count: 2092
list:
- accessibility: Open access
  additionDate: '2026-06-14T08:34:19.506926Z'
  biotoolsCURIE: biotools:phylo-movies
  biotoolsID: phylo-movies
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: enes@lbi-netmed.at
    fundrefid: null
    gridid: null
    name: Enes Berk Sakalli
    note: Corresponding software contact.
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    url: https://github.com/enesBerkSakalli
  - email: null
    fundrefid: null
    gridid: null
    name: Simon E. Haendeler
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Arndt von Haeseler
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Heiko A. Schmidt
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: Phylo-Movies is an open-source React and Flask web application, also
    available as a desktop app, for inspecting ordered phylogenetic tree series. It
    computes and visualizes subtree-prune-and-regraft transition frames between consecutive
    trees, helping users see which taxa or subtrees move across sliding-window analyses,
    bootstrap replicates, and curated tree-series comparisons. The viewer includes
    timeline playback, tree comparison, MSA context, coloring, analytics, image export,
    and recording tools.
  documentation:
  - note: Researcher-facing manual.
    type:
    - User manual
    url: https://enesberksakalli.github.io/phylo-movies/manual/
  - note: Project overview, installation, usage, citation, and links.
    type:
    - General
    url: https://github.com/enesBerkSakalli/phylo-movies/blob/main/README.md
  - note: Local source-checkout setup instructions.
    type:
    - Installation instructions
    url: https://github.com/enesBerkSakalli/phylo-movies/blob/main/docs/getting-started.md
  - note: Backend API documentation.
    type:
    - API documentation
    url: https://github.com/enesBerkSakalli/phylo-movies/blob/main/docs/api.md
  download:
  - note: Source checkout for full web application and backend workflows.
    type: Source code
    url: https://github.com/enesBerkSakalli/phylo-movies
    version: 0.98.1
  - note: Desktop convenience builds for macOS, Windows, and Linux.
    type: Binaries
    url: https://github.com/enesBerkSakalli/phylo-movies/releases/tag/v0.98.1
    version: 0.98.1
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Visualizes ordered phylogenetic tree series as animated transition movies
      with comparison, MSA context, movement analytics, image export, and recording
      support.
    operation:
    - term: Phylogenetic tree visualisation
      uri: http://edamontology.org/operation_0567
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    output:
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://enesberksakalli.github.io/phylo-movies/
  homepage_status: 0
  language:
  - Python
  - JavaScript
  - TypeScript
  lastUpdate: '2026-06-14T08:36:42.066838Z'
  license: MIT
  link:
  - note: Source code repository.
    type:
    - Repository
    url: https://github.com/enesBerkSakalli/phylo-movies
  - note: Static browser demo with precomputed example movies.
    type:
    - Service
    url: https://enesberksakalli.github.io/phylo-movies/demo/
  - note: null
    type:
    - Issue tracker
    url: https://github.com/enesBerkSakalli/phylo-movies/issues
  maturity: Mature
  name: Phylo-Movies
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: enes
  publication:
  - doi: 10.64898/2026.04.01.715821
    metadata: null
    note: bioRxiv preprint describing the Phylo-Movies method and examples.
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.5281/zenodo.20488923
    metadata: null
    note: Archived software release on Zenodo.
    pmcid: null
    pmid: null
    type:
    - Primary
    version: 0.98.1
  relation: []
  toolType:
  - Desktop application
  - Web application
  topic:
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 0
  version:
  - 0.98.1
- accessibility: Open access
  additionDate: '2026-06-09T14:59:46.648310Z'
  biotoolsCURIE: biotools:sigmacv
  biotoolsID: sigmacv
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: chretien.basile.jean.bernard.u4@s.mail.nagoya-u.ac.jp
    fundrefid: null
    gridid: null
    name: Basile Chrétien
    note: null
    orcidid: https://orcid.org/0000-0002-7483-2489
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    - Maintainer
    - Primary contact
    url: null
  description: Auto-generates clean, customizable academic CVs from open research
    data (OpenAlex, ORCID, Crossref, DataCite, Open Editors Plus). A single canonical
    CV object drives every output format (HTML, PDF, DOCX, LaTeX, Markdown); citations
    render through CSL; and the account holder is matched by persistent identifier
    (ORCID / OpenAlex ID) rather than name string. Free for individuals, open-source,
    and FAIR by design.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/BasileChretien/sigmacv#readme
  download:
  - note: null
    type: Source code
    url: https://github.com/BasileChretien/sigmacv
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data formatting
      uri: http://edamontology.org/operation_0335
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Annotation
      uri: http://edamontology.org/operation_0226
    output: []
  homepage: https://sigmacv.org
  homepage_status: 0
  language:
  - JavaScript
  - TypeScript
  lastUpdate: '2026-06-09T14:59:46.652232Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/BasileChretien/sigmacv
  - note: null
    type:
    - Issue tracker
    url: https://github.com/BasileChretien/sigmacv/issues
  maturity: Mature
  name: SigmaCV
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: basile
  publication:
  - doi: 10.5281/zenodo.20594123
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: 0.1.0
  relation: []
  toolType:
  - Web application
  topic: []
  validated: 0
  version:
  - 0.1.0
- accessibility: null
  additionDate: '2026-06-04T09:56:48.749854Z'
  biotoolsCURIE: biotools:NOVOPlasty
  biotoolsID: NOVOPlasty
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Nicolas Dierckxsens
    note: null
    orcidid: https://orcid.org/0000-0001-8051-6602
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: 'NOVOPlasty - The organelle assembler and heteroplasmy caller.


    NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular
    genomes..'
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/ndierckx/NOVOPlasty/wiki
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    output:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  - cmd: null
    input: []
    note: null
    operation:
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    output: []
  homepage: https://github.com/ndierckx/NOVOPlasty
  homepage_status: 0
  language:
  - Perl
  lastUpdate: '2026-06-04T09:56:48.751987Z'
  license: Other
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ndierckx/NOVOPlasty
  - note: null
    type:
    - Issue tracker
    url: https://github.com/ndierckx/NOVOPlasty/issues
  maturity: Mature
  name: NOVOPlasty
  operatingSystem: []
  otherID: []
  owner: aniehues
  publication:
  - doi: 10.1093/nar/gkw955
    metadata: null
    note: Primary publication for the tool.
    pmcid: PMC5389512
    pmid: '28204566'
    type:
    - Primary
    version: null
  - doi: 10.1093/nargab/lqz011
    metadata: null
    note: Primary publication for the heteroplasmy or variance calling option.
    pmcid: PMC7671380
    pmid: '33575563'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 0
  version:
  - NOVOPlasty4.3.5
- accessibility: null
  additionDate: '2026-06-04T08:25:03.738887Z'
  biotoolsCURIE: biotools:VerityMap
  biotoolsID: VerityMap
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: VerityMap is a tool for mapping long reads to assemblies of extra-long
    tandem repeats, producing SAM files and identifying potential heterozygous sites
    and assembly errors through analysis of rare k-mers. It supports PacBio HiFi and
    ONT reads and generates interactive HTML plots for variant analysis.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Mapping assembly
      uri: http://edamontology.org/operation_0523
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: BED
        uri: http://edamontology.org/format_3003
  homepage: https://github.com/ablab/VerityMap
  homepage_status: 0
  language:
  - C
  - CUDA
  - Python
  - C++
  lastUpdate: '2026-06-04T08:25:03.740814Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/ablab/tandemQUAST/issues
  maturity: Mature
  name: VerityMap
  operatingSystem: []
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.1093/bioinformatics/btaa440
    metadata: null
    note: null
    pmcid: PMC7355294
    pmid: '32657355'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-06-01T13:34:32.262833Z'
  biotoolsCURIE: biotools:flexrl
  biotoolsID: flexrl
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Kayané Robach
    note: null
    orcidid: https://orcid.org/0000-0002-5725-623X
    rorid: 05grdyy37
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://www.amsterdamumc.org/en/research/researchers/kayane-robach
  description: A Flexible Model For Record Linkage
  documentation:
  - note: null
    type:
    - API documentation
    url: https://rdrr.io/cran/FlexRL/api/
  - note: null
    type:
    - Installation instructions
    - Quick start guide
    - Training material
    - User manual
    url: https://github.com/robachowyk/FlexRL
  download:
  - note: null
    type: Source code
    url: https://github.com/robachowyk/FlexRL
    version: null
  - note: null
    type: Software package
    url: https://cran.r-project.org/package=FlexRL
    version: null
  editPermission:
    authors: []
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/robachowyk/FlexRL
  homepage_status: 0
  language:
  - C++
  - R
  lastUpdate: '2026-06-02T11:29:08.508018Z'
  license: GPL-3.0-or-later
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/robachowyk/FlexRL
  - note: null
    type:
    - Issue tracker
    url: https://github.com/robachowyk/FlexRL/issues
  - note: null
    type:
    - Helpdesk
    url: https://github.com/robachowyk/FlexRL/issues
  - note: null
    type:
    - Discussion forum
    url: https://github.com/robachowyk/FlexRL/issues
  maturity: Emerging
  name: FlexRL
  operatingSystem: []
  otherID: []
  owner: tpronk
  publication:
  - doi: 10.1093/jrsssc/qlaf016
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.48550/arXiv.2407.06835
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Data identity and mapping
    uri: http://edamontology.org/topic_3345
  validated: 0
  version:
  - 0.1.1
- accessibility: null
  additionDate: '2026-06-02T11:03:16.190851Z'
  biotoolsCURIE: biotools:MITObim
  biotoolsID: MITObim
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: christoph.hahn@uni-graz.at
    fundrefid: null
    gridid: null
    name: Christoph Hahn
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: MITObim - mitochondrial baiting and iterative mapping
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/chrishah/MITObim
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/chrishah/MITObim
  homepage_status: 0
  language:
  - Python
  - Perl
  lastUpdate: '2026-06-02T11:09:40.245903Z'
  license: MIT
  link:
  - note: null
    type:
    - Discussion forum
    url: https://groups.google.com/forum/#!forum/mitobim-users
  - note: null
    type:
    - Issue tracker
    url: https://github.com/chrishah/MITObim/issues
  - note: null
    type:
    - Repository
    url: https://github.com/chrishah/mitobim
  - note: This is a persistent identifier of version 1.9.1.
    type:
    - Other
    url: https://doi.org/10.5281/zenodo.1408102
  maturity: Mature
  name: MITObim
  operatingSystem: []
  otherID: []
  owner: aniehues
  publication:
  - doi: 10.1093/nar/gkt371
    metadata: null
    note: null
    pmcid: PMC3711436
    pmid: '23661685'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 0
  version:
  - v1.9.1
- accessibility: Open access
  additionDate: '2026-05-27T22:24:31.685869Z'
  biotoolsCURIE: biotools:pathogensurveillance
  biotoolsID: pathogensurveillance
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Pathogensurveillance is a population genomics pipeline for pathogen
    identification, variant detection, and biosurveillance. The pipeline accepts paths
    to raw reads for one or more organisms and creates reports in the form of an interactive
    HTML document. Significant features include the ability to analyze unidentified
    eukaryotic and prokaryotic samples, creation of reports for multiple user-defined
    groupings of samples, automated discovery and downloading of reference assemblies
    from NCBI RefSeq, and rapid initial identification based on k-mer sketches followed
    by a more robust multi gene phylogeny and SNP-based phylogeny.
  documentation:
  - note: null
    type:
    - User manual
    url: https://nf-co.re/pathogensurveillance
  download:
  - note: null
    type: Source code
    url: https://github.com/nf-core/pathogensurveillance/archive/refs/tags/1.1.0.tar.gz
    version: 1.1.0
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://nf-co.re/pathogensurveillance/
  homepage_status: 0
  language:
  - Groovy
  - R
  - Bash
  lastUpdate: '2026-05-27T22:31:22.963863Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/nf-core/pathogensurveillance
  - note: null
    type:
    - Issue tracker
    url: https://github.com/nf-core/pathogensurveillance/issues
  maturity: Emerging
  name: pathogensurveillance
  operatingSystem:
  - Linux
  otherID: []
  owner: zachary-foster
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - 1.1.0
- accessibility: null
  additionDate: '2018-07-25T09:20:55Z'
  biotoolsCURIE: biotools:phantasus
  biotoolsID: phantasus
  collectionID:
  - BioConductor
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: alsergbox@gmail.com
    fundrefid: null
    gridid: null
    name: Alexey Sergushichev
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: It is a web-application for visual and interactive gene expression
    analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation
    and analysis, which was integrated with an R environment via OpenCPU API. Aside
    from basic visualization and filtering methods, R-based methods such as k-means
    clustering, principal component analysis or differential expression analysis with
    limma package are supported.
  documentation:
  - note: null
    type:
    - User manual
    url: http://bioconductor.org/packages/release/bioc/manuals/phantasus/man/phantasus.pdf
  download:
  - note: null
    type: Software package
    url: http://bioconductor.org/packages/release/bioc/src/contrib/phantasus_1.0.2.tar.gz
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Clustering
      uri: http://edamontology.org/operation_3432
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Differential gene expression analysis
      uri: http://edamontology.org/operation_3223
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: http://bioconductor.org/packages/release/bioc/html/phantasus.html
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-05-14T22:23:09.969707Z'
  license: MIT
  link:
  - note: null
    type:
    - Mirror
    url: https://alserglab.wustl.edu/phantasus
  - note: null
    type:
    - Issue tracker
    url: https://github.com/alserglab/phantasus/issues
  - note: null
    type:
    - Repository
    url: https://github.com/alserglab/phantasus/issues
  maturity: null
  name: phantasus
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: alserg
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Microarray experiment
    uri: http://edamontology.org/topic_3518
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  validated: 1
  version:
  - 1.0.2
- accessibility: Open access
  additionDate: '2026-05-13T05:45:59.510938Z'
  biotoolsCURIE: biotools:framexplore
  biotoolsID: framexplore
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: vidhuvijay2003@gmail.com
    fundrefid: null
    gridid: null
    name: Vidhu S Vijay
    note: MS Bioinformatics student at Amrita Vishwa Vidyapeetham; creator and maintainer
      of FrameXplore.
    orcidid: https://orcid.org/0009-0009-1182-2089
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: https://github.com/Vidhusv
  description: FrameXplore is a Google Colab notebook that extends ColabFold to automatically
    identify and correct disulfide bonds in cysteine‑rich protein structures. After
    a standard ColabFold prediction, it extracts all cysteine residues, computes Cα–Cα
    and S–S distances, identifies true disulfide bonds using geometric cutoffs (Cα–Cα
    < 6.5 Å, S–S < 2.5 Å), writes a corrected PDB with proper CONECT records, and
    provides an interactive 3D view.
  documentation:
  - note: Quick start guide, example test case, methodology explanation, citation,
      and repository contents
    type:
    - General
    url: https://github.com/Vidhusv/FRAMEXPLORER/blob/main/README.md
  download:
  - note: Latest version of the complete repository as a ZIP file
    type: Source code
    url: https://github.com/Vidhusv/FRAMEXPLORER/archive/refs/heads/main.zip
    version: 1.0.0
  - note: Direct download of the Colab notebook (.ipynb file). Can be run locally
      or uploaded to Google Colab.
    type: Binaries
    url: https://raw.githubusercontent.com/Vidhusv/FRAMEXPLORER/main/FrameXplore.ipynb
    version: 1.0.0
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/Vidhusv/FRAMEXPLORER
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-13T06:23:55.557041Z'
  license: MIT
  link:
  - note: GitHub repository with source code, documentation, and logo
    type:
    - Repository
    url: https://github.com/Vidhusv/FRAMEXPLORER
  - note: Report bugs, suggest features, or ask questions
    type:
    - Issue tracker
    url: https://github.com/Vidhusv/FRAMEXPLORER/issues
  maturity: Emerging
  name: FrameXplore
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID:
  - type: doi
    value: doi:10.5281/zenodo.20135079
    version: null
  owner: vidhu
  publication:
  - doi: 10.1038/s41592-022-01488-1
    metadata: null
    note: 'ColabFold: making protein folding accessible to all. Nature Methods, 2022.'
    pmcid: PMC9184281
    pmid: '35637307'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Biosciences
    uri: http://edamontology.org/topic_4019
  validated: 0
  version:
  - 1.0.0
- accessibility: null
  additionDate: '2026-05-06T14:20:33.970341Z'
  biotoolsCURIE: biotools:paradigma
  biotoolsID: paradigma
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Paradigma is a toolbox for processing and feature extraction from wearable
    sensor data to identify digital biomarkers specifically tailored for Parkinson’s
    disease.
  documentation:
  - note: null
    type:
    - Training material
    - User manual
    url: https://biomarkersparkinson.github.io/paradigma/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Phenotype name
        uri: http://edamontology.org/data_3275
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Experimental measurement
        uri: http://edamontology.org/data_3108
      format:
      - term: Binary format
        uri: http://edamontology.org/format_2333
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
    - term: Data parsing
      uri: http://edamontology.org/operation_1812
    - term: Classification
      uri: http://edamontology.org/operation_2990
    - term: Feature extraction
      uri: http://edamontology.org/operation_3937
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: Binary format
        uri: http://edamontology.org/format_2333
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://github.com/biomarkersParkinson/paradigma
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-08T16:40:22.080190Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://research-software-directory.org/software/paradigma
  - note: null
    type:
    - Issue tracker
    url: https://github.com/biomarkersParkinson/paradigma/issues
  - note: null
    type:
    - Software catalogue
    url: https://pypi.org/p/paradigma
  maturity: Emerging
  name: paradigma
  operatingSystem:
  - Linux
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.5281/zenodo.13838392
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: null
  relation: []
  toolType:
  - Workflow
  - Suite
  topic:
  - term: Biomarkers
    uri: http://edamontology.org/topic_3360
  - term: Neurology
    uri: http://edamontology.org/topic_3334
  validated: 0
  version:
  - 1.1.1
- accessibility: Open access
  additionDate: '2026-05-08T09:48:10.559707Z'
  biotoolsCURIE: biotools:lightlogr
  biotoolsID: lightlogr
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: johannes.zauner@tum.de
    fundrefid: null
    gridid: null
    name: Johannes Zauner
    note: null
    orcidid: https://orcid.org/0000-0003-2171-4566
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    url: null
  description: "Process Data from Wearable Light Loggers and Optical Radiation Dosimeters.\
    \ \n\nImport, processing, validation, and visualization of personal light exposure\
    \ measurement data from wearable devices. The package for R statistical software\
    \ implements features such as the import of data and metadata files, conversion\
    \ of common file formats, validation of light logging data, verification of crucial\
    \ metadata, calculation of common parameters, and semi-automated analysis and\
    \ visualization."
  documentation:
  - note: null
    type:
    - General
    url: https://tscnlab.github.io/LightLogR/
  - note: null
    type:
    - Training material
    url: https://tscnlab.github.io/LightLogR_webinar/
  download:
  - note: 'in an R environment run:

      install.packages("LightLogR")'
    type: Software package
    url: https://cran.r-project.org/package=LightLogR
    version: 0.11.3
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://tscnlab.github.io/LightLogR/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-05-08T10:00:51.427165Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/tscnlab/LightLogR
  - note: null
    type:
    - Mailing list
    url: https://lists.lrz.de/mailman/listinfo/lightlogr-users
  - note: null
    type:
    - Issue tracker
    url: https://github.com/tscnlab/LightLogR/issues
  maturity: Mature
  name: LightLogR
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: johannes
  publication:
  - doi: 10.21105/joss.07601
    metadata: null
    note: null
    pmcid: PMC7617517
    pmid: '40123959'
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Open science
    uri: http://edamontology.org/topic_4010
  - term: Biosciences
    uri: http://edamontology.org/topic_4019
  - term: Preclinical and clinical studies
    uri: http://edamontology.org/topic_3379
  validated: 0
  version:
  - 0.10.3
- accessibility: Open access
  additionDate: '2026-04-20T14:52:49.621012Z'
  biotoolsCURIE: biotools:proteopy
  biotoolsID: proteopy
  collectionID:
  - mass spectrometry
  - proteomics
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: isabell.bludau@med.uni-heidelberg.de
    fundrefid: null
    gridid: null
    name: Isabell Bludau
    note: Junior Group Leader at the Department of Neuropathology, University Hospital
      Heidelberg
    orcidid: https://orcid.org/0000-0002-2601-238X
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: IanDirk.Fichtner@med.uni-heidelberg.de
    fundrefid: null
    gridid: null
    name: Ian Dirk Fichtner
    note: PhD student at the Department of Neuropathology, University Hospital Heidelberg
      and Division of Artificial Intelligence in Oncology, German Cancer Research
      Center (DKFZ)
    orcidid: https://orcid.org/0009-0002-3000-2907
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: ProteoPy is a lightweight Python library for protein- and peptide-level
    quantitative proteomics analysis, built around the AnnData class as its core data
    structure. It streamlines data import, preprocessing, and differential analysis
    while preserving all metadata within a single object.
  documentation:
  - note: null
    type:
    - General
    url: https://proteopy.readthedocs.io/en/latest/
  download:
  - note: null
    type: Source code
    url: https://github.com/UKHD-NP/proteopy/archive/refs/heads/main.zip
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://proteopy.readthedocs.io/en/latest/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-20T14:57:42.685298Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/UKHD-NP/proteopy
  - note: null
    type:
    - Discussion forum
    url: https://github.com/UKHD-NP/proteopy/discussions
  - note: null
    type:
    - Issue tracker
    url: https://github.com/UKHD-NP/proteopy/issues
  - note: Documentation
    type:
    - Other
    url: https://proteopy.readthedocs.io/en/latest/
  maturity: Emerging
  name: ProteoPy
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: ifichtner
  publication:
  - doi: 10.64898/2026.03.31.715273
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: null
  relation:
  - biotoolsID: anndata
    type: uses
  toolType:
  - Library
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  validated: 0
  version:
  - 0.1.1
- accessibility: Open access
  additionDate: '2026-04-06T14:44:11.549029Z'
  biotoolsCURIE: biotools:sambo_sequential_model-based_optimization
  biotoolsID: sambo_sequential_model-based_optimization
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Sequential and model-based optimization for Python with state-of-the-art
    performance.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://sambo-optimization.github.io/doc/sambo/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Optimisation and refinement
      uri: http://edamontology.org/operation_2425
    output: []
  homepage: https://sambo-optimization.github.io/
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-06T14:44:11.551236Z'
  license: AGPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/sambo-optimization/sambo
  - note: null
    type:
    - Issue tracker
    url: https://github.com/sambo-optimization/sambo/issues
  maturity: Mature
  name: SAMBO Optimization
  operatingSystem: []
  otherID: []
  owner: kurator
  publication:
  - doi: 10.5281/zenodo.14461363
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Applied mathematics
    uri: http://edamontology.org/topic_3569
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - v1.25.2
- accessibility: null
  additionDate: '2026-01-21T04:19:22.375410Z'
  biotoolsCURIE: biotools:rosalution
  biotoolsID: rosalution
  collectionID:
  - Rare Disease
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Angelina Uno-Antonison
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://github.com/SeriousHorncat
  description: Rosalution assists researchers study genetic variation 🧬 in patients
    🧑🏾‍🤝‍🧑🏼 by helping select candidate animal models 🐀🐁🐠🪱 to replicate the variation
    to further research to derive, diagnose, and provide therapies for ultra-rare
    diseases. Developed by the UAB Center for Computational Genomics and Data Science
    (CGDS).
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://github.com/uab-cgds-worthey/rosalution/releases/tag/0.8.8-er
    version: 0.8.8-er
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/uab-cgds-worthey/rosalution
  homepage_status: 0
  language:
  - JavaScript
  - Python
  lastUpdate: '2026-03-26T19:36:53.927081Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/uab-cgds-worthey/rosalution
  - note: null
    type:
    - Issue tracker
    url: https://github.com/uab-cgds-worthey/rosalution/issues
  maturity: Mature
  name: Rosalution
  operatingSystem: []
  otherID: []
  owner: sdhutchins
  publication:
  - doi: 10.21105/joss.05443
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  validated: 0
  version:
  - 0.8.8-er
- accessibility: Open access
  additionDate: '2018-12-12T12:35:31Z'
  biotoolsCURIE: biotools:bio.tools
  biotoolsID: bio.tools
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Contributors
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: https://biotools.readthedocs.io/en/latest/contributors.html
  description: The community registry of computational tools and data resources for
    biosciences.
  documentation:
  - note: API usage guide
    type:
    - API documentation
    url: https://biotools.readthedocs.io/en/latest/api_usage_guide.html
  - note: API Reference
    type:
    - API documentation
    url: https://biotools.readthedocs.io/en/latest/api_reference.html
  - note: null
    type:
    - Citation instructions
    url: https://biotools.readthedocs.io/en/latest/publications.html#citation
  - note: null
    type:
    - Contributions policy
    url: https://biotools.readthedocs.io/en/latest/contributors_guide.html
  - note: null
    type:
    - General
    url: https://biotools.readthedocs.io/en/latest/
  - note: null
    type:
    - Governance
    url: https://biotools.readthedocs.io/en/latest/governance.html
  - note: Curators Guide
    type:
    - User manual
    url: https://biotools.readthedocs.io/en/latest/curators_guide.html
  download:
  - note: null
    type: Source code
    url: https://github.com/bio-tools/biotoolsRegistry
    version: null
  editPermission:
    authors:
    - hans
    type: group
  elixirCommunity: []
  elixirNode:
  - Denmark
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Text
        uri: http://edamontology.org/data_3671
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output:
    - data:
        term: Tool metadata
        uri: http://edamontology.org/data_0958
      format:
      - term: YAML
        uri: http://edamontology.org/format_3750
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: XML
        uri: http://edamontology.org/format_2332
  homepage: https://bio.tools
  homepage_status: 0
  language:
  - JavaScript
  - Python
  lastUpdate: '2026-03-25T12:24:23.606945Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Helpdesk
    url: https://biotools.readthedocs.io/en/latest/support.html?highlight=help
  - note: null
    type:
    - Issue tracker
    url: https://github.com/bio-tools/biotoolsregistry/issues
  - note: null
    type:
    - Mailing list
    url: https://biotools.readthedocs.io/en/latest/contributors_guide.html#mailing-list
  - note: null
    type:
    - Repository
    url: https://github.com/bio-tools/biotoolsregistry/
  maturity: Emerging
  name: bio.tools
  operatingSystem: []
  otherID:
  - type: rrid
    value: RRID:SCR_014695
    version: null
  owner: jison
  publication:
  - doi: 10.1093/nar/gkv1116
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.12688/f1000research.12974.1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.1093/gigascience/gix022
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.1007/s10009-015-0392-z
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web API
  - Database portal
  - Web application
  topic:
  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2019-08-26T14:34:55Z'
  biotoolsCURIE: biotools:MINERVA_Platform
  biotoolsID: MINERVA_Platform
  collectionID:
  - LCSB
  - ELIXIR-LU
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Marek Ostaszewski
    note: null
    orcidid: https://orcid.org/0000-0003-1473-370X
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Piotr Gawron
    note: null
    orcidid: https://orcid.org/0000-0002-9328-8052
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Reinhard Schneider
    note: null
    orcidid: https://orcid.org/0000-0002-8278-1618
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Venkata Satagopam
    note: null
    orcidid: https://orcid.org/0000-0002-6532-5880
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Rudi Balling
    note: null
    orcidid: https://orcid.org/0000-0003-2902-5650
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: David Hoksza
    note: null
    orcidid: https://orcid.org/0000-0003-4679-0557
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ewa Smula
    note: null
    orcidid: https://orcid.org/0000-0001-7118-3164
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    url: null
  description: 'The MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform
    is a standalone webserver for visualization, exploration and management of molecular
    networks encoded in SBGN-compliant format, including files produced using CellDesigner
    or SBGN editors. Visualization of uploaded networks generated by the platform
    is accessible via a web browser to all viewers with the weblink to the resource.


    The MINERVA Platform is a webservice using the Java Server Faces 2 technology.
    The server side, including data parsing, integration, annotation and verification,
    is implemented in Java. The platform uses the Postgres SQL database for data storage
    and the Hibernate framework as a middle layer between web server and database.
    The user web-interface is generated using React.js. The displayed content is visualized
    by OpenLayers API, dedicated JavaScript and CSS.'
  documentation:
  - note: null
    type:
    - Quick start guide
    - Release notes
    - User manual
    - API documentation
    - Citation instructions
    - Terms of use
    url: https://minerva.uni.lu
  download:
  - note: Installation instructions, including debian package, virtual machine images
      and docker containers.
    type: Other
    url: https://minerva.pages.uni.lu/doc/install/
    version: 13.1.3 - 20.0.3
  editPermission:
    authors:
    - sascha.herzinger
    type: group
  elixirCommunity: []
  elixirNode:
  - Luxembourg
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Visualise systems biology diagrams online, on a standalone web server
    operation:
    - term: Pathway visualisation
      uri: http://edamontology.org/operation_3926
    output: []
  - cmd: null
    input: []
    note: Visualise omics data from multiple datasets on top of the diagrams
    operation:
    - term: Expression data visualisation
      uri: http://edamontology.org/operation_0571
    output: []
  - cmd: null
    input: []
    note: 'Convert between main systems biology layout formats: CellDeslgners SBML,
      SBML layout+render, SBGN-ML, GPML'
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output: []
  - cmd: null
    input: []
    note: Use MINERVA API to access systems biology formats for modelling
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output: []
  homepage: https://minerva.uni.lu
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-24T15:37:40.163855Z'
  license: AGPL-3.0
  link:
  - note: GiLab repository for core functionalities (data and format handling, service
      stability, API access)
    type:
    - Repository
    url: https://gitlab.lcsb.uni.lu/minerva/core/
  - note: Issue tracker for core functionalities (data and format handling, service
      stability, API access)
    type:
    - Issue tracker
    url: https://gitlab.lcsb.uni.lu/minerva/core/-/issues
  - note: GiLab repository for frontend functionalities
    type:
    - Repository
    url: https://gitlab.lcsb.uni.lu/minerva/frontend
  - note: Issue tracker for frontend functionalities
    type:
    - Issue tracker
    url: https://gitlab.lcsb.uni.lu/minerva/frontend/-/issues
  maturity: Mature
  name: The MINERVA Platform
  operatingSystem: []
  otherID: []
  owner: mjostaszewski
  publication:
  - doi: 10.1038/npjsba.2016.20
    metadata: null
    note: null
    pmcid: PMC5516855
    pmid: '28725475'
    type:
    - Primary
    version: '10.0'
  - doi: 10.1093/bioinformatics/btz286
    metadata: null
    note: null
    pmcid: PMC6821317
    pmid: '31074494'
    type:
    - Primary
    version: 12.2.3
  - doi: 10.1093/bib/bbz067
    metadata: null
    note: null
    pmcid: PMC7373180
    pmid: '31273380'
    type:
    - Primary
    version: 13.1.1
  - doi: 10.1089/big.2015.0057
    metadata: null
    note: null
    pmcid: PMC4932659
    pmid: '27441714'
    type:
    - Usage
    version: '10.0'
  - doi: 10.1016/j.envpol.2019.04.005
    metadata: null
    note: null
    pmcid: null
    pmid: '30991279'
    type: []
    version: 13.1.1
  relation:
  - biotoolsID: pathvisio
    type: uses
  - biotoolsID: sbgn
    type: uses
  - biotoolsID: libsbml
    type: uses
  toolType: []
  topic:
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Omics
    uri: http://edamontology.org/topic_3391
  - term: Translational medicine
    uri: http://edamontology.org/topic_3342
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  validated: 0
  version:
  - 13.1.3
  - 13.2.0
  - 14.0.13
  - 15.0.3
  - 16.4.0
  - 17.1.3
  - 18.1.1
  - 19.1.0
  - 19.1.3
  - 20.0.3
- 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:
    - Primary contact
    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
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Germany
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format:
      - term: COMBINE OMEX
        uri: http://edamontology.org/format_3686
      - term: SED-ML
        uri: http://edamontology.org/format_3685
      - term: CopasiML
        uri: http://edamontology.org/format_3239
      - term: SBML
        uri: http://edamontology.org/format_2585
    note: null
    operation:
    - term: Network simulation
      uri: http://edamontology.org/operation_3562
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    - term: Pathway visualisation
      uri: http://edamontology.org/operation_3926
    - term: Metabolic network modelling
      uri: http://edamontology.org/operation_3660
    output:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format:
      - term: COMBINE OMEX
        uri: http://edamontology.org/format_3686
      - term: SED-ML
        uri: http://edamontology.org/format_3685
      - term: CopasiML
        uri: http://edamontology.org/format_3239
      - term: SBML
        uri: http://edamontology.org/format_2585
  homepage: http://copasi.org/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-03-19T10:46:57.487072Z'
  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:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: frankbergmann
  publication:
  - doi: 10.1093/bioinformatics/btl485
    metadata: null
    note: null
    pmcid: null
    pmid: '17032683'
    type: []
    version: null
  - doi: 10.1007/978-1-59745-525-1_2
    metadata: null
    note: null
    pmcid: null
    pmid: '19399433'
    type: []
    version: null
  - doi: 10.1016/j.jbiotec.2017.06.1200
    metadata: null
    note: null
    pmcid: PMC5623632
    pmid: '28655634'
    type: []
    version: null
  relation:
  - biotoolsID: corc
    type: usedBy
  - biotoolsID: pycotools
    type: usedBy
  - biotoolsID: biosimulations
    type: includedIn
  - biotoolsID: sbmlwebapp
    type: usedBy
  - biotoolsID: libsbml
    type: uses
  - biotoolsID: basico
    type: usedBy
  toolType:
  - Command-line tool
  - Library
  - Desktop application
  topic:
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2015-08-24T08:35:55Z'
  biotoolsCURIE: biotools:bcftools
  biotoolsID: bcftools
  collectionID:
  - BCFtools
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: samtools@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Wellcome Sanger Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.sanger.ac.uk/
  - email: null
    fundrefid: null
    gridid: null
    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Support
    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: BCFtools is a set of utilities that manipulate variant calls in the
    Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently
    with both VCFs and BCFs, both uncompressed and BGZF-compressed.
  documentation:
  - note: null
    type:
    - General
    url: http://www.htslib.org/doc/bcftools.html
  - note: A workflow for BCFtools.
    type:
    - Other
    url: http://www.htslib.org/workflow/#mapping_to_variant
  download:
  - note: null
    type: Downloads page
    url: http://www.htslib.org/download/
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: BCF
        uri: http://edamontology.org/format_3020
      - term: VCF
        uri: http://edamontology.org/format_3016
    note: Multiple data munging operations.
    operation:
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: BCF
        uri: http://edamontology.org/format_3020
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-03-18T17:36:37.176917Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/samtools/bcftools
  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/bcftools/issues
  maturity: Mature
  name: BCFtools
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: awhitwham
  publication:
  - doi: 10.1093/bioinformatics/btp352
    metadata: null
    note: The Sequence Alignment/Map format and SAMtools.
    pmcid: PMC2723002
    pmid: '19505943'
    type:
    - Primary
    version: null
  - doi: 10.1093/gigascience/giab008
    metadata: null
    note: Twelve years of SAMtools and BCFtools.
    pmcid: PMC7931819
    pmid: '33590861'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: htslib
    type: uses
  toolType:
  - Suite
  - Command-line tool
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: GWAS study
    uri: http://edamontology.org/topic_3517
  - term: Genotyping experiment
    uri: http://edamontology.org/topic_3516
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - '1.3'
  - 1.3.1
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - 1.10.1
  - 1.10.2
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - '1.17'
  - '1.18'
  - '1.19'
  - '1.20'
  - '1.21'
  - 1.21.1
  - '1.22'
  - 1.22.1
  - '1.23'
  - 1.23.1
- accessibility: Open access
  additionDate: '2017-01-13T13:16:12Z'
  biotoolsCURIE: biotools:samtools
  biotoolsID: samtools
  collectionID:
  - Animal and Crop Genomics
  - Rare Disease
  - SAMtools
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: rd@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Richard Durbin
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: samtools@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Wellcome Sanger Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    - Primary contact
    url: https://www.sanger.ac.uk/
  - email: null
    fundrefid: null
    gridid: null
    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Support
    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: SAMtools and BCFtools are widely used programs for processing and analysing
    high-throughput sequencing data. They include tools for file format conversion
    and manipulation, sorting, querying, statistics, variant calling, and effect analysis
    amongst other methods.
  documentation:
  - note: HowTos for samtools
    type:
    - Other
    url: http://www.htslib.org/doc/#howtos
  - note: null
    type:
    - User manual
    url: http://www.htslib.org/doc/#manual-pages
  - note: null
    type:
    - Installation instructions
    url: http://www.htslib.org/download/
  download:
  - note: null
    type: Downloads page
    url: http://www.htslib.org/download/
    version: null
  editPermission:
    authors:
    - ELIXIR-EE
    - animalandcropgenomics
    - alice
    - awhitwham
    - sergitobara
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: SAM
        uri: http://edamontology.org/format_2573
    note: null
    operation:
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    - term: Data formatting
      uri: http://edamontology.org/operation_0335
    - term: Data editing
      uri: http://edamontology.org/operation_3096
    - term: Data parsing
      uri: http://edamontology.org/operation_1812
    - term: Data sorting
      uri: http://edamontology.org/operation_3802
    output:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: SAM
        uri: http://edamontology.org/format_2573
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-03-18T17:35:31.864480Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/samtools/samtools
  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/samtools/issues
  maturity: Mature
  name: SAMtools
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: awhitwham
  publication:
  - doi: 10.1093/bioinformatics/btp352
    metadata: null
    note: The Sequence Alignment/Map format and SAMtools.
    pmcid: PMC2723002
    pmid: '19505943'
    type:
    - Primary
    version: null
  - doi: 10.1093/gigascience/giab008
    metadata: null
    note: Twelve years of SAMtools and BCFtools.
    pmcid: PMC7931819
    pmid: '33590861'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/btr509
    metadata: null
    note: null
    pmcid: PMC3198575
    pmid: '21903627'
    type: []
    version: null
  relation:
  - biotoolsID: htslib
    type: uses
  toolType:
  - Suite
  - Command-line tool
  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - '1.3'
  - 1.3.1
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - 1.16.1
  - '1.17'
  - '1.18'
  - '1.19'
  - 1.19.1
  - 1.19.2
  - '1.20'
  - '1.21'
  - 1.21.1
  - '1.22'
  - 1.22.1
  - 1.22.2
  - '1.23'
  - 1.23.1
- accessibility: Open access
  additionDate: '2017-08-20T16:07:58Z'
  biotoolsCURIE: biotools:htslib
  biotoolsID: htslib
  collectionID:
  - Animal and Crop Genomics
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: samtools@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Wellcome Sanger Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    - Primary contact
    url: https://www.sanger.ac.uk/
  - email: null
    fundrefid: null
    gridid: null
    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Support
    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: The main purpose of HTSlib is to provide access to genomic information
    files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF
    and BCF formats). The library also provides interfaces to access and index genome
    reference data in FASTA format and tab-delimited files with genomic coordinates.
    It is utilized and incorporated into both SAMtools and BCFtools.
  documentation:
  - note: null
    type:
    - User manual
    url: http://www.htslib.org/doc/#manual-pages
  download:
  - note: null
    type: Downloads page
    url: http://www.htslib.org/download/
    version: null
  editPermission:
    authors:
    - animalandcropgenomics
    - smoe
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: BCF
        uri: http://edamontology.org/format_3020
      - term: VCF
        uri: http://edamontology.org/format_3016
    note: null
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: BCF
        uri: http://edamontology.org/format_3020
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-03-18T17:33:38.200309Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/samtools/htslib
  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/htslib/issues
  maturity: Mature
  name: HTSlib
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: awhitwham
  publication:
  - doi: 10.1093/gigascience/giab007
    metadata: null
    note: 'HTSlib: C library for reading/writing high-throughput sequencing data.'
    pmcid: PMC7931820
    pmid: '33594436'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: samtools
    type: usedBy
  - biotoolsID: bcftools
    type: usedBy
  toolType:
  - Library
  topic:
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - 1.2.1
  - '1.3'
  - 1.3.1
  - 1.3.2
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - 1.10.1
  - 1.10.2
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - '1.17'
  - '1.18'
  - '1.19'
  - '1.20'
  - 1.21.1
  - '1.22'
  - 1.22.1
  - 1.22.2
  - '1.23'
  - 1.23.1
- accessibility: null
  additionDate: '2021-11-29T10:31:42.544157Z'
  biotoolsCURIE: biotools:rhizovision-explorer
  biotoolsID: rhizovision-explorer
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: lmyork@noble.org
    fundrefid: null
    gridid: null
    name: Larry M. York
    note: null
    orcidid: https://orcid.org/0000-0002-1995-9479
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: RhizoVision Explorer is free and open-source software developed for
    estimating root traits from images acquired from a flatbed scanner or camera.
    Root images are expected to have a high contrast of roots with the background,
    homogenous lighting, and minimal overlapping of roots.
  documentation: []
  download: []
  editPermission:
    authors:
    - RDKing
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    - term: Feature extraction
      uri: http://edamontology.org/operation_3937
    output: []
  homepage: https://github.com/noble-research-institute/RhizoVisionExplorer
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-03-17T09:34:03.454691Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/rootphenomicslab/RhizoVisionExplorer/issues
  maturity: null
  name: RhizoVision Explorer
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1093/aobpla/plab056
    metadata:
      abstract: Roots are central to the function of natural and agricultural ecosystems
        by driving plant acquisition of soil resources and influencing the carbon
        cycle. Root characteristics like length, diameter and volume are critical
        to measure to understand plant and soil functions. RhizoVision Explorer is
        an open-source software designed to enable researchers interested in roots
        by providing an easy-To-use interface, fast image processing and reliable
        measurements. The default broken roots mode is intended for roots sampled
        from pots and soil cores, washed and typically scanned on a flatbed scanner,
        and provides measurements like length, diameter and volume. The optional whole
        root mode for complete root systems or root crowns provides additional measurements
        such as angles, root depth and convex hull. Both modes support providing measurements
        grouped by defined diameter ranges, the inclusion of multiple regions of interest
        and batch analysis. RhizoVision Explorer was successfully validated against
        ground truth data using a new copper wire image set. In comparison, the current
        reference software, the commercial WinRhizo™, drastically underestimated volume
        when wires of different diameters were in the same image. Additionally, measurements
        were compared with WinRhizo™ and IJ_Rhizo using a simulated root image set,
        showing general agreement in software measurements, except for root volume.
        Finally, scanned root image sets acquired in different labs for the crop,
        herbaceous and tree species were used to compare results from RhizoVision
        Explorer with WinRhizo™. The two software showed general agreement, except
        that WinRhizo™ substantially underestimated root volume relative to RhizoVision
        Explorer. In the current context of rapidly growing interest in root science,
        RhizoVision Explorer intends to become a reference software, improve the overall
        accuracy and replicability of root trait measurements and provide a foundation
        for collaborative improvement and reliable access to all.
      authors:
      - name: Seethepalli A.
      - name: Dhakal K.
      - name: Griffiths M.
      - name: Guo H.
      - name: Freschet G.T.
      - name: York L.M.
      citationCount: 130
      date: '2021-12-01T00:00:00Z'
      journal: AoB PLANTS
      title: 'RhizoVision Explorer: Open-source software for root image analysis and
        measurement standardization'
    note: null
    pmcid: PMC8598384
    pmid: '34804466'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Phenomics
    uri: http://edamontology.org/topic_3298
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2017-01-13T13:16:01Z'
  biotoolsCURIE: biotools:quast
  biotoolsID: quast
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: quast.support@cab.spbu.ru
    fundrefid: null
    gridid: null
    name: QUAST Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: "QUAST stands for QUality ASsessment Tool.  \nIt evaluates a quality\
    \ of genome assemblies by computing various metrics and providing nice reports."
  documentation:
  - note: null
    type:
    - General
    url: http://quast.bioinf.spbau.ru/
  download: []
  editPermission:
    authors:
    - ELIXIR-CZ
    - Keiler_Collier
    - rathor2611
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: quast -ek assembly.fa --out output_prefix
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: '# Running quast on a eukaryotic genome'
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Sequence assembly validation
      uri: http://edamontology.org/operation_3180
    output: []
  homepage: http://quast.sourceforge.net/quast
  homepage_status: 0
  language:
  - Perl
  - Python
  - C
  lastUpdate: '2026-03-13T09:39:06.494933Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ablab/quast
  - note: null
    type:
    - Issue tracker
    url: https://github.com/ablab/quast/issues
  maturity: Mature
  name: QUAST
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1093/bioinformatics/btt086
    metadata:
      abstract: Limitations of genome sequencing techniques have led to dozens of
        assembly algorithms, none of which is perfect. A number of methods for comparing
        assemblers have been developed, but none is yet a recognized benchmark. Further,
        most existing methods for comparing assemblies are only applicable to new
        assemblies of finished genomes; the problem of evaluating assemblies of previously
        unsequenced species has not been adequately considered. Here, we present QUAST
        - a quality assessment tool for evaluating and comparing genome assemblies.
        This tool improves on leading assembly comparison software with new ideas
        and quality metrics. QUAST can evaluate assemblies both with a reference genome,
        as well as without a reference. QUAST produces many reports, summary tables
        and plots to help scientists in their research and in their publications.
        In this study, we used QUAST to compare several genome assemblers on three
        datasets. QUAST tables and plots for all of them are available in the Supplementary
        Material, and interactive versions of these reports are on the QUAST website.
        © 2013 The Author.
      authors:
      - name: Gurevich A.
      - name: Saveliev V.
      - name: Vyahhi N.
      - name: Tesler G.
      citationCount: 6872
      date: '2013-04-15T00:00:00Z'
      journal: Bioinformatics
      title: 'QUAST: Quality assessment tool for genome assemblies'
    note: null
    pmcid: PMC3624806
    pmid: '23422339'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version:
  - v.5.3.0
- accessibility: Open access
  additionDate: '2016-03-17T13:51:10Z'
  biotoolsCURIE: biotools:webnma
  biotoolsID: webnma
  collectionID:
  - BiB tools
  - CBU tools
  - UiB tools
  - ELIXIR-NO
  - ELIXIR-Norway
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: Nathalie.Reuter@uib.no
    fundrefid: null
    gridid: null
    name: Nathalie Reuter
    note: null
    orcidid: https://orcid.org/0000-0002-3649-7675
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    url: http://www.cbu.uib.no/reuter/
  - email: null
    fundrefid: null
    gridid: null
    name: Sandhya P Tiwari
    note: null
    orcidid: https://orcid.org/0000-0002-0747-3826
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Kidane M Tekle
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Tristan Cragnolini
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Svenn H Grindhaug
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Lars Skjærven
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Gisle Salensminde
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Edvin Fuglebakk
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Siv M Hollup
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Department of Molecular Biology, University of Bergen, Norway
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Computational Biology Unit, Department of Informatics, University of Bergen,
      Norway
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: UiB
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: WEBnm@ provides quick, automated computation and analysis of low-frequency
    normal modes for protein structures.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: http://apps.cbu.uib.no/webnma3/howto/single
  - note: null
    type:
    - FAQ
    url: http://apps.cbu.uib.no/webnma3/qanda
  - note: null
    type:
    - General
    - Citation instructions
    url: http://apps.cbu.uib.no/webnma3/about
  download: []
  editPermission:
    authors:
    - eca008
    - korbinib
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Norway
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: Constructs elastic network model from alpha carbon coordinates of the protein,
      and computes properties to describe large scale conformations. Computes normal
      modes, fluctuation profiles, inter-residue correlations, conformational overlap
      analysis and vector field representations. Structural amino acid profiles, and
      normal mode characteristics describing protein motion, visualized in plots and
      decorated structure visualizations. White space delimited tabular data for normal
      modes and the provided plots
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Protein flexibility and motion analysis
      uri: http://edamontology.org/operation_0244
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Sequence profile
        uri: http://edamontology.org/data_1354
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Structure alignment
        uri: http://edamontology.org/data_0886
      format:
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: Performs comparative analysis of the normal modes of protein structures.
      Computes the Bhattacharyya Coefficient (BC) and the Root Mean Squared Inner
      Product (RMSIP) of aligned parts of the proteins. Alignment of sets of proteins
      to be compared. Multiple protein structures Heatmaps, dendrograms and structural
      amino acid profiles for visual comparison of structural similarity. White space
      delimited tabular data for the provided plots
    operation:
    - term: Protein structure comparison
      uri: http://edamontology.org/operation_2487
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Structural profile
        uri: http://edamontology.org/data_0889
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://apps.cbu.uib.no/webnma
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-03-11T08:56:55.566213Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    - Issue tracker
    url: https://github.com/reuter-group/webnma3
  - note: Helpdesk and support for ELIXIR Norway services.
    type:
    - Helpdesk
    url: https://elixir.no/helpdesk
  maturity: Mature
  name: WEBnma
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: UiB
  publication:
  - doi: 10.1186/s12859-014-0427-6
    metadata:
      abstract: 'Background: Normal mode analysis (NMA) using elastic network models
        is a reliable and cost-effective computational method to characterise protein
        flexibility and by extension, their dynamics. Further insight into the dynamics-function
        relationship can be gained by comparing protein motions between protein homologs
        and functional classifications. This can be achieved by comparing normal modes
        obtained from sets of evolutionary related proteins. Results: We have developed
        an automated tool for comparative NMA of a set of pre-aligned protein structures.
        The user can submit a sequence alignment in the FASTA format and the corresponding
        coordinate files in the Protein Data Bank (PDB) format. The computed normalised
        squared atomic fluctuations and atomic deformation energies of the submitted
        structures can be easily compared on graphs provided by the web user interface.
        The web server provides pairwise comparison of the dynamics of all proteins
        included in the submitted set using two measures: the Root Mean Squared Inner
        Product and the Bhattacharyya Coefficient. The Comparative Analysis has been
        implemented on our web server for NMA, WEBnmat, which also provides recently
        upgraded functionality for NMA of single protein structures. This includes
        new visualisations of protein motion, visualisation of inter-residue correlations
        and the analysis of conformational change using the. In addition, programmatic
        access to WEBnmat is now available through a SOAP-based web service. WEBnmat
        is available at. Conclusion: WEBnmat v2.0 is an online tool offering unique
        capability for comparative NMA on multiple protein structures. Along with
        a convenient web interface, powerful computing resources, and several methods
        for mode analyses, WEBnmat facilitates the assessment of protein flexibility
        within protein families and superfamilies. These analyses can give a good
        view of how the structures move and how the flexibility is conserved over
        the different structures.'
      authors:
      - name: Tiwari S.P.
      - name: Fuglebakk E.
      - name: Hollup S.M.
      - name: Skjaerven L.
      - name: Cragnolini T.
      - name: Grindhaug S.H.
      - name: Tekle K.M.
      - name: Reuter N.
      citationCount: 87
      date: '2014-12-30T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'WEBnmat v2.0: Web server and services for comparing protein flexibility'
    note: null
    pmcid: PMC4339738
    pmid: '25547242'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1186/1471-2105-6-52
    metadata:
      abstract: 'Background: Normal mode analysis (NMA) has become the method of choice
        to investigate the slowest motions in macromolecular systems. NMA is especially
        useful for large biomolecular assemblies, such as transmembrane channels or
        virus capsids. NMA relies on the hypothesis that the vibrational normal modes
        having the lowest frequencies (also named soft modes) describe the largest
        movements in a protein and are the ones that are functionally relevant. Results:
        We developed a web-based server to perform normal modes calculations and different
        types of analyses. Starting from a structure file provided by the user in
        the PDB format, the server calculates the normal modes and subsequently offers
        the user a series of automated calculations; normalized squared atomic displacements,
        vector field representation and animation of the first six vibrational modes.
        Each analysis is performed independently from the others and results can be
        visualized using only a web browser. No additional plug-in or software is
        required. For users who would like to analyze the results with their favorite
        software, raw results can also be downloaded. The application is available
        on http://www.bioinfo.no/tools/normalmodes. We present here the underlying
        theory, the application architecture and an illustration of its features using
        a large transmembrane protein as an example. Conclusion: We built an efficient
        and modular web application for normal mode analysis of proteins. Non specialists
        can easily and rapidly evaluate the degree of flexibility of multi-domain
        protein assemblies and characterize the large amplitude movements of their
        domains. © 2005 Hollup et al; licensee BioMed Central Ltd.'
      authors:
      - name: Hollup S.M.
      - name: Salensminde G.
      - name: Reuter N.
      citationCount: 105
      date: '2005-03-11T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'WEBnm@: A web application for normal mode analyses of proteins'
    note: null
    pmcid: PMC1274249
    pmid: '15762993'
    type:
    - Primary
    version: '1.0'
  relation:
  - biotoolsID: numpy
    type: uses
  - biotoolsID: biopython
    type: uses
  - biotoolsID: matplotlib
    type: uses
  - biotoolsID: mustang
    type: uses
  - biotoolsID: dssp
    type: uses
  toolType:
  - Web API
  - Suite
  topic:
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  validated: 1
  version:
  - '3.5'
- accessibility: null
  additionDate: '2026-02-22T16:11:47.056891Z'
  biotoolsCURIE: biotools:cnpscycle
  biotoolsID: cnpscycle
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: jingjing_friends@hotmail.com
    fundrefid: null
    gridid: null
    name: Jing Zhang
    note: null
    orcidid: https://orcid.org/0000-0001-5569-7763
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: yukun.zou@catas.cn
    fundrefid: null
    gridid: null
    name: Yukun Zou
    note: null
    orcidid: https://orcid.org/0000-0003-3622-9328
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: CNPS.cycle is an R package designed to streamline the analysis of shotgun
    metagenomic data related to biogeochemical cycles, providing users with visually
    informative outputs and automating key steps in data processing and analysis.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Differential gene expression profiling
      uri: http://edamontology.org/operation_3223
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    - term: Sequence assembly
      uri: http://edamontology.org/operation_0310
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    output: []
  homepage: https://github.com/yuezhengfu/CNPS.cycle/wiki
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-02-22T16:11:47.058922Z'
  license: null
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/yuezhengfu/CNPS.cycle/issues
  maturity: null
  name: CNPS.cycle
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1128/MSYSTEMS.01021-25
    metadata: null
    note: null
    pmcid: PMC12625701
    pmid: '41123363'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Carbon cycle
    uri: http://edamontology.org/topic_4020
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Metagenomic sequencing
    uri: http://edamontology.org/topic_3837
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-22T15:25:50.066712Z'
  biotoolsCURIE: biotools:meaanalysis
  biotoolsID: meaanalysis
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: emily.gordon@wadham.ox.ac.uk
    fundrefid: null
    gridid: null
    name: Emily A Gordon
    note: null
    orcidid: https://orcid.org/0009-0004-9490-5990
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: MEAanalysis is an open-source R package for visualizing burst parameters
    at the single-electrode level from AxIS Navigator MEA data, facilitating reproducible
    analysis and comparison of bursting parameters.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://egordon2.github.io/MEA-analysis-package/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-02-22T15:25:50.068898Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/egordon2/MEA-analysis-package/issues
  maturity: null
  name: MEAanalysis
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1093/BIOADV/VBAF160
    metadata: null
    note: null
    pmcid: PMC12311347
    pmid: '40746508'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Physiology
    uri: http://edamontology.org/topic_3300
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-22T15:25:38.814134Z'
  biotoolsCURIE: biotools:rqdeltact
  biotoolsID: rqdeltact
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: daniel.zalewski@umlub.pl
    fundrefid: null
    gridid: null
    name: Daniel Zalewski
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: RQdeltaCT is an R package designed for relative quantification of gene
    expression using delta Ct methods. It provides tools for data import, quality
    control, visualization, and statistical analysis of real-time PCR data, catering
    to both beginners and experienced R users.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: Regression analysis
      uri: http://edamontology.org/operation_3659
    - term: Scatter plot plotting
      uri: http://edamontology.org/operation_2940
    output: []
  homepage: https://CRAN.R-project.org/package=RQdeltaCT
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-02-22T15:25:38.817482Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/Donadelnal/RQdeltaCT/issues/1
  maturity: null
  name: RQdeltaCT
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1038/S41598-025-11822-0
    metadata: null
    note: null
    pmcid: PMC12350606
    pmid: '40804269'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Tomography
    uri: http://edamontology.org/topic_3452
  - term: PCR experiment
    uri: http://edamontology.org/topic_3519
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Probes and primers
    uri: http://edamontology.org/topic_0632
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-22T14:20:15.318545Z'
  biotoolsCURIE: biotools:eyeris
  biotoolsID: eyeris
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Shawn T Schwartz
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: eyeris is an R framework designed for flexible, extensible, and reproducible
    pupillometry preprocessing. It provides a complete workflow and addresses the
    need for standardized and FAIR data handling in pupillometry research.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    - term: Aggregation
      uri: http://edamontology.org/operation_3436
    - term: Splitting
      uri: http://edamontology.org/operation_3359
    output: []
  homepage: https://shawnschwartz.com/eyeris/reference/zscore.html
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-22T14:20:15.320606Z'
  license: MIT
  link:
  - note: null
    type:
    - Other
    url: https://shawnschwartz.com/eyeris
  - note: null
    type:
    - Repository
    url: https://cran.r-project.org/package=eyeris
  - note: null
    type:
    - Issue tracker
    url: https://github.com/shawntz/eyeris/issues
  maturity: null
  name: eyeris
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1101/2025.06.01.657312
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Electroencephalography
    uri: http://edamontology.org/topic_4014
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-22T13:39:33.222628Z'
  biotoolsCURIE: biotools:plantcv
  biotoolsID: plantcv
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: KMurphy@danforthcenter.org
    fundrefid: null
    gridid: null
    name: Katherine M Murphy
    note: null
    orcidid: https://orcid.org/0000-0002-8891-4274
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: PlantCV is a free and open-source package used for image analysis of
    plant phenotypes. It offers a pipeline for capturing, labeling, and transferring
    plant images, enabling quantification of traits such as plant size, height, and
    color.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    output: []
  homepage: https://plantcv.readthedocs.io/en/latest/
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-22T13:39:33.224517Z'
  license: null
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/danforthcenter/plantcv/issues
  maturity: null
  name: PlantCV
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.3791/67619
    metadata: null
    note: null
    pmcid: null
    pmid: '40228008'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Physiology
    uri: http://edamontology.org/topic_3300
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-22T13:39:01.895029Z'
  biotoolsCURIE: biotools:serobank
  biotoolsID: serobank
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: SeroBA(v2.0) is a tool and atlas designed to accurately identify pneumococcal
    serotypes based on genome sequencing. It provides a comprehensive library of known
    serotypes and incorporates a community-contribution system for updates.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Global alignment
      uri: http://edamontology.org/operation_0496
    output: []
  homepage: https://www.pneumogen.net/gps/#/serobank
  homepage_status: 0
  language: []
  lastUpdate: '2026-02-22T13:39:01.897168Z'
  license: null
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/GlobalPneumoSeq/seroba/issues
  maturity: null
  name: SeroBA(v2.0)
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1101/2025.04.16.648953
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Immunoproteins and antigens
    uri: http://edamontology.org/topic_2830
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-22T13:38:08.411538Z'
  biotoolsCURIE: biotools:mdciao
  biotoolsID: mdciao
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: guillermo.perez@charite.de
    fundrefid: null
    gridid: null
    name: Guillermo Pérez-Hernández
    note: null
    orcidid: https://orcid.org/0000-0002-9287-8704
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: mdciao is an open-source command-line tool and Python API for analyzing
    and visualizing molecular dynamics (MD) simulation data, particularly focused
    on residue-residue contact frequencies and enriched with domain-specific annotations.
  documentation:
  - note: null
    type:
    - General
    url: https://proteinformatics.uni-leipzig.de/mdciao/overview.html
  - note: null
    type:
    - Training material
    url: https://proteinformatics.uni-leipzig.de/mdciao/gallery.html#examples
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Simulation analysis
      uri: http://edamontology.org/operation_0244
    - term: Molecular dynamics
      uri: http://edamontology.org/operation_2476
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://www.mdciao.org
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-22T13:38:08.413715Z'
  license: LGPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://pypi.org/project/mdciao/
  - note: null
    type:
    - Issue tracker
    url: https://github.com/gph82/mdciao/issues
  maturity: null
  name: mdciao
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1371/JOURNAL.PCBI.1012837
    metadata: null
    note: null
    pmcid: PMC12011235
    pmid: '40258031'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Molecular dynamics
    uri: http://edamontology.org/topic_0176
  - term: Membrane and lipoproteins
    uri: http://edamontology.org/topic_0820
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 0
  version: []
- accessibility: null
  additionDate: '2021-11-01T10:50:55.880296Z'
  biotoolsCURIE: biotools:pastaq
  biotoolsID: pastaq
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: p.l.horvatovich@rug.nl
    fundrefid: null
    gridid: null
    name: Peter Horvatovich
    note: null
    orcidid: https://orcid.org/0000-0003-2218-1140
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: PASTAQ (Pipelines And Systems for Threshold Avoiding Quantification)
    provides a set of tools for high-performance pre-processing of LC-MS/MS data.
    Avoiding the use of arbitrary intensity thresholds in early stages of the pipeline
    can aid in the detection of important biological low intensity signals common
    in metabolomics and proteomics experiments.
  documentation: []
  download: []
  editPermission:
    authors:
    - n.m.palmblad@lumc.nl
    - peter2
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    - term: Deisotoping
      uri: http://edamontology.org/operation_3629
    - term: Peptide identification
      uri: http://edamontology.org/operation_3631
    - term: Peak detection
      uri: http://edamontology.org/operation_3215
    output: []
  homepage: https://pastaq.horvatovichlab.com
  homepage_status: 0
  language:
  - C++
  - Python
  lastUpdate: '2026-02-19T12:16:32.495761Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/PASTAQ-MS/PASTAQ
  - note: null
    type:
    - Issue tracker
    url: https://github.com/PASTAQ-MS/PASTAQ/issues
  maturity: null
  name: PASTAQ
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1021/acs.analchem.1c01892
    metadata:
      abstract: ''
      authors: []
      citationCount: 10
      date: '2021-08-17T00:00:00Z'
      journal: Analytical Chemistry
      title: Pipelines and Systems for Threshold-Avoiding Quantification of LC-MS/MS
        Data
    note: null
    pmcid: PMC8374884
    pmid: '34355890'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Workflow
  - Library
  topic:
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  validated: 0
  version: []
- accessibility: null
  additionDate: '2015-12-01T16:27:10Z'
  biotoolsCURIE: biotools:bridgedb
  biotoolsID: bridgedb
  collectionID:
  - Proteomics
  - ELIXIR-NL
  - BIGCAT-UM
  - BridgeDb
  - Rare Disease
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Maastricht University
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: BridgeDb is a framework to map identifiers between various databases.  It
    includes a Java library that provides an API to work with identifier-identifier
    mapping databases and resources.
  documentation:
  - note: null
    type:
    - General
    url: https://bridgedb.github.io/pages/docs.html
  download: []
  editPermission:
    authors:
    - proteomics.bio.tools
    - ChrisEvelo
    type: group
  elixirCommunity: []
  elixirNode:
  - Netherlands
  elixirPlatform:
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Gene identifier
        uri: http://edamontology.org/data_1025
      format: []
    note: API for converting gene identifiers (Ensembl, Entrez) to identifiers from
      another database. Depends on an identifier-identifier mapping database or service
      supported by the API.
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
    - data:
        term: Gene identifier
        uri: http://edamontology.org/data_1025
      format: []
  - cmd: null
    input:
    - data:
        term: Protein identifier
        uri: http://edamontology.org/data_0989
      format: []
    note: null
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
    - data:
        term: Protein identifier
        uri: http://edamontology.org/data_0989
      format: []
  - cmd: null
    input:
    - data:
        term: Compound identifier
        uri: http://edamontology.org/data_1086
      format: []
    note: API for converting compound identifiers (HMDB, ChEBI, ChemSpider, PubChem,
      etc) to identifiers from another database. Depends on an identifier-identifier
      mapping database or service supported by the API.
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
    - data:
        term: Compound identifier
        uri: http://edamontology.org/data_1086
      format: []
  homepage: http://bridgedb.github.io/
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2026-02-17T12:12:04.425822Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/bridgedb/BridgeDb
  - note: null
    type:
    - Issue tracker
    url: https://github.com/bridgedb/BridgeDb/issues
  - note: null
    type:
    - Social media
    url: https://fosstodon.org/@bridgedb
  maturity: Mature
  name: BridgeDb
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: egonw
  publication:
  - doi: 10.1186/1471-2105-11-5
    metadata: null
    note: null
    pmcid: PMC2824678
    pmid: '20047655'
    type: []
    version: null
  - doi: 10.1007/978-3-319-11964-9_7
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.3897/rio.8.e83031
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: identifiers.org
    type: uses
  - biotoolsID: bioregistry
    type: uses
  toolType:
  - Library
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  - term: Toxicology
    uri: http://edamontology.org/topic_2840
  validated: 1
  version:
  - 3.0.18
- accessibility: null
  additionDate: '2018-07-25T14:43:52Z'
  biotoolsCURIE: biotools:rwikipathways
  biotoolsID: rwikipathways
  collectionID:
  - Rare Disease
  - BioConductor
  - COVID-19
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: egon.willighagen@gmail.com
    fundrefid: null
    gridid: null
    name: Egon Willighagen
    note: null
    orcidid: https://orcid.org/0000-0001-7542-0286
    rorid: 02jz4aj89
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: alex.pico@gladstone.ucsf.edu
    fundrefid: null
    gridid: null
    name: Alexander Pico
    note: null
    orcidid: https://orcid.org/0000-0001-5706-2163
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Denise Slenter
    note: null
    orcidid: https://orcid.org/0000-0001-8449-1318
    rorid: 02jz4aj89
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Martina Kutmon
    note: null
    orcidid: https://orcid.org/0000-0002-7699-8191
    rorid: 02jz4aj89
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Susan Coort
    note: null
    orcidid: https://orcid.org/0000-0003-1224-9690
    rorid: 02jz4aj89
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Marvin Martens
    note: null
    orcidid: https://orcid.org/0000-0003-2230-0840
    rorid: 02jz4aj89
    typeEntity: Person
    typeRole: []
    url: null
  description: Use this package to interface with the WikiPathways API.
  documentation:
  - note: null
    type:
    - User manual
    url: http://bioconductor.org/packages/release/bioc/manuals/rWikiPathways/man/rWikiPathways.pdf
  download:
  - note: null
    type: Downloads page
    url: http://bioconductor.org/packages/release/bioc/src/contrib/rWikiPathways_1.0.0.tar.gz
    version: null
  editPermission:
    authors:
    - ChrisEvelo
    - LanfearJ
    - egonw
    type: group
  elixirCommunity:
  - Metabolomics
  elixirNode:
  - Netherlands
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Pathway ID (WikiPathways)
        uri: http://edamontology.org/data_3952
      format: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format:
      - term: GPML
        uri: http://edamontology.org/format_3657
  homepage: http://bioconductor.org/packages/release/bioc/html/rWikiPathways.html
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-02-17T11:52:55.435797Z'
  license: MIT
  link:
  - note: null
    type:
    - Mirror
    url: https://github.com/wikipathways/rwikipathways
  - note: null
    type:
    - Issue tracker
    url: https://github.com/wikipathways/rwikipathways/issues
  maturity: null
  name: rWikiPathways
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: egonw
  publication:
  - doi: 10.1093/nar/gkx1064
    metadata: null
    note: null
    pmcid: PMC5753270
    pmid: '29136241'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkad960
    metadata: null
    note: null
    pmcid: PMC10767877
    pmid: '37941138'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkaa1024
    metadata: null
    note: null
    pmcid: PMC7779061
    pmid: '33211851'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: bridgedbr
    type: usedBy
  - biotoolsID: wikipathways
    type: uses
  toolType:
  - Library
  topic:
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 1
  version:
  - 1.0.0
  - 1.26.0
- accessibility: null
  additionDate: '2023-06-07T03:22:25.847061Z'
  biotoolsCURIE: biotools:metabuli
  biotoolsID: metabuli
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'Metabuli: specific and sensitive metagenomic classification via joint
    analysis of DNA and amino acid'
  documentation: []
  download: []
  editPermission:
    authors:
    - vashokan
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format: []
  homepage: https://metabuli.steineggerlab.com
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-02-12T14:21:25.897853Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/steineggerlab/Metabuli/issues
  - note: github repository
    type:
    - Repository
    url: https://github.com/steineggerlab/Metabuli
  maturity: Mature
  name: metabuli
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: milot-mirdita
  publication:
  - doi: 10.1038/s41592-024-02273-y
    metadata: null
    note: null
    pmcid: null
    pmid: '38769467'
    type: []
    version: null
  relation:
  - biotoolsID: mmseqs2
    type: uses
  - biotoolsID: gtdb
    type: uses
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  validated: 0
  version: []
- accessibility: null
  additionDate: '2019-06-20T14:18:28Z'
  biotoolsCURIE: biotools:decompTumor2Sig
  biotoolsID: decompTumor2Sig
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: r.piro@fu-berlin.de
    fundrefid: null
    gridid: null
    name: Prof. Dr. Rosario M. Piro
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    url: null
  description: R package for identification of mutational signatures active in individual
    tumors. It decomposes an individual tumor genome into a given set of Alexandrov-type
    or Shiraishi-type signatures, thus quantifying the contribution of the corresponding
    mutational processes to the somatic mutations identified in the tumor.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/rmpiro/decompTumor2Sig/blob/master/decompTumor2Sig-manual.pdf
  download:
  - note: null
    type: Downloads page
    url: http://rmpiro.net/index.html#downloads
    version: null
  editPermission:
    authors:
    - ELIXIR-ITA-POLIMI
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    - term: Parsing
      uri: http://edamontology.org/operation_1812
    output: []
  homepage: http://rmpiro.net/decompTumor2Sig/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-02-12T13:42:21.288130Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/rmpiro/decompTumor2Sig/issues
  - note: null
    type:
    - Repository
    url: https://github.com/rmpiro/decompTumor2Sig
  - note: null
    type:
    - Software catalogue
    url: https://bioconductor.org/packages/release/bioc/html/decompTumor2Sig.html
  maturity: Mature
  name: decompTumor2Sig
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: rosario7
  publication:
  - doi: 10.1186/s12859-019-2688-6
    metadata:
      abstract: '© 2019 The Author(s).Background: The somatic mutations found in a
        tumor have in most cases been caused by multiple mutational processes such
        as those related to extrinsic carcinogens like cigarette smoke, and those
        related to intrinsic processes like age-related spontaneous deamination of
        5-methylcytosine. The effect of such mutational processes can be modeled by
        mutational signatures, of which two different conceptualizations exist: the
        model introduced by Alexandrov et al., Nature 500:415-421, 2013, and the model
        introduced by Shiraishi et al., PLoS Genetics 11(12):e1005657, 2015. The initial
        identification and definition of mutational signatures requires large sets
        of tumor samples. Results: Here, we present decompTumor2Sig, an easy to use
        R package that can decompose an individual tumor genome into a given set of
        Alexandrov-type or Shiraishi-type signatures, thus quantifying the contribution
        of the corresponding mutational processes to the somatic mutations identified
        in the tumor. Until now, such tools were available only for Alexandrov signatures.
        We demonstrate the correctness and usefulness of our approach with three test
        cases, using somatic mutations from 21 breast cancer genomes, from 435 tumor
        genomes of ten different tumor entities, and from simulated tumor genomes,
        respectively. Conclusions: The decompTumor2Sig package is freely available
        and has been accepted for inclusion in Bioconductor.'
      authors:
      - name: Kruger S.
      - name: Piro R.M.
      citationCount: 8
      date: '2019-04-18T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'DecompTumor2Sig: Identification of mutational signatures active in individual
        tumors'
    note: null
    pmcid: PMC6472187
    pmid: '30999866'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
  - 2.0.0
- accessibility: Open access
  additionDate: '2026-01-30T22:36:14.902508Z'
  biotoolsCURIE: biotools:pantas
  biotoolsID: pantas
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Differential quantification of alternative splicing events on spliced
    pangenome graphs.
  documentation:
  - note: null
    type:
    - General
    - Installation instructions
    - Quick start guide
    - Command-line options
    url: https://github.com/AlgoLab/pantas/blob/main/README.md
  download:
  - note: null
    type: Source code
    url: https://github.com/AlgoLab/pantas
    version: null
  - note: null
    type: Container file
    url: https://hub.docker.com/r/algolab/pantas
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Italy
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function: []
  homepage: https://github.com/algolab/pantas
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-30T22:36:14.904749Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/AlgoLab/pantas
  - note: null
    type:
    - Issue tracker
    url: https://github.com/AlgoLab/pantas/issues
  maturity: null
  name: pantas
  operatingSystem:
  - Linux
  otherID: []
  owner: yp
  publication:
  - doi: 10.1371/journal.pcbi.1012665
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: RNA splicing
    uri: http://edamontology.org/topic_3320
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-27T17:11:15.880698Z'
  biotoolsCURIE: biotools:recgraph
  biotoolsID: recgraph
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: RecGraph is a tool for computing optimal sequence-to-graph alignment
    with recombinations.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/AlgoLab/RecGraph/blob/main/README.md
  download:
  - note: null
    type: Binaries
    url: https://github.com/AlgoLab/RecGraph/releases/tag/v1.0.0
    version: 1.0.0
  - note: null
    type: Software package
    url: https://anaconda.org/channels/bioconda/packages/recgraph/overview
    version: null
  editPermission:
    authors: []
    type: group
  elixirCommunity: []
  elixirNode:
  - Italy
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function: []
  homepage: https://github.com/AlgoLab/RecGraph
  homepage_status: 0
  language:
  - Rust
  lastUpdate: '2026-01-30T22:07:27.044664Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/AlgoLab/RecGraph
  - note: null
    type:
    - Issue tracker
    url: https://github.com/AlgoLab/RecGraph/issues
  maturity: Emerging
  name: RecGraph
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: yp
  publication:
  - doi: 10.1093/bioinformatics/btae292
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: 1.0.0
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Population genomics
    uri: http://edamontology.org/topic_3796
  validated: 0
  version:
  - 1.0.0
- accessibility: Open access
  additionDate: '2021-05-08T17:25:21Z'
  biotoolsCURIE: biotools:bakta
  biotoolsID: bakta
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: oliver.schwengers@cb.jlug.de
    fundrefid: null
    gridid: null
    name: Oliver Schwengers
    note: null
    orcidid: https://orcid.org/0000-0003-4216-2721
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://github.com/oschwengers
  - email: null
    fundrefid: null
    gridid: null
    name: Justus Liebig University Giessen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.uni-giessen.de
  description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/oschwengers/bakta/blob/main/README.md
  - note: null
    type:
    - Contributions policy
    url: https://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.md
  - note: null
    type:
    - Code of conduct
    url: https://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.md
  - note: null
    type:
    - User manual
    url: https://bakta.readthedocs.io/
  download:
  - note: Mandatory annotation database
    type: Other
    url: https://zenodo.org/records/14916843
    version: v6.0
  editPermission:
    authors:
    - ELIXIR-CZ
    - bebatut
    type: group
  elixirCommunity: []
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fasta
    input:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence features metadata
        uri: http://edamontology.org/data_2914
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format:
      - term: GFF3
        uri: http://edamontology.org/format_1975
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Hidden Markov model
        uri: http://edamontology.org/data_1364
      format:
      - term: HMMER3
        uri: http://edamontology.org/format_3329
    note: null
    operation:
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    output:
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: GenBank format
        uri: http://edamontology.org/format_1936
      - term: GFF3
        uri: http://edamontology.org/format_1975
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Nucleic acid sequence record
        uri: http://edamontology.org/data_2887
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PNG
        uri: http://edamontology.org/format_3603
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://github.com/oschwengers/bakta
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-01-29T12:11:19.042627Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/oschwengers/bakta
  - note: null
    type:
    - Issue tracker
    url: https://github.com/oschwengers/bakta/issues
  - note: null
    type:
    - Other
    url: https://bioconda.github.io/recipes/bakta/README.html
  - note: null
    type:
    - Service
    url: https://bakta.computational.bio
  maturity: Mature
  name: Bakta
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: oschwengers
  publication:
  - doi: 10.1099/mgen.0.000685
    metadata: null
    note: null
    pmcid: PMC8743544
    pmid: '34739369'
    type:
    - Primary
    version: '1.1'
  - doi: 10.1093/nar/gkaf335
    metadata: null
    note: null
    pmcid: PMC12230652
    pmid: '40271661'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: diamond
    type: uses
  - biotoolsID: hmmer3
    type: uses
  - biotoolsID: infernal
    type: uses
  - biotoolsID: trnascan-se
    type: uses
  - biotoolsID: blast
    type: uses
  - biotoolsID: aragorn
    type: uses
  - biotoolsID: pilercr
    type: uses
  - biotoolsID: deepsig
    type: uses
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - v1.12.0
- accessibility: null
  additionDate: '2021-09-27T07:31:29.303373Z'
  biotoolsCURIE: biotools:icodon
  biotoolsID: icodon
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: arb@stowers.org
    fundrefid: null
    gridid: null
    name: Ariel Alejandro Bazzini
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: iCodon is a tool for ideal codon design for customized gene expression.
  documentation: []
  download: []
  editPermission:
    authors:
    - jian
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Nucleic acid design
      uri: http://edamontology.org/operation_3095
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: cis-regulatory element prediction
      uri: http://edamontology.org/operation_0441
    output: []
  homepage: https://bazzinilab.shinyapps.io/icodon/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-01-28T15:28:03.870976Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/santiago1234/iCodon
  - note: null
    type:
    - Issue tracker
    url: https://github.com/santiago1234/iCodon/issues
  maturity: null
  name: iCodon
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1101/2021.05.06.442969
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  - Library
  topic:
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Biotechnology
    uri: http://edamontology.org/topic_3297
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2019-09-13T12:51:16Z'
  biotoolsCURIE: biotools:kraken2
  biotoolsID: kraken2
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Derrick E. Wood
    note: null
    orcidid: http://orcid.org/0000-0002-7429-1854
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Jennifer Lu
    note: null
    orcidid: http://orcid.org/0000-0001-9167-2002
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: langmea@cs.jhu.edu
    fundrefid: null
    gridid: null
    name: Ben Langmead
    note: null
    orcidid: http://orcid.org/0000-0003-2437-1976
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: 'Kraken 2 is the newest version of Kraken, a taxonomic classification
    system using exact k-mer matches to achieve high accuracy and fast classification
    speeds. This classifier matches each k-mer within a query sequence to the lowest
    common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments
    inform the classification algorithm.

    Any assumption that Kraken’s raw read assignments can be directly translated into
    species or strain-level abundance estimates is flawed. Bracken (Bayesian Reestimation
    of Abundance after Classification with KrakEN), estimates species abundances in
    metagenomics samples by probabilistically re-distributing reads in the taxonomic
    tree. (Lu, Jennifer et al. “Bracken: estimating species abundance in metagenomics
    data.”)'
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/DerrickWood/kraken2/wiki/Manual
  - note: Links to multiple Kraken 2 and bracken databases and indexes
    type:
    - User manual
    url: https://benlangmead.github.io/aws-indexes/k2
  download:
  - note: null
    type: Source code
    url: https://github.com/DerrickWood/kraken2/archive/v2.0.8-beta.tar.gz
    version: 2.0.8-beta
  editPermission:
    authors:
    - vashokan
    - Keiler_Collier
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: '`kraken2 --db <kraken2_database> <input.fastq>`'
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://github.com/DerrickWood/kraken2
  homepage_status: 0
  language:
  - Perl
  - C++
  lastUpdate: '2026-01-28T10:34:30.102754Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/DerrickWood/kraken2
  - note: null
    type:
    - Issue tracker
    url: https://github.com/DerrickWood/kraken2/issues
  maturity: null
  name: kraken2
  operatingSystem: []
  otherID: []
  owner: anand-anshu
  publication:
  - doi: 10.1101/762302
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: kraken
    type: isNewVersionOf
  - biotoolsID: bracken
    type: usedBy
  - biotoolsID: gtdb
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  validated: 1
  version:
  - 2.0.8-beta
- accessibility: Open access
  additionDate: '2026-01-26T15:47:19.914992Z'
  biotoolsCURIE: biotools:dome_registry
  biotoolsID: dome_registry
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: gavinmichael.farrell@phd.unipd.it
    fundrefid: null
    gridid: null
    name: Gavin Farrell
    note: Curation and data support
    orcidid: https://orcid.org/0000-0001-5166-8551
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: null
  - email: omarabdelghani.attafi@studenti.unipd.it
    fundrefid: null
    gridid: null
    name: Omar Attafi
    note: null
    orcidid: https://orcid.org/0009-0002-2327-9430
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: A database of annotations for published papers describing machine learning
    methods in biology.
  documentation:
  - note: null
    type:
    - Installation instructions
    url: https://github.com/BioComputingUP/dome-registry
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Intrinsically Disordered Proteins
  elixirNode:
  - Italy
  - Greece
  elixirPlatform:
  - Data
  elixir_badge: 0
  function: []
  homepage: https://registry.dome-ml.org/
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-26T15:47:50.276247Z'
  license: CC-BY-NC-4.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/BioComputingUP/dome-registry/issues
  maturity: Mature
  name: DOME Registry
  operatingSystem: []
  otherID: []
  owner: gavin
  publication:
  - doi: 10.1093/gigascience/giae094
    metadata: null
    note: null
    pmcid: PMC11633452
    pmid: '39661723'
    type: []
    version: null
  relation:
  - biotoolsID: europepmc
    type: uses
  - biotoolsID: europepmc
    type: usedBy
  toolType:
  - Database portal
  - Web application
  topic:
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Biosciences
    uri: http://edamontology.org/topic_4019
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2026-01-26T10:32:11.701456Z'
  biotoolsCURIE: biotools:pyxlms
  biotoolsID: pyxlms
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: micha.birklbauer@fh-hagenberg.at
    fundrefid: null
    gridid: null
    name: Micha Johannes Birklbauer
    note: null
    orcidid: https://orcid.org/0009-0005-1051-179X
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    url: null
  - email: viktoria.dorfer@fh-hagenberg.at
    fundrefid: null
    gridid: null
    name: Viktoria Dorfer
    note: null
    orcidid: https://orcid.org/0000-0002-5332-5701
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: proteomics@fh-hagenberg.at
    fundrefid: null
    gridid: null
    name: Proteomics FHOÖ Campus Hagenberg
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole:
    - Primary contact
    url: null
  description: pyXLMS is a python package and web application with graphical user
    interface that aims to simplify and streamline the intermediate step of connecting
    crosslink search engine results with down-stream analysis tools, enabling researchers
    even without bioinformatics knowledge to conduct in-depth crosslink analyses and
    shifting the focus from data transformation to data interpretation and therefore
    gaining biological insight.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://hgb-bin-proteomics.github.io/pyXLMS/
  - note: null
    type:
    - User manual
    url: https://hgb-bin-proteomics.github.io/pyXLMS-docs
  - note: null
    type:
    - Code of conduct
    url: https://github.com/hgb-bin-proteomics/pyXLMS/blob/master/CODE_OF_CONDUCT.md
  - note: null
    type:
    - Contributions policy
    url: https://github.com/hgb-bin-proteomics/pyXLMS/blob/master/CONTRIBUTING.md
  - note: null
    type:
    - Release notes
    url: https://github.com/hgb-bin-proteomics/pyXLMS/releases
  download:
  - note: null
    type: Software package
    url: https://pypi.org/project/pyXLMS/
    version: null
  - note: null
    type: Source code
    url: https://github.com/hgb-bin-proteomics/pyXLMS
    version: null
  - note: null
    type: API specification
    url: https://hgb-bin-proteomics.github.io/pyXLMS/
    version: null
  - note: null
    type: Container file
    url: https://hub.docker.com/r/michabirklbauer/pyxlms
    version: null
  - note: null
    type: Tool wrapper (Other)
    url: https://hgb-bin-proteomics.github.io/pyXLMS-app
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: xlsx
        uri: http://edamontology.org/format_3620
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: mzIdentML
        uri: http://edamontology.org/format_3247
      - term: TSV
        uri: http://edamontology.org/format_3475
    note: null
    operation:
    - term: Protein interaction network analysis
      uri: http://edamontology.org/operation_0276
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    output:
    - data:
        term: Database search results
        uri: http://edamontology.org/data_2080
      format: []
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format: []
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format: []
  homepage: https://github.com/hgb-bin-proteomics/pyXLMS
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-01-26T11:27:09.160764Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/hgb-bin-proteomics/pyXLMS
  - note: null
    type:
    - Issue tracker
    url: https://github.com/hgb-bin-proteomics/pyXLMS/issues
  - note: API Documentation
    type:
    - Other
    url: https://hgb-bin-proteomics.github.io/pyXLMS/
  - note: User Guide
    type:
    - Other
    url: https://hgb-bin-proteomics.github.io/pyXLMS-docs
  - note: null
    type:
    - Service
    url: https://hgb-bin-proteomics.github.io/pyXLMS-app
  maturity: Mature
  name: pyXLMS
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: michabirklbauer
  publication:
  - doi: 10.64898/2025.12.18.695169
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: null
  relation:
  - biotoolsID: ms_annika
    type: uses
  - biotoolsID: maxquant
    type: uses
  - biotoolsID: merox
    type: uses
  - biotoolsID: plink-2
    type: uses
  - biotoolsID: pyteomics
    type: uses
  - biotoolsID: biopython
    type: uses
  toolType:
  - Library
  - Web application
  topic:
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  validated: 0
  version:
  - 1.7.5+
- accessibility: null
  additionDate: '2019-08-13T22:07:01Z'
  biotoolsCURIE: biotools:MicrobiomeR
  biotoolsID: MicrobiomeR
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: rgilmore@umc.edu
    fundrefid: null
    gridid: null
    name: Robert Gilmore
    note: null
    orcidid: http://orcid.org/0000-0001-8096-0180
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: shutchins2@umc.edu
    fundrefid: null
    gridid: null
    name: Shaurita D. Hutchins
    note: null
    orcidid: http://orcid.org/0000-0002-7687-0059
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: MicrobiomeR is an R package for microbiome analysis that incorporates
    phyloseq, metacoder, taxa, and microbiome in order to standardize and simplify
    common microbiome workflows.
  documentation:
  - note: null
    type:
    - General
    url: https://microbiomer.vallenderlab.science/
  download:
  - note: null
    type: Software package
    url: https://github.com/vallenderlab/MicrobiomeR/releases/download/v0.6.1/MicrobiomeR_0.6.1.tar.gz
    version: 0.6.1
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://vallenderlab.github.io/MicrobiomeR/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-01-21T04:08:50.540139Z'
  license: MIT
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/vallenderlab/MicrobiomeR/issues
  - note: null
    type:
    - Repository
    url: https://github.com/vallenderlab/MicrobiomeR
  maturity: null
  name: MicrobiomeR
  operatingSystem:
  - Windows
  - Linux
  otherID: []
  owner: sdhutchins
  publication:
  - doi: 10.21105/joss.01299
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 1
  version:
  - 0.6.1
- accessibility: null
  additionDate: '2026-01-15T12:21:21.624093Z'
  biotoolsCURIE: biotools:easypubplot
  biotoolsID: easypubplot
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: EasyPubPlot is a Shiny web application and associated R package designed
    for rapid omics data exploration and visualization. It simplifies the creation
    of publishable plots like scores plots, volcano plots, and heatmaps, guiding users
    through the process with minimal steps.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    - term: Box-Whisker plot plotting
      uri: http://edamontology.org/operation_2943
    - term: Dot plot plotting
      uri: http://edamontology.org/operation_0490
    - term: Principal component visualisation
      uri: http://edamontology.org/operation_2939
    output: []
  homepage: https://pharmaco-omicslab.shinyapps.io/EasyPubPlot
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-01-15T12:21:21.626214Z'
  license: null
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/Pharmaco-OmicsLab/EasyPubPlot/issues
  maturity: null
  name: EasyPubPlot
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1101/2024.11.26.625339
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Metabolomics
    uri: http://edamontology.org/topic_3172
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:56:46.229702Z'
  biotoolsCURIE: biotools:limelight
  biotoolsID: limelight
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Limelight is an open-source, web-based tool for analyzing, visualizing,
    and sharing mass spectrometry proteomics data. It supports various data formats
    from common search engines and enables collaborative interpretation of results.
  documentation:
  - note: null
    type:
    - Training material
    url: https://limelight.yeastrc.org/limelight/p/demo
  - note: null
    type:
    - User manual
    url: https://limelight-ms.readthedocs.io/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Peptide identification
      uri: http://edamontology.org/operation_3631
    - term: Protein-protein interaction analysis
      uri: http://edamontology.org/operation_2949
    output: []
  homepage: https://limelight-ms.org/
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T11:56:46.231326Z'
  license: null
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/yeastrc/limelight-core/issues
  maturity: null
  name: Limelight
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1101/2024.11.01.621597
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Protein modifications
    uri: http://edamontology.org/topic_0601
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T08:36:49.473036Z'
  biotoolsCURIE: biotools:spliceai
  biotoolsID: spliceai
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: gilbertma@chop.edu
    fundrefid: null
    gridid: null
    name: Melissa A. Gilbert
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: mcking@uw.edu
    fundrefid: null
    gridid: null
    name: Mary-Claire King
    note: null
    orcidid: https://orcid.org/0000-0001-9426-1743
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: SpliceAI Pangolin is a web service that predicts the impact of genetic
    variants on RNA splicing using SpliceAI and Pangolin models. It helps diagnose
    variants affecting splicing in diseases like Alagille syndrome.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    - term: Alternative splicing prediction
      uri: http://edamontology.org/operation_0264
    - term: Variant classification
      uri: http://edamontology.org/operation_3225
    - term: Splice site prediction
      uri: http://edamontology.org/operation_0433
    output: []
  homepage: https://spliceailookup.broadinstitute.org/
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T08:36:49.475246Z'
  license: null
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/broadinstitute/SpliceAI-lookup/issues
  maturity: null
  name: SpliceAI Pangolin
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1016/J.XHGG.2024.100351
    metadata: null
    note: null
    pmcid: PMC11440345
    pmid: '39244638'
    type: []
    version: null
  - doi: 10.1101/GR.279158.124
    metadata: null
    note: null
    pmcid: PMC11610570
    pmid: '39271294'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  - term: RNA splicing
    uri: http://edamontology.org/topic_3320
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T08:35:38.665803Z'
  biotoolsCURIE: biotools:geotox
  biotoolsID: geotox
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Kyle P Messier
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: GeoTox is an open-source R software package for characterizing the
    risk of perturbing molecular targets involved in adverse human health outcomes
    based on exposure to spatially-referenced stressor mixtures. It facilitates source-to-outcome
    continuum modeling for individual and population-level risk assessment.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://niehs.github.io/GeoTox/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-01-15T08:35:38.668010Z'
  license: null
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/NIEHS/GeoTox/issues
  maturity: null
  name: GeoTox
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1101/2024.09.23.24314096
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Toxicology
    uri: http://edamontology.org/topic_2840
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Biomarkers
    uri: http://edamontology.org/topic_3360
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-01-05T15:29:05.686915Z'
  biotoolsCURIE: biotools:winnow
  biotoolsID: winnow
  collectionID:
  - proteomics
  - Proteomics
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: j.daniel@instadeep.com
    fundrefid: null
    gridid: null
    name: Jemma Daniel
    note: null
    orcidid: https://orcid.org/0000-0002-1964-3976
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Documentor
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Amandla Mabona
    note: null
    orcidid: https://orcid.org/0009-0009-7514-677X
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    url: null
  - email: j.vangoey@instadeep.com
    fundrefid: null
    gridid: null
    name: Jeroen van Goey
    note: null
    orcidid: https://orcid.org/0000-0003-4480-5567
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Maintainer
    url: null
  - email: konka@dtu.dk
    fundrefid: null
    gridid: null
    name: Konstantinos Kalogeropoulos
    note: null
    orcidid: https://orcid.org/0000-0003-3907-9281
    rorid: null
    typeEntity: null
    typeRole:
    - Primary contact
    - Contributor
    url: null
  description: A confidence rescoring and FDR estimation workflow for de novo peptide
    sequencing.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://instadeepai.github.io/winnow/api/datasets/
  - note: null
    type:
    - Command-line options
    url: https://instadeepai.github.io/winnow/cli/
  - note: null
    type:
    - Contributions policy
    url: https://instadeepai.github.io/winnow/contributing/
  - note: null
    type:
    - Citation instructions
    url: https://instadeepai.github.io/winnow/#bibtex-entry-and-citation-info
  - note: null
    type:
    - Installation instructions
    url: https://instadeepai.github.io/winnow/#installation
  download:
  - note: null
    type: Source code
    url: https://github.com/instadeepai/winnow/archive/refs/tags/v1.0.3.zip
    version: 1.0.3
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: winnow predict --data-source instanovo --dataset-config-path test_config.yaml
      --method winnow  --fdr-threshold 0.01 --confidence-column confidence --output-folder
      ./predictions
    input:
    - data:
        term: Mass spectrum
        uri: http://edamontology.org/data_0943
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: MGF
        uri: http://edamontology.org/format_3651
    - data:
        term: Peptide identification
        uri: http://edamontology.org/data_0945
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: de Novo sequencing
      uri: http://edamontology.org/operation_3644
    output:
    - data:
        term: Peptide identification
        uri: http://edamontology.org/data_0945
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/instadeepai/winnow
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-01-06T07:50:06.065478Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/instadeepai/winnow
  - note: null
    type:
    - Issue tracker
    url: https://github.com/instadeepai/winnow/issues
  maturity: Emerging
  name: Winnow
  operatingSystem:
  - Linux
  otherID: []
  owner: Jemma
  publication:
  - doi: 10.48550/arXiv.2509.24952
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: '2'
  relation:
  - biotoolsID: instanovo
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - 1.0.3
- accessibility: Open access
  additionDate: '2025-12-15T17:27:55.661547Z'
  biotoolsCURIE: biotools:thaf
  biotoolsID: thaf
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: contact@verdanta.tech
    fundrefid: null
    gridid: null
    name: Audrius Meskauskas
    note: Verdanta is an early startup in Switzerland, providing curated RNASeq pipeline.
      Thaf is part of our software stack that is released open source.
    orcidid: https://orcid.org/0009-0006-1714-3691
    rorid: null
    typeEntity: Person
    typeRole: []
    url: https://verdanta.info
  description: thaf is a command-line tool to extract transcript sequences from a
    genome FASTA file based on GFF3 annotation files. It can also generate transcript-to-gene
    mapping files compatible with tools such as Salmon.
  documentation:
  - note: README provides enough information to use the tool
    type:
    - General
    url: https://crates.io/crates/thaf
  download:
  - note: Use Cargo commands to install the application. Cargo will build it from
      the source.
    type: Other
    url: https://crates.io/crates/thaf
    version: 0.0.4
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "thaf \\\n  -f <INPUT_GFF3> \\\n  -d <DNA_FASTA> \\\n  -t <OUTPUT_FASTA>\
      \ \\\n  [-g <GENEMAP_FILE>]\n  [-e <FEATURES>]"
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format: []
    note: Produce transcriptome file from genomic DNA and gff3
    operation:
    - term: Sequence coordinate conversion
      uri: http://edamontology.org/operation_3267
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format: []
  homepage: https://crates.io/crates/thaf
  homepage_status: 0
  language:
  - Rust
  lastUpdate: '2025-12-22T07:52:59.716256Z'
  license: BSD-3-Clause
  link:
  - note: Crates.io page providing installation instructions and README.
    type:
    - Software catalogue
    url: https://crates.io/crates/thaf
  - note: Source code. Also, use GitHub issue tracker to send bug reports and extension
      proposals.
    type:
    - Repository
    url: https://github.com/bourumir-wyngs/thaf
  - note: Verdanta page for thaf
    type:
    - Other
    url: https://verdanta.tech/open-source/
  maturity: Emerging
  name: thaf
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Bourumir
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 0
  version:
  - 0.0.4
- accessibility: Open access
  additionDate: '2019-02-13T17:01:40Z'
  biotoolsCURIE: biotools:Jalview
  biotoolsID: Jalview
  collectionID:
  - ELIXIR-UK
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Jim Procter
    note: null
    orcidid: https://orcid.org/0000-0002-7865-7382
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.lifesci.dundee.ac.uk/people/jim-procter
  - email: null
    fundrefid: null
    gridid: null
    name: Geoff Barton
    note: null
    orcidid: https://orcid.org/0000-0002-9014-5355
    rorid: null
    typeEntity: null
    typeRole: []
    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:
    - Citation instructions
    url: https://www.jalview.org/about/citation
  - note: Hands-on exercises, Training courses and Training videos
    type:
    - Training material
    url: https://www.jalview.org/training/
  - note: null
    type:
    - FAQ
    url: https://www.jalview.org/help/faq
  - note: null
    type:
    - User manual
    url: https://www.jalview.org/help/documentation/
  download:
  - note: null
    type: Downloads page
    url: https://www.jalview.org/download
    version: null
  - note: null
    type: Source code
    url: https://www.jalview.org/download/source/
    version: null
  - note: Binaries for all platforms
    type: Binaries
    url: https://www.jalview.org/download/?os=all
    version: null
  - note: null
    type: Icon
    url: https://www.jalview.org/favicon.svg
    version: null
  - note: Executable JAR file
    type: Binaries
    url: https://www.jalview.org/download/other/jar/
    version: null
  editPermission:
    authors:
    - ben_s
    - jimprocter
    type: group
  elixirCommunity: []
  elixirNode:
  - UK
  elixirPlatform:
  - Tools
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: GFF2-seq
        uri: http://edamontology.org/format_1938
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: RNAML
        uri: http://edamontology.org/format_3311
      - term: Format
        uri: http://edamontology.org/format_1915
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: mmCIF
        uri: http://edamontology.org/format_1477
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: GFF3-seq
        uri: http://edamontology.org/format_1939
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
    - data:
        term: Structure alignment
        uri: http://edamontology.org/data_0886
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    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);

      Predicted Aligned Error (PAE) Matrix File (.json)

      ...

      Other Output formats:

      PFAM (.pfam);

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

      Jalview Project File (.jvp);'
    operation:
    - term: Sequence alignment editing
      uri: http://edamontology.org/operation_3081
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: EPS
        uri: http://edamontology.org/format_3466
      - term: Format
        uri: http://edamontology.org/format_1915
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PNG
        uri: http://edamontology.org/format_3603
  homepage: https://www.jalview.org/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-11T14:16:30.074724Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Discussion forum
    url: https://discourse.jalview.org/
  - 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
    url: https://gitlab.jalview.org/jalview/jalview.git
  - note: Twitter feed
    type:
    - Social media
    url: https://twitter.com/Jalview
  - note: YouTube training videos
    type:
    - Social media
    url: https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/104771886/
  maturity: Mature
  name: Jalview
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: ben_s
  publication:
  - doi: 10.1093/bioinformatics/btp033
    metadata:
      abstract: ''
      authors: []
      citationCount: 7717
      date: '2009-05-07T00:00:00Z'
      journal: Bioinformatics
      title: Jalview Version 2-A multiple sequence alignment editor and analysis workbench
    note: null
    pmcid: PMC2672624
    pmid: '19151095'
    type: []
    version: null
  relation:
  - biotoolsID: jabaws
    type: uses
  - biotoolsID: chimera
    type: uses
  - biotoolsID: chimerax
    type: uses
  - biotoolsID: pymol
    type: uses
  - biotoolsID: bioconda
    type: includedIn
  - biotoolsID: 3d-beacons
    type: uses
  - biotoolsID: uniprot
    type: uses
  - biotoolsID: pfam
    type: uses
  - biotoolsID: ensembl
    type: uses
  - biotoolsID: pdb
    type: uses
  - biotoolsID: rfam
    type: uses
  - biotoolsID: 3d-beacons
    type: uses
  toolType:
  - Desktop application
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 1
  version:
  - 2.11.5.1
next: ?page=2
previous: null
