count: 32987
list:
- accessibility: null
  additionDate: '2026-04-06T11:38:43.105893Z'
  biotoolsCURIE: biotools:afktotogacor
  biotoolsID: afktotogacor
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: AFKTOTO dikenal sebagai situs gacor berlisensi yang menawarkan pengalaman
    bermain digital dengan sistem yang stabil dan akses yang mudah. Platform ini dirancang
    untuk memberikan kenyamanan bagi pengguna dalam menjelajahi berbagai fitur yang
    tersedia. buruan daftar dan ambil hadiah mu sekarang juga!!
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://kecebanget.info/
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-06T11:51:35.183127Z'
  license: null
  link: []
  maturity: null
  name: afktotogacor
  operatingSystem: []
  otherID: []
  owner: afktoto
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-04-03T22:41:05.770861Z'
  biotoolsCURIE: biotools:Platform.Bemo88
  biotoolsID: Platform.Bemo88
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: BEMO88 adalah platform permainan slot dan taruhan online dengan berbagai
    pilihan game seru, peluang jackpot besar, dan akses mudah kapan saja.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://lit.link/en/platformbemo88
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-03T22:41:05.773818Z'
  license: null
  link: []
  maturity: null
  name: Bemo88Disini
  operatingSystem: []
  otherID: []
  owner: PlatformBemo88
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-04-03T22:17:08.433069Z'
  biotoolsCURIE: biotools:PlatformBemo88
  biotoolsID: PlatformBemo88
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: BEMO88 adalah platform permainan slot dan taruhan online dengan berbagai
    pilihan game seru, peluang jackpot besar, dan akses mudah kapan saja.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://hoo.be/bemo88register
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-03T22:40:23.640934Z'
  license: null
  link: []
  maturity: null
  name: Bemo88Disini
  operatingSystem: []
  otherID: []
  owner: admin
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-04-03T22:06:40.989927Z'
  biotoolsCURIE: biotools:bemo88disini
  biotoolsID: bemo88disini
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Bemo88BEMO88 adalah platform permainan slot dan taruhan online dengan
    berbagai pilihan game seru untuk para semua pemain, peluang jackpot besar dan
    akses mudah kapan saja terpecaya no 1
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://bio.tools/register
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-03T22:09:58.105495Z'
  license: null
  link: []
  maturity: null
  name: Bemo88Disini
  operatingSystem: []
  otherID: []
  owner: admin
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-04-03T22:08:55.204237Z'
  biotoolsCURIE: biotools:rhino88
  biotoolsID: rhino88
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: '🚨 RHINO88 🚨

    Gacor tiap hari, banjir kemenangan! 🔥

    Bonus melimpah & WD super cepat ⚡

    Buruan join sebelum ketinggalan!'
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://hoo.be/rhino88
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-03T22:09:04.464295Z'
  license: null
  link: []
  maturity: null
  name: RHINO88
  operatingSystem: []
  otherID: []
  owner: Rhino88official
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-04-03T21:55:06.076211Z'
  biotoolsCURIE: biotools:inigamatogel
  biotoolsID: inigamatogel
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Selamat Datang dan Bergabung Bersama Link Situs Official GAMATOGEL
    - Akses Mudah Layanan Terpercaya Bermain Game Toto Online Terlengkap Indonesia.
    gamatogel telah di setujui sebagai bandar togel online resmi 4d terpercaya dan
    situs toto togel slot gacor di indonesia bet 100 perak.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://heylink.me/VVIPGAMAMURPHY91?utm_source=ig&utm_medium=social&utm_content=link_in_bio&fbclid=PAZXh0bgNhZW0CMTEAc3J0YwZhcHBfaWQMMjU2MjgxMDQwNTU4AAGni1YUAyefESmk2JRwN2gnat3OLLnG6s7jhSMY2zmryvS6nquiQCOfL4SzCuk_aem_cwxASPkXXnCcSIVAqdGW1A
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-03T21:56:46.470681Z'
  license: null
  link: []
  maturity: null
  name: INIGAMATOGEL
  operatingSystem: []
  otherID: []
  owner: admin
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-04-03T21:54:16.052743Z'
  biotoolsCURIE: biotools:bemo88-premium
  biotoolsID: bemo88-premium
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: BEMO88 hadir sebagai salah satu platform slot online yang menawarkan
    pengalaman bermain yang seru, cepat, dan penuh kejutan. Dengan tampilan modern
    serta pilihan game yang beragam, BEMO88 menjadi pilihan tepat bagi kamu yang ingin
    merasakan sensasi bermain slot dengan peluang kemenangan yang menarik.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://hoo.be/bemo88-premium
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-03T21:55:08.260341Z'
  license: null
  link: []
  maturity: null
  name: Bemo88-Premium
  operatingSystem: []
  otherID: []
  owner: BEMO88PREMIUM
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-04-03T21:51:17.447727Z'
  biotoolsCURIE: biotools:wira99hadir
  biotoolsID: wira99hadir
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: WIRA99 merupakan platform hiburan digital yang menawarkan sensasi bermain
    yang menarik, praktis, dan penuh keuntungan. Dengan teknologi canggih dan pelayanan
    profesional, setiap momen bermain terasa lebih maksimal.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://hoo.be/wra99
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-03T21:51:17.453508Z'
  license: null
  link: []
  maturity: null
  name: WIRA99HADIR
  operatingSystem: []
  otherID: []
  owner: wira99official
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-04-03T21:49:45.645389Z'
  biotoolsCURIE: biotools:badakrhino88
  biotoolsID: badakrhino88
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: '🦏 RHINO88 Official

    Platform terbaik untuk cuan tanpa batas 💎

    Minimal depo ringan, WD cepat tanpa drama ⚡

    Saatnya naik level jadi sultan!'
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://creator.hoo.be/me
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-03T21:49:52.773293Z'
  license: null
  link: []
  maturity: null
  name: BADAKRHINO88
  operatingSystem: []
  otherID: []
  owner: Rhino88
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-04-03T21:41:03.662184Z'
  biotoolsCURIE: biotools:bersamarumahduit
  biotoolsID: bersamarumahduit
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: “Rumahduit Gaming hadir sebagai pusat hiburan online dengan pengalaman
    bermain yang seru, cepat, dan penuh peluang. Didukung sistem modern dan layanan
    terbaik, setiap permainan menjadi lebih menyenangkan dan menguntungkan.”
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://sites.google.com/view/rumaharenagameonline/home
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-03T21:41:13.443424Z'
  license: null
  link: []
  maturity: null
  name: BERSAMARUMAHDUIT
  operatingSystem: []
  otherID: []
  owner: gamerumahduit
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-04-03T21:04:45.928572Z'
  biotoolsCURIE: biotools:groupgamatogel
  biotoolsID: groupgamatogel
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: “Gamatogel adalah platform hiburan online terpercaya yang menghadirkan
    berbagai permainan seru dengan sistem modern, akses cepat, dan pelayanan terbaik.
    Mengutamakan kenyamanan, keamanan, serta pengalaman bermain yang maksimal bagi
    setiap member.”
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://magic.ly/officialgamatogel
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-03T21:09:44.957252Z'
  license: null
  link: []
  maturity: null
  name: groupgamatogel
  operatingSystem: []
  otherID: []
  owner: admin
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: Open access (with restrictions)
  additionDate: '2026-03-28T10:21:22.720256Z'
  biotoolsCURIE: biotools:bionoculars
  biotoolsID: bionoculars
  collectionID: []
  confidence_flag: tool
  cost: Commercial
  credit: []
  description: "Life science search engine providing access to 80M+ articles, from\
    \ PubMed and OpenAlex, through complementary search pathways. \nCombines classical\
    \ keyword search with AI-assisted exploration, including semantic keyword grouping,\
    \ knowledge graph visualization, and AI-driven summarization. All AI-generated\
    \ insights are traceable to source articles. Designed to support transparent,\
    \ user-steered literature exploration for biology and biomedical research. Currently\
    \ in early access."
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://www.bionoculars.com/tutorial
  - note: null
    type:
    - Release notes
    url: https://www.bionoculars.com/blog/early-access
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Literature search
      uri: http://edamontology.org/operation_0305
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output: []
  homepage: https://www.bionoculars.com/
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-03T12:40:30.115237Z'
  license: Proprietary
  link: []
  maturity: Emerging
  name: Bionoculars
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID:
  - type: rrid
    value: RRID:SCR_028217
    version: null
  owner: SyllogistTeam
  publication: []
  relation: []
  toolType:
  - Web application
  - Web service
  topic:
  - term: Biomedical science
    uri: http://edamontology.org/topic_3344
  - term: Medicine
    uri: http://edamontology.org/topic_3303
  - term: Biology
    uri: http://edamontology.org/topic_3070
  - term: Natural language processing
    uri: http://edamontology.org/topic_0218
  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  - term: Literature and language
    uri: http://edamontology.org/topic_3068
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-10-29T08:08:30.731334Z'
  biotoolsCURIE: biotools:lethe_dicom_anonymizer
  biotoolsID: lethe_dicom_anonymizer
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Computational BioMedicine Laboratory, Foundation for Research and Technology
      Hellas (FORTH)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.ics.forth.gr/cbml/?lang=en
  description: "A DICOM Anonymization pipeline in a Docker container. This pipeline\
    \ is designed to anonymize DICOM files according to the EUCAIM standard and includes\
    \ the following steps:\n\nStep 1 (Optional): Perform OCR on DICOM pixel data to\
    \ remove sensitive information (burned-in information).\nStep 2: Deidentify DICOM\
    \ metadata using the RSNA CTP Anonymizer and the EUCAIM anonymization script.\
    \ \nStep 3 (Optional): Deidentify clinical data provided in CSV files so that\
    \ the referenced patient id is anonymized the same way CTP does in Step 2."
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/cbml-forth/lethe_anon_pipeline/blob/main/README.md
  download: []
  editPermission:
    authors:
    - ssfak
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
    note: null
    operation:
    - term: Anonymisation
      uri: http://edamontology.org/operation_3283
    output:
    - data:
        term: Raw image
        uri: http://edamontology.org/data_3424
      format:
      - term: DICOM format
        uri: http://edamontology.org/format_3548
  homepage: https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/lethe-dicom-anonymizer/info-tab
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-02T14:39:36.234580Z'
  license: EUPL-1.2
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/cbml-forth/lethe_anon_pipeline
  maturity: null
  name: Lethe DICOM Anonymizer
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: vkalokyri
  publication:
  - doi: 10.5281/zenodo.19097245
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Desktop application
  - Command-line tool
  topic:
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  - term: Data protection
    uri: http://edamontology.org/topic_4044
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  validated: 0
  version:
  - 0.9.12
  - 0.10.1
- accessibility: Open access
  additionDate: '2026-04-02T11:29:54.022786Z'
  biotoolsCURIE: biotools:pathotypr
  biotoolsID: pathotypr
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Paula Ruiz-Rodriguez
    note: null
    orcidid: https://orcid.org/0000-0003-0727-5974
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Mireia Coscolla
    note: null
    orcidid: https://orcid.org/0000-0003-0752-0538
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: I2SysBio (CSIC - Universitat de València)
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: PathoGenOmics Lab
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole:
    - Provider
    url: null
  description: 'A fast, offline, pathogen-agnostic toolkit for lineage classification
    and marker-driven genotyping from whole-genome sequencing data. Bring your own
    SNP marker panel for any microbial pathogen — pathotypr handles the rest. Ships
    with curated panels for Mycobacterium tuberculosis complex (MTBC): 3,707 lineage-defining
    SNPs and over 102,000 resistance-associated mutations. Works with assembled genomes
    (FASTA) and raw reads (FASTQ). Available as command-line interface and cross-platform
    desktop GUI (Tauri).'
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/PathoGenOmics-Lab/pathotypr/tree/main/docs
  download:
  - note: null
    type: Binaries
    url: https://github.com/PathoGenOmics-Lab/pathotypr/releases
    version: null
  - note: null
    type: Source code
    url: https://github.com/PathoGenOmics-Lab/pathotypr
    version: null
  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: FASTA
        uri: http://edamontology.org/format_1929
    note: train — Build a Random Forest classifier from labeled genomes.
    operation:
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output:
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: predict — Assign lineages to genomes using a pre-trained Random Forest model.
    operation:
    - term: Variant classification
      uri: http://edamontology.org/operation_3225
    output:
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: classify — Call known SNP markers in assembled genomes against a user-defined
      marker panel.
    operation:
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    - term: Variant classification
      uri: http://edamontology.org/operation_3225
    output:
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: split-fastq — Alignment-free genotyping directly from raw reads using k-mer
      matching.
    operation:
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output:
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: match — Find the closest reference genome from a set of references for raw
      reads.
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    output:
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://github.com/PathoGenOmics-Lab/pathotypr
  homepage_status: 0
  language:
  - Rust
  lastUpdate: '2026-04-02T11:29:54.029869Z'
  license: AGPL-3.0
  link: []
  maturity: Mature
  name: pathotypr
  operatingSystem: []
  otherID: []
  owner: paururo
  publication:
  - doi: 10.64898/2026.03.24.714002
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Public health and epidemiology
    uri: http://edamontology.org/topic_3305
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - 1.0.0
- accessibility: Restricted access
  additionDate: '2026-04-01T10:07:48.810565Z'
  biotoolsCURIE: biotools:covid19-dataset
  biotoolsID: covid19-dataset
  collectionID:
  - IMPaCT-Data
  - IMPaCT-ISCIII
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: angel.esteban@ffis.es
    fundrefid: null
    gridid: null
    name: Ángel Esteban
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: COVID-19 sequencing data obtained from hundreds of exomes.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://portfolio-covid19-dataset.imib.es/
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-01T10:07:48.812607Z'
  license: null
  link: []
  maturity: Emerging
  name: COVID19-dataset
  operatingSystem: []
  otherID: []
  owner: angel.esteban
  publication: []
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Omics
    uri: http://edamontology.org/topic_3391
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-04-01T09:54:16.773562Z'
  biotoolsCURIE: biotools:colportal
  biotoolsID: colportal
  collectionID:
  - IMPaCT-Data
  - IMPaCT-ISCIII
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: angel.esteban@ffis.es
    fundrefid: null
    gridid: null
    name: Ángel Esteban
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Platform for the combined analysis of clinical data and various omics
    data applied to a cohort of colorectal cancer patients.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://colportal.imib.es/
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-01T09:55:05.660444Z'
  license: null
  link: []
  maturity: Emerging
  name: COLPORTAL
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: angel.esteban
  publication: []
  relation: []
  toolType:
  - Database portal
  - Web application
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Omics
    uri: http://edamontology.org/topic_3391
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T11:57:34.490366Z'
  biotoolsCURIE: biotools:eddymotion
  biotoolsID: eddymotion
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Eddymotion is an open-source framework for volume-to-volume artifact
    estimation in neuroimaging, inspired by FSL’s eddy. It offers an alternative to
    FSL's eddy without commercial limitations and generalizes beyond eddy current
    distortions of diffusion MRI.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/nipreps/eddymotion
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-01T09:54:26.864866Z'
  license: null
  link: []
  maturity: Legacy
  name: eddymotion
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.31234/OSF.IO/GFNY9
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  validated: 0
  version: []
- accessibility: Restricted access
  additionDate: '2026-04-01T09:47:21.081699Z'
  biotoolsCURIE: biotools:digevar
  biotoolsID: digevar
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: angel.esteban@ffis.es
    fundrefid: null
    gridid: null
    name: Ángel Esteban
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Platform for analyzing genomic study results.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://portfolio-digevar.imib.es/
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-01T09:47:21.084818Z'
  license: null
  link: []
  maturity: Mature
  name: DIGEVAR
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: angel.esteban
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version: []
- accessibility: Restricted access
  additionDate: '2026-04-01T09:43:18.056267Z'
  biotoolsCURIE: biotools:dataraiders
  biotoolsID: dataraiders
  collectionID:
  - IMPaCT-ISCIII
  - IMPaCT-Data
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: angel.esteban@ffis.es
    fundrefid: null
    gridid: null
    name: Ángel Esteban
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Semantic enrichment of biomedical resources.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://portfolio-dataraiders.imib.es/
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-01T09:43:18.058742Z'
  license: null
  link: []
  maturity: Emerging
  name: DataRaiders
  operatingSystem: []
  otherID: []
  owner: angel.esteban
  publication: []
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  - term: Data integration and warehousing
    uri: http://edamontology.org/topic_3366
  - term: Natural language processing
    uri: http://edamontology.org/topic_0218
  validated: 0
  version: []
- accessibility: Restricted access
  additionDate: '2026-04-01T09:38:26.497572Z'
  biotoolsCURIE: biotools:elora
  biotoolsID: elora
  collectionID:
  - IMPaCT-Data
  - IMPaCT-ISCIII
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: angel.esteban@ffis.es
    fundrefid: null
    gridid: null
    name: Ángel Esteban
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Software for managing the lifecycle of biological samples—from collection
    to analysis.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://portfolio-elora.imib.es/
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-01T09:38:26.500307Z'
  license: null
  link: []
  maturity: Mature
  name: ELORA
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: angel.esteban
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Biobank
    uri: http://edamontology.org/topic_3337
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version: []
- accessibility: Restricted access
  additionDate: '2026-04-01T09:33:02.922356Z'
  biotoolsCURIE: biotools:semanticcrf
  biotoolsID: semanticcrf
  collectionID:
  - IMPaCT-ISCIII
  - IMPaCT-Data
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: angel.esteban@ffis.es
    fundrefid: null
    gridid: null
    name: Angel Esteban
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Web-based data collection forms.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://portfolio-semanticcrf.imib.es/
  homepage_status: 0
  language: []
  lastUpdate: '2026-04-01T09:33:02.924971Z'
  license: null
  link: []
  maturity: Emerging
  name: SemanticCRF
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: angel.esteban
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Data integration and warehousing
    uri: http://edamontology.org/topic_3366
  - term: Data governance
    uri: http://edamontology.org/topic_3571
  - term: Data identity and mapping
    uri: http://edamontology.org/topic_3345
  - term: Medical informatics
    uri: http://edamontology.org/topic_3063
  validated: 0
  version: []
- accessibility: Open access (with restrictions)
  additionDate: '2025-04-24T13:00:12.867477Z'
  biotoolsCURIE: biotools:eetl_toolset
  biotoolsID: eetl_toolset
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'Modular toolchain for an extensible and customizable ETL pipeline
    that extracts, transforms, and loads clinical data and medical imaging metadata,
    applying dataset-specific mappings to generate outputs compatible with the EUCAIM
    Common Data Model (CDM). Its design aims to minimize manual data preparation efforts
    and facilitate customization and integration with other components, such as data
    quality assurance tools.

    Containerized, currently supports input datasets in CSV, JSON, XLSX.'
  documentation:
  - note: Tool documentation from EUCAIM WP5 Task Force 2 effort
    type:
    - General
    url: https://docs.google.com/document/d/1QNiqAvVVVsg_3-YuUp1YGNWwakL8yap-
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode:
  - Spain
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data formatting
      uri: http://edamontology.org/operation_0335
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data deposition
      uri: http://edamontology.org/operation_3431
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output: []
  homepage: https://github.com/EUCAIM/etl-toolset/
  homepage_status: 0
  language:
  - Java
  - Python
  lastUpdate: '2026-03-31T09:51:42.443383Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/EUCAIM/etl-toolset/
  maturity: Emerging
  name: EUCAIM ETL toolset
  operatingSystem:
  - Linux
  - Windows
  otherID: []
  owner: victorsp
  publication: []
  relation:
  - biotoolsID: tabular_data_curator
    type: uses
  toolType:
  - Library
  - Workflow
  topic:
  - term: Data identity and mapping
    uri: http://edamontology.org/topic_3345
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  validated: 0
  version:
  - 0.1.1
  - 0.1.2
  - 0.2.1
- accessibility: null
  additionDate: '2026-03-31T09:30:07.983895Z'
  biotoolsCURIE: biotools:lipid-molecular-dynamics-simulation
  biotoolsID: lipid-molecular-dynamics-simulation
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Lipid molecular dynamics simulation is a powerful tool for investigating
    the structure and dynamics of biological membranes and their molecular interactions.
    Leveraging advanced computational biology and extensive experience, CD ComputaBio
    offers comprehensive lipid simulation services, spanning atomic to mesoscopic
    scales, to support drug development, materials science, and basic biology research.
    The simulation bridges the gap between theory and experiment, providing unparalleled
    insights into lipid membranes and their interactions.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/lipid-molecular-dynamics-simulation.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T09:30:07.985832Z'
  license: null
  link: []
  maturity: null
  name: Lipid Molecular Dynamics Simulation
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T09:27:37.603974Z'
  biotoolsCURIE: biotools:protein-molecular-dynamics-simulation
  biotoolsID: protein-molecular-dynamics-simulation
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Protein molecular dynamics simulation employs physical principles to
    computationally track the dynamic behavior of proteins at atomic resolution, revealing
    crucial insights into their conformational changes, interaction mechanisms, and
    functional regulation. CD ComputaBio integrates state-of-the-art algorithms, powerful
    computing resources, and artificial intelligence to provide clients with high-precision
    simulation services, driving advancements in drug design, enzyme engineering,
    and basic biological research.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/protein-molecular-dynamics-simulation.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T09:27:37.606182Z'
  license: null
  link: []
  maturity: null
  name: Protein Molecular Dynamics Simulation
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T09:23:51.094267Z'
  biotoolsCURIE: biotools:molecular-dynamics-simulation-service
  biotoolsID: molecular-dynamics-simulation-service
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Molecular dynamics (MD) is a computer simulation method for analyzing
    the physical movements of atoms and molecules. CD ComputaBio can simulate thousands
    or even millions of atoms and molecules, which are often used to simulate particles
    in liquids, ensembles of solids, and vapors, and can also use different force
    fields and boundary conditions to simulate all atoms, polymers, biological, metallic,
    granular and coarsening systems.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/molecular-dynamics-simulation-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T09:23:51.096714Z'
  license: null
  link: []
  maturity: null
  name: Molecular Dynamics Simulation Service
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T09:22:56.535087Z'
  biotoolsCURIE: biotools:carbohydrate-molecule-modeling-service
  biotoolsID: carbohydrate-molecule-modeling-service
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Carbohydrates, often referred to as glycans, are one of the four fundamental
    biomolecules essential for life, alongside proteins, lipids, and nucleic acids.
    Despite their critical roles in biological systems, carbohydrates remain understudied
    compared to their molecular counterparts. Carbohydrate modeling is crucial for
    understanding structure and function. It employs various methods, including molecular
    dynamics simulations, quantum chemical calculations, geometry optimization, and
    experimental data-driven structure prediction. CD ComputaBio provides its clients
    with high-quality computational modeling services, encompassing a wide range of
    scientific areas, including carbohydrate modeling.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/carbohydrate-molecule-modeling-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T09:22:56.537193Z'
  license: null
  link: []
  maturity: null
  name: Carbohydrate Molecule Modeling Service
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T09:21:45.471695Z'
  biotoolsCURIE: biotools:inhibitor-modeling-service
  biotoolsID: inhibitor-modeling-service
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Inhibitors are central to modern drug discovery, providing therapeutic
    opportunities through the selective blockade of disease-related proteins, enzymes,
    and signaling pathways. The global demand for targeted therapies has grown substantially,
    particularly in oncology, neurodegenerative disorders, and infectious diseases.
    As a premier CRO specializing in computational biotechnologies, CD ComputaBio
    offers comprehensive inhibitor modeling solutions designed to accelerate drug
    discovery initiatives.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/inhibitor-modeling-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T09:21:45.475729Z'
  license: null
  link: []
  maturity: null
  name: Inhibitor Modeling Service
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T09:20:39.418356Z'
  biotoolsCURIE: biotools:metal-complex-modeling-service
  biotoolsID: metal-complex-modeling-service
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Metal complexes are ubiquitous and essential components of biological
    systems, exhibiting a remarkable diversity in their structure and function. Metal
    complex modeling, a core competency at CD ComputaBio, provides a powerful lens
    through which to investigate these intricate molecules, offering invaluable insights
    for understanding fundamental biological processes and for the discovery and design
    of novel therapeutic agents inspired by nature.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/metal-complex-modeling-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T09:20:39.420422Z'
  license: null
  link: []
  maturity: null
  name: Metal Complex Modeling Service
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T09:12:43.035791Z'
  biotoolsCURIE: biotools:natural-product-modeling-service
  biotoolsID: natural-product-modeling-service
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Natural products, with their intricate structural diversity and remarkable
    biological activities, have long been a cornerstone of drug discovery. However,
    the journey from identifying a promising natural product to developing a life-saving
    therapeutic is often complex and resource-intensive. CD ComputaBio offers natural
    product modeling services, leveraging the power of computational chemistry and
    advanced modeling methods to accelerate your research and unlock the full potential
    of nature's pharmacy.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/natural-product-modeling-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T09:12:43.038462Z'
  license: null
  link: []
  maturity: null
  name: Natural Product Modeling Service
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T09:11:48.690318Z'
  biotoolsCURIE: biotools:small-molecule-modeling-services
  biotoolsID: small-molecule-modeling-services
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Small molecule modeling is a fundamental tool in computational biology
    and drug discovery, employing computer simulation to investigate interactions
    between potential drug candidates and biological macromolecules. By predicting
    binding modes, binding affinities, and molecular dynamics behavior, this method
    provides a scientific foundation for drug screening and optimization, facilitating
    a deeper understanding of molecular mechanisms and accelerating new drug development.
    CD ComputaBio provides small molecule modeling services to streamline drug discovery.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/small-molecule-modeling-services.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T09:11:48.692453Z'
  license: null
  link: []
  maturity: null
  name: Small Molecule Modeling Services
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T09:10:52.874541Z'
  biotoolsCURIE: biotools:cyclic-peptide-modeling-services
  biotoolsID: cyclic-peptide-modeling-services
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Cyclic peptides, with their unique structures, offer higher target
    affinity, metabolic stability, and membrane penetration than linear peptides,
    making them a focus in drug development. However, their complex conformations
    and verification challenges hinder their design. CD ComputaBio uses a top computational
    biology platform, combining AI, MD simulations, and QM calculations to offer comprehensive
    cyclic peptide modeling services, from design to evaluation, overcoming traditional
    experimental limitations.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/cyclic-peptide-structure-modeing-services.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T09:10:52.876846Z'
  license: null
  link: []
  maturity: null
  name: Cyclic Peptide Modeling Services
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T09:09:57.244299Z'
  biotoolsCURIE: biotools:signal_peptides_structure_modeling_services
  biotoolsID: signal_peptides_structure_modeling_services
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Signal peptides are short sequences of amino acids, typically between
    15 and 30 residues long, found at the N-terminal of proteins. They serve a critical
    function in directing the transport of proteins throughout the cell. CD ComputaBio
    offers a comprehensive suite of services dedicated to supporting your signal peptides
    discovery initiatives.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/signal-peptides-structure-modeling-services.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T09:09:57.246423Z'
  license: null
  link: []
  maturity: null
  name: Signal Peptides Structure Modeling Services
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T09:09:03.489615Z'
  biotoolsCURIE: biotools:peptide_modeling_services
  biotoolsID: peptide_modeling_services
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Peptides are made up of amino acid molecules, which are the "building
    blocks" of proteins. Peptides are short proteins, approximately 2-100 amino acids
    in length. CD ComputaBio offers a range of peptide modeling services to assist
    researchers and pharmaceutical companies in peptide drug discovery and development.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/peptide-modeling-services.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T09:09:03.492174Z'
  license: null
  link: []
  maturity: null
  name: Peptide Modeling Services
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T09:08:18.826777Z'
  biotoolsCURIE: biotools:antibody_modeling_services
  biotoolsID: antibody_modeling_services
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Antibodies are large, Y-shaped glycoproteins produced by B cells as
    the primary immune defense. CD ComputaBio is a professional service provider for
    the antibody modeling industry. With rich experience, our expert team has participated
    in some university scientific research projects and mastered a variety of advanced
    antibody modeling technologies.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/antibody-modeling-services.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T09:08:18.829908Z'
  license: null
  link: []
  maturity: null
  name: Antibody Modeling Services
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T09:07:08.089200Z'
  biotoolsCURIE: biotools:protein_modeling_service
  biotoolsID: protein_modeling_service
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: At CD ComputaBio, we have a proven track record of meeting our client's
    needs in protein modeling. One of our core competencies is our expertise in protein
    modeling services. Protein modeling is especially valuable for understanding the
    function of proteins, designing drugs, and studying the mechanisms of diseases.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/protein-modeling-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T09:07:08.091083Z'
  license: null
  link: []
  maturity: null
  name: Protein Modeling Service
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T09:06:06.499130Z'
  biotoolsCURIE: biotools:virtual_cell_modeling_service
  biotoolsID: virtual_cell_modeling_service
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Virtual cell modeling represents an emerging frontier at the intersection
    of artificial intelligence and biology, aiming to predict quantities such as responses
    to diverse perturbations quantitatively. However, autonomously building computational
    models for virtual cells is challenging due to the complexity of biological systems,
    the heterogeneity of data modalities, and the need for domain-specific expertise
    across multiple disciplines.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/virtual-cell-modeling-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T09:06:06.500955Z'
  license: null
  link: []
  maturity: null
  name: Virtual Cell Modeling Service
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T08:59:57.575542Z'
  biotoolsCURIE: biotools:antibody-antigen_docking_service
  biotoolsID: antibody-antigen_docking_service
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: The Antibody-Antigen Docking Service is a crucial tool in modern biomedical
    research. It allows for in-depth exploration of how antibodies bind to their specific
    antigens, which is fundamental for understanding immune responses and developing
    new treatments. CD ComputaBio's docking service is designed to aid researchers
    in their quest to develop more efficient and effective therapeutics.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/antibody-antigen-docking-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T08:59:57.577677Z'
  license: null
  link: []
  maturity: null
  name: Antibody-Antigen Docking Service
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T08:58:54.665985Z'
  biotoolsCURIE: biotools:protein-rna_docking_service
  biotoolsID: protein-rna_docking_service
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: The interactions between proteins and RNA molecules play a vital role
    in a wide array of biological processes. These interactions are implicated in
    gene expression regulation, RNA splicing, translation initiation, and many other
    essential cellular functions. At CD ComputaBio, we offer a sophisticated Protein-RNA
    Docking Service that aims to provide in-depth insights into these complex molecular
    associations.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/protein-rna-docking-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T08:58:54.667970Z'
  license: null
  link: []
  maturity: null
  name: Protein-RNA Docking Service
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T08:58:00.489874Z'
  biotoolsCURIE: biotools:protein-dna_docking_service
  biotoolsID: protein-dna_docking_service
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: With a professional background in computational biology, CD ComputaBio
    offers cutting-edge solutions for protein-DNA docking research. Our protein-DNA
    docking service enables researchers to explore the intricate interactions between
    proteins and DNA. Leveraging our expertise and sophisticated computational tools,
    we provide a comprehensive, customized approach to meet the unique needs of our
    clients.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/protein-dna-docking-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T08:58:00.492003Z'
  license: null
  link: []
  maturity: null
  name: Protein-DNA Docking Service
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T08:57:14.234038Z'
  biotoolsCURIE: biotools:protein-peptide_docking_service
  biotoolsID: protein-peptide_docking_service
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: CD ComputaBio offers specialized protein-peptide docking services that
    are designed to facilitate your research and development projects. Our deep expertise
    in computational biology, combined with advanced docking techniques, enables us
    to deliver insights that can drive innovations in various fields, including drug
    discovery, vaccine development, and therapeutic interventions.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/protein-peptide-docking-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T08:57:14.235856Z'
  license: null
  link: []
  maturity: null
  name: Protein-Peptide Docking Service
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T08:55:11.241433Z'
  biotoolsCURIE: biotools:protein-protein_docking_service
  biotoolsID: protein-protein_docking_service
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: 'Protein-protein interactions (PPIs) govern virtually every biological
    process, from signal transduction and immune recognition to enzymatic regulation
    and multi-protein complex assembly. Understanding how two proteins associate at
    the structural level is essential for mechanistic studies, antibody design, protein
    engineering, and therapeutic target validation. However, experimental determination
    of complex structures by X-ray crystallography, cryo-EM, or NMR remains time-consuming
    and resource-intensive.


    CD ComputaBio''s Protein-Protein Docking Service provides a robust and scientifically
    rigorous computational solution to predict biologically relevant protein complex
    structures with high confidence. By integrating advanced conformational sampling,
    multi-criteria scoring, structural refinement, and interface hotspot analysis,
    we deliver ranked docking models that are not only structurally plausible but
    also experimentally actionable.'
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/protein-protein-docking-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T08:55:11.244310Z'
  license: null
  link: []
  maturity: null
  name: Protein-Protein Docking Service
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-03-31T08:54:00.374906Z'
  biotoolsCURIE: biotools:molecular_docking_services
  biotoolsID: molecular_docking_services
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: CD ComputaBio provides a comprehensive molecular docking and structure-based
    drug design (SBDD) platform, offering high-accuracy simulations across small molecules,
    proteins, peptides, antibodies, RNA, and nucleic acids. Powered by proprietary
    AI engines—including BioAI-Dock, TurboAI-Screen, FlexAI-Fit, and FragAI-Grow—the
    service supports virtual screening, binding mode prediction, covalent docking,
    PPI modeling, peptide flexibility handling, and fragment-based drug design. Applications
    span small-molecule discovery, enzyme engineering, antibody design, RNA therapeutics,
    protein engineering, and macrocycle optimization. Through a streamlined workflow
    from consultation to data delivery, the platform enables researchers and biotech
    teams to accelerate hit identification, lead optimization, and complex biological
    interface analysis with speed, precision, and scientific rigor.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://www.computabio.com/molecular-docking-service.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-31T08:54:00.377679Z'
  license: null
  link: []
  maturity: null
  name: Molecular Docking Services
  operatingSystem: []
  otherID: []
  owner: CDComputaBio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2017-02-10T14:14:50Z'
  biotoolsCURIE: biotools:pal2nal
  biotoolsID: pal2nal
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: mikita@bioreg.kyushu-u.ac.jp
    fundrefid: null
    gridid: null
    name: Mikita Suyama
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: PAL2NAL converts a multiple sequence alignment of proteins and the
    corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks)
    and non-synonymous (Ka) substitution rates can be calculated.
  documentation: []
  download: []
  editPermission:
    authors:
    - Antonio_GS
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: DNA substitution modelling
      uri: http://edamontology.org/operation_0550
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    - term: Protein sequence analysis
      uri: http://edamontology.org/operation_2479
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output: []
  homepage: http://www.bork.embl.de/pal2nal/
  homepage_status: 0
  language:
  - Perl
  lastUpdate: '2026-03-30T20:15:48.108734Z'
  license: null
  link: []
  maturity: null
  name: PAL2NAL
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ELIXIR-EE
  publication:
  - doi: 10.1093/nar/gkl315
    metadata: null
    note: null
    pmcid: PMC1538804
    pmid: '16845082'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  - term: DNA
    uri: http://edamontology.org/topic_0654
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  validated: 1
  version: []
- accessibility: null
  additionDate: '2026-03-30T14:45:56.214720Z'
  biotoolsCURIE: biotools:search_ontologies
  biotoolsID: search_ontologies
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Search Ontologies is a tool for the automated extraction of ontology
    ID codes from web-based ontology repositories using metadata values. It supports
    the mapping of metadata fields from a structured Excel template to standardized
    ontology terms by using the BioPortal Search API.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/cim-unito/SearchOntologies
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-30T14:45:56.217379Z'
  license: null
  link: []
  maturity: null
  name: Search Ontologies
  operatingSystem: []
  otherID: []
  owner: francesco.gammaraccio
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-03-30T13:34:06.425220Z'
  biotoolsCURIE: biotools:autoencoder_rf_tabpfn_for_cross-cancer_metabolomics
  biotoolsID: autoencoder_rf_tabpfn_for_cross-cancer_metabolomics
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: haunss@informatik.uni-freiburg.de
    fundrefid: null
    gridid: null
    name: Sven Hauns
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: Accurate and rapid disease diagnosis, particularly in prostate cancer
    (PC) and breast cancer (BC), is critical for early intervention and improved patient
    outcomes. Metabolomic signatures represent a robust molecular framework for elucidating
    cancer-associated biochemical reprogramming. The use of Artificial Intelligence
    (AI) in biology in recent years has become widespread and promising. This study
    introduces a novel predictive method that integrates an Autoencoder, random forest
    based feature selection and Tabular Prior-data Fitted Network (TabPFN) to achieve
    high diagnostic accuracy from metabolomics data of prostate and breast cancer
    patients.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/SvenHauns/metabolomic_classifier.git
  download:
  - note: null
    type: Source code
    url: https://github.com/SvenHauns/metabolomic_classifier.git
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: 'python main.py --dataset {dataset_to_be_used} --setting {ae or rf} --size
      {size}


      python main.py --test_dataset {./data/toy_predict.csv} --dataset {./data/toy_train.csv}
      --predict True --setting {ae or rf} --size {size}


      see Readme for detailed instructions'
    input: []
    note: null
    operation:
    - term: Classification
      uri: http://edamontology.org/operation_2990
    output: []
  homepage: https://github.com/SvenHauns/metabolomic_classifier.git
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-03-30T13:34:06.427392Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/SvenHauns/metabolomic_classifier.git
  maturity: Emerging
  name: Autoencoder_RF_TabPFN for Cross-Cancer Metabolomics
  operatingSystem: []
  otherID: []
  owner: haunssv
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Human biology
    uri: http://edamontology.org/topic_2815
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version: []
- accessibility: null
  additionDate: '2021-03-19T08:57:45Z'
  biotoolsCURIE: biotools:bc-genexminer
  biotoolsID: bc-genexminer
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: pascal.jezequel@ico.unicancer.fr
    fundrefid: null
    gridid: null
    name: Pascal Jézéquel
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Breast cancer gene-expression miner (bc-GenExMiner) 4.5 is a mining
    module computes breast cancer differential gene expression analyses. It is a statistical
    mining tool of published annotated breast cancer transcriptomic data (DNA microarrays
    and RNA-seq). It offers the possibility to explore gene-expression of genes of
    interest in breast cancer.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Differential gene expression profiling
      uri: http://edamontology.org/operation_3223
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Expression correlation analysis
      uri: http://edamontology.org/operation_3463
    - term: Heat map generation
      uri: http://edamontology.org/operation_0531
    output: []
  homepage: http://bcgenex.ico.unicancer.fr
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-30T09:22:12.633153Z'
  license: null
  link: []
  maturity: null
  name: bc-GenExMiner
  operatingSystem: []
  otherID: []
  owner: w.gouraud
  publication:
  - doi: 10.1093/DATABASE/BAAB007
    metadata:
      abstract: '© 2021 The Author(s) 2021. Published by Oxford University Press.''Breast
        cancer gene-expression miner'' (bc-GenExMiner) is a breast cancer-associated
        web portal (http://bcgenex.ico.unicancer.fr). Here, we describe the development
        of a new statistical mining module, which permits several differential gene
        expression analyses, i.e. ''Expression'' module. Sixty-two breast cancer cohorts
        and one healthy breast cohort with their corresponding clinicopathological
        information are included in bc-GenExMiner v4.5 version. Analyses are based
        on microarray or RNAseq transcriptomic data. Thirty-nine differential gene
        expression analyses, grouped into 13 categories, according to clinicopathological
        and molecular characteristics (''Targeted'' and ''Exhaustive'') and gene expression
        (''Customized''), have been developed. Output results are visualized in four
        forms of plots. This new statistical mining module offers, among other things,
        the possibility to compare gene expression in healthy (cancer-free), tumour-adjacent
        and tumour tissues at once and in three triple-negative breast cancer subtypes
        (i.e. C1: molecular apocrine tumours; C2: basal-like tumours infiltrated by
        immune suppressive cells and C3: basal-like tumours triggering an ineffective
        immune response). Several validation tests showed that bioinformatics process
        did not alter the pathobiological information contained in the source data.
        In this work, we developed and demonstrated that bc-GenExMiner ''Expression''
        module can be used for exploratory and validation purposes. Database URL:
        http://bcgenex.ico.unicancer.fr'
      authors:
      - name: Jezequel P.
      - name: Gouraud W.
      - name: Ben Azzouz F.
      - name: Guerin-Charbonnel C.
      - name: Juin P.P.
      - name: Lasla H.
      - name: Campone M.
      citationCount: 6
      date: '2021-01-01T00:00:00Z'
      journal: Database
      title: 'Bc-GenExMiner 4.5: New mining module computes breast cancer differential
        gene expression analyses'
    note: null
    pmcid: PMC7904047
    pmid: '33599248'
    type: []
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Microarray experiment
    uri: http://edamontology.org/topic_3518
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 0
  version: []
- accessibility: null
  additionDate: '2017-08-20T17:18:10Z'
  biotoolsCURIE: biotools:provean
  biotoolsID: provean
  collectionID:
  - Animal and Crop Genomics
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://provean.jcvi.org/contact.php
  description: A software tool which predicts whether an amino acid substitution or
    indel has an impact on the biological function of a protein.
  documentation:
  - note: null
    type:
    - General
    url: http://provean.jcvi.org/index.php
  download: []
  editPermission:
    authors:
    - animalandcropgenomics
    - ahmad_raza
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence annotation
      uri: http://edamontology.org/operation_0361
    - term: Genetic variation analysis
      uri: http://edamontology.org/operation_3197
    output: []
  homepage: http://provean.jcvi.org/index.php
  homepage_status: 0
  language:
  - Shell
  lastUpdate: '2026-03-30T09:22:11.430833Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: PROVEAN
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ahmad_raza
  publication:
  - doi: 10.1371/journal.pone.0046688
    metadata:
      abstract: As next-generation sequencing projects generate massive genome-wide
        sequence variation data, bioinformatics tools are being developed to provide
        computational predictions on the functional effects of sequence variations
        and narrow down the search of casual variants for disease phenotypes. Different
        classes of sequence variations at the nucleotide level are involved in human
        diseases, including substitutions, insertions, deletions, frameshifts, and
        non-sense mutations. Frameshifts and non-sense mutations are likely to cause
        a negative effect on protein function. Existing prediction tools primarily
        focus on studying the deleterious effects of single amino acid substitutions
        through examining amino acid conservation at the position of interest among
        related sequences, an approach that is not directly applicable to insertions
        or deletions. Here, we introduce a versatile alignment-based score as a new
        metric to predict the damaging effects of variations not limited to single
        amino acid substitutions but also in-frame insertions, deletions, and multiple
        amino acid substitutions. This alignment-based score measures the change in
        sequence similarity of a query sequence to a protein sequence homolog before
        and after the introduction of an amino acid variation to the query sequence.
        Our results showed that the scoring scheme performs well in separating disease-associated
        variants (n = 21,662) from common polymorphisms (n = 37,022) for UniProt human
        protein variations, and also in separating deleterious variants (n = 15,179)
        from neutral variants (n = 17,891) for UniProt non-human protein variations.
        In our approach, the area under the receiver operating characteristic curve
        (AUC) for the human and non-human protein variation datasets is ~0.85. We
        also observed that the alignment-based score correlates with the deleteriousness
        of a sequence variation. In summary, we have developed a new algorithm, PROVEAN
        (Protein Variation Effect Analyzer), which provides a generalized approach
        to predict the functional effects of protein sequence variations including
        single or multiple amino acid substitutions, and in-frame insertions and deletions.
        The PROVEAN tool is available online at http://provean.jcvi.org. © 2012 Choi
        et al.
      authors:
      - name: Choi Y.
      - name: Sims G.E.
      - name: Murphy S.
      - name: Miller J.R.
      - name: Chan A.P.
      citationCount: 2199
      date: '2012-10-08T00:00:00Z'
      journal: PLoS ONE
      title: Predicting the Functional Effect of Amino Acid Substitutions and Indels
    note: null
    pmcid: PMC3466303
    pmid: '23056405'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Protein variants
    uri: http://edamontology.org/topic_3120
  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-10-03T14:08:36Z'
  biotoolsCURIE: biotools:gromacs
  biotoolsID: gromacs
  collectionID:
  - BioExcel
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: GROMACS support
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.gromacs.org/support/mailing_lists
  description: Versatile package to perform molecular dynamics, i.e. simulate the
    Newtonian equations of motion for systems with hundreds to millions of particles.
    It is primarily designed for biochemical molecules like proteins, lipids and nucleic
    acids that have a lot of complicated bonded interactions, but since it is extremely
    fast at calculating the nonbonded interactions (that usually dominate simulations)
    many groups are also using it for research on non-biological systems, e.g. polymers.
  documentation:
  - note: null
    type:
    - General
    url: http://www.gromacs.org/Documentation
  download:
  - note: null
    type: Software package
    url: http://www.gromacs.org/Downloads
    version: null
  editPermission:
    authors:
    - adam.hospital@irbbarcelona.org
    - gelpi@ub.edu
    - sergitobara
    - n.m.palmblad@lumc.nl
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Structure
        uri: http://edamontology.org/data_0883
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: null
    operation:
    - term: Molecular dynamics
      uri: http://edamontology.org/operation_2476
    output: []
  homepage: http://www.gromacs.org/
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-30T09:22:03.645037Z'
  license: LGPL-2.1
  link: []
  maturity: Mature
  name: Gromacs
  operatingSystem:
  - Linux
  otherID: []
  owner: jdianes
  publication:
  - doi: 10.1016/j.softx.2015.06.001
    metadata:
      abstract: GROMACS is one of the most widely used open-source and free software
        codes in chemistry, used primarily for dynamical simulations of biomolecules.
        It provides a rich set of calculation types, preparation and analysis tools.
        Several advanced techniques for free-energy calculations are supported. In
        version 5, it reaches new performance heights, through several new and enhanced
        parallelization algorithms. These work on every level; SIMD registers inside
        cores, multithreading, heterogeneous CPU-GPU acceleration, state-of-the-art
        3D domain decomposition, and ensemble-level parallelization through built-in
        replica exchange and the separate Copernicus framework. The latest best-in-class
        compressed trajectory storage format is supported.
      authors:
      - name: Abraham M.J.
      - name: Murtola T.
      - name: Schulz R.
      - name: Pall S.
      - name: Smith J.C.
      - name: Hess B.
      - name: Lindah E.
      citationCount: 15418
      date: '2015-01-01T00:00:00Z'
      journal: SoftwareX
      title: 'Gromacs: High performance molecular simulations through multi-level
        parallelism from laptops to supercomputers'
    note: null
    pmcid: null
    pmid: null
    type:
    - Benchmarking study
    version: null
  - doi: 10.1002/jcc.20291
    metadata:
      abstract: This article describes the software suite GROMACS (Groningen MAchine
        for Chemical Simulation) that was developed at the University of Groningen,
        The Netherlands, in the early 1990s. The software, written in ANSI C, originates
        from a parallel hardware project, and is well suited for parallelization on
        processor clusters. By careful optimization of neighbor searching and of inner
        loop performance, GROMACS is a very fast program for molecular dynamics simulation.
        It does not have a force field of its own, but is compatible with GROMOS,
        OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable
        shell models and flexible constraints. The program is versatile, as force
        routines can be added by the user, tabulated functions can be specified, and
        analyses can be easily customized. Nonequilibrium dynamics and free energy
        determinations are incorporated. Interfaces with popular quantum-chemical
        packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations.
        The package includes about 100 utility and analysis programs. GROMACS is in
        the public domain and distributed (with source code and documentation) under
        the GNU General Public License. It is maintained by a group of developers
        from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck
        Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.
        © 2005 Wiley Periodicals, Inc.
      authors:
      - name: Van Der Spoel D.
      - name: Lindahl E.
      - name: Hess B.
      - name: Groenhof G.
      - name: Mark A.E.
      - name: Berendsen H.J.C.
      citationCount: 14137
      date: '2005-12-01T00:00:00Z'
      journal: Journal of Computational Chemistry
      title: 'GROMACS: Fast, flexible, and free'
    note: null
    pmcid: null
    pmid: '16211538'
    type:
    - Benchmarking study
    version: null
  - doi: 10.1063/5.0018516
    metadata:
      abstract: The introduction of accelerator devices such as graphics processing
        units (GPUs) has had profound impact on molecular dynamics simulations and
        has enabled order-of-magnitude performance advances using commodity hardware.
        To fully reap these benefits, it has been necessary to reformulate some of
        the most fundamental algorithms, including the Verlet list, pair searching,
        and cutoffs. Here, we present the heterogeneous parallelization and acceleration
        design of molecular dynamics implemented in the GROMACS codebase over the
        last decade. The setup involves a general cluster-based approach to pair lists
        and non-bonded pair interactions that utilizes both GPU and central processing
        unit (CPU) single instruction, multiple data acceleration efficiently, including
        the ability to load-balance tasks between CPUs and GPUs. The algorithm work
        efficiency is tuned for each type of hardware, and to use accelerators more
        efficiently, we introduce dual pair lists with rolling pruning updates. Combined
        with new direct GPU-GPU communication and GPU integration, this enables excellent
        performance from single GPU simulations through strong scaling across multiple
        GPUs and efficient multi-node parallelization.
      authors:
      - name: Pall S.
      - name: Zhmurov A.
      - name: Bauer P.
      - name: Abraham M.
      - name: Lundborg M.
      - name: Gray A.
      - name: Hess B.
      - name: Lindahl E.
      citationCount: 349
      date: '2020-10-07T00:00:00Z'
      journal: Journal of Chemical Physics
      title: Heterogeneous parallelization and acceleration of molecular dynamics
        simulations in GROMACS
    note: null
    pmcid: null
    pmid: '33032406'
    type:
    - Benchmarking study
    version: null
  - doi: 10.1007/978-3-319-15976-8_1
    metadata:
      abstract: GROMACS is a widely used package for biomolecular simulation, and
        over the last two decades it has evolved from small-scale efficiency to advanced
        heterogeneous acceleration and multi-level parallelism targeting some of the
        largest supercomputers in the world. Here, we describe some of the ways we
        have been able to realize this through the use of parallelization on all levels,
        combined with a constant focus on absolute performance. Release 4.6 of GROMACS
        uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration,
        and both OpenMP and MPI parallelism within and between nodes, respectively.
        The recent work on acceleration made it necessary to revisit the fundamental
        algorithms of molecular simulation, including the concept of neighborsearching,
        and we discuss the present and future challenges we see for exascale simulation
        - in particular a very fine-grained task parallelism. We also discuss the
        software management, code peer review and continuous integration testing required
        for a project of this complexity.
      authors:
      - name: Pall S.
      - name: Abraham M.J.
      - name: Kutzner C.
      - name: Hess B.
      - name: Lindahl E.
      citationCount: 752
      date: '2015-01-01T00:00:00Z'
      journal: Lecture Notes in Computer Science (including subseries Lecture Notes
        in Artificial Intelligence and Lecture Notes in Bioinformatics)
      title: Tackling exascale software challenges in molecular dynamics simulations
        with GROMACS
    note: null
    pmcid: null
    pmid: null
    type:
    - Benchmarking study
    version: null
  - doi: 10.1093/bioinformatics/btt055
    metadata:
      abstract: 'Motivation: Molecular simulation has historically been a low-throughput
        technique, but faster computers and increasing amounts of genomic and structural
        data are changing this by enabling large-scale automated simulation of, for
        instance, many conformers or mutants of biomolecules with or without a range
        of ligands. At the same time, advances in performance and scaling now make
        it possible to model complex biomolecular interaction and function in a manner
        directly testable by experiment. These applications share a need for fast
        and efficient software that can be deployed on massive scale in clusters,
        web servers, distributed computing or cloud resources.Results: Here, we present
        a range of new simulation algorithms and features developed during the past
        4 years, leading up to the GROMACS 4.5 software package. The software now
        automatically handles wide classes of biomolecules, such as proteins, nucleic
        acids and lipids, and comes with all commonly used force fields for these
        molecules built-in. GROMACS supports several implicit solvent models, as well
        as new free-energy algorithms, and the software now uses multithreading for
        efficient parallelization even on low-end systems, including windows-based
        workstations. Together with hand-tuned assembly kernels and state-of-the-art
        parallelization, this provides extremely high performance and cost efficiency
        for high-throughput as well as massively parallel simulations. © 2013 The
        Author. Published by Oxford University Press. All rights reserved.'
      authors:
      - name: Pronk S.
      - name: Pall S.
      - name: Schulz R.
      - name: Larsson P.
      - name: Bjelkmar P.
      - name: Apostolov R.
      - name: Shirts M.R.
      - name: Smith J.C.
      - name: Kasson P.M.
      - name: Van Der Spoel D.
      - name: Hess B.
      - name: Lindahl E.
      citationCount: 5927
      date: '2013-04-01T00:00:00Z'
      journal: Bioinformatics
      title: 'GROMACS 4.5: A high-throughput and highly parallel open source molecular
        simulation toolkit'
    note: null
    pmcid: PMC3605599
    pmid: '23407358'
    type: []
    version: null
  - doi: 10.1021/ct700301q
    metadata:
      abstract: Molecular simulation is an extremely useful, but computationally very
        expensive tool for studies of chemical and biomolecular systems. Here, we
        present a new implementation of our molecular simulation toolkit GROMACS which
        now both achieves extremely high performance on single processors from algorithmic
        optimizations and hand-coded routines and simultaneously scales very well
        on parallel machines. The code encompasses a minimal-communication domain
        decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel
        constraint solver, and efficient virtual site algorithms that allow removal
        of hydrogen atom degrees of freedom to enable integration time steps up to
        5 fs for atomistic simulations also in parallel. To improve the scaling properties
        of the common particle mesh Ewald electrostatics algorithms, we have in addition
        used a Multiple-Program, Multiple-Data approach, with separate node domains
        responsible for direct and reciprocal space interactions. Not only does this
        combination of algorithms enable extremely long simulations of large systems
        but also it provides that simulation performance on quite modest numbers of
        standard cluster nodes. © 2008 American Chemical Society.
      authors:
      - name: Hess B.
      - name: Kutzner C.
      - name: Van Der Spoel D.
      - name: Lindahl E.
      citationCount: 13627
      date: '2008-03-01T00:00:00Z'
      journal: Journal of Chemical Theory and Computation
      title: 'GRGMACS 4: Algorithms for highly efficient, load-balanced, and scalable
        molecular simulation'
    note: null
    pmcid: null
    pmid: '26620784'
    type:
    - Benchmarking study
    version: null
  - doi: 10.1007/s008940100045
    metadata:
      abstract: GROMACS 3.0 is the latest release of a versatile and very well optimized
        package for molecular simulation. Much effort has been devoted to achieving
        extremely high performance on both workstations and parallel computers. The
        design includes an extraction of virial and periodic boundary conditions from
        the loops over pairwise interactions, and special software routines to enable
        rapid calculation of x-1/2. Inner loops are generated automatically in C or
        Fortran at compile time, with optimizations adapted to each architecture.
        Assembly loops using SSE and 3DNow! Multimedia instructions are provided for
        x86 processors, resulting in exceptional performance on inexpensive PC workstations.
        The interface is simple and easy to use (no scripting language), based on
        standard command line arguments with self-explanatory functionality and integrated
        documentation. All binary files are independent of hardware endian and can
        be read by versions of GROMACS compiled using different floating-point precision.
        A large collection of flexible tools for trajectory analysis is included,
        with output in the form of finished Xmgr/Grace graphs. A basic trajectory
        viewer is included, and several external visualization tools can read the
        GROMACS trajectory format.
      authors:
      - name: Lindahl E.
      - name: Hess B.
      - name: van der Spoel D.
      citationCount: 6227
      date: '2001-12-01T00:00:00Z'
      journal: Journal of Molecular Modeling
      title: 'GROMACS 3.0: A package for molecular simulation and trajectory analysis'
    note: null
    pmcid: null
    pmid: null
    type:
    - Benchmarking study
    version: null
  - doi: 10.1016/0010-4655(95)00042-E
    metadata:
      abstract: 'A parallel message-passing implementation of a molecular dynamics
        (MD) program that is useful for bio(macro)molecules in aqueous environment
        is described. The software has been developed for a custom-designed 32-processor
        ring GROMACS (GROningen MAchine for Chemical Simulation) with communication
        to and from left and right neighbours, but can run on any parallel system
        onto which a a ring of processors can be mapped and which supports PVM-like
        block send and receive calls. The GROMACS software consists of a preprocessor,
        a parallel MD and energy minimization program that can use an arbitrary number
        of processors (including one), an optional monitor, and several analysis tools.
        The programs are written in ANSI C and available by ftp (information: gromacs@chem.rug.nl).
        The functionality is based on the GROMOS (GROningen MOlecular Simulation)
        package (van Gunsteren and Berendsen, 1987; BIOMOS B.V., Nijenborgh 4, 9747
        AG Groningen). Conversion programs between GROMOS and GROMACS formats are
        included. The MD program can handle rectangular periodic boundary conditions
        with temperature and pressure scaling. The interactions that can be handled
        without modification are variable non-bonded pair interactions with Coulomb
        and Lennard-Jones or Buckingham potentials, using a twin-range cut-off based
        on charge groups, and fixed bonded interactions of either harmonic or constraint
        type for bonds and bond angles and either periodic or cosine power series
        interactions for dihedral angles. Special forces can be added to groups of
        particles (for non-equilibrium dynamics or for position restraining) or between
        particles (for distance restraints). The parallelism is based on particle
        decomposition. Interprocessor communication is largely limited to position
        and force distribution over the ring once per time step. © 1995.'
      authors:
      - name: Berendsen H.J.C.
      - name: van der Spoel D.
      - name: van Drunen R.
      citationCount: 8425
      date: '1995-09-02T00:00:00Z'
      journal: Computer Physics Communications
      title: 'GROMACS: A message-passing parallel molecular dynamics implementation'
    note: null
    pmcid: null
    pmid: null
    type:
    - Benchmarking study
    version: null
  - doi: 10.1002/jcc.24030
    metadata:
      abstract: The molecular dynamics simulation package GROMACS runs efficiently
        on a wide variety of hardware from commodity workstations to high performance
        computing clusters. Hardware features are well-exploited with a combination
        of single instruction multiple data, multithreading, and message passing interface
        (MPI)-based single program multiple data/multiple program multiple data parallelism
        while graphics processing units (GPUs) can be used as accelerators to compute
        interactions off-loaded from the CPU. Here, we evaluate which hardware produces
        trajectories with GROMACS 4.6 or 5.0 in the most economical way. We have assembled
        and benchmarked compute nodes with various CPU/GPU combinations to identify
        optimal compositions in terms of raw trajectory production rate, performance-to-price
        ratio, energy efficiency, and several other criteria. Although hardware prices
        are naturally subject to trends and fluctuations, general tendencies are clearly
        visible. Adding any type of GPU significantly boosts a node's simulation performance.
        For inexpensive consumer-class GPUs this improvement equally reflects in the
        performance-to-price ratio. Although memory issues in consumer-class GPUs
        could pass unnoticed as these cards do not support error checking and correction
        memory, unreliable GPUs can be sorted out with memory checking tools. Apart
        from the obvious determinants for cost-efficiency like hardware expenses and
        raw performance, the energy consumption of a node is a major cost factor.
        Over the typical hardware lifetime until replacement of a few years, the costs
        for electrical power and cooling can become larger than the costs of the hardware
        itself. Taking that into account, nodes with a well-balanced ratio of CPU
        and consumer-class GPU resources produce the maximum amount of GROMACS trajectory
        over their lifetime.
      authors:
      - name: Kutzner C.
      - name: Pall S.
      - name: Fechner M.
      - name: Esztermann A.
      - name: De Groot B.L.
      - name: Grubmuller H.
      citationCount: 198
      date: '2015-10-01T00:00:00Z'
      journal: Journal of Computational Chemistry
      title: 'Best bang for your buck: GPU nodes for GROMACS biomolecular simulations'
    note: null
    pmcid: PMC5042102
    pmid: '26238484'
    type:
    - Benchmarking study
    version: null
  - doi: 10.1002/jcc.26011
    metadata:
      abstract: We identify hardware that is optimal to produce molecular dynamics
        (MD) trajectories on Linux compute clusters with the GROMACS 2018 simulation
        package. Therefore, we benchmark the GROMACS performance on a diverse set
        of compute nodes and relate it to the costs of the nodes, which may include
        their lifetime costs for energy and cooling. In agreement with our earlier
        investigation using GROMACS 4.6 on hardware of 2014, the performance to price
        ratio of consumer GPU nodes is considerably higher than that of CPU nodes.
        However, with GROMACS 2018, the optimal CPU to GPU processing power balance
        has shifted even more toward the GPU. Hence, nodes optimized for GROMACS 2018
        and later versions enable a significantly higher performance to price ratio
        than nodes optimized for older GROMACS versions. Moreover, the shift toward
        GPU processing allows to cheaply upgrade old nodes with recent GPUs, yielding
        essentially the same performance as comparable brand-new hardware. © 2019
        Wiley Periodicals, Inc.
      authors:
      - name: Kutzner C.
      - name: Pall S.
      - name: Fechner M.
      - name: Esztermann A.
      - name: de Groot B.L.
      - name: Grubmuller H.
      citationCount: 288
      date: '2019-10-15T00:00:00Z'
      journal: Journal of Computational Chemistry
      title: 'More bang for your buck: Improved use of GPU nodes for GROMACS 2018'
    note: null
    pmcid: null
    pmid: '31260119'
    type:
    - Benchmarking study
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  - Suite
  topic:
  - term: Molecular dynamics
    uri: http://edamontology.org/topic_0176
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2026-03-26T02:15:51.819440Z'
  biotoolsCURIE: biotools:quac
  biotoolsID: quac
  collectionID:
  - Sequencing
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Manavalan Gajapathy
    note: null
    orcidid: https://orcid.org/0000-0002-8606-0113
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://github.com/ManavalanG
  description: QuaC is a snakemake-based pipeline that runs several QC tools for WGS/WES
    samples and then summarizes their results using pre-defined, configurable QC thresholds.
  documentation:
  - note: null
    type:
    - General
    url: https://quac.readthedocs.io/
  download:
  - note: null
    type: Source code
    url: https://github.com/uab-cgds-worthey/quac/releases/tag/2.0
    version: '2.0'
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    output: []
  homepage: https://github.com/uab-cgds-worthey/quac
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-03-28T20:53:47.092010Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/uab-cgds-worthey/quac
  maturity: Mature
  name: quac
  operatingSystem: []
  otherID: []
  owner: sdhutchins
  publication:
  - doi: 10.21105/joss.05313
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - '2.0'
- accessibility: Open access
  additionDate: '2026-03-28T18:52:56.484093Z'
  biotoolsCURIE: biotools:genxflo
  biotoolsID: genxflo
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit: []
  description: GenXflo is a no-code visual Nextflow pipeline builder for bioinformatics.
    Users design workflows on a drag-and-drop canvas and export clean, production-ready
    Nextflow DSL2 code. Supports Docker and Singularity containerisation, local, HPC,
    and cloud deployment on AWS, Azure, and Google Cloud, and includes AI-assisted
    workflow validation.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://genxflo.com/app/resources
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Design
      uri: http://edamontology.org/operation_2430
    output: []
  homepage: https://www.genxflo.com
  homepage_status: 0
  language:
  - JavaScript
  - Python
  - TypeScript
  - CWL
  lastUpdate: '2026-03-28T19:21:38.419258Z'
  license: null
  link:
  - note: documentation on how to use the tool
    type:
    - Software catalogue
    url: https://genxflo.com/app/resources
  - note: Product Overview
    type:
    - Other
    url: https://genxflo.com/product/overview
  maturity: Emerging
  name: Genxflo
  operatingSystem: []
  otherID: []
  owner: genxflo
  publication: []
  relation: []
  toolType:
  - Workbench
  topic:
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version: []
next: ?page=2
previous: null
