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  description: Open source Java library for bio- and cheminformatics.
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  homepage: http://github.com/cdk/cdk/
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  language:
  - Java
  lastUpdate: '2025-12-29T19:08:00.918429Z'
  license: LGPL-2.1
  link:
  - note: null
    type:
    - Repository
    url: http://github.com/cdk/cdk/
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    metadata:
      abstract: ''
      authors: []
      citationCount: 381
      date: '2017-06-06T00:00:00Z'
      journal: Journal of Cheminformatics
      title: 'The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular
        formulas, and substructure searching'
    note: null
    pmcid: PMC5461230
    pmid: '29086040'
    type: []
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  - doi: 10.1021/ci025584y
    metadata:
      abstract: ''
      authors: []
      citationCount: 935
      date: '2003-01-01T00:00:00Z'
      journal: Journal of Chemical Information and Computer Sciences
      title: 'The Chemistry Development Kit (CDK): An open-source Java library for
        chemo- and bioinformatics'
    note: null
    pmcid: PMC4901983
    pmid: '12653513'
    type:
    - Primary
    version: null
  - doi: 10.2174/138161206777585274
    metadata:
      abstract: ''
      authors: []
      citationCount: 445
      date: '2006-06-01T00:00:00Z'
      journal: Current Pharmaceutical Design
      title: Recent developments of the Chemistry Development Kit (CDK) - An open-source
        Java library for chemo- and bioinformatics
    note: null
    pmcid: null
    pmid: '16796559'
    type:
    - Other
    version: null
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  toolType:
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  topic:
  - term: Cheminformatics
    uri: http://edamontology.org/topic_2258
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 1
  version:
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- accessibility: Open access
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  biotoolsCURIE: biotools:opencausal
  biotoolsID: opencausal
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  credit:
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    fundrefid: null
    gridid: null
    name: Hüseyin Küçükali
    note: null
    orcidid: https://orcid.org/0000-0003-1669-3107
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    url: null
  description: An open platform for sharing, discussing and reusing causal graphs.
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  homepage: https://opencausal.org/
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  link: []
  maturity: Emerging
  name: Open Causal
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  owner: hkucukali
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2019-07-06T06:35:25Z'
  biotoolsCURIE: biotools:StructureProfiler
  biotoolsID: StructureProfiler
  collectionID: []
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    fundrefid: null
    gridid: null
    name: Matthias Rarey
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Tool for 3D protein structure profiling.
  documentation: []
  download:
  - note: NAOMI ChemBio Suite including the package
    type: Downloads page
    url: https://software.zbh.uni-hamburg.de/pages/getPackage
    version: null
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  function:
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    input: []
    note: null
    operation:
    - term: Protein geometry calculation
      uri: http://edamontology.org/operation_0249
    - term: Protein structure validation
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    - term: Protein-ligand docking
      uri: http://edamontology.org/operation_0482
    output: []
  homepage: https://www.zbh.uni-hamburg.de/forschung/amd/software/structureprofiler.html
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  license: Other
  link: []
  maturity: Mature
  name: StructureProfiler
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  - Linux
  - Windows
  - Mac
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  publication:
  - doi: 10.1093/bioinformatics/bty692
    metadata:
      abstract: Motivation Three-dimensional protein structures are important starting
        points for elucidating protein function and applications like drug design.
        Computational methods in this area rely on high quality validation datasets
        which are usually manually assembled. Due to the increase in published structures
        as well as the increasing demand for specially tailored validation datasets,
        automatic procedures should be adopted. Results StructureProfiler is a new
        tool for automatic, objective and customizable profiling of X-ray protein
        structures based on the most frequently applied selection criteria currently
        in use to assemble benchmark datasets. As examples, four dataset configurations
        (Astex, Iridium, Platinum, combined), all results of the combined tests and
        the list of all PDB Ids passing the combined criteria set are attached in
        theSupplementary Material.
      authors:
      - name: Meyder A.
      - name: Kampen S.
      - name: Sieg J.
      - name: Fahrrolfes R.
      - name: Friedrich N.-O.
      - name: Flachsenberg F.
      - name: Rarey M.
      citationCount: 4
      date: '2019-03-01T00:00:00Z'
      journal: Bioinformatics
      title: 'StructureProfiler: An all-in-one tool for 3D protein structure profiling'
    note: null
    pmcid: null
    pmid: '30124779'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Protein structural motifs and surfaces
    uri: http://edamontology.org/topic_0166
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-11-28T10:07:17Z'
  biotoolsCURIE: biotools:edia
  biotoolsID: edia
  collectionID:
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  - COVID-19
  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: University of Hamburg - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: null
  - email: rarey-office@zbh.uni-hamburg.de
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    gridid: null
    name: null
    note: null
    orcidid: null
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    typeEntity: Person
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  description: Easily interpretable electron density score for individual atoms. It
    quantifies the electron density support of each single atom by computing a weighted
    sum over an oversampled electron density grid in the proximity of the atom. Atomic
    EDIA values can also be combined with the help of the power mean to compute EDIA_m,
    an electron density score for small molecules, fragments, or residues.
  documentation:
  - note: null
    type:
    - General
    url: http://proteinsplus.zbh.uni-hamburg.de/help/index
  download: []
  editPermission:
    authors:
    - Bietz
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    type: group
  elixirCommunity:
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  elixirNode:
  - Germany
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: Score for structure quality assessment on a global or atomistic level
    operation:
    - term: Protein model validation
      uri: http://edamontology.org/operation_0321
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    output:
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
  homepage: http://proteinsplus.zbh.uni-hamburg.de/#edia
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-23T14:50:31.055029Z'
  license: null
  link: []
  maturity: null
  name: EDIA
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  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1021/acs.jcim.7b00391
    metadata:
      abstract: © 2017 American Chemical Society.Macromolecular structures resolved
        by X-ray crystallography are essential for life science research. While some
        methods exist to automatically quantify the quality of the electron density
        fit, none of them is without flaws. Especially the question of how well individual
        parts like atoms, small fragments, or molecules are supported by electron
        density is difficult to quantify. While taking experimental uncertainties
        correctly into account, they do not offer an answer on how reliable an individual
        atom position is. A rapid quantification of this atomic position reliability
        would be highly valuable in structure-based molecular design. To overcome
        this limitation, we introduce the electron density score EDIA for individual
        atoms and molecular fragments. EDIA assesses rapidly, automatically, and intuitively
        the fit of individual as well as multiple atoms (EDIAm) into electron density
        accompanied by an integrated error analysis. The computation is based on the
        standard 2fo - fc electron density map in combination with the model of the
        molecular structure. For evaluating partial structures, EDIAm shows significant
        advantages compared to the real-space R correlation coefficient (RSCC) and
        the real-space difference density Z score (RSZD) from the molecular modeler's
        point of view. Thus, EDIA abolishes the time-consuming step of visually inspecting
        the electron density during structure selection and curation. It supports
        daily modeling tasks of medicinal and computational chemists and enables a
        fully automated assembly of large-scale, high-quality structure data sets.
        Furthermore, EDIA scores can be applied for model validation and method development
        in computer-aided molecular design. In contrast to measuring the deviation
        from the structure model by root-mean-squared deviation, EDIA scores allow
        comparison to the underlying experimental data taking its uncertainty into
        account.
      authors:
      - name: Meyder A.
      - name: Nittinger E.
      - name: Lange G.
      - name: Klein R.
      - name: Rarey M.
      citationCount: 33
      date: '2017-10-23T00:00:00Z'
      journal: Journal of Chemical Information and Modeling
      title: Estimating Electron Density Support for Individual Atoms and Molecular
        Fragments in X-ray Structures
    note: null
    pmcid: null
    pmid: '28981269'
    type:
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    version: null
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  topic:
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    uri: http://edamontology.org/topic_0081
  - term: X-ray diffraction
    uri: http://edamontology.org/topic_2828
  validated: 1
  version: []
- accessibility: Open access (with restrictions)
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  biotoolsCURIE: biotools:dicom_image_similarity-duplicate_checker
  biotoolsID: dicom_image_similarity-duplicate_checker
  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'Detects duplicate or visually similar DICOM series using a tiered
    approach that combines metadata analysis, hash-based comparison, and pixel-level
    similarity metrics.

    Ideal for:

    1. High-level series comparison and classification, and

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


    For scenarios requiring strict, image-level deduplication based on pixel content,
    fully agnostic to metadata changes, consider using [https://bio.tools/image_duplicate_check_tool]'
  documentation:
  - note: null
    type:
    - General
    url: https://docs.google.com/document/d/10GsrgRCeyrZrdus04iI-967llth0o9yE/edit?usp=drive_link&ouid=108776251279939449410&rtpof=true&sd=true
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  homepage: https://www.med.auth.gr/en/content/laboratory-computing-medical-informatics-and-biomedical-imaging-technologies
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  language:
  - Python
  lastUpdate: '2025-12-23T13:24:16.938179Z'
  license: Apache-2.0
  link:
  - note: Link to the Harbor image
    type:
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    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/deduplication_tool
  maturity: Mature
  name: Image Duplicates Checker
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: difoto
  publication: []
  relation:
  - biotoolsID: data_integration_quality_check_tool_diqct
    type: includedIn
  toolType:
  - Command-line tool
  topic:
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 0
  version:
  - '2.0'
- accessibility: null
  additionDate: '2025-12-23T00:16:25.679615Z'
  biotoolsCURIE: biotools:spatial_proteomics
  biotoolsID: spatial_proteomics
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: lhhung@uw.edu
    fundrefid: null
    gridid: null
    name: Ling-Hong Hung
    note: null
    orcidid: https://orcid.org/0000-0002-5209-2248
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  - email: kayee@uw.edu
    fundrefid: null
    gridid: null
    name: Ka Yee Yeung
    note: null
    orcidid: https://orcid.org/0000-0002-1754-7577
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    url: null
  - email: fukudab@uw.edu
    fundrefid: null
    gridid: null
    name: Bryce Fukuda
    note: null
    orcidid: https://orcid.org/0009-0003-7203-5261
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  description: End-to-end spatial proteomics analysis workflow with QuPath integration.
    Our workflow consists of cell segmentation, batch correction, unsupervised clustering,
    validation of clusters on the image, and cell type clustering results visualization.
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://github.com/BioDepot/SpatialProteomics
    version: null
  editPermission:
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    type: private
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  homepage: https://github.com/BioDepot/SpatialProteomics
  homepage_status: 0
  language:
  - Python
  - R
  lastUpdate: '2025-12-23T00:29:13.711774Z'
  license: MIT
  link:
  - note: Demo video
    type:
    - Other
    url: https://youtu.be/vHjdCAZQhfE
  maturity: null
  name: Spatial Proteomics
  operatingSystem: []
  otherID:
  - type: rrid
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    version: null
  owner: kayee
  publication:
  - doi: 10.1101/2025.05.23.655879
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: '1'
  relation: []
  toolType:
  - Workflow
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-12-22T13:40:13.527477Z'
  biotoolsCURIE: biotools:fastoma
  biotoolsID: fastoma
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: FastOMA is a scalable software package to infer orthology relationship.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://github.com/DessimozLab/FastOMA/blob/main/README.md
  download: []
  editPermission:
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  elixirNode:
  - Switzerland
  elixirPlatform: []
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  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    note: null
    operation:
    - term: Phylogenetic tree reconciliation
      uri: http://edamontology.org/operation_3947
    - term: Protein sequence analysis
      uri: http://edamontology.org/operation_2479
    - term: Genome comparison
      uri: http://edamontology.org/operation_3209
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    - term: Phylogenetic inference (from molecular sequences)
      uri: http://edamontology.org/operation_0540
    output:
    - data:
        term: Sequence cluster (protein)
        uri: http://edamontology.org/data_1245
      format: []
    - data:
        term: Gene family report
        uri: http://edamontology.org/data_3148
      format:
      - term: OrthoXML
        uri: http://edamontology.org/format_3850
  homepage: https://github.com/dessimozlab/FastOMA
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-22T13:46:09.227488Z'
  license: MPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/dessimozlab/FastOMA
  - note: null
    type:
    - Service
    url: https://omabrowser.org
  maturity: Mature
  name: FastOMA
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: adrian.altenhoff
  publication:
  - doi: 10.1038/s41592-024-02552-8
    metadata:
      abstract: ''
      authors: []
      citationCount: 8
      date: '2025-02-01T00:00:00Z'
      journal: Nature Methods
      title: Orthology inference at scale with FastOMA
    note: null
    pmcid: PMC11810774
    pmid: '39753922'
    type: []
    version: null
  relation:
  - biotoolsID: omamer
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  validated: 0
  version:
  - 0.5.1
- accessibility: Open access
  additionDate: '2025-12-15T17:27:55.661547Z'
  biotoolsCURIE: biotools:thaf
  biotoolsID: thaf
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: contact@verdanta.tech
    fundrefid: null
    gridid: null
    name: Audrius Meskauskas
    note: Verdanta is an early startup in Switzerland, providing curated RNASeq pipeline.
      Thaf is part of our software stack that is released open source.
    orcidid: https://orcid.org/0009-0006-1714-3691
    rorid: null
    typeEntity: Person
    typeRole: []
    url: https://verdanta.info
  description: thaf is a command-line tool to extract transcript sequences from a
    genome FASTA file based on GFF3 annotation files. It can also generate transcript-to-gene
    mapping files compatible with tools such as Salmon.
  documentation:
  - note: README provides enough information to use the tool
    type:
    - General
    url: https://crates.io/crates/thaf
  download:
  - note: Use Cargo commands to install the application. Cargo will build it from
      the source.
    type: Other
    url: https://crates.io/crates/thaf
    version: 0.0.4
  editPermission:
    authors: []
    type: private
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: "thaf \\\n  -f <INPUT_GFF3> \\\n  -d <DNA_FASTA> \\\n  -t <OUTPUT_FASTA>\
      \ \\\n  [-g <GENEMAP_FILE>]\n  [-e <FEATURES>]"
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format: []
    note: Produce transcriptome file from genomic DNA and gff3
    operation:
    - term: Sequence coordinate conversion
      uri: http://edamontology.org/operation_3267
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format: []
  homepage: https://crates.io/crates/thaf
  homepage_status: 0
  language:
  - Rust
  lastUpdate: '2025-12-22T07:52:59.716256Z'
  license: BSD-3-Clause
  link:
  - note: Crates.io page providing installation instructions and README.
    type:
    - Software catalogue
    url: https://crates.io/crates/thaf
  - note: Source code. Also, use GitHub issue tracker to send bug reports and extension
      proposals.
    type:
    - Repository
    url: https://github.com/bourumir-wyngs/thaf
  - note: Verdanta page for thaf
    type:
    - Other
    url: https://verdanta.tech/open-source/
  maturity: Emerging
  name: thaf
  operatingSystem:
  - Mac
  - Linux
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  - doi: 10.1093/gigascience/giab008
    metadata:
      abstract: ''
      authors: []
      citationCount: 8157
      date: '2021-02-01T00:00:00Z'
      journal: GigaScience
      title: Twelve years of SAMtools and BCFtools
    note: Twelve years of SAMtools and BCFtools.
    pmcid: PMC7931819
    pmid: '33590861'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/btr509
    metadata:
      abstract: ''
      authors: []
      citationCount: 4643
      date: '2011-11-01T00:00:00Z'
      journal: Bioinformatics
      title: A statistical framework for SNP calling, mutation discovery, association
        mapping and population genetical parameter estimation from sequencing data
    note: null
    pmcid: PMC3198575
    pmid: '21903627'
    type: []
    version: null
  relation:
  - biotoolsID: htslib
    type: uses
  toolType:
  - Command-line tool
  - Suite
  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - '1.3'
  - 1.3.1
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - 1.16.1
  - '1.17'
  - '1.18'
  - '1.19'
  - 1.19.1
  - 1.19.2
  - '1.20'
  - '1.21'
  - '1.22'
  - '1.23'
- accessibility: Open access
  additionDate: '2017-08-20T16:07:58Z'
  biotoolsCURIE: biotools:htslib
  biotoolsID: htslib
  collectionID:
  - Animal and Crop Genomics
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: samtools@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Wellcome Sanger Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    - Primary contact
    url: https://www.sanger.ac.uk/
  - email: null
    fundrefid: null
    gridid: null
    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Support
    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: The main purpose of HTSlib is to provide access to genomic information
    files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF
    and BCF formats). The library also provides interfaces to access and index genome
    reference data in FASTA format and tab-delimited files with genomic coordinates.
    It is utilized and incorporated into both SAMtools and BCFtools.
  documentation:
  - note: null
    type:
    - User manual
    url: http://www.htslib.org/doc/#manual-pages
  download:
  - note: null
    type: Downloads page
    url: http://www.htslib.org/download/
    version: null
  editPermission:
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    - smoe
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: BCF
        uri: http://edamontology.org/format_3020
    note: null
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: BCF
        uri: http://edamontology.org/format_3020
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2025-12-16T15:41:44.904477Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/samtools/htslib
  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/htslib/issues
  maturity: Mature
  name: HTSlib
  operatingSystem:
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  - Linux
  - Windows
  otherID: []
  owner: awhitwham
  publication:
  - doi: 10.1093/gigascience/giab007
    metadata:
      abstract: ''
      authors: []
      citationCount: 236
      date: '2021-02-01T00:00:00Z'
      journal: GigaScience
      title: 'HTSlib: C library for reading/writing high-Throughput sequencing data'
    note: 'HTSlib: C library for reading/writing high-throughput sequencing data.'
    pmcid: PMC7931820
    pmid: '33594436'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: samtools
    type: usedBy
  - biotoolsID: bcftools
    type: usedBy
  toolType:
  - Library
  topic:
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - 1.2.1
  - '1.3'
  - 1.3.1
  - 1.3.2
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - 1.10.1
  - 1.10.2
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - '1.17'
  - '1.18'
  - '1.19'
  - '1.20'
  - '1.21'
  - '1.22'
  - 1.22.1
  - '1.23'
- accessibility: Open access
  additionDate: '2015-08-24T08:35:55Z'
  biotoolsCURIE: biotools:bcftools
  biotoolsID: bcftools
  collectionID:
  - BCFtools
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: samtools@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Wellcome Sanger Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.sanger.ac.uk/
  - email: null
    fundrefid: null
    gridid: null
    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Support
    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: BCFtools is a set of utilities that manipulate variant calls in the
    Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently
    with both VCFs and BCFs, both uncompressed and BGZF-compressed.
  documentation:
  - note: null
    type:
    - General
    url: http://www.htslib.org/doc/bcftools.html
  - note: A workflow for BCFtools.
    type:
    - Other
    url: http://www.htslib.org/workflow/#mapping_to_variant
  download:
  - note: null
    type: Downloads page
    url: http://www.htslib.org/download/
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: BCF
        uri: http://edamontology.org/format_3020
      - term: VCF
        uri: http://edamontology.org/format_3016
    note: Multiple data munging operations.
    operation:
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: BCF
        uri: http://edamontology.org/format_3020
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2025-12-16T15:40:43.213782Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/samtools/bcftools
  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/bcftools/issues
  maturity: Mature
  name: BCFtools
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: awhitwham
  publication:
  - doi: 10.1093/bioinformatics/btp352
    metadata:
      abstract: ''
      authors: []
      citationCount: 44891
      date: '2009-08-01T00:00:00Z'
      journal: Bioinformatics
      title: The Sequence Alignment/Map format and SAMtools
    note: The Sequence Alignment/Map format and SAMtools.
    pmcid: PMC2723002
    pmid: '19505943'
    type:
    - Primary
    version: null
  - doi: 10.1093/gigascience/giab008
    metadata:
      abstract: ''
      authors: []
      citationCount: 8157
      date: '2021-02-01T00:00:00Z'
      journal: GigaScience
      title: Twelve years of SAMtools and BCFtools
    note: Twelve years of SAMtools and BCFtools.
    pmcid: PMC7931819
    pmid: '33590861'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: htslib
    type: uses
  toolType:
  - Command-line tool
  - Suite
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: GWAS study
    uri: http://edamontology.org/topic_3517
  - term: Genotyping experiment
    uri: http://edamontology.org/topic_3516
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - '1.3'
  - 1.3.1
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - 1.10.1
  - 1.10.2
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - '1.17'
  - '1.18'
  - '1.19'
  - '1.20'
  - '1.21'
  - '1.22'
  - '1.23'
- accessibility: Open access
  additionDate: '2025-12-16T11:00:25.334832Z'
  biotoolsCURIE: biotools:globalamfungi
  biotoolsID: globalamfungi
  collectionID:
  - ELIXIR-CZ
  - Czech Republic
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: vetrovsky@biomed.cas.cz
    fundrefid: null
    gridid: null
    name: Tomas Vetrovsky
    note: null
    orcidid: https://orcid.org/0000-0002-0831-486X
    rorid: 02p1jz666
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-CZ
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole: []
    url: null
  description: The GlobalAMFungi Database is an open-access, global repository of
    arbuscular mycorrhizal (AM) fungal occurrence data compiled from high-throughput
    sequencing studies. It aggregates millions of DNA sequence observations of AM
    fungi from thousands of geographically referenced environmental samples, together
    with rich metadata on sampling location and environmental context, to map the
    global distribution and diversity of these key plant symbionts. The resource is
    designed to be community-driven and FAIR (Findable, Accessible, Interoperable,
    Reusable), supporting research into AM fungal ecology, biogeography, and how environmental
    factors shape their diversity.
  documentation:
  - note: null
    type:
    - User manual
    - Citation instructions
    - Quick start guide
    - Contributions policy
    - General
    url: https://globalamfungi.com/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Plant Sciences
  elixirNode:
  - Czech Republic
  elixirPlatform:
  - Data
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Data deposition
      uri: http://edamontology.org/operation_3431
    - term: Annotation
      uri: http://edamontology.org/operation_0226
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format:
      - term: FASTA-HTML
        uri: http://edamontology.org/format_2310
  homepage: https://globalamfungi.com/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-12-16T11:00:25.337448Z'
  license: CC-BY-4.0
  link:
  - note: null
    type:
    - Helpdesk
    - Repository
    - Service
    url: https://globalamfungi.com/
  maturity: Mature
  name: globalamfungi
  operatingSystem: []
  otherID: []
  owner: TomasVetrovsky
  publication:
  - doi: 10.1111/nph.19283
    metadata:
      abstract: null
      authors: []
      citationCount: 0
      date: null
      journal: null
      title: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Database portal
  - Web application
  topic:
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-12-16T08:20:17.123908Z'
  biotoolsCURIE: biotools:profiler
  biotoolsID: profiler
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: michel.salzet@univ-lille.fr
    fundrefid: null
    gridid: null
    name: Michel Salzet
    note: Professor Michel Salzet known for his work in immunology, oncology and proteomic
    orcidid: https://orcid.org/0000-0003-4318-0817
    rorid: null
    typeEntity: Person
    typeRole: []
    url: https://www.laboratoire-prism.fr/member/michel-salzet/
  description: 'Profiler is a peer-reviewed, open-source web platform and desktop
    version for end-to-end multi-omics data analysis, integrating statistical methods,
    machine learning, and artificial intelligence into a unified workflow.


    The platform supports proteomics, metabolomics, lipidomics, transcriptomics, genomics,
    and other omics datasets from raw or tabular inputs. Profiler provides automated
    preprocessing, data exploration, biomarker discovery, AI-driven modeling, survival
    analysis, and biological interpretation using enrichment analysis.


    Designed for both bioinformaticians and experimental scientists, Profiler enables
    reproducible, explainable, and high-performance omics analysis through an intuitive
    web interface.


    Profiler is developed by the PRISM U1192 laboratory and protected by INSERM Transfer.'
  documentation:
  - note: null
    type:
    - Citation instructions
    url: https://prism-profiler.univ-lille.fr/citation/
  download:
  - note: null
    type: Source code
    url: https://doi.org/10.5281/zenodo.17478158
    version: null
  - note: null
    type: Test data
    url: https://github.com/yanisZirem/Profiler_v1_requests_datatests
    version: '1.0'
  - note: null
    type: Software package
    url: https://prism-profiler.univ-lille.fr/app/
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Metabolomics
  - Proteomics
  - Rare Diseases
  elixirNode:
  - France
  elixirPlatform:
  - Tools
  - Training
  - Interoperability
  elixir_badge: 0
  function: []
  homepage: https://prism-profiler.univ-lille.fr/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-16T08:20:49.442259Z'
  license: Other
  link:
  - note: softeware link
    type:
    - Other
    url: https://prism-profiler.univ-lille.fr/
  - note: dataset examples
    type:
    - Repository
    url: https://github.com/yanisZirem/Profiler_v1_requests_datatests
  - note: Desktop version
    type:
    - Repository
    url: https://github.com/yanisZirem/prism-profiler
  maturity: Mature
  name: Profiler
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID:
  - type: doi
    value: doi:10.1093/bioinformatics/btaf644
    version: '1.0'
  owner: YZirem
  publication:
  - doi: 10.1093/bioinformatics/btaf644
    metadata: null
    note: null
    pmcid: null
    pmid: '41324558'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Desktop application
  - Web application
  - Workflow
  topic:
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2025-12-15T14:17:14.627791Z'
  biotoolsCURIE: biotools:asafind
  biotoolsID: asafind
  collectionID:
  - ELIXIR-CZ
  - Czech Republic
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: mvohnoutova@jcu.cz
    fundrefid: null
    gridid: null
    name: Marta Vohnoutová
    note: null
    orcidid: https://orcid.org/0000-0002-8915-8626
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    - Maintainer
    url: https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Vohnoutova_Marta_61699
  - email: agruber@prf.jcu.cz
    fundrefid: null
    gridid: null
    name: Ansgar Gruber
    note: null
    orcidid: https://orcid.org/0000-0002-5876-4391
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    url: https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gruber_Ansgar_118401
  description: "ASAFind is a software that predicts the intracellular location of\
    \ proteins in cells with four membrane-bound complex plastids of red algal origin.\
    \ \nThese plastids evolved via eukaryote-eukaryote endosymbiosis and for example\
    \ can be found in diatoms and cryptophytes. ASAFind uses protein sequence data\
    \ and external predictions of signal peptides (by the tools SignalP and TargetP),\
    \ and predicts plastid proteins, and proteins that are targeted to the periplastidic\
    \ compartment from these data; optionally, a graphical output can generated."
  documentation:
  - note: null
    type:
    - Installation instructions
    url: https://asafind.jcu.cz/download-page/
  download:
  - note: Download page on web-service, links to repository
    type: Downloads page
    url: https://asafind.jcu.cz/download-page/
    version: '2.0'
  editPermission:
    authors:
    - agruber
    type: group
  elixirCommunity:
  - Plant Sciences
  - Marine Metagenomics
  - Microbial Biotechnology
  elixirNode:
  - Czech Republic
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format: []
    note: null
    operation:
    - term: Subcellular localisation prediction
      uri: http://edamontology.org/operation_2489
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    - term: Protein cleavage site prediction
      uri: http://edamontology.org/operation_0422
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format: []
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format: []
  homepage: https://asafind.jcu.cz/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-15T17:36:43.189214Z'
  license: CC-BY-SA-4.0
  link:
  - note: Web Service
    type:
    - Service
    url: https://asafind.jcu.cz
  - note: Information and source code, for local installation or development
    type:
    - Repository
    url: https://github.com/ASAFind/ASAFind-2
  maturity: Mature
  name: ASAFind
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: martavohnoutova
  publication:
  - doi: 10.1111/tpj.70138
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-06-01T00:00:00Z'
      journal: Plant Journal
      title: 'ASAFind 2.0: multi-class protein targeting prediction for diatoms and
        algae with complex plastids'
    note: Publication of the current version of ASAFind (2.0)
    pmcid: PMC12136025
    pmid: '40464854'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1111/tpj.12734
    metadata:
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    type: Source code
    url: https://github.com/AuReMe/emapper2gbk.git
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    url: https://pypi.org/project/emapper2gbk/#files
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  function:
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        term: Sequence assembly
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      format:
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    - data:
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    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
    note: Genomic -single mode
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: GenBank-like format (text)
        uri: http://edamontology.org/format_2205
  homepage: https://github.com/AuReMe/emapper2gbk
  homepage_status: 0
  language:
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  lastUpdate: '2025-12-10T16:49:05.332576Z'
  license: LGPL-3.0
  link:
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    url: https://github.com/AuReMe/emapper2gbk
  - note: Access to Python library
    type:
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  maturity: Mature
  name: emapper2gbk
  operatingSystem:
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  otherID: []
  owner: Noe_Robert
  publication: []
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_4011
  validated: 0
  version:
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- accessibility: null
  additionDate: '2025-05-22T17:46:59.585364Z'
  biotoolsCURIE: biotools:mainzelliste
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  confidence_flag: null
  cost: Free of charge
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  description: Mainzelliste is a web-based first-level pseudonymization service. It
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    (IDAT), and thanks to the record linkage functionality, this is even possible
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    web interface. Mainzelliste also includes built-in consent management and supports
    FHIR APIs.
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  - note: null
    type:
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  - note: null
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  - note: null
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  license: AGPL-3.0
  link:
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    type:
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  owner: enola
  publication:
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    metadata:
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      authors: []
      citationCount: 76
      date: '2015-02-07T00:00:00Z'
      journal: BMC Medical Informatics and Decision Making
      title: A RESTful interface to pseudonymization services in modern web applications
    note: null
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    pmid: '25656224'
    type:
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    version: null
  relation: []
  toolType:
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  - Web API
  topic:
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  - term: Data identity and mapping
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  validated: 0
  version:
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  additionDate: '2019-11-05T14:50:05Z'
  biotoolsCURIE: biotools:acdtool
  biotoolsID: acdtool
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  cost: Free of charge
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  description: Web-server for the generic analysis of large data sets of counts.
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  license: null
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  name: ACDtool
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  owner: santini
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  toolType:
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  topic:
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  validated: 1
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  biotoolsCURIE: biotools:raptor-rnaseq
  biotoolsID: raptor-rnaseq
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  confidence_flag: tool
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  description: RAPTOR intelligently recommends and benchmarks RNA-seq pipelines by
    analyzing 20+ data characteristics (biological variation, depth, zero-inflation,
    sample size). Multi-criteria scoring provides personalized pipeline recommendations
    from eight production-ready workflows (STAR-RSEM-DESeq2, Salmon-edgeR, Kallisto-Sleuth,
    etc.) in 30 seconds with clear reasoning. Comprehensive benchmarking quantifies
    accuracy, efficiency, and reproducibility metrics across all pipelines on user
    data with customizable priority modes.
  documentation:
  - note: null
    type:
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    - Code of conduct
    - Command-line options
    - FAQ
    - General
    - Installation instructions
    - Quick start guide
    - Release notes
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    - Training material
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      format:
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      - term: Textual format
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      - term: CSV
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    note: 'Comprehensive statistical characterization of RNA-seq datasets: library
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      biological coefficient of variation (BCV), mean-variance relationships, sequencing
      depth assessment, and experimental design balance.'
    operation:
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    - term: Sequencing quality control
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    - term: Statistical calculation
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    output:
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      format:
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      - term: JSON
        uri: http://edamontology.org/format_3464
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
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  - cmd: raptor run --pipeline 3 --data your_fastq/ --output results/
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        term: Statistical estimate score
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      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
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      - term: CSV
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    note: 'Intelligent recommendation system analyzing data characteristics (library
      size variation, zero-inflation, BCV, sample size, sequencing depth, design complexity)
      and matching them to pipeline strengths using multi-criteria scoring (0-200).
      Recommends from 8 pipelines: STAR-RSEM-DESeq2 (high accuracy), HISAT2-StringTie-Ballgown
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      STAR-HTSeq-limma (complex designs), STAR-featureCounts-NOISeq (non-parametric),
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      modes: accuracy, speed, memory, or balanced.'
    operation:
    - term: Prediction and recognition
      uri: http://edamontology.org/operation_2423
    - term: Optimisation and refinement
      uri: http://edamontology.org/operation_2425
    - term: Comparison
      uri: http://edamontology.org/operation_2424
    output:
    - data:
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      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format:
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        uri: http://edamontology.org/format_3464
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
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        uri: http://edamontology.org/format_2331
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
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        uri: http://edamontology.org/format_2182
    - data:
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        uri: http://edamontology.org/data_0925
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        uri: http://edamontology.org/format_2305
    - data:
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        uri: http://edamontology.org/data_3112
      format:
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        uri: http://edamontology.org/format_3752
    note: 'Comprehensive benchmarking framework comparing 8 RNA-seq pipelines. Evaluates:
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      (2) Efficiency metrics: runtime, memory, CPU utilization, disk space; (3) Reproducibility
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      Benchmark datasets: simulated data (Polyester), SEQC/MAQC validation, and user
      data. Runtime: 2-4 hours (small datasets) to 8-24 hours (large datasets). Outputs:
      HTML dashboard, CSV/TSV tables, publication-ready figures.'
    operation:
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      uri: http://edamontology.org/operation_0337
    - term: Validation
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    - term: Comparison
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    output:
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    - data:
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    - data:
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      - term: PDF
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    - data:
        term: Gene expression profile
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    - data:
        term: Matrix
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      format:
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      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/AyehBlk/RAPTOR
  homepage_status: 0
  language:
  - Shell
  - Python
  - R
  lastUpdate: '2025-12-10T08:58:59.523684Z'
  license: MIT
  link:
  - note: null
    type:
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    url: https://github.com/AyehBlk/RAPTOR
  maturity: Emerging
  name: RAPTOR
  operatingSystem:
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  otherID:
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    version: v2.1.0
  owner: AyehBlk
  publication: []
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  toolType:
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  topic:
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2025-12-09T09:09:20.909736Z'
  biotoolsCURIE: biotools:dgenies
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    note: null
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  description: D-GENIES – for Dot plot large Genomes in an Interactive, Efficient
    and Simple way – is an online tool designed to compare two genomes. It supports
    large genome and you can interact with the dot plot to improve the visualisation.
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    note: null
    operation:
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    - data:
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      format: []
  homepage: https://dgenies.toulouse.inrae.fr/
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  license: GPL-3.0
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  maturity: Mature
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  owner: pbordron
  publication:
  - doi: 10.7717/peerj.4958
    metadata:
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      authors: []
      citationCount: 487
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      title: 'D-GENIES: Dot plot large genomes in an interactive, efficient and simple
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    note: null
    pmcid: PMC5991294
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    type:
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    version: null
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0622
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2021-01-02T12:42:50Z'
  biotoolsCURIE: biotools:mgse
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  confidence_flag: null
  cost: Free of charge
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    gridid: null
    name: Boas Pucker
    note: null
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  description: Mapping-based Genome Size Estimation (MGSE) predicts the size of a
    genome based on a (short) read mapping to an existing genome assembly. Low complexity
    sequences are often collapsed in a genome assembly thus the assembly size is smaller
    than the genome size. The actual copy number of sequences in the assembly is identified
    based on the coverage (sequencing depth) which allows the calculation of a genome
    size.
  documentation: []
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    type: Downloads page
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  license: null
  link:
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      journal: BMC Genomics
      title: Mapping-based genome size estimation
    note: null
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    type:
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    version: null
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  toolType:
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  - Script
  topic:
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    uri: http://edamontology.org/topic_0196
  - term: Sequence composition, complexity and repeats
    uri: http://edamontology.org/topic_0157
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  validated: 0
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- accessibility: Open access
  additionDate: '2025-10-15T07:25:34.085350Z'
  biotoolsCURIE: biotools:image_quality_assessment_metrics_iqa_for_xnat_platform
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    note: null
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    rorid: null
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  - email: preclinicaldata@eurobioimaging.eu
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  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:
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  function:
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      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/XNAT-Quality-Metrics/tree/main
  homepage_status: 0
  language:
  - Python
  - MATLAB
  lastUpdate: '2025-12-05T14:40:30.073701Z'
  license: CC-BY-NC-ND-4.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/FerielRamdhane/XNAT-Quality-Metrics/tree/main
  maturity: null
  name: Image Quality Assessment metrics  (IQA) for XNAT platform
  operatingSystem:
  - Linux
  - Windows
  - Mac
  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: '2025-06-30T08:52:48.500476Z'
  biotoolsCURIE: biotools:fair_eva_4_eucaim
  biotoolsID: fair_eva_4_eucaim
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Fernando Aguilar
    note: 'Creator and devloper of the main package FAIR EVA.

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

    This software started to be developed within IFCA-Advanced-Computing receives
    funding from the European Union’s Horizon 2020 research and innovation programme
    under grant agreement No 857647.'
  documentation:
  - note: Documentation for the main package, EUCAIM plugin specific documentation
      not included.
    type:
    - General
    url: https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.md
  - note: Wiki page with FAIR EVA for EUCAIM specific instructions.
    type:
    - User manual
    url: https://gitlabpages.ifca.es/fair-eva-guide-608baa/
  download: []
  editPermission:
    authors:
    - ines.ifca
    - davrodgon
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: python scripts/batch_runner.py --plugin eucaim_catalogue --out faireva_out
    input:
    - data:
        term: URL
        uri: http://edamontology.org/data_1052
      format: []
    note: null
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output:
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
  homepage: https://github.com/IFCA-Advanced-Computing/FAIR_eva
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-04T10:57:20.901575Z'
  license: Apache-2.0
  link:
  - note: Repository for FAIR EVA, without the EUCAIM specific plugin
    type:
    - Repository
    url: https://github.com/IFCA-Advanced-Computing/FAIR_eva
  maturity: Mature
  name: FAIR EVA for EUCAIM
  operatingSystem:
  - Linux
  otherID: []
  owner: davrodgon
  publication:
  - doi: 10.1038/s41597-023-02652-8
    metadata:
      abstract: null
      authors: []
      citationCount: 0
      date: null
      journal: null
      title: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Plug-in
  - Command-line tool
  - Web service
  topic:
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  validated: 0
  version:
  - EUCAIM_plugin_0.3
  - EUCAIM_plugin_0.3.1
  - EUCAIM_plugin_0.4.0
  - EUCAIM_0.4.2
- accessibility: Open access
  additionDate: '2023-01-25T22:49:31.072923Z'
  biotoolsCURIE: biotools:soluprotmutsupdb
  biotoolsID: soluprotmutsupdb
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: 222755@mail.muni.cz
    fundrefid: null
    gridid: null
    name: David Bednar
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: mazurenko@mail.muni.cz
    fundrefid: null
    gridid: null
    name: Stanislav Mazurenko
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Jan Velecký
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Marie Hamsikova
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: A manually curated database of protein solubility changes upon mutations.
  documentation: []
  download: []
  editPermission:
    authors:
    - velda
    - m.musil
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Protein solubility prediction
      uri: http://edamontology.org/operation_0409
    - term: Aggregation
      uri: http://edamontology.org/operation_3436
    - term: Variant effect prediction
      uri: http://edamontology.org/operation_0331
    output: []
  homepage: http://loschmidt.chemi.muni.cz/soluprotmutdb
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-03T12:49:50.125351Z'
  license: null
  link: []
  maturity: null
  name: SoluProtMutsupDB
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: velda
  publication:
  - doi: 10.1016/J.CSBJ.2022.11.009
    metadata:
      abstract: © 2022 The Author(s)Protein solubility is an attractive engineering
        target primarily due to its relation to yields in protein production and manufacturing.
        Moreover, better knowledge of the mutational effects on protein solubility
        could connect several serious human diseases with protein aggregation. However,
        we have limited understanding of the protein structural determinants of solubility,
        and the available data have mostly been scattered in the literature. Here,
        we present SoluProtMutDB – the first database containing data on protein solubility
        changes upon mutations. Our database accommodates 33 000 measurements of 17
        000 protein variants in 103 different proteins. The database can serve as
        an essential source of information for the researchers designing improved
        protein variants or those developing machine learning tools to predict the
        effects of mutations on solubility. The database comprises all the previously
        published solubility datasets and thousands of new data points from recent
        publications, including deep mutational scanning experiments. Moreover, it
        features many available experimental conditions known to affect protein solubility.
        The datasets have been manually curated with substantial corrections, improving
        suitability for machine learning applications. The database is available at
        loschmidt.chemi.muni.cz/soluprotmutdb.
      authors:
      - name: Velecky J.
      - name: Hamsikova M.
      - name: Stourac J.
      - name: Musil M.
      - name: Damborsky J.
      - name: Bednar D.
      - name: Mazurenko S.
      citationCount: 0
      date: '2022-01-01T00:00:00Z'
      journal: Computational and Structural Biotechnology Journal
      title: 'SoluProtMutDB: A manually curated database of protein solubility changes
        upon mutations'
    note: null
    pmcid: PMC9678803
    pmid: '36420168'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Data submission, annotation and curation
    uri: http://edamontology.org/topic_0219
  - term: Literature and language
    uri: http://edamontology.org/topic_3068
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2025-11-26T13:27:32.776575Z'
  biotoolsCURIE: biotools:iqa_dce_tool
  biotoolsID: iqa_dce_tool
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: The purpose of the tool is to provide a complete framework for automatic
    detection of image quality for Breast DCE MR images. The assessment is performed
    on the first post-contrast dynamic phase in order to assess the most clinically
    relevant sequence among a number of identical acquisitions. Two categories are
    available for image classification, i.e. high and low quality, depending on the
    level of noise, degree of blurring and presence of artifacts.
  documentation:
  - note: null
    type:
    - General
    url: https://docs.google.com/document/d/1hG_M21gvO4D8zkHmwtbavT8Dp6bliRU4/edit
  download:
  - note: null
    type: Container file
    url: https://hub.docker.com/r/billykforth/iqa_dce_tool
    version: '1.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://hub.docker.com/repository/docker/billykforth/iqa_dce_tool/general
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-03T06:46:13.717361Z'
  license: EUPL-1.1
  link: []
  maturity: Mature
  name: IQA DCE tool
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: billyk
  publication:
  - doi: 10.3390/jimaging11110417
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2025-11-29T18:03:55.516541Z'
  biotoolsCURIE: biotools:asparaginase_database
  biotoolsID: asparaginase_database
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Asparaginases are one of the most successful biopharmaceuticals that
    play a pivotal role in the treatment of acute lymphoblastic leukemia. In order
    to find new asparaginases with improved properties (stability, substrate affinity,
    immunogenicity) or to achieve these goals by enzyme engineering, it is essential
    to collect and accurately classify asparaginases from various sources. The database
    covers 101 experimentally studied proteins from the literature, a manually curated
    set of 127 sequences from SwissProt, and more than 100,000 automatically curated
    enzymes.
  documentation:
  - note: null
    type:
    - User manual
    url: https://asparaginasedb.cz/help.html
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Czech Republic
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://asparaginasedb.com/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-02T22:00:20.857626Z'
  license: CC-BY-4.0
  link: []
  maturity: Mature
  name: Asparaginase database
  operatingSystem:
  - Linux
  otherID: []
  owner: spiwokv
  publication: []
  relation: []
  toolType:
  - Database portal
  - Bioinformatics portal
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-04-30T10:28:37.002350Z'
  biotoolsCURIE: biotools:eucaim_wizard_tool
  biotoolsID: eucaim_wizard_tool
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Computational BioMedicine Laboratory, Foundation for Research and Technology
      Hellas (FORTH)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.ics.forth.gr/cbml/?lang=en
  description: The EUCAIM Wizard Tool performs an analysis of data re-identification
    risks of imaging and clinical data that follow the EUCAIM CDM. It includes and
    uses an EUCAIM specific configuration of the ARX Data Anonymization Tool (biotools:arx),
    by supporting a wide variety of privacy and risk models as well methods for analyzing
    the usefulness of output data.
  documentation:
  - note: null
    type:
    - User manual
    url: https://docs.google.com/document/d/1pi-7SvDKzVSYS78MhvnBX7PcXF3kZAc6/edit?usp=sharing&ouid=115998150174651530097&rtpof=true&sd=true
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Anonymisation
      uri: http://edamontology.org/operation_3283
    output: []
  homepage: https://github.com/cbml-forth/eucaim_wizard_tool
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2025-12-02T12:53:14.408095Z'
  license: EUPL-1.1
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/cbml-forth/eucaim_wizard_tool
  maturity: Emerging
  name: EUCAIM Wizard Tool
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: vkalokyri
  publication: []
  relation:
  - biotoolsID: arx
    type: includes
  - biotoolsID: arx
    type: uses
  toolType:
  - Desktop application
  topic:
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  - term: Data protection
    uri: http://edamontology.org/topic_4044
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  validated: 0
  version:
  - beta1.0
- accessibility: Open access
  additionDate: '2025-12-02T12:03:53.282983Z'
  biotoolsCURIE: biotools:aggreprot
  biotoolsID: aggreprot
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Joan Planas-Iglesias
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: David Bednar
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Jiri Damborsky
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Simeon Borko
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: AggreProt is a web server to predict and engineer protein aggregation.
    The tool provides a per-residue numerical aggregation propensity value and an
    overall protein aggregation propensity profile. Along with the protein solvent
    accessibility area and its transmembrane propensity, AggreProt predictions aid
    the users on designing soluble proteins.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Proteomics
  elixirNode:
  - Czech Republic
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function: []
  homepage: https://loschmidt.chemi.muni.cz/aggreprot/
  homepage_status: 0
  language:
  - Java
  - JavaScript
  lastUpdate: '2025-12-02T12:03:53.285771Z'
  license: Proprietary
  link: []
  maturity: Mature
  name: AggreProt
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: m.musil
  publication:
  - doi: 10.1093/nar/gkae420
    metadata:
      abstract: ''
      authors: []
      citationCount: 17
      date: '2024-07-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'AggreProt: A web server for predicting and engineering aggregation prone
        regions in proteins'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web service
  topic:
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2021-01-18T10:10:48Z'
  biotoolsCURIE: biotools:ape
  biotoolsID: ape
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: vedran.kasalica@health-ri.nl
    fundrefid: null
    gridid: null
    name: Vedran Kasalica
    note: null
    orcidid: https://orcid.org/0000-0002-0097-1056
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: anna-lena.lamprecht@uni-potsdam.de
    fundrefid: null
    gridid: null
    name: Anna-Lena Lamprecht
    note: null
    orcidid: https://orcid.org/0000-0003-1953-5606
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: APE (the Automated Pipeline Explorer) as a command-line tool and API
    for automated composition of scientific workflows. APE is easily configured to
    a new application domain by providing it with a domain ontology and semantically
    annotated tools. It can then be used to synthesize purpose-specific workflows
    based on a specification of the available workflow inputs, desired outputs and
    possibly additional constraints.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://ape-framework.readthedocs.io/
  download:
  - note: Download APE java library or the CLI
    type: Software package
    url: https://mvnrepository.com/artifact/io.github.sanctuuary/APE/2.1.7
    version: 2.1.7
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Workflow metadata
        uri: http://edamontology.org/data_0949
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Generation
      uri: http://edamontology.org/operation_3429
    output:
    - data:
        term: Workflow metadata
        uri: http://edamontology.org/data_0949
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: CWL
        uri: http://edamontology.org/format_3857
      - term: PNG
        uri: http://edamontology.org/format_3603
  homepage: https://github.com/sanctuuary/APE/
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2025-12-01T13:47:56.062392Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/sanctuuary/ape
  maturity: Mature
  name: APE
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: VKasalica
  publication:
  - doi: null
    metadata: null
    note: null
    pmcid: PMC7304703
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1021/acs.jproteome.0c00983
    metadata:
      abstract: ''
      authors: []
      citationCount: 7
      date: '2021-04-02T00:00:00Z'
      journal: Journal of Proteome Research
      title: 'APE in the Wild: Automated Exploration of Proteomics Workflows in the
        bio.tools Registry'
    note: null
    pmcid: PMC8041394
    pmid: '33720735'
    type:
    - Benchmarking study
    version: null
  relation: []
  toolType:
  - Library
  - Web API
  - Command-line tool
  topic:
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 1
  version:
  - 2.1.7
- accessibility: Open access
  additionDate: '2017-08-03T18:45:53Z'
  biotoolsCURIE: biotools:hbat
  biotoolsID: hbat
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Abhishek Tiwari
    note: null
    orcidid: https://orcid.org/0000-0003-2222-2395
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://www.abhishek-tiwari.com
  description: "HBAT (Hydrogen Bond Analysis Tool) is a package to automate the analysis\
    \ of potential hydrogen bonds and similar type of weak interactions in macromolecular\
    \ structures, available in Protein Data Bank (PDB) file format. HBAT uses a geometric\
    \ approach to identify molecular interactions by analysing distance and angular\
    \ criteria.\n\nHBAT 1.1 was released in 2007 as closed source Windows binary and\
    \ continue to be available via SourceForge. \n\nHBAT 2.0 was introduced in 2025\
    \ and a completed rewrite of original implementation with cross-platform support.\
    \ HBAT 2.0 is open sourced under MIT License."
  documentation:
  - note: null
    type:
    - General
    - API documentation
    - Citation instructions
    - Command-line options
    - Installation instructions
    - Quick start guide
    url: https://hbat.abhishek-tiwari.com
  download:
  - note: Cross-platform PyPI Python Package
    type: Software package
    url: https://pypi.org/project/hbat/
    version: 2.x
  - note: Mac and Linux Binaries including  AppImage, .deb, standalone executables.
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  license: CC-BY-NC-ND-4.0
  link:
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    url: https://segmenter.hope4kids.io/
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  name: Brain Glioma Segmenter
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  description: The Pediatric Brain Tumor Segmenter is a software tool developed by
    researchers from Universidad Politécnica de Madrid and Children’s National Hospital
    for the segmentation and analysis of pediatric brain tumors in magnetic resonance
    imaging (MRI). Built in Python, it enables precise quantitative analysis of pediatric
    brain tumors in MRI scans to support clinical decision-making in both diagnosis
    and prognosis.
  documentation:
  - note: null
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    url: https://docs.hope4kids.io/HOPE-Segmenter-Kids/
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  language:
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  lastUpdate: '2025-11-28T13:55:19.273705Z'
  license: CC-BY-NC-SA-4.0
  link:
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    url: https://segmenter.hope4kids.io/
  - note: GitHub repository
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    metadata:
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      title: Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging
    note: null
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      journal: Proceedings - International Symposium on Biomedical Imaging
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        with Adaptive Post-Processing'
    note: null
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  - doi: 10.48550/arXiv.2412.04094
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  toolType:
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  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
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    note: null
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  description: The Medical Imaging Interaction Toolkit (MITK) is a free open-source
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    Based on MITK, there is the MITK Workbench, a powerful and free application to
    view, process, and segment medical images.
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  license: BSD-3-Clause
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  - note: 'If you have any questions related to the use of or the development with
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      Note that you have to subscribe to the mailing list in order to send mails'
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    url: https://lists.sourceforge.net/lists/listinfo/mitk-users
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    metadata:
      abstract: Thoroughly designed, open-source toolkits emerge to boost progress
        in medical imaging. The Insight Toolkit (ITK) provides this for the algorithmic
        scope of medical imaging, especially for segmentation and registration. But
        medical imaging algorithms have to be clinically applied to be useful, which
        additionally requires visualization and interaction. The Visualization Toolkit
        (VTK) has powerful visualization capabilities, but only low-level support
        for interaction. In this paper, we present the Medical Imaging Interaction
        Toolkit (MITK). The goal of MITK is to significantly reduce the effort required
        to construct specifically tailored, interactive applications for medical image
        analysis. MITK allows an easy combination of algorithms developed by ITK with
        visualizations created by VTK and extends these two toolkits with those features,
        which are outside the scope of both. MITK adds support for complex interactions
        with multiple states as well as undo-capabilities, a very important prerequisite
        for convenient user interfaces. Furthermore, MITK facilitates the realization
        of multiple, different views of the same data (as a multiplanar reconstruction
        and a 3D rendering) and supports the visualization of 3D+t data, whereas VTK
        is only designed to create one kind of view of 2D or 3D data. MITK reuses
        virtually everything from ITK and VTK. Thus, it is not at all a competitor
        to ITK or VTK, but an extension, which eases the combination of both and adds
        the features required for interactive, convenient to use medical imaging software.
        MITK is an open-source project (www.mitk.org). © 2005 Elsevier B.V. All rights
        reserved.
      authors:
      - name: Wolf I.
      - name: Vetter M.
      - name: Wegner I.
      - name: Bottger T.
      - name: Nolden M.
      - name: Schobinger M.
      - name: Hastenteufel M.
      - name: Kunert T.
      - name: Meinzer H.-P.
      citationCount: 378
      date: '2005-12-01T00:00:00Z'
      journal: Medical Image Analysis
      title: The medical imaging interaction toolkit
    note: 'Nolden, Marco, et al. "The Medical Imaging Interaction Toolkit: challenges
      and advances: 10 years of open-source development."

      International journal of computer assisted radiology and surgery 8 (2013): 607-620'
    pmcid: null
    pmid: '15896995'
    type: []
    version: null
  - doi: 10.1007/s11548-013-0840-8
    metadata:
      abstract: 'Purpose: The Medical Imaging Interaction Toolkit (MITK) has been
        available as open-source software for almost 10 years now. In this period
        the requirements of software systems in the medical image processing domain
        have become increasingly complex. The aim of this paper is to show how MITK
        evolved into a software system that is able to cover all steps of a clinical
        workflow including data retrieval, image analysis, diagnosis, treatment planning,
        intervention support, and treatment control. Methods: MITK provides modularization
        and extensibility on different levels. In addition to the original toolkit,
        a module system, micro services for small, system-wide features, a service-oriented
        architecture based on the Open Services Gateway initiative (OSGi) standard,
        and an extensible and configurable application framework allow MITK to be
        used, extended and deployed as needed. A refined software process was implemented
        to deliver high-quality software, ease the fulfillment of regulatory requirements,
        and enable teamwork in mixed-competence teams. Results: MITK has been applied
        by a worldwide community and integrated into a variety of solutions, either
        at the toolkit level or as an application framework with custom extensions.
        The MITK Workbench has been released as a highly extensible and customizable
        end-user application. Optional support for tool tracking, image-guided therapy,
        diffusion imaging as well as various external packages (e.g. CTK, DCMTK, OpenCV,
        SOFA, Python) is available. MITK has also been used in several FDA/CE-certified
        applications, which demonstrates the high-quality software and rigorous development
        process. Conclusions: MITK provides a versatile platform with a high degree
        of modularization and interoperability and is well suited to meet the challenging
        tasks of today''s and tomorrow''s clinically motivated research. © 2013 CARS.'
      authors:
      - name: Nolden M.
      - name: Zelzer S.
      - name: Seitel A.
      - name: Wald D.
      - name: Muller M.
      - name: Franz A.M.
      - name: Maleike D.
      - name: Fangerau M.
      - name: Baumhauer M.
      - name: Maier-Hein L.
      - name: Maier-Hein K.H.
      - name: Meinzer H.-P.
      - name: Wolf I.
      citationCount: 354
      date: '2013-01-01T00:00:00Z'
      journal: International Journal of Computer Assisted Radiology and Surgery
      title: 'The medical imaging interaction toolkit: Challenges and advances: 10
        years of open-source development'
    note: 'Nolden, Marco, et al. "The Medical Imaging Interaction Toolkit: challenges
      and advances: 10 years of open-source development."

      International journal of computer assisted radiology and surgery 8 (2013): 607-620'
    pmcid: null
    pmid: '23588509'
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  description: 'Families and TAG Finder: a Snakemake workflow to identify gene families
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  description: The South Green Genome Hub is a suite of crop-specific community portals
    to manage genomic datasets with focus on tropical and Mediterranean plants. Currently
    developed on Banana, Cacao, Coffee, Grass, Rice, Vanilla, Citrus and Sugarcane,
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    information, metabolic pathways, gene families, transcriptomics and genetic markers).
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  - term: Transcriptomics
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    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: tgabaldon@crg.es
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://gabaldonlab.crg.es/
  description: Tool for the automated removal of spurious sequences or poorly aligned
    regions from a multiple sequence alignment.
  documentation:
  - note: Old versions
    type:
    - General
    url: http://trimal.cgenomics.org/
  - note: null
    type:
    - General
    url: https://trimal.readthedocs.io
  download:
  - note: null
    type: Source code
    url: https://github.com/inab/trimal
    version: 1.5.1
  - note: null
    type: Source code
    url: https://github.com/inab/trimal/tree/2.0_RC
    version: 2.0-RC
  editPermission:
    authors:
    - nico_bsc
    - sergitobara
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format: []
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
    - data:
        term: Alignment
        uri: http://edamontology.org/data_1916
      format:
      - term: phylipnon
        uri: http://edamontology.org/format_1998
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://trimal.readthedocs.io
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2025-11-26T09:30:50.611915Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/inab/trimal
  maturity: Mature
  name: trimAl
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: scapella
  publication:
  - doi: 10.1093/bioinformatics/btp348
    metadata:
      abstract: ''
      authors: []
      citationCount: 8679
      date: '2009-08-01T00:00:00Z'
      journal: Bioinformatics
      title: 'trimAl: A tool for automated alignment trimming in large-scale phylogenetic
        analyses'
    note: null
    pmcid: PMC2712344
    pmid: '19505945'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  validated: 1
  version:
  - 1.5.1
  - 2.0-RC
- accessibility: Open access
  additionDate: '2025-09-22T13:08:24.320192Z'
  biotoolsCURIE: biotools:nf-core_proteinfamilies
  biotoolsID: nf-core_proteinfamilies
  collectionID:
  - nf-core
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: nf-core/proteinfamilies is a bioinformatics pipeline that generates
    protein families from amino acid sequences and/or updates existing families with
    new sequences. It takes a protein fasta file as input, clusters the sequences
    and then generates protein family Hiden Markov Models (HMMs) along with their
    multiple sequence alignments (MSAs). Optionally, paths to existing family HMMs
    and MSAs can be given (must have matching base filenames one-to-one) in order
    to update with new sequences in case of matching hits.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/nf-core/proteinfamilies
  homepage_status: 0
  language:
  - Groovy
  lastUpdate: '2025-11-25T11:19:41.601191Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/nf-core/proteinfamilies
  maturity: Mature
  name: nf-core-proteinfamilies
  operatingSystem: []
  otherID:
  - type: rrid
    value: RRID:SCR_027374
    version: 1.3.0
  owner: vangelis
  publication:
  - doi: 10.1101/2025.08.12.670010
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  validated: 0
  version:
  - 2.0.0
  - 2.1.0
next: ?page=2
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