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  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
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    trees, helping users see which taxa or subtrees move across sliding-window analyses,
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    type:
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  - note: Desktop convenience builds for macOS, Windows, and Linux.
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  homepage_status: 0
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  lastUpdate: '2026-06-14T08:36:42.066838Z'
  license: MIT
  link:
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  - note: Static browser demo with precomputed example movies.
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  - note: null
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    note: water molecule placement
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  description: MicroMiner assists in identifying single-residue substitutions in protein
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    note: structural single-residue substitution search and analysis
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  - email: software.zbh@uni-hamburg.de
    fundrefid: null
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  description: JAMDA enables the preparation of individual protein structures and
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    retrieved 75% of the native poses in the three highest-ranked solutions for high-quality
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  documentation:
  - note: null
    type:
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  download:
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    type: Binaries
    url: https://uhh.de/naomi
    version: null
  editPermission:
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  description: Three-dimensional protein structures play a vital role in drug design.
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    type:
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  - note: Link to download the standalone tool from the NAOMI ChemBio Suite.
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  biotoolsCURIE: biotools:warpp
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  description: WarPP predicts the position and orientation of water molecules in small-molecule
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  description: LifeSoaks was designed to find solvent channels in macromolecular structures
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  description: The electron density score for individual atoms (EDIA) quantifies the
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  description: SIENA is a software pipeline enabling the fully automated construction
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  description: PoseEdit automatically generates 2D diagrams of protein-ligand complexes,
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    metadata: null
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  - term: Protein binding sites
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  description: PoseView automatically generates 2D diagrams of protein-ligand complexes,
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    types and simple geometric criteria. It adheres to the conventions of chemical
    structure diagram generation. The quality of the resulting diagrams is comparable
    to manually drawn examples from books and scientific publications.
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    - data:
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    note: 2D interaction diagram drawing
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    - term: Network visualisation
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    - term: Salt bridge calculation
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    - term: Protein-metal contact calculation
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    output:
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  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/poseview.html
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  lastUpdate: '2026-06-12T08:57:26.150042Z'
  license: Other
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  - note: A web API to run PoseView calculations for protein-ligand complexes.
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  name: PoseView
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  publication:
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    metadata: null
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    metadata: null
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  - doi: 10.1021/ci049958u
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  relation: []
  toolType:
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  topic:
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  - term: Molecular interactions, pathways and networks
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  - term: Protein binding sites
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  additionDate: '2016-11-28T10:07:16Z'
  biotoolsCURIE: biotools:protoss
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  description: Protoss is a fully automated hydrogen atom placement tool for protein-ligand
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    protonation states, tautomeric states, and hydrogen coordinates of both protein
    and ligand molecules by optimizing the hydrogen bond network.
  documentation:
  - note: null
    type:
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    input:
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      format:
      - term: SDF
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    note: prediction of protonation states and tautomers and placement of hydrogen
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    operation:
    - term: Hydrogen bond calculation
      uri: http://edamontology.org/operation_0394
    - term: Protein modelling
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    output:
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  homepage_status: 0
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  lastUpdate: '2026-06-12T08:56:32.130763Z'
  license: Other
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    type:
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    type:
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  maturity: Mature
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    metadata: null
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  relation:
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  topic:
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  - term: Structural biology
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  - term: Bioinformatics
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  - term: Molecular modelling
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  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Protein binding sites
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  - term: Structure prediction
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- accessibility: null
  additionDate: '2016-11-21T10:33:07Z'
  biotoolsCURIE: biotools:dogsitescorer
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  collectionID:
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  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
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  description: DoGSiteScorer is a grid-based automated pocket detection and analysis
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    protein. Global properties, describing the size, shape, and chemical features
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    score based on a linear combination of the three descriptors describing volume,
    hydrophobicity, and enclosure is provided for each (sub-)pocket. Furthermore,
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    and one). The higher the score, the more druggable the pocket is estimated to
    be.
  documentation:
  - note: null
    type:
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  download: []
  editPermission:
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  function:
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    - data:
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      format:
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    note: small molecule binding site detection and druggability assessment
    operation:
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    - term: Ligand-binding site prediction
      uri: http://edamontology.org/operation_3897
    - term: Protein structure analysis
      uri: http://edamontology.org/operation_2406
    output:
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    - data:
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      format: []
    - data:
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  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/dogsitescorer.html
  homepage_status: 0
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  lastUpdate: '2026-06-12T08:54:52.480543Z'
  license: Other
  link:
  - note: A web service to run DoGSiteScorer calculations for protein structures stored
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    type:
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  - note: A web API to run DoGSiteScorer calculations for protein structures stored
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    type:
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  maturity: Mature
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  operatingSystem:
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  otherID: []
  owner: ehrt
  publication:
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    metadata: null
    note: null
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    type:
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  - doi: 10.1093/bioinformatics/bts310
    metadata: null
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    pmid: '22628523'
    type:
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  relation: []
  toolType:
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  topic:
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  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Protein structure analysis
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  - term: Drug discovery
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  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Protein properties
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  validated: 1
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- accessibility: null
  additionDate: '2025-12-15T10:10:43.359638Z'
  biotoolsCURIE: biotools:dogsite3
  biotoolsID: dogsite3
  collectionID:
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  cost: Free of charge (with restrictions)
  credit:
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    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
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    typeRole:
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    url: null
  - email: software.zbh@uni-hamburg.de
    fundrefid: null
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    note: Primary Contact for Standalone Tool Issues
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    rorid: null
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    typeRole:
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  - email: null
    fundrefid: null
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  description: DoGSite3 was developed for predicting robust and reliable small molecule
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    procedure before binding site prediction. Known ligands in the structure can be
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    novel chemical binding site descriptors considering solvent accessibility. Compared
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    optimization. DoGSite3 runs finish within seconds.
  documentation:
  - note: null
    type:
    - General
    url: https://proteins.plus/help/index
  download:
  - note: Please register to download the tool.
    type: Binaries
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    version: null
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    note: small molecule binding site detection
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  lastUpdate: '2026-06-12T08:53:05.223278Z'
  license: Other
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    type:
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    url: https://proteins.plus
  - note: A web API to run DoGSite3 calculations for protein structures stored in
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    type:
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  - note: Link to download the standalone tool from the NAOMI ChemBio Suite.
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  name: DoGSite3
  operatingSystem:
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  - Linux
  otherID: []
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    metadata: null
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  - biotoolsID: geomine
    type: usedBy
  toolType:
  - Command-line tool
  - Web API
  - Web service
  topic:
  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  validated: 0
  version: []
- 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: '2026-06-04T08:08:16.771951Z'
  biotoolsCURIE: biotools:screen_assembly
  biotoolsID: screen_assembly
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Mark R. Davies
    note: null
    orcidid: https://orcid.org/0000-0001-6141-5179
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: 'Screen a bacterial assembly (contigs/CDS or proteins) for nucleotide
    or protein sequences.


    Pipeline that screens for presence of genes of interest (GOI) in bacterial assemblies.
    Generates multiple CSVs and plots that describe which genes are present and how
    variable their sequence is. Can use DNA or protein query sequences (GOIs) and
    DNA contigs/fastas or protein fastas as database (db) to search in.'
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/shimbalama/screen_assembly/wiki
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format: []
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format: []
  homepage: https://github.com/shimbalama/screen_assembly
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-06-04T08:08:16.774426Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/shimbalama/screen_assembly
  maturity: Mature
  name: screen_assembly
  operatingSystem: []
  otherID: []
  owner: aniehues
  publication:
  - doi: 10.1038/s41588-019-0417-8
    metadata: null
    note: null
    pmcid: PMC6650292
    pmid: '31133745'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Script
  - Command-line tool
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 0
  version:
  - v1
- accessibility: null
  additionDate: '2017-12-18T00:03:45Z'
  biotoolsCURIE: biotools:autodock_vina
  biotoolsID: autodock_vina
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://olegtrott.com/
  description: AutoDock Vina is a new open-source program for drug discovery, molecular
    docking and virtual screening, offering multi-core capability, high performance
    and enhanced accuracy and ease of use.
  documentation:
  - note: null
    type:
    - User manual
    url: http://vina.scripps.edu/manual.html
  download: []
  editPermission:
    authors:
    - ragibsiddique
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Molecular docking
      uri: http://edamontology.org/operation_0478
    output: []
  homepage: http://vina.scripps.edu/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-06-04T08:07:30.690513Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://www.mybiosoftware.com/autodock-vina-1-1-2-molecular-docking-virtual-screening-program.html
  maturity: null
  name: AutoDock Vina
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID:
  - type: rrid
    value: RRID:SCR_011958
    version: null
  owner: monami
  publication:
  - doi: 10.1002/jcc.21334
    metadata: null
    note: null
    pmcid: PMC3041641
    pmid: '19499576'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Molecular docking
    uri: http://edamontology.org/topic_2275
  validated: 1
  version:
  - 1.1.2
- accessibility: Open access
  additionDate: '2015-06-11T13:36:28Z'
  biotoolsCURIE: biotools:ega
  biotoolsID: ega
  collectionID:
  - RD-connect
  - Rare Disease
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: EMBL-EBI Databases
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: helpdesk@ega-archive.org
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: European genome-phenome Archive (EGA) - service for permanent archiving
    and sharing of all types of personally identifiable genetic and phenotypic data
    resulting from biomedical research projects.
  documentation:
  - note: null
    type:
    - General
    url: https://ega-archive.org/
  download: []
  editPermission:
    authors:
    - ELIXIR-EE
    - amy_jean
    type: group
  elixirCommunity: []
  elixirNode:
  - Spain
  elixirPlatform:
  - Data
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: EGA accession
        uri: http://edamontology.org/data_2383
      format: []
    note: null
    operation:
    - term: Deposition
      uri: http://edamontology.org/operation_3431
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    - term: Aggregation
      uri: http://edamontology.org/operation_3436
    output:
    - data:
        term: Experiment report
        uri: http://edamontology.org/data_2531
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://ega-archive.org/
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2026-06-04T08:07:27.522383Z'
  license: null
  link: []
  maturity: Mature
  name: EGA
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: EMBL-EBI_Databases
  publication:
  - doi: 10.1038/ng.3312
    metadata:
      abstract: © 2015 Nature America, Inc. All rights reserved.The European Genome-phenome
        Archive (EGA) is a permanent archive that promotes the distribution and sharing
        of genetic and phenotypic data consented for specific approved uses but not
        fully open, public distribution. The EGA follows strict protocols for information
        management, data storage, security and dissemination. Authorized access to
        the data is managed in partnership with the data-providing organizations.
        The EGA includes major reference data collections for human genetics research.
      authors:
      - name: Lappalainen I.
      - name: Almeida-King J.
      - name: Kumanduri V.
      - name: Senf A.
      - name: Spalding J.D.
      - name: Ur-Rehman S.
      - name: Saunders G.
      - name: Kandasamy J.
      - name: Caccamo M.
      - name: Leinonen R.
      - name: Vaughan B.
      - name: Laurent T.
      - name: Rowland F.
      - name: Marin-Garcia P.
      - name: Barker J.
      - name: Jokinen P.
      - name: Torres A.C.
      - name: De Argila J.R.
      - name: Llobet O.M.
      - name: Medina I.
      - name: Puy M.S.
      - name: Alberich M.
      - name: De La Torre S.
      - name: Navarro A.
      - name: Paschall J.
      - name: Flicek P.
      citationCount: 161
      date: '2015-01-01T00:00:00Z'
      journal: Nature Genetics
      title: The European Genome-phenome Archive of human data consented for biomedical
        research
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web API
  - Web application
  - Database portal
  topic:
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Laboratory information management
    uri: http://edamontology.org/topic_0607
  - term: Data security
    uri: http://edamontology.org/topic_3263
  - term: Data integration and warehousing
    uri: http://edamontology.org/topic_3366
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2020-06-05T08:52:25Z'
  biotoolsCURIE: biotools:calibracurve
  biotoolsID: calibracurve
  collectionID:
  - BioInfra.Prot
  - de.NBI
  - CUBiMed.RUB
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: martin.eisenacher@rub.de
    fundrefid: null
    gridid: null
    name: PD Dr. Martin Eisenacher
    note: If contacting use "SPARROW" in subject line to avoid mail deluge.
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: de.NBI
    note: Service provision and maintenance funded by de.NBI.
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Provider
    - Maintainer
    - Support
    url: https://www.denbi.de/
  - email: michael.kohl@rub.de
    fundrefid: null
    gridid: null
    name: Dr. Michael Kohl
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: A highly useful and flexible tool for calibration of targeted MS‐based
    measurements. CalibraCurve enables an automated batch-mode determination of dynamic
    linear ranges and quantification limits for both targeted proteomics and similar
    assays. The software uses a variety of measures to assess the accuracy of the
    calibration and provides intuitive visualizations.
  documentation:
  - note: null
    type:
    - Installation instructions
    - Citation instructions
    - General
    - User manual
    - Training material
    - Terms of use
    url: https://github.com/mpc-bioinformatics/CalibraCurve
  download:
  - note: null
    type: Downloads page
    url: https://github.com/mpc-bioinformatics/CalibraCurve
    version: '2.0'
  editPermission:
    authors:
    - karin
    type: group
  elixirCommunity:
  - Proteomics
  elixirNode:
  - Germany
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Analysis
      uri: http://edamontology.org/operation_2945
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: tiff
        uri: http://edamontology.org/format_3591
    - data:
        term: Text data
        uri: http://edamontology.org/data_2526
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://github.com/mpc-bioinformatics/CalibraCurve
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-06-04T08:07:22.002962Z'
  license: BSD-3-Clause
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/mpc-bioinformatics/CalibraCurve
  maturity: Mature
  name: CalibraCurve
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: BioInfra.Prot
  publication:
  - doi: 10.1002/pmic.201900143
    metadata:
      abstract: Targeted proteomics techniques allow accurate quantitative measurements
        of analytes in complex matrices with dynamic linear ranges that span up to
        4–5 orders of magnitude. Hence, targeted methods are promising for the development
        of robust protein assays in several sensitive areas, for example, in health
        care. However, exploiting the full method potential requires reliable determination
        of the dynamic range along with related quantification limits for each analyte.
        Here, a software named CalibraCurve that enables an automated batch-mode determination
        of dynamic linear ranges and quantification limits for both targeted proteomics
        and similar assays is presented. The software uses a variety of measures to
        assess the accuracy of the calibration, namely precision and trueness. Two
        different kinds of customizable graphs are created (calibration curves and
        response factor plots). The accuracy measures and the graphs offer an intuitive,
        detailed, and reliable opportunity to assess the quality of the model fit.
        Thus, CalibraCurve is deemed a highly useful and flexible tool to facilitate
        the development and control of reliable SRM/MRM-MS-based proteomics assays.
      authors:
      - name: Kohl M.
      - name: Stepath M.
      - name: Bracht T.
      - name: Megger D.A.
      - name: Sitek B.
      - name: Marcus K.
      - name: Eisenacher M.
      citationCount: 4
      date: '2020-06-01T00:00:00Z'
      journal: Proteomics
      title: 'CalibraCurve: A Tool for Calibration of Targeted MS-Based Measurements'
    note: null
    pmcid: null
    pmid: '32086983'
    type:
    - Primary
    version: '2.0'
  relation: []
  toolType:
  - Workflow
  - Script
  - Desktop application
  - Plug-in
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Experimental design and studies
    uri: http://edamontology.org/topic_3678
  validated: 1
  version:
  - '2.0'
- accessibility: null
  additionDate: '2026-06-03T05:24:59.073336Z'
  biotoolsCURIE: biotools:influential
  biotoolsID: influential
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: A comprehensive R package for identifying and ranking influential nodes
    in biological and other complex networks. The package implements the Integrated
    Value of Influence (IVI), Experimental data-based Integrative Ranking (ExIR),
    SIRIR, and numerous network centrality measures, enabling network topology analysis,
    influential node detection, feature prioritization, and candidate biomarker discovery.
    It also provides functions for network reconstruction, centrality assessment,
    visualization, and analysis of relationships between centrality measures.
  documentation:
  - note: null
    type:
    - User manual
    url: https://asalavaty.github.io/influential/articles/Vignettes.html
  download:
  - note: null
    type: Downloads page
    url: https://github.com/asalavaty/influential
    version: null
  - note: CRAN Version
    type: Downloads page
    url: https://cran.r-project.org/package=influential
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: 'ivi()

      exir()'
    input: []
    note: 'Identification of influential nodes

      Network centrality analysis

      Feature prioritization and ranking

      Network reconstruction

      Biomarker candidate discovery

      Topological network analysis

      Integrative ranking'
    operation:
    - term: Expression analysis
      uri: http://edamontology.org/operation_2495
    - term: Network analysis
      uri: http://edamontology.org/operation_3927
    output: []
  homepage: https://asalavaty.github.io/influential/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-06-03T05:24:59.075786Z'
  license: GPL-3.0
  link:
  - note: Source code
    type:
    - Repository
    url: https://github.com/asalavaty/influential
  - note: Documentation
    type:
    - Other
    url: https://asalavaty.github.io/influential/
  maturity: Mature
  name: influential
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: mania.abbas
  publication:
  - doi: 10.1016/j.patter.2020.100052
    metadata: null
    note: null
    pmcid: PMC7660386
    pmid: '33205118'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  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
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  description: Membrane Protein-Lipid Interaction Database. A large-scale experimentally
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  description: "Implemented by GIBI230, this tool is a Docker-based software designed\
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  description: 'The tool performs an automatic segmentation of the possible glioblastoma
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  description: The tool performs an automatic segmentation of the possible DIPG tumours
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  description: 'This tool is specifically designed and validated for automated detection
    and segmentation of neuroblastic tumours in T2-weighted magnetic resonance images
    (T2-MR) using deep learning. It processes DICOM or NIfTI input data and outputs
    in NIFTI or DICOM SEG.


    TRAINING & VALIDATION COHORTS:


    Initial Development (Veiga-Canuto 2022):

    -Training: 106 patients, 5-fold CV (median DSC 0.965 ± 0.018).

    -Internal validation: 26 patients (median DSC 0.918 ± 0.067).

    -Sources: La Fe (Spain), SIOPEN HR-NBL1/LINES, St. Anna (Austria), Pisa (Italy).

    -Mean age: 37.6 ± 39.3 months.

    -Median tumor volume: 116,518 mm³.


    External Validation (Veiga-Canuto 2023):

    -300 patients, 535 independent T2 MRI scans (486 at diagnosis, 49 post-chemotherapy).

    -Performance: median DSC 0.997 (0.944–1.000), 94% successful detection.

    -Sources: 12 European countries (HR-NBL1/SIOPEN 119, LINES/SIOPEN 107, German
    Registry 62, others 12).

    -Heterogeneous data: 1.5T (435), 3T (100); Siemens (318), Philips (109), GE (105),
    Canon (3).'
  documentation:
  - note: null
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    url: https://drive.eucaim.cancerimage.eu/s/tS2W8nb38Zs2ZzK
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    url: https://www.mdpi.com/2072-6694/14/15/3648
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    - Terms of use
    url: https://drive.eucaim.cancerimage.eu/s/44BxMSNpxwgsZiE
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    url: https://www.youtube.com/watch?v=c7XOEGRA9aQ&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=12
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      \ \\\n  --gpus all \\\n  harbor.eucaim.cancerimage.eu/processing-tools/mr_based_neuroblastoma_tumour_detection_and_segmentation:2.0.0\
      \ \\\n  --mode dicom-seg \\\n  --series-selector /output/config/series_to_segment.csv\
      \ \\\n  --seg-series-number 2302001 \\\n  --seg-algorithm-name \"nnUNet_Neuroblastoma_Primage_training\"\
      \ \\\n  --seg-coordinating-center \"EUCAIM Consortium\" \\\n  --keep-nifti false"
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        uri: http://edamontology.org/data_2968
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      - term: nii
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        uri: http://edamontology.org/format_3752
      - term: JSON
        uri: http://edamontology.org/format_3464
    note: null
    operation:
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      - term: nii
        uri: http://edamontology.org/format_3549
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/mr_based_neuroblastoma_tumour_detection_and_segmentation/info-tab
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  language:
  - Python
  lastUpdate: '2026-05-27T15:19:40.961989Z'
  license: CC-BY-NC-ND-4.0
  link:
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  name: MR-based neuroblastoma tumour detection and segmentation (EUCAIM-SW-019_T-01-02-002)
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  - term: Data architecture, analysis and design
    uri: http://edamontology.org/topic_3365
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  description: 'The tool is designed to perform a customisable image pre-processing
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    (NLM)), and another for the ANTs N4 and another for the ANT''s N4 bias correction
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    DWI and DCE sequences in neuroblastoma (NB) and paediatric brain tumours, but
    it can also be configured with some of their parameters using a JSON parameter
    configuration file.'
  documentation:
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    url: https://drive.eucaim.cancerimage.eu/s/wYJ7Fttnk6Dp7gc
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    url: https://drive.eucaim.cancerimage.eu/s/oseiKoeFZqwoRCA
  - note: null
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    url: https://www.youtube.com/watch?v=HkHqFGXGEbo&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=9
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    note: null
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      format:
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  - cmd: docker run --rm -v input_path:/input -v output_path:/output harbor.eucaim.cancerimage.eu/processin-tools/denoising_inhomogeneity_correction_tool:1.1.0
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      --denoising adf --conductance 0.5 --iterations 3 --time_step 0.0625 --n4 --bspline_size
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    input:
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    note: null
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  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/denoising_inhomogeneity_correction_tool/info-tab
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  lastUpdate: '2026-05-27T15:19:25.220262Z'
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  publication:
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    metadata: null
    note: null
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    metadata: null
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    pmcid: PMC7125275
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  topic:
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  validated: 0
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- accessibility: Open access (with restrictions)
  additionDate: '2025-11-25T09:58:37.569343Z'
  biotoolsCURIE: biotools:ml_model_for_mr_series_categorisation
  biotoolsID: ml_model_for_mr_series_categorisation
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  description: A tool based on artificial intelligence that is able to perform a categorisation
    of MRI series by using standardized DICOM tags. The categorisation includes the
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    DCE, ...), the presence of fat suppression and the detection of non-relevant /
    junk series (e.g. localizers, calibrations, screenshots...).
  documentation:
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    url: https://drive.eucaim.cancerimage.eu/s/8r3CzyQXrd7ERFp
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  maturity: Mature
  name: ML model for MR series categorisation (EUCAIM-SW-011_T-01-01-011)
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  description: 'Stress Knowledge Map:  A compilation of knowledge on mechanisms underlying
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next: ?page=2
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