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  - EBI Training Tools
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  description: Open-source software application for creating and solving mathematical
    models of biological processes such as metabolic networks, cell-signaling pathways,
    regulatory networks, infectious diseases, and many others. It includes features
    to define models of biological processes, simulate and analyze these models, generate
    analysis reports, and import/export models in SBML format.
  documentation:
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      - term: SED-ML
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    operation:
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    - term: Modelling and simulation
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    - term: Metabolic network modelling
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      format:
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      - term: SED-ML
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      - term: SBML
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  homepage: http://copasi.org/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-03-19T10:46:57.487072Z'
  license: Artistic-2.0
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    - Discussion forum
    url: https://groups.google.com/g/copasi-user-forum
  - note: Issue tracker
    type:
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  - note: null
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  maturity: Mature
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    metadata: null
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    metadata: null
    note: null
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  - doi: 10.1016/j.jbiotec.2017.06.1200
    metadata: null
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    type: usedBy
  toolType:
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  - Library
  - Desktop application
  topic:
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    uri: http://edamontology.org/topic_2259
  validated: 1
  version: []
- accessibility: null
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  biotoolsCURIE: biotools:lyrebird
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  description: 'Lyrebird is a module of SingleM specialized towards the profiling
    of viruses in metagenomic data. Currently, Lyrebird profiles dsDNA phages belonging
    to the Caudoviricetes.


    Lyrebird is similar to standard microbial SingleM, with some main conceptual differences:


    Since phage lack universal single copy marker genes, Lyrebird uses an expanded
    set of >500 marker genes, and does not assume each of them is present in each
    phage.

    Lyrebird uses a more sensitive homology search method to recruit reads to marker
    gene windows.

    Lyrebird does not use GTDB taxonomy, but instead uses a custom taxonomy based
    on vConTACT3 analysis of a custom collection of reference sequences derived from
    ICTV and IMG-VR.'
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  topic:
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  - term: Virology
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  validated: 0
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- accessibility: null
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  biotoolsCURIE: biotools:tipp3
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  description: 'TIPP3 is a metagenomic profiling method that solves the following
    problems:


    Taxonomic identification

    Input: A query read q

    Output: The taxonomic lineage of q (if identified)

    Abundance profiling

    Input: A set Q of query reads

    Output: An abundance profile estimated on Q

    TIPP3 continues the TIPP-family methods (prior methods: TIPP and TIPP2), which
    use a marker gene database to identify the taxonomic lineage of input reads (if
    the read comes from a marker gene). See the pipeline below for the TIPP3 workflow.


    Additionally, TIPP-SD, as a subcommand, can perform detection at the species level.'
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  license: null
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  maturity: null
  name: TIPP3
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  owner: vashokan
  publication:
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    metadata: null
    note: null
    pmcid: PMC11970662
    pmid: '40184383'
    type: []
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  relation: []
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  topic:
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    uri: http://edamontology.org/topic_3174
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2015-08-24T08:35:55Z'
  biotoolsCURIE: biotools:bcftools
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  confidence_flag: null
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    gridid: null
    name: Wellcome Sanger Institute
    note: null
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    rorid: null
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    typeRole:
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    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
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  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:
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  function:
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    input:
    - data:
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      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: '2026-03-18T17:36:37.176917Z'
  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:
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    url: https://github.com/samtools/bcftools/issues
  maturity: Mature
  name: BCFtools
  operatingSystem:
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  - Windows
  otherID: []
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  publication:
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    metadata: null
    note: The Sequence Alignment/Map format and SAMtools.
    pmcid: PMC2723002
    pmid: '19505943'
    type:
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    version: null
  - doi: 10.1093/gigascience/giab008
    metadata: null
    note: Twelve years of SAMtools and BCFtools.
    pmcid: PMC7931819
    pmid: '33590861'
    type:
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    version: null
  relation:
  - biotoolsID: htslib
    type: uses
  toolType:
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  topic:
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  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: GWAS study
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  - term: Genotyping experiment
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  validated: 1
  version:
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  - '1.17'
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  - '1.19'
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- accessibility: Open access
  additionDate: '2017-01-13T13:16:12Z'
  biotoolsCURIE: biotools:samtools
  biotoolsID: samtools
  collectionID:
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  confidence_flag: null
  cost: Free of charge
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    name: Richard Durbin
    note: null
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    url: null
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    typeEntity: Project
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  description: SAMtools and BCFtools are widely used programs for processing and analysing
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    and manipulation, sorting, querying, statistics, variant calling, and effect analysis
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  documentation:
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    type:
    - Other
    url: http://www.htslib.org/doc/#howtos
  - note: null
    type:
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  - note: null
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    note: null
    operation:
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    - term: Visualisation
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    - term: Data filtering
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    - term: Data formatting
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    - term: Data editing
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    - term: Data parsing
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    - term: Data sorting
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    output:
    - data:
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      format:
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      - term: CRAM
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      - term: SAM
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  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
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  lastUpdate: '2026-03-18T17:35:31.864480Z'
  license: MIT
  link:
  - note: null
    type:
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  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
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  maturity: Mature
  name: SAMtools
  operatingSystem:
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  otherID: []
  owner: awhitwham
  publication:
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    metadata: null
    note: The Sequence Alignment/Map format and SAMtools.
    pmcid: PMC2723002
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    type:
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    version: null
  - doi: 10.1093/gigascience/giab008
    metadata: null
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    pmcid: PMC7931819
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    type:
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    metadata: null
    note: null
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    type: []
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  toolType:
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  - Command-line tool
  topic:
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  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequencing
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  - term: Rare diseases
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  validated: 1
  version:
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  - 1.3.1
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  biotoolsCURIE: biotools:htslib
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  description: The main purpose of HTSlib is to provide access to genomic information
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  - note: null
    type:
    - User manual
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  link:
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  maturity: Mature
  name: HTSlib
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  otherID: []
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  publication:
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  toolType:
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  validated: 1
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  - 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
  - '1.22'
  - 1.22.1
  - 1.22.2
  - '1.23'
  - 1.23.1
- accessibility: Open access
  additionDate: '2025-07-21T09:43:28.406602Z'
  biotoolsCURIE: biotools:metabolink
  biotoolsID: metabolink
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: anamendesml@outlook.com
    fundrefid: null
    gridid: null
    name: Ana Mendes
    note: null
    orcidid: https://orcid.org/0009-0008-5170-0927
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: nils.f@bmb.sdu.dk
    fundrefid: null
    gridid: null
    name: Nils J Færgeman
    note: null
    orcidid: https://orcid.org/0000-0002-9281-5287
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: A web application for Streamlined Processing and Analysis of Large-Scale
    Untargeted Metabolomics Data.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/M3Metabolomics/MetaboLink/wiki
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Imputation
      uri: http://edamontology.org/operation_3557
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    output: []
  homepage: https://computproteomics.bmb.sdu.dk/MetaboLink/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-03-17T09:34:45.884481Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/M3Metabolomics/MetaboLink/
  maturity: Emerging
  name: MetaboLink
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/bioinformatics/btae459
    metadata: null
    note: null
    pmcid: PMC11269424
    pmid: '39018180'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Lipidomics
    uri: http://edamontology.org/topic_0153
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2026-03-17T09:01:01.731320Z'
  biotoolsCURIE: biotools:biogrowth
  biotoolsID: biogrowth
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Biogrowth provides an interface to the biogrowth package for R. It
    includes functions for describing population growth based on the principles of
    predictive microbiology. It can be used for making predictions (constant or dynamic
    environmental conditions; deterministic or dynamic) or model fitting (primary
    models, one-step primary and secondary models, dynamic models and global models).
    The whole project is Open Accesss.
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://github.com/albgarre/biogrowth4
    version: null
  editPermission:
    authors: []
    type: private
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  elixirNode: []
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  elixir_badge: 0
  function: []
  homepage: https://foodlab-upct.shinyapps.io/biogrowth4/
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-17T09:21:11.409928Z'
  license: GPL-3.0-or-later
  link:
  - note: null
    type:
    - Service
    url: https://foodlab-upct.shinyapps.io/biogrowth4/
  - note: null
    type:
    - Repository
    url: https://github.com/albgarre/biogrowth4
  maturity: Mature
  name: biogrowth
  operatingSystem: []
  otherID: []
  owner: albgarre
  publication:
  - doi: 10.18637/jss.v107.i01
    metadata: null
    note: Garre, A., Koomen, J., den Besten, H. M. W., & Zwietering, M. H. (2023).
      Modeling Population Growth in R with the biogrowth Package. Journal of Statistical
      Software, 107(1), 1–51. https://doi.org/10.18637/jss.v107.i01
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Applied mathematics
    uri: http://edamontology.org/topic_3569
  validated: 0
  version:
  - 1.0.8
- accessibility: Open access
  additionDate: '2026-03-16T11:37:02.408710Z'
  biotoolsCURIE: biotools:Freezing-Point
  biotoolsID: Freezing-Point
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: Freezing-Point is a user-friendly open-source software for the automated
    analysis of freezing behavior in rodents. Based on recorded videos or pose estimation
    files. An adaptive, data-driven algorithm automatically determines freezing detection
    thresholds, reducing subjective bias while preserving user oversight. Freezing-Point
    adopts a user-oriented design centered on a graphical interface that provides
    continuous visual access to original data, processing steps and analysis results.
    This design enables users to inspect, validate or refine results while minimizing
    unnecessary data manipulation.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://github.com/gillescourtand/Freezing-Point/blob/main/Doc/User_guide.md
  download:
  - note: null
    type: Binaries
    url: https://github.com/gillescourtand/Freezing-Point/releases
    version: 1.0.2
  editPermission:
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    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Optimisation and refinement
      uri: http://edamontology.org/operation_2425
    output: []
  homepage: https://github.com/gillescourtand/Freezing-Point
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-03-16T11:37:02.410724Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: Freezing-Point
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: gilles.courtand
  publication: []
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Neurobiology
    uri: http://edamontology.org/topic_3304
  validated: 0
  version:
  - 1.0.2
- accessibility: null
  additionDate: '2026-03-13T13:13:03.878846Z'
  biotoolsCURIE: biotools:macvector
  biotoolsID: macvector
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Applications for Molecular Biologists to simplify and speed up the
    analysis, manipulation, assembly and documentation of DNA and protein sequences.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://macvector.com/
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-13T13:56:37.541876Z'
  license: null
  link: []
  maturity: null
  name: MacVector
  operatingSystem:
  - Mac
  otherID: []
  owner: smoe
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - '18.8'
- accessibility: null
  additionDate: '2026-03-13T13:09:40.841224Z'
  biotoolsCURIE: biotools:snapgene
  biotoolsID: snapgene
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Tool to intuitively design, simulate, and visualise plasmids, primers,
    and DNA constructs.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.snapgene.com/
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-13T13:09:40.843781Z'
  license: null
  link: []
  maturity: null
  name: SnapGene
  operatingSystem: []
  otherID: []
  owner: smoe
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - '8.2'
- accessibility: null
  additionDate: '2026-03-13T11:04:15.445374Z'
  biotoolsCURIE: biotools:duphold
  biotoolsID: duphold
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: don't get DUP'ed or DEL'ed by your putative SVs.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/brentp/duphold
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-13T11:04:15.447199Z'
  license: null
  link: []
  maturity: null
  name: duphold
  operatingSystem: []
  otherID: []
  owner: camlloyd
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2017-01-13T13:16:01Z'
  biotoolsCURIE: biotools:quast
  biotoolsID: quast
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: quast.support@cab.spbu.ru
    fundrefid: null
    gridid: null
    name: QUAST Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: "QUAST stands for QUality ASsessment Tool.  \nIt evaluates a quality\
    \ of genome assemblies by computing various metrics and providing nice reports."
  documentation:
  - note: null
    type:
    - General
    url: http://quast.bioinf.spbau.ru/
  download: []
  editPermission:
    authors:
    - ELIXIR-CZ
    - Keiler_Collier
    - rathor2611
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: quast -ek assembly.fa --out output_prefix
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: '# Running quast on a eukaryotic genome'
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Sequence assembly validation
      uri: http://edamontology.org/operation_3180
    output: []
  homepage: http://quast.sourceforge.net/quast
  homepage_status: 0
  language:
  - Perl
  - Python
  - C
  lastUpdate: '2026-03-13T09:39:06.494933Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ablab/quast
  - note: null
    type:
    - Issue tracker
    url: https://github.com/ablab/quast/issues
  maturity: Mature
  name: QUAST
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1093/bioinformatics/btt086
    metadata:
      abstract: Limitations of genome sequencing techniques have led to dozens of
        assembly algorithms, none of which is perfect. A number of methods for comparing
        assemblers have been developed, but none is yet a recognized benchmark. Further,
        most existing methods for comparing assemblies are only applicable to new
        assemblies of finished genomes; the problem of evaluating assemblies of previously
        unsequenced species has not been adequately considered. Here, we present QUAST
        - a quality assessment tool for evaluating and comparing genome assemblies.
        This tool improves on leading assembly comparison software with new ideas
        and quality metrics. QUAST can evaluate assemblies both with a reference genome,
        as well as without a reference. QUAST produces many reports, summary tables
        and plots to help scientists in their research and in their publications.
        In this study, we used QUAST to compare several genome assemblers on three
        datasets. QUAST tables and plots for all of them are available in the Supplementary
        Material, and interactive versions of these reports are on the QUAST website.
        © 2013 The Author.
      authors:
      - name: Gurevich A.
      - name: Saveliev V.
      - name: Vyahhi N.
      - name: Tesler G.
      citationCount: 6872
      date: '2013-04-15T00:00:00Z'
      journal: Bioinformatics
      title: 'QUAST: Quality assessment tool for genome assemblies'
    note: null
    pmcid: PMC3624806
    pmid: '23422339'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version:
  - v.5.3.0
- accessibility: null
  additionDate: '2026-03-12T14:37:43.097466Z'
  biotoolsCURIE: biotools:agrischemas
  biotoolsID: agrischemas
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: 'AgriSchemas extends established standards – primarily schema.org and
    Bioschemas – adopting their philosophy of simple, practical modeling to enable
    interoperable data sharing. Unlike formal OWL-based

    ontologies, which can be computationally heavy and complex to implement, AgriSchemas
    utilizes a lightweight, low-formal schematization approach. This makes it highly
    suitable for the automatic integration of semi-structured and large datasets,
    enabling exploratory research (e.g., identifying candidate genes) through APIs,
    graph query languages, and annotated web pages. This approach complements highly
    formalized ontologies, providing a pragmatic pathway to share "farm-to-fork" data.'
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/Rothamsted/agri-schemas
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-12T14:37:43.100077Z'
  license: null
  link: []
  maturity: null
  name: AgriSchemas
  operatingSystem: []
  otherID: []
  owner: Arnedk
  publication: []
  relation:
  - biotoolsID: schema.org
    type: uses
  - biotoolsID: bioschemas
    type: uses
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-12T14:37:04.261554Z'
  biotoolsCURIE: biotools:bioschemas
  biotoolsID: bioschemas
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Bioschemas aims to improve the Findability on the Web of life sciences
    resources such as datasets, software, and training materials. It does this by
    encouraging people in the life sciences to use Schema.org markup in their websites
    so that they are indexable by search engines and other services. Bioschemas encourages
    the consistent use of markup to ease the consumption of the contained markup across
    many sites. This structured information then makes it easier to discover, collate,
    and analyse distributed resources.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://bioschemas.org/
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-12T14:37:04.263835Z'
  license: null
  link: []
  maturity: null
  name: Bioschemas
  operatingSystem: []
  otherID: []
  owner: Arnedk
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-12T14:29:10.025403Z'
  biotoolsCURIE: biotools:schema.org
  biotoolsID: schema.org
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Schema.org is a collaborative, community activity with a mission to
    create, maintain, and promote schemas for structured data on the Internet, on
    web pages, in email messages, and beyond.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://schema.org/
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-12T14:29:10.027479Z'
  license: null
  link: []
  maturity: null
  name: Schema.org
  operatingSystem: []
  otherID: []
  owner: Arnedk
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2021-01-18T08:31:10Z'
  biotoolsCURIE: biotools:knetminer
  biotoolsID: knetminer
  collectionID: []
  confidence_flag: tool
  cost: Commercial
  credit:
  - email: keywan@knetminer.com
    fundrefid: null
    gridid: null
    name: Keywan Hassani-Pak
    note: Founder & CEO
    orcidid: https://orcid.org/0000-0001-9625-0511
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: arne@knetminer.com
    fundrefid: null
    gridid: null
    name: Arné de Klerk
    note: Co-Founder & Product Manager
    orcidid: https://orcid.org/0000-0002-9525-6820
    rorid: null
    typeEntity: Person
    typeRole: []
    url: https://www.linkedin.com/in/arnedek/
  - email: marco@knetminer.com
    fundrefid: null
    gridid: null
    name: Marco Brandizi
    note: Co-Founder & Senior Software Developer
    orcidid: https://orcid.org/0000-0002-5427-2496
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: 'A comprehensive approach for supporting evidence-based gene discovery
    and complex trait analysis across species.


    KnetMiner is a web application to search and visualise genome-scale knowledge
    networks. It is used by scientists in academia and industry to accelerate gene-trait
    discovery research. KnetMiner offers features such as keyword, gene list, genome
    region search and GWAS Peak Search. Query refinement, gene ranking, gene set enrichment
    analysis and interactive visualisation of knowledge networks and genomic information
    are all core app competencies.


    KnetMiner also has an AI layer, called Graph Chat (https://knetminer.com/news/graph-chat-announcement),
    for more easily interpreting created knowledge networks.'
  documentation:
  - note: Navigate through the various KnetMiner repos for individual pieces of documentation.
    type:
    - User manual
    url: https://github.com/KnetMiner/
  download: []
  editPermission:
    authors:
    - Arnedk
    type: group
  elixirCommunity: []
  elixirNode:
  - UK
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Network visualisation
      uri: http://edamontology.org/operation_3925
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Genetic mapping
      uri: http://edamontology.org/operation_0282
    - term: Database search
      uri: http://edamontology.org/operation_2421
    output: []
  homepage: http://knetminer.com
  homepage_status: 0
  language:
  - Java
  - JavaScript
  lastUpdate: '2026-03-12T14:24:41.512890Z'
  license: MIT
  link:
  - note: null
    type:
    - Service
    url: https://app.knetminer.com
  - note: null
    type:
    - Other
    url: http://knetminer.com/
  - note: null
    type:
    - Repository
    url: https://github.com/KnetMiner/
  maturity: Mature
  name: KnetMiner
  operatingSystem: []
  otherID: []
  owner: Niclaskn
  publication:
  - doi: 10.1101/2020.04.02.017004
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web service
  topic:
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  - term: Literature and language
    uri: http://edamontology.org/topic_3068
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  validated: 0
  version:
  - Nova
- accessibility: null
  additionDate: '2025-04-14T16:46:40.806977Z'
  biotoolsCURIE: biotools:eucaim_dicom_anonymizer
  biotoolsID: eucaim_dicom_anonymizer
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit: []
  description: The EUCAIM DICOM Anonymizer  anonymizes a set of DICOM files. It supports
    both anonymization on a case-by-case scenario, meaning one DICOM Study at a time
    (single-mode) or on multiple cases concurrently (batch mode). Additionally it
    hashes and links clinical data.
  documentation:
  - note: null
    type:
    - User manual
    url: https://drive.google.com/file/d/1sY_EWl3HHt3_t0sZjzGNqD8fU6FkRBaK/view?usp=sharing
  download: []
  editPermission:
    authors:
    - vkalokyri
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Anonymisation
      uri: http://edamontology.org/operation_3283
    output: []
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/eucaim-anonymizer/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-03-12T10:24:13.299358Z'
  license: EUPL-1.2
  link: []
  maturity: null
  name: EUCAIM DICOM Anonymizer
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: vpapageor
  publication: []
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  - term: Data protection
    uri: http://edamontology.org/topic_4044
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  description: The Brain Metastasis Segmenter is a software tool developed by researchers
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  description: The Brain Glioma Segmenter is a software tool developed by researchers
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  description: DoGSite3 was developed for predicting robust and reliable small molecule
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  description: MicroMiner assists in identifying single-residue substitutions in protein
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  documentation:
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  description: GeoMine enables the automated mining of protein-ligand binding sites.
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  description: JAMDA enables the preparation of individual protein structures and
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  download:
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    type: Binaries
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  description: PoseView automatically generates 2D diagrams of protein-ligand complexes,
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  description: SIENA is a software pipeline enabling the fully automated construction
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  - doi: 10.1021/acs.jcim.5b00210
    metadata: null
    note: null
    pmcid: null
    pmid: '26098831'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Web API
  - Web service
  - Command-line tool
  topic:
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-11-28T10:07:17Z'
  biotoolsCURIE: biotools:edia
  biotoolsID: edia
  collectionID:
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  - de.NBI-biodata
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit:
  - email: proteinsplus.zbh@lists.uni-hamburg.de
    fundrefid: null
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    name: ProteinsPlus Support
    note: null
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    fundrefid: null
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    name: NAOMI ChemBio Suite Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Support
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: University of Hamburg, ZBH - Center for Bioinformatics
    note: null
    orcidid: null
    rorid: 00g30e956
    typeEntity: null
    typeRole:
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  description: The electron density score for individual atoms (EDIA) quantifies the
    electron density fit of each atom in a crystallographically resolved structure.
    Multiple EDIA values can be combined using the power mean to compute the EDIAm,
    i.e., the electron density score for a group of several atoms. It enables users
    to score a set of atoms, such as a ligand, a residue, or an active site.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download:
  - note: null
    type: Binaries
    url: https://uhh.de/naomi
    version: null
  editPermission:
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    type: private
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  function:
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        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
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        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
      - term: SDF
        uri: http://edamontology.org/format_3814
      - 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: 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
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/ediascorer.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-11T12:24:53.162379Z'
  license: Other
  link:
  - note: A web service to run EDIAscorer calculations for protein structures stored
      in the Protein Data Bank.
    type:
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    url: https://proteins.plus
  - note: A web API to run EDIAscorer calculations for protein structures stored in
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    type:
    - Service
    url: https://proteins.plus/help/edia_rest
  - note: A link to download the standalone tool from the NAOMI ChemBio Suite.
    type:
    - Software catalogue
    url: https://uhh.de/naomi
  maturity: Mature
  name: EDIAscorer
  operatingSystem:
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  - Linux
  - Mac
  otherID: []
  owner: ehrt
  publication:
  - doi: 10.1021/acs.jcim.7b00391
    metadata: null
    note: null
    pmcid: null
    pmid: '28981269'
    type:
    - Primary
    version: null
  relation:
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    type: usedBy
  toolType:
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  - Web service
  - Command-line tool
  topic:
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: X-ray diffraction
    uri: http://edamontology.org/topic_2828
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2016-03-17T13:51:10Z'
  biotoolsCURIE: biotools:webnma
  biotoolsID: webnma
  collectionID:
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  - CBU tools
  - UiB tools
  - ELIXIR-NO
  - ELIXIR-Norway
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: Nathalie.Reuter@uib.no
    fundrefid: null
    gridid: null
    name: Nathalie Reuter
    note: null
    orcidid: https://orcid.org/0000-0002-3649-7675
    rorid: null
    typeEntity: Person
    typeRole:
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    - Developer
    url: http://www.cbu.uib.no/reuter/
  - email: null
    fundrefid: null
    gridid: null
    name: Sandhya P Tiwari
    note: null
    orcidid: https://orcid.org/0000-0002-0747-3826
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Kidane M Tekle
    note: null
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    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: null
    fundrefid: null
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    name: Tristan Cragnolini
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    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Svenn H Grindhaug
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
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    name: Lars Skjærven
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Gisle Salensminde
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Edvin Fuglebakk
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Siv M Hollup
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Department of Molecular Biology, University of Bergen, Norway
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Computational Biology Unit, Department of Informatics, University of Bergen,
      Norway
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: UiB
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: WEBnm@ provides quick, automated computation and analysis of low-frequency
    normal modes for protein structures.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: http://apps.cbu.uib.no/webnma3/howto/single
  - note: null
    type:
    - FAQ
    url: http://apps.cbu.uib.no/webnma3/qanda
  - note: null
    type:
    - General
    - Citation instructions
    url: http://apps.cbu.uib.no/webnma3/about
  download: []
  editPermission:
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    type: group
  elixirCommunity:
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  elixirNode:
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  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: Constructs elastic network model from alpha carbon coordinates of the protein,
      and computes properties to describe large scale conformations. Computes normal
      modes, fluctuation profiles, inter-residue correlations, conformational overlap
      analysis and vector field representations. Structural amino acid profiles, and
      normal mode characteristics describing protein motion, visualized in plots and
      decorated structure visualizations. White space delimited tabular data for normal
      modes and the provided plots
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Protein flexibility and motion analysis
      uri: http://edamontology.org/operation_0244
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Sequence profile
        uri: http://edamontology.org/data_1354
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Structure alignment
        uri: http://edamontology.org/data_0886
      format:
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: Performs comparative analysis of the normal modes of protein structures.
      Computes the Bhattacharyya Coefficient (BC) and the Root Mean Squared Inner
      Product (RMSIP) of aligned parts of the proteins. Alignment of sets of proteins
      to be compared. Multiple protein structures Heatmaps, dendrograms and structural
      amino acid profiles for visual comparison of structural similarity. White space
      delimited tabular data for the provided plots
    operation:
    - term: Protein structure comparison
      uri: http://edamontology.org/operation_2487
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Structural profile
        uri: http://edamontology.org/data_0889
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://apps.cbu.uib.no/webnma
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-03-11T08:56:55.566213Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    - Issue tracker
    url: https://github.com/reuter-group/webnma3
  - note: Helpdesk and support for ELIXIR Norway services.
    type:
    - Helpdesk
    url: https://elixir.no/helpdesk
  maturity: Mature
  name: WEBnma
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: UiB
  publication:
  - doi: 10.1186/s12859-014-0427-6
    metadata:
      abstract: 'Background: Normal mode analysis (NMA) using elastic network models
        is a reliable and cost-effective computational method to characterise protein
        flexibility and by extension, their dynamics. Further insight into the dynamics-function
        relationship can be gained by comparing protein motions between protein homologs
        and functional classifications. This can be achieved by comparing normal modes
        obtained from sets of evolutionary related proteins. Results: We have developed
        an automated tool for comparative NMA of a set of pre-aligned protein structures.
        The user can submit a sequence alignment in the FASTA format and the corresponding
        coordinate files in the Protein Data Bank (PDB) format. The computed normalised
        squared atomic fluctuations and atomic deformation energies of the submitted
        structures can be easily compared on graphs provided by the web user interface.
        The web server provides pairwise comparison of the dynamics of all proteins
        included in the submitted set using two measures: the Root Mean Squared Inner
        Product and the Bhattacharyya Coefficient. The Comparative Analysis has been
        implemented on our web server for NMA, WEBnmat, which also provides recently
        upgraded functionality for NMA of single protein structures. This includes
        new visualisations of protein motion, visualisation of inter-residue correlations
        and the analysis of conformational change using the. In addition, programmatic
        access to WEBnmat is now available through a SOAP-based web service. WEBnmat
        is available at. Conclusion: WEBnmat v2.0 is an online tool offering unique
        capability for comparative NMA on multiple protein structures. Along with
        a convenient web interface, powerful computing resources, and several methods
        for mode analyses, WEBnmat facilitates the assessment of protein flexibility
        within protein families and superfamilies. These analyses can give a good
        view of how the structures move and how the flexibility is conserved over
        the different structures.'
      authors:
      - name: Tiwari S.P.
      - name: Fuglebakk E.
      - name: Hollup S.M.
      - name: Skjaerven L.
      - name: Cragnolini T.
      - name: Grindhaug S.H.
      - name: Tekle K.M.
      - name: Reuter N.
      citationCount: 87
      date: '2014-12-30T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'WEBnmat v2.0: Web server and services for comparing protein flexibility'
    note: null
    pmcid: PMC4339738
    pmid: '25547242'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1186/1471-2105-6-52
    metadata:
      abstract: 'Background: Normal mode analysis (NMA) has become the method of choice
        to investigate the slowest motions in macromolecular systems. NMA is especially
        useful for large biomolecular assemblies, such as transmembrane channels or
        virus capsids. NMA relies on the hypothesis that the vibrational normal modes
        having the lowest frequencies (also named soft modes) describe the largest
        movements in a protein and are the ones that are functionally relevant. Results:
        We developed a web-based server to perform normal modes calculations and different
        types of analyses. Starting from a structure file provided by the user in
        the PDB format, the server calculates the normal modes and subsequently offers
        the user a series of automated calculations; normalized squared atomic displacements,
        vector field representation and animation of the first six vibrational modes.
        Each analysis is performed independently from the others and results can be
        visualized using only a web browser. No additional plug-in or software is
        required. For users who would like to analyze the results with their favorite
        software, raw results can also be downloaded. The application is available
        on http://www.bioinfo.no/tools/normalmodes. We present here the underlying
        theory, the application architecture and an illustration of its features using
        a large transmembrane protein as an example. Conclusion: We built an efficient
        and modular web application for normal mode analysis of proteins. Non specialists
        can easily and rapidly evaluate the degree of flexibility of multi-domain
        protein assemblies and characterize the large amplitude movements of their
        domains. © 2005 Hollup et al; licensee BioMed Central Ltd.'
      authors:
      - name: Hollup S.M.
      - name: Salensminde G.
      - name: Reuter N.
      citationCount: 105
      date: '2005-03-11T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'WEBnm@: A web application for normal mode analyses of proteins'
    note: null
    pmcid: PMC1274249
    pmid: '15762993'
    type:
    - Primary
    version: '1.0'
  relation:
  - biotoolsID: numpy
    type: uses
  - biotoolsID: biopython
    type: uses
  - biotoolsID: matplotlib
    type: uses
  - biotoolsID: mustang
    type: uses
  - biotoolsID: dssp
    type: uses
  toolType:
  - Web API
  - Suite
  topic:
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  validated: 1
  version:
  - '3.5'
- accessibility: null
  additionDate: '2019-09-27T09:58:46Z'
  biotoolsCURIE: biotools:BioMercator
  biotoolsID: BioMercator
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: BioMercator is a software that provides a complete set of algorithms
    and visualization tool covering all steps required to perform QTL meta-analysis,
    graphical representation of large datasets. User may import sequence and genome
    annotations datasets within the software in order to display functional annotation
    related to QTL and meta-QTL.
  documentation: []
  download:
  - note: null
    type: Binaries
    url: https://sourcesup.renater.fr/frs/?group_id=2301
    version: 4.2.3
  editPermission:
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    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: QTL map
        uri: http://edamontology.org/data_1860
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Genome map
        uri: http://edamontology.org/data_1288
      format:
      - term: GFF3
        uri: http://edamontology.org/format_1975
    note: null
    operation:
    - term: Genetic mapping
      uri: http://edamontology.org/operation_0282
    - term: Physical mapping
      uri: http://edamontology.org/operation_2944
    output: []
  homepage: https://sourcesup.renater.fr/projects/biomercator
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2026-03-11T08:56:54.859634Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: BioMercator
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: admin
  publication:
  - doi: 10.1093/bioinformatics/bth230
    metadata:
      abstract: 'Summary: Breeding programs face the challenge of integrating information
        from genomics and from quantitative trait loci (QTL) analysis in order to
        identify genomic sequences controlling the variation of important traits.
        Despite the development of integrative databases, building a consensus map
        of genes, QTL and other loci gathered from multiple maps remains a manual
        and tedious task. Nevertheless, this is a critical step to reveal co-locations
        between genes and QTL. Another important matter is to determine whether QTL
        linked to same traits or related ones is detected in independent experiments
        and located in the same region, and represents a single locus or not. Statistical
        tools such as meta-analysis can be used to answer this question. BioMercator
        has been developed to automate map compilation and QTL meta-analysis, and
        to visualize co-locations between genes and QTL through a graphical interface.
        © Oxford University Press 2004; all rights reserved.'
      authors:
      - name: Arcade A.
      - name: Labourdette A.
      - name: Falque M.
      - name: Mangin B.
      - name: Chardon F.
      - name: Charcosset A.
      - name: Joets J.
      citationCount: 382
      date: '2004-09-22T00:00:00Z'
      journal: Bioinformatics
      title: 'BioMercator: Integrating genetic maps and QTL towards discovery of candidate
        genes'
    note: null
    pmcid: null
    pmid: '15059820'
    type: []
    version: '3'
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Quantitative genetics
    uri: http://edamontology.org/topic_3055
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  validated: 1
  version:
  - 4.2.3
- accessibility: Open access
  additionDate: '2025-09-25T00:18:49.762990Z'
  biotoolsCURIE: biotools:sertool
  biotoolsID: sertool
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: rennmeng@smail.nju.edu.cn
    fundrefid: null
    gridid: null
    name: Meng Ren
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: Detection of Sequence-Enriched Regions (SER) in Proteins and Nucleic
    Acids
  documentation:
  - note: null
    type:
    - User manual
    url: https://www.sertool.net/help
  download:
  - note: null
    type: Downloads page
    url: https://www.sertool.net/resource
    version: 1.0.1
  editPermission:
    authors: []
    type: public
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: python SERtool.py A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y --input test.fasta
      --start 20 --point 18 20 30 50
    input: []
    note: Independent scan for 20 amino acids
    operation:
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    output: []
  - cmd: python SERtool.py D-E --input test.fasta --start 20 --point 18 20 30 50
    input: []
    note: Same class D-E analysis
    operation:
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    output: []
  - cmd: python SERtool.py .S --input test.fasta --start 15 --point 5 10 10 30
    input: []
    note: 'Wildcard: all X-S motifs (e.g., DS, RS)'
    operation:
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    output: []
  homepage: https://github.com/rennmeng/SERtool
  homepage_status: 0
  language:
  - Rust
  - Python
  lastUpdate: '2026-03-11T03:31:16.480486Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/rennmeng/SERtool
  - note: null
    type:
    - Service
    url: https://www.sertool.net/
  maturity: Legacy
  name: SERtool
  operatingSystem:
  - Linux
  otherID: []
  owner: rennmeng
  publication: []
  relation: []
  toolType:
  - Bioinformatics portal
  - Web service
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  validated: 0
  version:
  - 1.0.1
- accessibility: Restricted access
  additionDate: '2025-05-16T09:56:39.880752Z'
  biotoolsCURIE: biotools:data_integration_quality_check_tool_diqct
  biotoolsID: data_integration_quality_check_tool_diqct
  collectionID:
  - eucaim
  confidence_flag: null
  cost: Commercial
  credit:
  - email: ioannach@auth.gr
    fundrefid: null
    gridid: null
    name: Ioanna Chouvarda
    note: null
    orcidid: https://orcid.org/0000-0001-8915-6658
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: A tool that checks the clinical metadata quality (validity, completeness),
    the integrity between images and clinical metadata provided as well as their accuracy,  the
    de-identification protocol applied, and existence of annotation together with
    the consistency between the images and the annotation files and informs the user
    on corrective actions prior to data upload.
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