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  additionDate: '2024-09-27T07:25:34.997795Z'
  biotoolsCURIE: biotools:navpa
  biotoolsID: navpa
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Navpa is non-software, deriving its name from nav pa', Klingon for
    paper town. Paper towns were fictional entities historically used to detect copyright
    violation of published works such as maps. Navpa itself does nothing, including
    in genomics. However, It can be used to test that services building on bio.tools
    can handle the special case of a tool with no inputs, outputs or operations.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/magnuspalmblad/navpa
  download: []
  editPermission:
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  language:
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  lastUpdate: '2025-09-14T08:39:13.825698Z'
  license: AGPL-3.0
  link: []
  maturity: Mature
  name: navpa
  operatingSystem:
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  - Linux
  - Windows
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Informatics
    uri: http://edamontology.org/topic_0605
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Genetics
    uri: http://edamontology.org/topic_3053
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2019-05-27T16:59:15Z'
  biotoolsCURIE: biotools:SLiM_software
  biotoolsID: SLiM_software
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Philipp Messer
    note: null
    orcidid: https://orcid.org/0000-0001-8453-9377
    rorid: null
    typeEntity: Person
    typeRole:
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    url: https://messerlab.org
  - email: bhaller@benhaller.com
    fundrefid: null
    gridid: null
    name: Benjamin C. Haller
    note: null
    orcidid: https://orcid.org/0000-0003-1874-8327
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://benhaller.com
  description: Evolutionary simulation framework that combines a powerful engine for
    population genetic simulations with the capability of modeling arbitrarily complex
    evolutionary scenarios.  Includes a graphical modeling environment.
  documentation:
  - note: The manual for SLiM itself
    type:
    - User manual
    url: http://benhaller.com/slim/SLiM_Manual.pdf
  - note: The manual for Eidos, the scripting language used by SLiM
    type:
    - User manual
    url: http://benhaller.com/slim/Eidos_Manual.pdf
  - note: Quick reference sheets for SLiM and Eidos
    type:
    - Quick start guide
    url: http://benhaller.com/slim/SLiMEidosRefSheets.zip
  download:
  - note: A source archive for the command-line `slim` tool only.  Complete source
      code is on GitHub, but most platforms have an installer anyway; see the manual,
      chapter 2, for installation instructions.
    type: Source code
    url: http://benhaller.com/slim/SLiM.zip
    version: null
  - note: The GitHub page for the current release version, to obtain full source code.
    type: Downloads page
    url: https://github.com/MesserLab/SLiM/releases/latest
    version: null
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  function:
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    input: []
    note: Run individual-based eco-evolutionary simulations with explicit genetics
    operation:
    - term: DNA substitution modelling
      uri: http://edamontology.org/operation_0550
    - term: Sequence generation
      uri: http://edamontology.org/operation_0230
    - term: Ecological modelling
      uri: http://edamontology.org/operation_3946
    output: []
  homepage: https://messerlab.org/slim/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2025-09-13T19:34:39.164982Z'
  license: GPL-3.0
  link:
  - note: SLiM home page in the Messer Lab website
    type:
    - Software catalogue
    url: https://messerlab.org/slim/
  - note: GitHub repository for SLiM
    type:
    - Repository
    url: https://github.com/MesserLab/SLiM
  - note: Discussion forum for SLiM questions
    type:
    - Discussion forum
    url: https://groups.google.com/g/slim-discuss
  - note: Announcements mailing list
    type:
    - Mailing list
    url: https://groups.google.com/g/slim-announce
  maturity: Mature
  name: SLiM
  operatingSystem:
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  - Mac
  - Windows
  otherID: []
  owner: bchaller
  publication:
  - doi: 10.1093/molbev/msy228
    metadata:
      abstract: ''
      authors: []
      citationCount: 541
      date: '2019-03-01T00:00:00Z'
      journal: Molecular Biology and Evolution
      title: 'SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model'
    note: 'B.C. Haller, P.W. Messer. (2019). SLiM 3: Forward genetic simulations beyond
      the Wright–Fisher Model. Molecular Biology and Evolution 36(3), 632–637.'
    pmcid: PMC6389312
    pmid: '30517680'
    type:
    - Primary
    version: '3.0'
  - doi: 10.1093/molbev/msy237
    metadata:
      abstract: ''
      authors: []
      citationCount: 13
      date: '2019-05-01T00:00:00Z'
      journal: Molecular Biology and Evolution
      title: Evolutionary Modeling in SLiM 3 for Beginners
    note: B.C. Haller, P.W. Messer. (2019). Evolutionary modeling in SLiM 3 for beginners.
      Molecular Biology and Evolution 36(5), 1101–1109.
    pmcid: PMC6501880
    pmid: '30590560'
    type:
    - Method
    version: '3.0'
  - doi: 10.1111/1755-0998.12968
    metadata:
      abstract: ''
      authors: []
      citationCount: 123
      date: '2019-03-01T00:00:00Z'
      journal: Molecular Ecology Resources
      title: Tree-sequence recording in SLiM opens new horizons for forward-time simulation
        of whole genomes
    note: B.C. Haller, J. Galloway, J. Kelleher, P.W. Messer, P.L. Ralph. (2019).
      Tree-sequence recording in SLiM opens new horizons for forward-time simulation
      of whole genomes. Molecular Ecology Resources 19(2), 552–566.
    pmcid: PMC6393187
    pmid: '30565882'
    type:
    - Primary
    version: '3.0'
  - doi: 10.1101/2025.08.07.669155
    metadata: null
    note: 'BC Haller, PL Ralph, PW Messer. (2025). SLiM 5: Eco-evolutionary simulations
      across multiple chromosomes and full genomes. bioRxiv, 2025.08. 07.669155'
    pmcid: PMC12363870
    pmid: '40832315'
    type:
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    version: '5.0'
  - doi: 10.1086/723601
    metadata:
      abstract: ''
      authors: []
      citationCount: 124
      date: '2023-05-01T00:00:00Z'
      journal: American Naturalist
      title: 'SLiM 4: Multispecies Eco-Evolutionary Modeling'
    note: 'B.C. Haller, P.W. Messer. (2023). SLiM 4: Multispecies eco-evolutionary
      modeling. The American Naturalist 201(5), E127–E139.'
    pmcid: PMC10793872
    pmid: '37130229'
    type:
    - Primary
    version: '4.0'
  relation: []
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2025-09-03T07:50:00.879412Z'
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  biotoolsID: cats-rf
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
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    note: null
    orcidid: https://orcid.org/0000-0002-1212-3302
    rorid: null
    typeEntity: Person
    typeRole:
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    - Maintainer
    - Documentor
    - Primary contact
    url: https://orcid.org/0000-0002-1212-3302
  description: CATS-rf evaluates transcriptome assemblies using RNA-seq reads without
    requiring a reference genome
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/bodulic/CATS-rf
  download:
  - note: null
    type: Source code
    url: https://github.com/bodulic/CATS-rf
    version: 1.0.2
  - note: null
    type: Software package
    url: https://anaconda.org/bioconda/cats-rf
    version: 1.0.2
  - note: null
    type: Container file
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  editPermission:
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  elixir_badge: 0
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    input:
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      format: []
    note: null
    operation:
    - term: Sequence assembly validation
      uri: http://edamontology.org/operation_3180
    output:
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        term: Statistical estimate score
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      format: []
  homepage: https://github.com/bodulic/CATS-rf
  homepage_status: 0
  language:
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  lastUpdate: '2025-09-13T17:36:18.188276Z'
  license: MIT
  link:
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  operatingSystem:
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  owner: bodulic
  publication:
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    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Omics
    uri: http://edamontology.org/topic_3391
  - term: Biology
    uri: http://edamontology.org/topic_3070
  - term: Biosciences
    uri: http://edamontology.org/topic_4019
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2021-01-18T09:10:00Z'
  biotoolsCURIE: biotools:atomic-charge-calculator-ii
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  confidence_flag: tool
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  credit:
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    fundrefid: null
    gridid: null
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    note: null
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    url: null
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    rorid: null
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  description: Atomic Charge Calculator II (ACC II) is a web application for fast
    calculation of partial atomic charges.
  documentation:
  - note: null
    type:
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    url: https://acc2.ncbr.muni.cz/static/manual.pdf
  download: []
  editPermission:
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  function:
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      - term: mmCIF
        uri: http://edamontology.org/format_1477
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: mmCIF
        uri: http://edamontology.org/format_1477
    note: Calculation of partial atomic charges
    operation:
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    output: []
  homepage: https://acc2.ncbr.muni.cz
  homepage_status: 0
  language:
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  - JavaScript
  - C++
  lastUpdate: '2025-09-11T08:26:42.258113Z'
  license: MIT
  link:
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  maturity: Mature
  name: Atomic Charge Calculator II
  operatingSystem: []
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  publication:
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    metadata:
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      authors: []
      citationCount: 46
      date: '2021-01-01T00:00:00Z'
      journal: Nucleic Acids Research
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    note: null
    pmcid: PMC7319571
    pmid: '32402071'
    type:
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    version: null
  relation: []
  toolType:
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  - Web API
  - Command-line tool
  topic:
  - term: Computational chemistry
    uri: http://edamontology.org/topic_3332
  validated: 0
  version:
  - '2'
- accessibility: Open access
  additionDate: '2025-09-10T13:36:20.945616Z'
  biotoolsCURIE: biotools:fastplong
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  confidence_flag: null
  cost: Free of charge
  credit:
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    name: OpenGene
    note: 'OpenGene - Open Source Genomics Toolbox

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    orcidid: null
    rorid: null
    typeEntity: null
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  description: Ultrafast preprocessing and quality control for long reads (Nanopore,
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  download: []
  editPermission:
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    note: null
    operation:
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    output: []
  - cmd: null
    input: []
    note: null
    operation:
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  homepage_status: 0
  language: []
  lastUpdate: '2025-09-10T14:13:36.859562Z'
  license: MIT
  link:
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    type:
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  - note: null
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    type:
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  topic:
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  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2016-03-24T16:22:28Z'
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    \ one produced by the TEdenovo pipeline, to provide TE annotations exported into\
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  elixirNode:
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  elixirPlatform:
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  language:
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  link:
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    pmid: null
    type:
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  relation: []
  toolType:
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  topic:
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  - term: DNA
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  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
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  version:
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  cost: Free of charge
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    note: null
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    typeRole:
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    - Support
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    url: https://urgi.versailles.inrae.fr/
  description: The PASTEClassifier (Pseudo Agent System for Transposable Elements
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    features. It browses the whole spectrum of possible classifications at order level
    using Wicker hierarchical system. It is also able to automatically classify other
    repeated elements like SSR (Simple Sequence Repeats), rDNA or potential repeated
    host genes. The output is designed to facilitate manual curation by providing
    to the biologist all characteristics that have been found on each TE sequence.
  documentation:
  - note: null
    type:
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  language:
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  - C++
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  license: CECILL-2.0
  link:
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    type:
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    url: https://urgi.versailles.inrae.fr/download/repet/
  maturity: Legacy
  name: PASTEClassifier
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  otherID: []
  owner: fruitshuang
  publication:
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    metadata:
      abstract: ''
      authors: []
      citationCount: 226
      date: '2014-05-02T00:00:00Z'
      journal: PLoS ONE
      title: 'PASTEC: An automatic transposable element classification tool'
    note: null
    pmcid: PMC4008368
    pmid: '24786468'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence composition, complexity and repeats
    uri: http://edamontology.org/topic_0157
  validated: 1
  version:
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- accessibility: null
  additionDate: '2024-01-10T12:54:25.092426Z'
  biotoolsCURIE: biotools:urgi
  biotoolsID: urgi
  collectionID:
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  confidence_flag: tool
  cost: Free of charge
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    name: Jerome Salse
    note: null
    orcidid: https://orcid.org/0000-0003-2942-1098
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    typeRole:
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    url: null
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    note: null
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    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
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    note: null
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    typeEntity: Division
    typeRole:
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  description: Comparative genomics-driven translational research tool.
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  function:
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    input: []
    note: null
    operation:
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    - term: Database search
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    output: []
  homepage: https://urgi.versailles.inrae.fr/synteny
  homepage_status: 0
  language: []
  lastUpdate: '2025-09-09T08:09:00.018602Z'
  license: Other
  link: []
  maturity: null
  name: SyntenyViewer
  operatingSystem:
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  - Linux
  - Windows
  otherID: []
  owner: raphael.flores
  publication:
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    metadata:
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      journal: Database
      title: 'SyntenyViewer: a comparative genomics-driven translational research
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    note: null
    pmcid: PMC10167986
    pmid: '37159239'
    type: []
    version: null
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0102
  - term: Plant biology
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  - term: Structural variation
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  - term: Paleogenomics
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  - term: Protein expression
    uri: http://edamontology.org/topic_0108
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  validated: 0
  version: []
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  additionDate: '2025-09-08T11:36:08.406899Z'
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  description: HVRLocator is a workflow to identify spanning hypervariable region(s)
    from amplicon sequencing variants or SRA public runs (SRR). It aligns query sequences
    to a reference E. coli full-length 16S rRNA gene and identifies the spanning region
    through alignment.
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  license: CC0-1.0
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    url: https://cloud.sylabs.io/library/jsaraiva/repo/hvrlocator
  maturity: null
  name: HVRLocator
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  owner: Kasmanas
  publication:
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    metadata: null
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  toolType:
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  topic:
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  - term: Probes and primers
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  validated: 0
  version: []
- accessibility: Open access
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    note: null
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    url: https://www.lifesci.dundee.ac.uk/people/geoff-barton
  description: Jalview is a free cross-platform program for multiple sequence alignment
    editing, visualisation and analysis. Use it to align, view and edit sequence alignments,
    analyse them with phylogenetic trees and principal components analysis (PCA) plots
    and explore molecular structures and annotation.
  documentation:
  - note: null
    type:
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  - note: null
    type:
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    type:
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  download:
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    version: null
  - note: Binaries for all platforms
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    url: https://www.jalview.org/download/?os=all
    version: null
  - note: null
    type: Icon
    url: https://www.jalview.org/favicon.svg
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  - note: Executable JAR file
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    version: null
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  function:
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      - term: FASTA-aln
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      - term: GFF2-seq
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      - term: BLC
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    - data:
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      format:
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    note: 'Other Input formats:

      AMSA (.amsa);

      JnetFile (.concise, .jnet);

      PFAM (.pfam);

      Substitution matrix (.matrix);

      Jalview Project File (.jvp);

      Jalview Feature File (.features, .jvfeatures);

      Jalview Annotations File (.annotations, .jvannotations);

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      ...

      Other Output formats:

      PFAM (.pfam);

      BioJS (.biojs) (interactive HTML/Javascript);

      Jalview Project File (.jvp);'
    operation:
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      - term: FASTA
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      - term: PHYLIP format
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      - term: GCG MSF
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      - term: Pileup
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      - term: ClustalW format
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    - data:
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      - term: HTML
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      - term: EPS
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      - term: SVG
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  homepage: https://www.jalview.org/
  homepage_status: 0
  language: []
  lastUpdate: '2025-09-04T13:26:28.643607Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Discussion forum
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  - note: null
    type:
    - Issue tracker
    url: https://issues.jalview.org/
  - note: Latest development version
    type:
    - Other
    url: https://www.jalview.org/development/jalview_develop/
  - note: null
    type:
    - Repository
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  - note: Twitter feed
    type:
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  - note: YouTube training videos
    type:
    - Social media
    url: https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw
  maturity: Mature
  name: Jalview
  operatingSystem:
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  otherID: []
  owner: ben_s
  publication:
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    metadata:
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      authors: []
      citationCount: 7499
      date: '2009-05-07T00:00:00Z'
      journal: Bioinformatics
      title: Jalview Version 2-A multiple sequence alignment editor and analysis workbench
    note: null
    pmcid: PMC2672624
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    type: []
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  relation:
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    type: uses
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  toolType:
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  topic:
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  validated: 1
  version:
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  additionDate: '2025-09-03T08:01:20.173602Z'
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  description: CATS-rb evaluates transcriptome assemblies using the reference genome
    of the corresponding species
  documentation:
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    note: null
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  publication:
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  relation: []
  toolType:
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  topic:
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  - term: Biology
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  additionDate: '2019-08-09T13:14:25Z'
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  description: Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine
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  topic:
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  - term: Proteomics experiment
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  biotoolsCURIE: biotools:omicflow
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  description: A generalised data structure for fast and efficient loading and data
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  documentation:
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  otherID: []
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  toolType:
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  topic:
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  - term: Microbial ecology
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  - term: Proteomics
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  validated: 0
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        of correction, filtration, imputation, and normalization steps. Manual execution
        across various applications often leads to inefficiencies, human-induced errors,
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        metabolomics datasets combining established methodologies and offering flexibility
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    be installed locally as a desktop app, Docker image, or R package.
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    metadata:
      abstract: Quality control (QC) is crucial for any scientific method producing
        data. Applying adequate QC introduces new challenges in the genomics field
        where large amounts of data are produced with complex technologies. For DNA
        microarrays, specific algorithms for QC and pre-processing including normalization
        have been developed by the scientific community, especially for expression
        chips of the Affymetrix platform. Many of these have been implemented in the
        statistical scripting language R and are available from the Bioconductor repository.
        However, application is hampered by lack of integrative tools that can be
        used by users of any experience level. To fill this gap, we developed a freely
        available tool for QC and pre-processing of Affymetrix gene expression results,
        extending, integrating and harmonizing functionality of Bioconductor packages.
        The tool can be easily accessed through a wizard-like web portal at http://www.arrayanalysis.org
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        and detailed technical documentation. It assists newcomers to the field in
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      - name: Jaillard M.
      - name: Adriaens M.E.
      - name: Gaj S.
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    note: null
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      abstract: 'Background: Illumina whole-genome expression bead arrays are a widely
        used platform for transcriptomics. Most of the tools available for the analysis
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        ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive
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        modules that provide support for additional types of data or extend workflows.
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        a free and user-friendly web interface for quality control and pre-processing
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        statistical and pathway analysis to provide a full workflow for Illumina gene
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        provided on the website or to generate processed input data for a broad range
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      - name: Goelela V.S.
      - name: Kelder T.
      - name: Adriaens M.E.
      - name: Evelo C.T.
      - name: Radonjic M.
      citationCount: 12
      date: '2015-06-30T00:00:00Z'
      journal: BMC Genomics
      title: A user-friendly workflow for analysis of Illumina gene expression bead
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    note: null
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    pmid: '26122086'
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    version: null
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  collectionID: []
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  cost: Free of charge
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  - email: rhernandvel@gmail.com
    fundrefid: null
    gridid: null
    name: Rodrigo Hernández Velázquez
    note: null
    orcidid: https://orcid.org/0009-0009-3048-8573
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: 'ViromeXplore conatains a set of bioinformatic workflows that can be
    used reproducibly, sequentially and interoperably between them and with other
    workflows. It allows multiple input types mand starting points that include raw
    reads, contigs, genomes, abbundance tables, phylogenies and taxonomies. ViromeXplore
    contains the most varied and comprehensive workflows to explore viral genes and
    genomes from viromes and metagenomes to date. The future aim for ViromeXplore
    is to continue expanding the workflows and including the most recent and efficient
    tools.


    The workflows are implemented in Nextflow, and additionally only Docker or Singularity
    are needed to run ViromeXplore.'
  documentation:
  - note: All the updated documentation can be found in readthedocs.
    type:
    - User manual
    url: https://viromexplore.readthedocs.io
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    url: https://github.com/rhernandvel/ViromeXplore
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  homepage_status: 0
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  lastUpdate: '2025-08-22T12:53:03.396154Z'
  license: BSD-3-Clause
  link:
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    type:
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  maturity: null
  name: ViromeXplore
  operatingSystem: []
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  owner: rhernandvel
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  topic: []
  validated: 0
  version:
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- accessibility: Open access
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  confidence_flag: null
  cost: Free of charge
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    fundrefid: null
    gridid: null
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    note: null
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    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Susan Carpenter
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    orcidid: https://orcid.org/0000-0002-5600-5404
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
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    gridid: null
    name: Karen McGinnis
    note: null
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    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
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    name: Andrew Nelson
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    rorid: null
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    typeRole: []
    url: null
  - email: null
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    gridid: null
    name: Keriayn Smith
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    orcidid: https://orcid.org/0000-0002-4351-2765
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Tian Hong
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    orcidid: https://orcid.org/0000-0002-8212-7050
    rorid: null
    typeEntity: null
    typeRole:
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    url: null
  description: EssSubgraph is a model algorithm that integrates omics data and network
    data to predict essential genes.
  documentation:
  - note: null
    type:
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    url: https://github.com/wenmm/EssSubgraph/tree/main
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  function:
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    input: []
    note: null
    operation:
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    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Gene prediction
      uri: http://edamontology.org/operation_2454
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Protein-protein interaction analysis
      uri: http://edamontology.org/operation_2949
    output: []
  homepage: https://github.com/wenmm/EssSubgraph/tree/main
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-08-20T18:13:15.065957Z'
  license: GPL-3.0
  link:
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    type:
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  maturity: Mature
  name: EssSubgraph
  operatingSystem:
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  owner: haimei
  publication:
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    metadata: null
    note: https://www.biorxiv.org/content/10.1101/2025.07.21.665218v1.abstract
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    pmid: null
    type:
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    version: null
  relation:
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    type: includes
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  topic:
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  - term: Computational biology
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  - term: Machine learning
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  - term: Biomarkers
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  validated: 0
  version: []
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    url: https://matheat.streamlit.app/
  description: MatHeat transforms your gene expression data into powerful insights,
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  license: null
  link:
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    type:
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  - note: Landing page of the MatHeat
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  topic:
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  - term: Gene expression
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  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Software engineering
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  - term: Bioinformatics
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  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  validated: 0
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- accessibility: Open access
  additionDate: '2025-08-12T09:03:01.228796Z'
  biotoolsCURIE: biotools:nf-cbra-snvs
  biotoolsID: nf-cbra-snvs
  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Workflow optimized for the analysis of rare diseases, designed to detect
    SNVs and INDELs in targeted sequencing data (CES/WES) and whole genome sequencing
    (WGS), built on Nextflow.
  documentation:
  - note: null
    type:
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    url: https://github.com/CIBERER/nf-CBRA-snvs
  download: []
  editPermission:
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  homepage: https://github.com/CIBERER/nf-CBRA-snvs
  homepage_status: 0
  language: []
  lastUpdate: '2025-08-12T09:05:51.626707Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/CIBERER/nf-CBRA-snvs
  maturity: Emerging
  name: nf-CBRA-snvs
  operatingSystem:
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  otherID: []
  owner: pminguez
  publication: []
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-08-12T08:52:25.808752Z'
  biotoolsCURIE: biotools:whale-fjd
  biotoolsID: whale-fjd
  collectionID:
  - IMPaCT-Data
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Pipeline based on Nextflow and nf-core for long-read DNA sequencing
    analysis.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/TBLabFJD/WHALE
  download: []
  editPermission:
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    - yolandabq
    type: group
  elixirCommunity: []
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  homepage: https://github.com/TBLabFJD/WHALE
  homepage_status: 0
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  lastUpdate: '2025-08-12T09:05:33.311501Z'
  license: CC-BY-SA-4.0
  link:
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    type:
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    url: https://github.com/TBLabFJD/WHALE
  maturity: Emerging
  name: WHALE-FJD
  operatingSystem:
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  otherID: []
  owner: pminguez
  publication: []
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0622
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-06-19T09:33:56.106410Z'
  biotoolsCURIE: biotools:parrot-fjd
  biotoolsID: parrot-fjd
  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Germline variant calling pipeline implemented in Nextflow which performs
    mapping, SNV/INDEL calling and annotation, and CNV calling and annotation for
    targeted sequencing (gene panels and WES) and whole genome sequencing.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/TBLabFJD/PARROT-FJD
  download: []
  editPermission:
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    type: private
  elixirCommunity:
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  elixirNode: []
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  homepage: https://github.com/TBLabFJD/PARROT-FJD
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  license: CC-BY-NC-4.0
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  maturity: Emerging
  name: PARROT-FJD
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  relation:
  - biotoolsID: fjd-pipeline
    type: isNewVersionOf
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    type: usedBy
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0622
  validated: 0
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- accessibility: Open access
  additionDate: '2022-03-21T17:29:40.559556Z'
  biotoolsCURIE: biotools:fjd-pipeline
  biotoolsID: fjd-pipeline
  collectionID:
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  confidence_flag: null
  cost: Free of charge
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    fundrefid: null
    gridid: null
    name: Bioinformatics Unit IIS-FJD
    note: null
    orcidid: https://orcid.org/0000-0003-4099-9421
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    typeEntity: Person
    typeRole:
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    url: https://www.translationalbioinformaticslab.es/
  description: 'Pipeline for Single Nucleotide Variants (SNVs) and Copy Number Variation
    (CNVs) variant calling. This tool is no longer maintained. See the new version:
    PARROT-FJD.'
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/TBLabFJD/VariantCallingFJD
  download: []
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  function:
  - cmd: null
    input:
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        term: Tool name (FASTA)
        uri: http://edamontology.org/data_1193
      format:
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        uri: http://edamontology.org/format_2545
    note: null
    operation:
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    - term: Copy number variation detection
      uri: http://edamontology.org/operation_3961
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: https://github.com/TBLabFJD/VariantCallingFJD
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  language:
  - Python
  - R
  - Bash
  lastUpdate: '2025-08-12T08:31:29.574795Z'
  license: CC-BY-NC-SA-4.0
  link:
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/TBLabFJD/VariantCallingFJD
  maturity: Emerging
  name: FJD-pipeline
  operatingSystem:
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  otherID: []
  owner: iiancu
  publication:
  - doi: 10.1038/s41525-021-00278-6
    metadata:
      abstract: Clinical exome (CE) sequencing has become a first-tier diagnostic
        test for hereditary diseases; however, its diagnostic rate is around 30–50%.
        In this study, we aimed to increase the diagnostic yield of CE using a custom
        reanalysis algorithm. Sequencing data were available for three cohorts using
        two commercial protocols applied as part of the diagnostic process. Using
        these cohorts, we compared the performance of general and clinically relevant
        variant calling and the efficacy of an in-house bioinformatic protocol (FJD-pipeline)
        in detecting causal variants as compared to commercial protocols. On the whole,
        the FJD-pipeline detected 99.74% of the causal variants identified by the
        commercial protocol in previously solved cases. In the unsolved cases, FJD-pipeline
        detects more INDELs and non-exonic variants, and is able to increase the diagnostic
        yield in 2.5% and 3.2% in the re-analysis of 78 cancer and 62 cardiovascular
        cases. These results were considered to design a reanalysis, filtering and
        prioritization algorithm that was tested by reassessing 68 inconclusive cases
        of monoallelic autosomal recessive retinal dystrophies increasing the diagnosis
        by 4.4%. In conclusion, a guided NGS reanalysis of unsolved cases increases
        the diagnostic yield in genetic disorders, making it a useful diagnostic tool
        in medical genetics.
      authors:
      - name: Romero R.
      - name: de la Fuente L.
      - name: Del Pozo-Valero M.
      - name: Riveiro-Alvarez R.
      - name: Trujillo-Tiebas M.J.
      - name: Martin-Merida I.
      - name: Avila-Fernandez A.
      - name: Iancu I.-F.
      - name: Perea-Romero I.
      - name: Nunez-Moreno G.
      - name: Damian A.
      - name: Rodilla C.
      - name: Almoguera B.
      - name: Corton M.
      - name: Ayuso C.
      - name: Minguez P.
      citationCount: 12
      date: '2022-12-01T00:00:00Z'
      journal: npj Genomic Medicine
      title: An evaluation of pipelines for DNA variant detection can guide a reanalysis
        protocol to increase the diagnostic ratio of genetic diseases
    note: null
    pmcid: PMC8795168
    pmid: '35087072'
    type:
    - Usage
    version: null
  relation:
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    type: hasNewVersion
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0091
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version: []
- accessibility: Open access
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  collectionID:
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  cost: Free of charge
  credit: []
  description: FREEPII (Feature Representation Enhancement End-to-end Protein Interaction
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    and feature representation enhancement for PPIs and protein complexes inference.
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  license: MIT
  link: []
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  name: FREEPII
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  owner: qqpigass
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  validated: 0
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- accessibility: Open access
  additionDate: '2023-07-25T12:35:27.605861Z'
  biotoolsCURIE: biotools:macpepdb_-_mass_centric_peptide_database
  biotoolsID: macpepdb_-_mass_centric_peptide_database
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  confidence_flag: null
  cost: Free of charge
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  - email: null
    fundrefid: null
    gridid: null
    name: Julian Uszkoreit
    note: null
    orcidid: http://orcid.org/0000-0001-7522-4007
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: dirk.winkelhardt@rub.de
    fundrefid: null
    gridid: null
    name: Dirk Winkelhardt
    note: null
    orcidid: https://orcid.org/0000-0001-8770-2221
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: PD Dr. Martin Eisenacher
    note: null
    orcidid: https://orcid.org/0000-0003-2687-7444
    rorid: null
    typeEntity: null
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    url: null
  description: A Database to Quickly Access All Tryptic Peptides of the UniProtKB
  documentation:
  - note: null
    type:
    - API documentation
    url: https://docs.rs/macpepdb/latest/macpepdb/web/index.html
  download: []
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  homepage: https://macpepdb.cubimed.rub.de/
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  language:
  - Rust
  - JavaScript
  - Other
  lastUpdate: '2025-07-31T09:03:29.192901Z'
  license: null
  link:
  - note: Backend implementation written in Rust / Axum
    type:
    - Repository
    url: https://github.com/medbioinf/macpepdb
  - note: Frontend implementation written in Rust / Dioxus
    type:
    - Repository
    url: https://github.com/medbioinf/macpepdb-frontend
  maturity: Mature
  name: MaCPepDB - Mass Centric Peptide Database
  operatingSystem: []
  otherID: []
  owner: di_hardt
  publication:
  - doi: 10.1021/acs.jproteome.0c00967
    metadata:
      abstract: Protein sequence databases play a crucial role in the majority of
        the currently applied mass-spectrometry-based proteomics workflows. Here UniProtKB
        serves as one of the major sources, as it combines the information of several
        smaller databases and enriches the entries with additional biological information.
        For the identification of peptides in a sample by tandem mass spectra, as
        generated by data-dependent acquisition, protein sequence databases provide
        the basis for most spectrum identification search engines. In addition, for
        targeted proteomics approaches like selected reaction monitoring (SRM) and
        parallel reaction monitoring (PRM), knowledge of the peptide sequences, their
        masses, and whether they are unique for a protein is essential. Because most
        bottom-up proteomics approaches use trypsin to cleave the proteins in a sample,
        the tryptic peptides contained in a protein database are of great interest.
        We present a database, called MaCPepDB (mass-centric peptide database), that
        consists of the complete tryptic digest of the Swiss-Prot and TrEMBL parts
        of UniProtKB. This database is especially designed to not only allow queries
        of peptide sequences and return the respective information about connected
        proteins and thus whether a peptide is unique but also allow queries of specific
        masses of peptides or precursors of MS/MS spectra. Furthermore, posttranslational
        modifications can be considered in a query as well as different mass deviations
        for posttranslational modifications. Hence the database can be used by a sequence
        query not only to, for example, check in which proteins of the UniProt database
        a tryptic peptide can be found but also to find possibly interfering peptides
        in PRM/SRM experiments using the mass query. The complete database contains
        currently 5 939 244 990 peptides from 185 561 610 proteins (UniProt version
        2020_03), for which a single query usually takes less than 1 s. For easy exploration
        of the data, a web interface was developed. A REST application programming
        interface (API) for programmatic and workflow access is also available at
        https://macpepdb.mpc.rub.de.
      authors:
      - name: Uszkoreit J.
      - name: Winkelhardt D.
      - name: Barkovits K.
      - name: Wulf M.
      - name: Roocke S.
      - name: Marcus K.
      - name: Eisenacher M.
      citationCount: 9
      date: '2021-04-02T00:00:00Z'
      journal: Journal of Proteome Research
      title: 'MaCPepDB: A Database to Quickly Access All Tryptic Peptides of the UniProtKB'
    note: null
    pmcid: null
    pmid: '33724838'
    type:
    - Primary
    version: '1.0'
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version:
  - 3.0.0
- accessibility: Open access
  additionDate: '2019-11-05T10:40:37Z'
  biotoolsCURIE: biotools:WheatIS
  biotoolsID: WheatIS
  collectionID:
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  - URGI
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: urgi-support@inrae.fr
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    note: null
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    - Support
    url: null
  description: "This project aims at building an International Wheat Information System\
    \ (WheatIS) to support the wheat research community. The main objective is to\
    \ provide a single-access web based system to access to the available data resources\
    \ and bioinformatics tools. The web portal indexes and makes findable any kind\
    \ of data from wheat related species. \nThe WheatIS search is an implementation\
    \ of DataDiscovery."
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    type:
    - General
    url: https://urgi.versailles.inra.fr/wheatis/about
  - note: null
    type:
    - Contributions policy
    url: https://urgi.versailles.inra.fr/wheatis/join
  - note: null
    type:
    - Terms of use
    url: https://urgi.versailles.inra.fr/wheatis/legal
  - note: null
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    - User manual
    url: https://urgi.versailles.inra.fr/wheatis/help
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        term: Ontology data
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      format: []
    note: null
    operation:
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      format: []
    - data:
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  homepage_status: 0
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  lastUpdate: '2025-07-29T13:42:41.391722Z'
  license: BSD-3-Clause
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    type:
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  maturity: Mature
  name: WheatIS
  operatingSystem: []
  otherID: []
  owner: jison
  publication:
  - doi: 10.1186/s13059-018-1491-4
    metadata:
      abstract: © 2018 The Author(s).The Wheat@URGI portal has been developed to provide
        the international community of researchers and breeders with access to the
        bread wheat reference genome sequence produced by the International Wheat
        Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools
        have been established for in-depth exploration of the genome sequence together
        with additional linked datasets including physical maps, sequence variations,
        gene expression, and genetic and phenomic data from other international collaborative
        projects already stored in the GnpIS information system. The portal provides
        enhanced search and browser features that will facilitate the deployment of
        the latest genomics resources in wheat improvement.
      authors:
      - name: Alaux M.
      - name: Rogers J.
      - name: Letellier T.
      - name: Flores R.
      - name: Alfama F.
      - name: Pommier C.
      - name: Mohellibi N.
      - name: Durand S.
      - name: Kimmel E.
      - name: Michotey C.
      - name: Guerche C.
      - name: Loaec M.
      - name: Laine M.
      - name: Steinbach D.
      - name: Choulet F.
      - name: Rimbert H.
      - name: Leroy P.
      - name: Guilhot N.
      - name: Salse J.
      - name: Feuillet C.
      - name: Paux E.
      - name: Eversole K.
      - name: Adam-Blondon A.-F.
      - name: Quesneville H.
      citationCount: 88
      date: '2018-08-17T00:00:00Z'
      journal: Genome Biology
      title: Linking the International Wheat Genome Sequencing Consortium bread wheat
        reference genome sequence to wheat genetic and phenomic data
    note: Alaux M, Rogers J, Letellier T, Flores R, Alfama  F, Pommier C, Mohellibi
      N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach D,
      Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, International
      Wheat Genome Sequencing Consortium, Paux E, Eversole K, Adam-Blondon A-F, Quesneville
      H (2018) Linking the International Wheat Genome Sequencing Consortium bread
      wheat reference genome sequence to wheat genetic and phenomic data. Genome Biology,
      19:111
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
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  topic:
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    uri: http://edamontology.org/topic_0780
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  - term: Biological databases
    uri: http://edamontology.org/topic_3071
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2020-02-13T15:34:59Z'
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  biotoolsID: RARe
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  credit:
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    gridid: null
    name: Support service
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
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    - Support
    url: null
  description: "RARe is a research infrastructure registered on the french national\
    \ roadmap that brings together five networks of BRCs conserving genetic, genomic,\
    \ and biological resources assembled and characterized by research on domestic\
    \ animals, model or cultivated plants, wild species related to domestic animals,\
    \ forest trees, micro-organisms of agronomic or agri-food interest, micro-organisms\
    \ and environmental organisms.\nThe purpose of this web portal is to facilitate\
    \ the discoverability of these data. \nRARe search is an implementation of DataDiscovery."
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  - note: null
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  - note: null
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    url: https://urgi.versailles.inrae.fr/rare/legal
  - note: null
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      format: []
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      format: []
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  license: BSD-3-Clause
  link:
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  maturity: Emerging
  name: RARe
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  owner: nfrancillon
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  relation:
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  - Web application
  - Web service
  - Database portal
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    uri: http://edamontology.org/topic_0780
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  - term: Biological databases
    uri: http://edamontology.org/topic_3071
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2020-01-21T16:40:38Z'
  biotoolsCURIE: biotools:DataDiscovery
  biotoolsID: DataDiscovery
  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit:
  - email: urgi-support@inrae.fr
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    typeRole:
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    url: null
  description: 'DataDiscovery aims at providing researchers a simple and fast access
    to relevant biological data using specific keywords and easy to use filters.


    This tool is expected to be easily customizable for specific filters, environments,
    or data schemas. Its current implementations supported by URGI are: WheatIS, Plant,
    RARe.'
  documentation:
  - note: General terms of use
    type:
    - Terms of use
    url: https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/LEGAL-MENTIONS.md
  - note: How to contribute
    type:
    - Contributions policy
    url: https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/README.md#contribute
  - note: How to use
    type:
    - User manual
    url: https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/HELP.md
  - note: How to install
    type:
    - Installation instructions
    url: https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/README.md#setup
  download: []
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  elixirNode:
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        uri: http://edamontology.org/data_2353
      format: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_2421
    - term: Relation extraction
      uri: http://edamontology.org/operation_3625
    - term: Indexing
      uri: http://edamontology.org/operation_0227
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      uri: http://edamontology.org/operation_3908
    output:
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        term: Database search results
        uri: http://edamontology.org/data_2080
      format: []
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        term: Data reference
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      format: []
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        term: Identifier
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      format: []
  homepage: https://urgi.versailles.inrae.fr/data-discovery/
  homepage_status: 0
  language:
  - JavaScript
  - Java
  - Bash
  lastUpdate: '2025-07-29T13:42:39.375595Z'
  license: BSD-3-Clause
  link:
  - note: GitLab code repository for DataDiscovery
    type:
    - Repository
    url: https://forgemia.inra.fr/urgi-is/data-discovery
  - note: Code repository mirror link for DataDiscovery
    type:
    - Mirror
    url: https://github.com/gnpis/DataDiscovery/
  maturity: Emerging
  name: DataDiscovery
  operatingSystem:
  - Linux
  otherID: []
  owner: nfrancillon
  publication:
  - doi: 10.3835/plantgenome2015.06.0038
    metadata:
      abstract: The genome sequences of many important Triticeae species, including
        bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained
        uncharacterized for a long time because their high repeat content, large sizes,
        and polyploidy. As a result of improvements in sequencing technologies and
        novel analyses strategies, several of these have recently been deciphered.
        These efforts have generated new insights into Triticeae biology and genome
        organization and have important implications for downstream usage by breeders,
        experimental biologists, and comparative genomicists. transPLANT (http://www.transplantdb.eu)
        is an EU-funded project aimed at constructing hardware, software, and data
        infrastructure for genome-scale research in the life sciences. Since the Triticeae
        data are intrinsically complex, heterogenous, and distributed, the transPLANT
        consortium has undertaken efforts to develop common data formats and tools
        that enable the exchange and integration of data from distributed resources.
        Here we present an overview of the individual Triticeae genome resources hosted
        by transPLANT partners, introduce the objectives of transPLANT, and outline
        common developments and interfaces supporting integrated data access.
      authors:
      - name: Spannagl M.
      - name: Alaux M.
      - name: Lange M.
      - name: Bolser D.M.
      - name: Bader K.C.
      - name: Letellier T.
      - name: Kimmel E.
      - name: Flores R.
      - name: Pommier C.
      - name: Kerhornou A.
      - name: Walts B.
      - name: Nussbaumer T.
      - name: Grabmuller C.
      - name: Chen J.
      - name: Colmsee C.
      - name: Beier S.
      - name: Mascher M.
      - name: Schmutzer T.
      - name: Arend D.
      - name: Thanki A.
      - name: Ramirez-Gonzalez R.
      - name: Ayling M.
      - name: Ayling S.
      - name: Caccamo M.
      - name: Mayer K.F.X.
      - name: Scholz U.
      - name: Steinbach D.
      - name: Quesneville H.
      - name: Kersey P.J.
      citationCount: 6
      date: '2016-03-01T00:00:00Z'
      journal: Plant Genome
      title: TransPLANT resources for triticeae genomic data
    note: "1-\tSpannagl, M., Alaux, M., Lange, M., Bolser, D. M., Bader, K. C., Letellier,\
      \ T., Kimmel, E., Flores, R.-G., Pommier, C., Kerhornou, A., Walts, B., Nussbaumer,\
      \ T., Grabmuller, C., Chen, J., Colmsee, C., Beier, S., Mascher, M., Schmutzer,\
      \ T., Arend, D., Thanki, A., Ramirez-Gonzalez, R., Ayling, M., Ayling, S., Caccamo,\
      \ M., Mayer, K. F. X., Scholz, U., Steinbach, D., Quesneville, H., Kersey, P.\
      \ (2016). TransPLANT resources for triticeae genomic data. Plant Genome, 9 (1),\
      \ 13 p."
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1038/hortres.2016.56
    metadata:
      abstract: Viticulture, like other fields of agriculture, is currently facing
        important challenges that will be addressed only through sustained, dedicated
        and coordinated research. Although the methods used in biology have evolved
        tremendously in recent years and now involve the routine production of large
        data sets of varied nature, in many domains of study, including grapevine
        research, there is a need to improve the findability, accessibility, interoperability
        and reusability (FAIR-ness) of these data. Considering the heterogeneous nature
        of the data produced, the transnational nature of the scientific community
        and the experience gained elsewhere, we have formed an open working group,
        in the framework of the International Grapevine Genome Program (www.vitaceae.org),
        to construct a coordinated federation of information systems holding grapevine
        data distributed around the world, providing an integrated set of interfaces
        supporting advanced data modeling, rich semantic integration and the next
        generation of data mining tools. To achieve this goal, it will be critical
        to develop, implement and adopt appropriate standards for data annotation
        and formatting. The development of this system, the GrapeIS, linking genotypes
        to phenotypes, and scientific research to agronomical and oeneological data,
        should provide new insights into grape biology, and allow the development
        of new varieties to meet the challenges of biotic and abiotic stress, environmental
        change, and consumer demand.
      authors:
      - name: Adam-Blondon A.-F.
      - name: Alaux M.
      - name: Pommier C.
      - name: Cantu D.
      - name: Cheng Z.-M.
      - name: Cramer G.
      - name: Davies C.
      - name: Delrot S.
      - name: Deluc L.
      - name: Di Gaspero G.
      - name: Grimplet J.
      - name: Fennell A.
      - name: Londo J.
      - name: Kersey P.
      - name: Mattivi F.
      - name: Naithani S.
      - name: Neveu P.
      - name: Nikolski M.
      - name: Pezzotti M.
      - name: Reisch B.
      - name: Topfer R.
      - name: Vivier M.
      - name: Ware D.
      - name: Quesneville H.
      citationCount: 37
      date: '2016-11-23T00:00:00Z'
      journal: Horticulture Research
      title: Towards an open grapevine information system
    note: "2-\tAdam-Blondon, A.-F., Alaux, M., Pommier, C., Cantu, D., Cheng, Z.-M.,\
      \ Cramer, G. R., Davies, C., Delrot, S., Deluc, L., di Gaspero, G., Grimplet,\
      \ J., Fennell, A., Londo, J. P., Kersey, P., Mattivi, F., Naithani, S., Neveu,\
      \ P., Nikolski, M., Pezzotti, M., Reisch, B. I., Topfer, R., Vivier, M., Ware,\
      \ D., Quesneville, H. (2016). Towards an open grapevine information system.\
      \ Horticulture Research, 3, 8 p. , DOI : 10.1038/hortres.2016.56"
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1186/s13059-018-1491-4
    metadata:
      abstract: The Wheat@URGI portal has been developed to provide the international
        community of researchers and breeders with access to the bread wheat reference
        genome sequence produced by the International Wheat Genome Sequencing Consortium.
        Genome browsers, BLAST, and InterMine tools have been established for in-depth
        exploration of the genome sequence together with additional linked datasets
        including physical maps, sequence variations, gene expression, and genetic
        and phenomic data from other international collaborative projects already
        stored in the GnpIS information system. The portal provides enhanced search
        and browser features that will facilitate the deployment of the latest genomics
        resources in wheat improvement.
      authors:
      - name: Alaux M.
      - name: Rogers J.
      - name: Letellier T.
      - name: Flores R.
      - name: Alfama F.
      - name: Pommier C.
      - name: Mohellibi N.
      - name: Durand S.
      - name: Kimmel E.
      - name: Michotey C.
      - name: Guerche C.
      - name: Loaec M.
      - name: Laine M.
      - name: Steinbach D.
      - name: Choulet F.
      - name: Rimbert H.
      - name: Leroy P.
      - name: Guilhot N.
      - name: Salse J.
      - name: Feuillet C.
      - name: Paux E.
      - name: Eversole K.
      - name: Adam-Blondon A.-F.
      - name: Quesneville H.
      citationCount: 181
      date: '2018-08-17T00:00:00Z'
      journal: Genome Biology
      title: Linking the International Wheat Genome Sequencing Consortium bread wheat
        reference genome sequence to wheat genetic and phenomic data
    note: "3-\tAlaux M, Rogers J, Letellier T, Flores R, Alfama  F, Pommier C, Mohellibi\
      \ N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach\
      \ D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, International\
      \ Wheat Genome Sequencing Consortium, Paux E, Eversole K, Adam-Blondon A-F,\
      \ Quesneville H (2018) Linking the International Wheat Genome Sequencing Consortium\
      \ bread wheat reference genome sequence to wheat genetic and phenomic data.\
      \ Genome Biology, 19:111."
    pmcid: null
    pmid: null
    type: []
    version: null
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    type: usedBy
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    type: usedBy
  toolType:
  - Web API
  - Web application
  - Web service
  - Database portal
  topic:
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  - term: Biological databases
    uri: http://edamontology.org/topic_3071
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  validated: 1
  version: []
- accessibility: null
  additionDate: '2019-11-27T10:47:08Z'
  biotoolsCURIE: biotools:OakMine
  biotoolsID: OakMine
  collectionID: []
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  cost: Free of charge
  credit: []
  description: Quercus robur annotation database
  documentation:
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  - note: null
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    url: https://flymine.readthedocs.io/en/latest/
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  elixir_badge: 0
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    input:
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        term: Sequence features
        uri: http://edamontology.org/data_1255
      format: []
    - data:
        term: Ontology data
        uri: http://edamontology.org/data_2353
      format: []
    note: null
    operation:
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    - term: Visualisation
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    - term: Gene-set enrichment analysis
      uri: http://edamontology.org/operation_2436
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
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        term: Over-representation data
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      format: []
    - data:
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        uri: http://edamontology.org/data_3786
      format: []
    - data:
        term: Sequence features
        uri: http://edamontology.org/data_1255
      format: []
  homepage: https://urgi.versailles.inra.fr/OakMine_PM1N
  homepage_status: 0
  language:
  - R
  - Ruby
  - Java
  - Python
  - JavaScript
  - Perl
  lastUpdate: '2025-07-29T13:42:35.424110Z'
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  link:
  - note: null
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    url: http://intermine.org
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  publication:
  - doi: 10.1093/bioinformatics/bts577
    metadata:
      abstract: InterMine is an open-source data warehouse system that facilitates
        the building of databases with complex data integration requirements and a
        need for a fast customizable query facility. Using InterMine, large biological
        databases can be created from a range of heterogeneous data sources, and the
        extensible data model allows for easy integration of new data types. The analysis
        tools include a flexible query builder, genomic region search and a library
        of 'widgets' performing various statistical analyses. The results can be exported
        in many commonly used formats. InterMine is a fully extensible framework where
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  - term: Proteomics
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  description: Python package to interact with the XNAT REST API in a python data-science
    way
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  description: XNAT is an open source imaging informatics platform developed by the
    Neuroinformatics Research Group at Washington University. XNAT was originally
    developed at Washington University in the Buckner Lab, which is now located at
    Harvard University. It facilitates common management, productivity, and quality
    assurance tasks for imaging and associated data. Thanks to its extensibility,
    XNAT can be used to support a wide range of imaging-based projects.
  documentation:
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  license: BSD-2-Clause
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  publication:
  - doi: 10.1385/ni:5:1:11
    metadata:
      abstract: The Extensible Neuroimaging Archive Toolkit (XNAT) is a software platform
        designed to facilitate common management and productivity tasks for neuroimaging
        and associated data. In particular, XNAT enables qualitycontrol procedures
        and provides secure access to and storage of data. XNAT follows a threetiered
        architecture that includes a data archive, user interface, and middleware
        engine. Data can be entered into the archive as XML or through data entry
        forms. Newly added data are stored in a virtual quarantine until an authorized
        user has validated it. XNAT subsequently maintains a history profile to track
        all changes made to the managed data. User access to the archive is provided
        by a secure web application. The web application provides a number of quality
        control and productivity features, including data entry forms, data-type-specific
        searches, searches that combine across data types, detailed reports, and listings
        of experimental data, upload/download tools, access to standard laboratory
        workflows, and administration and security tools. XNAT also includes an online
        image viewer that supports a number of common neuroimaging formats, including
        DICOM and Analyze. The viewer can be extended to support additional formats
        and to generate custom displays. By managing data with XNAT, laboratories
        are prepared to better maintain the long-term integrity of their data, to
        explore emergent relations across data types, and to share their data with
        the broader neuroimaging community. © Copyright 2007 by Humana Press Inc.
        All rights of any nature whatsoever are reserved.
      authors:
      - name: Marcus D.S.
      - name: Olsen T.R.
      - name: Ramaratnam M.
      - name: Buckner R.L.
      citationCount: 378
      date: '2007-03-01T00:00:00Z'
      journal: Neuroinformatics
      title: 'The extensible neuroimaging archive toolkit: An informatics platform
        for managing, exploring, and sharing neuroimaging data'
    note: null
    pmcid: null
    pmid: '17426351'
    type:
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    version: null
  - doi: 10.1162/jocn.2009.21407
    metadata:
      abstract: The Open Access Series of Imaging Studies is a series of neuroimaging
        data sets that are publicly available for study and analysis. The present
        MRI data set consists of a longitudinal collection of 150 subjects aged 60
        to 96 years all acquired on the same scanner using identical sequences. Each
        subject was scanned on two or more visits, separated by at least 1 year for
        a total of 373 imaging sessions. Subjects were characterized using the Clinical
        Dementia Rating (CDR) as either nondemented or with very mild tomild Alzheimer's
        disease. Seventy-two of the subjects were characterized as nondemented throughout
        the study. Sixty-four of the included subjects were characterized as demented
        at the time of their initial visits and remained so for subsequent scans,
        including 51 individuals with CDR 0.5 similar level of impairment to individuals
        elsewhere considered to have "mild cognitive impairment." Another 14 subjects
        were characterized as nondemented at the time of their initial visit (CDR
        0) and were subsequently characterized as demented at a later visit (CDR >
        0). The subjects were all right-handed and include bothmen (n=62) and women
        (n = 88). For each scanning session, three or four individual T1-weighted
        MRI scans were obtained. Multiple withinsession acquisitions provide extremely
        high contrast to noise, making the data amenable to a wide range of analytic
        approaches including automated computational analysis. Automated calculation
        of whole-brain volume is presented to demonstrate use of the data for measuring
        differences associated with normal aging and Alzheimer's disease. © 2010 Massachusetts
        Institute of Technology.
      authors:
      - name: Marcus D.S.
      - name: Fotenos A.F.
      - name: Csernansky J.G.
      - name: Morris J.C.
      - name: Buckner R.L.
      citationCount: 461
      date: '2010-12-01T00:00:00Z'
      journal: Journal of Cognitive Neuroscience
      title: 'Open access series of imaging studies: Longitudinal MRI data in nondemented
        and demented older adults'
    note: null
    pmcid: PMC2895005
    pmid: '19929323'
    type:
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    version: null
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  toolType:
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  - Web API
  topic:
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    uri: http://edamontology.org/topic_3384
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Bioimaging
    uri: http://edamontology.org/topic_3383
  - term: Tomography
    uri: http://edamontology.org/topic_3452
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
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- accessibility: Open access
  additionDate: '2025-07-23T10:27:57.572501Z'
  biotoolsCURIE: biotools:etenlnc
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    fundrefid: null
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    name: Pankaj Barah
    note: Assistant Professor at Department of Molecular Biology and Biotechnology,
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  description: ETENLNC (End-To-End-Novel-NonCoding) is a lncRNA identification and
    analysis framework
  documentation:
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    type:
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  download:
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    type: Biological data
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  function:
  - cmd: bash ETENLNC_docker.sh
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Genome map
        uri: http://edamontology.org/data_1288
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
      - term: GTF
        uri: http://edamontology.org/format_2306
      - term: GFF
        uri: http://edamontology.org/format_2305
    note: Run ETENLNC on paired-end raw RNA-Seq (.fastq) data
    operation:
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    - term: Sequencing quality control
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    - term: Transcriptome assembly
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    - term: Nucleic acid feature detection
      uri: http://edamontology.org/operation_0415
    - term: RNA-Seq quantification
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    - term: Differential gene expression profiling
      uri: http://edamontology.org/operation_3223
    - term: Heat map generation
      uri: http://edamontology.org/operation_0531
    - term: RNA secondary structure prediction
      uri: http://edamontology.org/operation_0278
    - term: k-mer counting
      uri: http://edamontology.org/operation_3472
    - term: Protein-nucleic acid interaction analysis
      uri: http://edamontology.org/operation_0389
    - term: RNA-binding protein prediction
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    - term: Gene regulatory network prediction
      uri: http://edamontology.org/operation_2437
    output:
    - data:
        term: Nucleic acid sequence record
        uri: http://edamontology.org/data_2887
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Heat map
        uri: http://edamontology.org/data_1636
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Protein interaction data
        uri: http://edamontology.org/data_0906
      format: []
  homepage: https://github.com/EvolOMICS-TU/ETENLNC
  homepage_status: 0
  language: []
  lastUpdate: '2025-07-23T10:27:57.574879Z'
  license: GPL-3.0
  link:
  - note: GitHub Repo
    type:
    - Repository
    url: https://github.com/EvolOMICS-TU/ETENLNC
  maturity: Emerging
  name: ETENLNC
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: prangannath
  publication:
  - doi: 10.1016/j.compbiolchem.2024.108140
    metadata:
      abstract: 'Long non-coding RNAs (lncRNAs) play crucial roles in the regulation
        of gene expression and maintenance of genomic integrity through various interactions
        with DNA, RNA, and proteins. The availability of large-scale sequence data
        from various high-throughput platforms has opened possibilities to identify,
        predict, and functionally annotate lncRNAs. As a result, there is a growing
        demand for an integrative computational framework capable of identifying known
        lncRNAs, predicting novel lncRNAs, and inferring the downstream regulatory
        interactions of lncRNAs at the genome-scale. We present ETENLNC (End-To-End-Novel-Long-NonCoding),
        a user-friendly, integrative, open-source, scalable, and modular computational
        framework for identifying and analyzing lncRNAs from raw RNA-Seq data. ETENLNC
        employs six stringent filtration steps to identify novel lncRNAs, performs
        differential expression analysis of mRNA and lncRNA transcripts, and predicts
        regulatory interactions between lncRNAs, mRNAs, miRNAs, and proteins. We benchmarked
        ETENLNC against six existing tools and optimized it for desktop workstations
        and high-performance computing environments using data from three different
        species. ETENLNC is freely available on GitHub: https://github.com/EvolOMICS-TU/ETENLNC.'
      authors:
      - name: Nath P.
      - name: Bhuyan K.
      - name: Bhattacharyya D.K.
      - name: Barah P.
      citationCount: 2
      date: '2024-10-01T00:00:00Z'
      journal: Computational Biology and Chemistry
      title: 'ETENLNC: An end to end lncRNA identification and analysis framework
        to facilitate construction of known and novel lncRNA regulatory networks'
    note: null
    pmcid: null
    pmid: '38996755'
    type:
    - Primary
    version: '.0'
  relation:
  - biotoolsID: hisat2
    type: uses
  - biotoolsID: salmon
    type: uses
  - biotoolsID: fastqc
    type: uses
  - biotoolsID: fastp
    type: uses
  - biotoolsID: stringtie
    type: uses
  - biotoolsID: gffcompare
    type: uses
  - biotoolsID: cpc2
    type: uses
  - biotoolsID: ncbi_blast_plus
    type: uses
  - biotoolsID: tximport
    type: uses
  - biotoolsID: deseq2
    type: uses
  - biotoolsID: lnctar
    type: uses
  - biotoolsID: capsule-lpi
    type: uses
  - biotoolsID: seekr
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2022-09-17T13:13:51.109638Z'
  biotoolsCURIE: biotools:physiboss
  biotoolsID: physiboss
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: alfonso.valencia@bsc.es
    fundrefid: null
    gridid: null
    name: Alfonso Valencia
    note: null
    orcidid: https://orcid.org/0000-0002-8937-6789
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Laurence Calzone
    note: null
    orcidid: https://orcid.org/0000-0002-7835-1148
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Emmanuel Barillot
    note: null
    orcidid: https://orcid.org/0000-0003-2724-2002
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Miguel Ponce-de-Leon
    note: null
    orcidid: https://orcid.org/0000-0002-7496-844X
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Arnau Montagud
    note: null
    orcidid: https://orcid.org/0000-0002-7696-1241
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: A sustainable integration of stochastic Boolean and agent-based modelling
    frameworks.
  documentation:
  - note: null
    type:
    - Code of conduct
    url: https://github.com/PhysiBoSS/PhysiBoSS/blob/master/CODE_OF_CONDUCT.md
  download: []
  editPermission:
    authors:
    - vincent-noel
    - ArnauMontagud
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    - term: Network analysis
      uri: http://edamontology.org/operation_3927
    output: []
  homepage: https://github.com/PhysiBoSS/PhysiBoSS
  homepage_status: 0
  language:
  - C++
  - Python
  - MATLAB
  lastUpdate: '2025-07-21T09:32:03.727618Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/PhysiBoSS/
  maturity: null
  name: PhysiBoSS
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Jennifer
  publication:
  - doi: 10.1101/2022.01.06.468363
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  validated: 1
  version:
  - '2.0'
- accessibility: Open access
  additionDate: '2025-07-18T19:35:58.827790Z'
  biotoolsCURIE: biotools:tinkerhap
  biotoolsID: tinkerhap
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Uri Hartmann
    note: null
    orcidid: https://orcid.org/0009-0002-0668-0249
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: 'TinkerHap is an accurate read-based phasing tool that integrates multiple
    methodologies to enhance phasing accuracy. It is designed to efficiently phase
    genomic data by linking sequencing reads across heterozygous sites, extending
    haplotype blocks, and incorporating pre-phased data when available.


    The full paper detailing the methodology and validation of TinkerHap is available
    at bioRxiv

    DOI: https://doi.org/10.1101/2025.02.16.638517.'
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
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  elixir_badge: 0
  function: []
  homepage: https://github.com/DZeevi-Lab/TinkerHap
  homepage_status: 0
  language: []
  lastUpdate: '2025-07-18T19:36:52.558166Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/DZeevi-Lab/TinkerHap
  - note: Full paper detailing the methodology and validation
    type:
    - Other
    url: https://doi.org/10.1101/2025.02.16.638517
  maturity: Emerging
  name: TinkerHap
  operatingSystem: []
  otherID: []
  owner: uri2x
  publication:
  - doi: 10.1101/2025.02.16.638517
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - 1.0.0
- accessibility: null
  additionDate: '2024-01-02T14:39:18.208505Z'
  biotoolsCURIE: biotools:pae_viewer
  biotoolsID: pae_viewer
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: jstuelk@gwdg.de
    fundrefid: null
    gridid: null
    name: Jörg Stülke
    note: null
    orcidid: https://orcid.org/0000-0001-5881-5390
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: christoph.elfmann@uni-goettingen.de
    fundrefid: null
    gridid: null
    name: Christoph Elfmann
    note: PhD student in charge of PAE Viewer.
    orcidid: https://orcid.org/0000-0002-7872-8232
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Webserver for the interactive visualization of the predicted aligned
    error for multimer structure predictions and crosslinks.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Protein structure prediction
      uri: http://edamontology.org/operation_0474
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: PTM site prediction
      uri: http://edamontology.org/operation_0417
    - term: Protein interaction prediction
      uri: http://edamontology.org/operation_2492
    - term: Protein structure validation
      uri: http://edamontology.org/operation_0321
    output: []
  homepage: https://pae-viewer.uni-goettingen.de/
  homepage_status: 0
  language: []
  lastUpdate: '2025-07-16T13:07:20.312542Z'
  license: null
  link:
  - note: null
    type:
    - Other
    url: https://gitlab.gwdg.de/general-microbiology/pae-viewer
  maturity: null
  name: PAE Viewer
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/nar/gkad350
    metadata:
      abstract: The development of AlphaFold for protein structure prediction has
        opened a new era in structural biology. This is even more the case for AlphaFold-Multimer
        for the prediction of protein complexes. The interpretation of these predictions
        has become more important than ever, but it is difficult for the non-specialist.
        While an evaluation of the prediction quality is provided for monomeric protein
        predictions by the AlphaFold Protein Structure Database, such a tool is missing
        for predicted complex structures. Here, we present the PAE Viewer webserver
        (http://www.subtiwiki.uni-goettingen.de/v4/paeViewerDemo), an online tool
        for the integrated visualization of predicted protein complexes using a 3D
        structure display combined with an interactive representation of the Predicted
        Aligned Error (PAE). This metric allows an estimation of the quality of the
        prediction. Importantly, our webserver also allows the integration of experimental
        cross-linking data which helps to interpret the reliability of the structure
        predictions. With the PAE Viewer, the user obtains a unique online tool which
        for the first time allows the intuitive evaluation of the PAE for protein
        complex structure predictions with integrated crosslinks.
      authors:
      - name: Elfmann C.
      - name: Stulke J.
      citationCount: 49
      date: '2023-07-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'PAE viewer: A webserver for the interactive visualization of the predicted
        aligned error for multimer structure predictions and crosslinks'
    note: null
    pmcid: PMC10320053
    pmid: '37140053'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  - term: Protein modifications
    uri: http://edamontology.org/topic_0601
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Computational chemistry
    uri: http://edamontology.org/topic_3332
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2022-03-13T11:27:48.265908Z'
  biotoolsCURIE: biotools:subtiwiki
  biotoolsID: subtiwiki
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: jstuelk@gwdg.de
    fundrefid: null
    gridid: null
    name: Jörg Stülke
    note: null
    orcidid: https://orcid.org/0000-0001-5881-5390
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: christoph.elfmann@uni-goettingen.de
    fundrefid: null
    gridid: null
    name: Christoph Elfmann
    note: PhD student in charge of SubtiWiki.
    orcidid: https://orcid.org/0000-0002-7872-8232
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: SubtiWiki is a database for the model organism Bacillus subtilis.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genome visualisation
      uri: http://edamontology.org/operation_3208
    - term: Operon prediction
      uri: http://edamontology.org/operation_0435
    - term: Gene regulatory network analysis
      uri: http://edamontology.org/operation_1781
    output: []
  homepage: https://subtiwiki.uni-goettingen.de/
  homepage_status: 0
  language: []
  lastUpdate: '2025-07-16T13:05:53.746014Z'
  license: null
  link: []
  maturity: null
  name: SubtiWiki
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: ChristophElfmann
  publication:
  - doi: 10.1093/nar/gkae957
    metadata:
      abstract: Bacillus subtilis is a Gram-positive model bacterium and one of the
        most-studied and best understood organisms. The complex information resulting
        from its investigation is compiled in the database SubtiWiki (https://subtiwiki.uni-goettingen.de/v5)
        in an integrated and intuitive manner. To enhance the utility of SubtiWiki,
        we have added novel features such as a viewer to interrogate conserved genomic
        organization, a widget that shows mutant fitness data for all non-essential
        genes, and a widget showing protein structures, structure predictions and
        complex structures. Moreover, we have integrated metabolites as new entities.
        The new framework also includes a documented API, enabling programmatic access
        to data for computational tasks. Here we present the recent developments of
        SubtiWiki and the current state of the data for this organism.
      authors:
      - name: Elfmann C.
      - name: Dumann V.
      - name: van den Berg T.
      - name: Stulke J.
      citationCount: 4
      date: '2025-01-06T00:00:00Z'
      journal: Nucleic Acids Research
      title: A new framework for SubtiWiki, the database for the model organism Bacillus
        subtilis
    note: null
    pmcid: PMC11701700
    pmid: '39441067'
    type:
    - Primary
    version: '5.0'
  relation: []
  toolType:
  - Web application
  - Database portal
  topic:
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Endocrinology and metabolism
    uri: http://edamontology.org/topic_3407
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2025-07-15T16:04:03.513732Z'
  biotoolsCURIE: biotools:GevaertLab_DUNE
  biotoolsID: GevaertLab_DUNE
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: thomas.barba@inserm.fr
    fundrefid: null
    gridid: null
    name: Thomas Barba
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: A versatile neuroimaging encoder for extracting deep features from
    multisequence brain MRIs
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://github.com/gevaertlab/DUNE/blob/main/README.md
  download:
  - note: null
    type: Source code
    url: https://github.com/gevaertlab/DUNE
    version: null
  editPermission:
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    type: private
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  elixir_badge: 0
  function:
  - cmd: python -m src.main process /path/to/dicom/folder /path/to/output
    input: []
    note: Extracts features from
    operation:
    - term: Feature extraction
      uri: http://edamontology.org/operation_3937
    output: []
  homepage: https://github.com/gevaertlab/DUNE
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-15T16:04:03.516083Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/gevaertlab/DUNE
  maturity: Mature
  name: DUNE
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: tbarba
  publication:
  - doi: 10.1101/2025.02.24.25322787
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version: []
- 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: 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: []
    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.'
  documentation:
  - note: Documentation for the main package, EUCAIM plugin specific documentation
      not included.
    type:
    - Quick start guide
    url: https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.md
  download: []
  editPermission:
    authors: []
    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/IFCA-Advanced-Computing/FAIR_eva
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-15T09:45:40.672775Z'
  license: Apache-2.0
  link: []
  maturity: Mature
  name: FAIR_EVA
  operatingSystem:
  - Linux
  otherID: []
  owner: davrodgon
  publication:
  - doi: 10.1038/s41597-023-02652-8
    metadata:
      abstract: The FAIR Principles are a set of good practices to improve the reproducibility
        and quality of data in an Open Science context. Different sets of indicators
        have been proposed to evaluate the FAIRness of digital objects, including
        datasets that are usually stored in repositories or data portals. However,
        indicators like those proposed by the Research Data Alliance are provided
        from a high-level perspective that can be interpreted and they are not always
        realistic to particular environments like multidisciplinary repositories.
        This paper describes FAIR EVA, a new tool developed within the European Open
        Science Cloud context that is oriented to particular data management systems
        like open repositories, which can be customized to a specific case in a scalable
        and automatic environment. It aims to be adaptive enough to work for different
        environments, repository software and disciplines, taking into account the
        flexibility of the FAIR Principles. As an example, we present DIGITAL.CSIC
        repository as the first target of the tool, gathering the particular needs
        of a multidisciplinary institution as well as its institutional repository.
      authors:
      - name: Aguilar Gomez F.
      - name: Bernal I.
      citationCount: 6
      date: '2023-12-01T00:00:00Z'
      journal: Scientific Data
      title: 'FAIR EVA: Bringing institutional multidisciplinary repositories into
        the FAIR picture'
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web service
  - Script
  topic:
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  validated: 0
  version:
  - EUCAIM_plugin_1
- accessibility: Open access
  additionDate: '2025-07-14T08:21:28.942611Z'
  biotoolsCURIE: biotools:UniversalMer
  biotoolsID: UniversalMer
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: UniversalMer is a k-mer counting tool for multiple size of k at once.
    It is available for DNA, RNA, and protein sequences. The program counts and summarizes
    the exact frequency of all k-mers from 1-mer to a user-defined maximum length
    (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in
    seconds. This program is designed for bioinformatics researchers and scientists.
  documentation: []
  download:
  - note: null
    type: Command-line specification
    url: https://sourceforge.net/projects/universal-mer/
    version: '2.0'
  editPermission:
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  elixirNode:
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  elixirPlatform:
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
    note: null
    operation:
    - term: k-mer counting
      uri: http://edamontology.org/operation_3472
    output:
    - data:
        term: Base word frequencies table
        uri: http://edamontology.org/data_1266
      format: []
    - data:
        term: Base frequencies table
        uri: http://edamontology.org/data_1265
      format: []
    - data:
        term: Text
        uri: http://edamontology.org/data_3671
      format: []
  homepage: https://ugrammer.github.io
  homepage_status: 0
  language:
  - C++
  - C
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  operatingSystem:
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  - Mac
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  owner: Ugrammer
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - 2.0.0
- accessibility: Open access
  additionDate: '2017-01-17T15:07:47Z'
  biotoolsCURIE: biotools:copasi
  biotoolsID: copasi
  collectionID:
  - de.NBI
  - EBI Training Tools
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://copasi.org/About/Team/
  - email: frank.bergmann@bioquant.uni-heidelberg.de
    fundrefid: null
    gridid: null
    name: Frank T. Bergmann
    note: null
    orcidid: https://orcid.org/0000-0001-5553-4702
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  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:
  - note: null
    type:
    - User manual
    url: http://copasi.org/Support/User_Manual/
  download:
  - note: Source and binary packages are available for download.
    type: Binaries
    url: http://copasi.org/Download/
    version: null
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    input:
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        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format:
      - term: SBML
        uri: http://edamontology.org/format_2585
      - term: CopasiML
        uri: http://edamontology.org/format_3239
      - term: SED-ML
        uri: http://edamontology.org/format_3685
      - term: COMBINE OMEX
        uri: http://edamontology.org/format_3686
    note: null
    operation:
    - term: Network simulation
      uri: http://edamontology.org/operation_3562
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    - term: Metabolic network modelling
      uri: http://edamontology.org/operation_3660
    - term: Pathway visualisation
      uri: http://edamontology.org/operation_3926
    output:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format:
      - term: SBML
        uri: http://edamontology.org/format_2585
      - term: CopasiML
        uri: http://edamontology.org/format_3239
      - term: SED-ML
        uri: http://edamontology.org/format_3685
      - term: COMBINE OMEX
        uri: http://edamontology.org/format_3686
  homepage: http://copasi.org/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2025-07-07T11:17:37.638447Z'
  license: Artistic-2.0
  link:
  - note: User Forum
    type:
    - Discussion forum
    url: https://groups.google.com/g/copasi-user-forum
  - note: Issue tracker
    type:
    - Issue tracker
    url: http://tracker.copasi.org/
  - note: Github Repo
    type:
    - Repository
    url: https://github.com/copasi/COPASI
  - note: null
    type:
    - Social media
    url: https://fosstodon.org/@copasi
  maturity: Mature
  name: COPASI
  operatingSystem:
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  - Windows
  - Mac
  otherID: []
  owner: frankbergmann
  publication:
  - doi: 10.1093/bioinformatics/btl485
    metadata:
      abstract: 'Motivation: Simulation and modeling is becoming a standard approach
        to understand complex biochemical processes. Therefore, there is a big need
        for software tools that allow access to diverse simulation and modeling methods
        as well as support for the usage of these methods. Results: Here, we present
        COPASI, a platform-independent and user-friendly biochemical simulator that
        offers several unique features. We discuss numerical issues with these features;
        in particular, the criteria to switch between stochastic and deterministic
        simulation methods, hybrid deterministic-stochastic methods, and the importance
        of random number generator numerical resolution in stochastic simulation.
        © 2006 Oxford University Press.'
      authors:
      - name: Hoops S.
      - name: Gauges R.
      - name: Lee C.
      - name: Pahle J.
      - name: Simus N.
      - name: Singhal M.
      - name: Xu L.
      - name: Mendes P.
      - name: Kummer U.
      citationCount: 2004
      date: '2006-12-15T00:00:00Z'
      journal: Bioinformatics
      title: COPASI - A COmplex PAthway SImulator
    note: null
    pmcid: null
    pmid: '17032683'
    type: []
    version: null
  - doi: 10.1007/978-1-59745-525-1_2
    metadata:
      abstract: Computational modeling and simulation of biochemical networks is at
        the core of systems biology and this includes many types of analyses that
        can aid understanding of how these systems work. COPASI is a generic software
        package for modeling and simulation of biochemical networks which provides
        many of these analyses in convenient ways that do not require the user to
        program or to have deep knowledge of the numerical algorithms. Here we provide
        a description of how these modeling techniques can be applied to biochemical
        models using COPASI. The focus is both on practical aspects of software usage
        as well as on the utility of these analyses in aiding biological understanding.
        Practical examples are described for steady-state and time-course simulations,
        stoichiometric analyses, parameter scanning, sensitivity analysis (including
        metabolic control analysis), global optimization, parameter estimation, and
        stochastic simulation. The examples used are all published models that are
        available in the BioModels database in SBML format. © 2009 Humana Press.
      authors:
      - name: Mendes P.
      - name: Hoops S.
      - name: Sahle S.
      - name: Gauges R.
      - name: Dada J.
      - name: Kummer U.
      citationCount: 171
      date: '2009-12-01T00:00:00Z'
      journal: Methods in Molecular Biology
      title: Computational modeling of biochemical networks using COPASI
    note: null
    pmcid: null
    pmid: '19399433'
    type: []
    version: null
  - doi: 10.1016/j.jbiotec.2017.06.1200
    metadata:
      abstract: COPASI is software used for the creation, modification, simulation
        and computational analysis of kinetic models in various fields. It is open-source,
        available for all major platforms and provides a user-friendly graphical user
        interface, but is also controllable via the command line and scripting languages.
        These are likely reasons for its wide acceptance. We begin this review with
        a short introduction describing the general approaches and techniques used
        in computational modeling in the biosciences. Next we introduce the COPASI
        package, and its capabilities, before looking at typical applications of COPASI
        in biotechnology.
      authors:
      - name: Bergmann F.T.
      - name: Hoops S.
      - name: Klahn B.
      - name: Kummer U.
      - name: Mendes P.
      - name: Pahle J.
      - name: Sahle S.
      citationCount: 81
      date: '2017-11-10T00:00:00Z'
      journal: Journal of Biotechnology
      title: COPASI and its applications in biotechnology
    note: null
    pmcid: PMC5623632
    pmid: '28655634'
    type: []
    version: null
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  - biotoolsID: corc
    type: usedBy
  - biotoolsID: pycotools
    type: usedBy
  - biotoolsID: biosimulations
    type: includedIn
  - biotoolsID: sbmlwebapp
    type: usedBy
  - biotoolsID: libsbml
    type: uses
  toolType:
  - Command-line tool
  - Library
  - Desktop application
  topic:
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2025-02-26T14:07:27.855714Z'
  biotoolsCURIE: biotools:basico
  biotoolsID: basico
  collectionID:
  - de.NBI
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: frank.bergmann@bioquant.uni-heidelberg.de
    fundrefid: null
    gridid: null
    name: Frank T. Bergmann
    note: null
    orcidid: https://orcid.org/0000-0001-5553-4702
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    url: null
  description: "BASICO, a simplified Python interface to COPASI. It provides a set\
    \ of functions\n that allow to create, edit, simulate and analyze models in an\
    \ automated way"
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://pypi.org/project/copasi-basico/
    version: null
  editPermission:
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    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
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    input:
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        term: Kinetic model
        uri: http://edamontology.org/data_3241
      format:
      - term: CopasiML
        uri: http://edamontology.org/format_3239
      - term: SBML
        uri: http://edamontology.org/format_2585
      - term: SED-ML
        uri: http://edamontology.org/format_3685
      - term: COMBINE OMEX
        uri: http://edamontology.org/format_3686
    note: null
    operation:
    - term: Metabolic network modelling
      uri: http://edamontology.org/operation_3660
    - term: Pathway analysis
      uri: http://edamontology.org/operation_3928
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output:
    - data:
        term: Kinetic model
        uri: http://edamontology.org/data_3241
      format:
      - term: CopasiML
        uri: http://edamontology.org/format_3239
      - term: SBML
        uri: http://edamontology.org/format_2585
      - term: SED-ML
        uri: http://edamontology.org/format_3685
      - term: COMBINE OMEX
        uri: http://edamontology.org/format_3686
  homepage: https://basico.readthedocs.io/en/latest/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-07T11:16:29.397538Z'
  license: Artistic-2.0
  link: []
  maturity: Mature
  name: basico
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: frankbergmann
  publication:
  - doi: 10.21105/joss.05553
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: copasi
    type: uses
  toolType:
  - Library
  - Script
  topic:
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2015-08-03T09:36:21Z'
  biotoolsCURIE: biotools:online_sbml_validator
  biotoolsID: online_sbml_validator
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Frank Bergmann
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Documentor
    url: https://www.biocatalogue.org
  - email: frank.bergmann@bioquant.uni-heidelberg.de
    fundrefid: null
    gridid: null
    name: Frank Bergmann
    note: null
    orcidid: https://orcid.org/0000-0001-5553-4702
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Check the syntax and internal consistency of files in SBML (The Systems
    Biology Markup Language) format.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://web.archive.org/web/20210507040418/http://sbml.org/Facilities/Documentation/Validator_Web_API
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Mathematical model
        uri: http://edamontology.org/data_0950
      format:
      - term: COMBINE OMEX
        uri: http://edamontology.org/format_3686
      - term: SBML
        uri: http://edamontology.org/format_2585
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output: []
  homepage: https://sbml.bioquant.uni-heidelberg.de/validator_servlet/
  homepage_status: 0
  language:
  - Java
  - Python
  lastUpdate: '2025-07-07T11:10:03.422874Z'
  license: LGPL-2.0
  link:
  - note: null
    type:
    - Service
    url: https://sbml.org/facilities/
  maturity: null
  name: Online SBML Validator
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: frankbergmann
  publication: []
  relation: []
  toolType:
  - Web API
  - Web application
  topic:
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2025-07-07T09:04:03.787249Z'
  biotoolsCURIE: biotools:sqanti3
  biotoolsID: sqanti3
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: ana.conesa@csic.es
    fundrefid: null
    gridid: null
    name: Ana Conesa
    note: null
    orcidid: https://orcid.org/0000-0001-9597-311X
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: pablo.atienza@csic.es
    fundrefid: null
    gridid: null
    name: Pablo Atienza
    note: Maintainer of SQANTI3
    orcidid: https://orcid.org/0009-0002-1093-693X
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    url: null
  - email: fabian.robledo@csic.es
    fundrefid: null
    gridid: null
    name: Fabián Robledo
    note: Maintainer of SQANTI3 and ELIXIR-related contact
    orcidid: https://orcid.org/0009-0005-9047-3315
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    url: null
  description: "SQANTI3 constitutes the first module of the Functional IsoTranscriptomics\
    \ (FIT) pipeline, which is an end-to-end strategy to perform isoform-level bioinformatics\
    \ analyses. \n\nThe SQANTI3 tool is designed to enable quality control and filtering\
    \ of long read-defined transcriptomes, which are often rich in artifacts and false-positive\
    \ isoforms. \n\nTherefore, a good curation of the transcriptome is indispensable\
    \ to proceed with FIT analysis and produce valid, biologically sound conclusions/hypothesis."
  documentation:
  - note: SQANTI3 main documentation resource
    type:
    - General
    url: https://github.com/ConesaLab/SQANTI3/wiki
  - note: null
    type:
    - Code of conduct
    url: https://github.com/ConesaLab/SQANTI3/blob/master/CODE_OF_CONDUCT.md
  - note: Command-line options and instructions for the QC submodule
    type:
    - Command-line options
    url: https://github.com/ConesaLab/SQANTI3/wiki/Running-SQANTI3-Quality-Control
  - note: Command-line options and instructions for the filter submodule
    type:
    - Command-line options
    url: https://github.com/ConesaLab/SQANTI3/wiki/Running-SQANTI3-filter
  - note: Command-line options and instructions for the rescue submodule
    type:
    - Command-line options
    url: https://github.com/ConesaLab/SQANTI3/wiki/Running-SQANTI3-rescue
  - note: Instructions to install and use sqanti, either in docker or apptainer containers
      or in a linux system
    type:
    - Installation instructions
    url: https://github.com/ConesaLab/SQANTI3/wiki/Dependencies-and-installation
  - note: Basic tutorial with examples to start using SQANTI3
    type:
    - Quick start guide
    url: https://github.com/ConesaLab/SQANTI3/wiki/Tutorial:-running-SQANTI3-on-an-example-dataset
  - note: Changelog and release notes for every version
    type:
    - Release notes
    url: https://github.com/ConesaLab/SQANTI3/releases
  - note: Citation instructions are on the end of the Github repository's main page
    type:
    - Citation instructions
    url: https://github.com/ConesaLab/SQANTI3?tab=readme-ov-file#how-to-cite-sqanti3
  - note: Benchmarking about the resources needed to run sqanti3 with multiple cores
    type:
    - Other
    url: https://github.com/ConesaLab/SQANTI3/wiki/SQANTI3-memory-requeriments-and-paralellization
  download:
  - note: null
    type: Downloads page
    url: https://github.com/ConesaLab/SQANTI3/releases
    version: null
  - note: Version 5.5 download link from github
    type: Binaries
    url: https://github.com/ConesaLab/SQANTI3/releases/download/v5.5/SQANTI3_v5.5.zip
    version: '5.5'
  editPermission:
    authors:
    - Fabian-RY
    type: group
  elixirCommunity: []
  elixirNode:
  - Spain
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/ConesaLab/SQANTI3
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-07-07T09:35:33.280160Z'
  license: GPL-3.0
  link:
  - note: Github repository for source code access and download
    type:
    - Repository
    url: https://github.com/ConesaLab/SQANTI3
  maturity: Mature
  name: SQANTI3
  operatingSystem:
  - Linux
  otherID: []
  owner: Fabian-RY
  publication:
  - doi: 10.1038/s41592-024-02229-2
    metadata:
      abstract: SQANTI3 offers a flexible tool for quality control, curation and annotation
        of long-read RNA sequencing data. SQANTI3 is a tool designed for the quality
        control, curation and annotation of long-read transcript models obtained with
        third-generation sequencing technologies. Leveraging its annotation framework,
        SQANTI3 calculates quality descriptors of transcript models, junctions and
        transcript ends. With this information, potential artifacts can be identified
        and replaced with reliable sequences. Furthermore, the integrated functional
        annotation feature enables subsequent functional iso-transcriptomics analyses.
      authors:
      - name: Pardo-Palacios F.J.
      - name: Arzalluz-Luque A.
      - name: Kondratova L.
      - name: Salguero P.
      - name: Mestre-Tomas J.
      - name: Amorin R.
      - name: Estevan-Morio E.
      - name: Liu T.
      - name: Nanni A.
      - name: McIntyre L.
      - name: Tseng E.
      - name: Conesa A.
      citationCount: 41
      date: '2024-05-01T00:00:00Z'
      journal: Nature Methods
      title: 'SQANTI3: curation of long-read transcriptomes for accurate identification
        of known and novel isoforms'
    note: Publication of SQANTI3
    pmcid: null
    pmid: null
    type:
    - Primary
    version: '5.1'
  - doi: 10.1101/gr.222976.117
    metadata:
      abstract: High-throughput sequencing of full-length transcripts using long reads
        has paved the way for the discovery of thousands of novel transcripts, even
        in well-annotated mammalian species. The advances in sequencing technology
        have created a need for studies and tools that can characterize these novel
        variants. Here, we present SQANTI, an automated pipeline for the classification
        of long-read transcripts that can assess the quality of data and the preprocessing
        pipeline using 47 unique descriptors. We apply SQANTI to a neuronal mouse
        transcriptome using Pacific Biosciences (PacBio) long reads and illustrate
        how the tool is effective in characterizing and describing the composition
        of the full-length transcriptome. We perform extensive evaluation of ToFU
        PacBio transcripts by PCR to reveal that an important number of the novel
        transcripts are technical artifacts of the sequencing approach and that SQANTI
        quality descriptors can be used to engineer a filtering strategy to remove
        them. Most novel transcripts in this curated transcriptome are novel combinations
        of existing splice sites, resulting more frequently in novel ORFs than novel
        UTRs, and are enriched in both general metabolic and neural-specific functions.
        We show that these new transcripts have a major impact in the correct quantification
        of transcript levels by state-of-the-art short-read-based quantification algorithms.
        By comparing our iso-transcriptome with public proteomics databases, we find
        that alternative isoforms are elusive to proteogenomics detection. SQANTI
        allows the user to maximize the analytical outcome of long-read technologies
        by providing the tools to deliver quality-evaluated and curated full-length
        transcriptomes.
      authors:
      - name: Tardaguila M.
      - name: De La Fuente L.
      - name: Marti C.
      - name: Pereira C.
      - name: Pardo-Palacios F.J.
      - name: Del Risco H.
      - name: Ferrell M.
      - name: Mellado M.
      - name: Macchietto M.
      - name: Verheggen K.
      - name: Edelmann M.
      - name: Ezkurdia I.
      - name: Vazquez J.
      - name: Tress M.
      - name: Mortazavi A.
      - name: Martens L.
      - name: Rodriguez-Navarro S.
      - name: Moreno-Manzano V.
      - name: Conesa A.
      citationCount: 256
      date: '2018-03-01T00:00:00Z'
      journal: Genome Research
      title: 'SQANTI: Extensive characterization of long-read transcript sequences
        for quality control in full-length transcriptome identification and quantification'
    note: Original SQANTI publication
    pmcid: null
    pmid: null
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  validated: 0
  version:
  - '5.5'
- accessibility: Open access
  additionDate: '2016-02-09T13:19:44Z'
  biotoolsCURIE: biotools:mirgen
  biotoolsID: mirgen
  collectionID:
  - UiO tools
  - ELIXIR-NO
  - ELIXIR-Norway
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: BastianFromm@gmail.com
    fundrefid: null
    gridid: null
    name: Bastian Fromm
    note: null
    orcidid: https://orcid.org/0000-0003-0352-3037
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    - Support
    url: null
  - email: kevin.j.peterson@dartmouth.edu
    fundrefid: null
    gridid: null
    name: Kevin J. Peterson
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  - email: support@elixir.no
    fundrefid: null
    gridid: null
    name: The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Support
    url: https://elixir.no/helpdesk
  - email: null
    fundrefid: 10.13039/501100005366
    gridid: grid.5510.1
    name: University of Oslo
    note: null
    orcidid: null
    rorid: 01xtthb56
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.uio.no/english/index.html
  description: MirGeneDB is a database of manually curated microRNA genes that have
    been validated and annotated as initially described in Fromm et al. 2015 , Fromm
    et al. 2020 and Fromm et al 2022. MirGeneDB 3.0 (Clarke and Hoye et al. 2024 )
    includes more than 21,000 microRNA gene entries representing more than 1,700 microRNA
    families from 114 metazoan species. All microRNAs can be browsed, searched and
    downloaded.
  documentation:
  - note: null
    type:
    - General
    url: https://www.mirgenedb.org/information
  download:
  - note: Sequence downloads for 75 species
    type: Biological data
    url: https://www.mirgenedb.org/download
    version: '3.0'
  editPermission:
    authors:
    - eca008
    type: group
  elixirCommunity: []
  elixirNode:
  - Norway
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence accession (nucleic acid)
        uri: http://edamontology.org/data_1097
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Organism identifier
        uri: http://edamontology.org/data_1869
      format: []
    note: 'Data retrieval: curated miRNA. Organism identifier: a specific miRNA identifier
      or a species  for all miRNAs for that species. Gene transcript report: with
      metadata and visualization. RNA secondary structure: the hairpin loop of the
      miRNA with bases.'
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output:
    - data:
        term: Gene transcript report
        uri: http://edamontology.org/data_3134
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: RNA secondary structure
        uri: http://edamontology.org/data_0880
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Sequence accession (nucleic acid)
        uri: http://edamontology.org/data_1097
      format: []
    note: null
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
      - term: BED
        uri: http://edamontology.org/format_3003
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://mirgenedb.org/
  homepage_status: 0
  language: []
  lastUpdate: '2025-07-05T22:33:30.082420Z'
  license: CC0-1.0
  link:
  - note: null
    type:
    - Helpdesk
    url: https://elixir.no/helpdesk
  maturity: Mature
  name: MirGeneDB
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID:
  - type: doi
    value: doi:10.25504/FAIRsharing.QXSgvF
    version: '2.0'
  owner: UiO
  publication:
  - doi: 10.1093/nar/gkab1101
    metadata:
      abstract: We describe an update of MirGeneDB, the manually curated microRNA
        gene database. Adhering to uniform and consistent criteria for microRNA annotation
        and nomenclature, we substantially expanded MirGeneDB with 30 additional species
        representing previously missing metazoan phyla such as sponges, jellyfish,
        rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning
        over ∼800 million years of animal evolution, and contains a total number of
        16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this
        update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new
        phylogenetically important species, especially those relevant for the study
        of whole genome duplication events, and through updating evolutionary nodes
        of origin for many families and genes, we were able to substantially refine
        our nomenclature system. All changes are traceable in the specifically developed
        MirGeneDB version tracker. The performance of read-pages is improved and microRNA
        expression matrices for all tissues and species are now also downloadable.
        Altogether, this update represents a significant step toward a complete sampling
        of all major metazoan phyla, and a widely needed foundation for comparative
        microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral
        and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.
      authors:
      - name: Fromm B.
      - name: Hoye E.
      - name: Domanska D.
      - name: Zhong X.
      - name: Aparicio-Puerta E.
      - name: Ovchinnikov V.
      - name: Umu S.U.
      - name: Chabot P.J.
      - name: Kang W.
      - name: Aslanzadeh M.
      - name: Tarbier M.
      - name: Marmol-Sanchez E.
      - name: Urgese G.
      - name: Johansen M.
      - name: Hovig E.
      - name: Hackenberg M.
      - name: Friedlander M.R.
      - name: Peterson K.J.
      citationCount: 95
      date: '2022-01-07T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MirGeneDB 2.1: Toward a complete sampling of all major animal phyla'
    note: null
    pmcid: PMC8728216
    pmid: '34850127'
    type:
    - Primary
    version: '2.1'
  - doi: 10.1093/nar/gkz885
    metadata:
      abstract: Small non-coding RNAs have gained substantial attention due to their
        roles in animal development and human disorders. Among them, microRNAs are
        special because individual gene sequences are conserved across the animal
        kingdom. In addition, unique and mechanistically well understood features
        can clearly distinguish bona fide miRNAs from the myriad other small RNAs
        generated by cells. However, making this distinction is not a common practice
        and, thus, not surprisingly, the heterogeneous quality of available miRNA
        complements has become a major concern in microRNA research. We addressed
        this by extensively expanding our curated microRNA gene database-MirGeneDB-to
        45 organisms, encompassing a wide phylogenetic swath of animal evolution.
        By consistently annotating and naming 10,899 microRNA genes in these organisms,
        we show that previous microRNA annotations contained not only many false positives,
        but surprisingly lacked >2000 bona fide microRNAs. Indeed, curated microRNA
        complements of closely related organisms are very similar and can be used
        to reconstruct ancestral miRNA repertoires. MirGeneDB represents a robust
        platform for microRNA-based research, providing deeper and more significant
        insights into the biology and evolution of miRNAs as well as biomedical and
        biomarker research. MirGeneDB is publicly and freely available at http://mirgenedb.org/.
      authors:
      - name: Fromm B.
      - name: Domanska D.
      - name: Hoye E.
      - name: Ovchinnikov V.
      - name: Kang W.
      - name: Aparicio-Puerta E.
      - name: Johansen M.
      - name: Flatmark K.
      - name: Mathelier A.
      - name: Hovig E.
      - name: Hackenberg M.
      - name: Friedlander M.R.
      - name: Peterson K.J.
      citationCount: 178
      date: '2020-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MirGeneDB 2.0: The metazoan microRNA complement'
    note: null
    pmcid: PMC6943042
    pmid: '31598695'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1146/annurev-genet-120213-092023
    metadata:
      abstract: Although microRNAs (miRNAs) are among the most intensively studied
        molecules of the past 20 years, determining what is and what is not a miRNA
        has not been straightforward. Here, we present a uniform system for the annotation
        and nomenclature of miRNA genes. We show that less than a third of the 1,881
        human miRBase entries, and only approximately 16% of the 7,095 metazoan miRBase
        entries, are robustly supported as miRNA genes. Furthermore, we show that
        the human repertoire of miRNAs has been shaped by periods of intense miRNA
        innovation and that mature gene products show a very different tempo and mode
        of sequence evolution than star products. We establish a new open access database-MirGeneDB
        (http://mirgenedb.org)-to catalog this set of miRNAs, which complements the
        efforts of miRBase but differs from it by annotating the mature versus star
        products and by imposing an evolutionary hierarchy upon this curated and consistently
        named repertoire.
      authors:
      - name: Fromm B.
      - name: Billipp T.
      - name: Peck L.E.
      - name: Johansen M.
      - name: Tarver J.E.
      - name: King B.L.
      - name: Newcomb J.M.
      - name: Sempere L.F.
      - name: Flatmark K.
      - name: Hovig E.
      - name: Peterson K.J.
      citationCount: 435
      date: '2015-11-23T00:00:00Z'
      journal: Annual Review of Genetics
      title: A Uniform System for the Annotation of Vertebrate microRNA Genes and
        the Evolution of the Human microRNAome
    note: null
    pmcid: PMC4743252
    pmid: '26473382'
    type:
    - Primary
    version: '1.0'
  - doi: 10.1093/nar/gkae1094
    metadata:
      abstract: We present a major update of MirGeneDB (3.0), the manually curated
        animal microRNA gene database. Beyond moving to a new server and the creation
        of a computational mirror, we have expanded the database with the addition
        of 33 invertebrate species, including representatives of 5 previously unsampled
        phyla, and 6 mammal species. MirGeneDB now contains entries for 21 822 microRNA
        genes (5160 of these from the new species) belonging to 1743 microRNA families.
        The inclusion of these new species allowed us to refine both the evolutionary
        node of appearance of a number of microRNA genes/families, as well as MirGeneDB's
        phylogenetically informed nomenclature system. Updated covariance models of
        all microRNA families, along with all smallRNA read data are now downloadable.
        These enhanced annotations will allow researchers to analyze microRNA properties
        such as secondary structure and features of their biogenesis within a robust
        phylogenetic context and without the database plagued with numerous false
        positives and false negatives. In light of these improvements, MirGeneDB 3.0
        will assume the responsibility for naming conserved novel metazoan microRNAs.
        MirGeneDB is part of RNAcentral and Elixir Norway and is publicly and freely
        available at mirgenedb.org.
      authors:
      - name: Clarke A.W.
      - name: Hoye E.
      - name: Hembrom A.A.
      - name: Paynter V.M.
      - name: Vinther J.
      - name: Wyrozemski L.
      - name: Biryukova I.
      - name: Formaggioni A.
      - name: Ovchinnikov V.
      - name: Herlyn H.
      - name: Pierce A.
      - name: Wu C.
      - name: Aslanzadeh M.
      - name: Cheneby J.
      - name: Martinez P.
      - name: Friedlander M.R.
      - name: Hovig E.
      - name: Hackenberg M.
      - name: Umu S.U.
      - name: Johansen M.
      - name: Peterson K.J.
      - name: Fromm B.
      citationCount: 6
      date: '2025-01-06T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MirGeneDB 3.0: Improved taxonomic sampling, uniform nomenclature of
        novel conserved microRNA families and updated covariance models'
    note: null
    pmcid: PMC11701709
    pmid: '39673268'
    type:
    - Primary
    version: '3.0'
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  - term: Gene regulation
    uri: http://edamontology.org/topic_0204
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  - term: Zoology
    uri: http://edamontology.org/topic_3500
  - term: Human biology
    uri: http://edamontology.org/topic_2815
  validated: 1
  version:
  - '3.0'
next: ?page=2
previous: null
