genomics workflows.


      Features include:

      - raw DNA format conversion

      - compatibility between major consumer DNA services

      - support for TSV and CSV genotype files

      - online processing without manual editing'
    type:
    - Service
    url: https://tendna.com/en/dna-converter
  maturity: Mature
  name: TenDNA DNA Format Converter
  operatingSystem:
  - Windows
  otherID:
  - type: doi
    value: doi:10.5281/zenodo.20185958
    version: 1.0.0
  owner: tendna
  publication:
  - doi: 10.5281/zenodo.20185958
    metadata: null
    note: https://doi.org/10.5281/zenodo.20185958
    pmcid: null
    pmid: null
    type: []
    version: 1.0.0
  - doi: 10.6084/m9.figshare.32493036
    metadata: null
    note: 10.6084/m9.figshare.32493036
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web service
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-05-27T22:24:31.685869Z'
  biotoolsCURIE: biotools:pathogensurveillance
  biotoolsID: pathogensurveillance
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Pathogensurveillance is a population genomics pipeline for pathogen
    identification, variant detection, and biosurveillance. The pipeline accepts paths
    to raw reads for one or more organisms and creates reports in the form of an interactive
    HTML document. Significant features include the ability to analyze unidentified
    eukaryotic and prokaryotic samples, creation of reports for multiple user-defined
    groupings of samples, automated discovery and downloading of reference assemblies
    from NCBI RefSeq, and rapid initial identification based on k-mer sketches followed
    by a more robust multi gene phylogeny and SNP-based phylogeny.
  documentation:
  - note: null
    type:
    - User manual
    url: https://nf-co.re/pathogensurveillance
  download:
  - note: null
    type: Source code
    url: https://github.com/nf-core/pathogensurveillance/archive/refs/tags/1.1.0.tar.gz
    version: 1.1.0
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://nf-co.re/pathogensurveillance/
  homepage_status: 0
  language:
  - Groovy
  - R
  - Bash
  lastUpdate: '2026-05-27T22:31:22.963863Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/nf-core/pathogensurveillance
  - note: null
    type:
    - Issue tracker
    url: https://github.com/nf-core/pathogensurveillance/issues
  maturity: Emerging
  name: pathogensurveillance
  operatingSystem:
  - Linux
  otherID: []
  owner: zachary-foster
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - 1.1.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T10:41:57.535794Z'
  biotoolsCURIE: biotools:cluster_based_harmonization
  biotoolsID: cluster_based_harmonization
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    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:
    - Developer
    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:
    - Primary contact
    - 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:
    authors:
    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: docker run --rm --cpus CPUS -v input_path:/input -v output_path:/output -v
      config_path:/config harbor.eucaim.cancerimage.eu/processing-tools/cluster_based_harmonization:1.1.0
      --config /config/config.json
    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
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
    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
  - 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:
  - Library
  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:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    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:
    - 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
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  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:
    authors:
    - 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
      true --zscore_p_low 1.0 --zscore_p_high 99.0 --denoise_method gaussian --gaussian_ksize
      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:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  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:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/2d_digital_mammography_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: 2D Digital Mammography Harmonization (EUCAIM-SW-046_T-01-03-008)
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
  - 1.1.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T10:38:08.771699Z'
  biotoolsCURIE: biotools:ct-based_neuroblastoma_tumour_detection_and_segmentation
  biotoolsID: ct-based_neuroblastoma_tumour_detection_and_segmentation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@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
    - Support
    url: null
  - email: adrian_galiana@iislafe.es
    fundrefid: null
    gridid: null
    name: Adrian Galiana-Bordera
    note: null
    orcidid: https://orcid.org/0000-0002-8324-8284
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  description: The tool performs by deep learning an automatic segmentation of the
    possible neuroblastoma tumours on Contrast Enhanced CT images (CE-CTs). Model
    architecture is Unet-based with residual operations, atrous dilation convolution
    and specific batch generator. It applies preprocessing steps as RAS conversion,
    resizing, z-score normalization, patching; and postprocessing operations. It takes
    DICOM images as input and generates tumoral masks in DICOM SEG or NIFTI formats.
  documentation:
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/GxJrJPrYBnzecqT
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=JQ0dtAE_6uc&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=37
  download: []
  editPermission:
    authors:
    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run --rm --gpus all \\\n\t-v /path/to/input:/input \\\n\t-v /path/to/output:/output\
      \ \\\n\tharbor.eucaim.cancerimage.eu/processing-tools/ct-based_neuroblastoma_tumour_detection_and_segmentation:2.0.0\
      \ \\\n\t--series_csv /output/config/series_to_segment.csv \\\n\t--output_dir\
      \ /output"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    - 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: 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/ct-based_neuroblastoma_tumour_detection_and_segmentation/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:20:51.076833Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ct-based_neuroblastoma_tumour_detection_and_segmentation/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: CT-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-022_T-01-02-005)
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: casopon
  publication:
  - doi: 10.3390/app11083508
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Usage
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - 2.0.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T12:09:16.704255Z'
  biotoolsCURIE: biotools:mr-based_glioblastoma_tumour_detection_and_segmentation
  biotoolsID: mr-based_glioblastoma_tumour_detection_and_segmentation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: maria_beser@iislafe.es
    fundrefid: null
    gridid: null
    name: Maria Beser-Robles
    note: null
    orcidid: https://orcid.org/0000-0002-0072-5525
    rorid: null
    typeEntity: Person
    typeRole:
    - 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
    - Developer
    - Support
    url: null
  - email: adrian_galiana@iislafe.es
    fundrefid: null
    gridid: null
    name: Adrian Galiana-Bordera
    note: null
    orcidid: https://orcid.org/0000-0002-8324-8284
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: 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:
    - Provider
    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 an automatic segmentation of the possible glioblastoma
    tumours on MRI images and its subregions: necrosis (Intratumoral necrotic core),
    edema (Peritumoral vasogenic edema), enhancing (Contrast-enhancing tumor region),
    total (Total tumor including edema and necrosis by a single model) and total-fused
    (Total tumor fusioning of necrosis+edema+enhancing). It applies preprocessing
    steps as skull stripping, intra-patient registration, z-score normalization, patching,
    among others. It takes DICOM images as input and generates tumoral masks in DICOM
    SEG or NIFTI formats.'
  documentation:
  - note: null
    type:
    - General
    url: https://pubmed.ncbi.nlm.nih.gov/38849632/
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/otrYTickHjDxnkP
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=8_OJPTQUKAw&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=22
  download: []
  editPermission:
    authors:
    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input \\\n  -v /path/to/output:/output\
      \ \\\n  harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest\
      \ \\\n  --series-selector /input/config/series.csv \\\n  --target total \\\n\
      \  --emit-config true"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    - 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: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input \\\n  -v /path/to/output:/output\
      \ \\\n  harbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest\
      \ \\\n  --series-list '[{\"dataset_id\":\"DS001\",\"patient_id\":\"PAT001\"\
      ,\"study_id\":\"ST001\",\"series_path\":\"/input/DICOM/DS001/PAT001/ST001/T1_POST\"\
      }]' \\\n  --target total-fused \\\n  --emit-config true"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    - 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: 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/mr-based_glioblastoma_tumour_detection_and_segmentation/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:20:39.690457Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_glioblastoma_tumour_detection_and_segmentation/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 glioblastoma tumour detection and segmentation (EUCAIM-SW-021_T-01-02-004)
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: casopon
  publication:
  - doi: 10.1007/s11548-024-03205-z
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - 2.1.1
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-29T09:19:51.404419Z'
  biotoolsCURIE: biotools:mr-based_dipg_tumour_detection_and_segmentation
  biotoolsID: mr-based_dipg_tumour_detection_and_segmentation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: matias_fernandez@iislafe.es
    fundrefid: null
    gridid: null
    name: Matias Fernandez-Paton
    note: null
    orcidid: https://orcid.org/0000-0001-9374-1411
    rorid: null
    typeEntity: Person
    typeRole:
    - 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
    - Developer
    - Documentor
    - Support
    url: null
  - email: adrian_galiana@iislafe.es
    fundrefid: null
    gridid: null
    name: Adrian Galiana-Bordera
    note: null
    orcidid: https://orcid.org/0000-0002-8324-8284
    rorid: null
    typeEntity: Person
    typeRole:
    - 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:
    - Documentor
    - Support
    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
    gridid: null
    name: Leonor Cerda-Alberich
    note: null
    orcidid: https://orcid.org/0000-0002-5567-4278
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    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 an automatic segmentation of the possible DIPG tumours
    on MR images. DIPG (Diffuse Intrinsic Pontine Glioma), or more recently, DMG (Diffuse
    Midline Glioma) is a H3 K27M–mutant pediatric brainstem cancer detected in T1W
    and Flair/T2-weighted magnetic resonance images. The tool includes a complete
    workflow from DICOM images to DICOM seg tumoral masks.
  documentation:
  - note: null
    type:
    - General
    url: https://link.springer.com/article/10.1007/s10278-025-01557-9
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/5CL2H8tyMDzFHex
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=f3DPS56z6oI&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=36
  download: []
  editPermission:
    authors:
    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input \\\n  -v /path/to/output:/output\
      \ \\\nharbor.eucaim.cancerimage.eu/processing-tools/mr-based_glioblastoma_tumour_detection_and_segmentation:latest\
      \ \\\n  --series-selector /input/config/series.csv"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
  - cmd: "docker run --rm --gpus all \\\n  -v /path/to/input:/input -v /path/to/output:/output\
      \ harbor.eucaim.cancerimage.eu/processing-tools/mr-based_dipg_tumour_detection_and_segmentation:latest\
      \ \\\n  --json-args '{\"dataset_id\":\"DS1\",\"patient_id\":\"P1\",\"study_id\"\
      :\"S1\",\"sequences\":{\"T1w\":\"/input/DICOM/DS1/P1/S1/T1\",\"FLAIR\":\"/input/DICOM/DS1/P1/S1/FLAIR\"\
      }}'"
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    note: null
    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
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_tumour_detection_and_segmentation/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:20:21.739269Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr-based_dipg_tumour_detection_and_segmentation/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 DIPG tumour detection and segmentation (EUCAIM-SW-020_T-01-02-003)
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: casopon
  publication:
  - doi: 10.1007/s10278-025-01557-9
    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: '2025-05-29T09:08:44.174795Z'
  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: eucaim_project@iislafe.es
    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: DICOM format
        uri: http://edamontology.org/format_3548
      - term: nii
        uri: http://edamontology.org/format_3549
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: 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/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
    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: '2025-11-25T09:58:37.569343Z'
  biotoolsCURIE: biotools:ml_model_for_mr_series_categorisation
  biotoolsID: ml_model_for_mr_series_categorisation
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: armago@alumni.uv.es
    fundrefid: null
    gridid: null
    name: Armando Gomis-Maya
    note: null
    orcidid: https://orcid.org/0000-0002-9527-8093
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: pedromiguel_martinez@iislafe.es
    fundrefid: null
    gridid: null
    name: Pedro-Miguel Martinez-Girones
    note: null
    orcidid: https://orcid.org/0000-0002-9506-9451
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: leonor_cerda@iislafe.es
    fundrefid: null
    gridid: null
    name: Leonor Cerda-Alberich
    note: null
    orcidid: https://orcid.org/0000-0002-5567-4278
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: luis_marti@iislafe.es
    fundrefid: null
    gridid: null
    name: Luis Marti-Bonmati
    note: null
    orcidid: https://orcid.org/0000-0002-8234-010X
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: A tool based on artificial intelligence that is able to perform a categorisation
    of MRI series by using standardized DICOM tags. The categorisation includes the
    type of sequence (e.g. spin echo, gradient echo), the weighting (e.g. T1W, T2W,
    DCE, ...), the presence of fat suppression and the detection of non-relevant /
    junk series (e.g. localizers, calibrations, screenshots...).
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/rpm56rD5FfXAHyb
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/8r3CzyQXrd7ERFp
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=gudDCiuJIf8&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=11
  download: []
  editPermission:
    authors:
    - casopon
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "docker run -it --rm --name my-container \\\n  -v \"<input_path>:/input\"\
      \ \\\n  -v \"<output_path>:/output\" \\\n  harbor.eucaim.cancerimage.eu/processing-tools/ml_model_for_mr_series_categorisation:<version>\
      \ \\\n  --config-string \"{'output_name': 'classification_results.json'}\""
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Classification
      uri: http://edamontology.org/operation_2990
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:19:08.404060Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/ml_model_for_mr_series_categorisation/artifacts-tab
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/grupo-de-investigaci%C3%B3n-biom%C3%A9dica-en-imagen/
  maturity: Mature
  name: ML model for MR series categorisation (EUCAIM-SW-011_T-01-01-011)
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: pedromiguel_martinez_HULAFE
  publication:
  - doi: 10.1186/s40537-025-01086-w
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  - term: Data acquisition
    uri: http://edamontology.org/topic_3077
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
  - 1.1.0
- accessibility: Open access (with restrictions)
  additionDate: '2025-11-21T13:49:36.578343Z'
  biotoolsCURIE: biotools:time_coherence_tool
  biotoolsID: time_coherence_tool
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: eucaim_project@iislafe.es
    fundrefid: null
    gridid: null
    name: GIBI230 - HULAFE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    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: 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:
    - Developer
    - Support
    url: null
  - email: carina_soler@iislafe.es
    fundrefid: null
    gridid: null
    name: Carina Soler-Pons
    note: null
    orcidid: https://orcid.org/0009-0000-2991-1391
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  description: "Tool that aims to validate visually the chronological order and logical\
    \ consistency of dates associated with a patient's medical history. It generates\
    \ a timeline visualization for each patient from an Excel file and highlights\
    \ rule violations.\n \nStatus : Containerized"
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/M23wDa4RWXenzxX
  - note: null
    type:
    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/9QbdWjnLBeMYSWR
  - note: null
    type:
    - Training material
    url: https://www.youtube.com/watch?v=j4J_UPQqYR4&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=10
  download: []
  editPermission:
    authors:
    - pedromiguel_martinez_HULAFE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: 'docker run -it --rm --name my-container -v "<input_path>:/input" -v "<output_path>:/output"
      harbor.eucaim.cancerimage.eu/processing-tools/time_coherence_tool:2.1.0 --config-string
      "{''data_file'': ''my_data.xlsx'', ''generate_pdf'': ''true''}"'
    input:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
    note: null
    operation:
    - term: Data analysis
      uri: http://edamontology.org/operation_2945
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: SVG
        uri: http://edamontology.org/format_3604
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/time_coherence_tool/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-27T15:18:38.027942Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/time_coherence_tool/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: Time Coherence Tool (EUCAIM-SW-001_T-01-01-001)
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: casopon
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  validated: 0
  version:
  - 1.1.0
- 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: eucaim_project@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: 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: '2023-06-14T13:47:49.064543Z'
  biotoolsCURIE: biotools:virtual_imaging_platform
  biotoolsID: virtual_imaging_platform
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: VIP is a web portal for medical imaging applications. It allows users
    to access scientific applications as a service (directly through the web browser
    with no installation required), as well as distributed computing resources in
    a transparent manner. It exploits the resources available in the biomed virtual
    organization of the EGI e-infrastructure to offer an open service to researchers
    worldwide.
  documentation:
  - note: null
    type:
    - Other
    url: https://github.com/virtual-imaging-platform/VIP-portal/wiki
  download:
  - note: null
    type: Source code
    url: https://github.com/virtual-imaging-platform/
    version: 3.0.1
  - note: VIP Docker image for development or testing (NOT for production)
    type: Container file
    url: https://hub.docker.com/layers/viplatform/vip-portal/4.6.1/images/sha256-5d47d27c3e285dec287506e2b3c436b343e2c1f92818b7c2cbf39afaed46fbb5
    version: 4.6.1
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: Binary format
        uri: http://edamontology.org/format_2333
    note: null
    operation:
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    output: []
  homepage: https://vip.creatis.insa-lyon.fr
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2026-05-27T07:35:36.149770Z'
  license: CECILL-B
  link:
  - note: null
    type:
    - Service
    url: https://vip.creatis.insa-lyon.fr/
  maturity: Mature
  name: Virtual Imaging Platform
  operatingSystem: []
  otherID: []
  owner: sorina.pop
  publication:
  - doi: 10.1109/tmi.2012.2220154
    metadata: null
    note: null
    pmcid: null
    pmid: '23014715'
    type: []
    version: null
  relation: []
  toolType:
  - Bioinformatics portal
  topic: []
  validated: 0
  version:
  - 3.0.1
  - 4.6.1
- 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:
    - Provider
    url: http://www.nib.si/
  - email: carissarobyn.bleker@nib.si
    fundrefid: null
    gridid: null
    name: Carissa Bleker
    note: null
    orcidid: https://orcid.org/0000-0003-1617-7145
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Kristina Gruden
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Živa Ramšak
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Vid Podpečan
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    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
  - Systems Biology
  elixirNode:
  - Slovenia
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    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:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output:
    - data:
        term: Mathematical model
        uri: http://edamontology.org/data_0950
      format:
      - term: SBML
        uri: http://edamontology.org/format_2585
      - 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:
    - Primary
    version: null
  relation:
  - biotoolsID: gomapman
    type: uses
  - biotoolsID: newt-ve
    type: uses
  toolType:
  - Database portal
  - Web application
  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 (with restrictions)
  additionDate: '2025-05-28T23:59:16.112917Z'
  biotoolsCURIE: biotools:dicom-seg_annotation
  biotoolsID: dicom-seg_annotation
  collectionID:
  - eucaim
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: This module provides a command line tool to validate DICOM SEG files
    against predefined requirements specified in an Excel file. It contains components
    for finding relevant DICOM files, loading and parsing validation requests and
    applying validation rules. The main validation process checks each DICOM file
    for compliance with the Type 1, 1C, 2, 2C and 3 attributes specified in the requirements
    file. A detailed report is generated highlighting issues such as missing, invalid
    or conditionally required attributes, including file paths and affected DICOM
    tags. The tool is designed to ensure data integrity and compliance with DICOM
    standards.
  documentation:
  - note: null
    type:
    - General
    url: https://drive.eucaim.cancerimage.eu/s/i4D6iMeBCxxHGXz
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/PgS6HJ5pBTk8THW
  download: []
  editPermission:
    authors:
    - authEucaim
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.med.auth.gr/en/content/laboratory-computing-medical-informatics-and-biomedical-imaging-technologies
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-21T11:59:37.802307Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/annotation_tool/info-tab
  maturity: Mature
  name: DICOM-SEG Annotation
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: difoto
  publication: []
  relation:
  - biotoolsID: data_integration_quality_check_tool_diqct
    type: includedIn
  toolType:
  - Desktop application
  - Command-line tool
  topic:
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 0
  version:
  - '0.1'
- accessibility: Open access
  additionDate: '2026-05-19T08:10:59.066569Z'
  biotoolsCURIE: biotools:jcvi
  biotoolsID: jcvi
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: tanghaibao@gmail.com
    fundrefid: null
    gridid: null
    name: Haibao Tang
    note: null
    orcidid: https://orcid.org/0000-0002-3460-8570
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: tanger_009@163.com
    fundrefid: null
    gridid: null
    name: Xingtan Zhang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: JCVI is a versatile toolkit for comparative genomics analysis. It is
    a collection of Python libraries to parse bioinformatics files, or perform computation
    related to assembly, annotation, and comparative genomics.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/tanghaibao/jcvi/wiki
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://github.com/tanghaibao/jcvi
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-21T09:01:41.228891Z'
  license: BSD-2-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://pypi.org/project/jcvi
  maturity: null
  name: JCVI
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: anitamnd
  publication:
  - doi: 10.1002/IMT2.211
    metadata: null
    note: null
    pmcid: PMC11316928
    pmid: '39135687'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2019-11-14T19:27:27Z'
  biotoolsCURIE: biotools:PolySTest
  biotoolsID: PolySTest
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: Robust statistical testing of quantitative proteomics data. The tool
    comprises and combines different tests and includes a new method for combined
    statistics of quantitative and missing values.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode:
  - Denmark
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Statistical modelling
      uri: http://edamontology.org/operation_3664
    - term: Differential protein expression profiling
      uri: http://edamontology.org/operation_3741
    output:
    - data:
        term: Q-value
        uri: http://edamontology.org/data_3932
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: P-value
        uri: http://edamontology.org/data_1669
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Heat map
        uri: http://edamontology.org/data_1636
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Histogram
        uri: http://edamontology.org/data_3905
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Gene expression profile
        uri: http://edamontology.org/data_0928
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: http://computproteomics.bmb.sdu.dk/app_direct/PolySTest
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-05-21T08:49:15.617162Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/computproteomics/PolySTest
  maturity: Mature
  name: PolySTest
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: veitveit11
  publication:
  - doi: 10.1074/mcp.RA119.001777
    metadata:
      abstract: ''
      authors: []
      citationCount: 26
      date: '2020-08-01T00:00:00Z'
      journal: Molecular and Cellular Proteomics
      title: 'PolySTest: Robust statistical testing of proteomics data with missing
        values improves detection of biologically relevant features'
    note: null
    pmcid: PMC8015005
    pmid: '32424025'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  validated: 1
  version: []
- accessibility: Open access (with restrictions)
  additionDate: '2025-05-28T23:55:08.439649Z'
  biotoolsCURIE: biotools:dicom_image_similarity-duplicate_checker
  biotoolsID: dicom_image_similarity-duplicate_checker
  collectionID:
  - eucaim
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'Automatically detects duplicate and near-duplicate DICOM image series
    in large medical imaging datasets. Uses a tiered pipeline combining DICOM metadata
    analysis, SHA-based pixel hashing, and image similarity metrics (SSIM, cosine,
    MAD) to identify exact copies, re-exported series, and near-identical acquisitions.
    All findings are reported for human expert review — no files are modified or deleted
    automatically.


    For scenarios requiring strict, image-level deduplication based on pixel content,
    fully agnostic to metadata changes, consider using [https://bio.tools/image_duplicate_check_tool]'
  documentation:
  - note: null
    type:
    - General
    url: https://drive.eucaim.cancerimage.eu/s/pELEgMjZL4xMWe3
  - note: null
    type:
    - User manual
    url: https://drive.eucaim.cancerimage.eu/s/ZxwyR5GTbSWSYjo
  download: []
  editPermission:
    authors:
    - authEucaim
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.med.auth.gr/en/content/laboratory-computing-medical-informatics-and-biomedical-imaging-technologies
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-21T00:27:06.913860Z'
  license: Apache-2.0
  link:
  - note: Link to the Harbor image
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/deduplication_tool/info-tab
  maturity: Mature
  name: Image Duplicates Checker
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: difoto
  publication: []
  relation:
  - biotoolsID: data_integration_quality_check_tool_diqct
    type: includedIn
  toolType:
  - Command-line tool
  topic:
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 0
  version:
  - '2.0'
- accessibility: Open access
  additionDate: '2026-05-19T13:51:52.767136Z'
  biotoolsCURIE: biotools:minigraph
  biotoolsID: minigraph
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: Minigraph is a sequence-to-graph mapper and graph constructor. For
    graph generation, it aligns a query sequence against a sequence graph and incrementally
    augments an existing graph with long query subsequences diverged from the graph.
  documentation:
  - note: null
    type:
    - General
    url: https://lh3.github.io/minigraph/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Alignment
      uri: http://edamontology.org/operation_2928
    output: []
  homepage: https://github.com/lh3/minigraph
  homepage_status: 0
  language:
  - C
  - JavaScript
  lastUpdate: '2026-05-20T09:16:39.920961Z'
  license: MIT
  link: []
  maturity: null
  name: minigraph
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: anitamnd
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-05-20T08:59:02.212508Z'
  biotoolsCURIE: biotools:snp-sites
  biotoolsID: snp-sites
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Finds SNP sites from a multi-FASTA alignment file.
  documentation:
  - note: null
    type:
    - General
    url: https://sanger-pathogens.github.io/snp-sites/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: 'snp-sites my_alignment.aln

      snp-sites my_gzipped_alignment.aln.gz'
    input:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: Relaxed PHYLIP Sequential
        uri: http://edamontology.org/format_3820
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: VCF
        uri: http://edamontology.org/format_3016
    note: null
    operation:
    - term: SNP detection
      uri: http://edamontology.org/operation_0484
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: Relaxed PHYLIP Sequential
        uri: http://edamontology.org/format_3820
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: https://sanger-pathogens.github.io/snp-sites/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-05-20T08:59:02.214591Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/sanger-pathogens/snp-sites
  maturity: null
  name: SNP-sites
  operatingSystem:
  - Linux
  otherID: []
  owner: aniehues
  publication:
  - doi: 10.1099/mgen.0.000056
    metadata: null
    note: null
    pmcid: PMC5320690
    pmid: '28348851'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  validated: 0
  version:
  - 2.5.1
- accessibility: Open access
  additionDate: '2026-05-19T21:38:22.336113Z'
  biotoolsCURIE: biotools:parsesnp21-26
  biotoolsID: parsesnp21-26
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: A small <720Kb C++ windows utility. That allows you to load  Ancestry,
    23andMe, FTDNA, or Genes for Good RAW DNA files search them, merge them. covert
    them to Ancestry format. But also create files from peer reviewed publications
    to compare with you loaded data to give your genetic disposition for the condition
    you have entered the data for an statistical risk if OR values are included. Included
    with the program are example files for Type 2 Diabetes risk factors. (As I have
    type 2 Diabetes so I could test the results).
  documentation:
  - note: pdf user manual
    type:
    - User manual
    url: https://raw.githubusercontent.com/BritRobin/ParseSNP/master/ParseSNP_Manual.pdf
  download:
  - note: Windows x64 or x86 installer
    type: Software package
    url: https://britrobin.github.io/ParseSNP/
    version: 1.1.1
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://britrobin.github.io/ParseSNP/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-05-20T00:58:03.254713Z'
  license: GPL-3.0
  link:
  - note: Git page for easy installer and pdf manual  download
    type:
    - Other
    url: https://britrobin.github.io/ParseSNP/
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/BritRobin/ParseSNP
  maturity: Emerging
  name: ParseSNP
  operatingSystem:
  - Windows
  otherID: []
  owner: RobinTaylor
  publication: []
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Personalised medicine
    uri: http://edamontology.org/topic_3577
  validated: 0
  version:
  - 1.1.1
- accessibility: Open access
  additionDate: '2026-05-20T00:15:17.437872Z'
  biotoolsCURIE: biotools:compucell3d
  biotoolsID: compucell3d
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: CompuCell3D is a multiscale multicellular virtual tissue modeling and
    simulation environment. CompuCell3D is written in C++ and provides Python bindings
    for model and simulation development in Python.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://compucell3d.org/
  - note: null
    type:
    - Training material
    url: https://compucell3d.org/Tutorials
  - note: null
    type:
    - Citation instructions
    url: https://compucell3d.org/Publications
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output: []
  homepage: https://compucell3d.org/SrcBin
  homepage_status: 0
  language:
  - Python
  - C++
  lastUpdate: '2026-05-20T00:31:43.306086Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://compucell3d.org/SrcBin
  - note: null
    type:
    - Discussion forum
    url: https://www.reddit.com/r/CompuCell3D/
  maturity: Mature
  name: CompuCell3D
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: VKasalica
  publication:
  - doi: 10.1016/b978-0-12-388403-9.00013-8
    metadata: null
    note: null
    pmcid: PMC3612985
    pmid: '22482955'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  validated: 0
  version:
  - 4.8.0
- accessibility: Open access
  additionDate: '2026-05-20T00:01:38.156396Z'
  biotoolsCURIE: biotools:nuclearphaser
  biotoolsID: nuclearphaser
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Jana Sperschneider
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://github.com/JanaSperschneider
  description: NuclearPhaser is a method for phasing of dikaryotic genomes into the
    two haplotypes using Hi-C contact graphs. This is an overview of the phasing pipeline
    for dikaryons.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://github.com/JanaSperschneider/NuclearPhaser/blob/main/README.md
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output: []
  homepage: https://github.com/JanaSperschneider/NuclearPhaser
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-20T00:10:43.605604Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/JanaSperschneider/NuclearPhaser
  maturity: Emerging
  name: NuclearPhaser
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: VKasalica
  publication: []
  relation: []
  toolType:
  - Script
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - '1.1'
- accessibility: Open access
  additionDate: '2026-05-19T23:23:06.270637Z'
  biotoolsCURIE: biotools:sam2interval
  biotoolsID: sam2interval
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A Python script that converts positional information from a SAM dataset
    into interval format with 0-based start and 1-based end. CIGAR string of SAM format
    is used to compute the end coordinate.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Galaxy
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
  homepage: https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-19T23:35:39.572272Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval
  maturity: Emerging
  name: sam2interval
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: VKasalica
  publication: []
  relation: []
  toolType:
  - Script
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version: []
- accessibility: Open access (with restrictions)
  additionDate: '2026-05-19T23:05:52.974836Z'
  biotoolsCURIE: biotools:miniconda
  biotoolsID: miniconda
  collectionID: []
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit: []
  description: Miniconda is a minimal Python distribution that includes the Conda
    package and environment manager plus only essential dependencies. It provides
    a lightweight way to create isolated environments and install Python packages
    as needed, without the large preinstalled package set of Anaconda.
  documentation:
  - note: null
    type:
    - General
    url: https://www.anaconda.com/docs/getting-started/miniconda/main
  download:
  - note: null
    type: Downloads page
    url: https://www.anaconda.com/download/success
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Service management
      uri: http://edamontology.org/operation_3760
    output: []
  homepage: https://www.anaconda.com/docs/getting-started/miniconda/main
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-19T23:18:02.374272Z'
  license: Proprietary
  link: []
  maturity: Mature
  name: miniconda
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: VKasalica
  publication: []
  relation: []
  toolType:
  - Suite
  - Command-line tool
  topic:
  - term: Software management
    uri: http://edamontology.org/topic_4047
  validated: 0
  version:
  - '26.3'
- accessibility: Open access (with restrictions)
  additionDate: '2025-04-24T13:00:12.867477Z'
  biotoolsCURIE: biotools:eetl_toolset
  biotoolsID: eetl_toolset
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'Modular toolchain for an extensible and customizable ETL pipeline
    that extracts, transforms, and loads clinical data and medical imaging metadata,
    applying dataset-specific mappings to generate outputs compatible with the EUCAIM
    Common Data Model (CDM). Its design aims to minimize manual data preparation efforts
    and facilitate customization and integration with other components, such as data
    quality assurance tools.

    Containerized, currently supports input datasets in CSV, JSON, XLSX.'
  documentation:
  - note: Tool documentation (updated)
    type:
    - General
    url: https://drive.eucaim.cancerimage.eu/s/zXE4xYDm3x3CWtQ
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Spain
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data formatting
      uri: http://edamontology.org/operation_0335
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data deposition
      uri: http://edamontology.org/operation_3431
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output: []
  homepage: https://github.com/EUCAIM/etl-toolset/
  homepage_status: 0
  language:
  - Python
  - Java
  lastUpdate: '2026-05-19T13:29:43.470985Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/EUCAIM/etl-toolset/
  maturity: Emerging
  name: EUCAIM ETL toolset
  operatingSystem:
  - Windows
  - Linux
  otherID: []
  owner: victorsp
  publication: []
  relation:
  - biotoolsID: tabular_data_curator
    type: uses
  toolType:
  - Workflow
  - Library
  topic:
  - term: Data identity and mapping
    uri: http://edamontology.org/topic_3345
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  validated: 0
  version:
  - 0.1.1
  - 0.1.2
  - 0.2.1
- accessibility: Open access
  additionDate: '2026-05-19T10:52:40.251441Z'
  biotoolsCURIE: biotools:alphafind_v2
  biotoolsID: alphafind_v2
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'AlphaFind v2 is a tool for fast, structure‑based search for protein
    structures against the AlphaFold DB (https://alphafold.ebi.ac.uk/) and TED DB
    (https://ted.cathdb.info/). The tool uses protein‑level embeddings to provide
    a rapid pre‑filter, with top candidates undergoing TM-Score, RMSD and residue‑level
    alignments computations. Four complementary search modes are available: (i) whole‑chain
    search, (ii) pLDDT‑aware search that restricts similarity to high‑confidence regions,
    (iii) domain search against the TED database, and (iv) multidomain search that
    combines several chain‑level matches into a single score. Users can restrict queries
    to a given organism, CATH superfamily or to proteins with experimental structures,
    and submit queries by UniProt/AlphaFold identifier. Results comprise a ranked
    list with similarity metrics, rich metadata and an interactive 3‑D superposition
    view. The service is freely accessible at https://alphafind.ics.muni.cz/.'
  documentation:
  - note: null
    type:
    - User manual
    url: https://alphafind.ics.muni.cz/manual
  download: []
  editPermission:
    authors: []
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Czech Republic
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format: []
    note: null
    operation:
    - term: Structural similarity search
      uri: http://edamontology.org/operation_0360
    output:
    - data:
        term: Structure similarity score
        uri: http://edamontology.org/data_0888
      format: []
  homepage: https://alphafind.ics.muni.cz/
  homepage_status: 0
  language: []
  lastUpdate: '2026-05-19T10:52:40.254162Z'
  license: null
  link:
  - note: null
    type:
    - Service
    url: https://alphafind.ics.muni.cz/
  maturity: Mature
  name: AlphaFind v2
  operatingSystem: []
  otherID: []
  owner: tslaninakova2
  publication:
  - doi: 10.1093/nar/gkag372
    metadata: null
    note: null
    pmcid: null
    pmid: '42028635'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: alphafind
    type: isNewVersionOf
  toolType:
  - Web application
  topic:
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-05-19T08:03:00.359212Z'
  biotoolsCURIE: biotools:circlator
  biotoolsID: circlator
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: mh12@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Martin Hunt
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Circlator is a tool to circularize genome assemblies. It will attempt
    to identify each circular sequence and output a linearised version of it. It does
    this by assembling all reads that map to contig ends and comparing the resulting
    contigs with the input assembly.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: Mapping assembly
      uri: http://edamontology.org/operation_0523
    output: []
  homepage: https://sanger-pathogens.github.io/circlator/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-19T08:04:05.768954Z'
  license: GD
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/sanger-pathogens/circlator
  maturity: Mature
  name: Circlator
  operatingSystem: []
  otherID: []
  owner: anitamnd
  publication:
  - doi: 10.1186/S13059-015-0849-0
    metadata: null
    note: null
    pmcid: PMC4699355
    pmid: '26714481'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-05-18T13:53:39.264896Z'
  biotoolsCURIE: biotools:gonetview
  biotoolsID: gonetview
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: jonas.marx3007@gmx.de
    fundrefid: null
    gridid: null
    name: Jonas Marx
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    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
  - note: null
    type:
    - User manual
    url: https://github.com/JonasMarx3007/GONetView/blob/main/docs/tutorial.md
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: GO concept ID
        uri: http://edamontology.org/data_1176
      format: []
    note: null
    operation:
    - term: Ontology visualisation
      uri: http://edamontology.org/operation_3559
    output:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PNG
        uri: http://edamontology.org/format_3603
  - cmd: null
    input:
    - data:
        term: Gene symbol
        uri: http://edamontology.org/data_1026
      format: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    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:
  - doi: 10.5281/zenodo.20271711
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: 0.1.0
  relation: []
  toolType:
  - Web application
  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
- accessibility: Open access
  additionDate: '2026-05-04T12:46:22.951830Z'
  biotoolsCURIE: biotools:dash_app_to_automate_metabolomics_data_analyses
  biotoolsID: dash_app_to_automate_metabolomics_data_analyses
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: An interactive platform that performs statistical analyses on metabolomics
    datasets and allows visualising results with ease. The interface gives users autonomy
    in creating figures suited to their reporting and publication needs.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/EdinOmics/A-Python-Dash-App-and-cPanel-workflow-to-automate-metabolomics-data-analyses-and-visualisation
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/EdinOmics/A-Python-Dash-App-and-cPanel-workflow-to-automate-metabolomics-data-analyses-and-visualisation
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-18T13:04:56.309902Z'
  license: CC-BY-4.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/EdinOmics/A-Python-Dash-App-and-cPanel-workflow-to-automate-metabolomics-data-analyses-and-visualisation
  maturity: Mature
  name: EdinOmics Dash App
  operatingSystem: []
  otherID: []
  owner: edinomics
  publication: []
  relation: []
  toolType:
  - Script
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Biosciences
    uri: http://edamontology.org/topic_4019
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-05-15T07:07:20.488935Z'
  biotoolsCURIE: biotools:open_neuroscience_graph
  biotoolsID: open_neuroscience_graph
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: stephen.whitmarsh@icm-institute.org
    fundrefid: null
    gridid: null
    name: Stephen Whitmarsh
    note: null
    orcidid: https://orcid.org/0000-0002-3969-6565
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://stephenwhitmarsh.com
  description: 'The Open Neuroscience Graph (openneuroscience.org) is an open-access,
    curated knowledge graph that maps the open science ecosystem in neuroscience as
    a browsable digital garden. Built from an Obsidian vault and published as a static
    website using Quartz, the project replaces traditional linear presentation with
    a networked structure of interlinked Markdown notes. Bidirectional links, full-text
    search, and an integrated graph visualization allow users to navigate thematic
    relationships dynamically rather than sequentially. The complete source material
    is openly available to sustain, replicate and extend the resource, includding
    all Markdown content, media attachments, Quartz configuration files, and site
    customizations. Researchers, educators, and open-science practitioners may explore
    the site directly, download the vault for offline use in Obsidian, or fork the
    material to build new, derivative knowledge bases.


    PID=https://doi.org/10.5281/zenodo.20181900'
  documentation:
  - note: null
    type:
    - Contributions policy
    url: https://gitlab.com/icm-institute/dac/opensciencegraph/-/blob/main/CONTRIBUTING.md?ref_type=heads
  download:
  - note: null
    type: Source code
    url: https://gitlab.com/icm-institute/dac/opensciencegraph
    version: 1.0.0
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - France
  elixirPlatform:
  - Training
  elixir_badge: 0
  function: []
  homepage: https://openneuroscience.org
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2026-05-15T07:07:30.968578Z'
  license: CC-BY-4.0
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.com/icm-institute/dac/opensciencegraph
  maturity: Emerging
  name: Open Neuroscience Graph
  operatingSystem:
  - Windows
  - iOS
  - Android
  - Linux
  - Mac
  otherID:
  - type: doi
    value: doi:10.5281/zenodo.20181900
    version: 1.0.0
  owner: stephen
  publication:
  - doi: 10.5281/zenodo.20181900
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: 1.0.0
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Biosciences
    uri: http://edamontology.org/topic_4019
  validated: 0
  version:
  - 1.0.0
- accessibility: Open access
  additionDate: '2025-10-15T07:25:34.085350Z'
  biotoolsCURIE: biotools:image_quality_assessment_metrics_iqa_for_xnat_platform
  biotoolsID: image_quality_assessment_metrics_iqa_for_xnat_platform
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: ferielromdhane@yahoo.fr
    fundrefid: null
    gridid: null
    name: Feriel Romdhane
    note: null
    orcidid: https://orcid.org/0000-0002-5854-9341
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: preclinicaldata@eurobioimaging.eu
    fundrefid: null
    gridid: null
    name: Euro-BioImaging ERIC
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://www.eurobioimaging.eu/
  - email: null
    fundrefid: null
    gridid: null
    name: National Research Council
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://www.ibb.cnr.it/
  description: Docker images developped at the Euro-BioImaging MED-Hub  and National
    Research Council (CNR) for the XNAT platform hosted by University of Turin. A
    suite of four Image Quality Assessment (IQA) metrics designed to evaluate the
    perceptual quality of preclinical and clinical image datasets within the XNAT
    platform at the scan and subject levels. The tool outputs Excel files containing
    the mean and median for each metric and scan, as well as PNG files with corresponding
    histogram plots.
  documentation:
  - note: null
    type:
    - General
    url: https://drive.eucaim.cancerimage.eu/s/Q7x86RTMiZJdq97
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
  homepage: https://github.com/FerielRamdhane/Image-Quality-Assessment-metrics-IQA-for-XNAT-platform
  homepage_status: 0
  language:
  - Python
  - MATLAB
  lastUpdate: '2026-05-13T08:27:23.849695Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/iqaxnat_scan/info-tab
  maturity: null
  name: Image Quality Assessment metrics  (IQA) for XNAT platform
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Feriel
  publication: []
  relation: []
  toolType:
  - Script
  - Command-line tool
  topic:
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2023-07-13T08:14:40.190855Z'
  biotoolsCURIE: biotools:nlmced_filter
  biotoolsID: nlmced_filter
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: ferielromdhane@yahoo.fr
    fundrefid: null
    gridid: null
    name: Feriel Romdhane
    note: null
    orcidid: https://orcid.org/0000-0002-5854-9341
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: The NLmCED (Non Local mean Coherence Enhancing Diffusion) filter is
    a denoising tool aimed to reduce Rician Noise in 3D MR images. It is a combination
    between two filters such as the Non-Local mean filter and the Anisotropic Diffusion
    tensor method with an estimator of Rician noise. The NLmCED filter can benefit
    from the noise reduction capabilities of the NLM filter while maintaining the
    edge-preserving characteristics of anisotropic diffusion.
  documentation:
  - note: null
    type:
    - General
    url: https://drive.eucaim.cancerimage.eu/s/L5iwmo6WknyLoWw
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: JPG
        uri: http://edamontology.org/format_3579
      - term: DICOM format
        uri: http://edamontology.org/format_3548
      - term: MAT
        uri: http://edamontology.org/format_3626
  homepage: https://github.com/FerielRamdhane/NLmCED-Filter/tree/main
  homepage_status: 0
  language:
  - Python
  - MATLAB
  lastUpdate: '2026-05-13T08:26:26.116424Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: Github Link
    type:
    - Repository
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nlmced/info-tab
  maturity: null
  name: NLmCED Filter
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Feriel
  publication:
  - doi: 10.1504/IJCVR.2018.090012
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1002/mrm.28676
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Script
  topic:
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version:
  - '1.0'
- 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
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  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: '2026-05-07T14:37:06.887814Z'
  biotoolsCURIE: biotools:bigr_xnattools
  biotoolsID: bigr_xnattools
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: m.starmans@erasmusmc.nl
    fundrefid: null
    gridid: null
    name: Martijn PA Starmans
    note: null
    orcidid: https://orcid.org/0000-0001-5086-7153
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://bigr.nl/member/martijn/
  - email: null
    fundrefid: null
    gridid: null
    name: Erasmus MC
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: 'xnattools is a python package with a set of modules for performing
    various operations on data stored in XNAT servers. The main purpose is to provide
    one standardized platform for running operations on XNAT servers. The package
    currently contains four tools that use this platform: dicom to nifty conversion,
    thumbnail generation from dicom, DICOM header data collection, in bulk downloading
    of a project.'
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://gitlab.com/radiology/radiomics/xnattools
    version: v0.0.1
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data editing
      uri: http://edamontology.org/operation_3096
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Aggregation
      uri: http://edamontology.org/operation_3436
    output: []
  homepage: https://gitlab.com/radiology/radiomics/xnattools
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-12T09:58:09.783339Z'
  license: Apache-2.0
  link: []
  maturity: Emerging
  name: BIGR xnattools
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: erik_h.m.
  publication: []
  relation:
  - biotoolsID: xnatpy
    type: uses
  - biotoolsID: xnat
    type: uses
  toolType:
  - Library
  topic: []
  validated: 0
  version:
  - v0.0.1
next: ?page=2
previous: null
