count: 33272
list:
- accessibility: Open access
  additionDate: '2026-06-26T00:29:30.740942Z'
  biotoolsCURIE: biotools:ab1lens
  biotoolsID: ab1lens
  collectionID:
  - fishka.bio
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: swim@fishka.bio
    fundrefid: null
    gridid: null
    name: Fishka Bio
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://fishka.bio
  description: Browser-based viewer for Sanger sequencing chromatograms in AB1/ABIF
    and SCF format, and for the .srd raw files of the Nanofor-05 capillary sequencer,
    converted to ABIF as they open. Shows raw and analysed traces, base calls (called
    or edited), per-base quality and the full ABIF directory, and puts two reads side
    by side with their tag tables aligned. A read aligns against a pasted or loaded
    reference, which reports identity, mismatches, indels and the ends that did not
    align, and flips the strand when the read is on the other one. End trimming (modified
    Mott or sliding window) has draggable handles, motif search is IUPAC-aware and
    finds primers, and QC metrics copy out as CSV. Drag on a trace to select a base
    range, then copy it as FASTA, zoom to it or export just that region. Exports the
    read as FASTA, FASTQ, .qual or ABIF and the chromatogram as a high-resolution
    PNG. Open files are kept as local sessions. Runs entirely in the browser — files
    are never uploaded.
  documentation:
  - note: Showcase gallery — an annotated screenshot per task, from quality control
      to aligning a read against a reference
    type:
    - Training material
    url: https://fishka.bio/ab1lens/showcase
  download:
  - note: Offline build — the same application as a self-contained archive, runs from
      local files with no server
    type: Downloads page
    url: https://fishka.bio/download
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: AB1
        uri: http://edamontology.org/format_3000
      - term: SCF
        uri: http://edamontology.org/format_1632
    note: null
    operation:
    - term: Chromatogram visualisation
      uri: http://edamontology.org/operation_3203
    - term: Reverse complement
      uri: http://edamontology.org/operation_0363
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    - term: Sequence trimming
      uri: http://edamontology.org/operation_3192
    - term: Sequence conversion
      uri: http://edamontology.org/operation_0233
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    output:
    - data:
        term: Sequence trace image
        uri: http://edamontology.org/data_2168
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
    - data:
        term: Sequence record
        uri: http://edamontology.org/data_0849
      format:
      - term: qual
        uri: http://edamontology.org/format_3607
      - term: AB1
        uri: http://edamontology.org/format_3000
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: AB1
        uri: http://edamontology.org/format_3000
    - data:
        term: Sequence record
        uri: http://edamontology.org/data_0849
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Pairwise sequence alignment
      uri: http://edamontology.org/operation_0491
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://fishka.bio/ab1lens
  homepage_status: 0
  language:
  - TypeScript
  lastUpdate: '2026-08-21T03:03:37.161093Z'
  license: Freeware
  link:
  - note: fishka.bio — the tool collection ab1lens belongs to
    type:
    - Software catalogue
    url: https://fishka.bio
  maturity: Mature
  name: ab1lens
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: fishka
  publication:
  - doi: 10.5281/zenodo.21444547
    metadata: null
    note: Software deposit (concept DOI — resolves to the latest version) covering
      the fishka.bio tools, including ab1lens.
    pmcid: null
    pmid: null
    type:
    - Other
    version: 2026.07.19
  relation: []
  toolType:
  - Desktop application
  - Web application
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-08-21T02:36:26.152495Z'
  biotoolsCURIE: biotools:readhit
  biotoolsID: readhit
  collectionID:
  - fishka.bio
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: swim@fishka.bio
    fundrefid: null
    gridid: null
    name: Fishka Bio
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://fishka.bio
  description: Browser-based viewer that maps sequencing reads onto one short reference
    — an amplicon, gene or plasmid. Reads open as Sanger AB1/ABIF, SCF, FASTA, FASTQ
    or a SAM somebody else already mapped (gzipped files are unpacked in place); the
    reference as FASTA, GenBank or a read. Both read orientations are tried automatically.
    The pileup reports per-position depth, where reads disagree with the target, and
    the consensus — phred-weighted for capillary reads, which keep their chromatogram
    under the letters. An optional protein lane translates target and consensus side
    by side. Reads are placed by minimap2 compiled to WebAssembly, or by the built-in
    aligner. One read or the whole alignment saves as FASTA. Runs entirely in the
    browser — files are never uploaded.
  documentation:
  - note: Showcase gallery — an annotated screenshot per task, from a handful of Sanger
      reads to an NGS pileup opened from a SAM
    type:
    - Training material
    url: https://fishka.bio/readhit/showcase
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence record
        uri: http://edamontology.org/data_0849
      format:
      - term: GenBank format
        uri: http://edamontology.org/format_1936
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: SAM
        uri: http://edamontology.org/format_2573
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: AB1
        uri: http://edamontology.org/format_3000
      - term: SCF
        uri: http://edamontology.org/format_1632
    note: null
    operation:
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    - term: Read mapping
      uri: http://edamontology.org/operation_3198
    - term: Pairwise sequence alignment
      uri: http://edamontology.org/operation_0491
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
    note: null
    operation:
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    - term: Chromatogram visualisation
      uri: http://edamontology.org/operation_3203
    - term: DNA translation
      uri: http://edamontology.org/operation_0371
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    output:
    - data:
        term: Sequence record
        uri: http://edamontology.org/data_0849
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://fishka.bio/readhit
  homepage_status: 0
  language:
  - TypeScript
  lastUpdate: '2026-08-21T02:36:26.155311Z'
  license: Freeware
  link:
  - note: fishka.bio — the tool collection readhit belongs to
    type:
    - Software catalogue
    url: https://fishka.bio
  maturity: Emerging
  name: readhit
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: fishka
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-07-19T01:15:04.193012Z'
  biotoolsCURIE: biotools:gbatlas
  biotoolsID: gbatlas
  collectionID:
  - fishka.bio
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: swim@fishka.bio
    fundrefid: null
    gridid: null
    name: Fishka Bio
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://fishka.bio
  description: "Browser-based viewer for GenBank and GenPept records — .gb, .gbk,\
    \ .gbff, .gp and plain GenBank text. Renders an interactive linear and circular\
    \ feature map, including circular plasmid maps, alongside the annotated source\
    \ text and the nucleotide/protein sequence. \n\nTranslates CDS features using\
    \ the record's own genetic code and translation qualifiers, flags where the stored\
    \ /translation disagrees with a plain translation, and adds optional computed\
    \ layers: ORF prediction and restriction-site mapping. Drag a range in the sequence\
    \ band to select it, then copy that stretch — either strand, as DNA or as protein,\
    \ plain or FASTA. Filters features by type, handles multi-record files, and keeps\
    \ open records as local sessions, so a closed tab can be picked up where it was\
    \ left. Runs entirely in the browser — files are never uploaded."
  documentation:
  - note: Showcase gallery — an annotated screenshot per task, from the circular plasmid
      map to CDS translation and restriction sites
    type:
    - Training material
    url: https://fishka.bio/gbatlas/showcase
  download:
  - note: Offline build — the same application as a self-contained archive, runs from
      local files with no server
    type: Downloads page
    url: https://fishka.bio/download
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence record
        uri: http://edamontology.org/data_0849
      format:
      - term: GenBank format
        uri: http://edamontology.org/format_1936
      - term: genpept
        uri: http://edamontology.org/format_1937
    note: null
    operation:
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    - term: Coding region prediction
      uri: http://edamontology.org/operation_0436
    - term: DNA translation
      uri: http://edamontology.org/operation_0371
    - term: Restriction site recognition
      uri: http://edamontology.org/operation_0431
    output:
    - data:
        term: Sequence record
        uri: http://edamontology.org/data_0849
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://fishka.bio/gbatlas
  homepage_status: 0
  language:
  - TypeScript
  lastUpdate: '2026-08-21T02:36:20.759005Z'
  license: Freeware
  link:
  - note: fishka.bio — the tool collection gbatlas belongs to
    type:
    - Software catalogue
    url: https://fishka.bio
  maturity: Mature
  name: gbatlas
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: fishka
  publication:
  - doi: 10.5281/zenodo.21444547
    metadata: null
    note: Software deposit (concept DOI — resolves to the latest version) covering
      the fishka.bio tools, including gbatlas.
    pmcid: null
    pmid: null
    type:
    - Other
    version: 2026.07.19
  relation: []
  toolType:
  - Desktop application
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Nucleic acid sites, features and motifs
    uri: http://edamontology.org/topic_3511
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-07-11T21:51:46.808639Z'
  biotoolsCURIE: biotools:picklet
  biotoolsID: picklet
  collectionID:
  - fishka.bio
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: swim@fishka.bio
    fundrefid: null
    gridid: null
    name: Fishka Bio
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://fishka.bio
  description: Browser-based tool to open almost any file that carries sequence —
    FASTA, FASTQ, GenBank, EMBL, Swiss-Prot, AB1/ABIF, SCF, Clustal, Stockholm, PHYLIP,
    NEXUS, MSF, PIR, MEGA, GFF3, SAM, BAM, GFA, PDB and ACE — see every sequence inside,
    pick the ones you want, and save them as FASTA. The format is detected from the
    file content, not from the extension, so unlabelled or misnamed files still open,
    and gzip-compressed files are unpacked in place. Records can be filtered by length,
    name, GC or sequence type, reverse-complemented, transcribed DNA↔RNA or translated
    to protein, deduplicated and reordered before saving. Runs entirely in the browser
    — files are never uploaded.
  documentation:
  - note: Showcase gallery — an annotated screenshot per task, from opening an unlabelled
      file to filtering, translating and saving the picked records
    type:
    - Training material
    url: https://fishka.bio/picklet/showcase
  download:
  - note: Offline build — the same application as a self-contained archive, runs from
      local files with no server
    type: Downloads page
    url: https://fishka.bio/download
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence record
        uri: http://edamontology.org/data_0849
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: GFF3
        uri: http://edamontology.org/format_1975
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: ACE
        uri: http://edamontology.org/format_3001
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: mega
        uri: http://edamontology.org/format_1991
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: GFA 2
        uri: http://edamontology.org/format_3976
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: SCF
        uri: http://edamontology.org/format_1632
      - term: GFA 1
        uri: http://edamontology.org/format_3975
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: AB1
        uri: http://edamontology.org/format_3000
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: Nexus format
        uri: http://edamontology.org/format_1912
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: UniProtKB format
        uri: http://edamontology.org/format_1963
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
      - term: GenBank format
        uri: http://edamontology.org/format_1936
    note: null
    operation:
    - term: Sequence file editing
      uri: http://edamontology.org/operation_2121
    - term: DNA translation
      uri: http://edamontology.org/operation_0371
    - term: Sequence conversion
      uri: http://edamontology.org/operation_0233
    - term: DNA transcription
      uri: http://edamontology.org/operation_0372
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://fishka.bio/picklet
  homepage_status: 0
  language:
  - TypeScript
  lastUpdate: '2026-08-21T02:36:18.912394Z'
  license: Freeware
  link:
  - note: fishka.bio — the tool collection picklet belongs to
    type:
    - Software catalogue
    url: https://fishka.bio
  maturity: Mature
  name: picklet
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: fishka
  publication:
  - doi: 10.5281/zenodo.21444547
    metadata: null
    note: Software deposit (concept DOI — resolves to the latest version) covering
      the fishka.bio tools, including picklet.
    pmcid: null
    pmid: null
    type:
    - Other
    version: 2026.07.19
  relation: []
  toolType:
  - Desktop application
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-08-20T18:05:41.024320Z'
  biotoolsCURIE: biotools:cognitionbiochem
  biotoolsID: cognitionbiochem
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: seung.jung@gmail.com
    fundrefid: null
    gridid: null
    name: Seung Ho Jung
    note: null
    orcidid: https://orcid.org/0000-0001-7914-5306
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  description: 'A structural pharmacology workbench for cognition-related CNS targets,
    built so that a displayed number must trace to a computation. Runs Boltz-2 locally
    for structure prediction, validates chemistry with RDKit, enforces a provenance
    record on every value, and reports eight studies pre-registered under content
    hashes before any data was seen. Its headline result is negative: designed peptides
    did not separate from composition-matched shuffles of their own amino acids.'
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/hopejsh/CognitionBioChem#readme
  - note: null
    type:
    - Citation instructions
    url: https://github.com/hopejsh/CognitionBioChem/blob/main/docs/REGISTRATION.md
  - note: 'The `license` field above is Apache-2.0, which covers this project''s code,
      but the repository is not single-licensed. It redistributes third-party scientific
      data that keeps its own terms: CC BY 4.0 (UniProt, AlphaFold DB), CC BY-SA 3.0
      (ChEMBL-derived files -- SHARE-ALIKE, so reuse carries an obligation onward),
      CC0 1.0 (RCSB depositions) and MIT (Boltz-2 model outputs). NOTICE lists which
      files fall under which.'
    type:
    - Terms of use
    url: https://github.com/hopejsh/CognitionBioChem/blob/main/NOTICE
  download:
  - note: null
    type: Source code
    url: https://github.com/hopejsh/CognitionBioChem/archive/refs/tags/v1.0.0.tar.gz
    version: 1.0.0
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Boltz-2 v2.2.1 runs locally; every predicted structure is retained under
      content-addressed custody with its confidence files.
    operation:
    - term: Protein structure prediction
      uri: http://edamontology.org/operation_0474
    output:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: mmCIF
        uri: http://edamontology.org/format_1477
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: mmCIF
        uri: http://edamontology.org/format_1477
    note: Backbone geometry, per-residue pLDDT and interface PAE are read from the
      model's own file; a value that was never computed renders as a label.
    operation:
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format: []
  - cmd: null
    input:
    - data:
        term: SMILES string
        uri: http://edamontology.org/data_2301
      format:
      - term: SMILES
        uri: http://edamontology.org/format_1196
    note: 'RDKit validation: parsing, molecular formula, InChIKey and stereochemistry
      completeness. A SMILES that fails to parse is shown as unverified.'
    operation:
    - term: Structure analysis
      uri: http://edamontology.org/operation_2480
    output:
    - data:
        term: Small molecule structure
        uri: http://edamontology.org/data_1463
      format: []
  homepage: https://github.com/hopejsh/CognitionBioChem
  homepage_status: 0
  language:
  - Python
  - JavaScript
  lastUpdate: '2026-08-20T18:06:12.321947Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/hopejsh/CognitionBioChem
  - note: null
    type:
    - Issue tracker
    url: https://github.com/hopejsh/CognitionBioChem/issues
  maturity: Mature
  name: CognitionBioChem
  operatingSystem:
  - Mac
  - Linux
  otherID:
  - type: doi
    value: doi:10.5281/zenodo.22032684
    version: concept DOI, resolves to the latest release
  - type: doi
    value: doi:10.5281/zenodo.22032685
    version: 1.0.0
  - type: rrid
    value: RRID:SCR_028851
    version: null
  owner: seung
  publication: []
  relation: []
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  validated: 0
  version:
  - 1.0.0
- accessibility: Open access (with restrictions)
  additionDate: '2026-08-19T00:51:31.640764Z'
  biotoolsCURIE: biotools:gelyze
  biotoolsID: gelyze
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: contact@bioinsight.co.jp
    fundrefid: null
    gridid: null
    name: BioInsight Co., Ltd.
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    - Primary contact
    url: https://bioinsight.co.jp
  description: 'Gelyze is a web-based image analysis tool for agarose gel electrophoresis
    of nucleic acids. A user uploads a gel image, confirms the proposed lane positions
    and the ladder baseline, and a deterministic algorithm then estimates fragment
    size from ladder calibration and quantifies relative band intensity by densitometry.
    Measurement and interpretation are kept separate: the numbers come from the algorithm,
    and an assistive AI layer explains the resulting pattern in plain language without
    producing any of the values. For research use only.'
  documentation:
  - note: null
    type:
    - User manual
    url: https://lab-ww.bioinsight.jp/help
  - note: null
    type:
    - FAQ
    url: https://lab-ww.bioinsight.jp/faq
  - note: null
    type:
    - Terms of use
    url: https://lab-ww.bioinsight.jp/terms
  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://lab-ww.bioinsight.jp
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-19T00:51:31.642994Z'
  license: Proprietary
  link: []
  maturity: Emerging
  name: Gelyze
  operatingSystem: []
  otherID: []
  owner: shunsuke1
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Molecular biology
    uri: http://edamontology.org/topic_3047
  validated: 0
  version: []
- accessibility: Open access (with restrictions)
  additionDate: '2026-08-17T23:27:23.095162Z'
  biotoolsCURIE: biotools:phonalab
  biotoolsID: phonalab
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: lucero@unb.br
    fundrefid: null
    gridid: null
    name: Jorge Carlos Lucero
    note: Professor of Computer Science at University of Brasília (Brazil)
    orcidid: https://orcid.org/0000-0003-0597-3808
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    url: https://lucerojc.github.io/
  - email: support@phonalab.com
    fundrefid: null
    gridid: null
    name: PhonaLab Inova Simples
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.phonalab/com
  description: PhonaLab is a browser-based platform for acoustic analysis of voice
    recordings, aimed at speech-language pathologists, voice clinicians, and researchers.
    It computes validated multiparametric acoustic indices — including the Acoustic
    Voice Quality Index (AVQI), Acoustic Breathiness Index (ABI), smoothed cepstral
    peak prominence (CPPS), and glottal-to-noise excitation ratio (GNE) — from sustained-vowel
    and connected-speech recordings, using Praat algorithms via the Parselmouth interface.
    Audio is processed in memory and not stored. Interface available in English, Brazilian
    Portuguese, and Spanish.
  documentation:
  - note: Peer-reviewed publication describing algorithm verification and concurrent
      validity of the platform's acoustic voice quality indices.
    type:
    - Citation instructions
    url: https://doi.org/10.1016/j.jvoice.2026.04.009
  - note: Explanatory guides on acoustic voice measures (CPPS, GNE, MPT/DSI) and clinical
      workflows.
    type:
    - Training material
    url: https://www.phonalab.com/guides
  - note: Audio is processed in memory and is not stored on the server.
    type:
    - Terms of use
    url: https://www.phonalab.com/terms
  - note: null
    type:
    - FAQ
    url: https://www.phonalab.com/faq
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://www.phonalab.com/
  homepage_status: 0
  language:
  - Python
  - JavaScript
  lastUpdate: '2026-08-18T22:06:01.693016Z'
  license: Proprietary
  link:
  - note: null
    type:
    - Social media
    url: https://www.instagram.com/phonalab.voice/
  maturity: Emerging
  name: PhonaLab
  operatingSystem: []
  otherID:
  - type: rrid
    value: RRID:SCR_028845
    version: null
  - type: doi
    value: DOI:10.5281/zenodo.21987370
    version: null
  owner: jorge_carlos
  publication:
  - doi: 10.1016/j.jvoice.2026.04.009
    metadata: null
    note: null
    pmcid: null
    pmid: '42049572'
    type:
    - Primary
    version: null
  - doi: 10.1016/j.jvoice.2026.07.051
    metadata: null
    note: null
    pmcid: null
    pmid: '42603770'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Medicine
    uri: http://edamontology.org/topic_3303
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-08-18T17:47:15.183333Z'
  biotoolsCURIE: biotools:membrane_visual_qc
  biotoolsID: membrane_visual_qc
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: trofimchikpavel@icloud.com
    fundrefid: null
    gridid: null
    name: Pavel Trofimchik
    note: null
    orcidid: https://orcid.org/0009-0007-6030-6019
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://github.com/TrPavel
  description: Open-source PyMOL plugin for membrane-aware review of predicted, designed
    and experimental protein structures. Membrane Visual QC provides planar membrane-relative
    geometry, residue core/interface classification, hydropathy and ligand-context
    review, solvent-accessibility context, PDBTM/OPM orientation-source checks, and
    reproducible batch reporting. It is designed as a review assistant rather than
    a biological structure validator.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/TrPavel/membrane-visual-qc/blob/main/docs/index.md
  - note: null
    type:
    - Quick start guide
    url: https://github.com/TrPavel/membrane-visual-qc/blob/main/docs/quick_start.md
  - note: null
    type:
    - User manual
    url: https://github.com/TrPavel/membrane-visual-qc/blob/main/docs/tutorial.md
  - note: v1.0 video walkthrough.
    type:
    - Training material
    url: https://youtu.be/lowQey_D610
  download:
  - note: Stable PyMOL Plugin Manager package.
    type: Software package
    url: https://github.com/TrPavel/membrane-visual-qc/releases/download/v1.0.0/MembraneVisualQC-1.0.0.zip
    version: 1.0.0
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/TrPavel/membrane-visual-qc
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-08-18T17:47:15.185629Z'
  license: MIT
  link:
  - note: Source code and project repository.
    type:
    - Repository
    url: https://github.com/TrPavel/membrane-visual-qc
  - note: Bug reports, feature requests and user feedback.
    type:
    - Issue tracker
    url: https://github.com/TrPavel/membrane-visual-qc/issues
  maturity: Emerging
  name: Membrane Visual QC
  operatingSystem:
  - Windows
  otherID: []
  owner: pavel
  publication: []
  relation: []
  toolType:
  - Desktop application
  - Plug-in
  - Command-line tool
  topic:
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Biochemistry
    uri: http://edamontology.org/topic_3292
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  validated: 0
  version:
  - 1.0.0
- accessibility: null
  additionDate: '2026-06-26T09:18:51.735249Z'
  biotoolsCURIE: biotools:PathBench-MIL
  biotoolsID: PathBench-MIL
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: PathBench-MIL is a comprehensive, flexible benchmarking/AutoML framework
    for multiple instance learning in histopathology. PathBench-MIL is expected to
    be deprecated and replaced by PathForge.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Data reference
        uri: http://edamontology.org/data_2093
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: TIFF
        uri: http://edamontology.org/format_3591
    note: null
    operation:
    - term: Optimisation and refinement
      uri: http://edamontology.org/operation_2425
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Regression analysis
      uri: http://edamontology.org/operation_3659
    - term: Classification
      uri: http://edamontology.org/operation_2990
    output:
    - data:
        term: Histogram
        uri: http://edamontology.org/data_3905
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: https://github.com/Sbrussee/PathBench-MIL
  homepage_status: 0
  language:
  - Shell
  - Python
  lastUpdate: '2026-08-18T09:47:11.729879Z'
  license: GPL-3.0
  link: []
  maturity: Legacy
  name: PathBench-MIL
  operatingSystem:
  - Linux
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.48550/arXiv.2512.17517
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: pathforge
    type: hasNewVersion
  toolType: []
  topic:
  - term: Pathology
    uri: http://edamontology.org/topic_0634
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-08-16T12:44:01.129997Z'
  biotoolsCURIE: biotools:pathforge
  biotoolsID: pathforge
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: PathForge is a modular benchmarking framework for multiple instance
    learning in computational pathology. It supports whole slide image feature extraction,
    HDF5 artifact generation, tile overviews, benchmarking, pipeline optimization,
    classification, regression, survival and retrieval tasks, and support for model
    inference and visualization.
  documentation:
  - note: null
    type:
    - General
    - Quick start guide
    - User manual
    url: https://pathforge.readthedocs.io/en/latest/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Data reference
        uri: http://edamontology.org/data_2093
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: TIFF
        uri: http://edamontology.org/format_3591
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Regression analysis
      uri: http://edamontology.org/operation_3659
    - term: Optimisation and refinement
      uri: http://edamontology.org/operation_2425
    - term: Classification
      uri: http://edamontology.org/operation_2990
    output:
    - data:
        term: Histogram
        uri: http://edamontology.org/data_3905
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: HDF5
        uri: http://edamontology.org/format_3590
  homepage: https://github.com/Sbrussee/PathForge
  homepage_status: 0
  language:
  - Shell
  - Python
  lastUpdate: '2026-08-18T09:43:04.240059Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/Sbrussee/PathForge
  - note: null
    type:
    - Other
    url: https://pathforge.readthedocs.io/en/latest/
  maturity: Mature
  name: PathForge
  operatingSystem:
  - Linux
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.48550/arXiv.2512.17517
    metadata: null
    note: Publication describes predecessor, PathBench-MIL
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: null
  relation:
  - biotoolsID: PathBench-MIL
    type: isNewVersionOf
  toolType:
  - Command-line tool
  topic:
  - term: Pathology
    uri: http://edamontology.org/topic_0634
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-08-18T09:37:38.223221Z'
  biotoolsCURIE: biotools:mailsdaddy_mbox_to_pst_converter
  biotoolsID: mailsdaddy_mbox_to_pst_converter
  collectionID: []
  confidence_flag: null
  cost: Commercial
  credit:
  - email: vishwakarmasomit205@gmail.com
    fundrefid: null
    gridid: null
    name: Somit Vishwakarma
    note: null
    orcidid: https://orcid.org/0000-0002-9579-0601
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: MailsDaddy MBOX to PST Converter is designed to move single or multiple
    MBOX file to Outlook PST, EML, MSG, HTML etc.
  documentation:
  - note: null
    type:
    - Installation instructions
    url: https://www.mailsdaddy.com/installation/mbox-to-pst-converter.pdf
  download:
  - note: null
    type: Software package
    url: https://www.mailsdaddy.com/dl/mbox-to-pst-converter.zip
    version: '8.1'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: convert data from MBOX-based email client to Outlook and others.
    input: []
    note: null
    operation:
    - term: Data management planning
      uri: http://edamontology.org/operation_4042
    output: []
  homepage: https://www.mailsdaddy.com/mbox-to-pst-converter/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-08-18T09:37:59.557406Z'
  license: Other
  link:
  - note: Thunderbbird to Outlook Converter
    type:
    - Service
    url: https://www.mailsdaddy.com/thunderbird-to-outlook-converter/
  maturity: null
  name: MailsDaddy MBOX to PST Converter
  operatingSystem:
  - Windows
  otherID: []
  owner: mailsdaddy
  publication:
  - doi: 10.5281/zenodo.21533078
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: '8.1'
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version:
  - '8.1'
- accessibility: Open access
  additionDate: '2026-08-18T08:32:45.894204Z'
  biotoolsCURIE: biotools:ft-itc-analysis
  biotoolsID: ft-itc-analysis
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: application@ft-itc.org
    fundrefid: null
    gridid: null
    name: Frederik Theisen
    note: null
    orcidid: https://orcid.org/0000-0002-3412-4242
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: FT-ITC Analysis is free, open-source desktop software for processing,
    fitting, and analysing isothermal titration calorimetry (ITC) data. It imports
    raw data from MicroCal, TA Instruments/NanoAnalyze, and PEAQ ITC project files,
    as well as integrated heat data and FT-ITC project files. The software supports
    baseline correction, injection integration, interaction-model fitting, global
    analysis, uncertainty estimation, advanced thermodynamic analyses, and publication-figure
    export on macOS, Windows, and Linux.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/FrederikTheisen/FT-ITC-Analysis/wiki
  download:
  - note: null
    type: Downloads page
    url: https://ft-itc.org/app-desktop
    version: null
  - note: null
    type: Source code
    url: https://github.com/FrederikTheisen/FT-ITC-Analysis
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://ft-itc.org
  homepage_status: 0
  language:
  - C#
  lastUpdate: '2026-08-18T08:33:03.631070Z'
  license: MIT
  link: []
  maturity: Emerging
  name: FT-ITC Analysis
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: frederik_friis
  publication: []
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Biophysics
    uri: http://edamontology.org/topic_3306
  - term: Chemistry
    uri: http://edamontology.org/topic_3314
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-08-18T03:14:42.132166Z'
  biotoolsCURIE: biotools:cuda-ising-osteo
  biotoolsID: cuda-ising-osteo
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: A GPU-accelerated Ising/QUBO optimisation pipeline for osteoporosis
    gene-target discovery. It performs expression-based feature selection and GWAS-seeded
    STRING network-module detection with a batched GPU parallel-tempering sampler
    (PyTorch/CUDA, with a NumPy CPU fallback), and includes a cross-cohort replication
    protocol and orthogonal validation of candidate genes.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/Oscarlee9203/cuda-ising-osteo
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-18T03:15:33.756666Z'
  license: null
  link: []
  maturity: null
  name: CUDA-Ising-Osteo
  operatingSystem: []
  otherID: []
  owner: oscar5
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - 1.0.0
- accessibility: Open access
  additionDate: '2026-08-17T15:22:16.224374Z'
  biotoolsCURIE: biotools:spoqc
  biotoolsID: spoqc
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: florian.heyl@dkfz-heidelberg.de
    fundrefid: null
    gridid: null
    name: Florian Heyl
    note: null
    orcidid: https://orcid.org/0000-0002-3651-5685
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ezgi Sen
    note: null
    orcidid: https://orcid.org/0009-0005-0816-2076
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Niklas Müller-Bötticher
    note: null
    orcidid: https://orcid.org/0000-0001-5103-7282
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: spoQC is a modular framework for multimodal quality control (QC) of
    imaging-based spatially resolved transcriptomics (SRT). It independently evaluates
    cell segmentation, imaging, and transcript data to identify high-quality regions
    (HQRs) across entire tissue sections. In addition, spoQC uses Markov random fields
    (MRFs) to incorporate spatial dependencies and generate spatially refined QC masks.
  documentation:
  - note: Complete documentation of spoQC
    type:
    - User manual
    url: https://spoqc.readthedocs.io/en/latest/
  download:
  - note: pip install
    type: Software package
    url: https://pypi.org/project/spoqc/
    version: 0.0.1
  - note: docker/singularity container
    type: Container file
    url: https://quay.io/repository/heylf/spoqc
    version: 0.0.1
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/heylf/spoQC
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-08-17T15:22:16.226347Z'
  license: MIT
  link: []
  maturity: Emerging
  name: spoQC
  operatingSystem: []
  otherID: []
  owner: florian4
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic: []
  validated: 0
  version:
  - 0.0.1
- accessibility: Open access
  additionDate: '2026-08-16T08:12:42.610611Z'
  biotoolsCURIE: biotools:par2-circadian
  biotoolsID: par2-circadian
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: mickwh@msn.com
    fundrefid: null
    gridid: null
    name: Michael Whiteside
    note: Author and maintainer
    orcidid: https://orcid.org/0009-0000-0643-5791
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    - Primary contact
    url: https://par2discovery.com
  description: 'Fits second-order autoregressive AR(2) models to gene expression time
    series and reports the eigenvalue modulus |lambda|, a single statistic quantifying
    temporal persistence: how strongly a gene''s recent past constrains its next value.
    Ranks genes into a clock/target/background hierarchy and reports correlation length,
    half-life and root type (real or complex) per gene.'
  documentation:
  - note: Installation, Python API and command-line usage
    type:
    - General
    url: https://github.com/mickwh2764/par2discovery#readme
  - note: CITATION.cff, schema 1.2.0
    type:
    - Citation instructions
    url: https://github.com/mickwh2764/par2discovery/blob/main/CITATION.cff
  - note: 'PolyForm Noncommercial 1.0.0: free for research and other noncommercial
      use; commercial use requires a separate licence. bio.tools has no SPDX entry
      for PolyForm, hence license: Other.'
    type:
    - Terms of use
    url: https://github.com/mickwh2764/par2discovery/blob/main/LICENSE
  download:
  - note: pip install par2-circadian
    type: Software package
    url: https://pypi.org/project/par2-circadian/
    version: 1.1.7
  - note: Git repository
    type: Source code
    url: https://github.com/mickwh2764/par2discovery
    version: 1.1.7
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: par2 expression.csv -o results.csv
    input:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: TSV
        uri: http://edamontology.org/format_3475
    note: Input is a matrix with genes as rows and evenly spaced timepoints as columns.
      Output is one row per gene giving the AR(2) coefficients, |lambda|, root type,
      correlation length and half-life, plus a hierarchy summary.
    operation:
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: Regression analysis
      uri: http://edamontology.org/operation_3659
    - term: RNA-seq time series data analysis
      uri: http://edamontology.org/operation_3565
    - term: Statistical modelling
      uri: http://edamontology.org/operation_3664
    output:
    - data:
        term: Statistical estimate score
        uri: http://edamontology.org/data_0951
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://github.com/mickwh2764/par2discovery
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-08-16T09:10:10.546971Z'
  license: Other
  link:
  - note: Source repository
    type:
    - Repository
    url: https://github.com/mickwh2764/par2discovery
  - note: Bug reports and feature requests
    type:
    - Issue tracker
    url: https://github.com/mickwh2764/par2discovery/issues
  - note: 'PAR(2) Discovery Engine: interactive analyses built on this package'
    type:
    - Other
    url: https://par2discovery.com
  - note: 'Reproducibility repository: analysis code, dataset accessions and expected
      results'
    type:
    - Other
    url: https://github.com/mickwh2764/par2-reproducibility
  - note: RRID:SCR_028837 (SciCrunch Registry)
    type:
    - Other
    url: https://scicrunch.org/resolver/RRID:SCR_028837
  maturity: Emerging
  name: par2-circadian
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID:
  - type: doi
    value: doi:10.5281/zenodo.21963192
    version: 1.1.7
  owner: michael
  publication:
  - doi: 10.21203/rs.3.rs-9283100/v1
    metadata: null
    note: Method preprint describing the AR(2) eigenvalue modulus and the clock/target/background
      hierarchy.
    pmcid: null
    pmid: null
    type:
    - Primary
    - Method
    version: null
  - doi: 10.5281/zenodo.21963192
    metadata: null
    note: Archived software, concept DOI resolving to the latest release.
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  - term: Mathematics
    uri: http://edamontology.org/topic_3315
  validated: 0
  version:
  - 1.1.7
- accessibility: Restricted access
  additionDate: '2026-08-15T11:18:20.560551Z'
  biotoolsCURIE: biotools:pan_bio
  biotoolsID: pan_bio
  collectionID: []
  confidence_flag: null
  cost: Commercial
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Pan.bio
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    - Developer
    url: https://pan.bio
  description: Pan.bio is a cloud genomics platform for pipeline execution, exploratory
    analysis, and clinical variant interpretation. Workflows runs validated Nextflow
    and nf-core pipelines including Sarek, rnaseq, scrnaseq, mag, ampliseq, chipseq
    and atacseq without local installation. Notebooks provides Python and R sessions
    with a preinstalled bioinformatics stack, importing public data from GEO, SRA
    and IPG by accession and reading Workflows outputs directly. VAIC applies ACMG/AMP
    variant classification with gene-specific rule sets from CanVIG-UK and ClinGen
    ENIGMA, with automated evidence criteria implemented for BRCA1 and BRCA2. Cohorts
    provides federated analysis of patient data within a Trusted Research Environment.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: 'Workflows: cloud execution of validated nf-core and Nextflow pipelines
      including Sarek for germline and somatic variant calling.'
    operation:
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
  - cmd: null
    input:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: Textual format
        uri: http://edamontology.org/format_2330
    note: 'VAIC: ACMG/AMP classification with gene-specific rules from CanVIG-UK and
      ClinGen ENIGMA. Automated evidence criteria are implemented for BRCA1 and BRCA2.
      Evidence is aggregated from ClinVar, CanVar, gnomAD v4.1, BayesDel, REVEL and
      SpliceAI. Accepts HGVS notation, variant lists and VCF on GRCh38 or GRCh37.
      Outputs include clinical reports plus FHIR and HL7 for EMR integration. Every
      criterion applied is shown with its strength and contribution. The final classification
      decision rests with the clinical user.'
    operation:
    - term: Variant classification
      uri: http://edamontology.org/operation_3225
    - term: Variant prioritisation
      uri: http://edamontology.org/operation_3226
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: PDF
        uri: http://edamontology.org/format_3508
  - cmd: null
    input:
    - data:
        term: Accession
        uri: http://edamontology.org/data_2091
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    note: 'Notebooks: Python and R analysis sessions with pandas, numpy, matplotlib,
      ggplot2, samtools and bedtools preinstalled. Imports datasets from GEO, SRA
      and IPG by accession and reads Workflows outputs without re-upload. The bioMind
      Notebook Agent generates analysis code from plain-language descriptions for
      the user to inspect and run.'
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://pan.bio
  homepage_status: 0
  language:
  - Python
  - R
  lastUpdate: '2026-08-15T11:18:50.823672Z'
  license: Proprietary
  link:
  - note: Contact and demo requests
    type:
    - Helpdesk
    url: https://pan.bio/company/contact/
  maturity: Mature
  name: Pan.bio
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: Pan.bio
  publication: []
  relation: []
  toolType:
  - Workflow
  - Web service
  - Web application
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Personalised medicine
    uri: http://edamontology.org/topic_3577
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Exome sequencing
    uri: http://edamontology.org/topic_3676
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 0
  version:
  - '1.0'
- accessibility: null
  additionDate: '2026-08-15T04:20:06.745455Z'
  biotoolsCURIE: biotools:nexcision
  biotoolsID: nexcision
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: rhys.white@phfscience.nz
    fundrefid: null
    gridid: null
    name: Rhys White
    note: null
    orcidid: https://orcid.org/0000-0001-6620-758X
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://www.phfscience.nz/staff-profiles/rhys-white/
  description: Exact, validated excision of coordinate-defined genomic regions from
    transposed NEXUS matrices.
  documentation:
  - note: Hosted NEXCISION documentation.
    type:
    - General
    url: https://nexcision.readthedocs.io/
  - note: Installation via PyPI, Bioconda, or tagged GitHub releases.
    type:
    - Installation instructions
    url: https://nexcision.readthedocs.io/en/latest/installation/
  - note: Workflow integration, provenance reporting, validation policies, and Snakemake
      examples.
    type:
    - User manual
    url: https://nexcision.readthedocs.io/en/latest/workflow-integration/
  download:
  - note: Tagged NEXCISION v0.1.1 source release.
    type: Source code
    url: https://github.com/RhysWhite/nexcision/releases/tag/v0.1.1
    version: 0.1.1
  - note: Python package for installation with pip.
    type: Software package
    url: https://pypi.org/project/nexcision/0.1.1/
    version: 0.1.1
  - note: Bioconda package for Conda-based environments.
    type: Software package
    url: https://anaconda.org/bioconda/nexcision
    version: 0.1.1
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: nexcise NEXUS REGIONS [options]
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nexus-seq
        uri: http://edamontology.org/format_1949
    - data:
        term: Sequence range
        uri: http://edamontology.org/data_1017
      format: []
    note: Remove coordinate-labelled NEXUS matrix rows overlapping user-defined 1-based
      inclusive genomic regions.
    operation:
    - term: Sequence alignment editing
      uri: http://edamontology.org/operation_3081
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nexus-seq
        uri: http://edamontology.org/format_1949
  homepage: https://github.com/RhysWhite/nexcision
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-08-15T04:20:15.574585Z'
  license: MIT
  link:
  - note: Source code and development repository.
    type:
    - Repository
    url: https://github.com/RhysWhite/nexcision
  - note: Bug reports and feature requests.
    type:
    - Issue tracker
    url: https://github.com/RhysWhite/nexcision/issues
  - note: Independent validation, adversarial testing, and scalability benchmarking
      materials.
    type:
    - Repository
    url: https://github.com/RhysWhite/nexcision-benchmarking
  maturity: Emerging
  name: NEXCISION
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID:
  - type: doi
    value: doi:10.5281/zenodo.21936049
    version: 0.1.1
  owner: rhys
  publication:
  - doi: 10.64898/2026.07.26.740842
    metadata: null
    note: Primary NEXCISION methods and validation preprint.
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  validated: 0
  version:
  - 0.1.1
- accessibility: null
  additionDate: '2026-08-14T16:23:03.786354Z'
  biotoolsCURIE: biotools:branchsnv
  biotoolsID: branchsnv
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: BRANCHSNV reports strict clade-exclusive nucleotide markers separately
    from single-nucleotide substitutions reconstructed on a selected edge of a rooted
    phylogenetic tree, while retaining ambiguity across equally parsimonious ancestral-state
    reconstructions.
  documentation:
  - note: null
    type:
    - FAQ
    url: https://branchsnv.readthedocs.io/en/latest/
  - note: null
    type:
    - Citation instructions
    url: https://branchsnv.readthedocs.io/en/latest/
  download:
  - note: null
    type: Software package
    url: https://pypi.org/project/branchsnv/
    version: null
  - note: null
    type: Downloads page
    url: https://github.com/RhysWhite/branchsnv/releases
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: "branchsnv find \\\n  --alignment alignment.nex \\\n  --tree tree.nwk \\\n\
      \  --outgroup-file outgroup_tips.txt \\\n  --clade-tips clade_tips.txt \\\n\
      \  --mode both \\\n  --output branch_snvs.tsv \\\n  --members-output branch_members.txt\
      \ \\\n  --report branchsnv_report.json"
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: Nexus format
        uri: http://edamontology.org/format_1912
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    note: Interrogates one selected branch of a rooted phylogeny, reporting strict
      clade-exclusive nucleotide markers separately from substitutions reconstructed
      on the focal edge under equal-cost parsimony.
    operation:
    - term: Phylogenetic analysis
      uri: http://edamontology.org/operation_0324
    output:
    - data:
        term: Sequence features
        uri: http://edamontology.org/data_1255
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://branchsnv.readthedocs.io/en/latest/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-08-14T16:23:14.011790Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/RhysWhite/branchsnv
  - note: null
    type:
    - Issue tracker
    url: https://github.com/RhysWhite/branchsnv/issues
  - note: null
    type:
    - Other
    url: https://github.com/RhysWhite/branchsnv-validation
  maturity: Emerging
  name: BRANCHSNV
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID:
  - type: doi
    value: doi:10.5281/zenodo.21919038
    version: 0.1.0
  owner: rhys
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - 0.1.0
- accessibility: null
  additionDate: '2018-08-24T13:49:33Z'
  biotoolsCURIE: biotools:p2rank
  biotoolsID: p2rank
  collectionID:
  - ELIXIR-CZ
  confidence_flag: null
  cost: null
  credit:
  - email: hoksza@ksi.mff.cuni.cz
    fundrefid: null
    gridid: null
    name: David Hoksza
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Novel machine learning-based method for prediction of ligand binding
    sites from protein structure.
  documentation:
  - note: null
    type:
    - General
    url: http://siret.ms.mff.cuni.cz/p2rank
  download: []
  editPermission:
    authors:
    - ayan
    type: group
  elixirCommunity: []
  elixirNode:
  - Czech Republic
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Protein binding site prediction
      uri: http://edamontology.org/operation_2575
    output: []
  homepage: http://siret.ms.mff.cuni.cz/p2rank
  homepage_status: 0
  language:
  - Java
  - Groovy
  lastUpdate: '2026-08-14T09:40:08.820438Z'
  license: MIT
  link: []
  maturity: null
  name: P2Rank
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: davidhokszamff
  publication:
  - doi: 10.1186/s13321-018-0285-8
    metadata:
      abstract: 'Background: Ligand binding site prediction from protein structure
        has many applications related to elucidation of protein function and structure
        based drug discovery. It often represents only one step of many in complex
        computational drug design efforts. Although many methods have been published
        to date, only few of them are suitable for use in automated pipelines or for
        processing large datasets. These use cases require stability and speed, which
        disqualifies many of the recently introduced tools that are either template
        based or available only as web servers. Results: We present P2Rank, a stand-alone
        template-free tool for prediction of ligand binding sites based on machine
        learning. It is based on prediction of ligandability of local chemical neighbourhoods
        that are centered on points placed on the solvent accessible surface of a
        protein. We show that P2Rank outperforms several existing tools, which include
        two widely used stand-alone tools (Fpocket, SiteHound), a comprehensive consensus
        based tool (MetaPocket 2.0), and a recent deep learning based method (DeepSite).
        P2Rank belongs to the fastest available tools (requires under 1 s for prediction
        on one protein), with additional advantage of multi-threaded implementation.
        Conclusions: P2Rank is a new open source software package for ligand binding
        site prediction from protein structure. It is available as a user-friendly
        stand-alone command line program and a Java library. P2Rank has a lightweight
        installation and does not depend on other bioinformatics tools or large structural
        or sequence databases. Thanks to its speed and ability to make fully automated
        predictions, it is particularly well suited for processing large datasets
        or as a component of scalable structural bioinformatics pipelines.'
      authors:
      - name: Krivak R.
      - name: Hoksza D.
      citationCount: 242
      date: '2018-12-01T00:00:00Z'
      journal: Journal of Cheminformatics
      title: 'P2Rank: machine learning based tool for rapid and accurate prediction
        of ligand binding sites from protein structure'
    note: null
    pmcid: PMC6091426
    pmid: '30109435'
    type: []
    version: null
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Cheminformatics
    uri: http://edamontology.org/topic_2258
  - term: Structural biology
    uri: http://edamontology.org/topic_1317
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  validated: 1
  version: []
- accessibility: null
  additionDate: '2021-01-18T11:19:37Z'
  biotoolsCURIE: biotools:asap-assemble
  biotoolsID: asap-assemble
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: puillandre@mnhn.fr
    fundrefid: null
    gridid: null
    name: Nicolas Puillandre
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: 'ASAP (Assemble Species by Automatic Partitioning) is a method to build
    species partitions from single locus sequence alignments.

    ASAP is the implementation of a hierarchical clustering algorithm that only uses
    pairwise genetic distances, avoiding the computational burden of phylogenetic
    reconstruction. Importantly, ASAP proposes species partitions ranked by a new
    scoring system that uses no biological prior insight of intraspecific diversity.'
  documentation:
  - note: null
    type:
    - General
    url: https://bioinfo.mnhn.fr/abi/public/asap/help_asap.html
  - note: null
    type:
    - FAQ
    url: https://bioinfo.mnhn.fr/abi/public/asap/FAQ_asap.html
  download: []
  editPermission:
    authors:
    - arkamukherjee
    - keqing
    - huda4
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Phylogenetic reconstruction
      uri: http://edamontology.org/operation_3478
    - term: DNA barcoding
      uri: http://edamontology.org/operation_3200
    - term: Sequence assembly
      uri: http://edamontology.org/operation_0310
    - term: Splitting
      uri: http://edamontology.org/operation_3359
    output: []
  homepage: https://bioinfo.mnhn.fr/abi/public/asap
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-14T09:40:06.996761Z'
  license: null
  link: []
  maturity: null
  name: ASAP
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1111/1755-0998.13281
    metadata:
      abstract: © 2020 John Wiley & Sons LtdHere, we describe Assemble Species by
        Automatic Partitioning (ASAP), a new method to build species partitions from
        single locus sequence alignments (i.e., barcode data sets). ASAP is efficient
        enough to split data sets as large 104 sequences into putative species in
        several minutes. Although grounded in evolutionary theory, ASAP is the implementation
        of a hierarchical clustering algorithm that only uses pairwise genetic distances,
        avoiding the computational burden of phylogenetic reconstruction. Importantly,
        ASAP proposes species partitions ranked by a new scoring system that uses
        no biological prior insight of intraspecific diversity. ASAP is a stand-alone
        program that can be used either through a graphical web-interface or that
        can be downloaded and compiled for local usage. We have assessed its power
        along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode
        data sets representing various degrees of challenge (from small and easy cases
        to large and complicated data sets). We also used Monte-Carlo simulations
        of a multispecies coalescent framework to assess the strengths and weaknesses
        of ASAP and the other programs. Through these analyses, we demonstrate that
        ASAP has the potential to become a major tool for taxonomists as it proposes
        rapidly in a full graphical exploratory interface relevant species hypothesis
        as a first step of the integrative taxonomy process.
      authors:
      - name: Puillandre N.
      - name: Brouillet S.
      - name: Achaz G.
      citationCount: 15
      date: '2021-02-01T00:00:00Z'
      journal: Molecular Ecology Resources
      title: 'ASAP: assemble species by automatic partitioning'
    note: null
    pmcid: null
    pmid: '33058550'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  - Desktop application
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 0
  version: []
- accessibility: Restricted access
  additionDate: '2026-02-23T13:56:07.187145Z'
  biotoolsCURIE: biotools:HelixInsight
  biotoolsID: HelixInsight
  collectionID: []
  confidence_flag: null
  cost: Commercial
  credit:
  - email: contact@helena.bio
    fundrefid: null
    gridid: null
    name: Helena Bioinformatics
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Developer
    url: https://helena.bio
  description: Deterministic, rule-based variant interpretation platform for clinical
    genetics laboratories. Automates ACMG/AMP 2015 classification using a Bayesian
    point-based framework (Tavtigian et al. 2018) with BayesDel ClinGen SVI-calibrated
    thresholds (Pejaver et al. 2022). Integrates 8 reference databases (gnomAD v4.1,
    ClinVar, dbNSFP 4.9c, SpliceAI, gnomAD Constraint, HPO, ClinGen, Ensembl VEP).
    Analyzes nuclear and mtDNA variants, structural and copy-number variants (SV/CNV),
    with trio/family and cohort analysis. Supports HPO-based phenotype matching, biomedical
    literature mining across 2M+ PubMed publications, and structured clinical report
    generation. AI assists in evidence synthesis but does not make classification
    decisions. EU-hosted on dedicated infrastructure in Helsinki, Finland (GDPR-compliant).
  documentation:
  - note: Complete production documentation covering every threshold, database version,
      and classification rule. Intended for clinical geneticists, laboratory directors,
      accreditation auditors, and bioinformaticians.
    type:
    - General
    url: https://folklore.helena.bio/docs
  - note: Seven-stage analysis pipeline (quality control, annotation, classification,
      phenotype matching, literature, screening, interpretation) transforming a raw
      VCF into a clinician-ready report, each stage producing traceable, auditable
      output.
    type:
    - General
    url: https://folklore.helena.bio/how-it-works
  - note: ACMG/AMP 2015 classification methodology (Richards et al. 2015) via Bayesian
      point-based system (Tavtigian et al. 2018), BayesDel ClinGen SVI-calibrated
      thresholds (Pejaver et al. 2022), and SpliceAI aligned to ClinGen SVI 2023 (Walker
      et al. 2023). Optional ClinGen VCEP overlay for ~50-60 genes. Strictly evidence-based,
      no ML determines pathogenicity.
    type:
    - General
    url: https://folklore.helena.bio/methodology
  - note: Mitochondrial DNA variant classification under the ClinGen Mitochondrial
      Disease Working Group (MMDWG) 2020 specification (McCormick et al. 2020). Operates
      as an independent module from the nuclear ACMG/AMP pipeline; every variant carries
      an explicit framework provenance label. Strength tiers follow ClinGen mtDNA
      VCEP v1.0.0.
    type:
    - General
    url: https://folklore.helena.bio/methodology/mtdna
  - note: Inheritance-aware evidence from trio (proband + both parents), duo, and
      proband-plus-sibling analyses. Implements ClinGen SVI 2018 de novo PS2/PM6 (PMID
      29543229), Jarvik & Browning 2016 LOD segregation framework (PMID 27236918),
      and ClinGen SVI 2021 PP1 strength bands. Augments the existing ACMG/AMP classification
      without re-calling variants.
    type:
    - General
    url: https://folklore.helena.bio/methodology/family-analysis
  - note: Structural and copy-number variant evaluation under the Riggs 2020 joint
      ACMG/ClinGen technical standard. Documents the point-based loss and gain metrics,
      dosage-sensitivity evidence, and five-tier classification, with reference data
      and documented limitations.
    type:
    - General
    url: https://folklore.helena.bio/methodology/sv
  - note: Prioritizes classified variants for clinical review. After ACMG classification
      determines what each variant is, screening determines which to review first
      based on patient-specific clinical relevance. Evaluates seven independent dimensions,
      applies clinical profile boosts, and produces a four-tier priority ranking with
      transparent, visible score components.
    type:
    - General
    url: https://folklore.helena.bio/screening-methodology
  - note: Canonical connector guide for Folklore Clinical Variant Interpretation MCP
      (io.github.helena-bioinformatics/folklore), version 1.2.2.
    type:
    - API documentation
    url: https://folklore.helena.bio/docs/folklore-connector
  - note: Public Apache-2.0 MCP protocol adapter README. The Folklore SaaS platform
      and clinical interpretation backend remain proprietary.
    type:
    - General
    url: https://github.com/helena-bioinformatics/folklore-mcp#readme
  - note: Release history for the public Folklore MCP protocol adapter.
    type:
    - Release notes
    url: https://github.com/helena-bioinformatics/folklore-mcp/blob/main/CHANGELOG.md
  download:
  - note: Apache-2.0 standalone MCP protocol adapter. Excludes proprietary clinical
      interpretation logic, private data, credentials and operational infrastructure.
    type: Source code
    url: https://github.com/helena-bioinformatics/folklore-mcp
    version: 1.2.2
  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: VCF
        uri: http://edamontology.org/format_3016
    note: null
    operation:
    - term: Variant classification
      uri: http://edamontology.org/operation_3225
    output:
    - data:
        term: Sequence report
        uri: http://edamontology.org/data_2955
      format: []
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format: []
    - data:
        term: Disease report
        uri: http://edamontology.org/data_1622
      format: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genetic variation analysis
      uri: http://edamontology.org/operation_3197
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Literature search
      uri: http://edamontology.org/operation_0305
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    output: []
  homepage: https://folklore.helena.bio
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-08-13T17:54:13.977787Z'
  license: Proprietary
  link:
  - note: Public Apache-2.0 MCP protocol adapter source; the Folklore SaaS platform
      and clinical interpretation backend remain proprietary.
    type:
    - Repository
    url: https://github.com/helena-bioinformatics/folklore-mcp
  - note: Public remote endpoint for Folklore Clinical Variant Interpretation MCP
      version 1.2.2.
    type:
    - Service
    url: https://api.helena.bio/folklore/v1/mcp
  - note: 'Official MCP Registry entry: io.github.helena-bioinformatics/folklore.'
    type:
    - Software catalogue
    url: https://registry.modelcontextprotocol.io/v0.1/servers?search=io.github.helena-bioinformatics%2Ffolklore&version=latest
  - note: Official Folklore integrations and MCP client connection page.
    type:
    - Other
    url: https://folklore.helena.bio/integrations
  - note: Public health and discovery metadata endpoint for the Folklore MCP service.
    type:
    - Technical monitoring
    url: https://api.helena.bio/folklore/v1/health
  maturity: Mature
  name: Folklore
  operatingSystem:
  - Linux
  otherID:
  - type: rrid
    value: RRID:SCR_028669
    version: 3.39.1
  owner: helenabio
  publication:
  - doi: 10.5281/zenodo.21105027
    metadata: null
    note: Methodological framework for real-world performance studies of the platform's
      variant classification, demonstrated on three internal validation cohorts.
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: '1.0'
  - doi: 10.5281/zenodo.21189571
    metadata: null
    note: 'A Deterministic Classification Core with an Agentic Interpretation Layer:
      An Architecture for Auditable, Human-Gated Clinical Variant Analysis'
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: '1.0'
  - doi: 10.5281/zenodo.21763096
    metadata: null
    note: 'Robustness and cross-cohort concordance of developmental regulons in endometrial
      carcinoma. Authors: Draga Toncheva, Vasil Sgurev and Vladimir Mitev.'
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: null
  - doi: 10.5281/zenodo.21922952
    metadata: null
    note: 'Archived public Apache-2.0 Folklore MCP adapter release. All-version DOI:
      10.5281/zenodo.21922951.'
    pmcid: null
    pmid: null
    type:
    - Other
    version: 1.2.2
  relation: []
  toolType:
  - Web API
  - Web application
  topic:
  - term: Human genetics
    uri: http://edamontology.org/topic_3574
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  validated: 0
  version:
  - 3.39.1
- accessibility: Open access
  additionDate: '2026-08-12T20:58:08.530146Z'
  biotoolsCURIE: biotools:peptide_reconstitution_calculator
  biotoolsID: peptide_reconstitution_calculator
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: hola@peptidomexico.com.mx
    fundrefid: null
    gridid: null
    name: Peptido México Open Science
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://github.com/PeptidoMexico/peptidomexico-open-science
  description: 'A transparent, unit-aware calculator for the mathematical relationship
    between peptide mass, target concentration and solution volume. It normalizes
    mg, micrograms, mL and microlitres, shows the formula and includes a reference
    syringe visualization. Research-use-only software: it does not select a solvent,
    validate a laboratory method, calculate a dose or provide administration guidance.'
  documentation:
  - note: README with installation, formula, assumptions, test vectors and research-use-only
      scope.
    type:
    - General
    url: https://github.com/PeptidoMexico/peptidomexico-open-science#readme
  download:
  - note: Source archive for the unit-aware calculation package, demo and reproducible
      fixtures.
    type: Source code
    url: https://github.com/PeptidoMexico/peptidomexico-open-science/archive/refs/heads/main.zip
    version: 0.1.0
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Calculation
      uri: http://edamontology.org/operation_3438
    output: []
  homepage: https://peptidomexico.com.mx/calculadora/
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-12T20:58:08.532610Z'
  license: MIT
  link:
  - note: Source repository, package code, demo, fixtures and reproducible test vectors.
    type:
    - Repository
    url: https://github.com/PeptidoMexico/peptidomexico-open-science
  - note: Public issue tracker for reproducibility questions and bug reports.
    type:
    - Issue tracker
    url: https://github.com/PeptidoMexico/peptidomexico-open-science/issues
  maturity: Emerging
  name: Peptide Reconstitution Calculator
  operatingSystem: []
  otherID: []
  owner: peptidomexico
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Chemistry
    uri: http://edamontology.org/topic_3314
  validated: 0
  version:
  - 0.1.0
- accessibility: null
  additionDate: '2026-08-12T11:51:25.085937Z'
  biotoolsCURIE: biotools:peptide-qc
  biotoolsID: peptide-qc
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: hola@peptidomexico.com.mx
    fundrefid: null
    gridid: null
    name: Péptido México
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    - Maintainer
    - Provider
    url: https://peptidomexico.com.mx/
  description: peptide-qc analyzes a standard peptide sequence and returns residue
    composition, elemental formula, average and monoisotopic mass, approximate charge
    and pI, and Kyte-Doolittle hydropathy. It is a deterministic command-line tool
    and JavaScript library for research software tests and teaching. It does not identify
    unknown samples, certify purity, model unusual chemistry or provide clinical interpretation.
  documentation:
  - note: null
    type:
    - User manual
    - Quick start guide
    url: https://peptidomexico-open-science.readthedocs.io/en/latest/peptide-qc/
  - note: null
    type:
    - Citation instructions
    url: https://github.com/PeptidoMexico/peptidomexico-open-science/blob/main/CITATION.cff
  download:
  - note: null
    type: Software package
    url: https://www.npmjs.com/package/peptide-qc
    version: 0.1.0
  - note: null
    type: Source code
    url: https://github.com/PeptidoMexico/peptidomexico-open-science
    version: 0.1.0
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: npx peptide-qc analyze --sequence ACDEFGHIK --ph 7 --json
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format: []
    note: Outputs deterministic sequence composition and approximate physicochemical
      properties for standard residues.
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output:
    - data:
        term: Molecular property
        uri: http://edamontology.org/data_2087
      format: []
  homepage: https://peptidomexico.com.mx/calculadora/
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2026-08-12T11:51:25.088151Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/PeptidoMexico/peptidomexico-open-science
  - note: null
    type:
    - Issue tracker
    url: https://github.com/PeptidoMexico/peptidomexico-open-science/issues
  maturity: null
  name: peptide-qc
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: peptidomexico
  publication: []
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - 0.1.0
- accessibility: Open access
  additionDate: '2026-08-12T08:49:12.529133Z'
  biotoolsCURIE: biotools:edfcore
  biotoolsID: edfcore
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: sarthaktayal2@gmail.com
    fundrefid: null
    gridid: null
    name: Sarthak Tayal
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://github.com/tayal-sarthak
  description: edfcore is a zero-dependency TypeScript library for reading EDF, EDF+,
    BDF, and BDF+ physiological recordings in browser and Node.js applications. It
    provides programmatic access to biosignal samples, channel metadata, per-channel
    sampling rates, physical units, annotations, and discontinuous recording timelines.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://edfcore.vercel.app/
  download:
  - note: null
    type: Software package
    url: https://www.npmjs.com/package/edfcore
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://edfcore.vercel.app/
  homepage_status: 0
  language:
  - JavaScript
  - TypeScript
  lastUpdate: '2026-08-12T08:52:34.040154Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/tayal-sarthak/edfcore
  - note: null
    type:
    - Service
    url: https://www.npmjs.com/package/edfcore
  maturity: Emerging
  name: edfcore
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: tayal-sarthak
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Neurobiology
    uri: http://edamontology.org/topic_3304
  - term: Informatics
    uri: http://edamontology.org/topic_0605
  - term: Computer science
    uri: http://edamontology.org/topic_3316
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-08-12T08:26:48.264972Z'
  biotoolsCURIE: biotools:mtbc_gene_atlas
  biotoolsID: mtbc_gene_atlas
  collectionID:
  - Mycobacterium tuberculosis complex
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: guyeux@gmail.com
    fundrefid: null
    gridid: null
    name: Christophe Guyeux
    note: FEMTO-ST Institute (CNRS UMR 6174), Universite Marie et Louis Pasteur, Besancon,
      France.
    orcidid: https://orcid.org/0000-0003-0195-4378
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: FEMTO-ST Institute, CNRS UMR 6174
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.femto-st.fr
  description: Continuously updated functional re-annotation of the Mycobacterium
    tuberculosis complex gene set, anchored on the MTBC0 ancestral genome rather than
    on a single strain. Serves one record per gene combining Pfam domains, ESMFold
    structures with Foldseek search, protein language-model features, orthology, curated
    knowledge, protein association networks and intra-species selection inferred from
    145209 sequenced genomes, with dated sources and a graded confidence level for
    every field. Intended as a successor to Mycobrowser, which is no longer maintained.
  documentation:
  - note: Scope, evidence layers, citation and coordinate-system conventions.
    type:
    - General
    url: https://mtbc.gclab.fr/about
  download:
  - note: 'Zenodo concept DOI: resolves to the latest archived release (per-gene records,
      consolidated layers, reproducibility bundle).'
    type: Downloads page
    url: https://doi.org/10.5281/zenodo.20815246
    version: null
  - note: Versioned read-only REST API over the served records.
    type: API specification
    url: https://mtbc.gclab.fr/api/v1
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Gene symbol
        uri: http://edamontology.org/data_1026
      format: []
    - data:
        term: Gene ID
        uri: http://edamontology.org/data_2295
      format: []
    note: Query by H37Rv locus tag (Rv1908c) or gene name (katG); every field carries
      its provenance and confidence.
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output:
    - data:
        term: Gene report
        uri: http://edamontology.org/data_0916
      format: []
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format: []
  - cmd: null
    input: []
    note: Structure-based leads for genes with no domain assignment, and population-scale
      selection signal per gene.
    operation:
    - term: Variant effect prediction
      uri: http://edamontology.org/operation_0331
    - term: Protein fold recognition
      uri: http://edamontology.org/operation_0303
    output: []
  homepage: https://mtbc.gclab.fr
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-08-12T08:26:48.267500Z'
  license: CC-BY-4.0
  link:
  - note: Source code repository, one script per evidence layer (MIT license).
    type:
    - Repository
    url: https://github.com/cguyeux/mtbc-gene-atlas
  maturity: Mature
  name: MTBC Gene Atlas
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: christophe
  publication:
  - doi: 10.5281/zenodo.20815246
    metadata: null
    note: Archived data and code releases (concept DOI). Replace or complement with
      the article DOI once the manuscript is accepted, keeping this entry so the data
      release stays citable on its own.
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web application
  - Database portal
  - Web API
  topic:
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Functional genomics
    uri: http://edamontology.org/topic_0085
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  validated: 0
  version:
  - '1'
- accessibility: null
  additionDate: '2026-08-11T15:36:24.023383Z'
  biotoolsCURIE: biotools:computase
  biotoolsID: computase
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Madhusudan Kulkarni
    note: null
    orcidid: https://orcid.org/0009-0004-0270-9731
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    - Primary contact
    url: https://github.com/madhusudan-kulkarni/computase
  description: Local Python sequence utilities for nucleotide composition, DNA and
    RNA reverse complements, NCBI genetic-code translation, six-frame candidate ORF
    enumeration, and IUPAC motif searches. Computase accepts raw nucleotide strings
    or one FASTA record and returns structured, bounded results with explicit scientific
    conventions.
  documentation:
  - note: null
    type:
    - General
    - Installation instructions
    - Quick start guide
    - Citation instructions
    url: https://github.com/madhusudan-kulkarni/computase#readme
  - note: null
    type:
    - Release notes
    url: https://github.com/madhusudan-kulkarni/computase/blob/main/CHANGELOG.md
  download:
  - note: null
    type: Software package
    url: https://pypi.org/project/computase/
    version: 0.1.1
  - note: null
    type: Source code
    url: https://github.com/madhusudan-kulkarni/computase/archive/refs/tags/v0.1.1.tar.gz
    version: 0.1.1
  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: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Reports composition, ambiguity-preserving GC bounds, and concrete-base GC
      skew.
    operation:
    - term: Sequence composition calculation
      uri: http://edamontology.org/operation_0236
    output:
    - data:
        term: Sequence composition report
        uri: http://edamontology.org/data_1261
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Preserves the DNA or RNA alphabet and supports IUPAC ambiguity symbols.
    operation:
    - term: Reverse complement
      uri: http://edamontology.org/operation_0363
    output:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Translates complete DNA or RNA codons with a selected NCBI genetic-code
      table.
    operation:
    - term: DNA translation
      uri: http://edamontology.org/operation_0371
    output:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Enumerates sequence-defined candidate ORFs in six frames; it does not predict
      genes.
    operation:
    - term: Sequence feature detection
      uri: http://edamontology.org/operation_0253
    output:
    - data:
        term: Sequence features
        uri: http://edamontology.org/data_1255
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence motif
        uri: http://edamontology.org/data_1353
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    note: Finds overlapping IUPAC motif matches on the forward, reverse, or both strands.
    operation:
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    output:
    - data:
        term: Sequence features
        uri: http://edamontology.org/data_1255
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://github.com/madhusudan-kulkarni/computase
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-08-11T15:40:38.679598Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/madhusudan-kulkarni/computase
  - note: null
    type:
    - Issue tracker
    url: https://github.com/madhusudan-kulkarni/computase/issues
  maturity: Emerging
  name: Computase
  operatingSystem:
  - Mac
  - Windows
  - Linux
  otherID: []
  owner: madhusudan-kulkarni
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Nucleic acids
    uri: http://edamontology.org/topic_0077
  validated: 0
  version:
  - 0.1.1
- accessibility: Open access (with restrictions)
  additionDate: '2026-06-30T01:57:07.663868Z'
  biotoolsCURIE: biotools:conspecta
  biotoolsID: conspecta
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit: []
  description: Conspecta is a browser-based research platform that brings microscopy
    image analysis, flow cytometry, molecular biology, sample tracking, and publication-ready
    figures into one connected workspace. It replaces the patchwork of disconnected
    tools most labs assemble, so a lab's data, samples, and results stay linked from
    experiment to figure with full traceability. Built for imaging-heavy and flow-heavy
    biology labs, new PIs, and early-stage biotech. Research-focused, not regulated
    or clinical. Free for you and one collaborator, every workspace included. Paid
    plans open it to the whole lab and add additional storage, AI object detection,
    external integrations via API, and bring-your-own AI assistant integration.
  documentation:
  - note: null
    type:
    - User manual
    url: https://conspecta.bio/guide/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Dimensionality reduction
      uri: http://edamontology.org/operation_3935
    output: []
  homepage: https://conspecta.bio
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-11T02:20:37.652980Z'
  license: Proprietary
  link: []
  maturity: Emerging
  name: Conspecta
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID:
  - type: rrid
    value: RRID:SCR_028623
    version: null
  owner: Conspecta
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Light microscopy
    uri: http://edamontology.org/topic_3385
  - term: Cytometry
    uri: http://edamontology.org/topic_3934
  - term: Molecular biology
    uri: http://edamontology.org/topic_3047
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-07-21T09:36:40.711284Z'
  biotoolsCURIE: biotools:nnunet
  biotoolsID: nnunet
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit:
  - email: r.floca@Dkfz-Heidelberg.de
    fundrefid: null
    gridid: null
    name: DKFZ Heidelberg
    note: Group Lead and Board Member, Medical Image Computing department, DKFZ Heidelberg
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    - Contributor
    - Maintainer
    url: https://www.dkfz.de/
  description: "nnU-Net is a self-configuring method for deep learning-based biomedical\
    \ image segmentation, developed by the Applied Computer Vision Lab (ACVL) of Helmholtz\
    \ Imaging and the Division of Medical Image Computing at the German Cancer Research\
    \ Center (DKFZ). It is designed to automatically adapt to a given dataset, analyzing\
    \ the provided training cases to configure a matching U-Net-based segmentation\
    \ pipeline without requiring expertise from the user.\nThe tool provides pretrained\
    \ models for \nPancreas and Pancreas tumor segmentation, Colon cancer primaries\
    \ segmentation, Abdominal organ segmentation, Liver and liver tumor segmentation,\
    \ Kidney and kidney tumor segmentation, Brain Tumor segmentation and Hippocampus\
    \ (MR data) segmentation"
  documentation:
  - note: GitHub Readme
    type:
    - General
    url: https://github.com/MIC-DKFZ/nnUNet/tree/nnunetv1
  - note: Docker containers and other relevant instructions
    type:
    - User manual
    url: https://github.com/MIC-DKFZ/nnunet-eucaim-docker/
  download: []
  editPermission:
    authors:
    - estegmeier
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: docker run --rm -v /host/dataset/study_001/:/home/eucaim/nnUNet_input -v
      /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-pancreas-tumour
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet pretrained on Task007_Pancreas targeting are pancras and pancreas
      tumor
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-liver-tumour
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet model pretrained on Task029_LiTS targeting are liver and liver
      tumor
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-hippocampus-segmentation
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet pretrained on Task004_Hippocampus MRI data targeting posterior
      and anterior parts of the hippocampus
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-colon-cancer
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet pretrained on Task010_Colon targeting are colon cancer primaries.
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-brain-tumour-pet
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUnet pretrained on Task169_BrainTumorPET targeting are brain tumor
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-abdominal-organ-segmentation
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUNet model pretrained on Task017_AbdominalOrganSegmentation targeting
      thirteen different abdominal organs
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  - cmd: docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output
      --gpus all nnunet-kidney-tumour
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: Run nnUNet model pretrained on Task135_KiTS2021 targeting are kidney, tumor
      and cyst.
    operation:
    - term: Image annotation
      uri: http://edamontology.org/operation_3553
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://github.com/MIC-DKFZ/nnUNet/tree/nnunetv1
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-08-10T14:05:16.089725Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nnunet-hippocampus-segmentation/artifacts-tab
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nnunet-kidney-tumour/artifacts-tab
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nnunet-abdominal-organ-segmentation/artifacts-tab
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nnunet-colon-cancer/artifacts-tab
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nnunet-brain-tumour-pet/artifacts-tab
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nnunet-liver-tumour/artifacts-tab
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nnunet-pancreas-tumour/artifacts-tab
  maturity: Mature
  name: nnUNet
  operatingSystem:
  - Linux
  otherID: []
  owner: ASHISR
  publication:
  - doi: 10.1038/s41592-020-01008-z
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic: []
  validated: 0
  version:
  - '1.0'
- accessibility: null
  additionDate: '2017-03-24T11:59:17Z'
  biotoolsCURIE: biotools:pharmagist
  biotoolsID: pharmagist
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: ppdock@tau.ac.il
    fundrefid: null
    gridid: null
    name: PharmaGist Administrator
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: PharmaGist is a web server for detecting pharmacophores or the spatial
    arrangement of features that enables a molecule to interact with a specific target
    receptor. Users input a set of structures of molecules that bind with the receptor
    for outputs of candidate pharmacophores that can be used in rational drug design.
  documentation:
  - note: null
    type:
    - General
    url: http://bioinfo3d.cs.tau.ac.il/pharma/help.html
  download: []
  editPermission:
    authors:
    - celebrity
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Protein-ligand docking
      uri: http://edamontology.org/operation_0482
    output: []
  homepage: http://bioinfo3d.cs.tau.ac.il/PharmaGist
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-10T10:29:08.045787Z'
  license: null
  link: []
  maturity: null
  name: PharmaGist
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: Sakasi
  publication:
  - doi: 10.1093/nar/gkn187
    metadata:
      abstract: Predicting molecular interactions is a major goal in rational drug
        design. Pharmacophore, which is the spatial arrangement of features that is
        essential for a molecule to interact with a specific target receptor, is an
        important model for achieving this goal. We present a freely available web
        server, named PharmaGist, for pharmacophore detection. The employed method
        is ligand based. Namely, it does not require the structure of the target receptor.
        Instead, the input is a set of structures of drug-like molecules that are
        known to bind to the receptor. The output consists of candidate pharmacophores
        that are computed by multiple flexible alignment of the input ligands. The
        method handles the flexibility of the input ligands explicitly and in deterministic
        manner within the alignment process. PharmaGist is also highly efficient,
        where a typical run with up to 32 drug-like molecules takes seconds to a few
        minutes on a stardard PC. Another important characteristic is the capability
        of detecting pharmacophores shared by different subsets of input molecules.
        This capability is a key advantage when the ligands belong to different binding
        modes or when the input contains outliers. The webserver has a user-friendly
        interface available at http://bioinfo3d.cs.tau.ac.il/PharmaGist.
      authors:
      - name: Schneidman-Duhovny D.
      - name: Dror O.
      - name: Inbar Y.
      - name: Nussinov R.
      - name: Wolfson H.J.
      citationCount: 253
      date: '2008-01-01T00:00:00Z'
      journal: Nucleic acids research
      title: 'PharmaGist: a webserver for ligand-based pharmacophore detection.'
    note: null
    pmcid: PMC2447755
    pmid: '18424800'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Medicinal chemistry
    uri: http://edamontology.org/topic_0209
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Protein folding, stability and design
    uri: http://edamontology.org/topic_0130
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  validated: 1
  version: []
- accessibility: Restricted access
  additionDate: '2026-08-08T08:00:42.930149Z'
  biotoolsCURIE: biotools:slidescope
  biotoolsID: slidescope
  collectionID: []
  confidence_flag: null
  cost: Commercial
  credit: []
  description: Desktop viewer for microscopy and whole slide pathology images on Windows
    and macOS. Opens whole slide scanner formats (Aperio SVS, Hamamatsu NDPI, MIRAX
    MRXS, Leica SCN, Ventana BIF) alongside acquisition formats (Zeiss CZI, Nikon
    ND2, DICOM, TIFF/OME-TIFF) in a single application, providing pyramid navigation
    of gigapixel images, metadata inspection, calibrated measurements, annotations,
    and on-device segmentation and object counting.
  documentation:
  - note: null
    type:
    - General
    url: https://slidescope.science/en/learn/
  download:
  - note: null
    type: Binaries
    url: https://slidescope.science/en/downloads/
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://slidescope.science/
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-08T08:15:24.500868Z'
  license: Proprietary
  link: []
  maturity: Mature
  name: SlideScope
  operatingSystem:
  - Windows
  - Mac
  otherID: []
  owner: ynevet
  publication: []
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Bioimaging
    uri: http://edamontology.org/topic_3383
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version:
  - 1.8.6
- 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: JSON
        uri: http://edamontology.org/format_3464
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: GFF3
        uri: http://edamontology.org/format_1975
      - 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: PNG
        uri: http://edamontology.org/format_3603
      - term: SVG
        uri: http://edamontology.org/format_3604
    - 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: '2026-08-07T07:24:30.787190Z'
  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
  toolType:
  - Command-line tool
  - Web application
  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:
  - v1.12.1
- accessibility: Open access
  additionDate: '2026-08-06T19:50:19.888266Z'
  biotoolsCURIE: biotools:viewpoly
  biotoolsID: viewpoly
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Provides a graphical user interface to integrate, visualize and explore
    results  from linkage and quantitative trait loci analysis, together with genomic
    information for autopolyploid species. The app is meant for interactive use and
    allows users to optionally upload different sources of information, including  gene
    annotation and alignment files, enabling the exploitation and search for candidate
    genes in a genome browser. In its current version, 'VIEWpoly' supports inputs
    from 'MAPpoly',  'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and
    'HIDECAN' packages.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: run_app()
    input: []
    note: Display Shiny Interface
    operation:
    - term: Genetic variation analysis
      uri: http://edamontology.org/operation_3197
    output: []
  homepage: https://github.com/Breeding-Insight/viewpoly
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-06T19:57:22.238627Z'
  license: AGPL-3.0
  link: []
  maturity: Mature
  name: VIEWpoly
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: chtaniguti
  publication: []
  relation: []
  toolType:
  - Bioinformatics portal
  topic:
  - term: Genetics
    uri: http://edamontology.org/topic_3053
  validated: 0
  version:
  - 1.0.3
- accessibility: null
  additionDate: '2026-08-06T19:48:56.915853Z'
  biotoolsCURIE: biotools:onemap
  biotoolsID: onemap
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Analysis of molecular marker data from model and non-model systems.  For
    the later, it allows statistical analysis by simultaneously estimating linkage
    and linkage phases (genetic map construction) according to Wu and colleagues (2002)
    <doi:10.1006/tpbi.2002.1577>. All analysis are based on multi-point  approaches
    using hidden Markov models.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/Cristianetaniguti/onemap
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-06T19:48:56.918390Z'
  license: null
  link: []
  maturity: null
  name: onemap
  operatingSystem: []
  otherID: []
  owner: chtaniguti
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - 3.2.6
- accessibility: null
  additionDate: '2026-08-06T19:47:11.129239Z'
  biotoolsCURIE: biotools:qploidy
  biotoolsID: qploidy
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Provides functions for estimating ploidy levels and detecting aneuploidy
    in individuals using allele intensities or allele count data from high-throughput
    genotyping platforms, including single nucleotide polymorphism (SNP) arrays and
    sequencing-based technologies. Implements method described in Taniguti et al.
    (2025) <doi:10.1002/tpg2.70044> an extended version of the 'PennCNV' signal standardization
    method by Wang et al. (2007) <doi:10.1101/gr.6861907> for higher ploidy  levels.
    Computes B-allele frequencies (BAF), z-scores, and identifies copy number variation
    patterns.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/Cristianetaniguti/Qploidy
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-06T19:47:11.134053Z'
  license: null
  link: []
  maturity: null
  name: Qploidy
  operatingSystem: []
  otherID: []
  owner: chtaniguti
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - 1.5.4
- accessibility: Open access
  additionDate: '2026-08-04T04:51:20.841163Z'
  biotoolsCURIE: biotools:bioszen
  biotoolsID: bioszen
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: bioszenf@gmail.com
    fundrefid: null
    gridid: null
    name: Benjamín Szenfeld
    note: null
    orcidid: https://orcid.org/0009-0003-4702-4149
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    - Primary contact
    url: null
  description: "BIOSZEN is an open-source R package and modular Shiny application\
    \ for reproducible analysis and visualization of experimental biological data\
    \ from Excel or CSV files. It supports statistical testing, control-based normalization,\
    \ replicate-aware quality control, and customizable scientific plots. \nIts microbial\
    \ growth-curve module analyzes optical-density time series and automatically extracts\
    \ quantitative growth parameters, including maximum specific growth rate (µMax),\
    \ doubling time, lag time, maximum optical density (ODmax), time to maximum growth,\
    \ area under the curve (AUC), and initial optical density (OD0). \nResults can\
    \ be exported as processed datasets, statistical summaries, analysis metadata,\
    \ scientific graphics, and editable PowerPoint figures."
  documentation:
  - note: null
    type:
    - General
    - User manual
    - Quick start guide
    url: https://github.com/bioszen/BIOSZEN#readme
  - note: Complete BIOSZEN user manual in English.
    type:
    - User manual
    url: https://github.com/bioszen/BIOSZEN/blob/main/inst/app/www/MANUAL_EN.md
  - note: null
    type:
    - Citation instructions
    url: https://github.com/bioszen/BIOSZEN#citation
  download:
  - note: Archived release files and permanent software record.
    type: Downloads page
    url: https://zenodo.org/records/18217210
    version: 2.1.1
  - note: Installable R package for BIOSZEN 2.1.1, including access to the Shiny application.
    type: Software package
    url: https://bioszen.r-universe.dev/BIOSZEN
    version: 2.1.1
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Statistical analysis, control-based normalization, replicate-aware quality
      control, and customizable visualization of experimental biological data from
      Excel or CSV files.
    operation:
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  - cmd: null
    input: []
    note: Analysis and visualization of microbial optical-density time series, including
      extraction of uMax, max_percap_time, doubling time, lag time, ODmax, max_time,
      AUC, OD0, and related growth parameters.
    operation:
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    - term: Data analysis
      uri: http://edamontology.org/operation_2945
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://github.com/bioszen/BIOSZEN
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-08-06T16:57:58.462807Z'
  license: GPL-3.0
  link:
  - note: Source code, example files, documentation, and development history.
    type:
    - Repository
    url: https://github.com/bioszen/BIOSZEN
  - note: Bug reports, installation problems, and feature suggestions.
    type:
    - Issue tracker
    url: https://github.com/bioszen/BIOSZEN/issues
  - note: Limited online demonstration of the BIOSZEN Shiny application.
    type:
    - Service
    url: https://bioszen-test.share.connect.posit.cloud
  maturity: null
  name: BIOSZEN
  operatingSystem:
  - Windows
  - Mac
  otherID: []
  owner: benjamin7
  publication:
  - doi: 10.5281/zenodo.18217210
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: all versions
  - doi: 10.5281/zenodo.18217522
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: 1.0.0
  relation: []
  toolType:
  - Desktop application
  - Web application
  topic:
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  validated: 0
  version:
  - 2.1.1
- accessibility: Open access (with restrictions)
  additionDate: '2026-08-06T14:21:39.858710Z'
  biotoolsCURIE: biotools:genome_of_slovakia_-_population_variant_browser
  biotoolsID: genome_of_slovakia_-_population_variant_browser
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: marcel.kucharik@uniba.sk
    fundrefid: null
    gridid: null
    name: Marcel Kucharík
    note: null
    orcidid: https://orcid.org/0000-0002-5373-8282
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    - Developer
    url: null
  - email: tomas.szemes@uniba.sk
    fundrefid: null
    gridid: null
    name: Tomáš Szemes
    note: null
    orcidid: https://orcid.org/0000-0002-0900-2534
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: jaroslav.budis@uniba.sk
    fundrefid: null
    gridid: null
    name: Jaroslav Budiš
    note: null
    orcidid: https://orcid.org/0000-0002-8667-6655
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: jan.radvanzsky@uniba.sk
    fundrefid: null
    gridid: null
    name: Ján Radvánszky
    note: null
    orcidid: https://orcid.org/0000-0001-9657-1198
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  - email: ingrid.lojova@uniba.sk
    fundrefid: null
    gridid: null
    name: Ingrid Lojová
    note: null
    orcidid: https://orcid.org/0000-0001-7659-0850
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: null
  description: The Genome of Slovakia Population Browser is an interactive tool for
    exploring genetic variation in the Slovak population, based on whole-genome sequencing
    data from >1000 individuals. It enables users to search genomic variants, examine
    their allele frequencies and distribution within the cohort, and compare population-specific
    observations with international reference datasets. The browser supports research,
    clinical variant interpretation, and the identification of variants that may be
    common, rare, or potentially specific to the Slovak population.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genetic variation analysis
      uri: http://edamontology.org/operation_3197
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Aggregation
      uri: http://edamontology.org/operation_3436
    output: []
  homepage: https://gos.cusp.uniba.sk/
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-06T14:21:55.117601Z'
  license: null
  link: []
  maturity: Mature
  name: Genome of Slovakia - Population variant browser
  operatingSystem:
  - Android
  - Windows
  - iOS
  - Mac
  - Linux
  otherID: []
  owner: marcel
  publication: []
  relation: []
  toolType:
  - Database portal
  - Web application
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Data integration and warehousing
    uri: http://edamontology.org/topic_3366
  - term: Population genetics
    uri: http://edamontology.org/topic_3056
  validated: 0
  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: VCF
        uri: http://edamontology.org/format_3016
      - term: BCF
        uri: http://edamontology.org/format_3020
    note: Multiple data munging operations.
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: BCF
        uri: http://edamontology.org/format_3020
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-08-05T14:16:46.233417Z'
  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:
  - Windows
  - Mac
  - Linux
  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:
  - Command-line tool
  - Suite
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: GWAS study
    uri: http://edamontology.org/topic_3517
  - term: Genotyping experiment
    uri: http://edamontology.org/topic_3516
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - '1.3'
  - 1.3.1
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - 1.10.1
  - 1.10.2
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - '1.17'
  - '1.18'
  - '1.19'
  - '1.20'
  - '1.21'
  - 1.21.1
  - '1.22'
  - 1.22.1
  - '1.23'
  - 1.23.1
  - '1.24'
- 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: SAM
        uri: http://edamontology.org/format_2573
      - term: CRAM
        uri: http://edamontology.org/format_3462
    note: null
    operation:
    - term: Data formatting
      uri: http://edamontology.org/operation_0335
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    - term: Data parsing
      uri: http://edamontology.org/operation_1812
    - term: Data editing
      uri: http://edamontology.org/operation_3096
    - 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: SAM
        uri: http://edamontology.org/format_2573
      - term: CRAM
        uri: http://edamontology.org/format_3462
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-08-05T14:15:50.643407Z'
  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:
  - Windows
  - Mac
  - Linux
  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:
  - Command-line tool
  - Suite
  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - '1.3'
  - 1.3.1
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - 1.16.1
  - '1.17'
  - '1.18'
  - '1.19'
  - 1.19.1
  - 1.19.2
  - '1.20'
  - '1.21'
  - 1.21.1
  - '1.22'
  - 1.22.1
  - 1.22.2
  - '1.23'
  - 1.23.1
  - '1.24'
- 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: BAM
        uri: http://edamontology.org/format_2572
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - 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: BAM
        uri: http://edamontology.org/format_2572
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - 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: '2026-08-05T14:15:15.562380Z'
  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
  - '1.24'
- accessibility: null
  additionDate: '2026-08-05T10:35:48.591622Z'
  biotoolsCURIE: biotools:samen_meten_data_portal
  biotoolsID: samen_meten_data_portal
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: samenmeten@rivm.nl
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: In the dataportal citizen science data and official measurement networks
    share their data. We combine and visualize the data. Citizen scientists can compare
    their data with other sensor data and official data. We provide a correction for
    relative humidity based on the official data and we give an estimate of the quality
    of the data, the “plausibility”.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://samenmeten.rivm.nl/
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-05T10:35:48.593592Z'
  license: null
  link: []
  maturity: null
  name: Samen Meten Data Portal
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-08-05T10:34:25.192259Z'
  biotoolsCURIE: biotools:samen_meten_knowledge_portal
  biotoolsID: samen_meten_knowledge_portal
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: samenmeten@rivm.nl
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: The (Dutch) knowledge portal focuses on the exchange of information.
    Technological developments enable anyone to measure for example air quality or
    noise with increasing accuracy. But when are measurements meaningful? how do you
    perform  measurements in the best possible way? and who else is developing new
    methods? To answer these questions, the knowledge portal offers an overview of
    the materials, sensors and devices that are available for environmental measurements.
    We also provide information about citizen science projects and the sharing and
    use of data.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.samenmeten.nl/
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-05T10:34:25.194296Z'
  license: null
  link: []
  maturity: null
  name: Samen Meten Knowledge Portal
  operatingSystem: []
  otherID: []
  owner: hkucukali
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-08-05T09:18:44.182905Z'
  biotoolsCURIE: biotools:proseqgo
  biotoolsID: proseqgo
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: ProSeqGO predicts Gene Ontology (GO) terms for protein sequences using
    ESM2 embeddings and a trained 1-Dimensional Convolutional Neural Network multi-label
    classifier. By integrating recent advances in protein language models, ProSeqGO
    facilitates large-scale, automated functional annotation directly from sequence
    input, empowering researchers to infer protein function, explore biological mechanisms,
    and accelerate discovery in genomics and proteomics.
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://github.com/BehRoooz/proseqgo/releases
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format: []
    note: Predicts the probability of Gene Ontology (GO) term membership for an input
      protein sequence using ESM2 embeddings and 1D CNN
    operation:
    - term: Protein function prediction
      uri: http://edamontology.org/operation_1777
    output:
    - data:
        term: Ontology concept
        uri: http://edamontology.org/data_2858
      format: []
  homepage: https://proseqgo.com/
  homepage_status: 0
  language:
  - Bash
  - SQL
  - Python
  lastUpdate: '2026-08-05T09:55:10.881591Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/BehRoooz/proseqgo
  maturity: null
  name: ProSeqGO
  operatingSystem: []
  otherID: []
  owner: behrouz
  publication: []
  relation: []
  toolType:
  - Web service
  - Command-line tool
  topic: []
  validated: 0
  version:
  - v1.0.0
- accessibility: Open access
  additionDate: '2026-08-05T08:49:43.567842Z'
  biotoolsCURIE: biotools:pdb2print
  biotoolsID: pdb2print
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: david@haeckes.de
    fundrefid: null
    gridid: null
    name: David Häckes
    note: null
    orcidid: https://orcid.org/0000-0002-2177-5206
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    url: null
  description: Converts Protein Data Bank structures into 3D-printable models. Each
    polymer chain is meshed separately and written as a named object in a single 3MF
    file, so a multi-material printer can assign one filament per chain. Protein chains
    can be rendered as a solvent-excluded surface, a cartoon, or a backbone tube;
    nucleic acids as a tube-and-rung form with the strands of a duplex welded at every
    base pair. Press-fit magnet pockets are optionally placed at chain interfaces,
    so a complex comes apart where its subunits actually meet. All meshes are checked
    for watertightness before export.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/davidtheadmin/pdb2print
  - note: null
    type:
    - Citation instructions
    url: https://github.com/davidtheadmin/pdb2print/blob/main/CITATION.cff
  download:
  - note: null
    type: Source code
    url: https://github.com/davidtheadmin/pdb2print
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  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
      - term: mmCIF
        uri: http://edamontology.org/format_1477
    - data:
        term: Nucleic acid structure
        uri: http://edamontology.org/data_1459
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
      - term: mmCIF
        uri: http://edamontology.org/format_1477
    note: Output is a 3MF file containing one named, separately coloured mesh object
      per polymer chain, ready for a multi-material slicer. 3MF is not yet represented
      in EDAM, so no output format term is given.
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    output: []
  homepage: https://pdb2print.org
  homepage_status: 0
  language:
  - Python
  - JavaScript
  lastUpdate: '2026-08-05T08:49:57.389077Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/davidtheadmin/pdb2print
  - note: null
    type:
    - Issue tracker
    url: https://github.com/davidtheadmin/pdb2print/issues
  maturity: Emerging
  name: pdb2print
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: david7
  publication:
  - doi: 10.5281/zenodo.21599702
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  - Library
  topic:
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  validated: 0
  version:
  - 1.2.0
- accessibility: Open access
  additionDate: '2025-06-30T08:52:48.500476Z'
  biotoolsCURIE: biotools:fair_eva_4_eucaim
  biotoolsID: fair_eva_4_eucaim
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Fernando Aguilar
    note: 'Creator and devloper of the main package FAIR EVA.

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

    This software started to be developed within IFCA-Advanced-Computing receives
    funding from the European Union’s Horizon 2020 research and innovation programme
    under grant agreement No 857647.'
  documentation:
  - note: Documentation for the main package, EUCAIM plugin specific documentation
      not included.
    type:
    - General
    url: https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.md
  - note: Wiki page with FAIR EVA for EUCAIM specific instructions.
    type:
    - User manual
    url: https://gitlabpages.ifca.es/fair-eva-guide-608baa/
  download: []
  editPermission:
    authors:
    - ines.ifca
    - davrodgon
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: fair-eva-cli batch -p eucaim_legacy
    input:
    - data:
        term: Database ID
        uri: http://edamontology.org/data_1048
      format: []
    note: null
    operation:
    - term: Validation
      uri: http://edamontology.org/operation_2428
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output:
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
  homepage: https://github.com/IFCA-Advanced-Computing/FAIR_eva
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-08-05T08:12:34.409744Z'
  license: Apache-2.0
  link:
  - note: Repository for FAIR EVA, without the EUCAIM specific plugin
    type:
    - Repository
    url: https://github.com/IFCA-Advanced-Computing/FAIR_eva
  - note: Repository for FAIR-EVA for eucaim plugin. Currently not public.
    type:
    - Repository
    url: https://gitlab.ifca.es/eucaim/fair_eucaim
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/fair_eucaim/artifacts-tab
  - note: null
    type:
    - Software catalogue
    url: https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/fair_eucaim_web/artifacts-tab
  maturity: Mature
  name: FAIR EVA for EUCAIM
  operatingSystem:
  - Linux
  otherID: []
  owner: davrodgon
  publication:
  - doi: 10.1038/s41597-023-02652-8
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Plug-in
  - Web service
  - Command-line tool
  topic:
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  validated: 0
  version:
  - EUCAIM_plugin_0.3
  - EUCAIM_plugin_0.3.1
  - EUCAIM_plugin_0.4.0
  - EUCAIM_0.4.2
  - v0.6.1
- accessibility: Open access
  additionDate: '2026-08-04T08:45:27.787408Z'
  biotoolsCURIE: biotools:pysmacks
  biotoolsID: pysmacks
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: bastien.molcrette@unibas.ch
    fundrefid: null
    gridid: null
    name: Bastien Molcrette
    note: full-stack developer of PySMACKS
    orcidid: https://orcid.org/0000-0002-5995-5376
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    - Contributor
    url: https://schmid.chemie.unibas.ch/en/
  - email: sonja.schmid@unibas.ch
    fundrefid: null
    gridid: null
    name: Sonja Schmid
    note: Team leader at the University of Basel, in which PySMACKS is developed
    orcidid: https://orcid.org/0000-0002-3710-5602
    rorid: null
    typeEntity: Person
    typeRole:
    - Support
    url: https://schmid.chemie.unibas.ch/en/
  description: Python computational framework for analysis of single-molecule FRET
    data
  documentation:
  - note: null
    type:
    - User manual
    - General
    - Installation instructions
    url: https://molcretb.github.io/PySMACKS
  download:
  - note: null
    type: Software package
    url: https://pypi.org/project/PySMACKS/
    version: 1.0.0b2
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: PySMACKS_GUI
    input: []
    note: Run the GUI of PySMACKS
    operation:
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    output: []
  homepage: https://github.com/molcretb/PySMACKS
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-08-04T08:45:27.789840Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/molcretb/PySMACKS
  - note: null
    type:
    - Issue tracker
    url: https://github.com/molcretb/PySMACKS/issues
  - note: Documentation
    type:
    - Other
    url: https://molcretb.github.io/PySMACKS/
  maturity: Emerging
  name: PySMACKS
  operatingSystem:
  - Linux
  - Windows
  otherID:
  - type: rrid
    value: RRID:SCR_028788
    version: null
  owner: bastien
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Biophysics
    uri: http://edamontology.org/topic_3306
  - term: Bioimaging
    uri: http://edamontology.org/topic_3383
  validated: 0
  version:
  - 1.0.0
- accessibility: null
  additionDate: '2026-08-03T17:25:29.657741Z'
  biotoolsCURIE: biotools:flasktrack
  biotoolsID: flasktrack
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: FlaskTrack is an AI-powered laboratory operations platform combining
    electronic laboratory notebook, laboratory information management, workflow execution,
    inventory management, molecular biology, and compliance capabilities. Researchers
    can create version-controlled protocols and workflows, execute guided procedures,
    track samples and batches, manage reagents, tools, plasmids, DNA sequences, primers,
    and assemblies, and preserve traceability through audit trails, approvals, and
    electronic signatures. AI-assisted features convert research papers, SOPs, and
    laboratory documentation into structured workflows for human review and approval.
    FlaskTrack supports role-based access, data exports, APIs, validation documentation,
    and workflows designed to assist laboratories working toward FDA 21 CFR Part 11
    requirements. It is intended for academic, biotechnology, pharmaceutical, CRO,
    tissue culture, synthetic biology, microbiology, and other life science laboratories.
  documentation:
  - note: User documentation for the day to day usage of the FlaskTrack lab operating
      platform
    type:
    - User manual
    - API documentation
    url: https://docs.flasktrack.com
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://flasktrack.com
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-03T17:28:37.919742Z'
  license: null
  link: []
  maturity: null
  name: FlaskTrack
  operatingSystem: []
  otherID: []
  owner: FlaskTrack
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2023-08-29T11:42:48.137925Z'
  biotoolsCURIE: biotools:biotools-linter
  biotoolsID: biotools-linter
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: 251814@mail.muni.cz
    fundrefid: null
    gridid: null
    name: Filip Rusz
    note: null
    orcidid: https://orcid.org/0009-0002-0046-9725
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: A rule-based checker for the bio.tools database.
  documentation:
  - note: null
    type:
    - General
    url: https://biotools-linter.biodata.ceitec.cz/docs
  - note: null
    type:
    - API documentation
    url: https://biotools-linter.biodata.ceitec.cz/api/documentation/
  download:
  - note: null
    type: Source code
    url: https://github.com/3top1a/biotools-linter
    version: null
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: --lint
    input: []
    note: null
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output:
    - data:
        term: Matrix
        uri: http://edamontology.org/data_2082
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
  homepage: https://biotools-linter.biodata.ceitec.cz/
  homepage_status: 0
  language:
  - Other
  - Python
  lastUpdate: '2026-08-03T08:28:36.844570Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/3top1a/biotools-linter
  - note: null
    type:
    - Technical monitoring
    url: https://biotools-linter.biodata.ceitec.cz/dash/
  maturity: Emerging
  name: biotools-linter
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: FilipRusz
  publication:
  - doi: 10.1093/nar/gkag420
    metadata: null
    note: null
    pmcid: PMC13355044
    pmid: '42363751'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web service
  - Web API
  - Command-line tool
  topic:
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 0
  version: []
- accessibility: null
  additionDate: '2017-02-10T11:35:10Z'
  biotoolsCURIE: biotools:jcat
  biotoolsID: jcat
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: andreas.grote@tu-bs.de
    fundrefid: null
    gridid: null
    name: Andreas Grote
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Tool that can adjust the codon usage of an input sequence to the selected
    organism. Useful for improving the expression of foreign genes in hosts with different
    codon usage.
  documentation:
  - note: null
    type:
    - General
    url: http://www.jcat.de/Introduction.jsp
  download: []
  editPermission:
    authors:
    - yanzixiang
    - lishentao
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Codon usage bias calculation
      uri: http://edamontology.org/operation_2962
    - term: Codon usage table comparison
      uri: http://edamontology.org/operation_0285
    - term: Codon usage analysis
      uri: http://edamontology.org/operation_0286
    - term: Codon usage table generation
      uri: http://edamontology.org/operation_0284
    - term: Codon usage fraction calculation
      uri: http://edamontology.org/operation_2964
    output: []
  homepage: http://www.jcat.de/
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-03T06:08:04.050221Z'
  license: null
  link: []
  maturity: null
  name: JCat
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: bilge
  publication:
  - doi: 10.1093/nar/gki376
    metadata:
      abstract: A novel method for the adaptation of target gene codon usage to most
        sequenced prokaryotes and selected eukaryotic gene expression hosts was developed
        to improve heterologous protein production. In contrast to existing tools,
        JCat (Java Codon Adaptation Tool) does not require the manual definition of
        highly expressed genes and is, therefore, a very rapid and easy method. Further
        options of JCat for codon adaptation include the avoidance of unwanted cleavage
        sites for restriction enzymes and Rho-independent transcription terminators.
        The output of JCat is both graphically and as Codon Adaptation Index (CAI)
        values given for the pasted sequence and the newly adapted sequence. Additionally,
        a list of genes in FASTA-format can be uploaded to calculate CAI values. In
        one example, all genes of the genome of Caenorhabditis elegans were adapted
        to Escherichia coli codon usage and further optimized to avoid commonly used
        restriction sites. In a second example, the Pseudomonas aeruginosa exbD gene
        codon usage was adapted to E.coli codon usage with parallel avoidance of the
        same restriction sites. For both, the degree of introduced changes was documented
        and evaluated. JCat is integrated into the PRODORIC database that hosts all
        required information on the various organisms to fulfill the requested calculations.
        JCat is freely accessible at http://www.prodoric.de/JCat. © 2005 Oxford University
        Press.
      authors:
      - name: Grote A.
      - name: Hiller K.
      - name: Scheer M.
      - name: Munch R.
      - name: Nortemann B.
      - name: Hempel D.C.
      - name: Jahn D.
      citationCount: 1055
      date: '2005-07-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'JCat: A novel tool to adapt codon usage of a target gene to its potential
        expression host'
    note: null
    pmcid: PMC1160137
    pmid: '15980527'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Zoology
    uri: http://edamontology.org/topic_3500
  validated: 1
  version: []
- accessibility: null
  additionDate: '2026-08-03T05:38:45.126785Z'
  biotoolsCURIE: biotools:protein_degrader
  biotoolsID: protein_degrader
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Creative Biogene offers an end-to-end solution for protein degrader
    development, integrating advanced computational screening, experimental validation,
    and optimization strategies to accelerate your drug discovery process.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.creative-biogene.com/
  homepage_status: 0
  language: []
  lastUpdate: '2026-08-03T05:38:45.129190Z'
  license: null
  link: []
  maturity: null
  name: Protein Degrader Discovery and Screening
  operatingSystem: []
  otherID: []
  owner: creativebiogene
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-08-02T21:31:09.264241Z'
  biotoolsCURIE: biotools:edf2csv
  biotoolsID: edf2csv
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: edf2csv is a local command-line tool for converting EDF, EDF+, BDF,
    and BDF+ physiological recordings into CSV and JSON files. It exports signal values,
    channel information, annotations, and recording metadata while preserving original
    sampling rates, physical units, and discontinuities.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output: []
  homepage: https://edf2csv.vercel.app/
  homepage_status: 0
  language:
  - TypeScript
  lastUpdate: '2026-08-02T21:31:09.268586Z'
  license: MIT
  link: []
  maturity: Emerging
  name: edf2csv
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: tayal-sarthak
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Biosciences
    uri: http://edamontology.org/topic_4019
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 0
  version: []
next: ?page=2
previous: null
